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ABINIT The user's manual - Université catholique de Louvain

1. abinis lt t6x files gt amp t69 log Y This job lasts about 20 minutes on a PC PIV Intel 2 2 GHz Because it is so long it was worth to run it before the examination of the input file Now you can examine it We need the usual part of the input file to perform a ground state calculation This is done in dataset 1 and at the end we print out the density We use a 4x4x4 FCC grid so 256 k points in the full Brillouin Zone shifted because it is the most economical It gives 10 k points in the Irreducible part of the Brillouin Zone However this k point grid does not contains the Gamma point and at present one cannot perform calculations of the self energy corrections for other k points than those present in the grid of k points in the KSS file Then in dataset 2 we perform a non self consistent calculation to calculate the Kohn Sham structure in a set of 19 k points in the Irreducible Brillouin Zone This set of k points is also derived from a 4x4x4 FCC grid but a NON SHIFTED one It has the same density of points as the 10 k point set but the symmetries are not used in a very efficient way However this set contains the Gamma point which allows us to tackle the computation of the band gap at this point In dataset 3 we calculate the screening The screening calculation is very time consuming So we have decided to weaken a bit the parameters found in the previous convergence studies Indeed ecutwfn has been decrea
2. 4 4 11 ptgroupma Mnemonics PoinT GROUP number for the MAgnetic space group Characteristic SYMMETRISER INTERNAL Variable type integer parameter Default 0 This internal variable characterizes a Shubnikov type III magnetic space group anti ferromagnetic space group The user is advised to consult The mathematical theory of symmetry in solids Representation theory for point groups and space groups 1972 C J Bradley and A P Cracknell Clarendon Press Oxford A Shubnikov type III magnetic space group might be defined by its Fedorov space group set of all spatial symmetries irrespective of their magnetic action and the halving space group only the symmetries that do not change the magnetisation The specification of the halving space group might be done by specifying for each point symmetry the magnetic action See Table 7 1 of the above mentioned reference Magnetic space groups are numbered from 1 to 58 4 4 12 spgaxor Mnemonics SPace Group AXes ORientation Characteristic SYMMETRISER Variable type integer parameter Default 1 It is taken into account only when spgroup 0 it allows one to define the axes orientation for the specific space groups for which this is needed Trigonal groups number 146 148 155 160 161 166 167 e 1 represents the hexagonal axes e 2 represents the rhombohedral axes Orthorhombic space groups there are six possibilities corresponding to the possible axes per mutations
3. diff til out Refs t11 out more You should get inoffensive differences like differences in the name of input files or timing differences like the following 5c5 lt Starting date Tue 4 Jul 2000 gt Starting date Thu 22 Jun 2000 TCT lt input file gt t11 in gt input file gt tl1 in 9 10c9 10 lt root for input files gt t1xi lt root for output files gt t1xo gt root for input files gt tili gt root for output files gt tilo 2 1 LESSON 1 THE H2 MOLECULE WITHOUT CONVERGENCE STUDIES 214c214 lt Total cpu time s m h 4 7 0 08 0 001 gt Total cpu time s m h 4 6 0 08 0 001 221 229c221 228 and what comes after that is related only to timing If you do not run on a PC under Linux you might also have small numerical differences on the order of 1 0 x 107 at most If you get something else you should ask for help Supposing everything went well we will now detail the different steps that took place how to run the code what is in the t11 in input file and later what is in the tll out and log output files 5 Running the code is described in the section 1 2 of the abinis_help file Please read it now 6 It is now time to edit the t11 in file You can have a first glance at it It is not very long about 40 lines mostly comments Do not try to understand everything immediately After having gone through it you should rea
4. without going further Run very fast on the order of the second e 3 gt stop in gstate before call scfev move or brdmin Useful to debug pseudopotentials e 4 stop in move after completion of all loops e 5 gt stop in brdmin after completion of all loops e 6 stop in scfcv after completion of all loops e 7 stop in vtorho after the first rho is obtained e 8 gt stop in vtowfk after the first k point is treated e 9 gt stop in cgwf after the first wf is optimized e 10 stop in getghc after the Hamiltonian is applied once This debugging feature is not yet activated in the RF routines Note that fftalg offers another option for debugging 4 3 34 prtwf Mnemonics PRinT the WaveFunction Characteristic Variable type integer parameter Default is 1 If set gt 1 provide output of wavefunction and eigenvalue file as described in section 6 7 of the main abinis help file For a standard ground state calculation the name of the wavefunction file will be the root output name followed by WFK If nqpt 1 the root name will be followed by WFQ For response function calculations the root name will be followed by 1WFx where x is the number of the perturbation The dataset information will be added as well if relevant No wavefunction output is provided by prtwf 0 117 4 4 GEOMETRY BUILDER SYMMETRY RELATED VARIABLES VARGEO 4 3 35 prtldm Mnemonics PRinT 1 DiMens
5. 3rd example ndtset 6 ecuti 10 ecut2 15 ecut3 20 ecut4 25 ecut5 30 ecut6 35 is equivalent to ndtset 6 ecut 10 ecut 5 In both cases there are six datasets with increasing values of ecut 61 3 2 THE INPUT FILE 3 2 5 Defining a double loop dataset To define a double loop dataset one has first to define the upper limit of two loop counters thanks to the variable udtset The inner loop will execute from 1 to udtset 2 and the outer loop will execute from 1 to udtset 1 Note that the largest value for udtset 1 and udtset 2 is 9 presently The value of ndtset must be coherent with udtset it must equal the product udtset 1 udtset 2 A dataset index is created by the concatenation of the outer loop index and the inner loop index For example if udtset 1 is 2 and udtset 2 is 4 the index will assume the following values 11 12 13 14 21 22 23 and 24 Independently of the use of udtset rules 2a and 2c will be used to define the value of an input variable 2a The question mark can be used as a metacharacter replacing any digit from 1 to 9 to define an index of a dataset For example ecut 1 means that the input value that follows it can be used for ecut for the datasets 01 11 21 31 41 51 61 71 81 and 91 2c If the variable name appended with the index of the dataset does not exist the code looks whether a double loop series has been defined for this keyword Series can be defined
6. 4 2 31 ortalg Mnemonics ORThogonalisation ALGorithm Characteristic DEVELOP Variable type integer parameter Default is 2 Allows to choose the algorithm for orthogonalisation Positive or zero values make two projections per line minimisation one before the precon ditioning one after This is the clean application of the band by band CG gradient for finding eigenfunctions Negative values make only one projection per line mininisation The orthogonalisation step is twice faster but the convergence is less good This actually calls to a better understanding of this effect ortalg 0 1 or 1 is the conventional coding actually identical to the one in versions prior to 1 7 ortalg 2 or 2 try to make better use of existing registers on the particular machine one is running More demanding use of registers is provided by ortalg 3 or 3 and so on The maximal value is presently 4 and 4 Tests have shown that ortalg 2 or 2 is suitable for use on the available platforms 104 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 2 32 qprtrb Mnemonics Q wavevector of the PERTurbation Characteristic DEVELOP Variable type integer array of three values Default wavevector is 0 0 0 Gives the wavevector in units of reciprocal lattice primitive translations of a perturbing potential of strength vprtrb See vprtrb for more explanation 4 2 33 useria userib useric userid userie Mnemonics
7. Copyright C 2000 2004 ABINIT group XG RC This file is distributed under the terms of the GNU General Public License see ABINIT Infos copyright or http www gnu org copyleft gp1 txt For the initials of contributors see ABINIT Infos contributors Before following the tutorial you should have read the new user s guide as well as the pages 1045 1058 of the paper Iterative minimization techniques for ab initio total energy calculations molecular dynamics and conjugate gradients by M C Payne M P Teter D C Allan T A Arias and J D Joannopoulos Rev Mod Phys 64 1045 1992 After the tutorial you might find useful to learn about the tests cases contained in directo ries ABINIT Test_fast ABINIT Test_vi ABINIT Test_v2 ABINIT Test_v3 and ABINIT Test_v4 that provide many example input files You should have a look at the README files of these directories Additional informations can be found in the ABINIT Infos directory including the description of the ABINIT project guide lines for developers more on the use of the code tuning Brief contents Lessons 1 4 present the basic concepts and form a whole you should not skip one of these e Lesson 1 deals with the H2 molecule get the total energy the electronic energies the charge density the bond length the atomization energy e Lesson 2 deals again with the H2 molecule convergence studies LDA versus GGA e Lesson 3 deals with crys
8. a 2 V3 2 x a c 4 1 where a c 1 0 If the angles are not all equal or if they are all 90 degrees one will have the following generic form e R1 1 0 0 e R2 a b 0 e R3 c d e where each of the vectors is normalized and form the desired angles with the others 4 1 3 ecut Mnemonics Energy CUToff Characteristic ENERGY Variable type real parameter Used for kinetic energy cutoff which controls number of planewaves at given k point by 1 2 27 k Gmaz ecut for Gmax All planewaves inside this basis sphere centered at k are included in the basis except if dilatmx is defined Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY characteristics 1 Ha 27 2113961 eV This is the single parameter which can have an enormous effect on the quality of a calculation basically the larger ecut is the better converged the calculation is For fixed geometry the total energy MUST always decrease as ecut is raised because of the variational nature of the problem Usually one runs at least several calculations at various ecut to investigate the convergence needed for reliable results For k points whose coordinates are build from 0 or 1 2 the implementation of time reversal symmetry that links coefficients of the wavefunctions in reciprocal space has been realized See the input variable istwfk If activated which corresponds to the Default mode this input variable istwfk wi
9. file as usual Edit the t68 in file and take the time to examine it Then issue abinis lt t6x files gt amp t68 log amp This small job lasts about 25 secs on a PC PIV Intel 2 2 GHz Edit the output file The number of bands used for the wavefunctions in the computation of the screening is mentioned in the fragments of output EPSILON 1 parameters EM1 file dimension of the eps 1 matrix 59 Gathering the macroscopic dielectric constant and GW energies for each number of bands one gets dielectric constant 102 1281 dielectric constant without local fields dimension of the eps 1 matrix 4 5 915 11 654 15 244 3 684 0 5 8 445 9 702 3 216 5 847 0 dielectric constant 101 2712 dielectric constant without local fields dimension of the eps 1 matrix 4 5 915 11 654 15 244 3 559 0 5 8 445 9 702 3 216 5 850 0 dielectric constant 101 2649 dielectric constant without local fields dimension of the eps 1 matrix 4 5 915 11 654 15 244 3 535 0 5 8 445 9 702 3 216 5 846 0 dielectric constant 101 1764 dielectric constant without local fields dimension of the eps 1 matrix 4 5 915 11 654 15 244 3 516 0 5 8 445 9 702 3 216 5 846 0 dielectric constant 101 1384 dielectric constant without local fields dimension of the eps 1 matrix 4 5 915 11 654 15 244 5 8 445 9 702 3 216 3 517 0 5 845 0 143 7244 59 806 0 241 11 579 0 075 5 990 811 0 232 9 18
10. 1 8438010986E 04 0 0000000000E 00 0 0000000000E 00 xcart 7 6091430410E 01 0 0000000000E 00 0 0000000000E 00 7 6091430410E 01 0 0000000000E 00 0 0000000000E 00 According to these data see xcart the optimal interatomic distance is about 1 520 Bohr in good agreement with the estimation of t12 out If you have time this is to be done at 12 CHAPTER 2 TUTORIAL home you might try to change the stopping criteria and redo the calculation to see the level of convergence of the interatomic distance Note that the final value of fcart in your run might differ slightly from the one shown above less than one percent change Such a fluctuation is quite often observed for a value converging to zero remember we ask the code to determine the equilibrium geometry that is forces should be zero when the same computation is done on different platforms 2 1 4 Computation of the charge density 1 We start from the optimized interatomic distance 1 522 Bohr and make a run at fixed geometry The input variable prtden must be set to 1 To understand correctly the content of the prtden description it is worth to read a much more detailed description of the files file in section 4 of the abinis_help file 2 The input file ABINIT Tutorial t14 in is an example of input file for a run that will print a density If you decide to use this file do not forget to change the file names in t1x files The run will take a
11. 5 577 0 817 0 225 8 960 0 743 9 188 number of plane waves for SigmaX 259 number of plane waves for SigmaC and W 169 Band EO VxcLDA SigX SigC E0 Z dSigC dE Sig E E EO E 4 5 915 11 654 15 247 3 779 0 804 0 244 11 504 0 150 6 065 5 8 445 9 702 3 218 5 577 0 817 0 225 8 961 0 741 9 186 number of plane waves for SigmaX 283 number of plane waves for SigmaC and W 169 Band EO VxcLDA SigX SigC EO0 Z dSigC dE Sig E E EO E 4 5 915 11 654 15 247 3 779 0 804 0 244 11 504 0 150 6 065 5 8 445 9 702 3 218 5 577 0 817 0 225 8 961 0 741 9 186 number of plane waves for SigmaX 283 number of plane waves for SigmaC and W 169 Band EO VxcLDA SigX SigC EO Z dSigC dE Sig E E EO E 4 5 915 11 654 15 247 3 779 0 804 0 244 11 504 0 150 6 065 5 8 445 9 702 3 218 5 577 0 817 0 225 8 961 0 741 9 186 So that npwsigr 169 ecutsigr 6 0 can be considered converged within 0 01 eV 2 6 5 Convergence on the number of bands to calculate the Self Energy At last as concerns the computation of the self energy we check the convergence on the number of bands in the calculation of the Sigma_X This will be done by defining five datasets with increasing nband ndtset 5 nband 50 nband 50 In directory ABINIT Tutorial Work6 copy the file t65 in and modify the t6x files file as usual Edit the t65 in file and take the time to examine it Then issue abinis lt t6x files gt amp t65 log amp This small job lasts a
12. ABINIT Tutorial t54 in in Work5 This is your input file You should edit it As for test 53 the changes with respect to the file ABINIT Tutorial t51 in are all gathered in the first part of this file Moreover the changes with respect to t53 in concern only the input variables rfatpol and rfdir Namely all the atoms will be displaced in all the directions There are six perturbations to consider So one might think that the CPU time will raise ac cordingly This is not true as ABINIT is able to determine which perturbations are the symmetric of another perturbation see section section 3 of the respfn_help file Now you can make the run It is a bit longer than one minute on a PIII at 450MHz You edit the file t54 out and notice that the response to two perturbations were computed explicitly while the response to the other four could be deduced by using the symmetries Nothing mysterious one of the two irreducible perturbations is for the Al atom placed in a rather symmetric local site and the other perturbation is for the As atom The phonon frequencies obtained by diagonalizing the dynamical matrix where the atomic masses have been taken into account see amu are given as follows Phonon wavevector reduced coordinates 0 00000 0 00000 0 00000 Phonon energies in Hartree 2 586632E 06 2 590723E 06 2 614440E 06 1 568560E 03 1 568560E 03 1 568560E 03 Phonon frequencies in cm 1 5 677000E 01 5 685980E 01 5 738033E 01 3 44259
13. Characteristic NON LINEAR 4 10 10 rf3atpol Mnemonics non linear Response Function 3rd mixed perturbation limits of ATomic POLarisa tions Characteristic NON LINEAR Variable type integer array of 2 elements Default is 1 1 Control the range of atoms for which displacements will be considered in phonon calculations atomic polarisations or in non linear computations using the 2n 1 theorem These values are only relevant to phonon response function calculations or non linear compu tations May take values from 1 to natom with rfatpol 1 lt rfatpol 2 The atoms to be moved will be defined by the do loop variable iatpol do iatpol rfatpol 1 rfatpol 2 For the calculation of a full dynamical matrix use rfatpol 1 1 and rfatpol 2 natom together with rfdir 1 1 1 For selected elements of the dynamical matrix use different values of rfatpol and or rfdir The name iatpol is used for the part of the internal variable ipert when it runs from 1 to natom The internal variable ipert can also assume values larger than natom of electric field or stress type see respfn help 4 10 11 rfdir Mnemonics Response Function DIRections Characteristic RESPFN 4 10 12 rfldir Mnemonics non linear Response Function 1st mixed perturbation DIRections Characteristic NON LINEAR 4 10 13 rf2dir Mnemonics non linear Response Function 2nd mixed perturbation DIRections Characteristic NON LINEAR 155 4 10 RESPONSE FU
14. Hamiltonian in the routine outkss f and so the size of the matrix the size of eigenvectors and the number of available states to be stored in the abo_KSS file If it is set to 0 then the planewave basis set defined by the usual Ground State input variable ecut is used to generate the superset of all planewaves used for all k points Note that this large planewave basis is the same for all k points Very important for the time being istwfk must be 1 for all the k points 4 6 9 nkptgw Mnemonics Number of GW PoinTs Characteristic GW Variable type integer 146 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Default 0 Only relevant if optdriver 4 that is GW calculations This input variable was called ngwpt in versions before v4 3 nkptgw gives the number of k points for which the GW calculation must be done It is used to dimension kptgw 4 6 10 nomegasrd Mnemonics Number of OMEGA to evaluate the Sigma Real axis Derivative Characteristic GW Variable type integer Default 9 Only relevant if optdriver 4 that is GW calculations The number of frequencies omega where sigma is calculation around the KS energy on the real axis From these values the derivative of Sigma with respect to omega and calculated at the KS energy is evaluated 4 6 11 npweps Mnemonics Number of PlaneWaves for EPSilon the dielectric matrix Characteristic GW Variable type integer Default 0 Only
15. Our values with a 4x4x1 grid a smearing of 0 04 Ha a kinetic energy cut off of 6 Ha the 13a1 981214 fhi pseudopotential still oscillate between 0 45 eV and 0 51 eV An error on the order of 0 016 eV is due to the thin vacuum layer Other sources of errors might have to be rechecked seeing the kind of accuracy that is needed Experimental data give a surface energy around 0 55 eV sorry the reference is to be provided 2 5 Lesson 5 Dynamical and dielectric properties of AlAs This lesson aims at showing how to get the following physical properties for an insulator e the phonon frequencies and eigenvectors at Gamma the dielectric constant e the Born effective charges e the LO TO splitting e the phonon frequencies and eigenvectors at other q points in the Brillouin Zone the interatomic force constants not yet e the phonon band structure from interatomic force constants not yet e associated thermodynamical properties not yet You will learn to use of response function features of ABINIT In a future version you will learn the use of the associated codes Mrgddb and Anaddb This lesson should take about to be provided hours to be done 2 5 1 The ground state geometry of AlAs Before beginning you might consider to work in a different subdirectory as for the other lessons Why not Workd The file ABINIT Tutorial t5x files lists the file names and root names You can copy it in the Work5 directory and c
16. Relevant only when optdriver 3 or 4 Indicate the file from which the dielectric matrix must be obtained As alternative one can use the input variable getkss When optdriver 3 or 4 at least one of irdkss or getscr must be non zero A non zero value of irdkss is treated in the same way as other ird variables see the section 4 of abinis_help 4 3 13 irdscr Mnemonics Integer that governs the ReaDing of EPSilon Characteristic GW Variable type integer parameter Default is 0 Relevant only when optdriver 4 Indicate the file from which the dielectric matrix must be obtained As alternative one can use the input variable getscr When optdriver 4 at least one of irdscr or getscr must be non zero A non zero value of irdscr is treated in the same way as other ird variables see the section 4 of abinis_help 4 3 14 irdwfk Mnemonics Integer that governs the ReaDing of WFK files 4 3 15 irdwfq Mnemonics Integer that governs the ReaDing of WFQ files 4 3 16 irdlwf Mnemonics Integer that governs the ReaDing of _1WF files 4 3 17 irdddk Mnemonics Integer that governs the ReaDing of DDK wavefunctions in 1WF files Characteristic Variable type integer parameter Default is 0 Indicates eventual starting wavefunctions As alternative one can use the input variables getwfk getwfq getlwf or getddk Ground state calculation e only irdwfk and getwfk have a meaning e at most one of irdwfk or getwfk can be no
17. There are different algorithms to do that See the input variable ionmov with values 2 3 and 7 In the present case with only one degree of freedom to be optimized the best choice is tonmov 3 You have also to define the maximal number of timesteps for this optimization Set the input variable ntime to 10 it will be largely enough For the stopping criterion tolmxf use the reasonable value of 5 0 x 1074 Ha Bohr This defines the force threshold to consider that the geometry is converged The code will stop if the residual forces are below that value before reaching ntime It is also worth to change the stopping criterion for the SCF cycle in order to be sure that the forces generated for each trial interatomic distance are sufficiently converged So change toldfe in toldff and set the latter input variable to ten times smaller than tolmxf The input file ABINIT Tutorial t13 in is an example of file that will do the job while ABINIT Tutorial Refs t13 o0ut is an example of output file If you decide to use these files do not forget to change the file names in the t1x files file So you run the code with your input file it should take less than one minute examine quietly this file which is much smaller than the t12 out file and get some significant output data gathered in the final echo of variables etotal 1 1058360628E 00 fcart 1 8438010986E 04 0 0000000000E 00 0 0000000000E 00
18. and 38 Sr For that unique pseudoatom to be generated here are the mixing coeeficients to be used to combine the Ba and Sr pseudopotentials ntypat 3 ntypalch 1 mixalch 0 25 0 75 Example 2 More complicated and illustrate some minor drawback of the design of input variables Suppose that one wants to generate Al 0 25 Ga 0 75 As 0 10 Sb 0 90 The input variables will be npsp 4 znucl 13 31 33 51 4 pseudopotentials should be read The atomic numbers All pseudopotentials will be used for some alchemical purpose ntypat 2 There will be two types of atoms ntypalch 2 None of the atoms will be pure Hence there will be npspalch 4 pseudopotentials to be used for alchemical purposes This array is a 4 2 array arranged in the usual Fortran order mixalch 0 25 O 0 0 0 134 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Minor drawback one should not forget to fill mixalch with the needed zero s in this later case 4 5 28 natsph Mnemonics Number of ATomic SPHeres for the atom projected density of states Characteristic Variable type integer parameter Default is natom This input variable is active only in the prtdos 3 case It gives the number of atoms around which the sphere for atom projected density of states will be build in the prtdos 3 case The indices of these atoms is given by iatsph The radius of these spher
19. default is 200 Allows to choose the algorithm for Fast Fourier Transforms These have to be used when applied to wavefunctions routine fourwf f as well as when applied to densities and potentials routine fourdp f Presently it is the concatenation of three digits labelled A B and C The first digit A is to be chosen among 1 2 3 and 4 e 1 gt use FFT routines written by S Goedecker e 2 gt use machine dependent FFT algorithm taken from the vendor library if it exists and if it has been implemented The bare fftalg 200 has little chance to be faster than fftalg 112 but it might be tried Implementing library subroutines with fftalg 4 200 has not yet been done Currently implemented library subroutines fftalg 200 are on HP z3dfft from Veclib on DEC Alpha zfft_3d from DXML on NEC ZFC3FB from ASL lib on SGI zfft3d from complib sgimath e 3 gt use serial or multi threaded FFTW fortran routines http www fftw org Currently implemented with fftalg 300 e 4 gt use FFT routines written by S Goedecker 2002 version that will be suited for MPI and OpenMP parallelism The second digit B is related to fourdp f e 0 only use Complex to complex FFT e 1 real to complex is also allowed only coded for A 1 The third digit C is related to fourwf f e 0 gt no use of zero padding e 1 gt use of zero padding only coded for A 1 and A 4 e 2 gt use of zero padding and
20. get variables can be used to chain the calculations Until now there are eight of them getwfk getwfq getddk get1wf getden getcell getured and getxcart 62 CHAPTER 3 ABINIS HELP getwfk allows to take the output wavefunctions of a previous dataset and use them as input wavefunctions getwfq getddk and get1wf do similar things for response function calculations getden does the same for the density getcell does the same for acell and rprim getzred and getxcart do the same for the atomic positions either in reduced coordinates or in cartesian coordinates The different variables corresponding to each dataset are echoed using the same indexing convention as for the input step For the last echo of the code variables some output variables are also summarized using the same conventions e etotal total energy e fcart cartesian forces e strten the stress tensor If you follow the tutorial you should go back to the tutorial window now 3 3 The files file Note This files file is called ab files in section 1 1 Contains the file names or root names needed to build file names These are listed below there are 5 names or root names for input output and temporaries and then a list of pseudopotentials These names may be provided from unit 05 interactively during the run but are more typically provided by piping from a file in unix the files file ab_in Filename of file containing the
21. positive or negative but non zero value of the STM bias stmbias This is a very approximate way to obtain STM profiles one can choose an equidensity surface and consider that the STM tip will follow this surface Such equidensity surface might be deter mined with the help of Cut3D and further post processing of it to be implemented The big approximations of this technique are neglect of the finite size of the tip and position independent transfer matrix elements between the tip and the surface The charge density is provided in units of electrons Bohr The name of the STM density file will be the root output name followed by STM Like a DEN file it can be analyzed by cut3d The file structure of this unformatted output file is described in section 6 5 of abinis_help For the STM charge density to be generated one must give as an input file the converged wavefunctions obtained from a previous run at exactly the same k points and cut off energy self consistently determined using the occupation numbers from occopt 7 In the run with positive prtstm one has to use e positive iscf occopt 7 with specification of tsmear nstep 1 e the tolwfr convergence criterion ionmov 0 this is the default value e optdriver 0 this is the default value Note that you might have to adjust the value of nband as well for the treatment of unoccupied states because the automatic determination of nband will often not include enough unoccup
22. prtgeo 114 prtkpt 115 prtpot 115 prtstm 116 prtvha 115 prtvhxc 115 prtvol 116 prtvxe 115 prtwf 117 pspso 140 pteroupma 122 qprtrb 105 qpt 140 qptn 150 qptnrm 141 ratsph 141 restartxf 168 flatpol 155 fldir 155 flelfd 156 flphon 157 f2atpol 155 f2dir 155 f2elfd 156 f2phon 157 f3atpol 155 f3dir 156 f3elfd 156 fasr 154 168 fatpol 154 fdir 155 felfd 156 fmeth 157 fphon 157 fstrs 157 fthrd 158 fuser 158 rprim 89 rprimd 89 T r T E r r T r r r r r T r E r r r r r sciss 158 shiftk 90 signperm 168 so_typat 140 soenergy 149 spgaxor 122 spgorig 123 spgroup 123 spgroupma 124 spinat 141 stmbias 142 strfact 169 strprecon 169 strtarget 169 symafm 142 symrel 91 td maxene 159 td mexcit 159 timopt 142 tnons 91 toldfe 91 toldff 92 tolmxf 169 tolvrs 92 tolwfr 92 tphysel 143 tsmear 143 typat 93 udtset 93 usepaw 151 useria userib useric userid userie 105 userra userrb userrc userrd userre 105 useylm 105 vaclst 124 vacnum 124 vacuum 143 vacwidth 144 vel 170 vis 170 vprtrb 105 wfoptalg 106 wtatcon 170 xangst 93 xcart 94 xred 94 zcut 149 znucl 94
23. scalar title beta and scalar title gamma sections all three must be present if one is present in the crystal section expecting the data in degrees e nsym symrel and tnons from the content of matrix sections in the symmetry section e natom from the number of items in the first atom sections in the atomArray section e typat from the attribute elementType in the atom sections in the atomArray section with identification of the pseudopotentials that have the correct nuclear charge according to the atomic symbol the first pseudopotential with the correct nuclear charge from the pseudopotential list will be used e xred from the attributes xFract yFract and zFract all three must be present if one is present in the atom sections in the atomArray section These limited parsing capabilities are enough for ABINIT to read the CML files it has created thanks to the use of the prtcml input variable 4 3 2 getden Mnemonics GET the DENsity from Characteristic Variable type integer parameter Default is 0 Eventually used when ndtset gt 0 multi dataset mode and in the case of a ground state calculation if iscf lt 0 non SCF calculation to indicate that the starting density is to be taken from the output of a previous dataset It is used to chain the calculations since it describes from which dataset the OUTPUT density ar
24. 0 50 5 0 5 It is used only when kptopt gt 0 and must be defined if nshiftk is larger than 1 shiftk 1 3 1 nshiftk defines nshiftk shifts of the homogeneous grid of k points based on ngkpt or kptrlatt The shifts induced by shiftk corresponds to the reduced coordinates in the coordinate system defining the k point lattice For example if the k point lattice is defined using ngkpt the point whose reciprocal space reduced coordinates are shiftk 1 ii ngkpt 1 shiftk 2 ii ngkpt 2 shiftk 3 ii ngkpt 3 belongs to the shifted grid number ii The user might rely on ABINIT to suggest suitable and efficients combinations of kptrlatt and shiftk The procedure to be followed is described with the input variables kptrlen In what follows we suggest some interesting values of the shifts to be used with even values of ngkpt This list is much less exhaustive than the above mentioned automatic procedure 1 When the primitive vectors of the lattice do NOT form a FCC or a BCC lattice the usual shifted Monkhorst Pack grids are formed by using nshiftk 1 and shiftk 0 5 0 5 0 5 This is often the preferred k point sampling For a non shifted Monkhorst Pack grid use nshiftk 1 and shiftk 0 0 0 0 0 0 but there is little reason to do that The FCC k point sampling defined with nshiftk 4 and shiftk oooo oonu oooo onon oooo noon is particularly efficient 2 When the primitive vectors of the lattice form a FCC lattice with rprim 0 0 0
25. 04 648 OV E44 bode eae SEE REPRE EEA The maim output Ble a 22G cac0ee e222 a a More on the main output file o o Tho header os ada eee ee ee ee ae da The density output file occ e ccsa 60 et dee ee eee Ee EEE EE GS The potential files 2 2 2 65 diia dG Ee ee hs The wavefunction output file o o o Cher output les s s sed eaaa ee da wt 3 6 Numerical quality of the calculations aooaa aa 37 Final remarks eoa ouy ai oe e g ee eee a ete eee D A Main ABINIT code input variables Complete list 4 1 Basic variables VARBAS 0 eee ee ee 4 1 1 4 1 2 4 1 3 4 1 4 NN 33 35 36 39 40 40 40 46 46 47 48 CONTENTS 4 2 GANS BE LADA AAA ee E ES ee Ee eRe Ges 81 ALG JGts6t oe a wae E Uae bh a ee 82 BA Al A a A a ee eg Re a ak 83 AUS Kept 2626 642 b bo eed eee e eee ae oot ee ewe 83 ALO io ser oe wR a ek Re 83 ELIO ato criar ee ERR aa EP ee 84 ALN o ce ea a RR EELS Gare PER eee od glk RRS 84 4112 ndet o as ooo et ee Ree hee ERE EE a A Re ee Gee eee Se a 85 ALIS DEDO lt lt 56s bd t bbe BAe e ee ee CEES PE ee 85 ALVA MEY 2 6 2 ke GS Goa ke Be eo ea AE amp Be ss 85 AAS Shit oe eae oe SER AROSE EE ES DEAS eo ee Ge 4 86 A ki koe ea BOS ee See AA Be a oS G 86 ALA AED rada da eee ee OAR ASA eee ee o a A 86 ALS ASTM 0 Gk we ee SO AA ee ER Oh oe Bw 4 87 S19 Mty pat a a padao RE ee ee ee ee be ee ee 87 o sce 2 ek bh awe PRES bee Ee A eee 2 8
26. 2 12 2 1 4 Computation of the charge density 004 13 2 1 5 Computation of the atomization energy 000 13 2 1 6 Answers to the questions section 1 1 10 04 15 2 2 Lesson 2 The H2 molecule with convergence studies 16 2 2 1 Summary of the previous lesson o e eens 16 22 2 The eonversence im ECUE io ee a sga a a e di 17 2 223 The convergence im ACB os q ee aa A 18 2 2 4 The final calculation in Local Spin Density Approximation 20 2 2 5 The use of the Generalized Gradient Approximation 20 Zo Lesson 3 Crystalline silicon s es s a aki ea A A 21 2 3 1 Computing the total energy of silicon at fixed number of k points 21 2 3 2 Starting the convergence study with respect to k points 22 2 3 3 Actually performing the convergence study with respect to k points 22 2 3 4 Determination of the lattice parameters osooso 23 2 3 5 Computing the band structure 2 2 6 See aa eee ee e ee aG 23 2 4 Lesson 4 Aluminum the bulk and the surface 20 25 2 4 1 Computing the total energy and lattice parameters of aluminum for a fixed smearing and number of k points o ee ee 26 2 4 2 The convergence study with respect to k points 27 2 4 3 The convergence study with respect to both number of k points AND broad enine factor SIE oc oe ae TR a A Bs 27 2 4 4 Determin
27. 3 rhohxc computes the Hartree and exchange correlation energy and potential and sometimes derivative of potential only the XC timing is reported excluding time connected to the FFTs xc pot fourdp 4 nonlop computes lt G Vnon locai C gt the matrix elements of the nonlocal pseudopotential 5 projbd Gram Schmidt orthogonalization In case of small jobs other initialisation routines may take a larger share and the sum of the times for the principal time consuming subroutine calls will not make 90 of the run time Tf the long printing option has been selected prtvol 1 the code gives much more information in the whole output file These should be rather self explanatory usually Some need more explanation In particular the cpu and wall times for major subroutines which are NOT independent of each other for example vtorho conducts the loop over k points and calls practically everything else In case of a ground state calculation at fixed atomic positions these subroutines are 1 abinit the main routine 2 driver select ground state or response calculations gstate the driver of the ground state calculations scfev the SCF cycle driver vtorho compute the density from the potential it includes a loop over spins and k points So SOU HS ee vtowfk compute the wavefunctions at one particular k point includes a non self consistent loop and a loop over bands 69 3 5 THE DIFFERENT OUTPUT FILES 7
28. 4 1 11 nband Mnemonics Number of BANDs Characteristic Variable type integer parameter Default is 1 Gives number of bands occupied plus possibly unoccupied for which wavefunctions are being computed along with eigenvalues Note if the parameter occopt see below is not set to 2 nband is a scalar integer but if the parameter occopt is set to 2 then nband must be an array nband nkpt nsppol giving the number of bands explicitly for each k point This option is provided in order to allow the number of bands treated to vary from k point to k point For the values of occopt 84 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST not equal to 0 or 2 nband can be omitted The number of bands will be set up thanks to the use of the variable fband The present Default will not be used If nspinor is 2 nband must be even for each k point In the case of a GW calculation optdriver 3 or 4 nband gives the number of bands to be treated to generate the screening susceptibility and dielectric matrix as well as the self energy However to generate the KSS file see kssform the relevant number of bands is given by nbandkss 4 1 12 ndtset Mnemonics Number of DaTaSETs Characteristic NO MULTI Variable type integer parameter Default is 0 no multi data set Gives the number of data sets to be treated If 0 means that the multi data set treatment is not used so that the root filenames will not be appended with
29. 5 0 5 0 5 0 0 0 5 0 5 0 5 0 0 the usual Monkhorst Pack sampling will be generated by using nshiftk 4 and shiftk oooo oonu oooo onon oooo noon 3 When the primitive vectors of the lattice form a BCC lattice with rprim However the simple sampling nshiftk 1 and shiftk 0 5 0 5 0 5 is excellent 4 For hexagonal lattices one can use nshiftk 1 and shiftk 0 0 0 0 0 5 90 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 1 24 symrel Mnemonics S Y Mmetry in REaL space Characteristic Variable type integer array symrel 3 3 nsym Default is the identity matrix for one symmetry Gives nsym 3x3 matrices expressing space group symmetries in terms of their action on the direct or real space primitive translations It turns out that these can always be expressed as integers Always give the identity matrix even if no other symmetries hold e g symrel 100010001 Also note that for this array as for all others the array elements are filled in a columnwise order as is usual for Fortran The relation between the above symmetry matrices symrel expressed in the basis of primitive translations and the same symmetry matrices expressed in cartesian coordinates is as follows Denote the matrix whose columns are the primitive translations as R and denote the cartesian symmetry matrix as S Then symrel R inverse S R where matrix multiplication is implied When the symmetry finder is used see nsym symrel
30. 9 183 dielectric constant 100 6436 dielectric constant without local fields 143 7240 number of bands 50 4 5 915 11 654 15 244 3 587 0 804 0 244 11 657 0 003 5 912 5 8 445 9 702 3 216 5 764 0 815 0 227 9 113 0 589 9 034 dielectric constant 101 1764 dielectric constant without local fields 143 7244 number of bands 100 4 5 915 11 654 15 244 3 516 0 804 0 244 11 714 0 060 5 855 5 8 445 9 702 3 216 5 846 0 811 0 233 9 182 0 520 8 965 dielectric constant 101 2028 dielectric constant without local fields 143 7244 number of bands 150 4 5 915 11 654 15 244 3 510 0 804 0 244 11 718 0 065 5 850 5 8 445 9 702 3 216 5 853 0 810 0 234 9 189 0 514 8 959 dielectric constant 101 2128 dielectric constant without local fields 143 7244 51 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION number of bands 4 5 915 11 654 15 244 3 509 5 8 445 9 702 3 216 5 854 O O 200 803 0 246 11 719 0 065 5 850 812 0 231 9 188 0 514 8 960 So that the computation using 100 bands can be considered converged within 0 01 eV 2 6 8 Convergence on the dimension of the e 1 matrix Third we check the convergence on the number of plane waves in the calculation of the screening This will be done by defining six datasets with increasing ecuteps 3 0 1 0 ecuteps ecuteps In directory ABINIT Tutorial Work6 copy the file t68 in and modify the t6x files
31. DEN GEO or CML xml files are output each time that a SCF cycle is finished The x of TIMx aims at giving each of these files a different name It is attributed as follows case 0nmov 1 there is an initialization phase that takes 4 calls to the SCF calculation The value of x will be A B C and D Then x will be 1 2 3 actually in agreement with the value of time see the keyword ntime other tonmov cases the initialisation phase take only one SCF call The value of x will be 0 for that call Then the value of x is 1 2 3 in agreement with the value of time see the keyword ntime tmp The temporary files created by the codes will have a name that is constructed from the root tmp tmp should usually be chosen such as to give access to a disk of the machine that is running the job not a remote NFS disk Under Unix the name might be something like tmp user_name temp The most important temporary files with their name created from the root tmp is the following tmp FFT not created if mffmem 1 contains a few arrays defined in real space on the FFT grid tmp KG not created if mkmem nkpt contains the data on G vectors inside the sphere around the different k points tmp_KGS created if iprcel 40 contains the data on G vectors inside the sphere around the different k points for the computation of the susceptibility tmp_WF1 and tmp_WF2 not created if mkmem nkpt contains the wavefunc
32. For d band metals use 0 01 Ha Always check the convergence of the calculation with respect to this parameter and simulta neously with respect to the sampling of k points see nkpt If occopt 3 tsmear is the physical temperature as the broadening is based on Fermi Dirac statistics However if occopt 4 5 6 or 7 the broadening is not based on Fermi Dirac statistics and tsmear is only a convergence parameter It is still possible to define a physical temperature thanks to the input variable tphysel See the paper by M Verstraete and X Gonze Phys Rev B 2002 4 5 54 vacuum Mnemonics VACUUM identification Characteristic NOT INTERNAL Variable type integer array vacuum 3 No Default Establishes the presence if 1 or absence if 0 of a vacuum layer along the three possible directions normal to the primitive axes 143 4 6 GW VARIABLES VARGW This information might be used to generate k point grids if kptopt 0 and neither ngkpt nor kptrlatt are defined see explanations with the input variable prtkpt It will allow to select a zero one two or three dimensional grid of k points The coordinate of the k points along vacuum directions is automatically set to zero If vacuum is not defined the input variable vacwidth will be used to determine automatically whether the distance between atoms is sufficient to have the presence or absence of vacuum 4 5 55 vacwidth Mnemonics VACuum WIDTH Characteristic
33. MAY EXCEED 132 CHARACTERS That is only the first 132 characters of each line of the input file will be read and parsed for input variables and their values The names of all the parameters can be found in the input variables file The definitions of all the parameters can be found in e Basic variables VARBAS e Developpement variables VARDEV e Geometry builder symmetry related variables VARGEO e Ground state calculation variables VARGS e Files handling variables VARFIL e Parallelisation variables VARPAR e Response Function variables VARRF e Structure optimization variables VARRLX In the actual input file these parameters may be given in any order desired and more than one may be given per line Spaces are used to separate values and additional spaces are ignored An as example of input the parameter for length scales is called acell and is an array acell 3 for the lengths of the primitive translations in bohr atomic units To input a typical Si diamond lattice one would have the line acell 10 25311 10 25311 10 25311 in the input file This may equivalently be written acell 3 10 25311 57 3 2 THE INPUT FILE and will still be parsed correctly Multiple spaces are ignored as is any text which does not contain the character strings which correspond to some input parameters In case of arrays only the needed numbers will be consid ered and the eventual numbers after those needed will also be ignor
34. Ob DN s ose se oa eK a ek Ae 120 SAR OD ar OBJ s ccs bk aa ED Pe ee 121 DAD SODIO ODIO oo 24 kaw ew a a od elk A 121 AAO Objet ODIO s 2 2 cee hee eee ebades ene Quad eee dads 121 AAA PUBrOUPMG s o 2 edb de Aa AERA Eee awe eee ees 122 LATA EOL a cara a a EG ee al 122 Alo SpE cx e yea a O RA dd e ae 123 WANE GROOM 2 Ge SR a ee eee A A O a D E 123 AMLO SPerOUpMG 224 4444 44 4 6 e OER R EA aA Dede ee Oda ade DA 124 BANG Vas niu ok koe oad eH ac ahh Oa oo 124 Bal VACHE o cvs 642 4 SHEER AD ae ee wea eee aa 124 Ground state calculation variables VARGS o e e 124 ADA Bale cocina a AA 124 ADA BADEY A ROE RE ee RE SRG WE ARE oe a 125 o IEA 125 ADAL DEONCBI RE oca e uae aaa e ii Go eee e a 126 AO DOUe oo 4 2 eos A A a ee AG BR ss a 126 A 6464 bbe bea Aa SEE OHM Sa Hea Meee eS EEE 126 ADT Rs 113333 a a Ae ee a ERA A Se ERS 127 ADS CURP o 26 60 2444 84 2S SOO eee Dh e de Yea ee 127 AGO epus ODUM ODUN s cacas rs a Goh OR 127 ADO ecu caras ek ee dira a ee hae 128 e AN 128 A A AN 128 ADS AUGE carios rasa A a OAS 128 A E A ee SSS BOE A ae G SE oe ee G 129 A era riss arada CHEE aaa eee Seed Pea 129 4 5 16 desdeltae 2 464 204024 844406200 8244 edd a ED 130 AUT O8 ld ce eee ESOS EERE DEERE AEG ee eee ed 130 AMS CRU oct S Sea aoa eg ee ER de a ee A 130 ALONG fband 22 oe ee kee ee eRe eRe eb eee 131 ABA DSO 2 ke eRe BSE A See A LA 131 WA N 6 aches oy OE Ee Pe ae e eee eG a 131 AGAR y o eck ew ee aon a CORRES EEG OER
35. Re Be Ge Gy ch ae ak ae Gres eee Ne A a we ee ee 158 a 664 4 RRA BUREN Sa He eee eee Baa 159 AMO ZO TAMBO asa SG A we Be a PARA a BES 159 Structure optimization variables VARRLX o e 159 AD A ack Se yin Ads RA A Be ee eo oa a we we a A 159 AL delayperm sa isese tita Oe ee EE OEE A be eee es 160 BAMA COAG en hk Am eee A EEE OO 160 ELA OA ee oe coo race gy Gade ae a aa A Re a 160 AJO COS ch ek ee a a EES RR oe Pe Pas 161 BO RE IDA acs ek AES eth EE be eA ra a a 161 ALT BOC sek ba ae ee aed SH eR ee Oh eh eG RH A 161 ALS COCA eos ae wa ek A A eR A A Oh ee Sh a 162 A oa a hE RSS ERDAS H DESDE ap DEER OE Ew YS we ws 162 A oe oa eh hae EERE ae a RRS ee RES SRE RS 162 CANER e foe ha REDO DEER Ae A EG ES 162 AAA TN a ee eR BARGES NN 163 A cece cae casey ge NE 163 e ak be RE OEE AR WEE ORE ERE owe Ba PAS 163 AM litio ek et Eee eat he be a ee ee AS 163 A 2 23 2 dd mean ASE RRMA SESE WHR OR RRR ARS 163 AM Oem 50 iia 164 AAU TSMC oos a ean DO DORE EP a at hk ERS Ges 165 ALIS cee ahha dk SAREE A ee pee OOS ee RR EEe OS SS 165 e II 165 e III E al GR ee Ee a wR Ew a aA 165 CONTENTS Index E AN 165 e RE 165 A o A Pd aea a eh ee a ROO ee eee eh eae a A 165 AMIS od AN 166 A UU PODOSCIDBP s Eoi aae e a a i a a a 166 STZ atime oe a paa aon e A a a A 166 ALISON DD curada a a a h G 167 AMIGO OptCE cidos ee ae RR eee EERE ra AA 167 o 64 6654 Raha DAA EEO AA Oe OEE EE i HA 168 AU AY a a ee Oe ee AE amp ee an 168 A
36. These are our final data for the local spin density approximation We have used izc 1 Other expressions for the local spin density approximation xc 2 3 7 are possible The values 1 2 3 and 7 should give about the same results since they all start from the XC energy of the homogeneous electron gas as determined by Quantum Monte Carlo calculations Other possibilities irc 4 5 6 are older local density functionals that could not rely on these data 2 2 5 The use of the Generalized Gradient Approximation We will use the Perdew Burke Ernzerhof functional proposed in Phys Rev Lett 77 3865 1996 In principle for GGA one should use another pseudopotential than for LDA However for the special case of Hydrogen and in general pseudopotentials with a very small core including only the 1s orbital pseudopotentials issued from the LDA and from the GGA are very similar So we will not change our pseudopotential This will save us lot of time as we should not redo an ecut convergence test ecut is often characteristic of the pseudopotentials that are used in a calculation Independently of the pseudopotential an acell convergence test should not be done again since the vacuum is treated similarly in LDA or GGA So our final values within GGA will be easily obtained by setting xc to 11 in the input file t24 in See ABINIT Tutorial t25 in for an example etotal11 1 1621428502E 00 etotal12 4 9869631857E 01 xcar
37. Used to control response function calculation of third order response Not implemented 4 10 26 rfuser Mnemonics Response Function USER defined Characteristic RESPFN Variable type integer parameter Default is 0 Available to the developpers to activate the use of ipert natom 5 and ipert natom 6 two sets of perturbations that the developpers can define e 0 no computations for ipert natom 5 or ipert natom 6 e 1 response with respect to perturbation natom 5 will be computed e 2 gt response with respect to perturbation natom 6 will be computed e 3 gt responses with respect to perturbations natom 5 and natom 6 will be computed In order to define and use correctly the new perturbations the developper might have to in clude code lines or additional routines at the level of the following routines cgwf3 f chkph3 f dyout3 f d2sym3 f eneou3 f eneres3 f gath3 f insy3 f loper3 f mkcor3 f nstdy3 f nstwf3 f re spfn f scfev3 f syper3 f vloca3 f vtorho3 f vtowfk3 f wings3 f In these routines the developper should pay a particular attention to the rfpert array defined in the routine respfn f as well as to the ipert local variable 4 10 27 sciss Mnemonics SCISSor operator Characteristic RESPFN ENERGY Variable type real parameter Default is 0 It is the value of the scissors operator the shift of conduction band eigenvalues used in response function calculations Can be specified in Ha t
38. WISP SIGN PEM cia OO ee RS ae a ee we 168 AIRE LE a a a ee eee wees Gee Gd he ele e Gangs ce ae e 169 ATL IASTEDICCON 642424434 20 aoe ERR ERA e Dee ee RO dae eda 169 A ss kd oe ER OR BR OE SM A 169 BV SOCOM 6 6 ee be Ro ERS ee eee be eR es 169 AAS VEL oia ee a RSME EERE A OER eee a aaa 170 ATLIS VS s o Goo eR REE RRO ERE EERE a ER Re 170 AU SO WtAtCON sss he ee op DS we a we A A a 170 173 Chapter 1 New User Guide Foreword The ABINIT package is written by the ABINIT group See the files X ABINIT Infos context and V ABINIT Infos planmning for more details about the ABINIT group and the ABINIT project You will find the welcome message and basic information about the Web site in the welcome address Before reading the present file you should get the paper Iterative minimization techniques for ab initio total energy calculations molecular dynamics and conjugate gradients M C Payne M P Teter D C Allan T A Arias and J D Joannopoulos Rev Mod Phys 64 1045 1097 1992 and read the introductory section After having gone through this beginner s introduction you should follow the tutorial 1 1 Introduction ABINIT is a package whose main program allows finding the total energy charge density and electronic structure of systems made of electrons and nuclei molecules and periodic solids within Density Functional Theory using pseudopotentials and a planewave basis ABINIT also includes options to optimize
39. a where x ecut kinetic_energy ecutsm Note that x2 3 2 x is 0 at x 0 with vanishing derivative and that at x 1 it is 1 with also vanishing derivative If ecutsm is zero the unmodified kinetic energy is used ecutsm can be specified in Ha the default Ry eV or Kelvin since ecutsm has the ENERGY characteristics 1 Ha 27 2113961 eV A few test for Silicon diamond structure 2 k points have shown 0 5 Ha to be largely enough for ecut between 2Ha and 6Ha to get smooth curves It is likely that this value is OK as soon as ecut is larger than 4Ha 4 11 6 friction Mnemonics internal FRICTION coefficient Characteristic Variable type real parameter Default is 0 001 Gives the internal friction coefficient atomic units for Langevin dynamics when ionmov 9 fixed temperature simulations with random forces The equation of motion is M d R dt Fr frictionMrd Rr dt Fandom 1 where Frandom 7 is a Gaussian random force with average zero and variance 2 frictionMykT The atomic unit of friction is Hartrees electronic mass atomic time units bohr See J Chelikowsky J Phys D Appl Phys 33 2000 R33 4 11 7 getcell Mnemonics GET CELL parameters from Characteristic Variable type integer parameter an instance of a get variable Default is 0 161 4 11 STRUCTURE OPTIMIZATION VARIABLES VARRLX This variable is typically used to chain the calculations in the multi datase
40. a working directory So you should create a subdirectory of this directory whose name might be Work so ABINIT Tutorial Work Change the working directory of windows 2 to Work CHAPTER 2 TUTORIAL mkdir Work cd Work You will do most of the actions of this tutorial in this working directory Copy the file tix files in Work cp tix files Edit the t1x files It is not very long only 6 lines It gives the informations needed for the code to build other file names You will discover more about this file in the section 1 1 of the abinis_help file Please read it now the third window shows up when you click on this link Modify the first and second lines of t1x files file so that they read tit in tit out Later you will again modify these lines to treat more cases Close the t1x files file Then copy the file ABINIT Tutorial t11 in in Work cp til in Also later we will look at this file and learn about its content For now you will try to run the code Its location is abinis So in the Work directory type abinis lt tix files gt amp log Wait a few seconds it s done You can look at the content of the Work directory ls Different output files have been created including a log file and the output file t11 out To check that everything is correct you can make a diff of t11 out with a reference file that used slightly different names
41. ae ee ee ee EP OE 132 D23 A 132 ADA IEDIDOMAS cocos ead HE ee A a rd HD Ro 133 A520 EP a 244444 See Oe RR RR 2 A haw es eS 133 4526 Epi cc io a 546494 FREE da de REA e es 133 AS e aaa A A a SG A 134 0 29 DSPE cecilia a da e e id de EG 135 A E 135 A NN 135 AOSI A ee ta ee ek a OSES eee OES ae he ee ee Ra DAS 136 A MRM 6454 54422 eee Ree ERE Pe hee et ee a 136 AOS UDE chk ee we Eee oe ER OR Sh HO eR es eR A 137 2 5 04 PP ea ow te a ce eae a ee ke eee Ee eee oS 137 4 5 90 tipspaleh oe se eee SAD SHOE DED H a a a ELE EEE GH 138 Wipe BOG ive oe Gs a A A ae eee ee a ee S 138 A537 NSpdetts lt 6 6 bbb SSa a A eee CES EEEE EE EG 138 oO es ERAN ae he a an a ee ee ee a i ee ee Re a a 138 vil CONTENTS 4 6 4 7 4 8 4 9 AO PAE a A A A a e de Ra a a a a 139 2 040 D NBDUTS ce a ae oh A A A a 139 o AN 139 ADA OBLAFVES 2 2 644 4b Do tar a 139 ADS SONDA a s e ee Se OR a ES Re Ge eR Dw 140 20 pepe obsolete 2 3 04 444 la eee ebb ee a 140 ASAS ADE se Rk ee eG RARER REE A Se Ee oe oR AS 140 E 2 ig eee RRR ERE EE Eb eee EE eee ee Ee a 141 ADAT PARSON oo 6 4 oe RAD AA EAA GD Oe CREME EE BH ES 141 ADAS AER EAN 141 ALDO stmbiis e ccs cea ee AA e ad ee e a 142 AI AAA A a we 142 4 5 01 o lt 6 44 4444 44 6 Ge bse aaa eee ee ede aaada 142 A552 GpRVSEL cos Gh oe ee ERK AL Oe Be LR abs oe Aw A 143 Lodo ISE cc bee oa ee A ee ea eee a 143 ADOT VANU oa sa baw Ge PRES bee RR oo eh b 143 AD Go WAOWIGtH oc ce ek eee eee eb eae a db aa
42. also combines actual FFT operations using 2 routines from Goedecker with important pre and post processing operations in order to maximize cache data reuse This is very efficient for cache architectures coded for A 1 and A 4 but A 4 is not yet sufficiently tested Internal representation as ngfft 7 4 2 9 fftcache Mnemonics Fast Fourier Transform CACHE size Characteristic DEVELOP Variable type integer parameter Default is 16 Not yet machine dependent Gives the cache size of the current machine in Kbytes Internal representation as ngfft 8 97 4 2 DEVELOPPEMENT VARIABLES VARDEV 4 2 10 freqsusin Mnemonics FREQuencies for the SUSceptibility matrix the INcrement Characteristic DEVELOP Variable type real parameter positive or zero Default is 0 0 Define with freqsuslo the series of imaginary frequencies at which the susceptibility matrix should be computed This is still under development 4 2 11 freqsuslo Mnemonics FREQuencies for the SUSceptibility matrix the LOwest frequency Characteristic DEVELOP Variable type real parameter positive or zero Default is 0 0 Define with freqsusin the series of imaginary frequencies at which the susceptibility matrix should be computed This is still under development 4 2 12 idyson Mnemonics Integer giving the choice of method for the DYSON equation Characteristic DEVELOP Variable type integer parameter Default value is 1 Choice
43. are described below Note however that the current version of ABINIT is able to read all these formats not to write them The format for version 4 1 was write unit header codvsn headform fform write unit header bantot date intxc ixc natom ngfft 1 3 4 amp nkpt nspden nspinor nsppol nsym npsp ntypat occopt pertcase amp amp ecut ecutsm ecut_eff qptn 1 3 rprimd 1 3 1 3 tphysel tsmear write unit header istwfk 1 nkpt nband 1 nkpt nsppol amp npwarr 1 nkpt so_typat 1 ntypat symafm 1 nsym amp symrel 1 3 1 3 1 nsym typat 1 natom amp kpt 1 3 1 nkpt occ 1 bantot tnons 1 3 1 nsym znucltypat 1 ntypat do ipsp 1 npsp npsp lines 1 for each pseudopotential npsp ntypat except if alchemical pseudo atoms write unit unit title znuclpsp zionpsp pspso pspdat pspcod pspxc enddo final record residm coordinates total energy Fermi energy write unit unit residm xred 1 3 1 natom etotal fermie The format for version 4 0 was write unit header codvsn headform fform write unit header bantot date intxc ixc natom ngfft 1 3 amp amp nkpt nspden nspinor nsppol nsym npsp ntypat occopt amp amp ecut ecutsm ecut_eff rprimd 1 3 1 3 tphysel tsmear write unit header istwfk 1 nkpt nband 1 nkpt nsppol amp npwarr 1 nkpt so_typat 1 ntypat symafm 1 nsym amp symrel 1 3 1 3 1 nsym typat 1 natom amp kpt 1 3 1 nkpt occ 1 bantot tnons 1 3 1 nsym znucltyp
44. be exact in the case of plane wave not PAW this ratio should be at least two If one uses a smaller ratio one will gain speed at the expense of accuracy In case of pure ground state calculation e g for the determination of geometries this is sensible However the wavefunctions that are obtained CANNOT be used for starting response function calculation 4 5 6 charge Mnemonics CHARGE Characteristic Variable type real number Default is 0 126 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Used to establish charge balance between the number of electrons filling the bands and the nominal charge associated with the atomic cores The code adds up the number of valence electrons provided by the pseudopotentials of each type call this zval then add charge to get the number of electrons per unit cell nelect Then if iscf is positive the code adds up the band occupancies given in array occ for all bands at each k point then multiplies by the k point weight wtk at each k point Call this sum nelect_occ for the number of electrons from occupation numbers Tt is then required that nelect_occ nelect To treat a neutral system which is desired in nearly all cases one must use charge 0 To treat a system missing one electron per unit cell set charge 1 4 5 7 chkexit Mnemonics CHecK whether the user want to EXIT Characteristic Variable type integer parameter Default is 2 for sequent
45. be the subject of the next section of the present tutorial The sections to be read are e the part of section 1 that had not yet been read e section 2 e section 4 e and for completeness section 5 You are now in the position to compute the full dynamical matrix at Gamma q 0 including the coupling with an homogeneous electric field You can copy the file ABINIT Tutorial t55 in in Work5 This is your input file You should edit it As for the other RF tests the changes with respect to the file ABINIT Tutorial t51 in are all gathered in the first part of this file Unlike the other tests however the multi dataset mode was used computing from scratch the ground state properties then computing the effect of the ddk perturbation then the effect of all other perturbations electric field as well as atomic displacements The run lasts about 3 minutes on a PIII 450MHz The analysis of the output file is even more cumbersome than the previous ones Let us skip the first dataset In the dataset 2 section one perturbation is correctly selected gt initialize data related to q vector lt The list of irreducible perturbations for this q vector is 1 idir 1 ipert 3 Perturbation wavevector in red coord 0 000000 0 000000 0 000000 Perturbation derivative vs k along direction 1 The analysis of the output for this particular perturbation is not particularly interesting except for the f sum rule ratio loper3 ek2
46. but also on the two values of the Compensation charge inside spheres a quantity written in the log file 4 9 3 pawlcutd Mnemonics PAW 1 L angular momentum used to CUT the development in moments of the Densitites Characteristic Variable type integer parameter The default is 10 Needed only when usepaw 1 The expansion of the densities in angular momenta is performed up to 1 pawlcutd 1 The choice made for this variable DOES have a bearing on the numerical accuracy of the results and as such should be the object of a convergence study The convergence test might be made on the total energy or derived quantities like forces but also on the two values of the Compensation charge inside spheres a quantity written in the log file 4 9 4 pawmgqgrdg Mnemonics PAW Max number of Q space GRid points for psp for the Double Grid Characteristic Variable type integer parameter The default is 1 Needed only when usepaw 1 Same use as mqgrid but for the fine grid instead of the coarse grid Tf set to 1 the step corresponding to mqgrid for the coarse grid defined by the energy cut off ecut is computed and then the same step is used for the fine grid defined by the energy cut off pawecutdg 4 9 5 pawnphi Mnemonics PAW Number of PHI angles used to discretize the sphere around each atom Characteristic Variable type integer parameter 152 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIS
47. code to use the KSS file calculated in the previous dataset Then three input variables describe the computation nband2 25 Bands to be used in the screening calculation ecutwfn2 2 1 Cut off energy of the planewave set to represent the wavefunctions ecuteps2 3 6 Cut off energy of the planewave set to represent the dielectric matrix In this case we use 25 bands to calculate the Kohn Sham response function es we use a cut off ecutwfn 2 1 Hartree giving 89 planewaves to represent the wavefunctions in the calculation of x2 The dimension of Yes as well as all the other matrices x is determined by ecuteps 3 6 Hartree giving 169 planewaves Finally we define the frequencies at which the screening must be evaluated w 0 0 eV and the imaginary frequency w i 16 7 eV The latter is determined by the input variable plasfrq plasfrq2 16 7 eV Imaginary frequency where to calculate the screening 42 CHAPTER 2 TUTORIAL The two frequencies are used to calculate the plasmon pole model parameters For the non zero frequency it is recommended to use a value close to the plasmon frequency for the plasmon pole model to work well Plasmons frequencies are usually close to 0 5 Hartree The parameters for the screening calculation are not far from the ones that give converged Energy Loss Function Im e spectra So that one can start up by using indications from EELS calculations existing in literature
48. crystal potential from the input atomic pseudopotentials then uses either an input wavefunction or simple gaussians to generate the initial charge density and screening potential then uses a self consistent algorithm to iteratively adjust the planewave coefficients until a sufficient convergence is reached in the energy Analytic derivatives of the energy with respect to atomic positions and unit cell primitive translations yield atomic forces and the stress tensor The code can optionally adjust atomic positions to move the forces toward zero and adjust unit cell parameters to move toward zero stress It can performs molecular dynamics It can also be used to find responses to atomic displacements and homogeneous electric field so that the full phonon band structure can be constructed In order to know more about ABINIT please follow the Tutorial Chapter 2 Tutorial This tutorial is aimed at teaching the use of ABINIT in the UNIX Linux OS and its variants OSF HP UX AIX It might be used for other operating systems but the commands have to be adapted Note that it can be accessed from the ABINIT web site as well as from your local ABINIT Infos Tutorial welcome html file The latter solution is of course preferable as the response time will be independent on the network traffic At present six lessons are available Each of them is at most two hours of student work Lessons 1 4 cover basics other lectures are more specialized
49. e 1 abc abc e 2 abc cab e 3 abc bca e 4 abc acb e 5 abc bac e 6 abc cba 122 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Monoclinic there are 3 or 9 possibilities depending on the space group See the space group help file for details In the log output file the notation used to describe the monoclinic groups is for example 15 c1 A2 a_c C2 c where e 15 represents the space group number e c1 the orientation as it appears on the web page e A is the real Bravais type lattice e 2 a the existent symmetry elements e _c marks the orientation of the two fold axis or of the mirror plane e C2 c represents the parent space group 4 4 13 spgorig Mnemonics SPace Group ORIGin Characteristic SYMMETRISER Variable type integer parameter Default 1 Gives the choice of origin for the axes system taken into account only when spgroup 0 It is defined according to the origin choice in the International Tables of Crystallography It applies only to the space groups 48 50 59 70 85 86 88 125 126 129 130 133 134 137 141 142 201 203 222 224 227 228 For details see the space group help file 4 4 14 spgroup Mnemonics SPace GROUP number Characteristic SYMMETRISER Variable type integer parameter Default 0 Gives the number of the space group If spgroup is 0 the code assumes that all the symmetries are input through the symrel matrices and the tnons vectors
50. each band is reasonable as well as the band widths but the band gaps are known to be qualitatively wrong Now we will compute the band gaps much more accurately using the so called GW approximation We start by an example in which we show how to perform in one shot the calculation of the ground state the Kohn Sham electronic structure the screening and the Self Energy matrix elements that is the GW corrections for one given k point for the highest occupied and the lowest empty bands We provide some reasonable parameters without checking convergence You 40 CHAPTER 2 TUTORIAL will see that this procedure is MUCH MORE time consuming than the corresponding calculation of the Kohn Sham eigenvalues So let us run immediately this calculation and while it is running we will explain what has been done In directory ABINIT Tutorial Work6 copy the files ABINIT Tutorial t6x files and t61 in and modify the t6x files file as usual Then issue abinis lt t6x files gt amp t61 log Y It is very important to run this job in background Indeed a PC Intel PIV 2 2 GHz will take about 6 minutes to complete it In the meantime you should read the following 1 The three steps of a GW calculation In order to complete a standard GW calculation one has to a Run a converged Ground State calculation at fixed lattice parameters and atomic positions to get self consistent density and potential and Kohn Sham
51. eigenvalues and eigenfunctions at the relevant k point as well as on a regular grid of k points b On the basis of these available Kohn Sham data compute the independent particle susceptibility matrix chi0 on a regular grid of wavevectors for at least two fre quencies usually zero frequency and a large frequency on the order of the plasmon frequency a dozen of eV then compute the dielectric matrix epsilon in the same conditions its inverse and the Random Phase susceptibility matrix chi c On this basis compute the self energy operator sigma at a given k point and derive the GW eigenvalues for the target states at this k point The input file t61 in has precisely that structure there are three datasets The first dataset starts a rather usual SCF calculation then will construct a specialized file t6xo_DS1_KSS _KSS for Kohn Sham Structure that contains the needed information to start step 2 The second dataset drives the computation of susceptibility and dielectric matrices giving another specialized file t6xo_DS2_EM1 _EM1 for Epsilon Minus 1 the inverse dielectric matrix Then in the third dataset one builds the eigenvalues of the 4th and 5th bands at the Gamma point So you can edit this t61 in file In the dataset independent part of this file the last half of the file there is the usual set of input variables describing the cell atom types number pos
52. for all pseudopotentials e If 3 treat spin orbit in the HFN form not allowed for all pseudopotentials Also so_typat 0 default to 1 2 or 3 according to the data contained in the pseudopotential file 1 there is no spin orbit information in the psp file 2 the spin orbit information is of the HGH form 3 the spin orbit information is of the HFN form 4 5 45 qpt Mnemonics Q PoinT Characteristic Variable type real array of 3 elements Default wavevector is 0 0 0 Define a q vector See qptnrm for extra normalization In ground state calculation if nqpt is 1 the vector qptn 1 3 qpt 1 3 qptnrm is added to each renormalized k point kpt 1 3 kptnrm to generate the normalized shifted set of k points kptns 1 3 1 nkpt In response function calculations qptn 1 3 qpt 1 3 qpturm is the wavevector of the phonon type calculation For insulators there is no restriction on the q points to be used for the perturbations By contrast for metals for the time being it is adviced to take q points for which the k and k q grids are the same when the periodicity in reciprocal space is taken into account Tests remains to be done to see whether other g points might be allowed perhaps with some modification of the code 140 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 5 46 qptnrm Mnemonics Q PoinTs NoRMalization Characteristic Variable type real parameter Default is 1 0 Provides re norma
53. for the inner loop index or the outer loop index Two signs will be appended to the variable name instead of one in the simple series case One of these signs must be a question mark again used as a metacharacter able to assume the values 1 to 9 If it is found in the first of the two positions it means that the series does not care about the outer loop index so the values generated are equal for all outer loop index values If it is found in the second of the two positions the series does not care about the inner loop index The other sign can be a colon a plus or a times as in the case of the series defined in 2a with the same meaning Rule 1 has precedence over them they have precedence over rules 3 or 4 rule 2a has precedence over rules 2b or 2c and the two latter cannot be used simultaneously for the same variable 4th example ndtset 6 udtset 2 3 acelli 10 10 10 acell2 15 15 15 ecut 5 ecut 1 is equivalent to ndtset 6 jdtset 11 12 13 21 22 23 acellii 10 10 10 ecutil 5 acelli2 10 10 10 ecut12 6 acell113 10 10 10 ecuti3 7 acell21 15 15 15 ecut21 5 acell22 15 15 15 ecut22 6 acell23 15 15 15 ecut23 7 More examples can be found in the directory Test_v1 cases 59 and later 3 2 6 File names in the multi dataset mode The root names for input and output files potential density wavefunctions and so on will receive an appendix DS followed by the index of the dataset See section 4 The
54. gradient optimisation of first order wavefunctions there is an instability situation when the q wavevector of the perturbation brings the eigenenergy of the highest treated band at some k point higher than the lowest untreated eigenenergy at some k q point If one accept a buffer of frozen states this instability can be made to disappear Frozen states receive automatically a residual value of 0 1d0 For a RF calculation with 3 lt occopt lt 7 supposing nbdbuf is not initialized in the input file then ABINIT will overcome the default nbdbuf value and automatically set nbdbuf to 2 This value might be too low in some cases Also the number of active bands in all cases is imposed to be at least 1 irrespective of the value of nbdbuf 4 5 30 nberry Mnemonics Number of BERRY phase computations Characteristic Variable type integer nberry Default is 1 Used for non zero values of berryopt 135 4 5 GROUND STATE CALCULATION VARIABLES VARGS Gives the number of Berry phase computations of polarisation or finite difference estima tions of the derivative of wavefunctions with respect to the wavevector each of which might be characterized by a different change of wavevector kberry When equal to 0 no Berry phase calculation of polarisation is performed The maximal value of nberry is 20 Note that the computation of the polarisation for a set of bands having different occupation numbers is meaningless although in the cas
55. i e the user may use xangst instead of xred or xcart to provide starting coordinates One and only one of xred xcart and xangst must be provided The conversion factor between Bohr and Ais 1 Bohr 0 5291772083 A See Physics Today Au gust 1989 p 8 Atomic positions evolve if ionmov 0 In constrast with xred and xcart xangst is not internal 4 1 33 xcart Mnemonics vectors X of atom positions in CARTesian coordinates Characteristic EVOLVING LENGTH Variable type real array xcart 3 natom or xcart 3 natrd if the geometry builder is used Gives the cartesian coordinates of atoms within unit cell This information is redundant with that supplied by array xred or xangst By default xcart is given in bohr atomic units 1 bohr 0 5291772083 A although Angstrom can be specified if preferred since xcart has the LENGTH characteristics If xred and xangst are ABSENT from the input file and xcart is provided then the values of xred will be computed from the provided xcart i e the user may use xcart instead of xred or xangst to provide starting coordinates Atomic positions evolve if ionmov 0 4 1 34 xred Mnemonics vectors X of atom positions in REDuced coordinates Characteristic EVOLVING Variable type real array xred 3 natom or xred 3 natrd if the geometry builder is used Default to all 0 0d0 Gives the atomic locations within unit cell in coordinates relative to real space primitive trans lations NOT in ca
56. in MEMory Characteristic Variable type integer parameter Default is 1 i e an in core solution Governs the choice of number of FFT arrays that will be kept permanently in core memory The allowed values are 0 in which case maximal use is made of disk space saving core memory at the expense of execution time not much usually or 1 in which case everything is kept in core memory More detailed explanations if mffmem 0 some arrays of size double precision xx nfft nsppol will be saved on disk when the wavefunctions are optimized or when the Hartree and xc potential is computed which can require some sizeable memory space also The number of these arrays is 10 if iscf 5 5 if iscf 1 and 4 if iscf 2 or 3 The saving of memory can be appreciable especially when iscf 5 and nsppol 2 4 3 20 mkmem Mnemonics Maximum number of K points in MEMory Characteristic Variable type integer parameter Default is nkpt i e in core solution Sets the maximum number of k points for which the ground state wavefunctions are kept in core memory at one time This value should either be 0 in which case an out of core solution will be used or else nkpt in which case an in core solution will be used Internal representation as mkmems 1 4 3 21 prtcml Mnemonics PRinT CML file Characteristic Variable type integer parameter Default is 0 If set to 1 or a larger value provide output of geometrical parameters using CML t
57. input variables is given in e Basic variables VARBAS e Developpement variables VARDEV e Geometry builder symmetry related variables VARGEO e Ground state calculation variables VARGS e GW variables VARGW e Files handling variables VARFIL e Parallelisation variables VARPAR e Projector Augmented Wave variables VARPAW e Response Function variables VARRF e Structure optimization variables VARRLX A set of examples aimed at guiding the beginner is available in the tutorial Other test cases more than 200 input files can be found in the ABINIT Test_fast ABINIT Test_v1 and ABINIT Test_v2 directories Many different sorts of pseudopotentials can be used with ABINIT Most of them can be found on the ABINIT web site There is a set of Teter hardness conserving potentials a set of Troullier Martins potentials a few Goedecker Teter Hutter pseudopotentials and Hartwigsen Goedecker Hutter potentials for the whole periodic table A subset of existing pseudopotentials are used for test cases and are located in the ABINIT Psps_for_tests directory Information on pseudopotential files can be found in the ABINIT help file and the ABINIT Infos Psp_infos directory 1 3 Other programs in the ABINIT package In addition to abinit there are utility programs mrgddb anaddb aim conducti newsp and cut3d are present in the package Others presently kptgen might be found on the Web site mrgddb and anaddb allow
58. is allowed 4 10 20 rfphon Mnemonics Response Function with respect to PHONons Characteristic RESPFN 4 10 21 rflphon Mnemonics non linear Response Function 1st mixed perturbation PHONons Characteristic NON LINEAR 4 10 22 rf2phon Mnemonics non linear Response Function 2nd mixed perturbation PHONons Characteristic NON LINEAR 4 10 23 rf2phon Mnemonics non linear Response Function 3rd mixed perturbation PHONons Characteristic NON LINEAR Variable type integer parameter Default is 0 It must be equal to 1 to run phonon response function calculations or to include some phonon perturbation in non linear computations 4 10 24 rfstrs Mnemonics Response Function with respect to STRainS Characteristic RESPFN Variable type integer parameter Default is 0 Used to run strain response function calculations e g needed to get elastic constants Define with rfdir the set of perturbations 157 4 10 RESPONSE FUNCTION VARIABLES VARRF e 0 no strain perturbation e 1 only uniaxial strain s ipert natom 3 is activated e 2 gt only shear strain s ipert natom 4 is activated e 3 both uniaxial and shear strain s both ipert natom 3 and ipert natom 4 are acti vated See the possible restrictions on the use of strain perturbations in the respfn_help file 4 10 25 rfthrd Mnemonics Response Function of THiRD order Characteristic RESPFN Variable type integer parameter Default is 0
59. is also a writing for each of the 5 first calls and the 10th call 4 2 21 istwfk Mnemonics Integer for choice of STorage of WaveFunction at each k point Characteristic Variable type integer array istwfk nkpt Default is 0 for all kK points for GS calculations For RF calculations the Default is not used ist wfk is forced to be 1 deep inside the code for all k points For spin orbit calculations nspinor 2 istwfk is also forced to be 1 for all k points Control the way the wavefunction for each k point is stored inside ABINIT in reciprocal space For the GS calculations in the cg array containing the wavefunction coefficients there is for each k point and each band a segment cg 1 2 l npw The full number of plane wave is determined by ecut However if the k point coordinates are build only from zeroes and halves see list below the use of time reversal symmetry that connects coefficients has been implemented in order to use real to complex FFTs see fftalg and to treat explicitly only half of the number of plane waves this being used as npw For the RF calculations there is not only the cg array but also the cgq and cgl arrays For the time reversal symmetry to decrease the number of plane waves of these arrays the q vector MUST be 0 0 0 Then for each k point the same rule as for the RF can be applied WARNING 991018 for the time being the time reversal symmetry c
60. k point this corresponds to the silicon case However the computation of phases inside nonlop is somehow time consuming Note internally nloalg is an array nloalg 1 4 that also allows to initialize in order jump mblkpw and mincat not documented However only the first component nloalg 1 is read as an input variable 103 4 2 DEVELOPPEMENT VARIABLES VARDEV 4 2 29 nnsclo Mnemonics Number of Non Self Consistent LOops Characteristic DEVELOP Variable type integer parameter Default is 0 Gives the maximum number of non self consistent loops of nline line minimisations in the SCF case when iscf gt 0 In the case iscf lt 0 the number of non self consistent loops is determined by nstep The Default value of 0 correspond to make the two first fixed potential determinations of wavefunctions have 2 non self consistent loops and the next ones to have only 1 non self consistent loop 4 2 30 optforces Mnemonics OPTions for the calculation of FORCES Characteristic DEVELOP Variable type integer parameter Default is 1 Allows to choose options for the calculation of forces e optforces 0 the forces are set to zero and many steps of the computation of forces are skipped e optforces 1 calculation of forces at each SCF iteration allowing to use forces as criterion to stop the SCF cycles e optforces 2 calculation of forces at the end of the SCF iterations like the stresses NOT YET IMPLEMENTED
61. needed and the file ABINIT Infos Psp_infos psp3 info e pspcod 4 or 5 old format pseudopotentials see ABINIT Infos Psp_infos psp45 info e pspcod 6 pseudopotentials from the fhi98pp code see ABINIT Infos Psp_infos psp6 info 3 5 The different output files Explanation of the output from the code Output from the code goes to several places listed below 3 5 1 The log file The log file this is the standard UNIX output file and corresponds to Fortran unit number 06 a file which echoes the values of the input parameters and describes various steps of the calculation typically in much more detail than is desired as a permanent record of the run This log file is intended to be informative in case of an error or for a fuller description of the run For a successful run the user will generally delete the log file afterwards There are four types of exception messages ERROR BUG WARNING and COMMENT messages ERROR and BUG messages cause the code to stop immediately or after a very small delay An ERROR is attributed to the user while a BUG is attributed to the developer A WARNING message indicates that something happened that is not as expected but this something is not so important as to make the code stop A COMMENT message gives some information to the user concerning something unusual None of them should appear when the run is completely normal After a run is completed always have a look at the end of the log
62. no linear term The difference between the ground state value 9 76268374500102E 00 hartree of the previous run and the perturbed value 9 76268124105590E 00 hartree of the present one is thus one half of the square of the co ordinate change 1 1000 times the 2D TE From these number the 2DTE is 5 00791024 Hartree Alternatively we can start from the reduced gradients The value of the reduced gradient with respect to a displacement of the Al atom along the first reduced axis is 0 005007930232 Hartree At first order this quantity is the product of the 2D TE by the reduced coordinate difference The estimate of the 2DTE is thus 5 007930232 Hartree The agreement with the other estimate is rather good 2 107 Hartree However it is possible to do much better thanks to the use of a higher order finite difference formula For this purpose one can perform another calculation in which the change of reduced coordinate along the first axis is 0 002 instead of 0 001 The doubling of the perturbation allows for a rather simple higher order estimation as we will see later The results of this calculation are as follows rms dE dt 7 1249E 03 max dE dt 1 0016E 02 dE dt below all hartree 1 0 010016299779 0 005097509981 0 005097509981 2 0 010016176675 0 005097455174 0 005097455174 Ewald 8 47987214716789E 00 resulting in Etotal 9 76267372899697E 00 hartree From these data taking into account that the perturbation was twice stron
63. number of divisions of each segment is defined by ndivk 4 5 25 kptrlatt Mnemonics K PoinTs grid Real space LATTice Characteristic Variable type integer array kptrlatt 3 3 No default This input variable is used only when kptopt is positive It partially defines the k point grid The other piece of information is contained in shiftk kptrlatt cannot be used together with ngkpt The values kptrlatt 1 3 1 kptrlatt 1 3 2 kptrlatt 1 3 3 are the coordinates of three vectors in real space expressed in the rprim coordinate system reduced coordinates They defines a super lattice in real space The k point lattice is the reciprocal of this super lattice eventually shifted see shiftk If neither ngkpt nor kptrlatt are defined ABINIT will automatically generate a set of k point grids and select the best combination of kptrlatt and shiftk that allows to reach a sufficient value of kptrlen See this latter variable for a complete description of this procedure 4 5 26 kptrlen Mnemonics K PoinTs grid Real space LENgth Characteristic Variable type real parameter Default 20 0d0 This input variable is used only when kptopt is positive and non zero Preliminary explanation The k point lattice defined by ngkpt or kptrlatt is used to perform integrations of periodic quantities in the Brillouin Zone like the density or the kinetic energy One can relate the error made by replacing the continuous integral by a sum over k p
64. of the three components of acell e optcell 2 full optimization of cell geometry modify acell and rprim normalize the vectors of rprim to generate the acell This is the usual mode for cell shape and volume optimization It takes into account the symmetry of the system so that only the effectively relevant degrees of freedom are optimized e optcell 3 constant volume optimization of cell geometry modify acell and rprim under constraint normalize the vectors of rprim to generate the acell e optcell 4 5 or 6 optimize acell 1 acell 2 or acell 3 respectively only works if the two other vectors are orthogonal to the optimized one the latter being along its cartesian axis e optcell 7 8 or 9 optimize the cell geometry while keeping the first second or third vector unchanged only works if the two other vectors are orthogonal to the one left unchanged the latter being along its cartesian axis NOTE that a few details require attention when performing unit cell optimisation e one has to get rid off the discontinuites due to discrete changes of plane wave number with cell size by using a suitable value of ecutsm e one has to allow for the possibility of a larger sphere of plane waves by using dilatmx e one might have to adjust the scale of stresses to the scale of forces by using strfact e if all the reduced coordinates of atoms are fixed by symmetry one cannot use toldff to stop the SCF cycle Suggestion
65. or obtained from the symmetry finder the default when nsym 0 It should be between 1 and 230 This option can be used to obtain all the atoms in the unit cell starting from the assymetric unit cell The references for computing the symmetry corresponding to the space groups are e International Tables for Crystallography 1983 Ed Theo Hahn D Reidel Publishing Com pany e The mathematical theory of symmetry in solids Representation theory for point groups and space groups 1972 C J Bradley and A P Cracknell Clarendon Press Oxford For details see the space group help file 123 4 5 GROUND STATE CALCULATION VARIABLES VARGS 4 4 15 spgroupma Mnemonics SPace GROUP number defining a MAgnetic space group Characteristic SYMMETRISER NOT INTERNAL Variable type integer parameter Default 0 This input variable might be used to define a Shubnikov magnetic space group anti ferromagnetic space group The user is advised to consult The mathematical theory of symmetry in solids Representation theory for point groups and space groups 1972 C J Bradley and A P Cracknell Clarendon Press Oxford A Shubnikov type IV magnetic space group might be defined by its Fedorov space group set of spatial symmetries that do not change the magnetisation and an additional magnetic space group number spgroupma A Shubnikov type III magnetic space group might be defined by its Fedorov space group set of all spatial symmetri
66. origin of coordinate thanks to the input variable boxcenter The maximal number of Kohn Sham excitations to be used to build the excited state TDDFT matrix can be defined by td_mexrcit or indirectly by the maximum Kohn Sham excitation energy td_maxene 4 1 5 ixc Mnemonics Integer for eXchange Correlation choice Characteristic Variable type integer parameter Default is izc 1 Teter parameterization However if all the pseudopotentials have the same value of pspxc the initial value of xc will be that common value Control the choice of exchange and correlation xc e 0 gt NO xc e 1 LDA or LSD Teter Pade parametrization 4 93 published in S Goedecker M Teter J Huetter Phys Rev B 54 1703 1996 which reproduces Perdew Wang which reproduces Ceperley Alder e 2 gt LDA Perdew Zunger Ceperley Alder no spin polarization e 3 gt LDA old Teter rational polynomial parametrization 4 91 fit to Ceperley Alder data no spin polarization 81 4 1 BASIC VARIABLES VARBAS 4 gt LDA Wigner functional no spin polarization e 5 gt LDA Hedin Lundqvist functional no spin polarization e 6 gt LDA X alpha functional no spin polarization e 7 gt LDA or LSD Perdew Wang 92 functional e 8 gt LDA or LSD x only part of the Perdew Wang 92 functional e 9 gt LDA or LSD x and RPA correlation part of the Perdew Wang 92 functional 11 gt GGA Perdew Burke Ernzerhof GGA functional 12
67. otherwise deduced from other input variables The k point coordinates as fractions of reciprocal lattice translations are therefore kpt mu ikpt kptnrm kptnrm defaults to 1 and can be ignored by the user It is introduced to avoid the need for many digits in representing numbers such as 1 3 It cannot be smaller than 1 0 4 1 9 kptopt Mnemonics KPoinTs OPTion Characteristic Variable type integer parameter Default is 0 Control the set up of the k points list The aim will be to initialize by straight reading or by a preprocessing approach based on other input variables the following input variables giving the k points their number and their weight kpt kptnrm nkpt and for iscf 4 2 wtk 83 4 1 BASIC VARIABLES VARBAS Often the k points will form a lattice in reciprocal space In this case one will also aim at initializing input variables that give the reciprocal of this k point lattice as well as its shift with respect to the origin ngkpt or kptrlatt as well as on nshiftk and shiftk e 0 read directly nkpt kpt kptnrm and wtk corresponds to the usage before version 2 1 One can use the kptgen utility to produce these input data e 1 gt rely on ngkpt or kptrlatt as well as on nshiftk and shiftk to set up the k points Take fully into account the symmetry to generate the k points in the Irreducible Brillouin Zone only This is the usual mode for GS calculations e 2 gt rely on ng
68. ponents are ignored As a side effect the wavefunctions are no more normalized and also no more orthogonal Also the set of plane waves can be much smaller for optdriver 3 than for optdriver 4 although a convergence study is needed to choose correctly both values This set of planewaves can also be determined by the other input variables npwwfn and nshwfn but these are much less convenient to use for general systems than the selection criterion based on the cut off energy 4 6 5 gwcalctyp Mnemonics GW CALCulation TYPe Characteristic GW Variable type integer Default 0 Only relevant if optdriver 3 or 4 that is GW calculations gwcalctyp governs the choice between plasmon pole approximation or full integration or to be described for development purposes 4 6 6 kptgw Mnemonics K PoinTs for GW calculations Characteristic GW Variable type real kptgw 3 nkptgw Default all 0 0 s For each k point with number igwpt in the range 1 nkptgw kptgw 1 igwpt is the reduced coordinate of the k point 145 4 6 GW VARIABLES VARGW At present not all k points are possible Only those corresponding to the k point grid defined with the same repetition parameters kptrlatt or ngkpt than the GS one but WITHOUT any shift are allowed 4 6 7 nbandkss Mnemonics Number of BaNDs STOred Characteristic Variable type integer parameter Default is 0 This input variable also called nbndsto
69. presented in sim ple terms in standard textbooks and should not be forgotten in doing ab initio calculations of phonon frequencies Thus we have now to treat correctly the homogeneous electric field type perturbation 2 5 5 Response function calculation of the effect of an homogeneous electric field The treatment of the homogeneous electric field perturbation is formally much more complex than the treatment of atomic displacements This is primarily because the change of potential associated with an homogeneous electric field is not periodic and thus does not satisfy the Born von Karman periodic boundary conditions For the purpose of the present tutorial one should read the section II C of the above mentioned paper P Giannozzi S de Gironcoli P Pavone and S Baroni Phys Rev B 43 7231 1991 36 CHAPTER 2 TUTORIAL The reader will find in X Gonze Phys Rev B 55 10337 1997 and X Gonze and C Lee Phys Rev B 55 10355 1997 more detailed information of this perturbation closely related to the ABINIT implementation There is also an extensive discussion of the Born effective charges by Ph Ghosez J P Michenaud and X Gonze Phys Rev B 58 6224 1998 In order to compute the response of solids to an homogeneous electric field as implemented in ABINIT the remaining sections of the respfn_help file should be read These also present the information needed to compute phonons with non zero q wavevector which will
70. pseudopotential core correction and Ewald energies e Next is the stress tensor 1 ucyo1 d Etot d straing for Etot total energy per unit cell and a b are x y or z components of strain The stress tensor is given in Cartesian coordinates in Hartree Bohr and GPa The basics of the stress tensor are described in O H Nielsen and Richard M Martin see the bibliography file Having finished all the calculations for the different datasets the code echoes the parameters listed in the input file using the latest values e g for xred vel and xcart and supplement them with the values obtained for the total energy the forces and stresses as well as occupation numbers The latter echoes are very convenient for a quick look at the result of calculation This is followed finally by the timing output both cpu time and wall clock time as provided by calls within the code The total cpu and wall clock times are reported first in seconds minutes and hours for convenient checking at a glance Next are the cpu and wall times for the principal time consuming subroutine calls each of which is independent of the others The sum of these times usually accounts for about 90 of the run time The main subroutines for BIG jobs are 1 fourwf the subroutine which performs the fast fourier transform for the wavefunctions 2 fourdp the subroutine which performs the fast fourier transform related to density and potential
71. respect to the unique perturbation take place iter 2DEtotal Ha deltaE Ha residm vres2 ETOT 1 6 5156051312863 1 464E 01 1 146E 02 1 947E 02 ETOT 2 5 0216331638978 1 494E 00 9 267E 04 2 027E 00 ETOT 3 5 0082678671217 1 337E 02 4 772E 06 7 929E 02 ETOT 4 5 0078677958105 4 001E 04 1 980E 07 2 712E 03 ETOT 5 5 0078558860285 1 191E 05 6 103E 09 5 074E 05 ETOT 6 5 0078557520180 1 340E 07 1 258E 10 9 613E 06 ETOT 7 5 0078557017091 5 031E 08 2 768E 11 3 841E 07 ETOT 8 5 0078557001188 1 590E 09 2 983E 12 6 089E 09 From these data you can see that the 2DTE determined by the response function technique is in excellent agreement with the higher order finite difference formula for the 2DTE determined in the previous section 5 0078555 Hartree from the energy differences and 5 0078552 Hartree from the force differences Now you can read the remaining of the section 6 2 of the respfn_help file Then you should also edit the t530_DDB file and read the corresponding section 6 4 of the respfn_help file Finally the excellent agreement between the finite difference formula and the response function approach calls for some accuracy considerations These can be found in section 7 of the respfn_ help file 35 2 5 LESSON 5 DYNAMICAL AND DIELECTRIC PROPERTIES OF ALAS 2 5 4 Response function calculation of the dynamical matrix at Gamma We are now in the position to compute the full dynamical matrix at Gamma q 0 You can copy the file
72. spin down Fermi energy Note for the time being only the spin down Fermi energy is written out in the main output file In the fixed magnetic moment case it differs from the spin up Fermi energy 4 5 21 iatsph Mnemonics Index for the ATomic SPHeres of the atom projected density of states Characteristic Variable type integer array iatsph 1 natsph Default is 1 2 natsph This input variable is active only in the prtdos 3 case It gives the number of the natsph atoms around which the sphere for atom projected density of states will be build in the prtdos 3 case The radius of these spheres is given by ratsph 131 4 5 GROUND STATE CALCULATION VARIABLES VARGS 4 5 22 iprcel Mnemonics Integer for PReConditioning of ELectron response Characteristic Variable type integer parameter Default is 0 Used when iscf gt 0 to define the SCF preconditioning scheme Potential based preconditioning schemes for the SCF loop electronic part are STILL UNDER DEVELOPMENT The present parameter electronic part describe the way the change of potential is derived from the residual The possible values of iprcel correspond to e 0 gt model dielectric function described by diemac dielng and diemix e larger or equal to 21 will compute the dielectric matrix according to diecut dielam diegap e Between 21 and 29 gt for the first few steps uses the same as option 0 then compute RPA dielectric function and use it as
73. such e Between 31 and 39 for the first few steps uses the same as option 0 then compute RPA dielectric function and use it with the mixing factor diemix e Between 41 and 49 gt compute the RPA dielectric matrix at the first step and recompute it at a later step and take into account the mixing factor diemix e Between 51 and 59 gt same as between 41 and 49 but compute the RPA dielectric matrix by another mean e Between 61 and 69 gt same as between 41 and 49 but compute the electronic dielectric matrix instead of the RPA one The step at which the dielectric matrix is computed or recomputed is determined by mod ulo iprcel 10 For non homogeneous cells relatively large iprcel 45 will likely give a large improvement over iprcel 0 For nsppol 2 with metallic occopt only iprcel 0 is allowed No meaning for RF calculations yet 4 5 23 kberry Mnemonics K wavevectors for BERRY phase computation Characteristic Variable type integer array kberry 3 nberry Default is an array of 0 Used for non zero values of berryopt This array defines for each Berry phase calculation the number of such calculations is defined by nberry the difference of wavevector between k points for which the overlap matrix must be computed The polarisation vector will be projected on the direction of that wavevector and the result of the computation will be the magnitude of this projection Doing more than one wavevector with different
74. that the preparatory GS calculations before a RF calculations must be highly converged Typical values for these preparatory runs are tolwfr between 1 0 x 10716 and 1 0 x 1072 Note that tolwfr is often used in the test cases but this is tolwfr purely for historical reasons except when iscf lt 0 other critera should be used 4 1 30 typat Mnemonics TYPE of atoms Characteristic Variable type integer array typat natom or typat natrd if the geometry builder is used Default is 1 for natom 1 Array giving an integer label to every atom in the unit cell to denote its type The different types of atoms are constructed from the pseudopotential files There are at most ntypat types of atoms As an example for BaTiO3 where the pseudopotential for Ba is number 1 the one of Ti is number 2 and the one of O is number 3 the actual value of the typat array might be typat 12333 The array typat has to agree with the actual locations of atoms given in xred xcart or xangst and the input of pseudopotentials has to be ordered to agree with the atoms identified in typat The nuclear charge of the elements given by the array znucl also must agree with the type of atoms designated in typat The array typat is not constrained to be increasing An internal representation of the list of atoms deep in the code array atindx groups the atoms of same type together This should be transparent to the user while keeping efficiency 4 1
75. the Web site All of its capabilities are present inside abinit however and are even more sophisticated At the level of graphics many commercial or free softwares can be used to visualize ABINIT outputs Some indications are contained in the ABINIT Infos Tutorial lesson_visual file but this topics has not yet been the subject of a systematic help file 1 4 Input variables to abinit The ABINIT help file describes the input variables and the output file As an overview the most important input variables are listed below acell 3 lattice constant of periodic cell in bohr ecut planewave kinetic energy cutoff in hartree lonmov when ionmov 0 the ions and cell shape are fixed 2 search for the equilibrium geometry 6 molecular dynamics iscf either a positive number for defining self consistent algorithm usual or 2 for band structure in fixed potential kptopt option for specifying the k point grid If kptopt 1 automatic generation using ngkpt and shiftk for the latter see abinis help natom total number of atoms in unit cell ngkpt 4 dimensions of the three dimensional grid of k points nstep maximal number of self consistent cycles on the order of 20 ntime number of molecular dynamics or relaxation steps ntypat number of types of atoms occopt set the occupation of electronic levels 1 for semiconductors 3 7 for metals rfelfd when 0 will do response calculation to electric field rfphon when 1 will do r
76. the output file The number of plane waves used for the wavefunctions in the computation of the screening is mentioned in the fragments of output EPSILON 1 parameters EM1 file dimension of the eps 1 matrix 169 number of plane waves for wavefunctions 59 Gathering the macroscopic dielectric constant and GW energies for each planewave set one gets dielectric constant 101 5301 dielectric constant without local fields 147 3095 number of plane waves for wavefunctions 59 4 5 915 11 654 15 244 3 799 0 806 0 241 11 486 0 168 6 083 5 8 445 9 702 3 216 5 555 0 816 0 225 8 942 0 761 9 206 dielectric constant 99 5265 dielectric constant without local fields 143 7208 number of plane waves for wavefunctions 113 4 5 915 11 654 15 244 3 769 0 804 0 244 11 510 0 143 6 059 5 8 445 9 702 3 216 5 582 0 815 0 226 8 964 0 738 9 183 dielectric constant 98 2598 dielectric constant without local fields 142 5982 number of plane waves for wavefunctions 137 4 5 915 11 654 15 244 3 762 0 801 0 248 11 517 0 137 6 052 5 8 445 9 702 3 216 5 588 0 815 0 227 8 970 0 733 9 178 dielectric constant 97 6265 dielectric constant without local fields 142 1664 number of plane waves for wavefunctions 169 4 5 915 11 654 15 244 3 759 0 804 0 244 11 519 0 135 6 050 5 8 445 9 702 3 216 5 590 0 815 0 227 8 972 0 731 9 176 dielectric constant 96 4286 dielectric constant without local fields 140 5466 numbe
77. the sphere input variables natsph and iatsph as well as the radius of this sphere input variable ratsph 4 3 24 prteig Mnemonics PRinT ElGenenergies Characteristic Variable type integer parameter Not yet active 4 3 25 prtfsurf Mnemonics PRinT Fermi SURFace file Characteristic Variable type integer parameter Default is 0 If set to 1 print Fermi surface file For the time being under development 4 3 26 prtgeo Mnemonics PRinT the GEOmetry analysis Characteristic Variable type integer parameter Default is 0 If set to 1 or a larger value provide output of geometrical analysis bond lengths and bond angles The value of prtgeo is taken by the code to be the maximum coordination number of atoms in the system It will deduce a maximum number of nearest and next nearest neighbors accordingly and compute corresponding bond lengths It will compute bond angles for the nearest neighbours only If ionmov 0 the name of the file will be the root output name followed by _GEO If ionmov 1 or 2 one file will be output at each time step with the name being made of e the root output name e followed by _TIMx where x is related to the timestep see later e then followed by GEO The content of the file should be rather self explanatory No output is provided by prtgeo is lower than or equal to 0 If prtgeo gt 0 the maximum number of atoms natom is 9999 114 CHAPTER 4
78. to optimize e 3 gt conduct structural optimization using the Broyden Fletcher Goldfarb Shanno minimiza tion BFGS modified to take into account the total energy as well as the gradients as in usual BFGS See the paper by Schlegel J Comp Chem 3 214 1982 Might be better than ionmov 2 for few degrees of freedom less than 3 or 4 e 4 gt conjugate gradient algorithm for simultaneous optimization of potential and ionic de grees of freedom It can be used with iscf 2 and iscf 5 or 6 WARNING this is under development and does not work very well in many cases optcell 4 0 is not available e 5 gt Simple relaxation of ionic positions according to converged forces Equivalent to ionmov 1 with zero masses albeit the relaxation coefficient is not vis but iprcfc optcell 4 0 is not available e 6 gt Molecular dynamics using the Verlet algorithm see Allen and Tildesley Computer simulation of liquids 1987 p 81 Although partly coded optcell 4 0 is not available The only related parameter is the time step dtion e 7 gt Quenched Molecular dynamics using the Verlet algorithm and stopping each atom for which the scalar product of velocity and force is negative Although partly coded optcell 4 0 is not available The only related parameter is the time step dtion The goal is not to produce a realistic dynamics but to go as fast as possible to the minimum For this purpose it is advised to set all the masses to the
79. to post process reponses to atomic displacements and or to homo geneous electric field as generated by abinit to produce full phonon band structures or thermo dynamical functions mrgddb is for Merge of Derivative DataBases while anaddb is for Analysis of Derivative DataBases Another utility is newsp whose main routine source is called newsp f It allows a crude inter polation among the wavefunctions at different k points and is useful in reformatting wavefunction files to restart jobs on either new unit cell geometries new planewave cutoffs or new k point grids Most of its capabilities have been transferred recently inside abinit however cut3d can be used to post process the three dimensional density or potential files generated by abinit It allows to deduce charge density in selected planes for isodensity plots along selected lines or at selected points It allows also to make the Hirshfeld decomposition of the charge density in atomic contributions aim is also a post processor of the three dimensional density files generated by abinit It performs the Bader Atom In Molecule decomposition of the charge density in atomic contribu tions CHAPTER 1 NEW USER GUIDE conducti allows to compute the frequency dependent optical conductivity A last one is kptgen that allows to find the symmetries of a set of atoms in a unit cell and to generate grids of k points It is available on
80. total energy with respect to the same atomic dis placement using the response function capabilities of ABINIT You can copy the file ABINIT Tutorial t53 inin Work5 This is your input file You should edit it The changes with respect to the file ABINIT Tutorial t51 in are all gathered in the first part of this file before HERRERA RRA RO RORORRRER RRA R RO HOHO HORROR RO RORORORRRRA AHH HEHEHE AHHH HARRAH Common input variables Accordingly you should get familiarized with the new input variables rfphon rfatpol rfdir Then pay attention to the special use of the kptopt input variable It will be explained in more detail later When you have understood the purpose of the input variable values specified before the Com mon input variables section you can make the code run It takes less than one minute on a PIII 450MHz Then we need to analyze the different output files For that purpose you should read the content of the section 6 of the respfn_help file Read it quickly as we will come back to the most important points hereafter ABINIT has created four different files e t53 1log the log file e t53 out the output file e t530_1WF1 the 1st order wavefunction file e t530_DDB the derivative database Let us have a look at the output file You can follow the description provided in the section 6 2 of the respfn_help file You should be able to find the place where the iterations for the minimization with
81. use toldfe with a small value like 1 0 x 10 167 4 11 STRUCTURE OPTIMIZATION VARIABLES VARRLX It is STRONGLY suggested first to optimize the ionic positions without cell shape and size optimization optcell 0 then start the cell shape and size optimization from the cell with relaxed ionic positions Presently v3 1 one cannot restart restartxf a calculation with a non zero optcell value from the x f history of another run with a different non zero optcell value There are still a few problems at that level 4 11 30 restartxf Mnemonics RESTART from X F history Characteristic Variable type integer parameter Default is 0 Control the restart of broyden minimisation Works only for ionmov 2 Broyden and when an input wavefunction file is specified thanks to the appropriate values of irdwfk or getwfk If positive the code reads from the input wf file the previous history of atomic coordinates and corresponding forces in order to continue the work done by the job that produced this wf file If optcell 0 the history of acell and rprim variables is also taken into account The code will take into consideration the whole history if restartxf 1 or discard the few first x f pairs and begin only at the pair whose number corresponds to restartxf If zero the Broyden minimization is done from scratch NOTE the input wf file must have been produced by a run that exited cleanly It cannot be one of the tempo
82. which dataset the OUTPUT wavefunctions are to be taken as INPUT of the present dataset If getkss 0 no such use of previously computed output KSS file is done 107 4 3 FILES HANDLING VARIABLES VARFIL If getkss is positive its value gives the index of the dataset from which the output KSS file is to be used as input If getkss is 1 the output KSS file of the previous dataset must be taken which is a frequently occuring case If getkss is a negative number it indicates the number of datasets to go backward to find the needed file In this case if one refers to a non existent data set prior to the first the KSS file is not initialised from a disk file so that it is as if getkss 0 for that initialisation 4 3 4 getocc Mnemonics GET OCC parameters from Characteristic Variable type integer parameter an instance of a get variable Default is 0 This variable is typically used to chain the calculations in the multi dataset mode ndtset gt 0 since it describes from which dataset the array occ is to be taken as input of the present dataset The occupation numbers are EVOLVING variables for which such a chain of calculations is useful If 0 no use of previously computed values must occur If it is positive its value gives the index of the dataset from which the data are to be used as input data It must be the index of a dataset already computed in the SAME run If equal to 1 the output data of
83. will be computed automatically 4 1 25 tnons Mnemonics Translation NON Symmorphic vectors Characteristic Variable type real array tnons 3 nsym Gives the nonsymmorphic translation vectors associated with the symmetries expressed in symrel These may all be 0 or may be fractional nonprimitive translations expressed relative to the real space primitive translations so using the reduced system of coordinates see xred If all elements of the space group leave 0 0 0 invariant then these are all 0 When the symmetry finder is used see nsym tnons is computed automatically 4 1 26 toldfe Mnemonics TOLerance on the DiFference of total Energy Characteristic Variable type real parameter Default is 0 0 stopping condition ignored Sets a tolerance for absolute differences of total energy that reached TWICE successively will cause one SCF cycle to stop and ions to be moved Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY charac teristics 1 Ha 27 2113961 eV If set to zero this stopping condition is ignored Effective only when SCF cycles are done iscf gt 0 In this case since toldfe toldff tolvrs and tolwfr are aimed at the same goal causing the SCF cycle to stop one and only one of these must be specified Because of machine precision it is not worth to try to obtain differences in energy that are smaller than about 1 0 x 1071 of the total energy T
84. 0 7 5084285443E 00 Bohr acell3 7 5013992940E 00 7 5013992940E 00 7 5013992940E 00 Bohr acell4 7 4990383260E 00 7 4990383260E 00 7 4990383260E 00 Bohr Note that there is usually a STRONG cross convergence effect between the number of k points and the value of the broadening tsmear The right procedure is for each value of tsmear get the convergence with respect with the number of k points then to compare the k point converged values for different values of tsmear In what follows we will restrict ourselves to the grids with nkpt 2 10 and 28 2 4 3 The convergence study with respect to both number of k points AND broadening factor tsmear The theoretical convergence rate for tsmear ending to 0 in the case of occopt 4 is quartic This is obtained in the hypothesis of infinitely dense k point grid We will check the evolution of acell as a function of tsmear for the following values of tsmear 0 01 0 02 0 03 and 0 04 Use the double loop capability of the multi dataset mode with the tsmear changes in the INNER loop This will saves CPU time as the wavefunctions of the previous dataset will be excellent no transfer to different k points The input file ABINIT Tutorial t43 in is an example while ABINIT Tutorial Refs t43 out is a reference output file From the output file here is the evolution of acell acellii 7 5622298688E 00 7 5622298688E 00 7 5622298688E 00 Bohr acelli2 7 5622412743E 00 7 5622412743E 00 7 56224127
85. 000E 00 xcart12 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 xcart21 7 6091430410E 01 0 0000000000E 00 0 0000000000E 00 7 6091430410E 01 0 0000000000E 00 0 0000000000E 00 xcart22 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 xcart31 7 5472620965E 01 0 0000000000E 00 0 0000000000E 00 7 5472620965E 01 0 0000000000E 00 0 0000000000E 00 xcart32 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 xcart41 7 5491934758E 01 0 0000000000E 00 0 0000000000E 00 7 5491934758E 01 0 0000000000E 00 0 0000000000E 00 xcart42 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 xcart51 7 5427689417E 01 0 0000000000E 00 0 0000000000E 00 7 5427689417E 01 0 0000000000E 00 0 0000000000E 00 xcart52 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 xcart61 7 5415539738E 01 0 0000000000E 00 0 0000000000E 00 7 5415539738E 01 0 0000000000E 00 0 0000000000E 00 xcart62 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 The corresponding atomization energies and interatomic distances are acell Bohr atomization energy Ha interatomic distance Bohr 8 1574 1 568 10 1656 1 522 12 1686 1 509 14 1691 1 510 16 1694 1 508 18 1695 1 508 In order to reach 0 2 convergence on the interatomic distance one needs acell 12 12 12 The atomization energy needs acell 14 14 14 to be converged at that level At 12 12 12 the difference is 0009 Ha 0 024eV which is sufficiently small for practical purposes We will use acell 12 12 12 for the
86. 01 istatshft 101 istwfk 101 ixc 81 jdtset 82 kberry 132 kpt 83 kptbounds 133 kptgw 145 kptnrm 83 kptns 149 kptopt 83 kptrlatt 133 kptrlen 133 kssform 111 Idgapp 102 localrdwf 151 mband 150 mdftemp 164 mditemp 165 mdwall 165 mffmem 112 mefft 150 mixalch 134 mklmem 153 mkmem 112 mkqmem 153 mpw 150 magrid 102 natcon 165 natfix 165 natfixx 165 natfixy 165 natfixz 165 natom 84 natrd 119 natsph 135 nband 84 nbandkss 146 nbandsus 102 nbdblock 102 nbdbuf 135 nberry 135 nconeq 166 ndivk 136 ndtset 85 ndyson 103 nelect 150 nfft 150 174 nfreqsus 103 ngfft 136 nefftdg 151 ngkpt 85 nkpt 85 nkptgw 146 nline 137 nloalg 103 nnsclo 104 nobj 119 nomegasrd 147 noseinert 166 npsp 137 npspalch 138 npweps 147 npwkss 146 npwsigx 147 npwwin 147 nqpt 138 nsheps 148 nshiftk 86 nshsigx 148 nshwfn 148 nspden 138 nspinor 138 nsppol 86 nstep 86 nsym 87 ntime 166 ntypalch 139 ntypat 87 167 ntyppure 139 objaat objbat 120 objaax objbax 120 objan objbn 120 objarf objbrf 121 objaro objbro 121 objatr objbtr 121 occ 139 occopt 88 omegasrdmax 148 optcell 167 optdriver 139 optforces 104 ortalg 104 pawecutdg 152 pawlcutd 152 pawmgaerdg 152 pawnphi 152 pawntheta 153 ppmfrq 148 prepanl 154 INDEX prtldm 118 prtbbb 154 prteml 112 prtden 113 prtdos 113 prteig 114 prtfsurf 114
87. 0355 1997 Effective charges in cartesian coordinates from electric field response and Effective charges in cartesian coordinates from phonon response Namely the Born effective charge of the Al atom is 2 104 and the one of the As atom is 2 127 The charge neutrality sum rule is not fulfilled exactly When ecut is increased and the sampling of k points is improved the sum of the two charges goes closer to zero Finally the phonon frequencies are computed Phonon wavevector reduced coordinates 0 00000 0 00000 0 00000 Phonon energies in Hartree 2 586632E 06 2 590723E 06 2 614440E 06 1 568560E 03 1 568560E 03 1 568560E 03 Phonon frequencies in cm 1 5 677000E 01 5 685980E 01 5 738033E 01 3 442590E 02 3 442590E 02 3 442590E 02 Phonon at Gamma with non analyticity in the direction cartesian coordinates 1 00000 0 00000 0 00000 Phonon energies in Hartree 2 590670E 06 2 590723E 06 4 101029E 06 1 568560E 03 1 568560E 03 1 729575E 03 Phonon frequencies in cm 1 5 685864E 01 5 685980E 01 9 000719E 01 3 442590E 02 3 442590E 02 3 795979E 02 Phonon at Gamma with non analyticity in the direction cartesian coordinates 0 00000 1 00000 0 00000 38 CHAPTER 2 TUTORIAL Phonon energies in Hartree 2 586632E 06 2 614440F 06 4 088526E 06 1 568560E 03 1 568560E 03 1 729575E 03 Phonon frequencies in cm 1 5 677000E 01 5 738033E 01 8 973277E 01 3 442590E 02 3 442590E 02 3 795979E 02 Phonon at Gamma
88. 0E 02 3 442590E 02 3 442590E 02 You might wonder about the dash sign present in the first column of the two lines giving the frequencies in cm 1 The first column of the main ABINIT output files is always dedicated to signs needed to automatic treat the comparison with respect to reference files Except if you become a ABINIT developer you should ignore these signs In the present case they should not be interpreted as a minus sign for the floating numbers that follow them There is a good news about this result and a bad news The good news is that there are indeed three acoustic mode with frequency rather close to zero less than 1 cm which is rather good The bad news comes when the three other frequencies are compared with experimental results or other theoretical results Indeed in the present run one obtains three degenerate modes while there should be a 2 1 splitting This can be seen in the paper Ab initio calculation of phonon dispersions in semiconductors by P Giannozzi S de Gironcoli P Pavone and S Baroni Phys Rev B 43 7231 1991 especially Fig 2 Actually we have forgotten to take into account the coupling between atomic displacements and the homogeneous electric field that exists in the case of polar insulators for so called Lon gitudinal Optic LO modes A splitting appears between these modes and the Transverse Optic TO modes This splitting Lyddane Sachs Teller LO TO splitting is
89. 1 6833336546E 01 f sum rule ratio 1 0028582985E 00 that should be close to 1 and becomes closer to it when ecut is increased and the sampling of k points is improved In the present status of ABINIT the f rule ratio is not computed correctly when ecutsm 4 0 In the third dataset section three irreducible perturbations are considered gt initialize data related to q vector lt The list of irreducible perturbations for this q vector is 1 idir 1 ipert 1 2 idir 1 ipert 2 3 idir 1 ipert 4 Much later the dielectric tensor is given 37 2 5 LESSON 5 DYNAMICAL AND DIELECTRIC PROPERTIES OF ALAS Dielectric tensor in cartesian coordinates j1 j2 matrix element dir pert dir pert real part imaginary part 1 4 1 4 9 7606048428 O 0000000000 1 4 2 4 O 0000000000 O 0000000000 1 4 3 4 O 0000000000 O 0000000000 2 4 1 4 O 0000000000 O 0000000000 7606048428 0000000000 2 4 3 4 O 0000000000 O 0000000000 N HS N HS co o 3 4 1 4 0 0000000000 0 0000000000 4 2 4 0 0000000000 0 0000000000 3 4 3 4 9 7606048428 0 0000000000 w It is diagonal and isotropic and corresponds to a dielectric constant of 9 7606048428 Then the Born effective charges are given either computed from the derivative of the wave functions with respect to the electric field or computed from the derivative of the wavefunctions with respect to an atomic displacement as explained in section II of X Gonze Phys Rev B 55 1
90. 15 1 1024495225E 00 etotal16 1 1005310615E 00 etotal17 1 0982871941E 00 etotal18 1 0957584182E 00 etotal19 1 0929800578E 00 etotal20 1 0899835224E 00 etotal21 1 0867972868E 00 You might try to plot these data see fig 2 1 The minimum of energy in the above list is clearly between dataset 11 and 12 that is xcart11 7 5000000000E 01 0 0000000000E 00 0 0000000000E 00 7 5000000000E 01 0 0000000000E 00 0 0000000000E 00 xcart12 7 7500000000E 01 0 0000000000E 00 0 0000000000E 00 7 7500000000E 01 0 0000000000E 00 0 0000000000E 00 corresponding to a distance of H atoms between 1 5 Bohr and 1 55 Bohr The forces vanish also between 1 5 Bohr and 1 55 Bohr fcart11 5 4963645520E 03 0 0000000000E 00 0 0000000000E 00 11 2 1 LESSON 1 THE H2 MOLECULE WITHOUT CONVERGENCE STUDIES 1 03 1 04 1 06 w 1 07 1 08 1 09 Y pre 1 1 bI n PS ee d 1 11 0 5 10 15 20 25 Figure 2 1 First figure 5 4963645520E 03 0 0000000000E 00 0 0000000000E 00 fcarti2 6 9585355532E 03 0 0000000000E 00 0 0000000000E 00 6 9585355532E 03 0 0000000000E 00 0 0000000000E 00 From these two values using a linear interpolation one get the optimal value of 1 522 Bohr Note that the number of SCF cycles drops from 7 to 5 when the wavefunctions are read from the previous dataset 2 1 3 Computation of the interatomic distance method 2 1 The other methodology is based on an automatic computation of the minimum
91. 16 11 132 12 334 1 257 0 775 0 290 11 089 0 043 5 659 5 8 357 10 157 5 951 3 336 0 779 0 284 9 480 0 677 9 034 E 0_gap 2 741 E GW_gap 3 375 DeltaE GW_gap 0 634 For the desired k point state 4 then state 5 one finds different information e EO is the Kohn Sham eigenenergy e VxcLDA gives the average Kohn Sham exchange correlation potential e SigX gives the exchange contribution to the self energy e SigC EO gives the correlation contribution to the self energy evaluated at the Kohn Sham eigenenergy e Zis the renormalization factor e dSigC dE is the energy derivative of SigC with respect to the energy e SigC E gives the correlation contribution to the self energy evaluated at the GW energy e E EO is the difference between GW energy and Kohn Sham eigenenergy e Eis the GW energy In this case the gap is also analyzed E 0_gap is the Kohn Sham one E GW_gap is the GW one and DeltaE GW_gap is the difference It is seen that the average Kohn Sham exchange correlation potential for the state 4 a valence state is very close to the exchange self energy correction For that state the corre lation correction is small and the difference between Kohn Sham and GW energies is also small 43 meV By contrast the exchange self energy is much smaller than the average 45 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION Kohn Sham potential for the state 5 a conducti
92. 2 Inner centered with a 2 b 2 c 2 associated translation e 3 Face centered with a 2 b 2 b 2 c 2 c 2 a 2 associated translations e 4 C centered with a 2 b 2 associated translation e 5 A centered with b 2 c 2 associated translation e 6 B centered with c 2 a 2 associated translation e 7 Rhombohedral lattice The user might also input directly these values although they might not be consistent with spgroup The space groups 146 148 155 160 161 166 167 when used with spgaxor 1 hexagonal axes will have brvltt 7 and two associated translations 2 3 1 3 1 3 and 1 3 2 3 2 3 For more details see the space group help file 118 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 4 2 genafm Mnemonics GENerator of the translation for Anti FerroMagnetic space group Characteristic SYMMETRISER Variable type real genafm 3 Default 3 0 This input variable might be used to define a Shubnikov type IV magnetic space group anti ferromagnetic space group The user is advised to consult The mathematical theory of symmetry in solids Representation theory for point groups and space groups 1972 C J Bradley and A P Cracknell Clarendon Press Oxford A Shubnikov type IV magnetic space group might be defined by its Fedorov space group set of spatial symmetries that do not change the magnatisation and one translation associated with a change of magnetisation genaf
93. 3 0 519 8 964 143 7244 113 804 0 243 11 680 0 026 5 889 811 0 233 9 185 0 517 8 962 143 7244 137 804 0 244 11 699 0 045 5 870 811 0 232 9 182 0 520 8 965 143 7244 169 804 0 244 11 714 0 060 5 855 811 0 233 9 182 0 520 8 965 143 7244 259 804 0 244 11 713 0 060 5 855 811 0 232 9 182 0 521 8 966 52 CHAPTER 2 TUTORIAL So that npweps 169 ecuteps 6 0 can be considered converged within 0 01 eV At this stage we know that for the screening computation we need ecutwfn 4 0 ecuteps 6 0 nband 100 Of course until now we have skipped the most difficult part of the convergence tests the number of k points It is as important to check the convergence on this parameter than on the other ones However this might be very time consuming since the CPU time scales as the square of the number of k points roughly and the number of k points can increase very rapidly from one possible grid to the next denser one This is why we will leave this out of the present tutorial and consider that we already know a sufficient k point grid for the last calculation 2 6 9 Calculation of the GW corrections for the band gap in Gamma Now we try to perform a GW calculation for a real problem the calculation of the GW corrections for the direct band gap of bulk Silicon in Gamma In directory ABINIT Tutorial Work6 copy the file t69 in and modify the t6x files file as usual DO NOT EDIT IT NOW Issue
94. 3 28 nkpt4 60 ABINIT computes this number of k point from the definition of the grid and the symmetries You might define an input nkpt value in which case ABINIT will compare its computed value with this input value We take this opportunity to examine the behavior of ABINIT when a problem is detected Let s suppose that with ngkpt1 4 4 4 one mentions nkpt1 2 The input file ABINIT Tutorial t32 in is an example Do not forget to change t3x files if you are using that file name The message that you get at the end of the log file is inkpts ERROR The input value of nkpt 2 does not match the number of k points generated by kptopt ngkpt shiftk ane the eventual symmetries that is nkpt 10 Action change nkpt in your input file or one of the other input variables This is a typical ABINIT error message It announce clearly that you should use nkpt 10 As the computation of nkpt for specific grids of k points is not an easy task while the even more important selection of specific economical grids the best ratio between the accuracy of the integration in the Brillouin zone and the number of k points is more difficult some help to the user is provided by ABINIT ABINIT is able to examine automatically different k point grids and to propose the best grids for integration This is described in the abinis_help file see the input variable prtkpt and the associated characterization of the integral accuracy described in kp
95. 31 udtset Mnemonics Upper limit on DaTa SETs Characteristic Variable type integer array udtset 2 No Default since it is not used when it is not defined Used to define the set of indices in the multi data set mode when a double loop is needed see later The values of udtset must be between 1 and 9 and their product must be equal to ndtset If udtset is used the input variable jdtset cannot be used wtk Mnemonics WeighTs for K points Characteristic Variable type real array wtk nkpt Default value is nkpt 1 0d0 Gives the k point weights The k point weights will have their sum normalized to 1 unless occopt 2 see description of occopt within the program and therefore may be input with any arbitrary normalization This feature helps avoid the need for many digits in representing fractional weights such as 1 3 wtk is ignored if iscf is not positive except if iscf 3 4 1 32 xangst Mnemonics vectors X of atom positions in cartesian coordinates length in ANGSTrom Characteristic NOT INTERNAL 93 4 1 BASIC VARIABLES VARBAS Variable type real array xangst 3 natom or xangst 3 natrd if the geometry builder is used Gives the cartesian coordinates of atoms within unit cell in angstrom This information is redundant with that supplied by array xred or xcart If xred and xangst are ABSENT from the input file and xcart is provided then the values of xred will be computed from the provided xcart
96. 4 5 6 and R3 7 8 9 Note carefully that the first three numbers input are the first column of rprim the next three are the second and the final three are the third This corresponds with the usual Fortran order for arrays The matrix whose columns are the reciprocal space primitive translations is the inverse transpose of the matrix whose columns are the direct space primitive translations Alternatively to rprim directions of dimensionless primitive vectors can be specified by using the input variable angdeg This is especially useful for hexagonal lattices with 120 or 60 degrees angles Indeed in order for symmetries to be recognized rprim must be symmetric up to 10 digits inducing a specification such as rprim 0 86602540378 0 5 0 0 0 86602540378 0 5 0 0 0 0 0 0 1 0 that can be avoided thanks to angdeg angdeg 90 90 120 4 1 22 rprimd Mnemonics Real space PRIMitive translations Dimensional Characteristic INTERNAL EVOLVING if ionmov 2 and optcell 4 0 Variable type real array rprimd 3 3 This internal variable gives the dimensional real space primitive vectors computed from acell and rprim Rip i rprimd i 1 rprim i 1 acell 1 for i 1 2 3 x y and z R2p i rprimd i 2 rprim i 2 acell 2 for i 1 2 3 2 3 R3p i rprimd i 3 rprim i 3 acell 3 for i 1 2 89 4 1 BASIC VARIABLES VARBAS 4 1 23 shiftk Mnemonics SHIFT for K points Characteristic Variable type real array shift 3 nshiftk Default 0 5
97. 43E 00 Bohr acell13 7 5622412745E 00 7 5622412745E 00 7 5622412745E 00 Bohr acell14 7 5622427067E 00 7 5622427067E 00 7 5622427067E 00 Bohr acell21 7 5071087625E 00 7 5071087625E 00 7 5071087625E 00 Bohr acel122 7 5071970473E 00 7 5071970473E 00 7 5071970473E 00 Bohr acel123 7 5032517079E 00 7 5032517079E 00 7 5032517079E 00 Bohr acell24 7 5055911048E 00 7 5055911048E 00 7 5055911048E 00 Bohr acell31 7 4958511018E 00 7 4958511018E 00 7 4958511018E 00 Bohr acel132 7 4952121945E 00 7 4952121945E 00 7 4952121945E 00 Bohr acell33 7 4965135656E 00 7 4965135656E 00 7 4965135656E 00 Bohr acell34 7 4990025833E 00 7 4990025833E 00 7 4990025833E 00 Bohr 27 2 4 LESSON 4 ALUMINUM THE BULK AND THE SURFACE These data should be analyzed properly For tsmear 0 01 the converged value contained in acell31 must be compared to acell11 and acell21 between acell21 and acell31 the difference is below 0 2 acell31 can be considered to be converged with respect to the number of k points at fixed tsmear This tsmear being the lowest one it is usually the most difficult to converge and the values acell31 32 88 and 34 are indeed well converged with respect to the k point number The use of the largest tsmear 0 04 giving acell34 induces only a small error in the lattice parameter For that particular value of tsmear one can use the second k point grid giving acell24 So to summarize We can choose to work with a 10 k point grid in the irreducib
98. 5 THE DIFFERENT OUTPUT FILES the change in Etot since last iteration deltaE the maximum squared residual residm over all bands and k points residm the residual measures the quality of the wavefunction convergence the squared residual of the potential in the SCF procedure vres2 the maximum change in the gradients of Etot with respect to fractional coordinates diffor in Hartree the rms value of the gradients of Etot with respect to fractional coordinates maxfor in hartree The latter two are directly related to forces on each atom Then comes an assessment of the SCF convergence the criterion for fulfillment of the SCF criterion defined by toldfe toldff tolwfr or tolurs might be satisfied or not Then the stresses are reported This ends the content of a fixed atomic position calculation Many such blocks can follow When the atomic positions have been eventually relaxed according to the value of ntime the code output more information The squared residuals for each band are reported k point by k point Then the fractional or reduced coordinates are given followed by the energy gradients followed by the cartesian coordinates in Angstroms followed by the cartesian forces in Hartree Bohr and eV Angstrom Also are given the rms force frms and the maximum absolute value of any force component max Next are the length scales of the unit cell in Bohr and in Angstroms Next are the eigenvalu
99. 5 3567080431E 08 5 3567080431E 08 0 Q0000000000E 00 0 0000000000E 00 0 0000000000E 00 The stress tensor is given in Hartree Bohr and the order of the components is 11 22 33 23 13 12 There is only a 0 13 relative difference between acelll and acell2 So our converged LDA value for Silicon with the 14si pspnc pseudopotential see the t3x files file is 10 217 Bohr that is 5 407 Angstrom The experimental value is 5 431 Angstrom at 25 degree Celsius see R W G Wyckoff Crystal structures Ed Wiley and sons New York 1963 2 3 5 Computing the band structure We fix the parameters acell to the theoretical value of 3 x 10 217 and we fix also the grid of k points the 4 x 4 x 4 FCC grid equivalent to a 8 x 8 x 8 Monkhorst pack grid We will ask for 8 bands 4 valence and 4 conduction 23 2 3 LESSON 3 CRYSTALLINE SILICON A band structure can be computed by solving the Kohn Sham equation for many different k points along different lines of the Brillouin zone The potential that enters the Kohn Sham must be derived from a previous self consistent calculation and will not vary during the scan of different k point lines Suppose that you want to make a L Gamma X U Gamma circuit with 10 12 and 17 divisions for each line each segment has a different length in reciprocal space and these divisions give approximately the same distance between points along a line The circuit will be obtained easily by the followin
100. 50E 00 However we will rely later on a more accurate more digits value of this total energy that can be found about a dozen of lines before this final echo Ewald 8 47989583509473E 00 resulting in Etotal 9 76268374500102E 00 hartree The output file also mention that the forces on both atoms vanish The run that you just made will be considered as defining a ground state configuration on top of which response functions will be computed The main output of this ground state run is the wavefunction file t51_oWFK that you can already rename as t51_iWFK Indeed it will be used in the next runs as an input file So in the corresponding files file third line pay attention to specify t51_i even if you change the root name for output files fourth line to t52_o or t530 2 5 2 Frozen phonon calculation of a second derivative of the total en ergy We will now aim at computing the second derivative of the total energy with respect to an atomic displacement by different means For that purpose you must first read section O and the first paragraph of section 1 of the respfn_help file the auxiliary help file that deals specifically with the response function features We will explain later in more detail the signification of the different input parameters intro duced in section 1 of the respfn_help file For now in order to be able to perform a direct comparison with the result of a response function calc
101. 74 show a small but non negligible difference between the two atoms Actually the forces should cancel each other exactly if the translation symmetry were perfect This is not the case but the breaking of this symmetry can be shown to arise only from the presence of the exchange correlation grid of points This grid does not move when atoms are displaced and so there is a very small variation of the total energy when the system is moved as a whole It is easy to restore the action reaction law by subtracting from every force component the mean of the forces on all atoms This is actually done when the gradient with respect to reduced coordinates are transformed into forces and specified in Cartesian coordinates as can be seen in the output file for the small displacement cartesian forces hartree bohr at end 1 0 00000421123276 0 00047199792687 0 00047199792687 2 0 00000421123276 0 00047199792687 0 00047199792687 34 CHAPTER 2 TUTORIAL This effect will be seen also at the level of 2DTE The so called acoustic sum rule imposing that the frequency of three modes called acoustic modes tend to zero with vanishing wavevector will also be slightly broken In this case also it will be rather easy to reimpose the acoustic sum rule In any case taking a finer XC grid will allow to reduce this effect 2 5 3 Response function calculation of a second derivative of the total energy We now compute the second derivative of the
102. 9667 0 9667 The zeta variable is the ratio between the spin density difference and the charge density It varies between 1 and 1 In the present case of Hydrogen there is no spin down density so the zeta variable is 1 The total energy is etotal 4 7010531340E 01 while the total energy of the H molecule is see test 13 etotal 1 1058360629E 00 The atomization energy is thus 0 1656 Ha At this stage we can compare our results e bond length 1 522 Bohr e atomization energy at that bond length 0 1656 Ha 4 506 eV with the experimental data as well as theoretical data using a much more accurate technique see Kolos and Roothaan Rev Mod Phys 32 219 1960 especially p 225 e bond length 1 401 Bohr e atomization energy 4 747 eV 14 CHAPTER 2 TUTORIAL The bond length is awful nearly 10 off and the atomization energy is a bit too low 5 off What is wrong Well are you sure that the input parameters that we did not discuss are correct These are e ecut the plane wave kinetic energy cut off e acell the supercell size e irc not even mentioned until now this input variable specifies what kind of exchange correlation functional is to be used e the pseudopotential We used 10 Ha as cut off energy a 10 x 10 x 10 Bohr supercell the local density approxi mation as well as the local spin density approximation in the Teter parameterization and a pseudopotential from th
103. 97 0 00000000000000 0 00000000000000 frms max avg 2 1595875E 02 3 7405152E 02 0 000E 00 0 000E 00 0 000E 00 h b On the first atom located at 0 7 0 0 in Cartesian coordinates in Bohr the force vector is pointing in the minus z direction and in the plus x direction for the second atom located at 0 7 0 0 The H2 molecule would like to expand 4 Q4 The eigenvalues in Hartree are mentioned at the lines 15 2 2 LESSON 2 THE H2 MOLECULE WITH CONVERGENCE STUDIES Eigenvalues hartree for nkpt 1 k points kpt 1 nband 2 wtk 1 00000 kpt 0 0000 0 0000 0 0000 reduced coord 0 36526 0 01379 As mentioned in the abinis_help file the absolute value of eigenenergies is not meaningful Only differences of eigenenergies as well as differences with the potential The difference is 0 35147 Hartree that is 9 564 eV Moreover remember that Kohn Sham eigenenergies are formally NOT connected to exper imental excitation energies Well more is to be said later about this 5 Q5 The maximum electronic density in electron per Bohr cube is reached at the mid point between the two H atoms Max el dens 2 6907E 01 el bohr 3 at reduced coord 0 0000 0 0000 0 0000 2 2 Lesson 2 The H2 molecule with convergence studies This lesson aims at showing how to get converged values for the following physical properties e the bond length e the atomization energy You will learn about the numerical quality of the calcul
104. ABINIT The User s Manual ABINIT group XG ed Zhenhua Yao Version 1 0 22 May 2004 ii Copyright 2004 ABINIT group XG Al rights reserved This document is free you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of the License or at your option any later version This document is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PUR POSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this document if not write to the Free Software Foundation Inc 675 Mass Ave Cambridge MA 02139 USA Contents 1 New User Guide 1 IU INTTOUCHOA cada A a wee G Pee 1 1 2 The sequential version of ABINIT abinis 1 1 3 Other programs in the ABINIT package o e 2 lA aput variables to ADD o ea ss o a A 3 1b A ee bbe eee eee dee Lhd bee e a a e 3 L6 What does the code de oi ss aa a koroe koe aoo See eee eae ees 4 2 Tutorial 5 2 1 Lesson 1 The H2 molecule without convergence studies 6 2 1 1 Computing the total energy and some associated quantities 6 2 1 2 Computation of the interatomic distance method 1 10 2 1 3 Computation of the interatomic distance method
105. Broyden structural optimization steps to be done if ionmov 1 or 2 respectively Note that at the present the option ionmov 1 is initialized with four Runge Kutta steps which costs some overhead in the startup By contrast the initialisation of other ionmov values is only one SCF call ntime is ignored if ionmov 0 166 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 11 28 ntypat Mnemonics Number of TYPEs of atoms Characteristic NO MULTI Variable type integer parameter Default is 1 Gives the number of types of atoms E g for a homopolar system e g pure Si ntypat is 1 The code tries to read the same number pseudopotential files The first pseudopotential is assigned type number 1 and so on 4 11 29 optcell Mnemonics OPTimize the CELL shape and dimensions Characteristic Variable type integer parameter The Default is optcell 0 Allows to optimize the unit cell shape and dimensions when ionmov 2 or 3 The configuration for which the stress almost vanish is iteratively determined by using the same algorithms as for the nuclei positions Will eventually modify acell and or rprim The ionic positions are ALWAYS updated according to the forces A target stress tensor might be defined see strtarget e optcell 0 modify nuclear positions since ionmov 2 but no cell shape and dimension op timisation e optcell 1 optimisation of volume only do not modify rprim and allow an homogeneous dilatation
106. Computing the GW energies In dataset 3 the calculation of the Self Energy matrix elements is performed One needs to define the driver option as well as the _KSS and _EM1 files optdriver3 4 Self Energy calculation getkss3 2 Obtain KSS file from dataset 1 geteps3 1 Obtain EM1 file from previous dataset The geteps input variable is also similar to other get input variables of ABINIT Then comes the definition of parameters needed to compute the self energy As for the computation of the susceptibility and dielectric matrices one must define the set of bands and two sets of planewaves nband3 100 Bands to be used in the Self Energy calculation ecutwfn3 5 0 Planewaves to be used to represent the wave functions ecutsigx3 6 0 Dimension of the G sum in Sigma_x the dimension in Sigma_c is controlled by npweps In this case nband controls the number of bands used to calculate the Self Energy ecutwfn defines as for optdriver 3 the number of planewaves used to represent the wavefunc tions ecutmat gives the dimension of the planewave sum needed to calculate Sigma_x the exchange part of the self energy which is diagonal The size of the planewave set needed to compute Sigma c the correlation part of the self energy is controlled by the dimension of the screening matrix read in the EM1 file However it is taken equal to the number of planewave of Sigma_x if the latter is smaller than the one for Sigma c Th
107. E Casida in Recent Developments and Applications of Modern Density Functional Theory edited by J M Seminario Elsevier Amsterdam 1996 is a NxN matrix where by default N is the product of the number of occupied states by the number of unoccupied states The input variable td_mexcit allows to diminish N it selects the first td_mexcit pairs of occupied and unoccupied states ordered with respect to increasing Kohn Sham energy difference However when td_mexcit is zero all pairs are allowed See td_maxene for an alternative way to decrease N 4 11 Structure optimization variables VARRLX 4 11 1 amu Mnemonics Atomic Mass Units Characteristic Variable type real array amu ntypat Default is provided by a database of atomic masses Gives the masses in atomic mass units for each kind of atom in cell These masses are used in performing molecular dynamical atomic motion if ionmov 1 6 7 or 8 Note that one may set all masses to 1 for certain cases in which merely structural relaxation is desired and not actual molecular dynamics Using 1986 recommended values 1 atomic mass unit 1 6605402e 27 kg In this unit the mass of Carbon 12 is exactly 12 A database of atomic masses is provided giving default values Note that the default database uses mixed isotope masses for Carbon the natural occurence of Carbon 13 is taken into account The values are those recommended by the commission on Atomic Weights and Isotopic Abun dances
108. ES NOT guarantee the convergence in the GW correction values at the end of the calculation In fact the dielectric constant is representative of only one element the head of the full dielectric matrix Even if the convergence on the dielectric constant with local fields takes somehow into account also other non diagonal elements In a GW calculation all the e7 matrix is used to build the Self Energy operator The dielectric constant here reported is the so called RPA dielectric constant due to the electrons Although evaluated at zero frequency it is understood that the ionic response is not included This is to be contrasted with the one computed in ANADDB The RPA dielectric constant restricted to electronic effects is also not the same as the one computed in the RESPFN part of ABINIT that includes exchange correlation effects We enter now the third dataset As for dataset 2 after some general information origin of KSS file header description of unit cell the echo of Kohn Sham eigenenergies in eV the evaluation of the wavefunction normalization the description of the FFT grid and Jellium parameters there is the echo of parameters for the plasmon pole model and the inverse dielectric function the screening The self energy operator has been constructed and one can evaluate the GW energies for each of the states The results follows k 0 125 0 000 0 000 Band EO lt VxcLDA gt SigX SigC E0 Z dSigC dE Sig E E EO E 4 5 6
109. F The input variable nspden describes the number of components of the density The first component the only one present when nspden 1 is always the total charge density When nspden 2 the second component is the density associated with spin up electrons The case nspden 4 is not yet implemented Note that the meaning of the different components of the density differs for the density array rhor and for the different potential arrays vxc see section 6 6 To identify the points in real space which correspond with the index ir above consider the following The first array value ir 1 corresponds with the first grid point which is at the origin of the unit cell x 0 y 0 z 0 The next grid point ir 2 lies along the first primitive translation at the next fft grid point which is 1 ngfft 1 acell 1 rprim mu 1 This is 1 ngfft 1 of the way along the first primitive translation 72 CHAPTER 3 ABINIS HELP The rest of the values up to ir ngfft 1 lie along this vector at ir 1 ngfft 1 of the way along the first primitive translation The point at ir ngfft 1 1 lies at 1 ngfft 2 along the second primitive translation The next points up to ir ngfft 1 ngfft 1 are displaced in the direction of the second primitive translation by 1 ngfft 2 and in the first translation by ir ngfft 1 1 ngfft 1 This pattern continues until ir ngfft 1 ngfft 2 The next point after that is displaced along the third primit
110. Hamada M Hwang and A J Freeman PRB 41 3620 1990 LDA PAW 2 53 eV B Arnaud and M Alouani PRB 62 4464 2000 LDA 2 53 eV present work GW 3 27 eV M S Hybertsen and S Louie PRL 55 1418 1985 GW 3 35 eV M S Hybertsen and S Louie PRB 34 5390 1986 GW 3 30 eV R W Godby M Schlueter L J Sham PRB 37 10159 1988 GW FLAPW 3 30eV N Hamada M Hwang and A J Freeman PRB 41 3620 1990 GW PAW 3 15 eV B Arnaud and M Alouani PRB 62 4464 2000 GW FLAPW 3 12eV W Ku and A G Eguiluz PRL 89 126401 2002 GW 3 17 eV present work The values are spread over an interval of 0 2 eV They depend on the details of the calculation In the case of pseudopotential calculations They depend of course on the pseudopotential used However a GW result is hardly meaningful beyond 0 1 eV in the present state of the art 54 Chapter 3 ABINIS Help Help file for the main code of the ABINIT package This document explains the i o parameters and format needed for the main code abinis in the ABINIT package The new user is advised to read first the new user s guide before reading the present file It will be easier to discover the present file with the help of the tutorial It is worthwhile to print this help file for ease of reading When the user is sufficiently familiarized with ABINIT the reading of the ABINIT Infos tuning file might be useful For response function calculations using abinis the compl
111. In order to obtain 0 2 relative accuracy on the bond length or atomization energy one should use a kinetic cut off energy of 30 Ha We will keep in mind this value for the final run Well 30 Ha is a large kinetic energy cut off The pseudopotential that we are using for Hydrogen is rather hard atomisation interatomic distance energy Ha Bohr 1656 1 522 1713 1 502 1737 1 480 1747 1 466 1753 1 460 1756 1 459 2 2 3 The convergence in acell The same technique as for ecut should be now used for the convergence in acell We will explore acell starting from 8 8 8 to 18 18 18 by step of 2 2 2 We keep ecut 10 for this study Indeed it 18 CHAPTER 2 TUTORIAL is a rather general rule that there is little cross influence between the convergence of ecut and the convergence of acell The file ABINIT Tutorial t23 in can be used as an example The CPU time needed is also in the order of a few minutes The output data ABINIT Tutorial Refs t23 out are as follows etotal11 1 1188128742E 00 etotal12 4 8074164342E 01 etotal21 1 1058360629E 00 etotal22 4 7010531340E 01 etotal31 1 1039109441E 00 etotal32 4 6767804747E 01 etotal41 1 1039012761E 00 etotal42 4 6743724167E 01 etotal51 1 1041439320E 00 etotal52 4 6735895144E 01 etotal61 1 1042058190E 00 etotal62 4 6736729686E 01 xcartil 7 8427119905E 01 0 0000000000E 00 0 0000000000E 00 7 8427119905E 01 0 0000000000E 00 0 0000000
112. Inorganic Chemistry Division IUPAC in Pure Appl Chem 60 841 1988 For Tc Pm Po to Ac Pa and beyond U none of the isotopes has a half life greater than 3 0 x 101 years and the values provided in the database do not come from that source For alchemical pseudoatoms 159 4 11 STRUCTURE OPTIMIZATION VARIABLES VARRLX the masses of the constituents atoms are mixed according to the alchemical miwing coefficients mixalch 4 11 2 delayperm Mnemonics DELAY between trials to PERMUTE atoms Characteristic Variable type integer Default is 0 Delay number of time steps between trials to permute two atoms in view of accelerated search of minima Still in development See the routine moldyn f See also signperm When delayperm is zero there is not permutation trials 4 11 3 dilatmx Mnemonics DILATation MaXimal value Characteristic Variable type real parameter Default is 1 0 Gives the maximal permitted scaling of the lattice parameters when the cell shape and dimen sion is varied see variable optcell It is used to define the sphere of plane waves and FFT box coherent with the possible modifications of the cell ionmov 2 and optcell 4 0 For these defi nitions it is equivalent to changing ecut by multiplying it by dilatmx the result is an effective ecut called internally ecut_eff other uses of ecut being not modified when dilatmx gt 1 0 Using dilatmxj1 0 is equivalent to changing ecut in all i
113. L 76 1212 1996 e 4 gt BPG for the ACFD This amounts to half the PGG kernel plus half the ALDA kernel for spin compensated systems K Burke M Petersilka and E K U Gross in Recent Advances in Density Functional Methods Vol III edited by P Fantucci and A Bencini World Scientific Singapore 2002 e 5 gt Linear energy optimized kernel J Dobson and J Wang PRB 62 10038 2000 e 6 gt Non linear energy optimized kernel J Dobson and J Wang PRB 62 10038 2000 For ACFD ALDA BPG and energy optimized kernels are highly experimental and not tested yet For ACFD calculations a cut off density has been defined for the ALDA BPG and en ergy optimized kernels let rhomin userre rhomax where rhomax is the maximum density in space then the actual density used to calculate the local part of these kernels at point r is max rho r rhomin 4 2 14 intexact Mnemonics INTegration using an EXACT scheme Characteristic DEVELOP Variable type integer parameter Default value is 0 Relates to the ACFD xc functionals only If intexact gt 0 the integration over the coupling constant will be performed analytically in the RPA and in the two electron PGG approximation for the ACFD exchange correlation energy Otherwise the integration over the coupling constant will be performed numerically also see ndyson and idyson Note that the program will stop in intexact gt 0 and ikhxc 4 1 RPA or ikhxc 4 3 PGG with two elect
114. LENGTH Variable type real parameter Default value is 10 0 Give a minimum projected distance between atoms to be found in order to declare that there is some vacuum present for each of the three directions By default given in bohr atomic units 1 Bohr 0 5291772083 A although Angstrom can be specified if preferred since vacwidth has the LENGTH characteristics The precise requirement is that a slab of width vacwidth delimited by two planes of constant reduced coordinates in the investigated direction must be empty of atoms 4 6 GW variables VARGW 4 6 1 bdgw Mnemonics BanDs for GW calculation Characteristic GW Variable type integer bdgw 2 nkptgw Default is all 0 s For each k point with number igwpt in the range 1 nkptgw bdgw 1 igwpt is the number of the lowest band for which the GW computation must be done and bdgw 2 igwpt is the number of the highest band for which the GW computation must be done 4 6 2 ecuteps Mnemonics Energy CUT off for EPSilon the dielectric matrix Characteristic GW Variable type real Default 0 0 Only relevant if optdriver 3 that is GW calculations ecuteps determines the cut off energy of the planewave set used to represent the independent particle susceptibility xo the dielectric matrix e and its inverse It is not worth to take ecuteps bigger than four times ecutwfn this latter limit corresponding to the highest Fourier components of a wavefunction convoluted
115. MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 3 27 prtkpt Mnemonics PRinT the K PoinTs sets Characteristic Variable type integer parameter Default is 0 If set 4 0 proceeds to a detailed analysis of different k point grids Works only if kptopt is positive and neither kptrlatt nor ngkpt are defined ABINIT will stop after this analysis Different sets of kK point grids are defined with common values of shiftk In each set ABINIT increases the length of vectors of the supercell see kptrlatt by integer steps The different sets are labelled by iset For each k point grid kptrlen and nkpt are computed the latter always invoking kptopt 1 that is full use of symmetries A series is finished when the computed kptrlen is twice larger than the input variable kptrlen After the examination of the different sets ABINIT summarizes for each nkpt the best possible grid that is the one with the largest computed kptrlen Note that this analysis is also performed when prtkpt 0 as soon as neither kptrlatt nor ngkpt are defined But in this case no analysis report is given and the code selects the grid with the smaller ngkpt for the desired kptrlen However this analysis takes some times well sometimes it is only a few seconds it depends on the value of the input kptrlen and it is better to examine the full analysis for a given cell and set of symmetries shiftk for all the production runs 4 3 28 prtpot Mnemonics P
116. N ABINIT CODE INPUT VARIABLES COMPLETE LIST Default is 1 for all indices Used for the generation of alchemical pseudopotentials that is when ntypalch is non zero Give the algorithm to be used to generate the ntypalch alchemical potentials from the different npspalch pseudopotentials dedicated to this use Presently algalch can only have the value 1 that is e the local potentials are mixed thanks to the mixalch mixing coefficients e the form factors of the non local projectors are all preserved and all considered to generate the alchemical potential e the scalar coefficients of the non local projectors are multiplied by the proportion of the corresponding type of atom that is present in mixalch e the characteristic radius for the core charge is a linear combination of the characteristic radii of the core charges build with the mixalch mixing coefficients e the core charge function f r rc is a linear combination of the core charge functions build with the mixalch mixing coefficients Later other algorithms for the mixing might be included 4 5 2 bdberry Mnemonics BanD limits for BERRY phase Characteristic Variable type integer array bdberry 4 Default is 4 0 Used for non zero values of berryopt Give the lower band and the upper band of the set of bands for which the Berry phase must be computed Irrelevant if nberry is not positive When nsppol is 1 no spin polarisation only the two first numbers giving
117. NCTION VARIABLES VARRF 4 10 14 rf3dir Mnemonics non linear Response Function 3rd mixed perturbation DIRections Characteristic NON LINEAR Variable type integer array of 3 elements Default is 0 0 0 Gives the directions to be considered for response function calculations or non linear compu tations The three elements corresponds to the three primitive vectors either in real space phonon calculations or in reciprocal space d dk and homogeneous electric field calculations So they generate a basis for the generation of the dynamical matrix or to macroscopic didlectric tensor of the effective charge tensors If equal to 1 response functions as defined by rfelfd rfphon rfdir and rfatpol are to be computed for the corresponding direction If 0 this direction should not be considered for non linear computations the corresponding input variables should be used 4 10 15 rfelfd Mnemonics Response Function with respect to the ELectric FielD Characteristic RESPFN 4 10 16 rflelfd Mnemonics non linear Response Function 1st mixed perturbation ELectric FielD Characteristic NON LINEAR 4 10 17 rf2elfd Mnemonics non linear Response Function 2nd mixed perturbation ELectric FielD Characteristic NON LINEAR 4 10 18 rf3elfd Mnemonics non linear Response Function 3rd mixed perturbation ELectric FielD Characteristic NON LINEAR Variable type integer parameter Default is 0 Turns on electric field resp
118. RinT the iotal kohn sham POTential 4 3 29 prtvha Mnemonics PRinT V_HArtree 4 3 30 prtvhxc Mnemonics PRinT V_ Hartree XC 4 3 31 prtvxc Mnemonics PRinT V_XC Characteristic Variable type integer parameter Default is 0 If set gt 1 provide output of different potentials For prtpot output the total Kohn Sham potential sum of local pseudo potential Hartree potential and xc potential For prtvha output the Hartree potential For prtvhxc output the sum of Hartree potential and xc potential For prtvxc output the exchange correlation potential If ionmov 0 the name of the potential file will be the root output name followed by _POT _VHA VHXC or VXC If ionmov 1 or 2 potential files will be output at each time step with the name being made of 115 4 3 FILES HANDLING VARIABLES VARFIL e the root output name e followed by _TIMx where x is related to the timestep see later e then followed by POT VHA VHXC or VXC The file structure of this unformatted output file is described in section 6 6 of abinis_help No output is provided by a negative value of these variables 4 3 32 prtstm Mnemonics PRinT the STM density Characteristic Variable type integer parameter Default is 0 If set to 1 or a larger value provide output of the electron density in real space rho r made only from the electrons close to the Fermi energy in a range of energy positive or negative determined by the
119. T The default is 13 Needed only when usepaw 1 Number of phi angles longitude used to discretize the data on the atomic spheres This discretization is completely defined by pawnphi and pawntheta 4 9 6 pawntheta Mnemonics PAW Number of THETA angles used to discretize the sphere around each atom Characteristic Variable type integer parameter The default is 12 Needed only when usepaw 1 Number of theta angles latitude used to discretize the data on the atomic spheres This discretization is completely defined by pawntheta and pawnphi 4 10 Response Function variables VARRF 4 10 1 dsifkpt Mnemonics DenSiFy K PoinTs Characteristic Variable type integer array dsifkpt 3 Default is 1 Can be used to density the k point grid along the lines that are parallel to the three primitive vectors in reciprocal space Should be useful for third order derivatives that include some deriva tive with respect to k points or electric field This part is in development For the time being consult ABINIT Infos nonlinear ps 4 10 2 mkqmem Mnemonics Maximum number of K Q points in MEMory 4 10 3 mklmem Mnemonics Maximum number of K points for 1st order wavefunctions kept in MEMory Characteristic RESPFN Variable type integer parameters Default is nkpt i e in core solution Plays a role similar to mkmem but for different sets of wavefunctions the ground state wave functions at k q and the first order wav
120. The file structure of the unformatted output file is described below see section 6 No output is provided by prtden lower or equal to 0 4 3 23 prtdos Mnemonics PRinT the Density Of States Characteristic Variable type integer parameter Default is 0 Provide output of Density of States if set to 1 2 or 3 Can either use a smearing technique prtdos 1 or the tetrahedron method prtdos 2 If prtdos 3 provide output of Local Density of States inside a sphere centered on an atom as well as the angular momentum projected DOS in the same sphere The resolution of the linear grid of energies for which the DOS is computed can be tuned thanks to dosdeltae If prtdos 1 the smeared density of states is obtained from the eigenvalues properly weighted at each k point using wtk and smeared according to occopt and tsmear All levels that are present in the calculation are taken into account occupied and unoccupied Note that occopt must be between 3 and 7 In order to compute the DOS of an insulator with prtdos 1 compute its density thanks to a self consistent calculation with a non metallic occopt value 0 1 or 2 then use prtdos 1 together with iscf 3 and a metallic occopt between 3 and 7 providing the needed smearing If prtdos 1 the name of the DOS file is the root name for the output files followed by DOS If prtdos 2 the DOS is computed using the tetrahedron method As in the case of prtdos 1 all levels that are
121. USER Integer variables A B C D and E Characteristic Variable type integers Default values are 0 These are user definable integers which the user may input and then utilize in subroutines of his her own design They are not used in the official versions of the ABINIT code and should ease independent developments hopefully integrated in the official version afterwards Internally they are available in the dtset structured datatype e g dtset useria 4 2 34 userra userrb userrc userrd userre Mnemonics USER Real variables A B C D and E Characteristic Variable type real numbers These are user definable with the same purpose as useri above Default value is 0 0 4 2 35 useylm Mnemonics USE YLM the spherical harmonics Characteristic DEVELOP Variable type integer parameter Default is 0 Not working yet purely for developpers 4 2 36 vprtrb Mnemonics potential V for the PeRTuRBation Characteristic DEVELOP ENERGY Variable type real array of 2 elements Default value is 0 d0 0 d0 Gives the real and imaginary parts of a scalar potential perturbation Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY characteristics This is made available for testing responses to such perturbations The form of the perturba tion which is added to the local potential is e vprtrb 1 I vprtrb 2 2 at G qprtrb and e vprtrb 1 I vprtrb 2 2 at G qprtrb see qprtrb als
122. VARIABLES VARRLX Variable type integer parameter Defaults are 0 no atoms held fixed Gives the number of atoms not to exceed natom which are to be held fixed during a structural optimization or molecular dynamics When natfix gt 0 natfix entries should be provided in array iatfix When natfixx gt 0 natfixx entries should be provided in array iatfixx and so on 4 11 25 nconeq Mnemonics Number of CONstraint EQuations Characteristic NO MULTI Variable type integer parameter Default is 0 Gives the number of independent equations constraining the motion of atoms during structural optimization or molecular dynamics see natcon iatcon and wtatcon 4 11 26 noseinert Mnemonics NOSE INERTia factor Characteristic Variable type real noseinert Default is 1 0d5 Give the inertia factor WT of the Nose Hoover thermostat when ionmov 8 in atomic units of weight length that is electron mass bohr The equations of motion are 2 M d Ri dX dR rr ae ar 15 and PX dBi Ma LMG 3NkgT 4 4 where J represent each nucleus M7 is the mass of each nucleus see amu Ry is the coordinate of each nucleus see xcart dX dt is a dynamical friction coefficient and T is the temperature of the thermostat see mditemp and mdftemp 4 11 27 ntime Mnemonics Number of TIME steps Characteristic Variable type integer parameter Default is 5 Gives the number of molecular dynamics time steps or
123. Variable type real parameter Default is 5 0d 5 hartree bohr Sets a maximal absolute force tolerance in hartree bohr below which BFGS structural relax ation iterations will stop Can also control tolerance on stresses when optcell 4 0 using the conversion factor strfact This tolerance applies to any particular cartesian component of any atom excluding fixed ones See the parameter ionmov This is to be used when trying to equilibrate a structure to its lowest energy configuration ionmov 2 169 4 11 STRUCTURE OPTIMIZATION VARIABLES VARRLX A value of about 5 0d 5 hartree bohr or smaller is suggested this corresponds to about 2 5d 3 eV A No meaning for RF calculations 4 11 37 vel Mnemonics VELocity Characteristic EVOLVING Variable type real array vel 3 natom Default is 3 natom 0 s Gives the starting velocities of atoms in cartesian coordinates in bohr atomic time units atomic time units given where dtion is described Irrelevant unless ionmov gt 0 For ionmov 8 Nose thermostat if vel is not initialized a random initial velocity giving the right kinetic energy will be generated If the geometry builder is used vel will be related to the preprocessed set of atoms generated by the geometry builder The user must thus foresee the effect of this geometry builder see objarf Velocities evolve is ionmov 1 4 11 38 vis Mnemonics VIScosity Characteristic Variable type real parameter D
124. _DSx where x is the dataset index defined by the input variable jdtset and also that input names with a dataset index are not allowed Otherwise ndtset 0 is equivalent to ndtset 1 4 1 13 ngkpt Mnemonics Number of Grid points for K Points generation Characteristic NOT INTERNAL Variable type integer array ngkpt 3 No Default Used when kptopt gt 0 if kptrlatt has not been defined kptrlatt and ngkpt are exclusive of each other Its three positive components give the number of k points of Monkhorst Pack grids defined with respect to primitive axis in reciprocal space in each of the three dimensions ngkpt will be used to generate the corresponding kptrlatt input variable The use of nshiftk and shiftk allows to generate shifted grids or Monkhorst Pack grids defined with respect to conventional unit cells When nshiftk 1 kptrlatt is initialized as a diagonal 3x3 matrix whose diagonal elements are the three values ngkpt 1 3 When nshiftk is greater than 1 ABINIT will try to generate kptrlatt on the basis of the primitive vectors of the k lattice the number of shifts might be reduced in which case kptrlatt will not be diagonal anymore Monkhorst Pack grids are usually the most efficient when their defining integer numbers are even For a measure of the efficiency see the input variable kptrlen 4 1 14 nkpt Mnemonics Number of K Points Characteristic Variable type integer parameter Default is 0 if kptopt40
125. able to deduce all symmetry operations leaving the lattice and atomic sublattices invariant see SYMMETRY FINDER Most of the variables can be used in the multi dataset mode see section 3 3 but those that must have a unique value throughout all the datasets are signaled with the indication NO MULTTY Most of the input variables do not change while a run is performed Some of them by contrast may evolve like the atomic positions the atomic velocities the cell shape and the occupation numbers Their echo after the run has proceeded will of course differ from their input value They are signaled by the indication EVOLVING The use of the atomic unit system e g the Hartree for energy about 27 211 eV and the Bohr for lengths about 0 529 Angstroms is strictly enforced within the code However the dimension of some input variables can be specified and read correctly At present this applies to two types of variables those that have the dimension of an energy and those that have a dimension of length The first class of variables have the characteristics ENERGY and can be specified in atomic units Hartree or electron volts or Rydbergs or even Kelvin The second class of variables have the characteristics LENGTH and can be specified in atomic units Bohr and angstrom The abinit parser recognize a dimension if it is specified after the list of numbers following the input variable keyword in the input file Th
126. ae Sa RR ee ee ee Re RR Be SG 101 ADO ISI cocoa ia a eee CEES EEG EG 101 AO MIG Rek tA de Se a AN 102 CONTENTS 4 3 4 4 A De MAGGIE IN 102 42 20 DDAMAS S cs ooo OL Dae A ha he oh ee 4 102 He a DADOS axel apd a PS Eee a ak 102 B20 Ddy 2 oo be SRE ee RARE ee ee oot ee wed 103 A tad IVC a oie wR OD ee A hE BO 103 ARAS MOAR oo ie Gee oe ERS ee eee bee AR es 103 AAD DAOC ee ee eA RRR ELLE Saas SEA eee od bh A a 104 Ls 10 9 8016 saiae a e a a a a e a A a e aa da 104 O29 ORE oc ia AA A ODA Oe a aA e dc i 104 CASO OPD iii we a a ARAS ra AE amp Be Bes 105 4 2 33 useria userib useric userid userie o o e e 105 4 2 34 userra userrb userrc userrd userre o o e eee 105 ADDO USE ccoo Aa a A 105 Hoe OO VPD car Rs a cb bd e 105 LL Woplall cocos cr AA a a a 106 Files handling variables VARFITL o 106 AS Culla oir dira a baas 106 Wd POG air RA a RR SRG We ARK oe 4 107 MY IE ay ee ee ee ae we ee a a 107 BOM PRIOR hbo we ee Ee EO Oe eS OS BE BS Go eee oe we 108 Mag DM og kde go e 2 a AA Se a EGG A A asa 108 AD Mew occiso Oe ee eae eee ede de Pee aad 109 Aer BOI 26 2458 A eke Be eee a PARA Ae EES 109 ASS MOVIE occa ee eee ESO B HO a A ee a ee 109 130 Petdde nck on eo ho Bw A a BR 109 ASO getldem 246 4044 04442 64 RRP a ee eek ome es ee haa 109 HAL Elida coda aea a aait ee Oe RR Bee ee he EE A ae a 109 ES WORES er OE Ee eee ee ee a eG be 110 Boas TOS an
127. amed plasfrq prior to v4 3 Only relevant if optdriver 3 that is GW calculations The present GW implementation is based on a plasmon pole model In this plasmon pole model the screening must be available at zero frequency as well as at another frequency imaginary on the order of the plasmon frequency the peak in the EELS spectrum This information is used to derive the behaviour of the dielectric matrix for all the frequencies complex ppmfrq defines the imaginary frequency at which the dielectric matrix is evaluated in addition to the zero frequency If the plasmon pole approximation is good then the choice of ppmfrq should have no influence on the final result One should check whether this is the case In general the plasmon frequencies of bulk solids are on the order of 0 5 Hartree 4 6 19 soenergy Mnemonics Scissor Operator ENERGY Characteristic GW ENERGY Variable type real Default 0 0 Only relevant if optdriver 3 that is GW calculations of screening The Scissor operator energy to be added to unoccupied levels for the screening calculation In some cases it mimics a second iteration self consistent GW calculation 4 6 20 zcut Mnemonics Z CUT Characteristic GW ENERGY Variable type real Default 0 1 eV 3 67493260 x 10 3 Ha Only relevant if optdriver 4 that is GW calculations It is meant to avoid some divergencies that might occur due to the numerical treatment of integrable poles along the integrati
128. and 1 if kptopt 0 If non zero nkpt gives the number of k points in the k point array kpt These points are used either to sample the Brillouin zone or to build a band structure along specified lines If nkpt is zero the code deduces from other input variables see the list in the description of kptopt the number of k points which is possible only when kptopt40 If kptopt 0 and the input value of nkpt40 then ABINIT will check that the number of k points generated from the other input variables is exactly the same than nkpt 85 4 1 BASIC VARIABLES VARBAS If kptopt is positive nkpt must be coherent with the values of kptrlatt nshiftk and shiftk For ground state calculations one should select the k point in the irreducible Brillouin Zone obtained by taking into account point symmetries and the time reversal symmetry For response function calculations one should select k points in the full Brillouin zone if the wavevector of the perturbation does not vanish or in a half of the Brillouin Zone if q 0 The code will automatically decrease the number of k points to the minimal set needed for each particular perturbation If kptopt is negative nkpt will be the sum of the number of points on the different lines of the band structure For example if kptopt 3 one will have three segments supposing ndivk is 10 12 17 the total number of k points of the circuit will be 10 12 17 1 for the final point 40 4 1 15 nshi
129. annot be used in the RF calculations y e 1 do NOT take advantage of the time reversal symmetry e 2 gt use time reversal symmetry for k 000 e 3 gt use time reversal symmetry for k 1 2 0 0 e 4 gt use time reversal symmetry for k 0 0 1 2 101 4 2 DEVELOPPEMENT VARIABLES VARDEV e 5 gt use time reversal symmetry for k 1 2 0 1 2 e 6 gt use time reversal symmetry for k 0 1 20 e 8 gt use time reversal symmetry for k 0 1 2 1 2 e 7 gt use time reversal symmetry for k 1 2 1 2 0 e 9 gt use time reversal symmetry for k 1 2 1 2 1 2 e 0 preprocessed for each k point choose automatically the appropriate time reversal option when it is allowed and chose istwfk 1 for all the other k points Note that the input variable mkmem also controls the wavefunction storage but at the level of core memory versus disk space 4 2 22 Idgapp Mnemonics Lein Dobson Gross approximation Characteristic DEVELOP Variable type integer parameter Default is 0 Concern only the ACFD computation of the correlation energy optdriver 3 If ldgapp gt 0 the Lein Dobson and Gross first order approximation to the correlation energy is also computed during the ACFD run See Lein Dobson and Gross J Comput Chem 20 12 1999 This is only implemented for the RPA for the PGG kernel and for the linear energy optimized kernel at the present time 4 2 23 magrid Mnemonic
130. ar in the variable tnons The code did an automatic analysis of symmetries They could alternatively be set by hand or using the symmetry builder to be described later e xangst and xred are alternative ways to xcart to specify the positions of atoms within the primitive cell Now you can start reading the description of the remaining of the t11 out file in the section 6 3 of the abinis_help file Look at the t11 out file at the same time 10 You have read completely an output file Could you answer the following questions e Q1 How many SCF cycles were needed to have the toldfe criterion satisfied e Q2 Is the energy likely more converged than toldfe e Q3 What is the value of the force on each atom in Ha Bohr e Q4 What is the difference of eigenenergies between the two electronic states e Q5 Where is located the maximum of the electronic density and how much is it in electrons Bohr answers are given at the end of the present file 2 1 2 Computation of the interatomic distance method 1 1 Starting from now everytime a new input variable is mentioned you should read the corre sponding descriptive section in the ABINIT help We will now complete the description of the meaning of each term there are still a few indications that you should be aware of even if you will not use them in the tutorial These might appear in the description of some input variables For this you should
131. ase etotal1 6 2547004716E 00 by contrast the difference with test 4 6 is less than 1 microHa giving the relaxed surface energy 0 0196 Ha 0 533 eV For the 4 aluminum layer case one has the non relaxed total energy ETOT 8 8 3546873347493 giving the unrelaxed surface energy 0 0186Ha 0 506 eV and for the relaxed case etotal2 8 3565574035E 00 giving the relaxed surface energy 0 0183 Ha 0 498 eV For the 5 aluminum layer case one has the non relaxed total energy ETOT 8 10 453642176501 giving the unrelaxed surface energy 0 0183Ha 0 498 eV and for the relaxed case etotal3 1 0454163549E 01 giving the relaxed surface energy 0 0180 Ha 0 490 eV The relative difference in the surface energy of the 4 and 5 layer cases is on the order of 1 5 In the framework of this tutorial we will not pursue this investigation which is a simple application of the concepts already explored Just for your information and as an additional warning when the work accomplished until now is completed with 6 and 7 layers without relaxation see ABINIT Tutorial t48 in and 31 2 5 LESSON 5 DYNAMICAL AND DIELECTRIC PROPERTIES OF ALAS ABINIT Tutorial Refs t48 out where 5 6 and 7 layers are treated this non relaxed energy number of aluminum layers surface energy 3 0 544 eV 4 0 506 eV surface energy behaves as follows 5 0 498 eV 6 0 449 eV 7 0 463 eV So the surface energy convergence is rather difficult to reach
132. at 1 ntypat do ipsp 1 npsp npsp lines 1 for each pseudopotential npsp ntypat except if alchemical pseudo atoms write unit unit title znuclpsp zionpsp pspso pspdat pspcod pspxc enddo final record residm coordinates total energy Fermi energy write unit unit residm xred 1 3 1 natom etotal fermie The format for version 3 4 was write unit header codvsn headform fform write unit header bantot date intxc ixc natom ngfft 1 3 amp amp nkpt nspden nspinor nsppol nsym npsp ntypat occopt ecut_eff rprimd 1 3 1 3 write unit header nband 1 nkpt nsppol amp npwarr 1 nkpt symrel 1 3 1 3 1 nsym typat 1 natom istwfk 1 nkpt amp kpt 1 3 1 nkpt occ 1 bantot tnons 1 3 1 nsym znucltypat 1 ntypat do ipsp 1 npsp npsp lines 1 for each pseudopotential npsp ntypat except if alchemical pseudo atoms write unit unit title znuclpsp zionpsp pspso pspdat pspcod pspxc enddo final record residm coordinates total energy Fermi energy write unit unit residm xred 1 3 1 natom etotal fermie The format for versions 2 3 to 3 3 was 71 3 5 THE DIFFERENT OUTPUT FILES write unit header codvsn headform fform write unit header bantot date intxc ixc natom ngfft 1 3 amp amp nkpt nspden nspinor nsppol nsym ntypat occopt acel1 1 3 8 amp ecut_eff rprimd 1 3 1 3 write unit header nband 1 nkpt nsppol amp npwarr 1 nkpt symrel 1 3 1 3 1 nsym typat 1 natom i
133. ate alchemical potentials from the available pseudopotentials See these input variables especially mixalch to understand how to use alchemical potentials in ABINIT 4 5 40 ntyppure Mnemonics Number of TYPe of atoms that are PURe Characteristic Inner Variable type integer parameter non negative ntyppure ntypat ntypalch 4 5 41 occ Mnemonics OCCupation numbers Characteristic EVOLVING Variable type real array occ nband Default occ is set to 0 s Gives occupation numbers for all bands in the problem Needed if occopt 0 or occopt 2 Ignored otherwise Also ignored when iscf 2 Typical band occupancy is either 2 or 0 but can be 1 for half occupied band or other choices in special circumstances If occopt is not 2 then the occupancies must be the same for each k point If occopt 2 then the band occupancies must be provided explicitly for each band EACH k POINT and EACH SPIN POLARIZATION in an array which runs over all bands k points and spin polarizations The order of entries in the array would correspond to all bands at the first k point spin up then all bands at the second k point spin up etc then all k points spin down The total number of array elements which must be provided is nband 1 nband 2 nband nkpt nsppol The occupation numbers evolve only for metallic occupations that is occopt gt 3 4 5 42 optdriver Mnemonics OPTions for the DRIVER Characteri
134. ation of the surface energy of aluminum 100 changing the ori entation OF the unit Gell os ww See eee Re ba a a a ee we a PES 28 2 4 5 Determination of the surface energy a 3 aluminum layer 1 vacuum layer slab calculation es e o o oak a eee ee A a ee AD 29 2 4 6 Determination of the surface energy increasing the number of vacuum layers 30 2 4 7 Determination of the surface energy increasing the number of aluminum 2 5 Lesson Byer E A 31 5 Dynamical and dielectric properties of AlAs 32 iii CONTENTS 2 5 1 2 5 2 2 5 3 2 5 4 2 5 5 2 5 6 2 0 1 2 6 Lesson 2 6 1 2 62 2 6 3 2 6 4 2 6 5 2 6 6 2 6 7 2 6 8 2 6 9 The ground state geometry of AlAs aoaaa aa e Frozen phonon calculation of a second derivative of the total energy Response function calculation of a second derivative of the total energy Response function calculation of the dynamical matrix at Gamma Response function calculation of the effect of an homogeneous electric field Response function calculation of phonon frequencies at non zerog The computation of full phonon band structures and thermodynamical prop AN 6 The quasi particle band structure of Silicon in the GW approximation Computation of the Silicon band gap at Gamma using a GW calculation Preparing convergence studies Kohn Sham structure KSS file and screen o oe eea eh oe RE Ee aw Sh ER ge ER Ble D Convergence on the number of plan
135. ations then make convergence studies with respect to the number of planewaves and the size of the supercell and finally consider the effect of the XC functional The problems related to the use of different pseudopotential are left for another lesson still to be written You will also finish to read the abinis_help file This lesson should take about 1 hour to be done 2 2 1 Summary of the previous lesson We studied the Hz molecule in a big box We used 10 Ha as cut off energy a 10 x 10 x 10 Bohr supercell the local density approximation as well as the local spin density approximation in the Teter parameterization ixc 1 the default and a pseudopotential from the Goedecker Hutter Teter table At this stage we compared our results e bond length 1 522 Bohr e atomization energy at that bond length 0 1656 Ha 4 506 eV with the experimental data as well as theoretical data using a much more accurate technique than DFT e bond length 1 401 Bohr e atomization energy 4 747 eV The bond length is awful nearly 10 off and the atomization energy is a bit too low 5 off 16 CHAPTER 2 TUTORIAL 2 2 2 The convergence in ecut 1 Computing the bond length and corresponding atomization energy in one run Before beginning you might consider to work in a different subdirectory as for lesson 1 Why not Work2 Because we will compute many times the bond length and atomization energy it is worth
136. ay as to be ignored by the parser when the data is read Case is irrelevant as the entire input string is mapped to upper case before parsing to remove case sensitivity More than one parameter per line may be given If a given parameter name is given more than once in the input file an error message is printed and the code stops If you follow the tutorial you should go back to the tutorial window now 3 2 2 More about ABINIT input variables In each section of the ABINIT input variables files a generic information on the input variable is given a mnemonics some characteristics the variable type and the default Then follows the description of the variable The mnemonics is indicated when available The characteristics can be of different types DEVELOP RESPFN GEOMETRY BUILDER SYMMETRISER SYMMETRY FINDER NO MULTI EVOLVING ENERGY LENGTH We now explain each of these classes DEVELOP refers to input variables that are not used in production runs but only during development time For non developers it is strongly advised to skip them Some input variables are related to response function features and are indicated RESPFN Detailed explanations related to response function features are to be found in the complementary respfn help file ABINIT Infos respfn_help html The initials RF are used for response func tion and non response function are often referred to as GS for ground state although thi
137. b lasts about 12 secs on a PC PIV Intel 2 2 GHz Edit the output file The number of plane waves used for Sigma_X is mentioned in the fragments of output SIGMA fundamental parameters PLASMON POLE MODEL number of plane waves for SigmaX 59 number of plane waves for SigmaC and W 59 Gathering the GW energies for each planewave set one gets number of plane waves for SigmaX 59 number of plane waves for SigmaC and W 59 Band EO VxcLDA SigX SigC EO Z dSigC dE 4 5 915 11 654 15 195 3 862 0 806 0 241 5 8 445 9 702 3 177 5 595 0 818 0 223 47 Sig E 11 395 8 941 E EO 0 259 0 761 E 6 174 9 206 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION number of plane waves for SigmaX 113 number of plane waves for SigmaC and W 113 Band EO VxcLDA SigX SigC EO Z dSigC dE Sig E E EO E 4 5 915 11 654 15 235 3 795 0 804 0 244 11 482 0 172 6 087 5 8 445 9 702 3 210 5 581 0 817 0 224 8 958 0 744 9 189 number of plane waves for SigmaX 137 number of plane waves for SigmaC and W 137 Band EO VxcLDA SigX SigC E0 Z dSigC dE Sig E E EO E 4 5 915 11 654 15 241 3 785 0 804 0 244 11 495 0 159 6 074 5 8 445 9 702 3 213 5 577 0 817 0 224 8 958 0 745 9 190 number of plane waves for SigmaX 169 number of plane waves for SigmaC and W 169 Band EO VxcLDA SigX SigC EO Z dSigC dE Sig E E EO E 4 5 915 11 654 15 244 3 779 0 804 0 244 11 502 0 151 6 066 5 8 445 9 702 3 216
138. be implemented this way For example nconeq 1 natcon 2 iatcon 1 2 wtatcon 0 0 100 1 could be used to constrain the relative height difference of two adsorbate atoms on a surface assuming their masses are equal since Fy FY 0 implies 21 z2 constant 171 4 11 STRUCTURE OPTIMIZATION VARIABLES VARRLX 172 Index abinis 56 fband 131 accesswff 95 fftalg 97 acell 79 fftcache 97 algalch 124 fixmom 131 amu 159 freqsusin 98 angdeg 79 freqsuslo 98 bdberry 125 bdgw 144 genafm 119 berryopt 125 getlden 109 boxcenter 126 getlwf 109 boxcutmin 126 getlwfden 109 brvltt 118 getcell 161 getddk 109 ceksph 95 getden 107 charge 126 getkss 107 chkexit 127 getocc 108 chkprim 127 getscr 108 cmlfile 106 getvel 162 cpus cpum cpuh 127 getwfk 109 getwfq 109 dedlnn 95 delayperm 160 densty 96 gwealctyp 145 diecut 128 diegap 128 iatcon 162 dielam 128 iatfix 163 dielng 128 iatfixx 163 diemac 129 iatfixy 163 diemix 129 iatfixz 163 dilatmx 160 iatsph 131 dosdeltae 130 idyson 98 dsifkpt 153 ikhxc 98 dtion 160 intexact 99 intxc 99 ecut 80 ionmov 163 ecuteps 144 iprcch 100 ecutsigx 145 iprcel 132 ecutsm 161 iprefe 100 ecutw n 145 irdlwf 110 effmass 96 irdddk 110 efield 130 irdkss 110 enunit 130 irdscr 110 eshift 96 irdwfk 110 exchn2n3 96 irdwfq 110 173 friction 161 getxcart 162 getxred 162 INDEX iscf 80 istatr 1
139. bout 12 secs on a PC PIV Intel 2 2 GHz 48 CHAPTER 2 TUTORIAL Edit the output file The number of bands used for the self energy is mentioned in the frag ments of output SIGMA fundamental parameters PLASMON POLE MODEL number of plane waves for SigmaX 169 number of plane waves for SigmaC and W 169 number of plane waves for wavefunctions 137 number of bands 50 Gathering the GW energies for each number of bands one gets number of bands 50 4 5 915 11 654 15 244 3 853 0 804 0 243 11 443 0 211 6 126 5 8 445 9 702 3 216 5 507 0 817 0 224 8 902 0 800 9 246 number of bands 100 4 5 915 11 654 15 244 3 779 0 804 0 244 11 502 0 151 6 066 5 8 445 9 702 3 216 5 577 0 817 0 225 8 960 0 743 9 188 number of bands 150 4 5 915 11 654 15 244 3 771 0 804 0 244 11 509 0 145 6 060 5 8 445 9 702 3 216 5 585 0 817 0 225 8 966 0 736 9 182 number of bands 200 4 5 915 11 654 15 244 3 769 0 804 0 244 11 510 0 143 6 059 5 8 445 9 702 3 216 5 587 0 817 0 225 8 967 0 735 9 180 number of bands 250 4 5 915 11 654 15 244 3 769 0 804 0 244 11 510 0 143 6 058 5 8 445 9 702 3 216 5 587 0 817 0 225 8 967 0 735 9 180 So that nband 100 can be considered converged within 0 01 eV At this stage we know that for the self energy computation we need ecutwfn 5 0 ecutmat 6 0 nband 100 2 6 6 Convergence on the number of planewaves in the wavefunctions to calculate the screening e Now we come back to the
140. calculation of the screening Adequate convergence studies will couple the change of parameters for optdriver 3 with a computation of the GW energy changes One cannot rely on the convergence of the macroscopic dielectric constant to assess the convergence of the GW energies As a consequence we will define a double loop over the datasets ndtset 10 udtset 5 2 The datasets 12 22 32 42 and 52 drive the computation of the GW energies Calculation of the Self Energy matrix elements GW corrections optdriver 2 4 geteps 2 1 ecutw n 2 5 0 ecutsigx 6 0 nband 2 100 49 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION The datasets 11 21 31 41 and 51 drive the corresponding computation of the screening tt Calculation of the screening epsilon 1 matrix optdriver 1 3 In this latter series we will have to vary the three different parameters ecutwfn ecuteps and nband First we check the convergence on the number of planewaves to describe the wavefunctions in the calculation of the screening This will be done by defining five datasets with increasing ecutwfn ecutw n 3 0 ecutw n 1 0 In directory ABINIT Tutorial Work6 copy the file t66 in and modify the t6x files file as usual Edit the t66 in file and take the time to examine it Then issue abinis lt t6x files gt amp t66 log This small job lasts about 15 secs on a PC PIV Intel 2 2 GHz Edit
141. ceptibility matrices ndyson gt 0 use ndyson more points in 0 1 4 2 27 nfreqsus Mnemonics Number of FREQuencies for the SUSceptibility matrix Characteristic DEVELOP Variable type integer parameter Default is 0 If 0 no computation of frequency dependent susceptibility matrix If 1 or larger will read freqsuslo and freqsusin to define the frequencies 1 is currently the only value allowed 4 2 28 nloalg Mnemonics Non Local ALGorithm Characteristic DEVELOP Variable type integer variable Default is 4 except for the NEC where it is 2 Allows to choose the algorithm for non local operator application On super scalar architec tures the Default nloalg 4 is the best but you can save memory by using nloalg 4 More detailed explanations e nloalg 2 Should be efficient on vector machines It is indeed the fastest algorithm for the NEC but actual tests on Fujitsu machine did not gave better performances than the other options e nloalg 3 same as nloalg 2 but the loop order is inverted e nloalg 4 same as nloalg 3 but maximal use of registers has been coded This should be especially efficient on scalar and super scalar machines This has been confirmed by tests Negative values of nloalg correspond positive ones where the phase precomputation has been suppressed in order to save memory space an array double precision ph3d 2 npw natom is saved typically half the space needed for the wavefunctions at 1
142. cgwf optimize one wavefunction in a fixed potential 8 getghc computes lt G H C gt that is applies the Hamiltonian operator to an input vector If you follow the tutorial you should go back to the tutorial window now 3 5 4 The header The wavefunction files density files and potential files all begins with the same records called the header This header is treated using a hdr_type datastructure inside ABINIT There are dedicated routines inside ABINIT for initializing a header updating it reading the header of an unformatted disk file writing a header to an unformatted disk file echoing a header to a formatted disk file cleaning a header datastructure The header is made of 4 npsp unformatted records obtained by the following Fortran90 instructions format 4 1 write unit header codvsn headform fform write unit header bantot date intxc ixc natom ngfft 1 3 amp amp nkpt nspden nspinor nsppol nsym npsp ntypat occopt pertcase amp amp ecut ecutsm ecut_eff qptn 1 3 rprimd 1 3 1 3 stmbias tphysel tsmear write unit header istwfk 1 nkpt nband 1 nkpt nsppol amp npwarr 1i nkpt so_typat 1 ntypat symafm 1 nsym symrel 1 3 1 3 1 nsym amp typat 1 natom amp kpt 1 3 1 nkpt occ 1 bantot tnons 1 3 1 nsym znucltypat 1 ntypat do ipsp 1 npsp npsp lines 1 for each pseudopotential npsp ntypat except if alchemical pseudo atoms write unit unit title znuclpsp zionpsp pspso ps
143. d is given as a single number and occ nband is an array of nband elements read in by the code The k point weights in array wtk nkpt are automatically normalized by the code to add to 1 e occopt 1 Same as occopt 0 except that the array occ is automatically generated by the code to give a semiconductor An error occurs when filling cannot be done with occupation numbers equal to 2 or 0 in each k point non spin polarized case or with occupation numbers equal to 1 or 0 in each k point spin polarized case e occopt 2 k points may optionally have different numbers of bands and different occupancies nband nkpt nsppol is given explicitly as an array of nkpt nsppol elements occ is given explicitly for all bands at each k point and eventually for each spin the total number of elements is the sum of nband ikpt over all k points and spins The k point weights wtk nkpt are NOT automatically normalized under this option occopt 3 4 5 6 and 7 Metallic occupation of levels using different occupation schemes see below The corresponding thermal broadening or cold smearing is defined by the input variable tsmear see below the variable xx is the energy in Ha divided by tsmear Like for occopt 1 the variable occ is not read All k points have the same number of bands nband is given as a single number read by the code The k point weights in array wtk nkpt are automatically normalized by the code to add to 1 occop
144. d general explanation about its content and the format of such input files in the section 3 1 of the abinis_help file 7 You might now examine in more details some input variables An alphabetically ordered index of all variables is provided and their description is found in the following files e Basic variables VARBAS e Development variables VARDEV e Files handling variables VARFIL e Geometry builder symmetry related variables VARGEO e Ground state calculation variables VARGS e GW variables VARGW e Internal variables VARINT e Parallelization variables VARPAR e Response Function variables VARRF e Structure optimization variables VARRLX However the number of such variables is rather large Note that a dozen of input variables were needed to run the first test case This is possible because there are defaults values for the other input variables When it exists the default value is mentioned at the end of the section related to each input variable in the corresponding input variables file Some input variables are also preprocessed in order to derive convenient values for other input variables Defaults are not existing or were avoided for the few input variables that you find in t11 in These are particularly important input variables So take a few minutes to have a look at the input variables of t11 in e acell e ntypat e znucl e natom e typat e xcart e ecut CHAPTER 2 TUTORIAL e
145. d objbat objbn Gives the list of atoms in either object a or object b This list is specified by giving for each atom its index in the list of coordinates xred xangst or xcart that also corresponds to a type of atom given by the array type These objects can be thought as molecules or groups of atoms or parts of molecules to be repeated rotated and translated to generate the full set of atoms Look at objarf and objbrf for further explanations objaat MUST be provided if nobj 1 objaat and objbat MUST be provided if nobj 2 Not present in the dtset array no internal 4 4 6 objaax objbax Mnemonics OBJect A AXis OBJect B AXis Characteristic GEOMETRY BUILDER NO INTERNAL LENGTH Variable type real arrays objaax 6 and objbax 6 Gives for each object the cartesian coordinates of two points first point objaax 1 3 or objbax 1 3 second point objaax 4 6 or objbax 4 6 By default given in bohr atomic units 1 bohr 0 5291772083 A although Angstrom can be specified if preferred since these variables have the LENGTH characteristics The two points define an axis of rotation of the corresponding object Note that the rotation of the object is done BEFORE the object is translated The sign of the rotation angle is positive if the object is to be rotated clockwise when looking to it along the axis from point 1 coordinates 1 3 toward point 2 coordinates 4 6 objaat MUST be provided if nobj 1 and one compo
146. ded with DSx_WFK is done If getwfk is positive its value gives the index of the dataset for which the output wavefunction file appended with WFK must be used If getwfk is 1 the output wf file with WFK of the previous dataset must be taken which is a frequently occuring case If getwfk is a negative number it indicates the number of datasets to go backward to find the needed wavefunction file In this case if one refers to a non existent data set prior to the first the wavefunctions are not initialised from a disk file so that it is as if getwfk 0 for that initialisation Thanks to this rule the use of getwfk 1 is rather straightforward except for the first wavefunctions that are not initialized by reading a disk file the output wavefunction of one dataset is input of the next one In the case of a ddk calculation in a multidataset run in order to compute correctly the localisation tensor it is mandatory to declare give getddk the value of the current dataset i e getddk3 3 this is a bit strange and should be changed in the future 4 3 10 getlden Mnemonics GET the wavefunctions from WFK file DenSIFied to be completed 4 3 11 getlwfden Mnemonics GET the wavefunctions from WFK file DenSIFied to be completed 109 4 3 FILES HANDLING VARIABLES VARFIL 4 3 12 irdkss Mnemonics Integer that governs the ReaDing of KSS file Characteristic GW Variable type integer parameter Default is 0
147. dentified We will focus only on cut and acell This is because e the convergence of the SCF cycle and geometry determination are well under control thanks to toldfe toldff and tolmaf this might not be the case for other physical prop erties e there is no k point convergence study to be done for an isolated system in a big box no additional information is gained by adding a k point beyond one e the boxcut value is automatically chosen larger than 2 by ABINIT see the determination of the input variable ngfft by preprocessing e we are using ionmov 3 for the determination of the geometry For the check of convergence with respect to ecut you have the choice between doing different runs of the t21 in file with different values of ecut or doing a double loop of datasets as proposed in ABINIT Tutorial t22 in The values of ecut have been chosen between 10Ha and 35Ha by step of 5 Ha If you want to make a double loop you might benefit of reading again the double loop section of the abinis_help file 3 You have likely seen a big increase of the CPU time needed to do the calculation now a few minutes You should also look at the increase of the memory needed to do the calculation go back to the beginning of the output file The output data are as follows 17 2 2 LESSON 2 THE H2 MOLECULE WITH CONVERGENCE STUDIES etotal11 etotal12 etotal21 etotal22 etotal31 etotal32 etotal41 etotal42 etotal51 etotal52 e
148. der development The present parameter charge part mixed electronic atomic describe the way a change of density is derived from a change of atomic position Supported values e 0 fixed charge e 1 gt rigid ion hypothesis atomic charge moves with atom used to correct the forces e 2 rigid ion hypothesis atomic charge moves with atom used to correct forces and density e 3 gt a different implementation of the rigid ion hypothesis atomic charge moves with atom used to correct forces and density For the time being the choice 3 must be used with ionmov 4 and iscf 5 Otherwise use the choice 2 No meaning for RF calculations 4 2 17 prefe Mnemonics Integer for PReConditioner of Force Constants Characteristic DEVELOP Variable type integer parameter Default for iprcfe is 0 Used when iscf gt 0 to define the SCF preconditioning scheme Potential based preconditioning schemes for the SCF loop are still under development The present parameter force constant part describe the way the a change of force is derived from a change of atomic position Supported values e 0 hessian is the identity matrix e 1 hessian is 0 5 times the identity matrix e 2 gt hessian is 0 25 times the identity matrix e 1 gt hessian is twice the identity matrix e simply corresponding power of 2 times the identity matrix No meaning for RF calculations 4 2 18 isecur Mnemonics Integer for level of SECURity choice Cha
149. dimensional k point grid If the system is confined in a tube a one dimensional k point grid will be generated For a cluster this procedure will only generate the Gamma point 4 5 27 mixalch Mnemonics MIXing coefficients for ALCHemical potentials Characteristic Variable type integer array mixalch npspalch ntypalch Default is 0 d0 will not accepted Used for the generation of alchemical pseudoatoms that is when ntypalch is non zero This array gives for each type of alchemical pseudatom there are ntypalch such pseudoatoms the mixing coefficients of the basic npspalch pseudopotentials for alchemical use For each type of alchemical pseudoatom the sum of the mixing coefficients must equal 1 The actual use of the mixing coefficients is defined by the input variable algalch Example 1 Suppose that we want to describe Ba 0 25 Sr 0 75 Ti O3 The input variables related to the construction of the alchemical Ba 0 25 Sr 0 75 potential will be npsp 4 4 pseudopotentials should be read znucl 8 40 56 38 The nuclear charges Note that the two atoms whose pseudopotentials are to be mixed are mentioned at the end of the series There will be three types of atoms One pseudoatom will be alchemical Hence there will be ntyppure 2 pure pseudoatoms with znucl 8 0 and 40 Ti corresponding to the two first pseudopotentials Out of the four pseudopotentials npspalch 2 are left for alchemical purposes with znucl 56 Ba
150. ding to the value of getden if ndtset 4 0 The name of the density file must be given as indicated in the section 4 of abinis_help iscf 2 would be used for band structure calculations to permit computation of the eigenvalues of occupied and unoccupied states at arbitrary k points in the fixed self consistent potential produced by some integration grid of k points To compute the eigenvalues and wavefunctions of unoccupied states in a separate non selfconsistent run the user should save the self consistent rho r and then run iscf 2 for the intended set of k points and bands To prepare a run with iscf 2 a density file can be produced using the parameter prtden see its description When a self consistent set of wavefunctions is already available abinit can be used with nstep 0 see Test_v2 t47 in and the adequate value of prtden e 3 gt like 2 but initialize occ and wtk directly or indirectly using ngkpt or kptrlatt depending on the value of occopt For GS this option might be used to generate Density of states thanks to prtdos or to produce STM charge density map thanks to prtstm For RF this option is needed to compute the response to ddk perturbation e 1 like 2 but the non self consistent calculation is followed by the determination of excited states within TDDFT This is only possible for nkpt 1 kpt 0 0 0 nsppol 1 Note that the oscillator strength needs to be defined with respect to an
151. e 144 GW variables VARGW acma aaa iuei iii ee 144 AGM BOW rro aH alee eh a eo ER eA we ee eS 144 AO GUEPI dine a wwe oo PEO e DEES Oey oes 144 M05 SEUS isa BAe Se oe ee DEG Ge ee asa G 145 AGA ECU 6s ben bd bata SPORE eae ee eee PEE EaS 145 A65 MWe 64464 4 4 eke Be ee a PERERA Se EGS 145 o oo 4 44 veh oe POPE DAG EEDA PEG he Yee a es 145 Moor BD ies Ss a a BO 146 AOR MPWEES 2444404404442 468 REE eae ee dee ee das 146 AOO DEG os bk ee eae ee Ra Ve Oe SES HS GE EO a 146 4 6 10 nome gastd ociosa a ee Se ee a ee 147 ALI PWES is da BAS oe a EERE OQ OOOS Dae he ae oe a A A 147 LOIS POSEE iaa ee RAE Bee SS OEE EE ee ee Yo 147 A613 2654524444424 68 Oe eae eee Seed e 147 A AI cee eke Bee eee a ARE RRR 148 AGS mshsigx oc ocas a 644 ee a e Ge e LS eee ee 148 ANG DSN aS Sea aoa eg eR ERS eS eee ee ee AS 148 607 OMESAST MBX cio ara eee Eee ORE AA A 148 a A A Ae OR ERS eee A A 148 46 19 o lt 2 06 e a ee RR a Pe aa a ee ee ee be 149 BOAO AGE ask wc oe oo a ORR EEE OG OEE a ee ee eG EAP AE 149 Internal variables VARINT o eee ee 149 Moa MURS AAA 149 Ml SUDAN ci a dk ee ee eR le A ae ee eae a 150 ATS MBH kaa hhh EEE EGA SEER EERE OGG Ye et 150 A Pi iat ee A eee ee ea ee 150 ATO MEOE 2c 65 bG4 4455406648 Reo dee EEE de 150 Mee Dae a a aa a i a RARA 150 C Pillo E E E eR RRS aaa a a 150 ATS UPIN ooi oe gaed hina aa ESOS e A A a E AA A 151 Parallelisation variables VARPAR onana a 151 A ecua A 151 Projector Augmented Wave va
152. e Goedecker Hutter Teter table Phys Rev B 54 1703 1996 We will see in the next lesson how to address the choice of these parameters except the pseudopotential 2 1 6 Answers to the questions section 1 1 10 NOTE there might be numerical differences from platform to platform in the quoted results 1 Q1 7 SCF cycles were needed iter Etot hartree deltaE h residm vres2 diffor maxfor ETOT 1 1 1013391225241 1 101E 00 4 220E 04 8 396E 00 2 458E 02 2 458E 02 ETOT 2 1 1034123727266 2 073E 03 4 367E 09 1 668E 00 8 602E 03 3 318E 02 ETOT 3 1 1037064870489 2 941E 04 1 836E 05 3 207E 01 4 922E 03 3 810E 02 ETOT 4 1 1037182046373 1 172E 05 1 090E 07 8 675E 02 3 620E 04 3 774E 02 ETOT 5 1 1037224013769 4 197E 06 1 436E 07 1 829E 04 3 593E 04 3 738E 02 ETOT 6 1 1037224209642 1 959E 08 1 123E 09 1 445E 05 3 106E 05 3 741E 02 ETOT 7 1 1037224213176 3 534E 10 6 528E 12 8 113E 07 4 102E 06 3 741E 02 At SCF step 7 etot is converged for the second time diff in etot 3 534E 10 lt toldfe 1 000E 06 2 Q2 Yes the energy is more converged than toldfe since the stopping criterion asked for the difference between successive evaluations of the energy to be smaller than toldfe twice in a row while the evolution of the energy is nice and always decreasing by smaller and smaller amounts 3 Q3 These values are cartesian forces hartree bohr at end 1 0 03740515236097 0 00000000000000 0 00000000000000 2 0 037405152360
153. e actual margin to be taken into account should come with experience Note that only one of these three parameters can be defined in a single input file A zero value has no action of the job Internally only cpus is used in the dtset array adequate conversion factors are used to generate it from cpum or cpuh 127 4 5 GROUND STATE CALCULATION VARIABLES VARGS 4 5 10 diecut Mnemonics Dlelectric matrix Energy CU Toff Characteristic DEVELOP ENERGY Variable type real parameter Default diecut is 2 2d0 Ha Kinetic energy cutoff that controls the number of planewaves used to represent the dielectric matrix 1 2 27 Gmaz ecut for Gmaz Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY charac teristics 1 Ha 27 2113961 eV All planewaves inside this basis sphere centered at G 0 are included in the basis This is useful only when iprcel gt 21 which means that a preconditioning scheme based on the dielectric matrix is used NOTE a negative diecut will define the same dielectric basis sphere as the corresponding positive value but the FFT grid will be identical to the one used for the wavefunctions The much smaller FFT grid used when diecut is positive gives exactly the same results No meaning for RF calculations yet 4 5 11 diegap Mnemonics Dlelectric matrix GAP Characteristic DEVELOP ENERGY Variable type real parameter Default diegap is 0 1 Ha Gives a ro
154. e an input file that will do the computation described above interatomic distances from 1 0 Bohr to 2 0 Bohr by steps of 0 05 Bohr You might start from t11 in Try to define a series and to use the getwfk input variable the latter will make the computation much faster You should likely have a look at the section that describes the irdwfk and getwfk input variables in particular look at the meaning of getwfk 1 Also define explicitly the number of states or supercell bands to be one using the input variables nband The input file ABINIT Tutorial t12 in is an example of file that will do the job while ABINIT Tutorial Refs t12 out is an example of output file If you decide to use the ABINIT Tutorial t12 in file do not forget to change the file names in the t1x files file So you run the code with your input file this might take one or two minutes examine the output file quickly there are many repetition of sections for the different datasets and get the output energies gathered in the final echo of variables etotali 1 0368223891E 00 etotal2 1 0538645432E 00 etotal3 1 0674504850E 00 etotal4 1 0781904896E 00 etotal5 1 0865814785E 00 etotal6 1 0930286804E 00 etotal7 1 0978628207E 00 etotal8 1 1013539124E 00 etotal9 1 1037224213E 00 etotal10 1 1051483730E 00 etotal11 1 1057788247E 00 etotal12 1 1057340254E 00 etotal13 1 1051125108E 00 etotal14 1 1039953253E 00 etotal
155. e and the ABINIT group are explained in the file ABINIT Infos context and ABINIT Infos planning or some recent version of them Please send questions and constructive criticisms of the code or this documentation as well as bug reports see ABINIT Infos bug_report to 76 CHAPTER 3 ABINIS HELP Xavier Gonze Unit PCPM Universit Catholique de Louvain 1 place Croix du Sud B 1348 Louvain la Neuve Belgium tel 32 10 472076 fax 32 10 473452 email gonze pcpm ucl ac be or to Douglas C Allan SP FR 05 Corning Incorporated Corning NY 14831 USA tel 1 607 974 3498 fax 1 607 974 3675 email allandc corning com Correspondence by email is usually most convenient 77 3 7 FINAL REMARKS 78 Chapter 4 Main ABINIT code input variables Complete list This document lists the names keywords of all input variables to be used in the main input file of the abinis code The new user is advised to read first the new user s guide before reading the present file It will be easier to discover the present file with the help of the tutorial When the user is sufficiently familiarized with ABINIT the reading of the ABINIT Infos tuning file might be useful For response function calculations using abinis the complementary file ABINIT Infos respfn_help is needed Copyright C 1998 2004 ABINIT group DCA XG RC This file is distributed under the terms of the GNU General Public L
156. e changes with respect to the file ABINIT Tutorial t51 in are all gathered in the first part of this file The multi dataset mode is used computing from scratch the ground state properties then computing different dynamical matrices The run is rather long about 30 minutes on a PIII 450MHz So you would better leave your computer 39 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION running and either read more of the ABINIT documentation why not the mrgddb_help and the anaddb_help or make a walk The results of this simulation can be compared to those provided in the Gianozzi et al paper The agreement is rather good despite the low cut off energy and different pseudopotentials At X they get 95 cm 216 cm 337 cm and 393 cm while we get 92 5 cm 204 6 cm 313 9 cm and 375 9 cm With ecut 6 Hartree we get 89 7 cm 212 3 cm 328 5 cm and 385 8 cm At L they get 71 cm7 212 cm 352 cm and 372 cm while we get 69 0 cm 202 5 cm 332 6 cm and 352 3 cm With ecut 6 Hartree we get 68 1 cm 208 5 cm 346 7 em and 362 6 cm At q 0 1 0 0 we get 31 6 cm 63 6 cm 342 0 cm and 379 7 cm The acoustic modes tends nearly linearly to zero while the optic modes are close to their values at Gamma 344 3 cm and 379 6 cm7 2 5 7 The computation of full phonon band structures and th
157. e is no primitive cell of bulk aluminum based on these vectors but a doubled cell We will first compute the total energy associated with this doubled cell This is not strictly needed but it is a valuable intermediate step towards the study of the surface You might start from t43 in You have to change rprim Still try to keep acell at the values of bulk aluminum that were determined previously But it is not all the most difficult part in the passage to this doubled cell is the definition of the k point grid Of course one could just take a homogeneous simple cubic grid of k points but this will not correspond exactly to the k point grid used in the primitive cell in t43 in This would not be a big problem but you would miss some error cancellation The answer to this problem is given in the input file ABINIT Tutorial t44 in The proce dure to do the exact translation of the k point grid will not be explained here sorry for this If you do not see how to do it just use homogeneous simple cubic grids with about the same resolution as for the primitive cell case There is a simple rule to estimate ROUGHLY whether 28 CHAPTER 2 TUTORIAL two grids for different cells have the same resolution simply multiply the linear dimensions of the k point grids by the number of sublattices by the number of atoms in the cell For example the corresponding product for the usual 10 k point grid is 4x4x4 x 4 x 1 256 In the file t44 i
158. e of file containing output wavefunction coefficients if ngpt 0 The wavefunction file is unformatted and can be very large abo_WFQ Same as abo_WFK but for the case ngpt 1 The wavefunctions are always output either with the name abo_WFK or with the name abo_WFQ abo_1WFxx Same as abo_WFK but for first order wavefunctions xx is the index of the perturbation see the section 6 3 of the respfn_help htm1 file abo _ DDB The derivative database produced by a response function dataset see the section 6 5 of the respfn_help html file abo_DEN Filename of file containing density in the case ionmov 0 See the keyword prtden This file is unformatted but can be read by cut3d abo_TIMx_DEN Filenames of files containing density in the case ionmov40 The value of x after TIM is described hereafter See the keyword prtden This file is unformatted but can be read by cut3d abo_POT Filename of file containing Kohn Sham potential See the keyword prtopt This file is unfor matted but can be read by cut3d abo_TIMx_POT Filenames of files containing Kohn Sham potential in the case ionmov40 The value of x after TIM is described hereafter See the keyword prtopt This file is unformatted but can be read by cut3d abo_DOS Filename of file containing density of states See the keyword prtdos This file is formatted abo_TIMx_DOS Filenames of files containing the density of states in the case prtdos 2 and io
159. e of spin polarized calculations the spin up bands might have an identical occupation number that might differ from the identical occupation number of spin down bands Although meaningless ABINIT will perform such computation if required by the user The input variable bdberry governs the set of bands for which a Berry phase is computed The computation of the Berry phase is not yet implemented for spinor wavefunctions nspinor 2 Moreover it is not yet implemented in the parallel version of ABINIT 4 5 31 ndivk Mnemonics Number of DIVisions of K lines Characteristic NOT INTERNAL Variable type integer array ndivk abs kptopt No default Gives the number of divisions of each of the segments of the band structure whose path is determined by kptopt and kptbounds This is only needed when kptopt is negative In this case the absolute value of kptopt is the number of such segments For example suppose that the number of segment is just one kptopt 1 a value ndivk 4 will lead to the computation of points with relative coordinates 0 0 0 25 0 5 0 75 and 1 0 along the segment in consideration Now suppose that there are two segments kptopt 2 with ndivk 1 4 and ndivk 2 2 the computation of the eigenvalues will be done at 7 points 5 belonging to the first segment with relative coordinates 0 0 0 25 0 5 0 75 and 1 0 the last one being also the starting point of the next segment for which two other points must be compu
160. e oo a ee ed OSE A a OAS 110 A TOV Le ee a ee ee ESS OS RES oe ee Ss 110 AGO MW o lt 0 625544444 24 68 OE a e eee ede de Pee aaa 110 ASG WAI 6 A LAGS GS ca ee ee Bee eee a ee ARERR 110 ASAT wdddk o 42 6 ee ee Bee OHSS 2 bE DS EAE G LE Ree ee 110 AGUS SSI oS Sea aoa ge ee ERS eS eS eee ee A 111 ASO WE sii a eee RR dass 112 ASA ORAM ce kk ee BS a ied ee OER See A LA 112 Sal Premio sous a ye pida ae e eee Gb ee 112 Ae POB cacas ee haan a ORES A ee eG Ea AA 113 o a a a a a a ce a a e e a ar 113 BGAN UGS nek a a eR HO OR ES hk HD ODO 114 odo PBI oia Bk ee ee eR EE A AA eee eae 114 ct boas SSO DODRS GY EEES DEE OGG Yb we ee a 114 e ait oe So oak a ee a ee ee eR SG a A 115 Boe PPOs lt o6 e bane bbe E a a E HHEe eed oe GEHL EH ES 115 Good EUV ae a 2 we Ge E 115 ESO PUTO ccc ee Rara y a 115 ASSL PVR dades ee ea PSOE OE OEE ee e ba PDS 115 oa DIS io ee GRE eee EERE RO ee hae ee a 116 Boo PUYOL a hk 6 he AAN 116 A PEE oat koe oe ELAR le eee ee eee he ee eo 117 AO Prld ao ee a ba eee Poe Sede a eee dhe hehe hee e a 118 Geometry builder symmetry related variables VARGEO 118 AAW DI 224622464444 45 44808 Oe eda de ee eG hGeGeb send 118 Male BOALO da amp dat tana dae we ee da i a we eo aa 119 vi CONTENTS 4 5 CAS OO AER AAA a A A A Ee eRe ene 119 AAD BOD sc Aas ewe SoS Se Rew O Ob Paw a a aoaaa Uh ee bh eae 119 HA OD Gat OID scada ES s aod 120 AAG Objaak OBIDAE sio bt keh ee eA ED er OO AR eee eed 120 AAT ODIO
161. e specification can be upper or lower case or a mix thereof Here is the list of recognized chains of characters e Ry gt Rydberg for energies e eV gt electron volts for energies e K gt Kelvin for energies e Angstr Angstrom for lengths Except in the case of Angstr the abbreviation must be used i e Rydberg will not be recognized presently Other character chains like au for atomic units or Hartree or Bohr are not recognized but make the parser choose by default atomic units which is the correct behaviour Example acell 8 8 8 angstrom ecut 8 Ry tsmear 1000 K or acell 3 10 Bohr ecut 270 eV tsmear 0 01 The use of the atomic units is mandatory for other dimensioned input variables like the tolerance on forces toldff parameters that define an object objaaz objbaz objatr objbtr and the initial velocity of atoms vel if needed The initial atomic positions can be input in Bohr or Angstrom through xcart but also independently in Angstrom through xangst or even in reduced coordinates through xred Reduced cartesian coordinates must be used for the eventual translations accompanying symmetry operations tnons 59 3 2 THE INPUT FILE In addition to giving the input variables the input file can be useful for another purpose placing the word exit on the top line will cause the job to end smoothly on the
162. e the experimental value is 8 2 The agreement is not very good a fact that can be attributed to the LDA lack of polarization dependence X Gonze Ph Ghosez and R Godby Phys Rev Lett 1995 Still the agreement of our calculation with the theoretical result is not very good With ecut 3 Hartree we have 9 76 Changing it to 6 Hartree gives 10 40 A better k point sampling 8x8x8 with ecut 6 Hartree reduces the value to 9 89 Changing pseudopotentials finally improves the agreement with the much harder 13al pspgth and 33as psphgh pseudopotentials with adequate ecut 16 Hartree and 8x8x8 Monkhorst Pack sampling we reach a value of 9 37 This illustrates that the dielectric tensor is a much more sensitive quantity than the others 2 5 6 Response function calculation of phonon frequencies at non zero q The computation of phonon frequencies at non zero q is actually simpler than the one at Gamma One must distinguish two cases Either the q wavevector connects k points that belong to the same grid or the wavevector q is general In any case the computation within the response function formalism is more efficient than using the frozen phonon technique the use of supercell is completely avoided For an explanation of this fact see for example section IV of X Gonze Phys Rev B55 10337 1997 You can copy the file ABINIT Tutorial t56 inin Work5 This is your input file You should edit it As for the other RF tests th
163. e to be taken as INPUT density of the present dataset If getden 0 no such use of previously computed output density file is done If getden is positive its value gives the index of the dataset from which the output density is to be used as input If getden is 1 the output density of the previous dataset must be taken which is a frequently occuring case If getden is a negative number it indicates the number of datasets to go backward to find the needed file In this case if one refers to a non existant data set prior to the first the density is not initialised from a disk file so that it is as if getden 0 for that initialisation Thanks to this rule the use of getden 1 is rather straightforward except for the first density that is not initialized by reading a disk file the output density of one dataset is input of the next one Be careful the output density file of a run with non zero ionmov does not have the proper name it has a TIM indication for use as an input of an iscf lt 0 calculation One should use the output density of a ionmov 0 run 4 3 3 getkss Mnemonics GET Kohn Sham Structure from Characteristic GW Variable type integer parameter Default is 0 Used when ndtset gt 0 multi dataset mode and optdriver 3 or 4 a GW calculation to indicate that the KSS wavefunction file is to be taken from the output of a previous dataset It is used to chain the calculations since it describes from
164. e variable is zero that is for the wave functions that are not kept in core memory e 0 gt Use standard Fortran IO routines e 1 Use MPI IO routines this option is only available in parallel e 2 gt Use NetCDF routines this option is not yet available The MPI IO routines might be much more efficient than usual Fortran IO routines in the case of a large number of processors with a pool of disks attached globally to the processors but not one disk attached to each processor For a cluster of workstations where each processor has his own temporaries the use of accesswff 0 might be perfectly allright 4 2 2 ceksph Mnemonics CEnter K SPHere Characteristic DEVELOP Variable type integer parameter Default is 0 Control the set of plane waves in a sphere generated for each k point e 0 gt do not center the sphere on Gamma e 1 do center the sphere on Gamma this option is allowed only in the program newsp not in abinis or abinip The value 0 is desirable for all usual band structure calculation since this choice allows the symmetry to be preserved at each k points so that degeneracies are correct The value 1 is used to generate input wavefunctions to the GW code of Rex Gody and coworkers This option is only allowed in newsp 4 2 3 dedlnn Mnemonics Characteristic ENERGY Variable type real parameter Default dedlnn is 0 i e no correction Gives a value for derivative d Etotal d log Npw for given val
165. ed For example natom 3 This gives the number of atoms typat 112 2 3 typat 1 natom gives the type of each atom only the three first data are read since natom 3 A given variable is identified by the parser by having at least one blank before it and af ter it again multiple blanks are irrelevant ABINIT has also some very limited interpretor capabilities e It can identify one slash sign being placed between two numbers without a separating blank as being the definition of a fraction e g 1 3 will be interpreted as 0 33333333333333d0 e It can identify sqrt or sqrt as being the definition of a square root when applied to one valid number also without a separating blank e g sqrt 0 75 will be interpreted as 0 8660254038d0 e Note however that these capabilities are NOT recursive and cannot be used one with the other e g sqrt 3 4 is invalid To include comments it is recommended that they be placed to the right of the comment characters or anything to the right of a or a on any line is simply ignored by the parser Additional text not preceeded by a or a would not otherwise cause trouble unless the text inadvertantly contained character strings which were the same as variable names e g acell The characters or can also be used to store old values of variables or place anything else of convenience into the file in such a w
166. efault is 100 Gives the viscosity atomic units for linear frictional damping term applied to molecular dynamics when ionmov 1 Used for eventual relaxation of structure however ionmov 2 is in general more efficient The equation of motion is M d R dt Fy visdRy dt The atomic unit of viscosity is hartrees atomic time units bohr Units are not critical as this is a ficitious damping used to relax structures A typical value for silicon is 400 with dtion of 350 and atomic mass 28 amu Critical damping is most desirable and is found only by optimizing vis for a given situation 4 11 39 wtatcon Mnemonics WeighTs for AToms in CONstraint equations Characteristic NO MULTI Variable type real array wtatcon 3 natcon nconeq Default is 0 Gives the weights determining how the motion of atoms is constrained during structural opti mization or molecular dynamics see nconeq natcon and iatcon For each of the nconeq inde pendent constraint equations wtatcon is a 3 natcon array giving weights Wz for the x y and z components of each of the atoms labeled by J in the list of indices iatcon Prior to taking an atomic step the calculated forces Fy are replaced by projected forces F which satisfy the set of constraint equations No gt Wmut Fina 0 for each of the nconeg arrays Wy mu x y 2 1 natcon 170 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Different types of motion constraints can
167. efunctions Only needed for response calculations Internal representation as mkmems 2 and mkmems 3 Note 991019 that although the effective number of k points can be reduced thanks to sym metry for different perturbations mkqmem and mklmem are presently still compared with the input nkpt This should be changed later 153 4 10 RESPONSE FUNCTION VARIABLES VARRF 4 10 4 prepanl Mnemonics PREPAre Non Linear response calculation Characteristic RESPFN Variable type integer parameter Default is 0 The computation of third order derivatives from the 2n 1 theorem requires the first order wavefunctions and densities obtained from a linear response calculation The standard approach in a linear response calculation is i to compute only the irreductible perturbations and ii to use symmetries to reduce the number of k points for the k point integration This approach cannot be applied presently v4 1 if the first order wavefunctions are to be used to compute third order derivatives First for electric fields the code needs the derivatives along the three directions Still in case of phonons only the irreducible perturbations are required Second for both electric fields and phonons the wavefunctions must be available in half the BZ kptopt 2 or the full BZ kptopt 3 During the linear response calculation in order to prepare a non linear calculation one should put prepanl to 1 in order to force ABINIT i to co
168. eh o G 88 ALAL TOMMY ascitis eee eee Eee ee ee Ge eee ee a 89 BAS POA ce ke eee be SS ERRORS SSE i AA ae 89 ATLAS COU oaii ensa eek eee ee ee Ee ee ee 90 AMIA igymirel ce ee he SE OOS Re EES DES Goh eet ee 4 91 AN DOr TONE ok ae eae IA RR A D 91 4 126 tole ccc riesit bata SEE eae ee eee Pee dad 91 AMO TOM 6 6 ASS A A oe ee a PARA A Se ERE SS 92 AAS COVES oa da EE ESBS ERED Shh Yee ead 92 PRASAD GOW a ie oe ee he Bw EO IS a 92 ISO type i654 422 64 404442 468 REE eee ee dee ee ae 93 HMO MOG AA 93 S132 RANGE coo oc RR Re a ee ee be 93 eA REO cee ee we ae a eo OSE te PODS Baek a ee oe Ra AS 94 AA MEd Goi 2 2Re we ada See eee A Eee oe ee 94 E ERAN 94 Developpement variables VARDEV 95 AD gecessWil oc aaa serada a e de e dee eee eH 95 ADD SEBA a AAA A e ee AG 95 Zo dela 0d eke ie veia A a 95 ADA ASNT ene a E Se ORE RS ee A LRA a 96 Heo o ote ee ee ee eee Gb eS 96 BO MO caia ew ee aon a CRESS EOE A eo EAE 96 OO NAAA 96 MOS Tale ook Fh ae ee A AAA ee ek A Do 97 429 CIDE ante ee we AR OR EE Le AA hee e ete 97 A DAO Mesui ck ee A ES EES PEELS Yaa ed 98 A et Se Ge eo os ke REE ee ee we eS Ga SS 98 AQ ANS 26 oe ob be ada CERES EE de e 98 ole PENRO 22 2 we Ge a ak ak a ee oe Boece a AE ee Re a aA 98 Lala DERIO ria EA aa a ee ee A 99 AO UR as a AR A a e ds ad 99 BONO IDEA oder rr ad eo ed 100 A E AAN 100 BONS ISE NO caia oe EE ERR ee a a a 100 ADU istati o eci aa d t A A EERE REE EHH 101 ALO ASS Slik ye SR
169. elf Energy We begin by the convergence study on the three parameters needed in the self energy calculation optdriver 4 This is because for these we will not need a double dataset loop to check this convergence and we will rely on the previously determined EM1 file First we check the convergence on the number of planewaves to describe the wavefunctions in the calculation of the Self Energy This will be done by defining five datasets with increasing ecutwfn ndtset 5 ecutw n 3 0 ecutw n 1 0 In directory ABINIT Tutorial Work6 copy the file t63 in and modify the t6x files file as usual Edit the t63 in file and take the time to examine it Then issue abinis lt t6x files gt amp t63 log amp This small job lasts about 10 secs on a PC PIV Intel 2 2 GHz Edit the output file The number of plane waves used for the wavefunctions in the computation of the self energy is mentioned in the fragments of output SIGMA fundamental parameters PLASMON POLE MODEL number of plane waves for SigmaX 169 number of plane waves for SigmaC and W 169 number of plane waves for wavefunctions 59 Gathering the GW energies for each planewave set one gets 46 CHAPTER 2 TUTORIAL number of plane waves for wavefunctions 59 Band EO VxcLDA SigX SigC E0 Z dSigC dE Sig E E EO E 4 5 915 11 651 15 237 3 897 0 806 0 240 11 401 0 251 6 166 5 8 445 9 669 3 222 5 460 0 819 0 222 8 861 0 808 9 253 number of plane waves fo
170. ementary resp n help file ABINIT Infos respfn_help html is needed Copyright C 1998 2004 ABINIT group DCA XG This file is distributed under the terms of the GNU General Public License see ABINIT Infos copyright or http www gnu org copyleft gpl txt For the initials of contributors see ABINIT Infos contributors 3 1 How to run the code 3 1 1 Introducing the files file Given an input file parameters described below and the required pseudopotential files the user must create a files file which lists names for the files the job will require including the main input file the main output file root names for other input output or temporary files and different pseudopotential file names The files file called for example ab files could look like e ab_in e ab_out e abi Es e abo e tmp e 14si psp In this example e the main input file is called ab_in 595 3 1 HOW TO RUN THE CODE e the main output will be put into the file called ab_out e the name of input wavefunctions if any will be built from the root abi namely abi_WFK see later e the output wavefunctions will be written to abo_WFK Other output files might be build from this root e the temporary files will have a name that use the root tmp for example tmp_STATUS e the pseudopotential needed for this job is 14si psp Other examples are given in the ABINIT Test_fast directory The maximal leng
171. en come the parameters defining the k points and states for which the electronic energy must be computed nkptgw3 1 number of k point where to calculate the GW correction kptgw3 k points 0 125 0 000 0 000 bdgw3 4 5 calculate GW corrections for bands from 4 to 5 nkptgw tells the number of k points for which the GW corrections must be computed The k points coordinates are given in kptgw At present they must belong to the grid of k points defined with the same repetition parameters kptrlatt or ngkpt than the GS one but WITHOUT any shift bdgw gives the minimum maximum band whose energies are calculated There is an additional parameter called zcut related to the self energy computation It is meant to avoid some divergences that might occur in the calculation due to integrable poles along the integration path Examination of the output file Let us hope now that your calculation has been completed and that we can examine the output file So please edit the t61 out file 43 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION The first departure from the usual information present in the output file for usual GS cal culations appears after the SCF cycles of DATASET 1 Calculating and writing out Kohn Sham electronic Structure file Using diagonalized wavefunctions and energies kssform 1 number of Gamma centered plane waves 483 number of Gamma centered shells 25 number o
172. er file On the other hand this is the file that is usually kept for archival purposes In addition wavefunctions can be input starting point or output result of the calculation and possibly charge density and or electrostatic potential if they have been asked for These three sets of data are stored in unformatted files The Density Of States DOS can also be an output as a formatted readable file An analysis of geometry can also be provided GEO file The name of these files is constructed from a root name that must be different for input files and output files and that is provided by the user to which the code will append a descriptor like WFK for wavefunctions DEN for the density POT for the potential DOS for the density of states There are also different temporary files A root name should be provided by the user from which the code generate a full name Amongst these files there is a status file summarizing the current status of advancement of the code in long jobs ABINIT abinis_help contains more details 1 6 What does the code do The simplest sort of job computes an electronic structure for a fixed set of atomic positions within a periodic unit cell By electronic structure we mean a set of eigenvalues and wavefunctions which achieve the lowest DFT energy possible for that basis set that number of planewaves The code takes the description of the unit cell and atomic positions and assembles a
173. ermody namical properties This section is still to be written You might have a look at the tests 26 to 32 of the directory ABINIT Infos Test_v2 The ABINIT tutorial is now finished It might be worth to read the full list of abinis input variables Then proceeds to the ABINIT Infos Dirs_and_files file to have a global view of ABINIT 2 6 Lesson 6 The quasi particle band structure of Silicon in the GW approximation This lesson aims at showing how to get self energy corrections to the DFT Kohn Sham eigenvalues in the GW approximation The GW formalism will NOT be explained in this tutorial The reader might consult the review e Quasiparticle calculations in solids by Aulbur W G Jonsson L Wilkins J W in Solid State Physics 54 1 218 2000 also available at http www physics ohio state edu wilkins vita gw_review ps The different formulas of the GW formalism that have been implemented in ABINIT have been written in a pdf document by Valerio Olevano who also wrote the first version of this tutorial see ABINIT Infos Theory gwa pdf This lesson should take about 2 hours to be done 2 6 1 Computation of the Silicon band gap at Gamma using a GW calculation Before beginning you might consider to work in a different subdirectory as for the other lessons Why not Work6 At the end of lesson 3 you computed the Kohn Sham band structure of Silicon In this approximation the variation of eigenvalues inside
174. es irrespective of their magnetic action and an additional magnetic space group number spgroupma For the additional number spgroupma we follow the definition of Table 7 4 of the above mentioned Bradley and Cracknell textbook Thus one way to specify a Shubnikov IV magnetic space group is to define both spgroup and spgroupma For example the group P2_1 c has spgroup 14 and spgroupma 78 Alternatively for Shubnikov IV magnetic groups one might define spgroup and genafm For both the type III and IV one might define by hand the set of symmetries using symrel tnons and symafm 4 4 16 vaclst Mnemonics VACancies LiST Characteristic GEOMETRY BUILDER NOT INTERNAL Variable type integer array vaclst vacnum No Default Gives the identification number s of atoms to be subtracted from the set of atoms that are obtained after having rotated translated and repeated the objects Useful to created vacancies 4 4 17 vacnum Mnemonics VACancies NUMber Characteristic GEOMETRY BUILDER Variable type integer parameter Default value is 0 Gives the number of atoms to be subtracted from the list of atoms after the rotations trans lations and repetitions have been done The list of these atoms is contained in vaclst 4 5 Ground state calculation variables VARGS 4 5 1 algalch Mnemonics ALGorithm for generating ALCHemical pseudopotentials Characteristic Variable type integer array algalch ntypalch 124 CHAPTER 4 MAI
175. es is given by ratsph 4 5 29 nbdbuf Mnemonics Number of BanDs for the BUF fer Characteristic Variable type integer parameter Default 0 However the default is changed to 2 in some cases see later nbdbuf gives the number of bands the highest in energy that among the nband bands are to be considered as part of a buffer This concept is useful in two situations in non self consistent calculations for the determination of the convergence tolerance for response functions of metals to avoid instabilities In non self consistent GS calculations iscf lt 0 the highest levels might be difficult to con verge if they are degenerate with another level that does not belong to the set of bands treated Then it might take extremely long to reach tolwfr although the other bands are already extremely well converged and the energy of the highest bands whose residual are not yet good enough is also rather well converged In response to this problem for non zero nbdbuf the largest residual residm to be later com pared with tolwfr will be computed only in the set of non buffer bands this modification applies for non self consistent as well as self consistent calculation for GS as well as RF calculations For a GS calculation with iscf lt 0 supposing nbdbuf is not initialized in the input file then ABINIT will overcome the default nbdbuf value and automatically set nbdbuf to 2 In metallic RF calculations in the conjugate
176. es of each band for each k point in eV or hartree or both depending on the choice of enunit NOTE that the average electrostatic potential of a periodically repeated cell is UNDE FINED In the present implementation the average Hartree potential and local potential are imposed to be zero but not the average exchange correlation potential This definition gives some meaning to the absolute values of eigenenergies thanks to Janak s theorem they are deriva tives of the total energy with respect to occupation number Indeed the G 0 contributions of the Hartree local potential and ion ion to the total energy is independent of the occu pation number in the present implementation With this noticeable exception one should always work with differences in eigenenergies as well as differences between eigenenergies and the potential For example the absolute eigenenergies of a bulk cell should not be used to try to predict a work function The latter quantity should be obtained in a supercell geometry by comparing the Fermi energy in a slab and the potential in the vacuum in the same supercell Next are the minimum and maximum values for charge density and next smaller or larger values in order to see degeneracies Next are the components of the total energy broken down into kinetic 68 CHAPTER 3 ABINIS HELP Hartree exchange and correlation xc local pseudopotential nonlocal pseudopotential local
177. esponse calculation to atomic displacements rprim 3 3 dimensionless primitive translations of periodic cell each COLUMN of this array is one primitive translation typat natom sequence of integers specifying the type of each atom NOTE the atomic coordinates xangst xcart or xred must be spec ified in the same order tolmxf force tolerance for structural relaxation in hartree bohr tolvrs tolerance on self consistent convergence xangst 3 natom cartesian coordinates Angstrom of atoms in unit cell NOTE only used when xred and xcart are absent xcart 3 natom cartesian coordinates bohr of atoms in unit cell NOTE only used when xred and xangst are absent xred 3 natom fractional coordinates for atomic locations NOTE leave out if xangst or xcart is used znucl ntypat Nuclear charge of each type of element must agree with nuclear charge found in psp file 1 5 Output files Output from a abinis run shows up in several files and in the standard output Usually one runs the command with a pipe of standard output to a log file which can be inspected for warnings or error messages if anything goes wrong or otherwise can be discarded at the end of a run The 3 1 6 WHAT DOES THE CODE DO more easily readable formatted output goes to the output file whose name is given in the files file i e you provide the name of the formatted output file No error message is reported in the latt
178. etization or with spin orbit if one allows for spontaneous non collinear magnetism Not yet available for forces stresses response functions The default nspden nsppol does not suit the case of vector magnetization 4 5 38 nspinor Mnemonics Number of SPINORial components of the wavefunctions Characteristic DEVELOP Variable type integer parameter The Default is 1 If nspinor 1 usual case scalar wavefunction compatible with nsppol 1 nspden 1 as well as nsppol 2 nspden 2 If nspinor 2 the wavefunction is a spinor compatible with nsppol 1 with nspden 1 or 4 but not with nsppol 2 When nspinor is 2 the values of istwfk are automatically set to 1 Also the number of bands for each k point should be even 138 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 5 39 ntypalch Mnemonics Number of TYPe of atoms that are ALCHemical Characteristic Variable type integer parameter The default is 0 Used for the generation of alchemical pseudopotentials when ntypalch is non zero alchemical mixing will be used Among the ntypat types of atoms the last ntypalch will be alchemical pseudoatoms while only the first ntyppure will be uniquely associated with a pseudopotential the ntyppure first of these actually The ntypalch types of alchemical pseudoatoms are to be made from the remaining npspalch pseudopotentials In this case the input variables algalch mixalch are active and gener
179. ewaves in the wavefunctions to calculate the Sel Pmerey sg a a PG a OE Pe ye ee Aa Mek ee Pe SG Convergence on the number of planewaves to calculate Sigma x Convergence on the number of bands to calculate the Self Energy Convergence on the number of planewaves in the wavefunctions to calculate A he hhh oe eee ue YE ES Convergence on the number of bands to calculate the screening Convergence on the dimension of the e7 matrix Calculation of the GW corrections for the band gap in Gamma 3 ABINIS Help 3 1 How to Tun the code acandit aa danara aani kaaa aa dll 3 1 2 ld Introducing the files file s cc o bee ee ee eee ees Runiing the Geode ooo cidcid a ea The underlying theoretical framework and algorithms oo WRG mpat Ble ica ak Oo a ee ee ee Dee Be eee ee ees 3al 3 2 2 IAI 3 2 4 3 2 0 3 2 6 Format of the input file so lt a osos soa aa mami taa ae More about ABINIT input variables oaoa The multi dataset modes a o sisa deaa o oaoa A ee EE a a a Denning a series o i o ea ea RA ee a Defining a double loop dataset o cc cia cooo rbaa aaa g sees File names in the multi dataset mode o oe Mhe ies HE ve nk we RRE AAD a 3 4 The pseudopotential files 0 020 202 02 ee ee eee 3 5 The different output Bles lt o sa coea a ee ed Ge ee eG 3 5 1 3 5 2 3 5 3 3 5 4 3 5 5 3 5 6 3 5 7 3 5 8 The logfile 2 244448
180. examine some variables that were NOT defined in the input file but that appear in the echo written in t11 out e nband its value is 2 It is the number of electronic states that will be treated by the code It has been com puted by counting the number of valence electrons in the unit cell summing the valence electrons brought by each pseudopotential then occupying the lowest states look at the occ variable and adding some states at least one maybe more depending on the size of the system e ngfft its value is 30 30 30 It is the number of points of the three dimensional FFT grid It has been derived from ecut and the dimension of the cell acell The maximal number of plane waves mpw is mentioned in the memory evaluation section it is 752 Well this is not completely right as the code took advantage of the time reversal symmetry valid for the k point 0 0 0 to decrease the number of planewave by about a factor of two The full set of plane waves is 1503 see later in the t11 out file The code indicates the time reversal symmetry by a value of istwfk 2 instead of the usual istwfk 1 default 2 1 LESSON 1 THE H2 MOLECULE WITHOUT CONVERGENCE STUDIES e nsym its value is 16 It is the number of symmetries of the system The 3 x 3 matrices symrel define the symmetries operation In this case none of the symmetries is accompanied by a trans lation that would appe
181. f bands 283 This section was issued when the Hamiltonian at the different k points were diagonalized after the SCF cycles in order to generate the KSS file Then comes the output of the numer ous eigenvalues at the different k points Finally the normalization and orthogonalization of the eigenvectors is tested One should obtain perfect normalization and orthogonalization at that stage Test on the normalization of the wavefunctions min sum_G la n k G 1 000000 max sum_G a n k G 1 000000 Test on the orthogonalization of the wavefunctions min sum_G a n k G a n k G 0 000000 max sum_G a n k G a n k G 0 000000 Then follows the usual information for the dataset 1 The dataset 2 drives the computation of the susceptibility and dielectric matrices in preparation of the GW energy calculation of dataset 3 After some general information origin of KSS file header description of unit cell comes the echo of Kohn Sham eigenenergies in eV and then the evaluation of the wavefunction normalization and orthogonalization USING ONLY THE PLANEWAVE SET DEFINED BY ecutwfn npwwfn or nshwfn Thus there is no surprise that these relations are not fulfilled test on the normalization of the wavefunctions min sum_G la n k G 0 497559 max sum_G a n k G 0 995840 test on the orthogonalization of the wavefunctions min sum_G a n k G a n k G 0 000000 max sum_G a n k G a n k G 0 179460 The squared norm of o
182. f e g the total energy within some range of planewave number or ecut It is appropriate to attempt to optimize this convergence especially for difficult atoms like oxygen or copper as long as one does not significantly compromise the quality or transferability of the pseu dopotential There are many people working on new techniques for optimizing convergence For information on extended norm conservation see E L Shirley D C Allan R M Martin and J D Joannopoulos Phys Rev B 40 3652 1989 For information on optimizing the convergence of pseudopotentials see A M Rappe K M Rabe E Kaxiras and J D Joannopoulos Phys Rev B 41 1227 1990 In addition to achieving convergence in the number of planewaves in the basis one must ensure that the SCF iterations which solve the electronic structure for a given set of atomic coordinates are also converged This convergence is controlled by the parameters toldfe toldff tolwfr and tolurs as well as the parameter nstep One of the tolerance parameters must be chosen and when the required level of tolerance is fulfilled the SCF cycles will stop The nstep variable also controls convergence in preconditioned conjugate gradient iterations by forcing the calculation to stop whenever the number of such iterations exceeds nstep Usually one wants nstep to be set larger than needed to reach a given tolerance or else one wants to restart insufficiently converged calculations until
183. ferent spin We will define by hand the occupation of each spin see the input variables occopt to be set to 2 and occ Finally in order to make numerical errors cancel it is important to compute the above mentioned difference in the same box for the same cut off and even for a location in the box that is similar to the molecule case although the latter might not be so important The input file ABINIT Tutorial t15 in is an example of file that will do the job while ABINIT Tutorial Refs t15 o0ut is an example of output file If you decide to use the t15 in file do not forget to change the file names in the tix files file The run lasts a few seconds You should read the output file and note the tiny differences related with the spin polarization e the electronic eigenvalues are now given for both spin up and spin down cases Eigenvalues hartree for nkpt 1 k points SPIN UP kpt 1 nband 1 wtk 1 00000 kpt 0 0000 0 0000 0 0000 reduced coord 0 26422 Eigenvalues hartree for nkpt 1 k points SPIN DOWN kpt 1 nband 1 wtk 1 00000 kpt 0 0000 0 0000 0 0000 reduced coord 0 11117 e the spin polarization at each point of the FFT grid is also analyzed Min spin pol zeta 1 0000E 00 at reduced coord 0 0000 0 0000 0 0000 next min 1 0000E 00 at reduced coord 0 0333 0 0000 0 0000 Max spin pol zeta 1 0000E 00 at reduced coord 0 9667 0 9667 0 9667 3 next max 1 0000E 00 at reduced coord 0 9333 0
184. few seconds The density will be output in the tlxo_DEN file Try to edit it No luck This file is unformatted not written using the ASCII code Even if you cannot read it its description is provided in the abinis_help It contains first a header then the density numbers The description of the header is presented in section 6 4 of the abinis_help file while the body of the _DEN file in presented in section 6 5 It is the appropriate time to read also the description of the potential files and wavefunctions files as these files contain the same header as the density file see sections 6 6 and 6 7 3 Such a density file can be read by ABINIT to restart a calculation see the input variable iscf when its value is 2 but more usually by an utility called cut3d This utility is available in the ABINIT package You might try to use it now to generate two dimensional cuts in the density and visualize the charge density contours Read the corresponding cut3d help file Then try to run cut3d to analyze t1xo_DEN You should first try to translate the unformatted density data to indexed formatted data by using option 6 in the adequate menu Save the indexed formatted data to file t1xo_DEN_indexed Then edit this file to have an idea of the content of the _DEN files For further treatment you might choose to select another option than 6 In particular if you have access to MATLAB choose option 5 With minor modifications set ngr
185. ffects are important since these schemes compute their own mixing factor for self consistency 4 5 16 dosdeltae Mnemonics DOS Delta in Energy Characteristic ENERGY Variable type real parameter Default is 0 0 Defines the linear grid resolution energy increment to be used for the computation of the Density Of States when prtdos is non zero If dosdeltae is set to zero the default value the actual increment is 0 001 Ha if prtdos 1 and the much smaller value 0 00005 Ha if prtdos 2 This different default value arises because the prtdos 1 case based on a smearing technique gives a quite smooth DOS while the DOS from the tetrahedron method prtdos 2 is rapidly varying 4 5 17 efield Mnemonics Electric FIELD Characteristic Variable type real array efield 3 Default is 3 0 0 In case berryopt 4 a finite electric field calculation is performed The value of this electric field and its direction is determined by efield It must be given in atomic units 1 a u of electric field 514220624373 482 V m see note below in cartesian coordinates References for the calculation under electric field based on multi k point Berry phase e Nunes and Vanderbilt PRL 73 712 1994 real space version of the finite field Hamiltonian e Nunes and Gonze PRB 63 155197 2001 reciprocal space version of the finite field Hamil tonian the one presently implemented and extensive theoretical analysis e Souza Iniguez and Vanderb
186. file to see whether an ERROR or a BUG occurred Also the code gives the number of WARNING or COMMENT it issued It is advised to read at least the WARNING messages during the first month of ABINIT use If you follow the tutorial you should go back to the tutorial window now 66 CHAPTER 3 ABINIS HELP 3 5 2 The main output file The main output file is a formatted output file to be kept as the permanent record of the run Note that it is expected not to exist at the beginning of the run If a file with the name specified in the files file already exists the code will generate from the given one another name appended with A If this new name already exists it will try to append B and so on until Z Then the code stops and asks you to clean the directory The main output file starts with a heading e version number and specified platform copyright notice and distribution licence e date echo of files file except pseudopotential name Then for each dataset it reports the point symmetry group and Bravais lattice and the expected memory needs It echoes the input data and report on checks of data consistency for each dataset If you follow the tutorial you should go back to the tutorial window now 3 5 3 More on the main output file Then for each dataset the real computation is done and the code will report on some initialisa tions the SCF convergence and the final analysis of results for
187. final run For most solids the size of the unit cell will be smaller than that We are treating a lot of vacuum in this supercell So the Hz study with this pseudopotential turns out to be not really easy Of course the number of states to be treated is minimal This allows to have reasonable CPU time still 19 2 2 LESSON 2 THE H2 MOLECULE WITH CONVERGENCE STUDIES 2 2 4 The final calculation in Local Spin Density Approximation We now use the correct values of both ecut and acell Well you should modify the t23 in file to make a calculation with acell 12 12 12 and ecut 30 You can still use the double loop feature with udtset 1 2 which reduces to a single loop to minimize the modifications to the file The file ABINIT Tutorial t24 in can be taken as an example of input file and ABINIT Tutorial Refs t24 out as an example of output file Since we are doing the calculation at a single ecut acell pair the total CPU time is not as much as for the previous determinations of optimal values through series calculations However the memory needs have still increased a bit The output data are etotal11 1 1329372052E 00 etotal12 4 7765320649E 01 xcartil 7 2661954446E 01 0 0000000000E 00 0 0000000000E 00 7 2661954446E 01 0 0000000000E 00 0 0000000000E 00 xcarti2 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 e The corresponding atomization energy is 0 1776 Ha 4 833 eV e The interatomic distance is 1 4532 Bohr e
188. for the method used to solve the Dyson equation in the calculation of the interacting susceptibility matrix or and in the calculation of the ACFD exchange correlation energy e idyson 1 Solve the Dyson equation by direct matrix inversion e idyson 2 Solve the Dyson equation as a first order differential equation with respect to the coupling constant lambda only implemented for the RPA at the present stage see header of dyson_de f for details e idyson 3 Calculate only the diagonal of the interacting susceptibility matrix by self consistently computing the linear density change in response to a set of perturbations Only implemented for the RPA at the present stage and entirely experimental see dyson_sc f for details 4 2 13 ikhxc Mnemonics Integer option for KHXC Hartree XC kernel Characteristic Variable type integer parameter Default value is 1 Define the HXC kernel in the cases for which it can be dissociated with the choice of the HXC functional given by ixc namely the TD DFT computation of excited states iscf 1 and the computation of the susceptibility matrix for ACFD purposes Options 2 to 6 are for the ACFD only e 0 gt RPA for the TDDFT but no kernel for the ACFD testing purposes 98 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST e 1 gt RPA for the TDDFT and ACFD e 2 gt ALDA PW92 for the ACFD e 3 gt PGG for the ACFD M Petersilka U J Gossmann and E K U Gross PR
189. fr Indeed the two upper bands by default have not been taken into account to apply this convergence criterion they constitute a buffer The number of such buffer bands is governed by the input variable nbdbuf It can happen that the highest or two highest band s if not separated by a gap from non treated bands can exhibit a very slow convergence rate This buffer allows to achieve convergence of important non buffer bands In the present case 6 bands have been converged with a residual better than tolwfr while the two upper bands are less converged still sufficiently for graphical representation of the band structure In order to achieve the same convergence for all 8 bands it is advised to use nband 10 that is 8 2 2 4 Lesson 4 Aluminum the bulk and the surface This lesson aims at showing how to get the following physical properties for a metal and for a surface e the total energy 25 2 4 LESSON 4 ALUMINUM THE BULK AND THE SURFACE e the lattice parameter e the relaxation of surface atoms e the surface energy You will learn about the smearing of the Brillouin zone integration and also a bit about preconditioning the SCF cycle This lesson should take about 1 hour and 30 minutes to be done 2 4 1 Computing the total energy and lattice parameters of aluminum for a fixed smearing and number of k points Before beginning you might consider to work in a different subdirectory as f
190. ftk Mnemonics Number of SHIFTs for k point grids Characteristic Variable type integer parameter The Default is 1 This parameter gives the number of shifted grids to be used concurrently to generate the full grid of k points It can be used with primitive grids defined either from ngkpt or kptrlatt The maximum allowed value of nshiftk is 8 The values of the shifts are given by shiftk 4 1 16 nsppol Mnemonics Number of SPin POLarization Characteristic Variable type integer parameter The Default is 1 Give the number of independent spin polarisations Can take the values 1 or 2 If nsppol 1 one has an unpolarized calculation nspinor 1 nspden 1 or an antiferromag netic system nspinor 1 nspden 2 or a calculation in which spin up and spin down cannot be disantengled nspinor 2 non collinear magnetism or presence of spin orbit coupling for which one needs spinor wavefunctions If nsppol 2 one has a spin polarized calculation with separate and different wavefunctions for up and down spin electrons for each band and k point Compatible only with nspinor 1 nspden 2 In the present status of development with nsppol 1 all values of ixc are allowed while with nsppol 2 only ixc 0 1 7 and 11 are allowed See also the input variable nspden for the components of the density matrix with respect to the spin polarization 4 1 17 nstep Mnemonics Number of self consistent field STEPS Characteristic Variable type i
191. g choice of segment end points L 1 2 0 0 Gamma 0 O 0 X o 1 2 1 2 Gamma 1 1 1 Note 1 the last Gamma point is in another cell of the reciprocal space than the first one this choice allows to construct the X U Gamma line easily 2 the k points are specified using reduced coordinates in agreement with the input setting of the primitive 2 atom unit cell in standard textbooks you will often find the L Gamma or X point given in coordinates of the conventional 8 atom cell the above mentioned circuit is then 1 2 1 2 1 2 0 0 0 1 0 0 1 1 1 but such coordinates cannot be used with the 2 atom cell So you should set up in your input file for the first dataset a usual SCF calculation in which you output the density priden 1 and for the second dataset fix iscf to 2 to make a non self consistent calculation e define getden 1 to take the output density of dataset 1 e set nband to 8 e set kptopt to 3 to define three segments in the Brillouin Zone e set ndivk to 10 12 17 this means a circuit defined by 4 points with 10 divisions of the first segment 12 divisions of the second 17 divisions of the third e set kptbounds to L point Gamma point X point Gamma point in another cell e OOO O O O A PO0O0O O A O O PO0O0O 0 O 5 0 e set enunit to 1 in order to have eigenenergies in eV e the only tolerance criterion admitted for non self consistent calcu
192. g less states Another way to reduce the load of the diagonalization is made possible through the use of npwkss It governs the size of the plane wave basis set in which the Hamiltonian matrix will be expressed and diagonalized The default value leaves the number of plane wave equal to the one of the SCF ground state calculation Another relevant input variable related also to the specific set up of the _KSS file is kssform In this first dataset we asked also the self consistent cycle to be done for nine bands nband1 9 Number of occ and empty bands to be computed Only four bands would be needed for Si The purpose of defining more bands in the ground state determination is to verify that at least the first Kohn Sham eigenvalues obtained through the diagonalization are sufficiently close to those determined in the self consistent procedure At present the comparison is not done automatically so please check well sometimes that the Kohn Sham eigenvalues given in the self consistency part with a residual are close to those given after the diagonalization 3 Generating the screening the EM1 file In dataset 2 the calculation of the screening susceptibility dielectric matrix is performed We need to set optdriver 3 to do that optdriver2 3 Screening calculation The getkss input variable is similar to other get input variables of ABINIT getkss2 1 Obtain KSS file from previous dataset In this case it tells the
193. gate gradient minimization for each band The Default 4 is fine Special cases with degeneracies or near degeneracies of levels at the Fermi energy may require a larger value of nline 5 or 6 Line minimizations will be stopped anyway when improvement gets small With the input variable nnsclo governs the convergence of the wavefunctions for fixed potential Note that nline 0 can be used to diagonalize the Hamiltonian matrix in the subspace spanned by the input wavefunctions 4 5 34 npsp Mnemonics Number PSeudoPotentials Characteristic NO MULTI Variable type integer parameter Default is ntypat Usually the number of pseudopotentials to be read is equal to the number of type of atoms However in the case an alchemical mixing of pseudopotential is to be used often the number of pseudopotentials to be read will not equal the number of types of atoms Alchemical pseudopotentials will be present when ntypalch is non zero See ntypalch to under stand how to use alchemical potentials in ABINIT The input variables ntypalch algalch mixalch are active and generate alchemical potentials from the available pseudopotentials Also the inner variables ntyppure npspalch becomes active See these input variables especially mixalch to understand how to use alchemical potentials in ABINIT 137 4 5 GROUND STATE CALCULATION VARIABLES VARGS 4 5 35 npspalch Mnemonics Number of PSeudoPotentials that are ALCHemical Characterist
194. ger the same procedure than above leads to the values 5 00800270 Hartree from finite difference of energy and 5 009149889 Hartree from finite difference of forces the value 0 010016299779 has to be multiplied by 1000 2 The combination of these data with the previous estimate can be done thanks to an higher order finite difference formula in which the difference of estimations the largest perturbation minus the smallest one is divided by three and then subtracted from the smallest estimation As far as the total energy estimation is concerned the difference is 0 0001104 Ha which divided by three and subtracted from 5 00789230 Hartree gives 5 0078555 Hartree The same higher order procedure for force estimates gives 5 0078552 Hartree So the agreement between total energy estimate and force estimate of the 2DTE can be observed up to the 7th digit inclusive Before comparing this result with the 2DTE directly computed from the response function capabilities of ABINIT a last comment is in order One can observe that the action eaction law is fulfilled only approximately by the system Indeed the force created on the second atom should be exactly equal in magnitude to the force on the first atom The values of dE dt mentioned above for example for the doubled displacement rms dE dt 7 1249E 03 max dE dt 1 0016E 02 dE dt below all hartree 1 0 010016299779 0 005097509981 0 005097509981 2 0 010016176675 0 005097455174 0 0050974551
195. gt GGA x only part of Perdew Burke Ernzerhof GGA functional 13 gt GGA potential of van Leeuwen Baerends while for energy Perdew Wang 92 functional 14 gt GGA revPBE of Y Zhang and W Yang Phys Rev Lett 80 890 1998 15 gt GGA RPBE of B Hammer L B Hansen and J K Norskov Phys Rev B 59 7413 1999 16 gt GGA HTCH of F A Hamprecht A J Cohen D J Tozer N C Handy J Chem Phys 109 6264 1998 e 20 gt Fermi Amaldi xc 1 N Hartree energy where N is the number of electrons per cell G 0 is not taken into account however for TDDFT tests No spin pol Does not work for RF e 21 gt same as 20 except that the xc kernel is the LDA ixc 1 one for TDDFT tests e 22 gt same as 20 except that the xc kernel is the Burke Petersilka Gross hybrid for TDDFT tests Note that the choice made here should agree with the choice made in generating the original pseudopotential except for ixc 0 usually only used for debugging A warning is issued if this is not the case However the choices izc 1 2 3 and 7 are fits to the same data from Ceperley Alder and are rather similar at least for spin unpolarized systems The choice between the LDA or the LSD is governed by the value of nsppol see below NOTE in the implementation of the spin dependence of these functionals and in order to avoid divergences in their derivatives the interpolating function between spin unpolarized and fully spin polarized functi
196. hange it as usual Note that two pseudopotentials are mentioned in this files file one for the Aluminum atom and one for the Arsenic atom The first to be mentioned for Al will define the first type of atom The second to be mentioned for As will define the second type of atom It is the first time that you encounter this situation in the tutorials You can also copy the file ABINIT Tutorial t51 in in Work5 This is your input file You should edit it read it carefully and because of the use of two types of atoms have a look at the following input variables e ntypat e typat 32 CHAPTER 2 TUTORIAL Note that the value of tolurs is rather stringent This is because the wavefunctions determined by the present run will be used later as starting point of the response function calculation You will work at fixed ecut 3Ha and k point grid defined by kptrlatt the 4x4x4 Monkhorst Pack grid It is implicit that in real life you should do a convergence test with respect to both convergence parameters We postpone the discussion of the accuracy of these choices and the choice of pseudopotential to the last section of this tutorial LINK TO BE GIVEN They give acceptable results not very accurate but more important the speed is reasonable for a tutorial You should make the run a dozen of second on a PIII at 450 MHz and obtain the following value for the energy in the final echo section etotal 9 76268374
197. hat the sum of atomic DOS for all angular momenta and atoms integrated on the energy range of the occupied states gives back the total charge If this is not an issue one could rely on the half of the nearest neighbour distances or any scheme that allows to define an atomic radius Note that the choice of this radius is however critical for the balance between the s p and d components Indeed the integrated charge within a given radius behave as a different power of the radius for the different channels s p d At the limit of very small radii the s component dominates the charge contained in the sphere 4 5 48 spinat Mnemonics SPIN for AToms Characteristic Variable type real array spinat 3 natom or spinat 3 natrd if the symmetriser is used Default is 0 0d0 Gives the initial electronic spin magnetisation for each atom in unit of h bar 2 Note that if nspden 2 the z component must be given for each atom in triplets 0 0 z component For example the electron of an hydrogen atom can be spin up 0 0 1 0 or spin down 0 0 1 0 This value is only used to create the first exchange and correlation potential and is not used anymore afterwards It is not checked against the initial occupation numbers occ for each spin channel 141 4 5 GROUND STATE CALCULATION VARIABLES VARGS It is meant to give an easy way to break the spin symmetry and to allow to find stable local spin fluctuations for example antiferromag
198. he Chemical Markup Language see papers by P Murray Rust and H Rzepa especially J Chem Inf Comput Sci 39 928 942 1998 and the Web site http www xml cml org Such file can be treated automatically by tools developed to handle XML formatted files Such a CML file contains e The crystallographic information space group number and the needed unit cell parameters and angles e The list of symmetry elements e The list of atoms in the cell symbols and reduced coordinates If ionmov 0 the name of the CML file will be the root output name followed by CML xml If ionmov 1 or 2 the CML file will be output at each time step with the name being made of e the root output name e followed by _TIMx where x is related to the timestep see later 112 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST e then followed by CML xml No output is provided by prtcml lower or equal to 0 4 3 22 prtden Mnemonics PRinT the DENsity Characteristic Variable type integer parameter Default is 0 If set to 1 or a larger value provide output of electron density in real space rho r in units of electrons Bohr If ionmov 0 the name of the density file will be the root output name followed by _DEN If ionmov 1 or 2 density files will be output at each time step with the name being made of e the root output name e followed by _TIMx where x is related to the timestep see later e then followed by _DEN
199. he default Ry eV or Kelvin since ecut has the ENERGY characteristics 1 Ha 27 2113961 eV Typical use is for response to electric field rfelfd 3 but NOT for d dk rfelfd 2 and phonon responses 158 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 10 28 td_ maxene Mnemonics Time Dependent dft MAXimal kohn sham ENErgy difference Characteristic TDDFT Variable type real parameter Default is huge The Matrix to be diagonalized in the Casida framework see Time Dependent Density Func tional Response Theory of Molecular systems Theory Computational Methods and Functionals by M E Casida in Recent Developments and Applications of Modern Density Functional Theory edited by J M Seminario Elsevier Amsterdam 1996 is a NxN matrix where by default N is the product of the number of occupied states by the number of unoccupied states The input variable td maxene allows to diminish N it selects only the pairs of occupied and unoccupied states for which the Kohn Sham energy difference is less than td maxene See td mexcit for an alternative way to decrease N 4 10 29 td_mexcit Mnemonics Time Dependent dft Maximal number of EXCITations Characteristic TDDFT Variable type real parameter Default is 0 The Matrix to be diagonalized in the Casida framework see Time Dependent Density Func tional Response Theory of Molecular systems Theory Computational Methods and Functionals by M
200. he primitive set of atoms using the following order it will process each atom in the primitive list one by one determine whether it belongs to either object a or object b and then repeat it taking into account the proper rotation and translation with the fastest varying repetition factor being the first then the second then the third In the final list of atoms one will first find the atoms generated from atom 1 in the primitive list then those generated from atom 2 in the primitive list and so on If the geometry builder is only used to rotate or translate an object without repeating it simply use 1 1 1 which is also the Default value Not present in the dtset array no internal 4 4 9 objaro objbro Mnemonics OBJect A ROtations OBJect B ROtations Characteristic GEOMETRY BUILDER NO INTERNAL Variable type real arrays objaro 4 and objbro 4 Default is 4 0 0d0 no rotation Give for each object the angles of rotation in degrees to be applied to the corresponding object The rotation is applied before the translation and the axis is defined by the variables objaax and objbax See the latter variables for the definition of the sign of the rotation The first component objaro 1 and objbro 1 gives the angle of rotation to be applied to the first instance of the object The second third or fourth component resp gives the increment of rotation angle from one instance to the next instance defined by the first second or
201. ht at K 0 diel K is imposed to be 1 If the preconditioning were perfect the change of potential would lead to an exceedingly fast solution of the self consistency problem two or three steps The present model dielectric function is excellent for rather homogeneous unit cells When K 0 it tends to the macroscopic dielectric constant eventually divided by the mixing factor diemix For metals simply put diemac to a very large value 10 is OK The screening length dielng governs the length scale to go from the macroscopic regime to the microscopic regime where it is known that the dielectric function should tend to 1 It is on the order of 1 bohr for metals with medium density of states at the Fermi level like Molybdenum and for Silicon For metals with a larger DOS at the Fermi level like Iron the screening will be more effective so that dielng has to be decreased by a factor of 2 4 This works for GS and RF calculation 4 5 14 diemac Mnemonics model DIElectric MACroscopic constant Characteristic Variable type real parameter Default is 106 metallic damping A rough knowledge of the macroscopic dielectric constant diemac of the system is a useful help to speed up the SCF procedure a model dielectric function see the keyword dielng is used for that purpose It is especially useful for speeding up the treatment of rather homogeneous unit cells Some hint The value of diemac should usually be bigger than 1 0d0 on ph
202. ial version of ABINIT 1 for parallel version of ABINIT If chkexit is 1 or 2 ABINIT will check whether the user wants to interrupt the run using the keyword exit on the top of the input file or creating a file named abinit exit see the end of section 3 2 of abinis_help If chkexit 0 the check is not performed at all If chkexit 1 the check is not performed frequently after each SCF step If chkexit 2 the check is performed frequently after a few bands at each k point 4 5 8 chkprim Mnemonics CHecK whether the cell is PRIMitive Characteristic SYMMETRY FINDER Variable type integer parameter Default is 1 If the symmetry finder is used see nsym a non zero value of chkprim will make the code stop if a non primitive cell is used If chkprim 0 a warning is issued but the run does not stop If you are generating the atomic and cell geometry using spgroup you might generate a PRIM ITIVE cell using brvlatt 1 4 5 9 cpus cpum cpuh Mnemonics CPU time limit in Seconds Minutes Hours Characteristic NO MULTI for cpum and cpuh NO INTERNAL Variable type real parameters Default is 0 0d0 One of these three real parameters can be defined in the input file to set up a CPU time limit When the job reaches that limit it will try to end smoothly However note that this might still take some time If the user want a firm CPU time limit the present parameter must be reduced sufficiently Intuition about th
203. ic Inner Variable type integer parameter non negative npspalch npsp ntyppure 4 5 36 nqpt Mnemonics Number of Q POINTs Characteristic Variable type integer parameter Default is 0 Determines whether one g point must be read See the variables qpt and qptnrm Can be either 0 or 1 If 1 and used in ground state calculation a global shift of all the k points is applied to give calculation at k q In this case the output wavefunction will be appended by WFQ instead of WFK see the section 4 of abinis_help Also if 1 and a RF calculation is done defines the wavevector of the perturbation 4 5 37 nspden Mnemonics Number of SPin DENsity components Characteristic DEVELOP Variable type integer parameter The Default is the value of nsppol If nspden 1 no spin magnetisation the density matrix is diagonal with same values spin up and spin down compatible with nsppol 1 only for both nspinor 1 or 2 If nspden 2 scalar magnetization the axis is arbitrarily fixed in the z direction the density matrix is diagonal with different values for spin up and spin down compatible with nspinor 1 either with nsppol 2 general collinear magnetisation or nsppol 1 antiferromagnetism If nspden 4 vector magnetization the density matrix is full with allowed x y and z mag netisation useful only with nspinor 2 and nsppol 1 either because there is spin orbit without time reversal symmetry and thus spontaneous magn
204. ic translations vectors will be input in array tnons If there is no symmetry in the problem then set nsym to 1 because the identity is still a symmetry In case of a RF calculation the code is able to use the symmetries of the system to decrease the number of perturbations to be calculated and to decrease of the number of special k points to be used for the sampling of the Brillouin zone After the response to the perturbations have been calculated the symmetries are used to generate as many as possible elements of the 2DTE from those already computed SYMMETRY FINDER mode Default mode Tf nsym is 0 all the atomic coordinates must be explicitely given one cannot use the geometry builder and the symmetrizer the code will then find automatically the symmetry operations that leave the lattice and each atomic sublattice invariant It also checks whether the cell is primitive see chkprim Note that the tolerance on symmetric atomic positions and lattice is rather stringent for a symmetry operation to be admitted the lattice and atomic positions must map on themselves within 1 0e 8 The user is allowed to set up systems with non primitive unit cells i e conventional FCC or BCC cells or supercells without any distortion In this case pure translations will be identified as symmetries of the system by the symmetry finder Then the combined pure translation usual rotation and inversion symmetry operations can be very numerous Fo
205. icense see ABINIT Infos copyright or http www gnu org copyleft gpl txt For the initials of contributors see ABINIT Infos contributors 4 1 Basic variables VARBAS 4 1 1 acell Mnemonics scAle CELL Characteristic EVOLVING LENGTH Variable type real array acell 3 Gives the length scales by which dimensionless primitive translations in rprim are to be multiplied By default given in Bohr atomic units 1 Bohr 0 5291772083 A although Angstrom can be specified if preferred since acell has the LENGTH characteristics See further description of acell related to the rprim input variable 4 1 2 angdeg Mnemonics ANGles in DEGrees Characteristic Variable type real array angdeg 3 No Default use rprim as Default Gives the angles between directions of primitive vectors of the unit cell in degrees as an alternative to the input array rprim Will be used to set up rprim that together with the array acell will be used to define the primitive vectors e angdeg 1 is the angle between the 2nd and 3rd vectors 79 4 1 BASIC VARIABLES VARBAS e angdeg 2 is the angle between the 1st and 3rd vectors e angdeg 3 is the angle between the 1st and 2nd vectors If the three angles are equal within 1 0 x 1071 except if they are exactly 90 degrees the three primitive vectors are chosen so that the trigonal symmetry that exchange them is along the z cartesian axis R1 a 0 c R2 a 2 V3 2 x a c R3
206. ied states When prtstm is non zero the stress tensor is set to zero No output of STM file is provided by prtstm lower or equal to 0 4 3 33 prtvol Mnemonics PRinT VOLume Characteristic Variable type integer parameter Default is 0 116 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Control the volume of printed output Standard choice is 0 Positive values print more in the output and log files while negative values are for debugging or preprocessing only and cause the code to stop at some point e 0 gt there is a limit on the number of k points for which related information will be written This limit is presently 50 Due to some subtlety if for some dataset prtvol is non zero the limit for input and output echoes cannot be enforced so it is like if prtvol 1 for the all the dataset for which prtvol was set to 0 e 1 gt there is no such limit for the input and output echoes in the main output file e 2 gt there is no such limit in the whole main output file e 3 gt there is no such limit in both output and log files e 10 gt no limit on the number of k points and moreover the eigenvalues are printed for every SCF iteration as well as other additions to be specified in the future Debugging options e 1 stop in abinis main program before call gstate Useful to see the effect of the preprocessing of input variables memory needed effect of symmetries k points
207. ilt PRL 89 117602 2003 implementation of the finite field Hamiltonian reciprocal space version See also Umari Pasquarello PRL 90 027401 2003 The atomic unit of electric field strength is ecy 4m 9a where ec is the electronic charge in Coulomb 1 602176462e 19 eo is the electric constant 8 854187817d 12 F m and ag is the Bohr radius in meter 0 5291772083e 10 4 5 18 enunit Mnemonics ENergy UNITs Characteristic Variable type integer parameter Default is 0 eigenvalues in hartree and phonon frequencies in Hartree and cm 1 Governs the units to be used for output of eigenvalues and eventual phonon frequencies e 0 print eigenvalues in hartree e 1 print eigenvalues in eV e 2 gt print eigenvalues in both hartree and eV 130 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST If phonon frequencies are to computed e 0 phonon frequencies in Hartree and cm 1 e 1 phonon frequencies in eV and THz e 2 phonon frequencies in hartree eV cm 1 Thz and Kelvin 4 5 19 fband Mnemonics Factor for the number of BANDs Characteristic NO INTERNAL Variable type real parameter positive or zero Default is 0 125 in case occopt 1 insulating case and 0 500 for other values of occopt metallic case Not used in case occopt 0 or 2 Governs the number of bands to be used in the code in the case the parameter nband is not defined in the input file which means that occopt is not equal
208. independent direction allows to find the full polarisation vector However note that converged results need oriented grids denser along the difference wavevector than usual Monkhorst Pack grids The difference of wavevector is computed in the coordinate system defined by the k points grid see ngkpt and kptrlatt so that the values of kberry are integers Of course such a k point grid must exist and all the corresponding wavefunctions must be available so that the computation is 132 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST allowed only when kptopt is equal to 3 In order to save computing time it is suggested to make a preliminary calculation of the wavefunctions on the irreducible part of the grid with kptopt equal to 1 and then use these converged wavefunctions in the entire Brillouin zone by reading them to initialize the kptopt 3 computation 4 5 24 kptbounds Mnemonics K PoinTs BOUNDarieS Characteristic NOT INTERNAL Variable type real array kptbounds 3 abs kptopt 1 No Default It is used to generate the circuit to be followed by the band structure when kptopt is negative it is not read if kptopt is zero or positive There are abs kptopt segments to be defined each of which wich start from the end point of the preceeding one Thus the number of points to be input is abs kptopt 1 They form a circuit starting at kptbounds 1 3 1 kptnrm and ending at kptbounds 1 3 abs kptopt 1 kptnrm The
209. input data described in the preceeding sections ab_out Filename of the main file in which formatted output will be placed the main output file Error messages and other diagnostics will NOT be placed in this file but sent to unit 06 terminal or log file the unit 06 output can be ignored unless something goes wrong The code repeats a lot of information to both unit 06 and to the main output file The unit 06 output is intended to be discarded if the run completes successfully with the main output file keeping the record of the run in a nicer looking format abi The other files READ by the code will have a name that is constructed from the root abi This apply to optionally read wavefunction density or potential files In the multi dataset mode this root will be complemented by _DS and the dataset index The list of possible input files with their name created from the root abi is the following a similar list exist when DS and the dataset index are appended to abi e abi WFK filename of file containing input wavefunction coefficients created from an earlier run with nqpt 0 Will be opened and read if irdwfk is 1 The wavefunction file is unformatted and can be very large Warning in the multi dataset mode if getwfk is non zero a wavefunction file build from abo will be read e abi WFQ filename of file containing input wavefunction coefficients created from an earlier run with nqpt 1 as needed for res
210. input variables the existence of defaults the actions of the preprocessor and the use of the multi dataset feature You will also learn about the two output files as well as the density file This first lesson covers the sections 1 3 4 and 6 of the abinis_help file The very first step is a detailed tour of the input and output files you are like a tourist and you discover a town in a coach You will have a bit more freedom after that first step It is supposed that you have some good knowledge of UNIX Linux This lesson should take about 2 hours to be done 2 1 1 Computing the total energy and some associated quantities This is the first step the most important and the most difficult Note that the present tutorial will use four different windows one to visualize the html text of the tutorial the present windows a second to run the code a third to visualize sections of the abinis_help file that will open automatically and a fourth one for the html input variables that will also open automatically Try to manage adequately these four windows 1 In addition to the present windows open the second windows Go to the Tutorial directory that we refer as ABINIT Tutorial cd ABINIT Tutorial In that directory you will find the necessary input files to run the examples related to this tutorial Take a few seconds to read the names of the files and directories already present in ABINIT Tutorial 2 You also need
211. ional potential and density Characteristic Variable type integer parameter Default is 0 If set gt 1 provide one dimensional projection of potential and density for each of the three axis This corresponds to averaging the potential or the density on bi dimensional slices of the FFT grid 4 4 Geometry builder symmetry related variables VAR GEO 4 4 1 brvltt Mnemonics BRaVais La T Tice type Characteristic SYMMETRIZER Variable type integer parameter Default is 0 Set the type of Bravais lattice needed only if spgroup 4 0 In this case the cell defined by acell and rprim or angdeg should be the CONVENTIONAL cell If brvltt 0 the code will assign brvltt from the space group information spgroup and produce the symmetry operations for the conventional unit cell If the conventional cell is not primitive the user should set chkprim 0 If brvltt 1 the code will assign brvltt from the space group information then reduce the unit cell to a primitive unit cell The echo of acell and rprim might thus differ from those derived directly from the input variables Also the input variable xred will refer to the CONVENTIONAL unit cell but its echo will refer to the preprocessed PRIMITIVE unit cell There is of course no problem with xangst and xcart as they are independent of the unit cell The echo of brvltt in the output file will be one of the following Bravais lattices e 1 Primitive with no associated translations e
212. ition planewave cut off energy SCF convergence parameters than in the t35 in file driving the Kohn Sham band structure calculation Then for the three datasets you will find specialized additional input variables 2 Generating the Kohn Sham band structure the KSS file In dataset 1 apart from the usual input variables we are acquainted to through the previous tutorials there is a new input variable nbandkss 1 Number of bands in KSS file 1 means the maximum possible This input variable tells the program to calculate the Kohn Sham electronic structure by the in this case full diagonalization of the Kohn Sham Hamiltonian evaluated at the converged density and calculated in each one of the k points of the grid Note that this diagonalization is performed in a routine outkss f separated from the usual SCF cycle so that there is additional control of the wavefunction actually stored if needed In particular the number of bands to be computed in this routine is NOT determined by the usual input variable nband 41 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION nbandkss is the key variable to create a _KSS file If it is zero no _KSS file will be created 1 lead to the generation and storage of the maximum possible number of states or bands common to all points This might lead to quite time consuming calculations One can reduce the load in the diagonalization by requirin
213. ive translation by 1 ngfft 3 and so forth until ir varies all the way from 1 to ngfft 1 ngfft 2 ngfft 3 This last point is in the corner diagonally opposite from the origin or right alongside the origin if the whole grid is viewed as being periodically repeated 3 5 6 The potential files Also unformatted files consisting of the header records and do ispden 1 nspden write unit potential ir ir 1 cplex ngfft 1 ngfft 2 ngfft 3 enddo where potential can be either the sum of the Hartree potential exchange correlation and local pseudopotential see prtopt the Hartree potential see prtuha the Hartree XC potential see prtvhxc or the XC potential see prtvrc These are defined on the real space grid in Hartree energy units The underlying grid is as described above If nspden 2 the different components are the spin up potential and the spin down potential The case nspden 4 is not yet implemented Note that the Hartree potential is NOT spin dependent but in order to use the same format as for the other potential files the spin independent array is written twice once for spin up and one for spin down 3 5 7 The wavefunction output file This is an unformatted data file containing the planewaves coefficients of all the wavefunctions and different supplementary data The ground state wf file consists of the header records and data written with the following lines of FORTRAN version 4 0 and more recent versions ba
214. kpt or kptrlatt as well as on nshiftk and shiftk to set up the k points Take into account only the time reversal symmetry k points will be generated in half the Brillouin zone This is to be used when preparing or executing a RF calculation at q 0 0 0 e 3 gt rely on ngkpt or kptrlatt as well as on nshiftk and shiftk to set up the k points Do not take into account any symmetry k points will be generated in the full Brillouin zone This is to be used when preparing or executing a RF calculation at non zero q e 4 gt has been replaced by negative values in version 2 3 e A negative value gt rely on kptbounds and ndivk to set up a band structure calculation along different lines allowed only for iscf 2 The absolute value of kptopt gives the number of segments of the band structure In the case of a grid of k points the auxiliary variables kptrlen ngkpt and prtkpt might help you to select the optimal grid 4 1 10 natom Mnemonics Number of ATOMs Characteristic Variable type integer parameter Default is 1 Gives the total number of atoms in the unit cell Default is 1 but you will obviously want to input this value explicitly Note that natom refers to all atoms in the unit cell not only to the irreducible set of atoms in the unit cell using symmetry operations this set allows to recover all atoms If you want to specify only the irreducible set of atoms use the symmetriser see the input variable natrd
215. l then the eigenenergy computation along different lines For that purpose the multi dataset mode has been implemented It allows the code to treat in one run different sets of data and to chain them The number of datasets to be treated is specified by the variable ndtset while the indices of the datasets by default 1 2 3 and so on can be eventually provided by the array jdtset For each dataset to be treated characterized by some index each input variable will determined by the following rules actually it is easier to understand when one looks at examples see below 1 ABINIT looks whether the variable name e g ecut appended with the index of the dataset e g jdtset 2 exists e g ecut2 It will take the data that follows this keyword if it exist 2 If this modified variable name does not exist it will look whether a metacharacter a series or a double loop data set has been defined see sections 3 4 or 3 5 3 If the variable name appended with the index of the dataset does not exist and if there is no series nor double loop dataset for this keyword it looks for an occurence of the variable name without any index appended and take the corresponding data This corresponds to the single dataset mode 4 If such occurences do not exist it takes the default value Also similar to the single dataset mode 1st example ndtset 2 acell 8 8 8 ecuti 10 ecut2 15 means that there are 2 datasets a fi
216. l be unstable If dtion is too small then the molecular dynamics will move inefficiently slowly A consensus exists in the community that forces larger than about 0 1 eV Angstrom are really too large to consider the relaxation to be converged It is best for the user to get experience with this in his her own application The option tonmov 2 3 or 7 are also available This uses the Broyden BFGS scheme for structural optimization and is much more efficient than viscous damping for structural relaxation 6 If you are running supercell calculations i e an isolated atom or molecule in a big box or a defect in a solid or a slab calculation you must check the convergence of your calculation with respect to the supercell and system size e For an isolated molecule in a big box increase concurrently the three dimensions of your supercell acell and check the convergence of your physical property e For a defect in a solid your supercell must bu a multiple of the primitive cell of the bulk solid so you have less freedom Still be sure that your supercell is large enough for your properties of interest to be accurate at the level you want it to be e For aslab calculation you must increase the vacuum in the cell but also the thickness of your slab systematically If you follow the tutorial you should go back to the tutorial window now 3 7 Final remarks The ABINIT package is developped by the ABINIT group The status of this packag
217. lations is tolwfr You should set it to 1 0 x 107 or so and suppress toldfe The input file ABINIT Tutorial t35 in is an example while ABINIT Tutorial Refs t35 out is a reference output file You should find the band structure starting at second dataset Eigenvalues eV for nkpt 40 k points kpt 1 nband 8 wtk 1 00000 kpt 0 5000 0 0000 0 0000 reduced coord 3 78987 1 16032 4 69394 4 69394 7 38389 9 23579 9 23579 13 45363 kpt 2 nband 8 wtk 1 00000 kpt 0 4500 0 0000 0 0000 reduced coord 24 CHAPTER 2 TUTORIAL 3 92925 0 95943 4 71018 4 71018 7 40286 9 25271 9 25271 13 48581 kpt 3 nband 8 wtk 1 00000 kpt 0 4000 0 0000 0 0000 reduced coord 4 25584 0 44579 4 76451 4 76451 7 46440 9 30899 9 30899 13 57381 kpt 4 nband 8 wtk 1 00000 kpt 0 3500 0 0000 0 0000 reduced coord 4 64158 0 24736 4 85456 4 85456 7 56450 9 38020 9 38020 13 64227 One needs a graphical tool to represent all these data For the MAPR 2451 lecture try with MATLAB Even without a graphical tool we will have a quick look at the values at L Gamma X and Gamma again kpt 1 nband 8 wtk 1 00000 kpt 0 5000 0 0000 0 0000 reduced coord 3 78987 1 16032 4 69394 4 69394 7 38389 9 23579 9 23579 13 45363 kpt 11 nband 8 wtk 1 00000 kpt 0 0000 0 0000 0 0000 reduced coord 6 17102 5 91515 5 91515 5 91515 8 44524 8 44524 8 44524 9 17125 kpt 23 nband 8 wtk 1 00000 kpt 0 0000 0 5000 0 5000 reduced c
218. le Brillouin zone and the associated tsmear 0 04 with less than 0 1 error on the lattice parameter NOTE that this error due to the Brillouin zone sampling could add to the error due to the choice of ecut that was mentioned previously to be on the order of 0 2 In what follows we will stick to these values of ecut and tsmear and try to use k point grids with a similar resolution Our final value for the aluminum lattice parameter in the LDA using the 13a1 981214 fhi pseudopotential is thus 7 5056 Bohr that is 3 9718 A The experimental value at 25 degree Celsius is 4 04958 The associated total energy and accuracy can be deduced from etotal11 2 0915880134E 00 etotal12 2 0931821220E 00 etotal13 2 0947762307E 00 etotal14 2 0963703493E 00 etotal21 2 0969479910E 00 etotal22 2 0975288692E 00 etotal23 2 0977992413E 00 etotal24 2 0979739819E 00 etotal31 2 0983273553E 00 etotal32 2 0982967240E 00 etotal33 2 0983057844E 00 etotal34 2 0983969839E 00 etotal24 is 2 0979739819E 00 Ha with an accuracy of 0 0005 Ha 2 4 4 Determination of the surface energy of aluminum 100 changing the orientation of the unit cell In order to study the Aluminum 100 surface we will have to set up a supercell representing a slab This supercell should be chosen as to be compatible with the primitive surface unit cell The corresponding directions are 1 1 0 and 1 1 0 The direction perpendicular to the surface is 0 0 1 Ther
219. lization of qpt Must be positive non zero The actual q vector renormal ized is qptn 1 3 qpt 1 3 qptnrm 4 5 47 ratsph Mnemonics Radius of the ATomic SPHere Characteristic Variable type real parameter Default is 2 0 Bohr Active only in the prtdos 3 case for the time being Provides the radius of the spheres around the natsph atoms of indices iatsph in which the local DOS and its angular momentum projections will be analysed Note that as presently implemented the SAME radius is used for all the atoms So one might have to perform different calculations to obtain the set of relevant DOS each corresponding to one atom type for each of which a different radius might be used NOTE The choice of this radius is quite arbitrary In a plane wave basis set there is no natural definition of an atomic sphere However it might be wise to use the following well defined and physically motivated procedure in version 4 2 this procedure is NOT implemented unfortunately from the Bader analysis one can define the radius of the sphere that contains the same charge as the Bader volume This Equivalent Bader charge atomic radius might then be used to perform the present analysis See the AIM Bader help file for more explanations Another physically motivated choice would be to rely on another charge partitioning like the Hirshfeld one see the cut3d utility The advantage of using charge partitioning schemes comes from the fact t
220. ll allow to divide the number of plane wave npw treated explicitly by a factor of two Still the final result should be identical with the full set of plane waves See the input variable ecutsm for the smoothing of the kinetic energy needed to optimize unit cell parameters 4 1 4 iscf Mnemonics Integer for Self Consistent Field cycles Characteristic Variable type integer parameter Default is 5 Control the self consistency Positive non zero values this is the usual choice for doing the usual ground state GS calculations or for structural relaxation where the potential has to be determined self consistently The choice between different algorithms for SCF is possible 80 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST e 1 gt get the largest eigenvalue of the SCF cycle DEVELOP option used with irdwfk 1 or irdwfq 1 e 2 gt SCF cycle simple mixing e 3 gt SCF cycle anderson mixing e 5 gt SCF cycle CG based on the minim of the energy e Other positive including zero values are not allowed The preferred option is 5 which is quite robust The value 3 can be faster but sometimes the SCF iterations will not converge with iscf 3 Other negative options e 2 a non self consistent calculation is to be done in this case an electron density rho r on a real space grid produced in a previous calculation will be read from a disk file automatically if ndtset 0 or accor
221. localrdwf 0 should be much more efficient if you really need temporary disk storage switch to localrdwf 1 In the case of a cluster of nodes with a different file system for each machine the input wavefunction file must be available on all nodes if localrdwf 1 while it is needed only for the master node if localrdwf 0 4 9 Projector Augmented Wave variables VARPAW 4 9 1 ngfftdg Mnemonics Number of Grid points for Fast Fourier Transform Double Grid Characteristic Variable type integer array ngfftdg 3 Default Needed only when usepaw 1 151 4 9 PROJECTOR AUGMENTED WAVE VARIABLES VARPAW To be documented 4 9 2 pawecutdg Mnemonics PAW Energy CUToff for the Double Grid Characteristic ENERGY Variable type real parameter Default 1 25 times ecut Needed only when usepaw 1 Define the energy cut off for the fine FFT grid that allow to transfer data from the normal coarse FFT grid to the spherical grid around each atom pawecutdg must be larger or equal to ecut If equal to it then no fine grid is used The results are not very accurate but the computations proceed quite fast The default value is sometimes a bit too low but does not slow down the computation The choice made for this variable DOES have a bearing on the numerical accuracy of the results and as such should be the object of a convergence study The convergence test might be made on the total energy or derived quantities like forces
222. m is precisely this translation in reduced coordinates like xred Thus one way to specify a Shubnikov IV magnetic space group is to define both spgroup and genafm Alternatively one might define spgroup and spgroupma or define by hand the set of symmetries using symrel tnons and symafm 4 4 3 natrd Mnemonics Number of AToms ReaD Characteristic GEOMETRY BUILDER SYMMETRISER Variable type integer parameter Default is natom Gives the number of atoms to be read from the input file in the case the geometry builder or the symmetriser is used In this case natrd is also used to dimension the array typat and the arrays xred xangst and xcart Must take into account the vacancies see vacnum and vaclst Despite possible vacancies cannot be bigger than natom 4 4 4 nobj Mnemonics Number of OBJects Characteristic GEOMETRY BUILDER NO INTERNAL Variable type integer parameter Default is 0 no use of the geometry builder Gives the number of objects to be used by the geometry builder in order to find the full set of atoms At present only one or two objects can be defined identified as objects a and b Related variables for object a are objan objaat objarf objatr objaro objaax Related variables for object b are objbn objbat objbrf objbtr objbro objbax More detailed explanation when the geometry builder is used i e when nobj 1 or nobj 2 the code will be given a primitive se
223. mpute the electric field perturbation along the three directions explicitely and ii to keep the full number of k points 4 10 5 prtbbb Mnemonics PRinT Band By Band decomposition Characteristic RESPFN Variable type integer parameter Default is 0 If prtbbb is 1 print the band by band decomposition of Born effective charges and localization tensor in case they are computed See Ph Ghosez and X Gonze J Phys Condens Matter 12 9179 2000 and M Veithen X Gonze and Ph Ghosez to be published 4 10 6 rfasr Mnemonics Response Function Acoustic Sum Rule Characteristic RESPFN Variable type integer parameter Default is 0 Control the evaluation of the acoustic sum rule in effective charge calculations within a response function calculation e 0 no acoustic sum rule imposed e 1 gt acoustic sum rule imposed with extra charge evenly distributed among atoms e 2 gt acoustic sum rule imposed with extra charge given proportionally to those atoms with the largest effective charge 4 10 7 rfatpol Mnemonics Response Function limits of ATomic POLarisations Characteristic RESPFN 154 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 10 8 rflatpol Mnemonics non linear Response Function 1st mixed perturbation limits of ATomic POLarisa tions Characteristic NON LINEAR 4 10 9 rf2atpol Mnemonics non linear Response Function 2nd mixed perturbation limits of ATomic POLarisa tions
224. n one has 4x4x4 x 2 x 2 256 The grids of k points should not be too anisotropic for this rough estimation to be valid Note also the input variables rprim and chkprim in this input file So you run t44 in only a few seconds the reference file is ABINIT Tutorial Refs t44 out and you find the following total energy etotal 4 1962972596E 00 It is not exactly twice the total energy for the primitive cell mentioned above but the difference is less than 0 0005 Ha It is due to the different FFT grids used in the two runs and affect the exchange correlation energy These grids are always homogeneous primitive 3D grids so that changing the orientation of the lattice will give mutually incompatible lattices Increasing the size of the FFT grid would improve the agreement 2 4 5 Determination of the surface energy a 3 aluminum layer 1 vacuum layer slab calculation We will first compute the total energy associated with only three layers of aluminum separated by only one layer of vacuum This is kind of a minimal slab e one surface layer e one bulk layer e one surface layer e one vacuum layer o It is convenient to take the vacuum region as having a multiple of the width of the aluminum layers but this is not mandatory The supercell to use is the double of the previous cell that had two layers of Aluminum atoms along the 0 0 1 direction Of course the relaxation of the surface might give an important co
225. n zero 110 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST if irdwfk and getwfk are both zero initialize wavefunctions with random numbers for ground state calculation if irdwfk 1 read ground state wavefunctions from a disk file appended with _WFK produced in a previous ground state calculation see the section 4 of abinis_help Response function calculation one and only one of irdwfk or getwfk MUST be non zero if irdwfk 1 read ground state k wavefunctions from a disk file appended with _WFK produced in a previous ground state calculation see the section 4 of abinis_help only one of irdwfq or getwfq can be non zero if both of them are non zero use as k q file the one defined by irdwfk and or getwfk if irdwfq 1 read ground state k q wavefunctions from a disk file appended with _WFQ produced in a previous ground state calculation see the section 4 of abinis_help at most one of irdlwf or getlwf can be non zero if both are zero initialize first order wavefunctions to 0 s if irdlwf 1 read first order wavefunctions from a disk file appended with _1WFx produced in a previous response function calculation see the section 4 of abinis_help at most one of irdddk or getddk can be non zero one of them must be non zero if an homogeneous electric field calculation is done presently a ddk calculation in the same dataset is not allowed if irdddk 1 read first order ddk wavefunctions fr
226. nce toldfe toldff tolvrs and tolwfr are aimed at the same goal causing the SCF cycle to stop one and only one of these must be specified To get accurate stresses may be quite demanding 4 1 29 tolwfr Mnemonics TOLerance on WaveFunction squared Residual Characteristic Variable type real parameter Default is 0 0d0 stopping criterion ignored Gives a convergence tolerance for the largest squared residual defined below for any given band The squared residual is lt nk H E nk gt E lt nk H nk gt 4 2 which clearly is nonnegative and goes to 0 as the iterations converge to an eigenstate With the squared residual expressed in Hartrees2 Hartrees squared the largest squared residual called residm encountered over all bands and k points must be less than tolwfr for iterations to halt due to successful convergence Note that if iscf gt 0 this criterion should be replaced by those based on toldfe preferred for ionmov 0 toldff preferred for ionmov 0 or tolvrs preferred for theoretical reasons When tolwfr is 0 0 this criterion is ignored and a finite value of toldfe toldff or tolvrs must be specified This also imposes a restriction on taking an ion step ion steps are not permitted unless the largest squared residual is less than tolwfr ensuring accurate forces To get accurate stresses may be quite demanding 92 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Note
227. nd of the ntime timesteps 4 11 19 mdwall Mnemonics Molecular Dynamics WALL location Characteristic Variable type real parameter Default is 10000 0 Bohr the walls are extremely far away Gives the location atomic units of walls on which the atoms will bounce back when ion mov 6 7 8 or 9 For each cartesian direction idir 1 2 or 3 there is a pair of walls with coordinates xcart idir wall and xcart idir rprimd idir idir wall Supposing the particle will cross the wall its velocity normal to the wall is reversed so that it bounces back By default given in bohr atomic units 1 bohr 0 5291772083 A although Angstrom can be specified if preferred since mdwall has the LENGTH characteristics 4 11 20 natcon Mnemonics Number of AToms in CONstraint equations Characteristic NO MULTI Variable type integer array of length nconeq Default is 0 Gives the number of atoms appearing in each of the nconeq independent equations constraining the motion of atoms during structural optimization or molecular dynamics see nconeq iatcon and wtatcon 4 11 21 natfix Mnemonics Number of Atoms that are FIXed 4 11 22 natfixx Mnemonics Number of Atoms that are FIXed along the X direction 4 11 23 natfixy Mnemonics Number of Atoms that are FIXed along the Y direction 4 11 24 natfixz Mnemonics Number of Atoms that are FIXed along the Z direction Characteristic NOT INTERNAL 165 4 11 STRUCTURE OPTIMIZATION
228. nd the description of the cell provided by acell rprim and or angdeg 4 7 5 nelect Mnemonics Number of ELECTrons Characteristic INTERNAL Variable type real number This internal variable gives the number of electrons per unit cell as computed from the sum of the valence electrons related to each atom given by the pseudopotential that is called zval and the input variable charge nelect zval charge 4 7 6 nfft Mnemonics Number of FFT points Characteristic INTERNAL Variable type integer If the space parallelisation is not used this internal variable gives the number of Fast Fourier Transform points in the grid generated by nefft 1 3 It is simply the product of the three components of ngfft If the space parallelisation is used then it becomes the number of Fast Fourier Transform points attributed to this particular processor It is no more the above mentioned simple product but a number usually close to this product divided by the number of processors on which the space is shared 4 7 7 qptn Mnemonics Q PoinT re Normalized Characteristic INTERNAL 150 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Variable type real array qptn 3 Used if nqpt 1 This internal variable is derived from qpt and qptnrm qptn 1 3 qpt 1 3 qptnrm 4 7 8 usepaw Mnemonics USE Projector Augmented Waves method Characteristic INTERNAL Variable type integer parameter Value is set by the pseudopote
229. ne of the wavefunctions is even as low as one half This should lead us to question the choice of ecutwfn that we have made we will need a convergence study see later The parameters of the FFT grid needed to represent the wavefunction and compute their convolution so as to get the screening matrices are then given Then the grid of g point in the irreducible part of the Brillouin Zone on which the sus ceptibility and dielectric matrices will be computed is given It is a grid of points with the same repetition parameters kptrlatt or ngkpt than the GS one but WITHOUT any shift On the basis of only the average density one can obtain the plasmon frequency of metallic Jellium homogeneous electron gas placed in a neutralizing background The next lines start from the average density of the system and evaluate the r parameter of the Jellium then compute the plasmon frequency THIS IS A ROUGH ESTIMATE In particular it will be questionable for strongly inhomogeneous systems Also the choice of pseudopotential inclusion of core states will have an effect on this estimate So take it cautiously It is better to try a few values of plasfrq than to rely blindly on this value At the end of the screening calculation the macroscopic dielectric constant is printed 44 CHAPTER 2 TUTORIAL dielectric constant 13 8476 dielectric constant without local fields 15 5520 Note that the convergence in the dielectric constant DO
230. nent of objaro does not vanish objaat and objbat MUST be provided if nobj 2 and one component of objbro does not vanish Not present in the dtset array no internal 4 4 7 objan objbn Mnemonics OBJect A Number of atoms OBJect B Number of atoms Characteristic GEOMETRY BUILDER NO INTERNAL Variable type integer parameters Gives the number of atoms in either object a or object b The list of atoms is given by the variables objaat and objbat objan MUST be provided if nobj 1 objan and objbn MUST be provided if nobj 2 Not present in the dtset array no internal 120 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 4 8 objarf objbrf Mnemonics OBJect A Repetition Factors OBJect B Repetition Factors Characteristic GEOMETRY BUILDER NO INTERNAL Variable type integer arrays objarf 3 and objbrf 3 Default is 1 1 1 Gives three repetition factors of the objects a or b This gives the opportunity to generate a three dimensional set of repeated objects although a simple one dimensional repetition will be easily obtained through the specification of nrep 1 1 where nrep is the 1D repetition factor The initial rotation and translation of the object as well as the increment of rotation or translation from one object to the next are specified by the variables objaro and objatr for object a and objbro and objbtr for object b Note that the geometry builder will generate the full set of atoms from t
231. netism or the spontaneous spatial spin separation of elongated H2 molecule If the geometry builder is used spinat will be related to the preprocessed set of atoms generated by the geometry builder The user must thus foresee the effect of this geometry builder see objarf If the geometry builder is not used and the symmetries are not specified by the user nsym 0 spinat will be used if present to determine the anti ferromagnetic characteristics of the symmetry operations see symafm If the symmetries are specified and the irreducible set of atoms is specified the anti ferromagnetic characteristics of the symmetry operations symafm will be used to generate spinat for all the non irreducible atoms 4 5 49 stmbias Mnemonics Scanning Tunneling Microscopy BIAS voltage Characteristic ENERGY Variable type real parameter Default is 0 00 Gives in Hartree the bias of the STM tip with respect to the sample in order to generate the STM density map Used with positive iscf occopt 7 metallic gaussian nstep 1 and positive prtstm this value is used to generate a charge density map from electrons close to the Fermi energy in a positive or negative energy range Positive stmbias will lead to the inclusion of occupied valence states only while negative stmbias will lead to the inclusion of unoccupied conduction states only Can be specified in Ha the default Ry eV or Kelvin since stmbias has the ENERGY characteris
232. ngkpt and shiftk are used to generate the list of k points kpt and their weights wtk You should read the information about kpt and wtk From the output file here is the evolution of total energy per unit cell etotal1l 8 8662238960E 00 etotal2 8 8724909739E 00 etotal3 8 8726017429E 00 etotal4 8 8726056405E 00 The difference between dataset 3 and dataset 4 is rather small Even the dataset 2 gives an accuracy of about 0 0001 Ha So our converged value for the total energy at fixed acell fixed ecut is 8 872 Ha 2 3 4 Determination of the lattice parameters The input variable optcell governs the automatic optimization of cell shape and volume For the automatic optimization of cell volume use opcell 1 ionmov 3 ntime 10 dilatmx 1 05 ecutsm 0 5 You should read the indications about dilatmz and ecutsm Do not test all the k point grids only those with nkpt 2 and 10 The input file ABINIT Tutorial t34 in is an example while ABINIT Tutorial Refs t34 out is a reference output file This run might last a few minutes You should obtain the following evolution of the lattice parameters acell1 1 0230001904E 01 1 0230001904E 01 1 0230001904E 01 Bohr acell2 1 0216682464E 01 1 0216682464E 01 1 0216682464E 01 Bohr with the following very small residual stresses strtenl 2 5365388633E 08 2 5365388633E 08 2 5365388633E 08 0 Q0000000000E 00 0 0000000000E 00 0 0000000000E 00 strten2 5 3567080431E 08
233. ngy ngz to 30 you will be able to use the file dim m present in ABINIT Tutorial to visualize the 3 Dimensional isosurfaces Another option might be to use the XCrysDen software for which you need to use option 9 2 1 5 Computation of the atomization energy 1 The atomization energy is the energy needed to separate a molecule in its constituent atoms each being neutral In the present case one must compute first the total energy of an isolated hydrogen atom The atomization energy will be the difference between the total energy of H gt and twice the total energy of H There are some subtleties in the calculation of an isolated atom e in many cases the ground state of an isolated atom is spin polarized see the variables nsppol and spinat e the highest occupied level might be degenerate with the lowest unoccupied level of the same spin in which case techniques usually appropriate for metals are to be used see lesson 4 13 2 1 LESSON 1 THE H2 MOLECULE WITHOUT CONVERGENCE STUDIES e also often the symmetry of the ground state charge density will NOT be spherical so that the automatic determination of symmetries by the code based on the atomic coordinates should be disabled see the input variable nsym to be set to 1 in this case For Hydrogen we are lucky that the ground state is spherical 1s orbital and that the highest occupied level and lowest unoccupied level although degenerate have a dif
234. nkpt e nstep e toldfe e diemac o diemiz Have also a look at kpt and iscf It is now time to have a look at the two output files of the run First edit the log file You can begin to read it It is nasty Jump to its end You will find there the number of WARNINGS and COMMENTS that were issued by the code during execution You might try to find them in the file localize the keywords WARNING or COMMENT in this file Some of them are for the experienced user For the present time we will ignore them You can find more information about messages in the log file in the section 6 1 of the abinis_help file Then edit the t11 out file You find some general information about the output file in section 6 2 of the abinis_help file You should also e examine the header of t11 out e examine the report on memory needs do not read each value of parameters e examine the echo of preprocessed input data until you reach the message chkinp Checking input parameters for consistency If the code does not stop there the input parameters are consistent At this stage many default values have been provided and the preprocessing is finished It is worth to come back to the echo of preprocessed input data You should first examine the t11 in file in more details and read the meaning of each of its variables in the corresponding input variables file if it has not yet been done Then you should
235. nmov 1 or 2 The value of x after TIM is described hereafter See also the keyword prtdos This file is formatted 64 CHAPTER 3 ABINIS HELP abo GEO Filename of file containing the geometrical analysis bond lengths and bond angles in the case ionmov 0 See the keyword prtgeo This file is formatted abo TIMx_GEO Filenames of files containing the geometrical analysis bond lengths and bond angles in the case ionmov 1 or 2 The value of x after TIM is described hereafter See also the keyword prtgeo This file is formatted abo_CML xml filename of file containing the Chemical Markup Language description of the system crys tallographic data symmetry data atomic symbols and reduced coordinates in the case ionmov 0 See the keyword prtcml This file is formatted abo_TIMx_GEO Filenames of files containing the Chemical Markup Language description of the system crys tallographic data symmetry data atomic symbols and reduced coordinates in the case ion mov 1 or 2 The value of x after TIM is described hereafter See also the keyword prtcml This file is formatted abo STO Filename of file containing output wavefunction coefficients if nbandkss 0 This wave function file is unformatted and can be very large Its purpose is to start a GW calcula tion using M Torrent s code A different format than for abo_WFK is used see the file ABINIT Infos format_STO When onmov 0 the POT
236. nspinor nband lt for each k point write unit kg 1 3 1 npw lt plane wave reduced coordinates do iband 1 nband write unit eigen jband iband 1 nband bantot jband 1 2 nband lt column of eigenvalue matrix write unit cg ii 1i 1 2 npw nspinor lt wavefunction coefficients enddo for a single band and k point bantot bantot nband enddo enddo In version previous to 4 0 npw and nspinor were combined write unit npw nspinor nband while the planewave coordinate record was not present in both GS and RF cases Note that there is an alternative format _KSS for the output of the wavefunction coefficients activated by a non zero value of nbandkss 3 5 8 Other output files There are many other output files optionally written all formatted files at present Their use is usually governed by a specific input variable Please consult the description of this input variable in order to have more information on such files e prtcml to print a CML file with geometry information e prtdos to print a file with the electronic Density Of States e prtgeo to print a file with a geometrical analysis bond lengths and bond angles that also contains an XMOL section e prtidm to print a one dimensional projection of potential and density for the three axes If you follow the tutorial you should go back to the tutorial window now 3 6 Numerical quality of the calculations The following section describes various parameter
237. nteger parameter Default is 1 Gives the maximum number of SCF cycles or iterations Full convergence from random numbers if usually achieved in 12 20 SCF iterations Each can take from minutes to hours In certain difficult cases usually related to a small or zero bandgap convergence performance may be much worse When the convergence tolerance tolwfr on the wavefunctions is satisfied iterations will stop so for well converged calculations you should set nstep to a value larger than you think will be needed for full convergence e g if 20 steps usually converges the system set nstep to 30 86 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST NOTE that a choice of nstep 0 is permitted this will either read wavefunctions from disk with irdwfk 1 or irdwfq 1 or non zero getwfk or getwfq in the case of multi dataset and compute the density the total energy and stop or else with all of the above vanishing will initialize randomly the wavefunctions and compute the resulting density and total energy This is provided for testing purposes One can output the density by using prtden Unlike the forces the stress tensor also gets computed with nstep 0 4 1 18 nsym Mnemonics Number of SYMmetry operations Characteristic SYMMETRY FINDER Variable type integer parameter Default is 0 Gives number of space group symmetries to be applied in this problem Symmetries will be input in array symrel and nonsymmorph
238. ntial files either PAW or norm conserving If the user wants to use the Projector Augmented Method then usepaw must be 1 This variable is determined by the pseudopotentials files Indeed special PAW pseudo projector files must be used these are the equivalent of the pseudopotential files for the pseudopotential method Such files are NOT yet available for the entire periodic table Also forces and stresses are not yet computed in the PAW method as implemented in ABINIT v4 1 Other limitations are present as well precluding the use of PAW for real production work These limitations will be waived as time passes Related variables pawecutdg pawlcutd pawmqgrdg pawnphi pawntheta 4 8 Parallelisation variables VARPAR 4 8 1 localrdwf Mnemonics LOCAL ReaD WaveFunctions Characteristic DEVELOP PARALLEL Variable type integer Default is 1 This input variable is used only in abinip If localrdwf 1 the input wavefunction disk file is read locally by each processor while if localrdwf 0 only one processor reads it and BCAST it to other processors The option localrdwf 0 is NOT allowed when mkmem 0 or for RF when mkqmem 0 or mklmem 0 that is when the wavefunctions are stored on disk This is still to be coded In the case of a parallel computer with a unique file system both options are as convenient for the user However if the I O are slow compared to communications between processors e g for CRAY T3E machines
239. ntot 0 lt counts over all bands do isppol 1 nsppol do ikpt 1 nkpt write unit npw nspinor nband lt for each k point write unit kg 1 3 1 npw lt plane wave reduced coordinates write unit eigen 1 bantot nband bantot lt eigenvalues for this k point occ 1 bantot nbandtbantot lt occupation numbers for this k point do iband 1 nband write unit cg iit ii 1 2 npw nspinor lt wavefunction coefficients enddo for a single band and k point bantot bantot nband enddo enddo If the job ended without problem and if one is not using newsp a few supplementary lines are added in order to give the history of atomic positions and corresponding forces The integer nxfh gives the number of pairs x f of positions and forces in reduced coordinates write unit nxfh do ixfh 1 nxfh write unit xred 1 3 1 natom ixfh dummy 1 3 1 4 amp 73 3 6 NUMERICAL QUALITY OF THE CALCULATIONS amp fred 1 3 1 natom ixfh dummy 1 3 1 4 enddo The dummy variables might contain in the future the description of the unit cell and the stresses The type of the different variables is integer kg nband npw nspinor nxfh double precision cg dummy eigen fred occ xred The response function wf file consists of the header records and data written with the following lines of FORTRAN version 4 0 and more recent versions bantot 0 lt counts over all bands do isppol 1 nsppol do ikpt 1 nkpt write unit npw
240. ntribution to the total energy You should start from t44 in You have to modify rprim double the cell along 0 0 1 the atomic positions as well as the k point mesh For the latter it is supposed that the electrons cannot propagate from one slab to its image in the 0 0 1 direction so that the k component of the special k points can be taken 0 only one layer of k points is needed along the z direction You should also allow the relaxation of atomic positions but not the relaxation of lattice parameters the lattice parameters along x or y must be considered fixed to the bulk value while for the z direction there is no interest to allow the vacuum region to collapse The input file ABINIT Tutorial t45 in is an example while ABINIT Tutorial Refs t45 out is a reference output file The run might last one minute The total energy after the first SCF cycle when the atomic positions are equal to their starting values is ETOT 7 6 2619731934699 Note that the total energy of three aluminum atoms in the bulk from section 4 3 etotal24 is 6 293922 Ha So that the non elaxed surface energy per surface unit cell there are two surfaces in our simulation cell is 29 2 4 LESSON 4 ALUMINUM THE BULK AND THE SURFACE 0 015975 Ha 0 435 eV The total energy after the Broyden relaxation is etotal 6 2622233982E 00 so that the relaxed surface energy per surface unit cell is 0 015849 Ha 0 431 eV It seem
241. o 105 4 3 FILES HANDLING VARIABLES VARFIL 4 2 37 wfoptalg Mnemonics WaveFunction OPTimisation ALGorithm Characteristic DEVELOP Variable type integer parameter Default is 0 Allows to choose the algorithm for the optimisation of the wavefunctions The different possi bilities are e wfoptalg 0 standard state by state conjugate gradient algorithm with no possibility to parallelize over the states wfoptalg 1 blocked conjugate gradient algorithm with possibility to parallelize over the states or bands but at the expense of a few more operations when a block of states has been optimized separately to obtain a coherent set of wavefunctions The number of states in a block is defined in nbdblock wfoptalg 2 minimisation of the residual with respect to different shifts in order to cover the whole set of occupied bands with possibility to parallelize over blocks of states or bands The number of states in a block is defined in nbdblock THIS IS STILL IN DEVELOP MENT wfoptalg 3 minimisation of the residual with respect to a shift Available only in the non self consistent case iscf 2 in order to find eigenvalues and wavefunctions close to a prescribed value 4 3 Files handling variables VARFIL 4 3 1 cmlfile Mnemonics Chemical Markup Language FILE Characteristic NO INTERNAL Variable type character string Default is no file Used to import some of the data from one or more Chemical Markup Lang
242. o get accurate stresses may be quite demand ing 91 4 1 BASIC VARIABLES VARBAS 4 1 27 toldff Mnemonics TOLerance on the DiFference of Forces Characteristic Variable type real parameter Default is 0 0 stopping condition ignored Sets a tolerance for differences of forces in hartree bohr that reached TWICE successively will cause one SCF cycle to stop and ions to be moved If set to zero this stopping condition is ignored Effective only when SCF cycles are done iscf gt 0 In this case since toldfe toldff tolvrs and tolwfr are aimed at the same goal causing the SCF cycle to stop one and only one of these must be specified This tolerance applies to any particular cartesian component of any atom INCLUDING fixed ones This is to be used when trying to equilibrate a structure to its lowest energy configuration ionmov 2 or in case of molecular dynamics ionmov 1 A value ten times smaller than tolmxf is suggested for example 5 0 x 107 Hartree Bohr This stopping criterion is not allowed for RF calculations 4 1 28 tolvrs Mnemonics TOLerance on the potential V r ReSidual Characteristic Variable type real parameter Default is 0 0 stopping condition ignored Sets a tolerance for potential residual that when reached will cause one SCF cycle to stop and ions to be moved If set to zero this stopping condition is ignored Effective only when SCF cycles are done iscf gt 0 In this case si
243. oint lattice to the Fourier transform of the periodic quantity Erroneous contributions will appear only for the vectors in real space that belong to the reciprocal of the k point lattice except the origin Moreover the expected size of these contributions usually decreases exponentially with the distance So the length of the smallest of these real space vectors is a measure of the accuracy of the k point grid When either ngkpt or kptrlatt is defined kptrlen is not used as an input variable but the length of the smallest vector will be placed in this variable and echoed in the output file On the other hand when neither ngkpt nor kptrlatt are defined ABINIT will automatically generate a large set of possible k point grids and select among this set the grids that give a 133 4 5 GROUND STATE CALCULATION VARIABLES VARGS length of smallest vector LARGER than kptrlen and among these grids the one that when used with kptopt 1 reduces to the smallest number of k points Note that this procedure can be time consuming It is worth to do it once for a given unit cell and set of symmetries but not use this procedure by default The best is then to set prtkpt 1 in order to get a detailed analysis of the set of grids If some layer of vacuum is detected in the unit cell see the input variable vacuum the computation of kptrlen will ignore the dimension related to the direction perpendicular to the vacuum layer and generate a bi
244. om a disk file appended with 1WFx produced in a previous response function calculation see the section 4 of abinis_help 4 3 18 kssform Mnemonics Kohn Sham Structure file FORMat Characteristic Variable type integer parameter Default is 1 i e the KSS format Governs the choice of the format for the file that contains the Kohn Sham electronic structure information for use in GW calculations see the input variables optdriver and nbandkss obsolete kssform 0 the STA file is generated together with a VKB file containing infor mation on the pseudopotential kssform 1 a single file kss double precision containing complete information on the Kohn Sham Structure eigenstates and the pseudopotentials used will be generated through full diagonalization of the complete Hamiltonian matrix The file has at the beginning the standard abinit header obsolete kssform 2 the same as 1 but most of the relevant informations are in single precision kssform 3 a single file kss double precision containing complete information on the Kohn Sham Structure eigenstates and the pseudopotentials used will be generated through the usual conjugate gradient algorithm so a restricted number of states The file has at the beginning the standard abinit header Very important for the time being istwfk must be 1 for all the k points 111 4 3 FILES HANDLING VARIABLES VARFIL 4 3 19 mffmem Mnemonics Maximum number of FFt grids
245. on has been slightly modified by including a zeta rescaled by 1 d0 1 d 6 This should affect total energy at the level of 1 d 6Ha and should have an even smaller effect on differences of energies or derivatives The value izc 10 is used internally gives the difference between izc 7 and izc 9 for use with an accurate RPA correlation energy 4 1 6 jdtset Mnemonics index J for DaTaSETs Characteristic NO MULTI Variable type integer array jdtset ndtset Default the series 1 2 3 ndtset Gives the dataset index of each of the datasets This index will be used e to determine which input variables are specific to each dataset since the variable names for this dataset will be made from the bare variable name concatenated with this index and only if such a composite variable name does not exist the code will consider the bare variable name or even the Default 82 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST e to characterize output variable names if their content differs from dataset to dataset e to characterize output files root names appended with DSx where x is the dataset index The allowed index values are between 1 and 99 An input variable name appended with 0 is not allowed When ndtset 0 this array is not used and moreover no input variable name appended with a digit is allowed This array might be initialized thanks to the use of the input variable udtset In this case jdtse
246. on path If the denominator becomes smaller than zcut a small imaginary part depending on zcut is added in order to avoid the divergence Ideally one should make a convergence study of zcut decreasing for increasing number of k points 4 7 Internal variables VARINT 4 7 1 kptns Mnemonics K PoinTs re Normalized and Shifted Characteristic INTERNAL Variable type real array kptns 3 nkpt If nqpt 0 or if one is doing a reponse calculation this internal variable is derived from kpt and kptnrm kptns 1 3 kpt 1 3 kptnrm so that it is kpt renormalized by kptnrm If nqpt 1 and one is not doing a ground state calculation this internal variable is derived from kpt kptnrm and qptn kptns 1 3 kpt 1 3 kptnrm qptn 1 3 so that it is kpt renormalized by kptnrm then shifted by qptn 1 3 149 4 7 INTERNAL VARIABLES VARINT 4 7 2 mband Mnemonics Maximum number of BANDs Characteristic INTERNAL Variable type integer This internal variable deduces from nband 1 nkpt nsppol the maximum number of bands over all k points and spin polarisation 4 7 3 mefft Mnemonics Maximum of nGFFT Characteristic INTERNAL Variable type integer This internal variable gives the maximum of ngfft 1 3 4 7 4 mpw Mnemonics Maximum number of Plane Waves Characteristic INTERNAL Variable type integer This internal variable gives the maximum of the number of plane waves over all k points It is computed from ecut a
247. on state but the correlation correction is much larger than for state 4 On the whole the difference between Kohn Sham and GW energies is not very large but nevertheless it is quite important when compared with the size of the gap 2 6 2 Preparing convergence studies Kohn Sham structure KSS file and screening EM1 file In the following sections we will perform different convergence analyses because this is such an important task In order to keep the CPU time at a reasonable level we will use fake KSS and screening data by limiting ourselves to the Gamma point only In that way we will verify convergence aspects that could be very cumbersome at least in the framework of a tutorial if more k points were used In directory ABINIT Tutorial Work6 copy the file t62 in and modify the t6x files file as usual Edit the t62 in file and take the time to examine it Note that the SCF cycles have been disconnected from the generation of the KSS file Then issue abinis lt t6x files gt amp t62 log This small job lasts about 10 secs on a PC PIV Intel 2 2 GHz After that step you will need the KSS and EM1 files produced in this run for the next runs up to 6 8 Move t6xo_DS2_KSS to t6xo_DS1_KSS and t6xo_DS3_EM1 to t6xo_DS1_EM1 The next 6 sections are intended to show you how to find the converged parameters for a GW calculation 2 6 3 Convergence on the number of planewaves in the wavefunctions to calculate the S
248. onse function calculations or non linear computation including the electric field perturbation Actually such calculations requires first the non self consistent calculation of derivatives with respect to k independently of the electric field perturbation itself e 0 no electric field perturbation e 1 gt full calculation with first the derivative of ground state wavefunction with respect to k d dk calculation by a non self consistent calculation then the generation of the e first order response to an homogeneous electric field e 2 only the derivative of ground state wavefunctions with respect to k 156 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST e 3 gt only the generation of the first order response to the electric field assuming that the data on derivative of ground state wavefunction with respect to k is available on disk Note because the tolerances to be used for derivatives or homogeneous electric field are different one often does the calculation of derivatives in a separate dataset followed by calculation of electric field response as well as phonon The options 2 and 3 proves useful in that context also in case a scissor shift is to be used it is usually not applied for the d dk response 4 10 19 rfmeth Mnemonics Response Function METHod Characteristic RESPFN Variable type integer parameter Default is 1 Selects method used in response function calculations Presently only 1
249. oord 1 96598 1 96598 3 00347 3 00347 6 50928 6 50928 15 94976 16 44101 kpt 40 nband 8 wtk 1 00000 kpt 1 0000 1 0000 1 0000 reduced coord 6 17102 5 91515 5 91515 5 91515 8 44524 8 44524 8 44524 9 17125 The last gamma is exactly equivalent to the first gamma It can be checked that the top of the valence band is obtained at Gamma 15 56202 eV The width of the valence band is 12 09 eV the lowest unoccupied state at X is 0 594 eV higher than the top of the valence band at Gamma The Si is described as an indirect band gap material this is correct with a band gap of about 0 594 eV this is quantitatively quite wrong the experimental value 1 17 eV is at 25 degree Celsius The minimum of the conduction band is even slightly displaced with respect to X see kpt 21 This underestimation of the band gap is well known the famous DFT band gap problem In order to obtain correct band gaps you need to go beyond the Kohn Sham Density Functional Theory use the GW approximation This is described in the sixth lesson of the tutorial For experimental data and band structure representation see M L Cohen and J R Che likowski Electronic structure and optical properties of semiconductors Springer Verlag New York 1988 There is a subtlety that is worth to comment about In non self consistent calculations like those performed in the present band structure calculation with iscf 2 not all bands are converged within the tolerance tolw
250. or dtion is about 100 The user must try several values for dtion in order to establish the stable and efficient choice for the accompanying amu atom types and positions and vis viscosity 160 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST For quenched dynamics ionmov 7 a larger time step might be taken for example 200 No meaning for RF calculations 4 11 5 ecutsm Mnemonics Energy CUToff SMearing Characteristic ENERGY Variable type real parameter in Hartree Default is 0 d0 This input variable is important when performing relaxation of unit cell size and shape non zero optcell Using a non zero ecutsm the total energy curves as a function of ecut or acell can be smoothed keeping consistency with the stress and automatically including the Pulay stress The recommended value is 0 5 Ha Actually when optcell 4 0 ABINIT requires ecutsm to be larger than zero If you want to optimize cell shape and size without smoothing the total energy curve a dangerous thing to do use a very smalle ecutsm on the order of one microHartree Technical information See Bernasconi et al J Phys Chem Solids 56 501 1995 for a related method ecutsm allows to define an effective kinetic energy for plane waves close to but lower than the maximal kinetic energy ecut For kinetic energies less than ecut ecutsm nothing is modified while between ecut ecutsm and ecut the kinetic energy is multiplied by 1 0 2 3 2x
251. or lesson 1 2 or 3 Why not Work4 The file ABINIT Tutorial t4x files lists the file names and root names You can copy it in the Work4 directory and change it as usual You can also copy the file ABINIT Tutorial t41 in in Work4 This is your input file You should edit it read it carefully and have a look at the following new input variables and their explanation e occopt e tsmear Note also the following 1 You will work at fixed ecut 6Ha It is implicit that in real life you should do a convergence test with respect to ecut Here a suitable ecut is given to you It will allow to obtain 0 2 relative accuracy on lattice parameters Note that this is the softer pseudopotential of those that we have used until now the 01h pspgth for H needed 30 Ha it was rather hard the 14si pspnc for Si needed 8 Ha 2 The input variable diemac has been suppressed Aluminum is a metal and the default is taylored for that case When you have read the input file you can run the code as usual it will take a few seconds Then read the output file quietly You should note that the Fermi energy and occupation numbers have been computed automatically Fermi energy hartree 0 26800 Eigenvalues hartree for nkpt 2 k points kpt 1 nband 3 wtk 0 75000 kpt 0 2500 0 5000 0 0000 reduced coord 0 09391 0 25391 0 41846 occupation numbers for kpt 1 2 00003 1 33306 0 00014 kpt 2 nband 3 wtk 0 25000 kp
252. ote that the use of getxcart and getxred differs when acell and rprim are different from one dataset to the other If 0 no use of previously computed values must occur If it is positive its value gives the index of the dataset from which the data are to be used as input data It must be the index of a dataset already computed in the SAME run If equal to 1 the output data of the previous dataset must be taken which is a frequently occuring case However if the first dataset is treated 1 is equivalent to 0 since no dataset has yet been computed in the same run If another negative number it indicates the number of datasets to go backward to find the needed data once again going back beyond the first dataset is equivalent to using a null get variable Note getxred and getxcart cannot be simultaneously non zero for the same dataset On the other hand the use of getvel with getxred is allowed despite the different coordinate system 4 11 11 iatcon Mnemonics Indices of AToms in CONstraint equations Characteristic NO MULTI NOT INTERNAL Variable type integer array iatcon natcon nconeq 162 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Default is 0 Gives the indices of the atoms appearing in each of the nconeq independent equations con straining the motion of atoms during structural optimization or molecular dynamics see nconeq natcon and wtatcon Note combined with wtatcon to give internal
253. ould be tested against larger values of ngfft When boxcut is larger than 2 ngfft could be reduced without 136 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST loss of accuracy In this case the small variations that are observed are solely due to the xc quadrature that may be handled with intxc 1 to even reduce this effect Internally ngfft is an array of size 18 The present components are stored in ngfft 1 3 while e ngfft 4 6 contains slightly different larger values modified for efficiency of the FFT e ngfft 7 is f talg e ngfft 8 is fftcache e ngfft 9 is set to 0 if the parallelization of the FFT is not activated while it is set to 1 if it is activated ngfft 10 is the number of processors of the FFT group ngfft 11 is the index of the processor in the group of processors ngfft 12 is n2proc the number of x z planes in reciprocal space treated by the processor ngfft 13 is n3proc the number of x y planes in real space treated by the processor ngfft 14 is mpi comm fft the handle on the MPI communicator in charge of the FFT parallelisation e ngfft 15 18 are not yet used The number of points stored by this processor in real space is n1 n2 n3proc while in reciprocal space it is nl n2proc n3 4 5 33 nline Mnemonics Number of LINE minimisations Characteristic Variable type integer parameter Default is 4 Gives maximum number of line minimizations allowed in preconditioned conju
254. pdat pspcod pspxc enddo final record residm coordinates total energy Fermi energy write unit unit residm xred 1 3 1 natom etotal fermie where the type of the different variables is character 6 codvsn integer headform fform integer bantot date intxc ixc natom ngfft 3 nkpt nspden nspinor nsppol nsym ntypat occopt pertcase double precision acell 3 ecut ecutsm ecut_eff qptn 3 rprimd 3 3 amp amp tphysel tsmear integer istwfk nkpt nband nkpt nsppol npwarr nkpt so_typat ntypat amp amp stmbias amp symafm nsym symrel 3 3 nsym typat natom double precision kpt 3 nkpt occ bantot tnons 3 nsym znucltypat ntypat character 132 title double precision znuclpsp zionpsp integer pspso pspdat pspcod pspxc lmax lloc mmax integers double precision residm xred 3 natom etotal fermie NOTE etotal is set to its true value only for density and potential files For other files it is set to 1 0d20 NOTE ecut_eff ecut dilatmx2 NOTE In pre v4 1 fermie is set to zero for non metallic occupation numbers or for non self consistent calculations In v4 1 and later for all cases where occupation numbers are defined that is positive iscf and iscf 3 and for non metallic occupation numbers the Fermi energy is set to the highest occupied eigenenergy 70 CHAPTER 3 ABINIS HELP The header might differ for different versions of ABINIT The pre v4 2 formats
255. ponse function salculations The wavefunction file is unformatted and can be very large Warning in the multi dataset mode if getwfk is non zero a wavefunction file build from abo will be read e abi_1WFxx filename of file containing input first order wavefunctions created from an earlier RF run xx is the index of the perturbation 63 3 3 THE FILES FILE abi DEN filename of file containing density created from an earlier run See explanations related to negative values of iscf This file is also unformatted Warning in the multi dataset mode if getwfk is non zero a density file build from abo will be read abi_HES filename of file containing an approximate hessian for eventual re initialisation of Broyden minimisation See brdmin f routine The use of restartxf is preferred abo Except ab_out and log the other files WRITTEN by the code will have a name that is constructed from the root abo This apply to optionally written wavefunction density potential or density of states files In the multi dataset mode this root will be complemented by DS and the dataset index Also in the multi dataset mode the root abo can be used to build the name of input files thanks to the get variables The list of possible input files with their name created from the root abo is the following a similar list exists when DS and the dataset index are appended to abo abo_WFK Filenam
256. present in the calculation are taken into account occupied and unoccupied In this case the k points must have been defined using the input variable ngkpt or the input variable kptrlatt There must be at least two non equivalent points in the Irreducible Brillouin Zone to use prtdos 2 There is no need to take care of the occopt or tsmear input variables and there is no subtlety to be taken into account for insulators The computation can be done in the self consistent case as well as in the non self consistent case using iscf 3 This allows to refine the DOS at fixed starting density In that case if ionmov 0 the name of the potential file will be the root output name followed by _DOS like in the prtdos 1 case 113 4 3 FILES HANDLING VARIABLES VARFIL However if ionmov 1 or 2 potential files will be output at each time step with the name being made of e the root output name e followed by TIMx where x is related to the timestep see later e then followed by DOS If prtdos 3 the same tetrahedron method as for prtdos 2 is used but the DOS inside a sphere centered on some atom is delivered as well as the angular momentum projected 1 0 1 2 3 4 DOS in the same sphere The preparation of this case the parameters under which the computation is to be done and the file denomination is similar to the prtdos 2 case However three additional input variables might be provided describing the atoms that are the center of
257. prior to v4 3 is used for the preparation of a GW calculation it will be used in a GS run where optdriver 0 to generate a KSS file In this run nbandkss should be non zero Then this GS run should be followed with a run where optdriver 3 e If nbandkss 0 no KSS file is created e If nbandkss 1 all the available eigenstates energies and eigenfunctions are stored in a abo_KSS file at the end of the ground state calculation The number of states is forced to be e the same for all k points it will be the minimum of the number of plane waves over all k points e If nbandkss is greater than 0 abinit stores about nbandkss eigenstates in a abo_KSS file This number of states is forced to be the same for all k points See npwkss for the selection of the number of the planewave components of the eigenstates to be stored Very important for the time being istwfk must be 1 for all the k points For more details about the format of the abo_KSS file see the routine outkss f 4 6 8 npwkss Mnemonics Number of planewave COMponents STOred Characteristic Variable type integer parameter Default is 0 This input variable was called ncomsto prior to v4 3 is used for the preparation of a GW calculation the GS run where optdriver 1 and nbandkss 4 0 should be followed with a run where optdriver 3 Also if nbandkss 0 no use of npwkss npwkss defines the number of planewave components of the Kohn Sham states to build the
258. r example a conventional FCC cell has 192 symmetry operations instead of the 48 ones of the primitive cell A maximum limit of 384 symmetry operations is hard coded This corresponds to the maximum number of symmetry operations of a 2x2x2 undistorted supercell Going beyond that number will make the code stop very rapidly If you want nevertheless for testing purposes to treat a larger number of symmetries change the initialization of msym in the abinit f main routine then recompile the code 4 1 19 ntypat Mnemonics Number of TYPEs of atoms Characteristic NO MULTI Variable type integer parameter Default is 1 Gives the number of types of atoms E g for a homopolar system e g pure Si ntypat is 1 while for BaTiO3 ntypat is 3 Except when alchemical mixing of pseudopotentials is used the number of types of atoms will be equal to the number of pseudopotentials npsp to be provided by the user Thus The code will try to read the same number of pseudopotential files whose names should have been given in the files file The first pseudopotential will be assigned the type number 1 and so on 87 4 1 BASIC VARIABLES VARBAS 4 1 20 occopt Mnemonics OCCupation OPTion Characteristic Variable type integer option parameter The Default is occopt 1 Control how input parameters nband occ and wtk are handled e occopt 0 All k points have the same number of bands and the same occupancies of bands nban
259. r of plane waves for wavefunctions 259 4 5 915 11 654 15 244 3 760 0 803 0 245 11 518 0 136 6 051 5 8 445 9 702 3 216 5 592 0 815 0 227 8 973 0 730 9 175 50 CHAPTER 2 TUTORIAL So that npwwfn 113 ecutwfn 4 0 can be considered converged within 0 01 eV 2 6 7 Convergence on the number of bands to calculate the screening Second we check the convergence on the number of bands in the calculation of the screening This will be done by defining five datasets with increasing nband nband11 nband21 nband31 nband41 nband51 25 50 100 150 200 In directory ABINIT Tutorial Work6 copy the file t67 in and modify the t6x files file as usual Edit the t67 in file and take the time to examine it Then issue abinis lt t6x files gt amp t67 log amp This small job lasts about 22 secs on a PC PIV Intel 2 2 GHz Edit the output file The number of bands used for the wavefunctions in the computation of the screening is mentioned in the fragments of output EPSILON 1 parameters EM1 file dimension of the eps 1 matrix 169 number of plane waves for wavefunctions 113 number of bands 25 Gathering the macroscopic dielectric constant and GW energies for each number of bands one gets dielectric constant 99 5265 dielectric constant without local fields 143 7208 number of bands 25 4 5 915 11 654 15 244 3 769 0 804 0 244 11 510 0 143 6 059 5 8 445 9 702 3 216 5 582 0 815 0 226 8 964 0 738
260. r wavefunctions 113 Band EO VxcLDA SigX SigC EO Z dSigC dE Sig E E EO E 4 5 915 11 654 15 244 3 789 0 804 0 244 11 495 0 159 6 075 5 8 445 9 691 3 213 5 564 0 817 0 224 8 944 0 747 9 192 number of plane waves for wavefunctions 137 Band EO VxcLDA SigX SigC EO Z dSigC dE Sig E E EO E 4 6 915 11 654 15 244 3 779 0 804 0 244 11 502 0 151 6 066 5 8 445 9 702 3 216 5 577 0 817 0 225 8 960 0 743 9 188 number of plane waves for wavefunctions 169 Band EO VxcLDA SigX SigC EO Z dSigC dE Sig E E EO E 4 5 915 11 651 15 242 3 770 0 804 0 245 11 508 0 144 6 059 5 8 445 9 718 3 221 5 584 0 817 0 225 8 972 0 745 9 190 number of plane waves for wavefunctions 259 Band EO VxcLDA SigX SigC E0 Z dSigC dE Sig E E EO E 4 5 915 11 667 15 253 3 766 0 803 0 245 11 522 0 145 6 060 5 8 445 9 716 3 219 5 591 0 816 0 225 8 977 0 740 9 185 So that npwwfn 137 ecutwfn 5 0 can be considered converged within 0 01eV 2 6 4 Convergence on the number of planewaves to calculate Sigma_x Second we check the convergence on the number of planewaves in the calculation of the Sigma_X This will be done by defining five datasets with increasing ecutmat ndtset 7 ecutsigx 3 1 0 ecutsigx 0 In directory ABINIT Tutorial Work6 copy the file t64 in and modify the t6x files file as usual Edit the t64 in file and take the time to examine it Then issue abinis lt t6x files gt amp t64 log This small jo
261. racteristic DEVELOP Variable type integer Default is 0 In the presently used algorithms there is a compromise between speed and robustness that can be tuned by using isecur 100 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST If isecur 0 an extrapolation of out of line data is allowed and might save one non SCF cal culation every two line minimisation when some stability conditions are fulfilled since there are 2 non SCF calculations per line minimisation 1 out of 4 is saved Using isecur 1 or higher integers will raise gradually the threshold to make extrapolation Using isecur 2 will allow to save 2 non SCF calculations every three line minimisation but this can make the algorithm unstable Lower values of isecur allows for more tentative savings In any case there must be one non SCF computation per line minimisation No meaning for RF calculations yet 4 2 19 istatr Mnemonics Integer for STATus file repetition Rate 4 2 20 istatshft Mnemonics Integer for STATus file SHiFT Characteristic DEVELOP NO MULTI Variable type integer parameter Default istatr is 49 and 149 for Cray T3E slow I Os Values lower than 10 may not work on some machines Default istatshft is 1 Govern the rate of output of the status file This status file is written when the number of the call to the status subroutine is equal to istatshft modulo istatr so that it is written once every istatr call There
262. ramework and algorithms See the bibliography file The methods employed in this computer code to solve the electronic structure problem are de scribed in part in different review papers as well as research papers The code is an implementation of the Local Density Approximation to the Density Functional Theory based upon a plane wave basis set and separable pseudopotentials The iterative minimization algorithm is a combination of fixed potential preconditioned conjugate gradient optimization of wavefunction and a choice of different algorithms for the update of the potential one of which is a potential based conjugate gradient algorithm The representation of potential density and wavefunctions in real space will be done on a regular 3D grid of points Its spacing will be determined by the cut off energy see the input variable ecut of the planewave basis in reciprocal space This grid of points will also be the starting point of Fast Fourier Transforms between real and reciprocal space The number of such points called ngfft should be sufficiently large for adequate representation of the functions but not too large for reason of computational efficiency The trade off between accuracy and computational efficiency is present in many places in the code and addressed briefly at the end of the present help file 56 CHAPTER 3 ABINIS HELP We recommend a good introduction to many different concepts valid for this code a
263. rary wf files that exist when a job crashed Presently v3 1 one cannot restart a calculation with a non zero optcell value from the x f history of another run with a different non zero optcell value There are still a few problems at that level Starting a non zero optcell run from a zero optcell run should work 4 11 31 rfasr Mnemonics Response Function Acoustic Sum Rule Characteristic RESPFN Variable type integer parameter Default is 0 Control the evaluation of the acoustic sum rule in effective charge calculations within a response function calculation e 0 no acoustic sum rule imposed e 1 acoustic sum rule imposed with extra charge evenly distributed among atoms e 2 gt acoustic sum rule imposed with extra charge given proportionally to those atoms with the largest effective charge 4 11 32 signperm Mnemonics SIGN of PERMutation potential Characteristic Variable type integer Default is 1 In development See the routine moldyn f See also delayperm 1 favors alternation of species 1 favors segregation 168 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 11 33 strfact Mnemonics STRess FACTor Characteristic Variable type real parameter Default is 100 0 Bohr The stresses multiplied by strfact will be treated like forces in the process of optimization ionmov 2 non zero optcell For example the stopping criterion defined by tolmxf relates to these scaled stresse
264. read the section 3 2 of the abinis_help file 2 There are three methodologies to compute the optimal distance between the two Hydrogen atoms e one could compute the TOTAL ENERGY for different values of the interatomic distance make a fit through the different points and determine the minimum of the fitting function e one could compute the FORCES for different values of the interatomic distance make a fit through the different values and determine the zero of the fitting function e one could use an automatic algorithm for minimizing the energy or finding the zero of forces We will begin with the computation of energy and forces for different values of the interatomic distance This exercise will allow you to learn how to use multiple datasets The interatomic distance in the t11 in file was 1 4 Bohr Suppose you decide to examine the interatomic distances from 1 0 Bohr to 2 0 Bohr by steps of 0 05 Bohr That is 21 calculations If you are a UNIX guru it will be easy for you to write a script that will drive these 21 calculations changing automatically the variable xcart in the input file and then gather all the data in a convenient form to be plotted 10 CHAPTER 2 TUTORIAL Well are you a UNIX guru If not there is an easier path all within ABINIT This is the multi dataset mode Detailed explanations about it can be found in sections 3 3 3 4 3 5 and 3 6 of the abinis_help file Now can you writ
265. relevant if optdriver 3 that is GW calculations npweps determines the size of the planewave set used to represent the independent particle susceptibility xo the dielectric matrix e and its inverse See ecuteps preferred over npweps for more information 4 6 12 npwsigx Mnemonics Number of PlaneWaves for SIGma eXchange Characteristic GW Variable type integer Default 0 Only relevant if optdriver 4 that is GW calculations This input variable wxas previously called npwmat npwsigx determines the cut off energy of the planewave set used to generate the exchange part of the self energy operator See ecutsigx preferred over npwsigx for more information 4 6 13 npwwfn Mnemonics Number of PlaneWaves for WaveFunctioNs Characteristic GW Variable type integer Default 0 Only relevant if optdriver 3 or 4 that is GW calculations npwwfn determines the size of the planewave set used to represent the wavefunctions in the formula that generates the independent particle susceptibility x2 147 4 6 GW VARIABLES VARGW See ecutwfn preferred over nshwfn for more information 4 6 14 nsheps Mnemonics Number of SHells for EPSilon the dielectric matrix Characteristic GW Variable type integer Default 0 Only relevant if optdriver 3 that is GW calculations nsheps determines the size of the planewave set used to represent the independent particle susceptibility A the dielectric matrix e and its inver
266. representation of the latter this should be described 4 11 12 iatfix Mnemonics Indices of AToms that are FIXed 4 11 13 iatfixx Mnemonics Indices of AToms that are FIXed along the X direction 4 11 14 iatfixy Mnemonics Indices of AToms that are FIXed along the Y direction 4 11 15 iatfixz Mnemonics Indices of AToms that are FIXed along the Z direction Characteristic iatfixx iatfixy and iatfixz are NOT INTERNAL Variable type integer arrays of length natfix natfixx natfixy or natfixz No Default ignored unless natfix natfixx natfixy or natfixz gt 0 Give the index in the range 1 to natom of each atom which is to be held fixed for structural optimization or molecular dynamics The variable iatfix lists those fixed in the three directions while the other variables allow to fix some atoms along x y or z directions or a combination of these WARNING The implementation is inconsistent For ionmov 1 the fixing of directions was done in cartesian coordinates while for the other values of ionmov it was done in reduced coordinates Sorry for this There is no harm in fixing one atom in the three directions using iatfix then fixing it again in other directions by mentioning it in iatfixx iatfixy or iatfixz The internal representation of these input data is done by the mean of one variable iat fix 3 natom defined for each direction and each atom being 0 if the atom is not fixed along the direction and 1 if the atom i
267. responds to an average radius a u of the density and is used to generate a gaussian density If set to 0 0d0 an optimized value is used No meaning for RF calculations 4 2 5 effmass Mnemonics EFFective MASS Characteristic DEVELOP Variable type real number Default value is one This parameter allows to change the electron mass with respect to its experimental value 4 2 6 eshift Mnemonics Energy SHIFT Characteristic DEVELOP ENERGY Variable type real number Default value is zero Used only if wfoptalg 3 eshift gives the shift of the energy used in the shifted Hamiltonian squared The algorithm will determine eigenvalues and eigenvectors centered on eshift Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY charac teristics 1 Ha 27 2113961 eV 4 2 7 exchn2n3 Mnemonics EXCHange N2 and N3 Characteristic DEVELOP Variable type integer parameter Default is 0 If exchn2n3 is 1 the internal representation of the FFT arrays in reciprocal space will be array n1 n3 n2 where the second and third dimensions have been switched This is to allow to be coherent with the exchn2n3 4xx FFT treatment 96 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 2 8 fftalg Mnemonics Fast Fourier Transform ALGorithm Characteristic DEVELOP Variable type integer parameter Default is 112 except for VPP Fujitsu for which the Default is 111 and for NEC for which the
268. riables VARPAW o o 151 AL UE co ee a A a e ta a e de ds a e e 151 LUZ PAE a AA ee Eee oe aoe e 152 AOS Pawlcutd esca 4444 5440608 ada e EERE 152 AOA DOQUIER A oe ae se Gok eh ww Bs a ays 152 CONTENTS 4 10 4 11 a IE 152 ADE pawitheta lt o cara Pawan a eda de A eee 153 Response Function variables VARRE 0 o e e 153 MAG SUGGS oo 4 eg po EWR ea aa dr meal 153 LIS MEE e a we ee SO a ek A 153 ES MEMES os gaa a ee EE RR aa e ee 153 MAGA PEDAL ooo eo A RR ERLE A ba a 154 ANGE PBB 6 6 42 ek ee bee Reh ERLE eb ee he eee 4 dh a 154 ONG AI 154 LIOFT PEDO aaa ae AAA era Se RARER Re Bales 154 AOS Tatpol so oc ae A e DE Wee eae a es 155 AO PIAS ooo Se ES ye A Bee Gh hin ia ke es Be aie a 155 ANG NOPBATOON coord AAA eR ER a a 155 CARA a dor rr arc be 155 MUTE eag RNA 155 WAG MAGE us RARE A a aa 155 ANG EIR sois mir eee EE eG ee eR eee ee a aE 156 MAGARIN ou Ge RAR RES S REO A ERS RE ARE OAS 156 MAG LOPERA cidos ala hd de A eo OE RRA Re a a 156 MAG PESO os ee ae ee Oa ee ee ae ae ae 156 AIIE oc Bike ea a Md a a ee A kG BAe OHS 156 UA a e a a oo eG dA eae CEO GES Eee Meee ee thas 157 AAG 2OPPNOR 6 4 4 5 8 a Gye Rw A ER RE ARERR SSS BERS 157 AIOI pPbOb ooo EEO BES Dee Bh hw EA a ee 157 WAG QI NOM fine eee ba aw EO Se ee Ooo eee ae eG EE 157 ANGORA II 157 MAG QOS cece ke A eee A AE EOD SORE REG EE HES Don 157 a eco case E NN 158 AUTE aco ese ka a a ed oe OSE A eee ea OAS 158 MU RRS ca
269. rons 4 2 15 intxc Mnemonics INTerpolation for eXchange Correlation Characteristic DEVELOP Variable type integer parameter Default value is 0 e 0 gt do usual xc quadrature on fft grid e 1 gt do higher accuracy xc quadrature using fft grid and additional points at the centers of each cube doubles number of grid points the high accuracy version is only valid for boxcut gt 2 If boxcut 2 the code stops For RF calculations only intxc 0 is allowed yet Moreover the GS preparation runs giving the density file and zero order wavefunctions must be done with intxc 0 Prior to ABINIT v2 3 the choice intxc 1 was favoured it was the default but the continuation of the development of the code lead to prefer the default intxc 0 Indeed the benefit of intxc 1 is rather small while making it available for all cases is a non negligible development effort Other targets are prioritary You will notice that many automatice tests use intxc 1 Please do not follow this historical choice for your production runs 99 4 2 DEVELOPPEMENT VARIABLES VARDEV 4 2 16 iprcch Mnemonics Integer for PReConditioning of CHarge response Characteristic DEVELOP Variable type integer parameter Default for iprech is 2 unless ionmov 4 and iscf 5 in which case iprech is automatically put to 3 Used when iscf gt 0 to define the SCF preconditioning scheme Potential based preconditioning schemes for the SCF loop are still un
270. rst in which acell 8 8 8 ecut 10 has to be used and a second in which acell 8 8 8 ecut 15 60 CHAPTER 3 ABINIS HELP has to be used 2nd example ndtset 2 jdtset 4 5 acell 888 acell5 10 10 10 ecuti 10 ecut2 15 ecut3 20 ecut4 25 ecut5 30 this means that there are still two datasets but now characterized by the indices 4 and 5 so that the first run will use the generic acell and ecut4 acell 8 8 8 ecut 25 and the second run will use acell5 and ecut5 acell 10 10 10 ecut 30 Note that ecut1 ecut2 and ecut3 are not used 3 2 4 Defining a series Rules 2 is split in three parts 2a 2b and 2c Series relate with 2b 2b If the variable name appended with the index of the dataset does not exist the code looks whether a series has been defined for this keyword There are two kinds of series e arithmetic series constant increment between terms of the series e geometric series constant ratio between terms of the series The first term of the series is defined by the keyword appended with a colon e g ecut while the increment of an arithmetic series is defined by the keyword appended with a plus e g ecut and the factor of a geometric series is defined by the keyword appended with a times e g ecut If the index of the dataset is 1 the first term of the series is used while for index N the appropriate input data is obtained by considering the Nth term of the series
271. rtesian coordinates Thus these are fractional numbers typically between 0 and 1 and are dimensionless The cartesian coordinates of atoms are given by teartesian tl x rl xal t2 x r2 a2 t3 r3 a3 where t1 t2 t3 are the reduced coordinates given in columns of xred r1 r2 r3 are the columns of dimensionless array rprim and al a2 a3 are the elements of the array acell giving length scales in bohr If you prefer to work only with cartesian coordinates you may work entirely with xcart or xangst and ignore xred in which case xred must be absent from the input file One and only one of xred xcart and Atomic positions evolve if ionmov 0 4 1 35 znucl Mnemonics charge Z of the NUCLeus Characteristic NO MULTI Variable type real array znucl npsp Gives nuclear charge for each type of pseudopotential in order If znucl does not agree with nuclear charge as given in pseudopotential files the program writes an error message and stops N B In the pseudopotential files znucl is called zatom 94 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 2 Developpement variables VARDEV 4 2 1 accessw f Mnemonics ACCESS to WaveFunction Files Characteristic DEVELOP Variable type integer parameter Default is 0 Governs the method of access to the internal wavefunction files Relevant only for the wave functions files for which the corresponding mkmem typ
272. s 4 11 34 strprecon Mnemonics STRess PRECONditioner Characteristic Variable type real parameter Default is 1 0 This is a scaling factor to initialize the part of the Hessian related to the treatment of the stresses optimisation of the unit cell In case there is an instability decrease the default value e g set it to 0 1 4 11 35 strtarget Mnemonics STRess TARGET Characteristic Variable type real array strtarget 6 Default is 6 0 0 Ha Bohr 3 The optimization of cell size and shape as might be asked through optcell will target the stress tensor defined by by strtarget or part thereof if restricted optimizations are asked like fixed shape Presently this required target stress is not taken into account for the determination of the symmetries If it breaks the symmetries of the input unit cell so that symrel disagrees with strtarget the result will be unreliable Also presently the thermodynamical potential to be used n this situation the free energy does not replace the total energy so that for exemple ionmov 3 cannot be used since this algorithm is taking into account the total energy The components of the stress tensor must be stored according to 1 1 gt 1 2 2 2 3 3 3 2 3 gt 4 3 1 gt 5 1 2 6 The conversion factor between Ha Bohr and GPa is 1 Ha Bohr 29421 033d0 GPa Not used if optcell 0 4 11 36 tolmxf Mnemonics TOLerance on the MaXimal Force Characteristic
273. s Maximum number of Q space GRID points for pseudopotentials Characteristic DEVELOP Variable type integer parameter Default is 1201 Govern the size of the one dimensional information related to pseudopotentials in reciprocal space potentials or projector functions 4 2 24 nbandsus Mnemonics Number of BANDs to compute the SUSceptibility Characteristic Variable type integer parameter Default value is nband Number of bands to be used in the calculation of the susceptibility matrix ACFD only 4 2 25 nbdblock Mnemonics Number of BanDs in a BLOCK Characteristic DEVELOP Variable type integer parameter Default is 1 102 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST In case of non standard blocked algorithms for the optimization of the wavefunctions that is if wfoptalg 4 0 nbdblock defines the number of bands or states in a block 4 2 26 ndyson Mnemonics Number of points to be added for the solution of the DYSON equation Characteristic Variable type integer parameter Default value is 1 Number of points to be added to lambda 0 and lambda 1 that are always calculated for the integration ober the coupling constant lambda in the ACFD calculation of the exchange correlation energy e ndyson 1 let the code decide how many points to use presently 3 points for idyson 1 or 3 and 9 points for idyson 2 e ndyson 0 only compute the non interacting and fully interacting sus
274. s latter designation is not really satisfactory There are also parameters related to the geometry builder a preprocessor of the input file aimed at easing the work of the user when there are molecules to be manipulated rotation and translation or group of atoms to be repeated The indication GEOMETRY BUILDER is given for them These can also be skipped for the first few steps in the use of the code Indeed it should be easy to set up the geometry of systems with less than 20 40 atoms without this 58 CHAPTER 3 ABINIS HELP geometry builder Even for larger systems its functionalities could eventually be of no help For a step to step description of this geometry builder look at the variable nobj Alternatively to the geometry builder there is also a symmetriser It allows to generate the full set of atoms in the primitive cell from the knowledge of the symmetry operations and the atoms in the asymetric cell It also allows to generate the symmetry operations from the knowledge of the number of the space group according to the international crystallographic tables The indication SYMMETRISER is given for the variables related to its use Look at the variable spgroup You may find in the space group help file the crystallographic equivalence of the parameters belonging to the symmetriser Still as an alternative to the geometry builder and the symmetriser if all the coordinates of the atoms are given the code is
275. s fixed along the direction When some atoms are fixed along 1 or 2 directions the use of symmetries is restricted to symmetry operations whose 3x3 matrices symrel are diagonal If the geometry builder is used iatfix will be related to the preprocessed set of atoms generated by the geometry builder The user must thus foresee the effect of this geometry builder see objarf 4 11 16 ionmov Mnemonics IONic MOVEs Characteristic Variable type integer parameter Default for ionmov is 0 Control the displacements of ions and eventually see optcell changes of cell shape and size 163 4 11 STRUCTURE OPTIMIZATION VARIABLES VARRLX e 0 gt do not move ions e 1 gt move atoms using molecular dynamics with optional viscous damping friction linearly proportional to velocity The viscous damping is controlled by the parameter vis If actual undamped molecular dynamics is desired set vis to 0 The implemented algorithm is the generalisation of the Numerov technique 6th order but is NOT invariant upon time reversal so that the energy is not conserved The value ionmov 6 will usually be preferred although the algorithm that is implemented is lower order opcell 4 0 is not available e 2 gt conduct structural optimization using the Broyden Fletcher Goldfarb Shanno minimiza tion BFGS This is much more efficient for structural optimization than viscous damping when there are less than let s say 10 degrees of freedom
276. s that the relaxation energy is very small compared to the surface energy but we need to do the convergence studies 2 4 6 Determination of the surface energy increasing the number of vacuum layers One should now increase the number of vacuum layers 2 and 3 layers instead of only 1 It is preferable to define atomic positions in cartesian coordinates The same coordinates will work for both 2 and 3 vacuum layers while this is not the case for reduced coordinates as the cell size increases The input file ABINIT Tutorial t46 in is an example input file while ABINIT Tutorial Refs t46 out is a reference output file The run might take a few minutes In the Broyden step 0 of the first dataset you will notice the WARNING scprqt WARNING nstep 10 was not enough SCF cycles to converge maximum force difference 1 716E 04 exceeds toldff 5 000E 05 The SCF convergence is indeed getting more difficult This is because the default preconditioner see the notice of the input variable dielng is not very good for the metal vacuum case For the interpretation of the present run this is not critical as the convergence criterion was close of being fulfilled but one should keep this in mind as you will see For the 2 vacuum layer case one has the non relaxed total energy ETOT 10 6 2538519290781 that is inaccurate at the 1 0d 4Ha level giving the unrelaxed surface energy 0 0200 Ha 0 544 eV and for the relaxed case eto
277. s which affect convergence and the numerical quality of calculations The list of these input parameters is 1 ecut 74 CHAPTER 3 ABINIS HELP 2 3 4 5 6 toldfe toldff tolwfr and tolurs as well as nstep nkpt ngfft tolmxf as well as amu dtion vis ntime acell and rprim The technical design of the pseudopotential also affects the quality of the results 1 The first issue regarding convergence is the number of planewaves in the basis for a given set of atoms Some atoms notably those in the first row or first transition series row have relatively deep pseudopotentials which require many planewaves for convergence In contrast are atoms like Si for which fewer planewaves are needed A typical value of ecut for silicon might be 5 10 Hartree for quite good convergence while the value for oxygen might be 25 35 hartree or more depending on the convergence desired and the design of the pseudo potential NOTE It is necessary in every new problem to TEST the convergence by RAISING ecut for a given calculation until the results being computed are constant to within some tolerance This is up to the user and is very important For a given acell and rprim ecut is the parameter which controls the number of planewaves Of course if rprim or acell is varied then the number of planewaves will also change Let us reiterate that extremely careful pseudopotential design can optimize the convergence o
278. same value for example use the Carbon mass i e set amu to 12 for all type of atoms e 8 gt Molecular dynamics with Nose Hoover thermostat using the Verlet algorithm Although partly coded optcell 0 is not available Related parameters the time step dtion the initial temperature mditemp the final temperature mdftemp and the thermostat mass noseinert e 9 gt Langevin molecular dynamics Although partly coded optcell 4 0 is not available Related parameters the time step dtion the initial temperature mditemp the final temperature mdftemp and the friction coefficient friction No meaning for RF calculations 4 11 17 mdftemp Mnemonics Molecular Dynamics Final Temperature Characteristic Variable type real mdftemp Default is mdftemp mditemp Give the final temperature for itime ntime of the Nose Hoover thermostat ionmov 8 and Langevin dynamics ionmov 9 in Kelvin This temperature will change linearly from mditemp at itime 1 to the final temperature mdftemp at the end of the ntime timesteps 164 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 11 18 mditemp Mnemonics Molecular Dynamics Initial Temperature Characteristic Variable type real mditemp Default is 300 Give the initial temperature for itime 1 of the Nose Hoover thermostat ionmov 8 and Langevin dynamics ionmov 9 in Kelvin This temperature will change linearly to reach the temperature mdftemp at the e
279. se See ecuteps preferred over nsheps for more information 4 6 15 nshsigx Mnemonics Number of SHells for MAT Characteristic GW Variable type integer Default 0 Only relevant if optdriver 4 that is GW calculations This input variable was named nshma prior to v4 3 nshsigx determines the cut off energy of the planewave set used to generate the exchange part of the self energy operator See ecutsigx preferred over nshsigx for more information 4 6 16 nshwfn Mnemonics Number of SHells for WaveFunctioNs Characteristic GW Variable type integer Default 0 Only relevant if optdriver 3 or 4 that is GW calculations nshwfn determines the number of shells of the planewave set used to represent the wavefunctions in the formula that generates the independent particle susceptibility xE See ecutwfn preferred over nshwfn for more information 4 6 17 omegasrdmax Mnemonics OMEGA to evaluate the Sigma Real axis Derivative MAXimal value Characteristic GW Variable type real Default 1 0 eV Only relevant if GW calculations The maximum distance from the KS energy where to evaluate Sigma Sigma is evaluated at KS energy maxomegasrd KS_energy maxomegasrd sampled nomegasrd times 4 6 18 ppmfrq Mnemonics Plasmon Pole Model FReQuency Characteristic ENERGY GW 148 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST Variable type real Default 0 0 Ha This input variable was n
280. sed from 4 0 to 3 6 This is rather innocuous Also nband has been decreased from 100 to 25 This is a drastic change The CPU time of this part is linear with respect to this parameter or more exactly with the number of conduction bands Thus the CPU time has been decreased by a factor of 4 Referring to our previous convergence study we see that the absolute accuracy on the GW energies is now on the order of 0 2 eV only However the gap energy difference between valence and conduction states is likely correct within 0 02 eV Finally in dataset 4 we calculate the self energy matrix element in Gamma using the previously determined parameters You should obtain the following results k 0 000 0 000 0 000 Band EO VxcLDA SigX SigC E0 Z dSigC dE Sig E E EO E 4 5 915 11 255 12 425 0 861 0 771 0 296 11 493 0 238 5 677 5 8 445 10 067 5 858 3 690 0 772 0 296 9 666 0 401 8 846 E 0_gap 2 530 E GW_gap 3 169 DeltaE GW_gap 0 639 53 2 6 LESSON 6 THE QUASI PARTICLE BAND STRUCTURE OF SILICON IN THE GW APPROXIMATION So that the LDA energy gap in Gamma is about 2 53 eV while the GW correction is about 0 64 eV so that the GW band gap found is 3 17 eV One can compare now what have been obtained to what one can get from the literature EXP 3 40 eV Landolt Boernstein LDA 2 57 eV L Hedin Phys Rev 139 A796 1965 LDA 2 57 eV M S Hybertsen and S Louie PRL 55 1418 1985 LDA FLAPW 2 55eV N
281. stic Variable type integer parameter The Default is optdriver 0 For each dataset choose the task to be done at the level of the driver routine The choice is between e optdriver 0 ground state calculation GS routine gstate 139 4 5 GROUND STATE CALCULATION VARIABLES VARGS e optdriver 1 response function calculation RF routine respfn e optdriver 2 susceptibility calculation SUS routine suscep e optdriver 3 susceptibility and dielectric matrix calculation CHI routine screening see the input variables ecutwfn ecuteps plasfrq getkss as well as nbandkss and nband e optdriver 4 self energy calculation SIG routine sigma e optdriver 5 non linear response functions using the 2n 1 theorem routine nonlinear If one of rfphon rfelfd or rfstrs is non zero while optdriver is not defined in the input file ABINIT will set optdriver to 1 automatically These input variables rfphon rfelfd and rfstrs must be zero if optdriver is not set to 1 4 5 43 so typat Mnemonics Spin Orbit TYPe of each pseudo ATom 4 5 44 pspso obsolete Mnemonics PSeudoPotential treatment of Spin Orbit interaction Characteristic Variable type integer array so_typat ntypat Default is ntypat 1 For each type of atom each pseudopotential specify the spin orbit interaction e If 1 no spin orbit interaction even if nspinor 2 e If 2 treat spin orbit in the HGH form not allowed
282. stwfk 1 nkpt amp kpt 1 3 1 nkpt occ 1 bantot tnons 1 3 1 nsym znucl 1 ntypat do itypat 1 ntypat ntypat lines 1 for each psp write unit unit title znucl zion pspso pspdat pspcod pspxc amp amp 1lmax lloc mmax enddo final record residm coordinates total energy Fermi energy write unit unit residm xred 1 3 1 natom etotal fermie The format for versions 2 0 2 1 and 2 2 was write unit header codvsn fform write unit header bantot date intxc ixc natom ngfft 1 3 amp nkpt nsppol nsym ntypat acel1 1 3 ecut_eff rprimd 1 3 1 3 write unit header nband 1 nkpt nsppol amp npwarr 1 nkpt symrel 1 3 1 3 1 nsym typat 1 natom istwfk 1 nkpt amp kpt 1 3 1 nkpt occ 1 bantot tnons 1 3 1 nsym znucl 1 ntypat do itypat 1 ntypat ntypat lines 1 for each psp write unit unit title znucl zion pspdat pspcod pspxc lmax lloc mmax enddo final record residm coordinates total energy write unit unit residm xred 1 3 1 natom etotal 3 5 5 The density output file This is an unformatted data file containing the electron density on the real space FFT grid It consists of the header records followed by do ispden 1 nspden write unit rhor ir ir 1 cplex ngfft 1 ngfft 2 ngfft 3 enddo where rhor is the electron density in electrons bohr and cplex is the number of complex components of the density cplex 1 for GS calculations the density is real and cplex 1 or 2 for R
283. t 1 2 or 3 the variable rfdir must be used to specify the primitive vector along which the projection of the polarization or the ddk will be computed For example if berryopt 1 and rfdir 1 0 0 the projection of the polarization along the reciprocal lattice vector G is computed In case rfdir 1 1 1 ABINIT computes the projection of P along G1 G2 and G3 and transforms the results to cartesian coordinates e efield rfdir in case of berryopt 4 The cases berryopt 1 2 3 and 4 work only if kptopt 3 nsppol 1 nspinor 1 and occopt 1 4 5 4 boxcenter Mnemonics BOX CENTER Characteristic Variable type real array boxcenter 3 Default boxcenter 1 3 is 0 5 0 5 0 5 Defines the center of the box in reduced coordinates At present this information is only used in the case of Time Dependent DFT computation of the oscillator strength One must take boxcenter such as to be roughly the center of the cluster or molecule The default is sensible when the vacuum surrounding the cluster or molecule has xred 0 or 1 On the contrary when the cluster or molecule is close to the origin it is better to take boxcenter 0 0 0 4 5 5 boxcutmin Mnemonics BOX CUT off MINimum Characteristic Variable type real Default is 2 0 The box cut off ratio is the ratio between the wavefunction plane wave sphere radius and the radius of the sphere that can be inserted in the FFT box in reciprocal space In order for the density to
284. t 0 2500 0 0000 0 0000 reduced coord 0 07058 0 41033 0 68787 occupation numbers for kpt 2 2 00000 0 00030 0 00000 You should also note that the components of the total energy include an entropy term Eight components of total free energy hartree are kinetic 8 70148725738375E 01 Hartree 3 84240572509002E 03 xc 8 08093663953667E 01 loc psp 8 21205082511040E 02 nl psp 4 52424282437438E 01 pspcore 3 78200676875296E 02 kT entropy 7 99762559838938E 03 internal energy 2 08996839059198E 00 Ewald 2 72823071647785E 00 resulting in Etotal 2 09796601619037E 00 hartree Also Etotal 5 70885576267268E 01 eV Eeig band energy 3 5951203776E 01 Ha 26 CHAPTER 2 TUTORIAL 2 4 2 The convergence study with respect to k points There is of course a convergence study associated to the sampling of the Brillouin zone You should examine different grids of increasing resolution You might try the following series of grids ngkptl 22 2 ngkpt2 444 ngkpt3 6 6 6 ngkpt4 88 8 with the associated nkpt nkpti 2 nkpt2 10 nkpt3 28 nkpt4 60 The input file ABINIT Tutorial t42 in is an example while ABINIT Tutorial Refs t42 out is a reference output file The run might take more than one minute You will see that FOR THE PARTICULAR VALUE OF tsmear 0 05 Ha the lattice param eter is already converged with nkpt 10 acell1 7 5623662498E 00 7 5623662498E 00 7 5623662498E 00 Bohr acell2 7 5084285443E 00 7 5084285443E 0
285. t 3 Fermi Dirac smearing finite temperature metal Smeared delta function 0 2540 cosh xx 2 0d0 2 occopt 4 Cold smearing of N Marzari see his thesis work with a 5634 minimization of the bump Smeared delta function exp xx2 sqrt pi 1 5d0 xx a 1 5d0 xx 1 0d0 a xx occopt 5 Cold smearing of N Marzari see his thesis work with a 8165 monotonic function in the tail Same smeared delta function as occopt 4 with different a occopt 6 Smearing of Methfessel and Paxton PRB40 3616 1989 with Hermite polynomial of degree 2 corresponding to Cold smearing of N Marzari with a 0 so same smeared delta function as occopt 4 with different a occopt 7 Gaussian smearing corresponding to the 0 order Hermite polynomial of Methfessel and Paxton Smeared delta function 1 0d0 exp xx 2 sqrt pi WARNING one can use metallic occupation of levels in the case of a molecule in order to avoid any problem with degenerate levels However it is adviced NOT to use occopt 6 and to a lesser extent occopt 4 and 5 since the associated number of electron versus the Fermi energy is NOT garanteed to be a monotonic function For true metals AND a sufficiently dense sampling 88 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST of the Brillouin zone this should not happen but be cautious As an indication of this problem a small variation of input parameters might lead to a j
286. t cannot be used 4 1 7 kpt Mnemonics K PoinTs Characteristic Variable type real array kpt 3 nkpt Default is 0 0 0 for just one k point Contains the k points in terms of reciprocal space primitive translations NOT in cartesian coordinates Needed ONLY if kptopt 0 otherwise deduced from other input variables It contains dimensionless numbers in terms of which the cartesian coordinates would be k_cartesian k1 G1 k2 G2 k3 G3 where k1 k2 k3 represent the dimensionless reduced coordinates and G1 G2 G3 are the cartesian coordinates of the primitive translation vectors G1 G2 G3 are related to the choice of direct space primitive translation vectors made in rprim Note that an overall norm for the k points is supplied by kptnrm This allows one to avoid supplying many digits for the k points to represent such points as 1 1 1 3 Note one of the algorithms used to set up the sphere of G vectors for the basis needs compo nents of k points in the range 1 1 so the remapping is easily done by adding or subtracting 1 from each component until it is in the range 1 1 That is given the k point normalization kptnrm described below each component must lie in kptnrm kptnrm Not read if kptopt 4 0 4 1 8 kptnrm Mnemonics K PoinT s NoRMalization Characteristic Variable type real parameter Default is 1 Establishes a normalizing denominator for each k point Needed only if kptopt lt 0
287. t mode ndtset gt 0 since it describes from which dataset acell and rprim are to be taken as input of the present dataset The cell parameters are EVOLVING variables for which such a chain of calculations is useful If 0 no use of previously computed values must occur If it is positive its value gives the index of the dataset from which the data are to be used as input data It must be the index of a dataset already computed in the SAME run If equal to 1 the output data of the previous dataset must be taken which is a frequently occuring case However if the first dataset is treated 1 is equivalent to 0 since no dataset has yet been computed in the same run If another negative number it indicates the number of datasets to go backward to find the needed data once again going back beyond the first dataset is equivalent to using a null get variable 4 11 8 getxcart Mnemonics GET XCART from 4 11 9 getxred Mnemonics GET XRED from 4 11 10 getvel Mnemonics GET VEL from Characteristic Variable type integer parameters instances of get variables Default is 0 These variables are typically used to chain the calculations in the multi dataset mode ndtset gt 0 since they describe from which dataset the corresponding output variables are to be taken as input of the present dataset The atomic positions and velocities are EVOLVING variables for which such a chain of calculation is useful N
288. t names You can copy it in the Work3 directory and change it as you did for the t1x files and t2x files files You can also copy the file ABINIT Tutorial t31 in in Work3 This is your input file You should edit it read it carefully have a look at the following new input variables and their explanation e rprim e zred used instead of xcart e kptopt ngkpt nshiftk shiftk kptrlatt not easy take your time e diemac compared to isolated molecules another value is used while diemiz has been sup pressed Note also the following you will work at fixed ecut 8Ha It is implicit that in real life you should do a convergence test with respect to ecut Here a suitable ecut is given to you It will allow to obtain 0 2 relative accuracy on lattice parameters When you have read the input file you can run the code as usual it will run a few seconds Then read the output file and note the total energy etotal 8 8662238960E 00 21 2 3 LESSON 3 CRYSTALLINE SILICON 2 3 2 Starting the convergence study with respect to k points There is of course a convergence study associated to the sampling of the Brillouin zone You should examine different grids of increasing resolution You might try the following series of grids ngkpt1 22 2 ngkpt2 444 ngkpt3 6 6 6 ngkpt4 88 8 However the associated number of k points in the irreducible Brillouin zone grows very fast It is nkpti 2 nkpt2 10 nkpt
289. t of atoms from which it will have to deduce the full set of atoms An object will be specified by the number of atoms it includes objan or objbn and the list of these atoms objaat or objbat Examples of physical realisation of an object can be a molecule or a group of atom to be repeated or a part of a molecule to be rotated The geometry builder can indeed repeat these objects objarf or objbrf rotate them objaro or objbro with respect to an axis objaax or objbax and translate them objatr or objbtr After having generated a geometry thanks to rotation translation and repetition of objects it is possible to remove some atoms in order to create vacancies vacnum and vaclst The number of atoms in the primitive set those that will be read from the input file is specified by the variable natrd It will be always smaller than the final 119 4 4 GEOMETRY BUILDER SYMMETRY RELATED VARIABLES VARGEO number of atoms given by the variable natom The code checks whether the primitive number of atoms plus those obtained by the repetition operation is coherent with the variable natom taking into account possible vacancies You should look at the other variables for more information Go to objan for example Not present in the dtset array no internal 4 4 5 objaat objbat Mnemonics OBJect A list of AToms OBJect B list of AToms Characteristic GEOMETRY BUILDER NO INTERNAL Variable type integer arrays objaat objan an
290. t11 7 1203906739E 01 0 0000000000E 00 0 0000000000E 00 7 1203906739E 01 0 0000000000E 00 0 0000000000E 00 xcarti2 0 0000000000E 00 0 0000000000E 00 0 0000000000E 00 e The corresponding atomization energy is 0 1647 Ha 4 482 eV e The interatomic distance is 1 4241 Bohr 20 CHAPTER 2 TUTORIAL e These are our final data for the generalized gradient approximation Once more here are the experimental data e bond length 1 401 Bohr e atomization energy 4 747 eV In GGA we are within 2 of the experimental bond length but 5 of the experimental atomization energy In LDA we were within 4 of the experimental bond length and within 2 of the experimental atomization energy Do not forget that the typical accuracy of LDA and GGA varies with the class of materials studied 2 3 Lesson 3 Crystalline silicon This lesson aims at showing you how to get the following physical properties for an insulator e the total energy e the lattice parameter e the band structure actually the Kohn Sham band structure You will learn about the use of k points as well as the smearing of the planewave kinetic energy cut off This lesson should take about 1 hour to be done 2 3 1 Computing the total energy of silicon at fixed number of k points Before beginning you might consider to work in a different subdirectory as for lesson 1 or lesson 2 Why not Work3 The file ABINIT Tutorial t3x files lists the file names and roo
291. tal1 6 2546977224E 00 this one is converged to the required level giving the relaxed surface energy 0 0196 Ha 0 533 eV Note that the difference between unrelaxed and relaxed case is a bit larger than in the case of one vacuum layer This is because there was some interaction between slabs of different supercells For the 3 vacuum layer case the self consistency problem becomes even more severe than with 2 vacuum layers The Broyden steps 0 and 1 are NOT sufficiently converged one might set nstep to a larger value but the best is to change the preconditioner as described below However for the Broyden steps number 2 and beyond because one takes advantage of the previous wavefunctions a sufficient convergence is reached The total energy in the relaxed case is total2 6 2559056529E 00 giving the relaxed surface energy 0 0190 Ha 0 515 eV There is a rather small 0 018 eV difference with the 2 vacuum layer case For the next run we will keep the 2 vacuum layer case and we know that the accuracy of the coming calculation cannot be better than 0 016 eV One might investigate the 4 vacuum layer case but this is not worth in the present tutorial 30 CHAPTER 2 TUTORIAL 2 4 7 Determination of the surface energy increasing the number of aluminum layers One should now increase the number of aluminum layers while keeping 2 vacuum layers We will consider 4 and 5 aluminum layers This is rather straightforward to set
292. talline silicon an insulator the definition of a k point grid the smearing of the cut off energy the computation of a band structure and again convergence studies e Lesson 4 deals with crystalline aluminum a metal and its surface occupation numbers smearing the Fermi Dirac distribution the surface energy and again convergence studies Lessons 5 and beyond present more specialized topics You can pick one of these at random with lessons 1 4 you know enough to start one of the others 2 1 LESSON 1 THE H2 MOLECULE WITHOUT CONVERGENCE STUDIES e The fifth lesson deals with the dynamical and dielectric properties of AlAs an insulator phonons at Gamma dielectric constant Born effective charges LO TO splitting phonons in the whole Brillouin zone in the future it should also present the interatomic forces and the computation of thermodynamical properties e The sixth lesson deals with the computation of the quasi particle band structure of Silicon in the GW approximation so much better than the Kohn Sham LDA band structure That s all for now The following topics should be covered later e the choice of pseudopotentials 2 1 Lesson 1 The H2 molecule without convergence stud ies This lesson aims at showing how to get the following physical properties e The pseudo total energy e The bond length e The charge density e The atomization energy You will learn about the two input files the basic
293. ted with relative coordinates 0 5 and 1 0 It is easy to compute disconnected circuits non chained segments by separating the circuits with the value ndivk 1 for the intermediate segment connecting the end of one circuit with the beginning of the next one in which case no intermediate point is computed along this segment 4 5 32 ngfft Mnemonics Number of Grid points for Fast Fourier Transform Characteristic Variable type integer array ngfft 3 Default is 0 0 0 so automatic selection of optimal values Gives the size of fast fourier transform fft grid in three dimensions Each number must be composed of the factors 2 3 and 5 to be consistent with the radices available in our fft If no ngfft is provided or if ngfft is set to 0 0 0 the code will automatically provide an optimal set of ngfft values based on acell rprim and ecut This is the recommended procedure of course The total number of FFT points is the product ngfft 1 x ngfft 2 x ngfft 3 nfft When ngfft is made smaller than recommended values the code runs faster and the equations in effect are approximated by a low pass fourier filter The code reports to standard output unit 06 a parameter boxcut which is the smallest ratio of the fft box side to the G vector basis sphere diameter When boxcut is less than 2 the fourier filter approximation is being used When boxcut gets less than about 1 5 the approximation may be too severe for realistic results and sh
294. th of names for the main input or output files is presently 132 characters It is 112 characters for the root strings since they will be supplemented by different character strings If you follow the tutorial you should go back to the tutorial window now 3 1 2 Running the code The main executable files are called abinis sequential version or abinip parallel version In the present help file we will concentrate on the sequential version There is a brief introduction to the use of the parallel version in the ABINIT Infos paral_use file Supposing that the files file is called ab files and that the executable is placed in your working directory abinis is run interactively in Unix with the command abinis lt ab files gt amp log or in the background with the command abinis lt ab files gt amp log amp where standard out and standard error are piped to the log file called log piping the standard error thanks to the amp sign placed after is really important for the analysis of eventual failures when not due to ABINIT but to other sources like disk full problem The user can specify any names he she wishes for any of these files Variations of the above commands could be needed depending on the flavor of UNIX that is used on the platform that is considered for running the code If you follow the tutorial you should go back to the tutorial window now 3 1 3 The underlying theoretical f
295. the geometry according to the DFT forces and stresses or to perform molec ular dynamics simulation using these forces or to generate dynamical matrices Born effective charges and dielectric tensors In addition to the main ABINIT code different utility programs are provided We will use the name ABINIT to refer to the directory that contains the ABINIT package In practice a version number is appended to this name to give for example ABINITv1 0 1 ABINIT contains different subdirectories For example the present file as well as other descriptive files should be found in ABINIT Infos Other subdirectories will be described later 1 2 The sequential version of ABINIT abinis The main code exists in a sequential version with the name abinis ABINIT sequential and in a parallel version with the name abinip ABINIT parallel In the present new user s help file we will suppose that the sequential version is used After installation it is present in the package as ABINIT abinis To run abinis you need four things e Access to the executable abinis e An input file e A files file list of file names in a file 1 3 OTHER PROGRAMS IN THE ABINIT PACKAGE e A pseudopotential input file for each kind of element in the unit cell With these items a job can be run The full list of input variables all of which are provided in the single input file is given in the ABINIT input variables file The detailed description of
296. the lower and highest bands are significant Their occupation number is assumed to be 2 When nsppol is 2 spin polarized calculation the two first numbers give the lowest and highest bands for spin up and the third and fourth numbers give the lowest and highest bands for spin down Their occupation number is assumed to be 1 Presently bdband MUST be initialized by the user in case of Berry phase calculation the above mentioned default will cause an early exit 4 5 3 berryopt Mnemonics BERRY phase options Characteristic Variable type integer berryopt Default is 0 e 0 no computation of expressions relying on a Berry phase default e 1 gt the computation of Berry phases is activated berryphase routine e 2 gt the computation of derivatives with respect to the wavevector thanks to the Berry phase finite difference formula is activated uderiv routine e 3 gt same as option 1 and 2 together e 4 finite electric field calculation 125 4 5 GROUND STATE CALCULATION VARIABLES VARGS e 1 alternative computation of Berry phases berryphase_new routine e 2 alternative computation of derivatives with respect to the wavevector thanks to the Berry phase finite difference formula berryphase_new routine e 3 gt same as option 1 and 2 together The other related input variables are e in case of berryopt 1 2 or 3 bdberry and kberry also nberry must be larger than 0 e in case of berryop
297. the output variable boxcut is less than 2 boxcut is the smallest ratio of the fft box side to the planewave basis sphere diameter If this ratio is 2 or larger then e g the calculation of the Hartree potential from the charge density is done without approximation NOTE the values of ngfft 1 3 are chosen automatically by the code to give boxcut 2 if ngfft has not been set by hand At ratios smaller than 2 certain of the highest fourier components are corrupted in the convolution If the basis is nearly complete this fourier filter can be an excellent approximation In this case values of boxcut can be as small as about 1 5 without incurring significant error For a given ecut acell and rprim one should run tests for which ngfft is large enough to give boxcut j 2 and then one may try smaller values of ngfft if the results are not significantly altered See the descriptions of these variables above 5 If you are running calculations to relax or equilibrate structures i e with ionmov 1 and possibly vis 0 then the quality of your molecular dynamics or relaxation will be affected by the parameters amu dtion vis ntime tolmaf Clearly if you want a relaxed structure you must either run long enough or make repeated runs until the largest force in the problem output as fmax is smaller than what you will tolerate see tolmxf If dtion is too large for the given values of masses amu and viscosity vis then the molecular dynamics wil
298. the previous dataset must be taken which is a frequently occuring case However if the first dataset is treated 1 is equivalent to 0 since no dataset has yet been computed in the same run If another negative number it indicates the number of datasets to go backward to find the needed data once again going back beyond the first dataset is equivalent to using a null get variable NOTE that a non zero getocc MUST be used with occopt 2 so that the number of bands has to be initialized for each k point Of course these numbers of bands must be identical with the numbers of bands of the dataset from which occ will be copied The same is true for the number of k points 4 3 5 getscr Mnemonics GET SCReening the inverse dielectric matrix from Characteristic GW Variable type integer parameter Default is 0 Used when ndtset gt 0 multi dataset mode and optdriver 4 sigma step of a GW calculation to indicate that the dielectric matrix EPS file is to be taken from the output of a previous dataset It is used to chain the calculations since it describes from which dataset the OUTPUT dielectric matrix are to be taken as INPUT of the present dataset If getscr 0 no such use of previously computed output EPS file is done If getscr is positive its value gives the index of the dataset from which the output EPS file is to be used as input If getscr is 1 the output EPS file of the previous dataset must be taken
299. the required tolerance is reached Note that if the gap in the system closes e g due to defect formation or if the system is metallic in the first place the presently coded algorithm will be slower to converge than for insulating materials Convergence trouble during iterations usually signals closure of the gap The code will suggest to treat at least one unoccupied state or band in order to be able to monitor such a closure For self consistent calculations iscf positive it is important to test the adequacy of the k point integration If symmetry is used then one usually tests a set of special point grids Otherwise one tests the addition of more and more k points presumably on uniform grids to ensure that a sufficient number has been included for good k point integration The parameter nkpt indicates how many k points are being used and their coordinates are given by kpt and kptnrm described above The weight given to each k point is provided 75 3 7 FINAL REMARKS by input variable wtk Systematic tests of k point integration are much more difficult than tests of the adequacy of the number of planewaves The difficulty I refer to is simply the lack of a very systematic method for generating k point grids for tests 4 It is possible to run calculations for which the fft box is not quite large enough to avoid aliasing error in fft convolutions An aliasing error or a fourier filter approximation is occurring when
300. third repetition factor resp This allows to generate 3D arrays of molecules with different rotation angles Not present in the dtset array no internal 4 4 10 objatr objbtr Mnemonics OBJect A TRanslations OBJect B TRanslations Characteristic GEOMETRY BUILDER NO INTERNAL LENGTH Variable type real arrays objatr 3 4 and objbtr 3 4 Default is 12 0 0d0 no translation Give for each object the vectors of translations in cartesian coordinates to be applied to the corresponding object By default given in bohr atomic units 1 bohr 0 5291772083 A although Angstrom can be specified if preferred since these variables have the LENGTH characteristics The translation is applied after the rotation 121 4 4 GEOMETRY BUILDER SYMMETRY RELATED VARIABLES VARGEO The first vector objatr 3 1 and objbro 3 1 gives the translation to be applied to the first instance of the object The second third or fourth component resp gives the increment of translation from one instance to the next instance defined by the first second or third repetition factor resp This allows to generate 3D arrays of molecules In general when the objects are repeated a translation vector must be given since otherwise the repeated objects pack in the same region of space As an exception one can have a set of molecules regularly spaced on a circle in which case only rotations are needed Not present in the dtset array no internal
301. this dataset Each of these phases is now described in more details The code reports e the real and reciprocal space translation vectors Note the definition of the reciprocal vector is such that R G delta e the volume of the unit cell e the ratio between linear dimension of the FFT box and the sphere of plane waves called boxcut e It must be above 2 for exact treatment of convolutions by FFT ngfft has been automatically chosen to give a boxcut value larger than 2 but not much larger since more CPU time is needed for larger FFT grids e the code also mention that for the same FFT grid you might treat slightly larger ecut so with a rather small increase of CPU time e the heading for each pseudopotential which has been input e from the inwffil subroutine a description of the wavefunction initialization random num ber initialization or input from a disk file that is a report of the number of planewaves npw in the basis at each k point e from the setup2 subroutine the average number of planewaves over all k points is reported in two forms arithmetic average and geometric average Until here the output of a ground state computation is identical to the one of a response function calculation See the respfn_help document for the latter especially section 6 2 Next the code reports information for each SCF iteration e the iteration number e the total energy Etot in Hartree 67 3
302. tics 0 001 Ha 27 2113961 meV 315 773 Kelvin With occopt 7 one has also to specify an independent broadening tsmear 4 5 50 symafm Mnemonics SYMmetries Anti FerroMagnetic characteristics Characteristic Variable type integer array symafm nsym Default is nsym 1 In case the material is magnetic well this is only interesting in the case of antiferromagnetism additional symmetries might appear that change the sign of the magnetisation They have been introduced by Shubnikov 1951 They can be used by ABINIT to decrease the CPU time by using them to decrease the number of k points symafm should be set to 1 for all the usual symmetry operations that do not change the sign of the magnetisation while it should be set to 1 for the magnetisation changing symmetries If the symmetry operations are not specified by the user in the input file that is if nsym 0 then ABINIT will use the values of spinat to determine the content of symafm 4 5 51 timopt Mnemonics TIMing OPTion Characteristic NO MULTI DEVELOP Variable type integer parameter Default is 1 for sequential code 2 for parallel code This input variable allows to modulate the use of the timing routines 142 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST e If 0 as soon as possible suppresses all calls to timing routines e If 1 usual timing behaviour with short analysis appropriate for sequential execution e If 2 gt close to
303. timopt 1 except that the analysis routine does not time the timer appro priate for parallel execution e If 1 gt a full analysis of timings is delivered e If 2 a full analysis of timings is delivered except timing the timer 4 5 52 tphysel Mnemonics Temperature PHYSical of the ELectrons Characteristic ENERGY Variable type real parameter Default is 0 00 Gives in Hartree the physical temperature of the system in case occopt 4 5 6 or 7 Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY char acteristics 0 001 Ha 27 2113961 meV 315 773 Kelvin One has to specify an independent broadening tsmear The combination of the two parameters tphysel and tsmear is described in a paper by M Verstraete and X Gonze Phys Rev B 2002 Note that the signification of the entropy is modified with respect to the usual entropy The choice has been made to use tsmear as a prefactor of the entropy to define the entropy contribution to the free energy 4 5 53 tsmear Mnemonics Temperature of SMEARing Characteristic ENERGY Variable type real parameter Default is 0 04 Gives the broadening of occupation numbers occ in the metallic cases occopt 3 4 5 6 and 7 Can be specified in Ha the default eV Ry or Kelvin since tsmear has the ENERGY characteristics 0 001 Ha 27 2113961 meV 315 773 Kelvin Default is 0 04 Ha This should be OK for a free electron metal like Al
304. tions in the process of the calculation 65 3 4 THE PSEUDOPOTENTIAL FILES e tmp STATUS gives the status of advancement of the calculation and is updated very frequently psp1 filename of first pseudopotential input file The pseudopotential data files are formatted There must be as many filenames provided sequentially here as there are types of atoms in the system and the order in which the names are given establishes the identity of the atoms in the unit cell psp2 psp3 If you follow the tutorial you should go back to the tutorial window now 3 4 The pseudopotential files The following section describes the file structure used for the pseudopotential files with different formats Actually no real understanding of these files is needed to run the code but for different other reasons it might be useful to be able to understand the file structures Different format are possible labelled 1 to 6 presently The associated internal variable is called pspcod Example of use are found in ABINIT Test_v1 Informations on the file structure can be found in the ABINIT Infos Psp_infos directory e pspcod 1 Troullier Martins pseudopotentials generated by D C Allan and A Khein see ABINIT Infos Psp_infos psp1 info pspcod 2 Goedecker Teter Hutter GTH pseudopotentials See Phys Rev B 54 1703 1996 if needed e pspcod 3 Hartwigsen Goedecker Hutter pseudopotentials See Phys Rev B 58 3641 1998 if
305. to 0 or 2 In case fband is 0 0d0 the code computes from the pseudopotential files and the geometry data contained in the input file the number of electrons present in the system Then it computes the minimum number of bands that can accomodate them and use that value for nband In case fband differs from zero other bands will be added just larger than fband times the number of atoms This parameter is not echoed in the top of the main output file but only the parameter nband that it allowed to compute It is also not present in the dtset array no internal The default values are chosen such as to give naturally some conduction bands This improves the robustness of the code since this allows to identify lack of convergence coming from near degeneracies at the Fermi level In the metallic case the number of bands generated might be too small if the smearing factor is large The occupation numbers of the higher bands should be small enough such as to neglect higher bands It is difficult to automate this so a fixed default value has been chosen 4 5 20 fixmom Mnemonics FIX the magnetic MOMent Characteristic Variable type real parameter Default is 99 99 This input variable is active only in the nsppol 2 case If fixmom is not the magic value of 99 99 the magnetic moment of the system will be fixed to the value of fixmom Otherwise the magnetic moment will be determined self consistently by having the same spin up and
306. to make a single input file that will do all the associated operations You should try to use 2 datasets try to combine ABINIT Tutorial t13 in with ABINIT Tutorial t15 in Do not try to have the same position of the H atom as one of the Hz atoms in the optimized geometry The input file ABINIT Tutorial t21 in is an example of file that will do the job while ABINIT Tutorial Refs t21 o0ut is an example of output file You might use ABINIT Tutorial t2x files as files file do not forget to modify it although it does not differ from ABINIT Tutorial tix files The run should take less than one minute You should obtain the values etotali 1 1058360629E 00 etotal2 4 7010531340E 01 and xcarti 7 6091430410E 01 0 0000000000E 00 0 0000000000E 00 7 6091430410E 01 0 0000000000E 00 0 0000000000E 00 These are similar to those determined in lesson 1 although they have been obtained in one run You can also check that the residual forces are lower than 5 0 x 1074 Convergence issues are discussed in section 7 of the abinis_help file By the way you have read all the most important parts of the abinis_help file You are missing the sections 2 5 8 You are also missing the description of many input variables We suggest that you finish to read entirely the above mentioned sections of the abinis_help file now while the knowledge of the input variables will come in the long run 2 Many convergence parameters have been already i
307. total61 etotal62 xcart11 xcart12 xcart21 xcart22 xcart31 xcart32 xcart41 xcart42 xcart51 xcart52 xcart61 xcart62 1058360629E 00 7010531340E 01 1218715957E 00 7529731218E 01 1291943792E 00 7773586216E 01 1326879404E 00 1899907995E 01 1346739190E 00 1972721394E 01 1359660026E 00 8022016187E 01 6091430410E 01 6091430410E 01 0000000000E 00 5104996718E 01 5104996718E 01 OOO0000000E 00 3977137323E 01 3977137323E 01 0000000000E 00 3304297557E 01 3304297557E 01 0000000000E 00 3001593298E 01 3001593298E 01 0000000000E 00 2955932741E 01 2955932741E 01 0000000000E 00 0 0 0 0 0 0 0 0 0 O 0 0 0 0 0 0 0 0 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 OO OO OO O O OO OO OOO Om One 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 0000000000E 00 The corresponding atomization energies and interatomic distances are ecut Ha 10 15 20 25 30 35
308. trlen The generation of lists of k point sets is done in different test cases in the directory Test_v2 You can directly have a look at the output files in ABINIT Test_v2 Refs the output files for the tests 61 to 73 When one begins the study of a new material it is strongly advised to examine first the list of k points grids and select at least three efficient ones for the k point convergence study Do not forget that the CPU time will be linearly proportional to the number of k points to be treated using 10 k points will take five more time than using 2 k points Even for a similar accuracy of the Brillouin zone integration about the same value of kptrlen it might be easy to generate a grid that will fold to 10 k in the irreducible Brillouin zone as well as one that will fold to 2 k points in the irreducible Brillouin zone The latter is clearly to be preferred 2 3 3 Actually performing the convergence study with respect to k points In order to understand k point grids you should read the Monkhorst and Pack paper Phys Rev B 13 5188 1976 Well maybe not immediately In the meantime you can try the above mentioned convergence study The input file ABINIT Tutorial t33 in is an example while ABINIT Tutorial Refs t33 out is a reference output file In this output file you should have a look at the echo of input 22 CHAPTER 2 TUTORIAL variables As you know these are preprocessed and in particular
309. ts uses This is allowed although its meaning is no longer related to a maximal expected scaling Setting dilatmx to a large value leads to waste of CPU time and memory Supposing you think that the optimized acell values might be 10 larger than your input values use simply dilatmx 1 1 This will already lead to an increase of the number of planewaves by a factor 1 1 3 1 331 and a corresponding increase in CPU time and memory It is possible to use dilatmx when optcell 0 but a value larger than 1 0 will be a waste Must be 1 0 for RF calculations 4 11 4 dtion Mnemonics Delta Time for IONs Characteristic Variable type real parameter Default is 100 Used for controlling ion time steps If ionmov is set to 1 6 or 7 then molecular dynamics is used to update atomic positions in response to forces The parameter dtion is a time step in atomic units of time One atomic time unit is 2 418884e 17 seconds which is the value of Planck s constant in hartree sec In this case the atomic masses in amu given in array amu are used in Newton s equation and the viscosity for ionmov 1 and number of time steps are provided to the code using input variables vis and ntime The code actually converts from masses in amu to masses in atomic units in units of electron masses but the user enters masses in amu The conversion from amu to atomic units electron masses is 1822 88851 electron masses amu A typical good value f
310. uage 2 CML2 file s one per dataset Unlike most of the other input variables it refers to a character string e g cmlfile t67 in_CML xml The file is preprocessed and the relevant information is translated in order to be used as an alternative to the usual input variables Note that the input variables directly defined in the usual input file have precedence over the CML data the latter are used only when there is no occurence of the corresponding keyword in the input file The ABINIT CML parser is still quite primitive The mechanism followed to parse the CML file is described afterwards The ABINIT CML parser will localize in the CML file the first occurence of a molecule markup section It will ignore all other occurences of molecule Inside this molecule section it will localize the first occurences of the crystal symmetry and atomArray sections All other occurences and all other sections are ignored The following ABINIT input variables will be extracted from these sections of the CML file if the data is available 999 6699 9 e acell from the first scalar title a scalar title b and scalar c sections all three must be present if one is present in the crystal section expecting the data in Angstrom 106 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 99 6 9 e angdeg from the first scalar title alpha
311. ue of ecut Here log refers to a natural base e logarithm Since Etotal is an energy dedlnn is also an energy Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY characteristics 1 Ha 27 2113961 eV dedlnn is used to compute the Pulay correction to the stress tensor using correction 1 ucvol dedlnn See the discussion on the stress tensor given below 95 4 2 DEVELOPPEMENT VARIABLES VARDEV This value must be computed independently by making several runs at fixed geometry and variable ecut generally within 3 of the desired ecut and using the Etotal npw data to compute the derivative NOTE ABINIT computes the stress tensor whenever a self consistent energy run is performed but the values along the diagonal of the stress tensor can have large systematic errors unless a user provided value of dedlnn is input so that the appropriate Pulay correction to the diagonal stress tensor is computed An alternative and more elegant way to correct these systematic errors is provided through the use of the ecutsm input variable 4 2 4 densty Mnemonics initial DENSity for each TYpe of atom Characteristic DEVELOP Variable type real array densty ntypat Default is 0 0d0 Gives a rough description of the initial GS density for each type of atom This value is only used to create the first exchange and correlation potential and is not used anymore afterwards For the time being it cor
312. ugh estimation of the dielectric gap between the highest energy level computed in the run and the set of bands not represented Used to extrapolate dielectric matrix when iprcel gt 21 Can be specified in Ha the default Ry eV or Kelvin since ecut has the ENERGY charac teristics 1 Ha 27 2113961 eV No meaning for RF calculations yet 4 5 12 dielam Mnemonics Dlelectric matrix LAMbda Characteristic DEVELOP Variable type real parameter between 0 and 1 Default dielam is 0 5 Gives the amount of occupied states with mean energy given by the highest level computed in the run included in the extrapolation of the dielectric matrix Used when iprcel gt 21 No meaning for RF calculations yet 4 5 13 dielng Mnemonics model DIElectric screening LeNGth Characteristic Variable type real parameter Default is 1 0774841d0 bohr for historical reasons Used for screening length in bohr of the model dielectric function diagonal in reciprocal space By default given in bohr atomic units 1 bohr 0 5291772083 A although Angstrom can be specified if preferred since dielng has the LENGTH characteristics 128 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST This model dielectric function is as follows 1 dielng K 1 diemac dielng K diemix diel K The inverse of this model dielectric function will be applied to the residual to give the precon ditioned change of potential Rig
313. ulation we choose as a perturbation the displacement of the Al atom along the first axis of the reduced coordinates You can copy the file ABINIT Tutorial t52 inin Work5 This is your input file You should edit it and briefly look at the two changes with respect to the file ABINIT Tutorial t51 in the change of zred and the reading of the wavefunction file using the irdwfk input variable Then you can make the run The symmetry is lowered with respect to the ground state geometry so that the number of k points increases a lot and of course the CPU time about one minute on a PIII 450 MHz From this run it is possible to get the values of the total energy and the value of the gradient of the total energy with respect to change of reduced coordinate rms dE dt 3 5517E 03 max dE dt 5 0079E 03 dE dt below all hartree 1 0 005007930232 0 002526304574 0 002526304574 2 0 005007868293 0 002526274885 0 002526274885 Ewald 8 47988991313938E 00 resulting in Etotal 9 76268124105590E 00 hartree The change of reduced coordinate of the Al atom along the first axis was rather small 1 1000 and we can make an estimate of the second derivative of the total energy with respect to the reduced coordinate thanks to finite difference formulas 33 2 5 LESSON 5 DYNAMICAL AND DIELECTRIC PROPERTIES OF ALAS We start first from the total energy difference The total energy is symmetric with re spect to that perturbation so that it has
314. ump of total energy because there might be two or even three possible values of the Fermi energy and the bissection algorithm find one or the other 4 1 21 rprim Mnemonics Real space PRIMitive translations Characteristic EVOLVING if ionmov 2 and optcell 4 0 Variable type real array rprim 3 3 Default 3x3 unity matrix Give in columnwise entry the three dimensionless primitive translations in real space If the Default is used that is rprim is the the unity matrix the three dimensionless primitive vectors are three unit vectors in cartesian coordinates Each will be multiplied by the corresponding acell value to give the dimensional primitive vectors called rprimd In the general case the dimensional cartesian coordinates of the crystal primitive translations R1p R2p and R3p see rprimd are Rip i rprim i 1 acell 1 for i 1 2 3 x y and z R2p i rprim i 2 acel1 2 for i 1 2 3 R3p i rprim i 3 acel1 3 for i 1 2 3 The rprim variable is thus used to define directions of the primitive vectors that will be multiplied by the appropriate length scale acell 1 acell 2 or acell 3 respectively to give the dimensional primitive translations in real space in cartesian coordinates Presently it is requested that the mixed product R1xR2 R3 is positive If this is not the case simply exchange a pair of vectors To be more specific rprim 1 2 3 4 5 6 7 8 9 corresponds to input of the three primitive translations R1 1 2 3 R2
315. up but the problem with the preconditioner is more embarrassing One could use an effective dielectric constant of about 3 or 5 with a rather small mixing coefficient on the order of 0 2 However there is also another possibility using an estimation of the dielectric matrix governed by prcel 45 For comparison with the previous treatment of SCF one can recompute the result with 3 aluminum layers The input file ABINIT Tutorial t47 inis an example while ABINIT Tutorial Refs t47 out is a reference output file This run might take a few minutes and is the longer of the tutorial You should start it now You can monitor its evolution by editing from time to time the t47_STATUS file that the code updates regularly The status file that refer to the skeleton of the code is described in the ABINIT Infos Notes_for_coding programmer_guide You might take advantage of the time of the run to explore the files contained in the ABINIT Infos directory and the ABINIT Infos Notes_for_coding directory The README files provided interesting entry points in the documentation of the code Coming back to the file t47 out You will notice that the SCF convergence is now excellent for all the cases 3 4 or 5 metal layers For the 3 aluminum layer case one has the non relaxed total energy ETOT 7 6 2539524354404 this quantity is converged unlike in test 4 6 giving the unrelaxed surface energy 0 0200 Ha 0 544 eV and for the relaxed c
316. vailable in a Reviews of Modern Physics article Iterative minimization techniques for ab initio total energy calculations molecular dynamics and conjugate gradients M C Payne M P Teter D C Allan T A Arias and J D Joannopoulos Rev Mod Phys 64 1045 1097 1992 This paper does NOT reflect the present status of the code ABINIT is closer in spirit to the paper of of Kresse and Furthmuller see the bibliography list except that it does not use ultrasoft pseudopotentials and that response functions have been implemented in ABINIT 3 2 The input file 3 2 1 Format of the input file Note that this input file was called ab_in in the example of section 1 1 We first explain the content of the input file without use of the multi dataset possibility that will be explained in section 3 3 The parameters are input to the code from a single input file Each parameter value is provided by giving the name of the input variable and then placing the numerical value s beside the name separated by one or more spaces Depending on the input variable the numerical value may be an integer or a real number internal representation as double precision number and may actually represent an array of values If it represents an array the next set of numbers separated by spaces are taken as the values for the array Do NOT separate a minus sign from the number to which it applies Do NOT use tabs NOTE THAT NO LINE OF THE INPUT FILE
317. very next iteration This functions because the program closes and reopens the input file on every iteration and checks the top line for the keyword exit THE WORD MUST BE PLACED WITH SPACES BLANKS ON BOTH SIDES Thus placing exit on the top line of the input file WHILE THE JOB IS ALREADY RUNNING will force the job to end smoothly on the very next iteration On some machines this does not work always we do not know why Another possibility is offered one can create a file named abinit exit in the directory where the job was started The code should also smoothly end In both cases the stop is not immediate It can take a significant fraction about 20 at most of one SCF step to execute properly the instruction still needed If you follow the tutorial you should go back to the tutorial window now 3 2 3 The multi dataset mode Until now we have assumed that the user wants to make computations corresponding to one set of data for example determination of the total energy for some geometry with some set of plane waves and some set of k points It is often needed to redo the calculations for different values of some parameter letting all the other things equal As typical examples we have convergence studies needed to determine which cut off energy gives the needed accuracy In other cases one makes chains of calculations in order to compute the band structure first a self consistent calculation of the density and potentia
318. which is a frequently occuring case If getscr is a negative number it indicates the number of datasets to go backward to find the needed file In this case if one refers to a non existent data set prior to the first the EPS file is not initialised from a disk file so that it is as if getscr 0 for that initialisation 108 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 3 6 getwfk Mnemonics GET the wavefunctions from _WFK file 4 3 7 getwfq Mnemonics GET the wavefunctions from _WFQ file 4 3 8 getlwf Mnemonics GET the first order wavefunctions from _1WF file 4 3 9 getddk Mnemonics GET the ddk wavefunctions from _1WF file Characteristic Variable type integer parameter Default is 0 Eventually used when ndtset gt 0 in the multi dataset mode to indicate starting wavefunc tions as an alternative to irdwfk irdwfq irdlwf or irdddk One should first read the explanations given for these latter variables The getwfk getwfq getlwf and getddk variables are typically used to chain the calculations in the multi dataset mode since they describe from which dataset the OUTPUT wavefunctions are to be taken as INPUT wavefunctions of the present dataset We now focus on the getwfk input variable the only one used in ground state calculations but the rules for getwfq and getlwf are similar with WFK replaced by WFQ or _1WF If getwfk 0 no use of previously computed output wavefunction file appen
319. with itself Usually even twice the value of ecutwfn might overkill In any case a convergence study is worth This set of planewaves can also be determined by the other input variables npweps and nsheps but these are much less convenient to use for general systems than the selection criterion based on a cut off energy 144 CHAPTER 4 MAIN ABINIT CODE INPUT VARIABLES COMPLETE LIST 4 6 3 ecutsigx Mnemonics Energy CUT off for MAT Characteristic GW Variable type real Default 0 0 Only relevant if optdriver 4 that is GW calculations This input variable was named ecut mat prior to v4 3 ecutsigx determines the cut off energy of the planewave set used to generate the exchange part of the self energy operator This set of planewaves can also be determined by the other input variables npwsigx and nshsigx but these are much less convenient to use for general systems than the selection criterion based on the cut off energy 4 6 4 ecutwfn Mnemonics Energy CUT off for WaveFunctions Characteristic GW Variable type real Default 0 0 Only relevant if optdriver 3 or 4 that is GW calculations ecutwfn determines the cut off energy of the planewave set used to represent the wavefunctions in the formula that generates the independent particle susceptibility xe for optdriver 3 or the self energy for optdriver 4 Usually ecutwfn is smaller than ecut so that the wavefunctions are filtered and some com
320. with non analyticity in the direction cartesian coordinates 0 00000 0 00000 1 00000 Phonon energies in Hartree 2 590723E 06 2 610339E 06 4 088540E 06 1 568560E 03 1 568560E 03 1 729575E 03 Phonon frequencies in cm 1 5 685980E 01 5 729031E 01 8 973308E 01 3 442590E 02 3 442590E 02 3 795979E 02 The first few lines discard any effect of the homogeneous electric field while the next sections consider it along the three Cartesian coordinates In the present material the directionality of the electric field has no influence We note that there are still three acoustic mode below 1 cm7 while the optic modes have the correct degeneracies two TO modes at 344 3 cm and one LO mode at 379 6 cm These values can be compared to experimental 361 cm 402 cm as well as theoretical 363 cm 400 cm values again the Gianozzi et al paper mentioned above Most of the discrepancy comes from the too low value of ecut Using ABINIT with ecut 6 Hartree gives 358 8 cm 389 8 cm The remaining of the discrepancy may come partly from the pseudopotentials that are particularly soft The comparison of Born effective charges is also interesting After imposition of the neutrality sum rule the Al Born effective charge is 2 116 The value from Gianozzi et al is 2 17 the experimental value is 2 18 Increasing ecut to 6 Hartree in ABINIT gives 2 168 For the dielectric tensor it is more delicate The value from Gianozzi et al is 9 2 whil
321. ysical grounds For metals simply put diemac to a very large value the default 106 is OK For silicon use 12 0 A similar value is likely to work well for other semiconductors For wider gap insulators use 2 0 4 0 For molecules in an otherwise empty big box try 1 5 3 0 Systems that combine a highly polarisable part and some vacuum are rather badly treated by the present version of ABINIT You have to experiment a bit to find the best diemac If you let diemac to its default value you might even never obtain the self consistent convergence For response function calculations use the same values as for GS The improvement in speed can be considerable for small but non zero values of the wavevector 4 5 15 diemix Mnemonics model DIElectric MIXing factor Characteristic Variable type real parameter Default is 1 0 Gives overall factor of the preconditioned residual potential to be transferred in the SCF cycle It should be between 0 0 and 1 0 If the model dielectric function were perfect diemix should be 1 0 By contrast if the model dielectric function does nothing when diemac 1 0d0 or dielng is larger than the size of the cell diemix can be used to damp the amplifying factor inherent to the SCF loop For molecules a value on the order 0 5 or 0 33 is rather usual 129 4 5 GROUND STATE CALCULATION VARIABLES VARGS When iscf 3 or iscf 5 diemix is only important at the few first iterations when anharmonic e

ABINIT The user's manual - Université catholique de Louvain

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ABINIT The user's manual - Universit&eacute; catholique de Louvain

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ABINIT The user's manual - Université catholique de Louvain