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User's Guide for Quantum ESPRESSO

1. This problem is usually more severe for GGA than with LDA because the GGA functionals have functional forms that vary more strongly with the position particularly so for isolated molecules or system with significant portions of vacuum because in the exponential tail of the charge density a the finite cutoff hence there is an effect due to cutoff induces oscillations in rho and b the reduced gradient is diverging info by Stefano de Gironcoli June 2008 ph x yields really lousy phonons with bad or negative frequencies or wrong sym metries or gross ASR violations Possible reasons 69 e if this happens only for acoustic modes at q 0 that should have w 0 Acoustic Sum Rule violation see the item before this one e wrong data file read e wrong atomic masses given in input will yield wrong frequencies but the content of file fildyn should be valid since the force constants not the dynamical matrix are written to file e convergence threshold for either SCF conv_thr or phonon calculation tr2_ph too large try to reduce them e maybe your system does have negative or strange phonon frequencies with the approx imations you used A negative frequency signals a mechanical instability of the chosen structure Check that the structure is reasonable and check the following parameters The cutoff for wavefunctions ecutwfc For USPP the cutoff for the charge density ecutrho The k point grid especially
2. iotk an Input Output Toolkit BLAS and LAPACK Finally several additional packages that exploit data produced by QUANTUM ESPRESSO or patch some QUANTUM ESPRESSO routines can be installed as plug ins Wannier90 maximally localized Wannier functions http www wannier org writ ten by A Mostofi J Yates Y S Lee WanT quantum transport properties with Wannier functions http www wannier transport org originally written by A Ferretti A Calzolari and M Buongiorno Nardelli YAMBO electronic excitations within Many Body Perturbation Theory GW and Bethe Salpeter equation http www yambo code org originally written by A Marini PLUMED calculation of free energy surface through metadynamics M Bonomi et al Comp Phys Comm 180 1961 2009 http merlino mi infm it plumed PLUMED GIPAW Gauge Independent Projector Augmented Waves NMR chemical shifts and EPR g tensor written by Davide Ceresoli Univ Oxford Emine Kucukbenli SISSA Ari Seitsonen Univ Zurich Uwe Gerstmann Francesco Mauri Univ Paris VI Available at http qe forge org frs group_id 37 see also http www gipaw net This guide documents PWscf NEB CP PHonon PostProc The remaining packages have sepa rate documentation The QUANTUM ESPRESSO codes work on many different types of Unix machines in cluding parallel machines using both OpenMP and MPI Message Passing Interface Running QUANTUM ESPRESSO on Mac OS X and MS Windows i
3. t at least plain DFT GGA and the like If you are still convinced that it is see above Is there a converter from format XYZ to UPF What is available no warranty is in directory upftools You are most welcome to contribute a new converter 12 4 Input data A large percentage of the problems reported to the mailing list are caused by incorrect input data Before reporting a problem with strange crashes or strange results please have a look at your structure with XCrySDen XCrySDen can directly visualize the structure from both PWscf input data xcrysden pwi input data file and from PWscf output as well xcrysden pwo output file Unlike most other visualizers XCrySDen is periodicity aware you can easily visualize period ically repeated cells You are advised to always use XCrySDen to check your input data 72 Where can I find the crystal structure atomic positions of XYZ The following site contains a lot of crystal structures http cst www nrl navy mil lattice Since this seems to come up often I d like to point out that the American Mineralogist Crystal Structure Database http rruff geo arizona edu AMS amcsd is another excellent place to find structures though you will have to use it in conjunction with the Bilbao crystallography server http www cryst ehu es and have some understanding of space groups and Wyckoff positions See also http cci 1b1 gov cctbx index html My crystal has a H
4. 13 ia32 Intel 32 bit machines x86 running Linux ia64 Intel 64 bit Itanium running Linux x86_64 Intel and AMD 64 bit running Linux see note below aix IBM AIX machines solaris PC s running SUN Solaris sparc Sun SPARC machines crayxt4 Cray XT4 5 machines macppc Apple PowerPC machines running Mac OS X mac686 Apple Intel machines running Mac OS X cygwin MS Windows PCs with Cygwin necsx NEC SX 6 and SX 8 machines ppc64 Linux PowerPC machines 64 bits ppc64 mn as above with IBM xlf compiler ppc64 bg IBM BlueGene Note x86_64 replaces amd64 since v 4 1 Cray Unicos machines SGI machines with MIPS architecture HP Compaq Alphas are no longer supported since v 4 3 2 Finally configure recognizes the following command line options enable parallel compile for parallel execution if possible default yes enable openmp compile for openmp execution if possible default no enable shared use shared libraries if available default yes disable wrappers disable C to fortran wrapper check default enabled enable signals enable signal trapping default disabled and the following optional packages with internal blas compile with internal BLAS default no with internal lapack compile with internal LAPACK default no with scalapack use ScaLAPACK if available default yes enable exx compile enabling the use of hybrid functionals exact exchange If you want to modify the configure script advanced users o
5. What are the units for quantity XYZ Unless otherwise specified all PWscf input and output quantities are in atomic Rydberg units i e energies in Ry lengths in Bohr radii etc Note that CP uses instead atomic Hartree units energies in Ha lengths in Bohr radii 74 Self consistency is slow or does not converge at all In most cases your input data is bad or else your system is metallic and you are treating it as an insulator If this is not the case reduce mixing beta to 0 3 0 1 or smaller try the mixing mode value that is more appropriate for your problem What is the difference between total and absolute magnetization The total mag netization is the integral of the magnetization in the cell Mr ice Nason ar The absolute magnetization is the integral of the absolute value of the magnetization in the cell Ma J ep E In a simple ferromagnetic material they should be equal except possibly for an overall sign In simple antiferromagnets like FeO NiO Mr is zero and M4 is twice the magnetization of each of the two atoms info by Stefano de Gironcoli How can I calculate magnetic moments for each atom There is no right way of defining the local magnetic moment around an atom in a multi atom system However an approximate way to define it is via the projected density of states on the atomic orbitals code projwfc x see example08 for its use as a postprocessing tool This code generate many
6. and is based on his GUIB concept http www k3 ijs si kokalj guib e atomic was written by Andrea Dal Corso and it is the result of many additions to the original code by Paolo Giannozzi and others Lorenzo Paulatto wrote the PAW extension iotk http www s3 infm it iotk was written by Giovanni Bussi SISSA XSPECTRA was written by Matteo Calandra Univ Paris VI and collaborators VON was contributed by Huy Viet Nguyen SISSA GWW was written by Paolo Umari and Geoffrey Stenuit Democritos QHA and PlotPhon were contributed by Eyvaz Isaev Moscow Steel and Alloy Inst and Linkoping and Uppsala Univ TD DFPT written by Stefano Baroni SISSA Ralph Gebauer ICTP Baris Malcioglu Dario Rocca Brent Walker Other relevant contributions to QUANTUM ESPRESSO Minoru Otani AIST Yoshio Miura Tohoku U Nicephore Bonet MIT Nicola Marzari Univ Oxford Brandon Wood LLNL Tadashi Ogitsu LLNL contributed Effective Screening Method PRB 73 115407 2006 Brian Kolb and Timo Thonhauser Wake Forest University implemented the vdW DF and vdW DF2 functionals with support from Riccardo Sabatini and Stefano de Gironcoli SISSA and DEMOCRITOS Andrea Ferretti Univ Oxford contributed the qexml and sumpdos utility helped with file formats and with various problems Hannu Pekka Komsa CSEA Lausanne contributed the HSE functional Dispersions interaction in the framework of DFT D were contributed by Daniel Forrer
7. are provided only for PWgui Stable releases of the QUANTUM ESPRESSO source package current version is 4 3 2 can be downloaded from this URL http www quantum espresso org download php Uncompress and unpack the core distribution using the command tar zxvf espresso X Y Z tar gz a hyphen before zxvf is optional where X Y Z stands for the version number If your version of tar doesn t recognize the a flag gunzip c espresso X Y Z tar gz tar xvf 10 A directory espresso X Y Z will be created Given the size of the complete distribution you may need to download more packages and to unpack them following the same procedure they will unpack into the same directory Plug ins such as YAMBO or PLUMED should instead be downloaded into subdirectory archive but NOT UNPACKED OR UNCOMPRESSED command make will take care of this during in stallation GIPAW is automatically downloaded from http qe forge org frs group_id 37 and compiled by typing make gipaw from the main espresso directory Occasionally patches for the current version fixing some errors and bugs may be distributed as a diff file In order to install a patch for instance cd espresso X Y Z patch p1 lt path to the diff file patch file diff If more than one patch is present they should be applied in the correct order Daily snapshots of the development version can be downloaded from the developers site qe forge org follow the link
8. hey are independent of the system size but dependent on the size of the augmentation charge an atomic property that doesn t vary that much for different systems and on the real space resolution needed by augmentation charges rule of thumb ecutrho is between 6 and 12 times ecutwfc The small boxes should be set as small as possible but large enough to contain the core of the largest element in your system The formula for estimating the box size is quite simple nrib 2R L x nri and the like where Reut is largest cut off radius among the various atom types present in the system L is the physical length of your box along the x axis You have to round your result to the nearest larger integer In practice nr1b etc are often in the region of 20 24 28 testing seems again a necessity The core charge is in principle finite only at the core region as defined by some Rreut and vanishes out side the core Numerically the charge is represented in a Fourier series which may give rise to small charge oscillations outside the core and even to negative charge density but only if the cut off is too low Having these small boxes removes the charge oscillations problem at least outside the box and also offers some numerical advantages in going to higher cut offs info by Nicola Marzari 10 Performances 10 1 Execution time Since v 4 2 QUANTUM ESPRESSO prints real wall time instead of CPU time The following is a rough estimate o
9. 00 0 00000 1 The two main parameters are force pairing true which forces the paired electrons to be the same sic sic_mac which instructs the code to use Mauri s correction Remember to add an extra column in ATOMIC_POSITIONS with 1 to activate SIC for those atoms Warning This approach has known problems for dissociation mechanism driven by excess electrons Comment 1 Two parameters sic_alpha and sic_epsilon have been introduced follow ing the suggestion of M Sprik ICR 05 to treat the radical OH H2O In any case a complete ab initio approach is followed using sic_alpha 1 sic_epsilon 1 Comment 2 When you apply this SIC scheme to a molecule or to an atom which are neutral remember to add the correction to the energy level as proposed by Landau in a neutral system subtracting the self interaction the unpaired electron feels a charged system even if using a compensating positive background For a cubic box the correction term due to the Madelung energy is approx given by 1 4186 Lror 1 047 Lpor where Lu is the linear dimension of your box celldm 1 The Madelung coefficient is taken from I Dabo et al PRB 77 115139 2007 info by F Baletto francesca baletto kcl ac uk 9 4 2 ensemble DFT The ensemble DFT eDFT is a robust method to simulate the metals in the framework of ab initio molecular dynamics It was introduced in 1997 by Marzari et al 54 The specific subroutines
10. 2008 How do I calculate the work function Work function average potential in the vac uum Fermi Energy The former is estimated in a supercell with the slab geometry by looking at the average of the electrostatic potential typically without the XC part See the example in examples WorkF ct_example 128 Phonons Is there a simple way to determine the symmetry of a given phonon mode A symmetry analyzer was added in v 3 2 by Andrea Dal Corso Other packages that perform symmetry analysis of phonons and normal modes 76 ISOTROPY package http stokes byu edu iso isotropy html ACKJ ACMI packages http www cpc cs qub ac uk I am not getting zero acoustic mode frequencies why Because the Acoustic Sum Rule ASR i e the translational invariance is violated in approximated calculations In PW calculations the main and most irreducible violation comes from the discreteness of the FFT grid There may be other reasons though notably insufficient convergence Recently I found that the parameters tr2_ph for the phonons and conv_thr for the ground state can affect the quality of the phonon calculation especially the vanishing frequencies for molecules Info from Katalyn Gaal Nagy Anyway if the nonzero frequencies are small you can impose the ASR to the dynamical matrix usually with excellent results Nonzero frequencies for rotational modes of a molecule are a fictitious effect of the finite supercell size o
11. CO DEMOCRITOS DEmocritos MOdeling Center for Y Research In aTOmistic Simulation IOM User s Guide for QUANTUM ESPRESSO version 4 3 2 Contents 1 pt ed yas EE Oe ee ae 3 RN 4 1 3 SEET GT o mob a a a a aww dd bd ee 7 1 3 1 Guidelines for posting to the mailing bet 7 14 Terms Au 8 8 SL Download 20 4 4 4 4 4 4 aa e dee BG dee See AD eo hk oe as 8 de ee ee ee ee a ee ee ee 10 29 a AAN foe ee eu ee ee OE EES we eS 10 2 3 1 Manual configuration ge da ee eee ee bee eR PRE eR Eee oS 12 24 Libraries ce ross Be ee ew a e we hs we er ee me o a 13 2 4 1 If optimized libraries are not found 14 BEEN 14 pure aaa Bae e eee re E ee 17 de a o o 2h a a 19 2 7 1 AU architectures 2 2 aaa 19 ama ie ee eee ee See ee ee a 19 23 IPI reg si aa tpa rr Gee de Bod oe eee EEN a 20 2 7 4 IBM BlueGene e 20 2Co LINUX BOI oa ao AO Be aw ee Yaw YR aw Oe SEA eee a aa 20 2 7 6 Linux PC clusters with MPI aoaaa 23 2 017 Intel MacOSX e eieaa ee a a a a B 24 AI ee pe eee d e 25 2 Parallelism 26 E E hes oe Sag A 26 ia rad AA e A a 26 3 3 Parallelization levels o 27 3 3 1 Understanding parallel I O o o o 29 a a Bode ee a Br 30 32 AE e rd ra Bred a A oe ee 32 4 2 Data files a 33 kamen Olea Oot 33 A ec AAA A eee ee 34 5 Using PWscf 34 5 1 Electronic structure calculations lt i oa be seri 35 EE 36 5 3 Direct interface with CAS
12. CPU each copy lives in a different world with its own private set of data and communicates with other executables only via calls to MPI libraries MPI parallelization requires compilation for parallel execution linking with MPI libraries execution using a launcher program depending upon the specific machine The number of CPUs used is specified at run time either as an option to the launcher or by the batch queue system 2 OpenMP A single executable spawn subprocesses threads that perform in parallel spe cific tasks OpenMP can be implemented via compiler directives explicit OpenMP or via multithreading libraries library OpenMP Explicit OpenMP require compilation for OpenMP execution library OpenMP requires only linking to a multithreading version of mathematical libraries e g ESSLSMP ACML_MP MKL the latter is natively multi threading The number of threads is specified at run time in the environment variable OMP_NUM_THREADS MPI is the well established general purpose parallelization In QUANTUM ESPRESSO several parallelization levels specified at run time via command line options to the executable are implemented with MPI This is your first choice for execution on a parallel machine Library OpenMP is a low effort parallelization suitable for multicore CPUs Its effectiveness relies upon the quality of the multithreading libraries and the availability of multithreading FFTs If you are using MKL you may want to select
13. Padua Univ and Michele Pavone Naples Univ Federico II Filippo Spiga Univ Milano Bicocca contributed the mixed MPI OpenMP paralleliza tion The initial BlueGene porting was done by Costas Bekas and Alessandro Curioni IBM Zurich Gerardo Ballabio wrote the first configure for QUANTUM ESPRESSO Audrius Alkauskas IRRMA Uli Aschauer Princeton Simon Binnie Univ College London Guido Fratesi Axel Kohlmeyer UPenn Konstantin Kudin Princeton Sergey Lisenkov Univ Arkansas Nicolas Mounet MIT William Parker Ohio State Univ Guido Roma CEA Gabriele Sclauzero IRRMA Sylvie Stucki IRRMA Pascal Thibaudeau CEA Vittorio Zecca Federico Zipoli Princeton answered questions on the mailing list found bugs helped in porting to new architectures wrote some code An alphabetical list of further contributors includes Dario Alf Alain Allouche Francesco Antoniella Francesca Baletto Mauro Boero Nicola Bonini Claudia Bungaro Paolo Cazzato Gabriele Cipriani Jiayu Dai Cesar Da Silva Alberto Debernardi Gernot Deinzer Yves Ferro Martin Hilgeman Yosuke Kanai Nicolas Lacorne Stephane Lefranc Kurt Maeder Andrea Marini Pasquale Pavone Mickael Profeta Kurt Stokbro Paul Tangney Antonio Tilocca Jaro Tobik Malgorzata Wierzbowska Silviu Zilberman and let us apologize to everybody we have forgotten This guide was mostly written by Paolo Giannozzi Gerardo Ballabio and Carlo Cavazzoni wrote the section o
14. all pw_X in should be already present A detailed description of all NEB specific input variables is contained in files Doc INPUT_NEB See Example 17 A NEB calculation will produce a number of files in the current directory De in the directory were the code is run containing additional information on the minimum energy path The files are organized as following where prefix is specified in the input file prefix dat is a three column file containing the position of each image on the reaction co ordinate arb units its energy in eV relative to the energy of the first image and the residual error for the image in eV ap prefix int contains an interpolation of the path energy profile that pass exactly through each image it is computed using both the image energies and their derivatives prefix path information used by QUANTUM ESPRESSO to restart a path calculation its format depends on the input details and is undocumented prefix axsf atomic positions of all path images in the XCrySDen animation format to visu alize it use xcrysden axsf prefix axsf prefix xyz atomic positions of all path images in the generic xyz format used by many quantum chemistry softwares prefix crd path information in the input format used by pw x suitable for a manual restart of the calculation NEB calculation are a bit tricky in general and require extreme care to be setup correctly NEB also takes easily hundreds of iteration to converge of c
15. and trial and error Remember also that the convergence to the equilibrium positions depends on the energy threshold for the electronic GS in fact correct forces required to move ions toward the minimum are obtained only when electrons are in their GS Then a small threshold on forces could not be satisfied if you do not require an even smaller threshold on total energy Let us now move to case 2 randomization of positions If you have relaxed the system or if the starting system is already in the equilibrium po sitions then you need to displace ions from the equilibrium positions otherwise they will not move in a dynamics simulation After the randomization you should bring electrons on the GS again in order to start a dynamic with the correct forces and with electrons in the GS Then you should switch off the ionic dynamics and activate the randomization for each species specifying the amplitude of the randomization itself This could be done with the following amp IONS namelist amp ions ion_dynamics none tranp 1 TRUE tranp 2 TRUE amprp 1 0 01 amprp 2 0 01 In this way a random displacement of max 0 01 a u is added to atoms of species 1 and 2 All other input parameters could remain the same Note that the difference in the total energy etot between relaxed and randomized positions can be used to estimate the temperature that will be reached by the system In fact starting with zero ionic velo
16. compiler do I need to compile QUANTUM ESPRESSO Any non buggy or not too buggy fortran 95 compiler should work with minimal or no changes to the code configuremay not be able to recognize your system though Why is configure saying that I have no fortran compiler Because you haven t one really or maybe you have one but it is not in your execution path or maybe it has been given an unusual name by your system manager Install a compiler if you have none if you have one fix your execution path or define an alias if it has a strange name Do not pass an executable with the path as an argument to configure asine g configure F90 some strange f95 it doesn t work Why is configure saying that my fortran compiler doesn t work Because it doesn t work really more exactly configure has tried to compile a small test program and didn t succeed Your compiler may not be properly installed For Intel compiler on PC s you may have forgotten to run the required initialization script for the compiler See also above configure doesn t recognize my system what should I do If compilation linking works never mind otherwise try to supply a suitable supported architecture or and manually edit the make sys file Detailed instructions in Sec 2 2 Why doesn t configure recognize that I have a parallel machine You need a properly configured complete parallel environment If any piece is missing configure will revert to serial
17. defined in include c_defs h Note that QUANTUM ESPRESSO is self contained with the exception of MPI libraries for parallel compilation if system libraries are missing the problem is in your compiler library combination or in their usage not in QUANTUM ESPRESSO If you get mysterious errors in the provided tests and examples your compiler or your mathematical libraries or MPI libraries or a combination thereof is very likely buggy Al though the presence of subtle bugs in QUANTUM ESPRESSO that are not revealed during the testing phase can never be ruled out it is very unlikely that this happens on the provided tests and examples 2 7 2 Cray XT machines Use configure ARCH crayxt4 or else configurewill not recognize the Cray specific software environment Older Cray machines T3D T3E X1 are no longer supported 2 7 3 IBM AIX v 4 3 1 of the CP code Wannier function dynamics crashes with segmentation violation on some AIX v 6 machines Workaround compile it with mpx1f95 instead of mpx1f90 Info by Roberto Scipioni June 2011 On IBM machines with ESSL libraries installed there is a potential conflict between a few LAPACK routines that are also part of ESSL but with a different calling sequence The appearance of run time errors like ON ENTRY TO ZHPEV PARAMETER NUMBER 1 HAD 21 AN ILLEGAL VALUE is a signal that you are calling the bad routine If you have defined D ESSL you should load ESSL before LAPACK see variabl
18. for metallic systems Note that negative frequencies are actually imaginary the negative sign flags eigenvalues of the dynamical matrix for which w lt 0 Wrong degeneracy error in star_q Verify the q vector for which you are calculating phonons In order to check whether a symmetry operation belongs to the small group of q the code compares q and the rotated q with an acceptance tolerance of 10 set in routine PW eqvect f90 You may run into trouble if your q vector differs from a high symmetry point by an amount in that order of magnitude 12 Frequently Asked Questions FAQ 12 1 General If you search information on QUANTUM ESPRESSO the best starting point is the web site html www quantum espresso org See in particular the links learn for documentation contacts if you need somebody to talk with The mailing list pw_forum is the typical place where to ask questions about QUANTUM ESPRESSO 12 2 Installation Most installation problems have obvious origins and can be solved by reading error messages and acting accordingly Sometimes the reason for a failure is less obvious In such a case you should look into Bech 2 and into the pw_forum archive to see if a similar problem with solution is described If you get really weird error messages during installation look for them with your preferred Internet search engine such as Google very often you will find an explanation and a workaround 70 What Fortran
19. for specific questions about coding proposals offers of help etc send a message to the developers mailing list user q e developers address qe forge org 1 3 1 Guidelines for posting to the mailing list Life for subscribers of pw forum will be easier if everybody complies with the following guide lines e Before posting please browse or search the archives links are available in the Contacts page of the QUANTUM ESPRESSO web site http www quantum espresso org contacts php Most questions are asked over and over again Also make an attempt to search the available documentation notably the FAQs and the User Guide The answer to most questions is already there e Sign your post with your name and affiliation e Choose a meaningful subject Do not use reply to start a new thread it will confuse the ordering of messages into threads that most mailers can do In particular do not use reply to a Digest e Be short no need to send 128 copies of the same error message just because you this is what came out of your 128 processor run No need to send the entire compilation log for a single error appearing at the end e Avoid excessive or irrelevant quoting of previous messages Your message must be imme diately visible and easily readable not hidden into a sea of quoted text e Remember that even experts cannot guess where a problem lies in the absence of sufficient information e Remember that the mai
20. for the eDFT are in CPV ensemble_dft 90 where you define all the quantities of interest The subroutine CPV inner_loop_cold f90 called by cg_sub 90 control the inner loop and so the minimization of the free energy A with respect to the occupation matrix To select a eDFT calculations the user has to set calculation cp occupations ensemble tcg true passop 0 3 maxiter 250 to use the CG procedure In the eDFT it is also the outer loop where the energy is minimized with respect to the wavefunction keeping fixed the occupation matrix While the specific parameters for the inner loop Since eDFT was born to treat metals keep in mind that we want to describe the broadening of the occupations around the Fermi energy Below the new parameters in the electrons list are listed e smearing used to select the occupation distribution there are two options Fermi Dirac smearing fd cold smearing smearing cs recommended e degauss is the electronic temperature it controls the broadening of the occupation numbers around the Fermi energy e ninner is the number of iterative cycles in the inner loop done to minimize the free energy A with respect the occupation numbers The typical range is 2 8 e conv thr is the threshold value to stop the search of the minimum free energy e niter_cold_restart controls the frequency at which a full iterative inner cycle is done It is in the range 1 ninner
21. group only if the double bond is aligned along one of the crystal axis if Ceo is rotated in some arbitrary way pw x may not find any symmetry apart from inversion e they contain a fractional translation that is incompatible with the FFT grid see next paragraph Note that if you change cutoff or unit cell volume the automatically com puted FFT grid changes and this may explain changes in symmetry and in the number of k points as a consequence for no apparent good reason only if you have fractional translations in the system though e a fractional translation without rotation is a symmetry operation of the system This means that the cell is actually a supercell In this case all symmetry operations containing 65 fractional translations are disabled The reason is that in this rather exotic case there is no simple way to select those symmetry operations forming a true group in the mathematical sense of the term Warning symmetry operation N not allowed This is not an error If a symmetry operation contains a fractional translation that is incompatible with the FFT grid it is discarded in order to prevent problems with symmetrization Typical fractional translations are 1 2 or 1 3 of a lattice vector If the FFT grid dimension along that direction is not divisible respectively by 2 or by 3 the symmetry operation will not transform the FFT grid into itself Self consistency is slow or does not converge at all Bad input data
22. http www netlib org lapack for linear algebra e FETW http www fftw org for Fast Fourier Transforms A copy of the needed routines is provided with the distribution However when available optimized vendor specific libraries should be used this often yields huge performance gains BLAS and LAPACK QUANTUM ESPRESSO can use the following architecture specific replacements for BLAS and LAPACK MKL for Intel Linux PCs ACML for AMD Linux PCs ESSL for IBM machines SCSL for SGI Altix SUNperf for Sun If none of these is available we suggest that you use the optimized ATLAS library see http math atlas sourceforge net Note that ATLAS is not a complete replacement for LAPACK it contains all of the BLAS plus the LU code plus the full storage Cholesky code Follow the instructions in the ATLAS distributions to produce a full LAPACK replacement Sergei Lisenkov reported success and good performances with optimized BLAS by Kazushige Goto They can be freely downloaded but not redistributed See the GotoBLAS2 item at http www tacc utexas edu tacc projects FFT QUANTUM ESPRESSO has an internal copy of an old FFTW version and it can use the following vendor specific FFT libraries IBM ESSL SGI SCSL SUN sunperf NEC ASL AMD ACML configure will first search for vendor specific FFT libraries if none is found it will search for an external FFTW v 3 library if none is found it will fall back to the internal copy of FFTW
23. in which a 43 band structure calculation with calculation phonon was performed as an intermediate step is no longer implemented since version 4 1 It is also no longer needed to specify Inscf true for q 0 The output data file appear in the directory specified by variables outdir with names specified by variable prefix After the output file s has been produced do not remove any of the files unless you know which are used and which are not you can run ph x The first input line of ph x is a job identifier At the second line the namelist amp INPUTPH starts The meaning of the variables in the namelist most of them having a default value is described in file Doc INPUT_PH Variables outdir and prefix must be the same as in the input data of pw x Presently you must also specify amass i a real variable the atomic mass of atomic type i After the namelist you must specify the q vector of the phonon mode in Cartesian coordi nates and in units of 27 a Notice that the dynamical matrix calculated by ph x at q 0 does not contain the non analytic term occurring in polar materials i e there is no LO TO splitting in insulators Moreover no Acoustic Sum Rule ASR is applied In order to have the complete dynamical matrix at q 0 including the non analytic terms you need to calculate effective charges by specifying option epsil true to ph x This is however not possible because not physical for metals i e any system subj
24. installed on that machine Ask your system administrator for instructions To run a single example go to the corresponding directory e g example example01 and execute run_example This will create a subdirectory results containing the input and output files generated by the calculation Some examples take only a few seconds to run while others may require several minutes depending on your system To run all the examples in one go execute run_all_examples from the examples directory On a single processor machine this typically takes a few hours The make_clean script cleans the examples tree by removing all the results sub directories However if additional subdirectories have been created they aren t deleted In each example s directory the reference subdirectory contains verified output files that you can check your results against They were generated on a Linux PC using the Intel compiler On different architectures the precise numbers could be slightly different in particular if different FFT dimensions are automatically selected For this reason a plain diff of your results against the reference data doesn t work or at least it requires human inspection of the results 20 2 7 Installation tricks and problems 2 7 1 All architectures Working Fortran 95 and C compilers are needed in order to compile QUANTUM ESPRESSO Most Fortran 90 compilers actually implement the Fortran 95 standard but old
25. of pools into which processors are to be grouped pw x only e the number of task groups into which processors are to be grouped e the number of processors performing iterative diagonalization for pw x or orthonor malization for cp x Items 1 and 2 are machine and installation dependent and may be different for interactive and batch execution Note that large parallel machines are often configured so as to disallow interactive execution ifin doubt ask your system administrator Item 3 also depend on your specific configuration shell execution path etc Item 4 is optional but may be important see the following section for the meaning of the various options For illustration here is how to run pw x on 16 processors partitioned into 8 pools 2 pro cessors each for several typical cases IBM SP machines batch pw x npool 8 lt input This should also work interactively with environment variables NPROC set to 16 MP_HOSTFILE set to the file containing a list of processors IBM SP machines interactive using poe poe pw x procs 16 npool 8 lt input PC clusters using mpiexec mpiexec n 16 pw x npool 8 lt input SGI Altix and PC clusters using mpirun mpirun np 16 pw x npool 8 lt input IBM BlueGene using mpirun mpirun np 16 exe path to executable pw x args npool 8 in path to input cwd path to work directory If you want to run in parallel the examples distributed with QUANTUM ESP
26. problems with YAMBO If simply typing make yambo produces an error such as undefined reference to MAIN__ you need to run the YAMBO configure by yourself specifying the appropriate compiler option for instance nofor_main for intel compiler or Mnomain for PGI If you do not manage to solve the problem consult the official YAMBO web site http www yambo code org for specific information 68 11 4 PostProc Some postprocessing codes complain that they do not find some files For Linux PC clusters in parallel execution in at least some versions of MPICH the current directory is set to the directory where the executable code resides instead of being set to the directory where the code is executed This MPICH weirdness may cause unexpected failures in some postprocessing codes that expect a data file in the current directory Workaround use symbolic links or copy the executable to the current directory error in davcio in postprocessing codes Most likely you are not reading the correct data files or you are not following the correct procedure for postprocessing In parallel execution if you did not set wf_collect true the number of processors and pools for the phonon run should be the same as for the self consistent run all files must be visible to all processors 11 5 ph x errors ph x stops with error reading file The data file produced by pw x is bad or incomplete or produced by an incompatible version of the code In p
27. typically shows up under the form of mysterious errors when 32 reading data If this happens use the option in or inp or input followed by the input file name Example pw x in inputfile npool 4 gt outputfile Of course the input file must be accessible by the processor that must read it only one processor reads the input file and subsequently broadcasts its contents to all other processors Apparently the LSF implementation of MPI libraries manages to ignore or to confuse even the in inp input mechanism that is present in all QUANTUM ESPRESSO codes In this case use the i option of mpirun 1sf to provide an input file Trouble with MKL and MPI parallelization If you notice very bad parallel performances with MPI and MKL libraries it is very likely that the OpenMP parallelization performed by the latter is colliding with MPI Recent versions of MKL enable autoparallelization by default on multicore machines You must set the environmental variable OMP_NUM_THREADS to 1 to disable it Note that if for some reason the correct setting of variable OMP_NUM_THREADS does not propagate to all processors you may equally run into trouble Lorenzo Paulatto Nov 2008 suggests to use the x option to mpirun to propagate OMP_NUM_THREADS to all processors Axel Kohlmeyer suggests the following April 2008 I ve found that Intel is now turning on multithreading without any warning and that is for example why their FFT seems faster than
28. 3 x yr structure how does this translate to QE input data There are several different way to specify structures described in detail in Doc INPUT_PW How can I generate a supercell If you need to create a supercell and are too lazy to create a small program to translate atoms you can e use the spacegroup program in EXCITING package http exciting code org to gen erate the supercell use fropho http fropho sourceforge net to check the symmetry Kun Yin April 2009 e use the PHON code http www homepages ucl ac uk ucftbdxa Eyvaz Isaev April 2009 Where can I find the Brillouin Zone high symmetry points irreps for XYZ You might find this web site useful http www cryst ehu es cryst get_kvec html info by Cyrille Barreteau nov 2007 Or else in textbooks such as e g The mathematical theory of symmetry in solids by Bradley and Cracknell Where can I find Monkhorst Pack grids of k points Auxiliary code kpoints x found in pwtools and produced by make tools generates uniform grids of k points that are equiv alent to Monkhorst Pack grids 12 5 Parallel execution Effective usage of parallelism requires some basic knowledge on how parallel machines work and how parallelism is implemented in QUANTUM ESPRESSO If you have no experience and no clear ideas or not idea at all consider reading Sec 3 How do I choose the number of processors how do I setup my parallel calculation Ple
29. AMD CPUs at least some versions of ifort 10 1 miscompile subroutine write_rho_xml in Module xml_io_base f 90 with O2 optimization Using O1 instead solves the problem info by Carlo Cavazzoni March 2008 The intel compiler version 10 1 008 miscompiles a lot of codes I have proof for CP2K and CPMD and needs to be updated in any case info by Axel Kohlmeyer May 2008 ifort v 9 The latest July 2006 32 bit version of ifort 9 1 works Earlier versions yielded Compiler Internal Error Linux PCs with MKL libraries On Intel CPUs it is very convenient to use Intel MKL libraries They can be also used for AMD CPU selecting the appropriate machine optimized libraries and also together with non Intel compilers Note however that recent versions of MKL 10 2 and following do not perform well on AMD machines configure should recognize properly installed MKL libraries By default the non threaded version of MKL is linked unless option configure with openmp is specified In case of trouble refer to the following web page to find the correct way to link MKL http software intel com en us articles intel mkl link line advisor MKL contains optimized FFT routines and a FFTW interface to be separately compiled For 64 bit Intel Core2 processors they are slightly faster than FFTW MKL v 10 FFTW v 3 fortran interface reported by P Giannozzi November 2008 For parallel MPI execution on multiprocessor SMP machines set the environment
30. Dal Corso 2007 07 27 See Example 13 for non collinear magnetism Example 22 for spin orbit interactions DFT U DFT U formerly known as LDA U calculation can be performed within a sim plified rotationally invariant form of the U Hubbard correction See Example 25 and references quoted therein Dispersion Interactions DFT D For DFT D DFT semiempirical dispersion inter actions see the description of input variables london sample files tests vdw and the comments in source file Modules mm_dispersion f90 37 Hartree Fock and Hybrid functionals Calculations in the Hartree Fock approximation or using hybrid XC functionals that include some Hartree Fock exchange currently require that DEXX is added to the preprocessing options DFLAGS in file make sys before compilation if you change this after the first compilation make clean recompile Documentation on usage can be found in subdirectory examples EXX_example The algorithm is quite standard see for instance Chawla and Voth JCP bf 108 4697 1998 Sorouri Foulkes and Hine JCP 124 064105 2006 Spencer and Alavi PRB 77 193110 2008 Basically one generates auxiliary densities p_ Ou Wk in real space and transforms them to reciprocal space using FFT the Poisson equation is solved and the resulting potential is transformed back to real space using FFT then multiplied by ou and the results are accumulated The only tricky point is the treatment of the q 0 limit
31. FFTW For serial and OpenMP based runs this makes no difference in fact the multi threaded FFT helps but if you run MPI locally you actually lose performance Also if you use the numactl tool on linux to bind a job to a specific cpu core MKL will still try to use all available cores and slow down badly The cleanest way of avoiding this mess is to either link with 1mk1_intel_1p64 1mk1_sequential 1mk1_core on 64 bit x86_64 ia64 1mk1_intel lmkl_sequential lmkl_core on 32 bit i e ia32 or edit the libmkl_ platform a file I m using now a file 1ibmk110 a with GROUP libmkl_intel_1p64 a libmkl_sequential a libmkl_core a It works like a charm UPDATE Since v 4 2 configure links by default MKL without multithreaded support Trouble with compilers and MPI libraries Many users of QUANTUM ESPRESSO in particular those working on PC clusters have to rely on themselves or on less than adequate system managers for the correct configuration of software for parallel execution Mysteri ous and irreproducible crashes in parallel execution are sometimes due to bugs in QUANTUM ESPRESSO but more often than not are a consequence of buggy compilers or of buggy or miscompiled MPI libraries Very useful step by step instructions to compile and install MPI libraries can be found in the following post by Javier Antonio Montoya http www democritos it pipermail pw_forum 2008 April 008818 htm On a Xeon quadriprocessor cluster
32. FFTW3 set CPPFLAGS D__FFTW3 in make sys and to link with the MKL interface to FFTW3 You will get a decent speedup 25 on two cores Explicit OpenMP is a very recent addition still at an experimental stage devised to increase scalability on large multicore parallel machines Explicit OpenMP is devised to be run together with MPI and also together with multithreaded libraries BEWARE you have to be VERY careful to prevent conflicts between the various kinds of parallelization If you don t know how to run MPI processes and OpenMP threads in a controlled manner forget about mixed OpenMP MPI parallelization 3 2 Running on parallel machines Parallel execution is strongly system and installation dependent Typically one has to specify 1 a launcher program not always needed such as poe mpirun mpiexec with the appro priate options if any 2 the number of processors typically as an option to the launcher program but in some cases to be specified after the name of the program to be executed 3 the program to be executed with the proper path if needed for instance pw x or pw x or HOME bin pw x or whatever applies Beware MKL v 10 2 2 has a buggy dsyev yielding wrong results with more than one thread fixed in v 10 2 4 28 4 other QUANTUM ESPRESSO specific parallelization options to be read and interpreted by the running code e the number of images used by NEB or phonon calculations e the number
33. INO 2 aa 37 6_NEB calculations 39 7 Phonon calculations 41 RE EE a e as a a 41 ES 42 AA E 42 7 4 Distributed Phonon calculations 0 0 43 8 Post processing 43 beh Fone Sea ee Bee Bek aes ee 43 ra We er ye ee ha ee ee ee e a 44 gh ie Ss E NE 44 8 4 Wannier functions oo e a a a 44 8 5 Other tools 2 45 45 IIA E E E ee 47 ad A a ri Se oa a a 47 A d e RR 50 wh aoe aa as E eee ee e e eae ce 51 9 4 1 Self interaction Correction 0 0 0 00 00 000 eee ee 51 9 4 2 ensemble DEI 52 SE ae ee EE E ea 55 9 4 4 Treatment of USPPs o 55 10 Performances 55 10 1 Execution time 55 IES AAA A A ee 57 A A 57 10 4 Parallelization issues 57 11 Troubleshooting 58 E E E E EE 59 11 2 Compilation problems with PLUMED e 66 11 3 Compilation problems with YAMBU e EE EE EE E EE ar ar 66 MENS AE 67 ey AA A e A AAA E oe 67 12 Frequently Asked Questions FAQ 68 PAM EI 68 era a he ep Ree ion Rt ee ia a e 68 ar Base oes ok Gy Sache ks ok WERE pends Wah es he a oie oe wie E 70 a a es ok ON ete E es ee oe a 70 Se ody ot Ge Bee od ane ae Prd we PO Se he n 71 KSC Se E Se ok RA ee oe ee e a 72 12 7 Self A oa ses kk GRR READE RE ERE REARS EG OEE e 72 ise Po ea o o o aia e 74 1 Introduction This guide covers the installation and usage of QUANTUM ESPRESSO opEn Source Package for Research in Electronic Structure Simulation and Optimization version 4 3 2 The QUANTUM ESPRESSO distribut
34. If you have recent versions v 10 or later of MKL installed you may use the FFTW3 interface provided with MKL This can be directly linked in MKL distributed with v 12 of the Intel compiler In earlier versions only sources are distributed you have to compile them and to modify file make sys accordingly MKL must be linked after the FFTW MKL interface MPI libraries MPI libraries are usually needed for parallel execution unless you are happy with OpenMP multicore parallelization In well configured machines configure should find the appropriate parallel compiler for you and this should find the appropriate libraries Since often this doesn t happen especially on PC clusters see Sec 2 7 6 15 Other libraries QUANTUM ESPRESSO can use the MASS vector math library from IBM if available only on AIX 2 4 1 If optimized libraries are not found The configure script attempts to find optimized libraries but may fail if they have been in stalled in non standard places You should examine the final value of BLAS_LIBS LAPACK_LIBS FFT_LIBS MPI_LIBS if needed MASS_LIBS IBM only either in the output of configure or in the generated make sys to check whether it found all the libraries that you intend to use If some library was not found you can specify a list of directories to search in the envi ronment variable LIBDIRS and rerun configure directories in the list must be separated by spaces For example configure LIBDIRS op
35. It is a trick to speed up the calculation e lambda_cold is the length step along the search line for the best value for A when the iterative cycle is not performed The value is close to 0 03 smaller for large and complicated metallic systems NOTE degauss is in Hartree while in PWscfis in Ry The typical range is 0 01 0 02 Ha The input for an Al surface is amp CONTROL calculation cp restart_mode from_scratch nstep 10 iprint 5 isave 5 dt 125 0d0 prefix Aluminum_surface pseudo_dir UPF outdir scratch ndr 50 59 ndw 51 SYSTEM ibrav 14 celldm 1 21 694d0 celldm 2 1 00D0 celldm 3 2 121D0 celldm 4 0 0d0 celldm 5 0 0d0 celldm 6 0 0d0 nat 96 ntyp 1 nspin 1 ecutwfc 15 nbnd 160 input_dft pbe occupations ensemble smearing cs degauss 0 018 amp ELECTRONS orthogonalization Gram Schmidt startingwfc random ampre 0 02 tcg true passop 0 3 maxiter 250 emass_cutoff 3 00 conv_thr 1 d 6 n_inner 2 lambda_cold 0 03 niter_cold_restart 2 amp IONS ion_dynamics verlet ion_temperature nose fnosep 4 0d0 tempw 500 d0 ATOMIC_SPECIES Al 26 89 Al pbe UPF NOTA1 remember that the time step is to integrate the ionic dynamics so you can choose something in the range of 1 5 fs NOTA2 with eDFT you are simulating metals or systems fo
36. Quantum ESPRESSO then SCM Beware the develop ment version is well under development use at your own risk The bravest may access the development version via anonymous access to the Subversion SVN repository see the De veloper Manual Doc developer man pdf section Using SVN The QUANTUM ESPRESSO distribution contains several directories Some of them are common to all packages Modules source files for modules that are common to all programs include files h included by fortran and C source files clib external libraries written in C flib external libraries written in Fortran extlibs archive of external libraries LAPACK BLAS and iotk install installation scripts and utilities pseudo pseudopotential files used by examples upftools converters to unified pseudopotential format UPF examples sample input and output files Doc general documentation archive contains plug ins in tar gz form while others are specific to a single package PW PWscf source files for scf calculations pw x pwtools PWscf source files for miscellaneous analysis programs tests PWscf automated tests NEB PWneb source files for NEB calculations neb x PP PostProc source files for post processing of pw x data file PH PHonon source files for phonon calculations ph x and analysis Gamma PHonon source files for Gamma only phonon calculation phcg x D3 PHonon source files for third order derivative calculations d3
37. RESSO see Sec 2 6 set PARA_PREFIX to everything before the executable pw x in the above examples PARA POSTFIX to what follows it until the first redirection sign lt gt if any For execution using OpenMP on N threads set PARA_PREFIX to env OMP_NUM_THREADS N 3 3 Parallelization levels Data structures are distributed across processors Processors are organized in a hierarchy of groups which are identified by different MPI communicators level The groups hierarchy is as follow 29 pools _ task groups world _ images linear algebra groups world is the group of all processors MPI COMM WORLD images Processors can then be divided into different images corresponding to a point in configuration space i e to a different set of atomic positions for NEB calculations to one or more than one irrep or wave vector in phonon calculations pools When k point sampling is used each image group can be subpartitioned into pools and k points can distributed to pools Within each pool reciprocal space basis set PWs and real space grids are distributed across processors This is usually referred to as PW paralleliza tion All linear algebra operations on array of PW real space grids are automatically and effectively parallelized 3D FFT is used to transform electronic wave functions from reciprocal to real space and vice versa The 3D FFT is parallelized by distributing planes of the 3D grid in
38. TM images selected squared wavefunction ELF electron localization function planar averages integrated local density of states Various types of plotting along a line on a plane three dimensional polar and output formats including the popular cube format can be specified The output files can be directly read by the free plotting system Gnuplot 1D or 2D plots or by code plotrho x that comes with PostProc 2D plots or by advanced plotting software XCrySDen and gOpenMol 3D plots See file Doc INPUT_PP for a detailed description of the input for code pp x See Example 05 for an example of a charge density plot Example 16 for an example of STM image simulation 8 2 Band structure Fermi surface The code bands x reads data file s extracts eigenvalues regroups them into bands the algo rithm used to order bands and to resolve crossings may not work in all circumstances though The output is written to a file in a simple format that can be directly read by plotting program plotband x Unpredictable plots may results if k points are not in sequence along lines See Example 05 directory for a simple band plot The code bands x performs as well a symmetry analysis of the band structure see Example 01 The calculation of Fermi surface can be performed using kvecs_FS x and bands_FS x The resulting file in xsf format can be read and plotted using XCrySDen See Example 08 for an example of Fermi surface visualization Ni includi
39. al variable OMP_NUM_THREADS to 1 unless you know what you are doing See Sec 3 for more info on this and on the difference between MPI and OpenMP parallelization Linux PCs with ACML libraries For AMD CPUs especially recent ones you may find convenient to link AMD acml libraries can be freely downloaded from AMD web site configure should recognize properly installed acml libraries together with the compilers most frequently used on AMD systems pgf90 pathscale openf95 sunf95 24 2 7 6 Linux PC clusters with MPI PC clusters running some version of MPI are a very popular computational platform nowadays QUANTUM ESPRESSO is known to work with at least two of the major MPI implementations MPICH LAM MPI plus with the newer MPICH2 and OpenMPI implementation configure should automatically recognize a properly installed parallel environment and prepare for parallel compilation Unfortunately this not always happens In fact e configure tries to locate a parallel compiler in a logical place with a logical name but if it has a strange names or it is located in a strange location you will have to instruct configure to find it Note that in many PC clusters Beowulf there is no parallel Fortran 95 compiler in default installations you have to configure an appropriate script such as mpif90 e configure tries to locate libraries both mathematical and parallel libraries in the usual places with usual names but if they have strange nam
40. al check that compilation was successful you may want to run some or all of the examples You should first of all ensure that you have downloaded and correctly unpacked the package containing examples since v 4 1 in a separate package tar zxvf path to package espresso X Y Z examples tar gz will unpack several subdirectories into espresso X Y Z There are two different types of examples e automated tests in directories tests and cptests Quick and exhaustive but not meant to be realistic implemented only for pw x and cp x e examples in directory examples Cover many more programs and features of the QUANTUM ESPRESSO distribution but they require manual inspection of the results Let us first consider the tests Automated tests for pw x are in directory tests File tests README contains a list of what is tested To run tests follow the directions in the header if file check_pw x j edit variables PARA PREFIX PARA_POSTFIX if needed see below Same for cp x this time in directory cptests Let us now consider examples A list of examples and of what each example does is contained in examples README For details see the README file in each example s directory If you find that any relevant feature isn t being tested please contact us or even better write and send us a new example yourself To run the examples you should follow this procedure 1 Go to the examples directory and edit the environment_variables file
41. amelist amp CONTROL Most variables in namelists have default values Only the following variables in amp SYSTEM must always be specified ibrav integer Bravais lattice index celldm real dimension 6 crystallographic constants nat integer number of atoms in the unit cell ntyp integer number of types of atoms in the unit cell ecutwfc real kinetic energy cutoff Ry for wavefunctions For metallic systems you have to specify how metallicity is treated in variable occupations If you choose occupations smearing you have to specify the smearing width degauss and optionally the smearing type smearing Spin polarized systems must be treated as metallic system except the special case of a single k point for which occupation numbers can be fixed occupations from input and card OCCUPATIONS Explanations for the meaning of variables ibrav and celldm as well as on alternative ways to input structural data are in files Doc INPUT_PW for pw x and Doc INPUT_CP for cp x These files are the reference for input data and describe a large number of other variables as well Almost all variables have default values which may or may not fit your needs After the namelists you have several fields cards introduced by keywords with self explanatory names ATOMIC_SPECIES ATOMIC_POSITIONS K POINTS CELL PARAMETERS optional OCCUPATIONS optional 34 The keywords may be followed on the same line by an option Un
42. an perform the following types of calculations e phonon frequencies and eigenvectors at a generic wave vector using Density Functional Perturbation Theory e effective charges and dielectric tensors e electron phonon interaction coefficients for metals 5 e interatomic force constants in real space e third order anharmonic phonon lifetimes e Infrared and Raman nonresonant cross section PHonon can be used whenever PWscf can be used with the exceptions of DFT U nonlocal VdW and hybrid functionals USPP and PAW are not implemented for higher order response calculations See the header of file PH phonon f90 for a complete and updated list of what PHonon can and cannot do Calculations in the Quasi Harmonic approximations of the vibra tional free energy can be performed using the QHA package PostProc can perform the following types of calculations e Scanning Tunneling Microscopy STM images e plots of Electron Localization Functions ELF e Density of States DOS and Projected DOS PDOS e Lowdin charges e planar and spherical averages plus interfacing with a number of graphical utilities and with external codes CP can perform Car Parrinello molecular dynamics including variable cell dynamics and free energy surface calculation at fixed cell through meta dynamics if patched with PLUMED 1 2 People In the following the cited affiliation is either the current one or the one where the last known contribution
43. annot bracket Ef Possible reasons e serious error in data such as bad number of electrons insufficient number of bands absurd value of broadening e the Fermi energy is found by bisection assuming that the integrated DOS N E is an in creasing function of the energy This is not guaranteed for Methfessel Paxton smearing of order 1 and can give problems when very few k points are used Use some other smearing function simple Gaussian broadening or better Marzari Vanderbilt cold smearing pw x yields internal error cannot bracket Ef message but does not stop This may happen under special circumstances when you are calculating the band structure for selected high symmetry lines The message signals that occupations and Fermi energy are not correct but eigenvalues and eigenvectors are Remove occupations tetrahedra in the input data to get rid of the message pw x runs but nothing happens Possible reasons e in parallel execution the code died on just one processor Unpredictable behavior may follow e in serial execution the code encountered a floating point error and goes on producing NaNs Not a Number forever unless exception handling is on and usually it isn t In both cases look for one of the reasons given above e maybe your calculation will take more time than you expect pw x yields weird results If results are really weird as opposed to misinterpreted e if this happens after a change in the code o
44. ar scaling thanks to the increase in serial speed coming from the reduction of data size making it easier for the machine to keep data in the cache VERY IMPORTANT For each system there is an optimal range of number of processors on which to run the job A too large number of processors will yield performance degradation If the size of pools is especially delicate N should not exceed Na and N 3 and should ideally be no larger than 1 2 1 4N3 and or N 3 In order to increase scalability it is often convenient to further subdivide a pool of processors into task groups When the number of processors exceeds the number of FFT planes data can be redistributed to task groups so that each group can process several wavefunctions at the same time The optimal number of processors for linear algebra parallelization taking care of mul tiplication and diagonalization of M x M matrices should be determined by observing the performances of cdiagh rdiagh pw x or ortho cp x for different numbers of processors in the linear algebra group must be a square integer Actual parallel performances will also depend on the available software MPI libraries and on the available communication hardware For PC clusters OpenMPI http www openmpi org seems to yield better performances than other implementations info by Kostantin Kudin Note however that you need a decent communication hardware at least Gigabit ethernet in order to have ac
45. arallel execution if you did not set wf_collect true the number of processors and pools for the phonon run should be the same as for the self consistent run all files must be visible to all processors ph x mumbles something like cannot recover or error reading recover file You have a bad restart file from a preceding failed execution Remove all files recover in outdir ph x says occupation numbers probably wrong and continues You have a metallic or spin polarized system but occupations are not set to smearing ph x does not yield acoustic modes with zero frequency at q 0 This may not be an error the Acoustic Sum Rule ASR is never exactly verified because the system is never exactly translationally invariant as it should be The calculated frequency of the acoustic mode is typically less than 10 cm but in some cases it may be much higher up to 100 cm The ultimate test is to diagonalize the dynamical matrix with program dynmat x imposing the ASR If you obtain an acoustic mode with a much smaller w let us say lt lem with all other modes virtually unchanged you can trust your results The problem is in the fact that the XC energy is computed in real space on a discrete grid and hence the total energy is invariant only for translation in the FFT grid Increasing the charge density cutoff increases the grid density thus making the integral more exact thus reducing the problem unfortunately rather slowly
46. ase see above Why is my parallel job running in such a lousy way A frequent reason for lousy parallel performances is a conflict between MPI parallelization implemented in QUANTUM ESPRESSO and the autoparallelizing feature of MKL libraries Set the environment variable OPEN_MP_THREADS to 1 See SecB for more info Why is my parallel job crashing when reading input data doing nothing If the same data work in serial execution use code inp input_file instead of code lt input_file Some MPI libraries do not properly handle input redirection 73 The code stops with an error reading namelist xxxx Most likely there is a misspelled variable in namelist xxxx If there isn t any have you looked carefully really REALLY beware control characters like DOS control M they can confuse the namelist reading code If this happens to the first namelist to be read usually amp CONTROL in parallel execution see above 12 6 Frequent errors during execution Why is my job crashing with segmentation fault Possible reasons too much mem ory requested executable or libraries fitted to a different hardware code bug compiler bug The latter are typically not reproducible on different architectures or compilers code bugs may sometimes be elusive but typically yield a more reproducible pattern of problems Mysterious unpredictable erratic errors in parallel execution are almost always coming from bugs in the compiler or and i
47. ating system If you get errors like IPO Error unresolved suml_cos2 at the linking stage your compiler is optimized to use the SSE version of sine cosine etc contained in the SVML library Append 1svml to the list of libraries in your make sys file info by Axel Kohlmeyer oct 2007 Linux PCs with Portland compiler pgf90 QUANTUM ESPRESSO does not work reliably or not at all with many old versions lt 6 1 of the Portland Group compiler pgf90 Use the latest version of each release of the compiler with patches if available see the Portland Group web site http www pgroup com Linux PCs with Pathscale compiler Version 2 99 of the Pathscale EKO compiler web site http www pathscale com works and is recognized by configure but the preprocessing command pathcc E causes a mysterious error in compilation of iotk and should be replaced by lib cpp P traditional The MVAPICH parallel environment with Pathscale compilers also works info by Paolo Gian nozzi July 2008 Version 3 1 and version 4 open source of the Pathscale EKO compiler also work info by Cezary Sliwa April 2011 and Carlo Nervi June 2011 In case of mysterious errors while compiling iotk remove all lines like 22 1 iotk_base spp from all iotk source files Linux PCs with gfortran Old gfortran versions often produce nonfunctional phonon ex ecutables segmentation faults and the like other versions miscompile iotk the executab
48. ceptable performances with PW parallelization Do not expect good scaling with cheap hardware PW calculations are by no means an embarrassing parallel problem Also note that multiprocessor motherboards for Intel Pentium CPUs typically have just one memory bus for all processors This dramatically slows down any code doing massive access to memory as most codes in the QUANTUM ESPRESSO distribution do that runs on processors of the same motherboard 11 Troubleshooting Almost all problems in QUANTUM ESPRESSO arise from incorrect input data and result in error stops Error messages should be self explanatory but unfortunately this is not always true If the code issues a warning messages and continues pay attention to it but do not assume that something is necessarily wrong in your calculation most warning messages signal harmless problems 60 11 1 pw x problems pw x says error while loading shared libraries or cannot open shared object file and does not start Possible reasons e If you are running on the same machines on which the code was compiled this is a library configuration problem The solution is machine dependent On Linux find the path to the missing libraries then either add it to file etc 1d so conf and run ldconfig must be done as root or add it to variable LD _LIBRARY_PATH and export it Another possibility is to load non shared version of libraries ending with a instead of shared ones ending w
49. chines using PC hardware may or may not have the needed software If not you need either to buy a commercial product e g Portland or to install an open source compiler like gfortran or g95 Note that several commercial compilers are available free of charge under some license for academic or personal usage e g Intel Sun 2 3 configure To install the QUANTUM ESPRESSO source package run the configure script This is ac tually a wrapper to the true configure located in the insta11 subdirectory configure will try to detect compilers and libraries available on your machine and set up things accordingly Presently it is expected to work on most Linux 32 and 64 bit PCs all Intel and AMD CPUs and PC clusters SGI Altix IBM SP and BlueGene machines NEC SX Cray XT machines Mac OS X MS Windows PCs A GPU enabled version is currently available as a separate branch of the svn repository See the following message and instructions http www democritos it pipermail pw_forum 2011 May 020399 html Instructions for the impatient cd espresso X Y Z configure make all Symlinks to executable programs will be placed in the bin subdirectory Note that both C and Fortran compilers must be in your execution path as specified in the PATH environment variable Additional instructions for special machines configure ARCH crayxt4r for CRAY XT machines configure ARCH necsx for NEC SX machines configure ARCH ppc64 mn PowerPC Linux x
50. cities all the difference is potential energy but in a dynamics simulation the energy will be equipartitioned between 51 kinetic and potential then to estimate the temperature take the difference in energy de convert it in Kelvin divide for the number of atoms and multiply by 2 3 Randomization could be useful also while we are relaxing the system especially when we suspect that the ions are in a local minimum or in an energy plateau 9 3 CP dynamics At this point after having minimized the electrons and with ions displaced from their equi librium positions we are ready to start a CP dynamics We need to specify verlet both in ionic and electronic dynamics The threshold in control input section will be ignored like any parameter related to minimization strategy The first time we perform a CP run after a minimization it is always better to put velocities equal to zero unless we have velocities from a previous simulation to specify in the input file Restore the proper masses for the ions In this way we will sample the microcanonical ensemble The input section changes as follow amp electrons emass 400 d0 emass_cutoff 2 5d0 electron_dynamics verlet electron_velocities zero amp ions ion_dynamics verlet ion_velocities zero ATOMIC_SPECIES C 12 0d0 c_blyp_gia pp H 1 00d0 h ps If you want to specify the initial velocities for ions you have to set ion velocities fro
51. compilation Detailed instructions in Sec 2 2 Compilation fails with internal error what should I do Any message during com pilation saying something like internal compiler error and the like means that your compiler is buggy You should report the problem to the compiler maker especially if you paid real money for it Sometimes reducing the optimization level or rearranging the code in a strategic place will make the problem disappear In other cases you will need to move to a different compiler or to a less buggy version or buggy in a different way that doesn t bug you of the same compiler Compilation fails at linking stage symbol not found If the missing symbols i e routines that are called but not found are in the code itself most likely the fortran to C conventions used in file include c_defs h are not appropriate Edit this file and retry If the missing symbols are in external libraries BLAS LAPACK FFT MPI libraries there is a name mismatch between what the compiler expects and what the library provides See Sec 2 2 If the missing symbols aren t found anywhere either in the code or in the libraries they are system library symbols i If they are called by external libraries you need to add a missing system library or to use a different set of external libraries compiled with the same compiler you are using ii If you are using no external libraries and still getting missing symbols your compiler and compiler
52. cule calculation cp restart_mode from_scratch ndr 51 ndw 51 nstep 100 47 iprint 10 isave 100 tstress TRUE tprnfor TRUE dt 5 000 etot_conv_thr ekin_conv_thr 1 d 4 prefix c6h6 pseudo_dir scratch benzene outdir scratch benzene Out Pp T LO system ibrav 14 celldm 1 16 0 celldm 2 celldm 3 celldm 4 celldm 5 celldm 6 nat 12 ntyp 2 nbnd 15 ecutwfc 40 0 nrib 10 nr2b 10 nr3b 10 input_dft BLYP e CO OO OO OO tz CO OO OO Om CH e amp electrons emass 400 d0 emass_cutoff 2 5d0 electron_dynamics sd amp ions ion_dynamics none amp cell cell_dynamics none press 0 0d0 ATOMIC_SPECIES C 12 0d0 c_blyp_gia pp H 1 00d0 h ps ATOMIC_POSITIONS bohr C 2 6 0 0 0 0 C 1 3 1 C i C 2 C 1 48 D P DO D DO CH N ON GG M H BW D N You can find the description of the input variables in file Doc INPUT_CP 9 1 Reaching the electronic ground state The first run when starting from scratch is always an electronic minimization with fixed ions and cell to bring the electronic system on the ground state GS relative to the starting atomic configuration This step is conceptually very similar to self consistency in a pw x run Sometimes a single run is not enough to reach the GS In this case you need to re run the electronic mini
53. d through an optional auxiliary input file named pw2casino dat see below Note that in versions prior to 4 3 this functionality was provided through separate post processing utilities available in the PP directory these are no longer supported For QMC MD runs PWSCF etc previously needed to be patched using the patch script PP pw2casino MDloop sh this is no longer necessary How to generate xwfn data files with PWscf Use the pw2casino option when invoking pw x e g pw x pw2casino lt input_file gt output_file The xfwn data file will then be generated automatically PWscf is capable of doing the plane wave to blip conversion directly the blip utility provided in the CASINO distribution is not required and so by default PWscf produces the binary blip wave function file bwfn data b1 Various options may be modified by providing a file pw2casino dat in outdir with the following format amp inputpp blip_convert true blip_binary true blip_single_prec false blip_multiplicity 1 d0 n_points_for_test 0 Some or all of the 5 keywords may be provided in any order The default values are as given above and these are used if the pw2casino dat file is not present The meanings of the keywords are as follows blip_convert reexpand the converged plane wave orbitals in localized blip functions prior to writing the CASINO wave function file This is almost always done since wave functions expanded in b
54. der 2 neb x does not read from standard input You cannot use input redirection as in neb x lt neb in A NEB calculation can be run in two different ways 1 by reading a single input file to be specified using command line options neb x inp or neb x input 2 by specifying the number N of images i e points in the configuration space using command line option neb x input_images N and providing input data in a neb dat file and in files pw_X in X 1 N For case 1 the input file contains KEYWORDS see below for format specifications These KEYWORDS enable the code to distinguish which part of the file contains NEB specific data and which parts contains input data for the energy and force computational engine currently only PW After the parsing different files are generated neb dat with NEB specific input data and a set of PWscf input files pw_1 in pw_N in PWscf input files one for each set of atomic position All options for a single SCF calculation apply The general structure of the file to be parsed is 41 BEGIN BEGIN_PATH_INPUT neb specific namelists and cards END_PATH_INPUT BEGIN_ENGINE_INPUT BEGIN_ENGINE_INPUT 7 pw specific namelists and cards BEGIN_POSITIONS FIRST_IMAGE pw ATOMIC_POSITIONS card INTERMEDIATE_IMAGE pw ATOMIC_POSITIONS card LAST_IMAGE pw ATOMIC_POSITIONS card END_POSITIONS other pw specific cards END_ENGINE_INPUT END For case 2 the neb dat file and
55. dition one would like to have linear scaling of the RAM per processor Oy Op N so that large memory systems fit into the RAM of each processor As a general rule image parallelization e may give good scaling but the slowest image will determine the overall performances load balancing may be a problem e requires very little communications suitable for ethernet communications e does not reduce the required memory per processor unsuitable for large memory jobs Parallelization on k points e guarantees almost linear scaling if the number of k points is a multiple of the number of pools 99 e requires little communications suitable for ethernet communications e does not reduce the required memory per processor unsuitable for large memory jobs Parallelization on PWs e yields good to very good scaling especially if the number of processors in a pool is a divisor of Na and Na the dimensions along the z axis of the FFT grids nr3 and nr3s which coincide for NCPPs e requires heavy communications suitable for Gigabit ethernet up to 4 8 CPUs at most specialized communication hardware needed for 8 or more processors e yields almost linear reduction of memory per processor with the number of processors in the pool A note on scaling optimal serial performances are achieved when the data are as much as possible kept into the cache As a side effect PW parallelization may yield superlinear better than line
56. e LAPACK LIBS in make sys 2 7 4 IBM BlueGene The current configure is tested and works only on the machine at J lich For other sites you should try something like configure ARCH ppc64 bg BLAS_LIBS LAPACK_LIBS SCALAPACK_DIR BLACS_DIR where the various _LIBS and _DIR suggest where the various libraries are located 2 7 5 Linux PC Both AMD and Intel CPUs 32 bit and 64 bit are supported and work either in 32 bit emu lation and in 64 bit mode 64 bit executables can address a much larger memory space than 32 bit executable but there is no gain in speed Beware the default integer type for 64 bit machine is typically 32 bit long You should be able to use 64 bit integers as well but it will not give you any advantage and you may run into trouble Currently the following compilers are supported by configure Intel ifort Portland pgf90 gfortran g95 Pathscale pathf95 Sun Studio sunf95 AMD Open64 openf95 The ordering approximately reflects the quality of support Both Intel MKL and AMD acml mathematical libraries are supported Some combinations of compilers and of libraries may however require manual editing of make sys It is usually convenient to create semi statically linked executables with only libc libm libpthread dynamically linked If you want to produce a binary that runs on different machines compile it on the oldest machine you have i e the one with the oldest version of the oper
57. e atomic 1d1 x for pseudopotential generation see specific doc umentation in atomic_doc e make upf produces utilities for pseudopotential conversion in directory upftools e make cp produces the Car Parrinello code CPV cp x and the postprocessing code CPV cppp x e make all produces all of the above e make plumed uncompress and move rename PLUMED patches PW CPV and clib routines and compiles PW and CPV e make w90 uncompress and move rename wannier90 copy an appropriate make sys and produces all executables in textttW90 wannier90 x and in bin e make want uncompress and move rename want run want s configure and produces all want executables in WANT bin e make yambo uncompress and move rename yambo run yambo s configure and produces all yambo executables in YAMBO bin e make gipaw download QE GIPAW uncompress and move rename gipaw run gipaw s configure and produces all gipaw executables in GIPAW bin and in bin For the setup of the GUI refer to the PWgui X Y Z INSTALL file where X Y Z stands for the version number of the GUI should be the same as the general version number If you are using the SVN sources see the GUI README file instead The codes for data postprocessing in PP are 17 Note ware pp x extracts the specified data from files produced by pw x prepares data for plotting by writing them into formats that can be read by several plotting programs bands x extracts and reorders eigenvalues fro
58. e list of allowed XC functionals and of their acronyms can be found in Modules funct f90 More documentation on pseudopotentials and on the UPF format can be found in the Wiki 5 Using PWscf Code pw x performs various kinds of electronic and ionic structure calculations We may distinguish the following typical cases of usage for pw x 2 36 5 1 Electronic structure calculations Single point fixed ion SCF calculation Set calculation scf this is actually the default Namelists amp IONS and amp CELL will be ignored See Example 01 Band structure calculation First perform a SCF calculation as above then do a non SCF calculation with the desired k point grid and number nbnd of bands Use calculation bands if you are interested in calculating only the Kohn Sham states for the given set of k points e g along symmetry lines see for instance http www cryst ehu es cryst get_kvec htm1 Specify instead calculation nscf if you are interested in further processing of the results of non SCF calculations for instance in DOS calculations In the latter case you should specify a uniform grid of points For DOS calculations you should choose occupations tetrahedra together with an automatically generated uniform k point grid card K POINTS with option automatic Specify nosym true to avoid generation of additional k points in low symme try cases Variables prefix and outdir which determine the names of inpu
59. ect to a broadening At q 0 use program dynmat x to calculate the correct LO TO splitting IR cross sections and to impose various forms of ASR If ph x was instructed to calculate Raman coefficients dynmat x will also calculate Raman cross sections for a typical experimental setup Input documentation in the header of PH dynmat f90 A sample phonon calculation is performed in Example 02 7 2 Calculation of interatomic force constants in real space First dynamical matrices are calculated and saved for a suitable uniform grid of q vectors only those in the Irreducible Brillouin Zone of the crystal are needed Although this can be done one q vector at the time a simpler procedure is to specify variable 1disp true and to set variables nq1 nq2 nq3 to some suitable Monkhorst Pack grid that will be automatically generated centered at q 0 Do not forget to specify epsil true in the input data of ph x if you want the correct TO LO splitting in polar materials Second code q2r x reads the dynamical matrices produced in the preceding step and Fourier transform them writing a file of Interatomic Force Constants in real space up to a distance that depends on the size of the grid of q vectors Input documentation in the header of PH q2r f90 Program matdyn x may be used to produce phonon modes and frequencies at any q us ing the Interatomic Force Constants file as input Input documentation in the header of PH matdyn 90 For more de
60. er versions may not be Fortran 95 compliant Moreover C and Fortran compilers must be in your PATH If configure says that you have no working compiler well you have no working compiler at least not in your PATH and not among those recognized by configure If you get Compiler Internal Error or similar messages your compiler version is buggy Try to lower the optimization level or to remove optimization just for the routine that has problems If it doesn t work or if you experience weird problems at run time try to install patches for your version of the compiler most vendors release at least a few patches for free or to upgrade to a more recent compiler version If you get error messages at the loading phase that look like file XYZ o unknown not recognized invalid wrong file type file format module version one of the following things have happened 1 you have leftover object files from a compilation with another compiler run make clean and recompile 2 make did not stop at the first compilation error it may happen in some software con figurations Remove the file o that triggers the error message recompile look for a compilation error If many symbols are missing in the loading phase you did not specify the location of all needed libraries LAPACK BLAS FFTW machine specific optimized libraries in the needed order If only symbols from clib are missing verify that you have the correct C to Fortran bindings
61. erratic crashes in parallel execution have been reported apparently correlated with ifort 10 1 info by Nathalie Vast and Jelena Sjakste May 2008 33 4 Using QUANTUM ESPRESSO Input files for PWscf codes may be either written by hand or produced via the PWgui graph ical interface by Anton Kokalj included in the QUANTUM ESPRESSO distribution See PWgui x y z INSTALL where x y z is the version number for more info on PWgui or GUI README if you are using SVN sources You may take the examples distributed with QUANTUM ESPRESSO as templates for writing your own input files see Sec 2 6 In the following whenever we mention Example N we refer to those Input files are those in the results subdirectories with names ending with in they will appear after you have run the examples 4 1 Input data Input data for the basic codes of the QUANTUM ESPRESSO distribution pw x and cp x is organized as several namelists followed by other fields introduced by keywords The namelists are amp CONTROL general variables controlling the run amp SYSTEM structural information on the system under investigation amp ELECTRONS electronic variables self consistency smearing amp IONS optional ionic variables relaxation dynamics amp CELL optional variable cell optimization or dynamics Optional namelist may be omitted if the calculation to be performed does not require them This depends on the value of variable calculation in n
62. es or strange locations you will have to rename move them or to instruct configure to find them If MPI libraries are not found parallel compilation is disabled e configure tests that the compiler and the libraries are compatible i e the compiler may link the libraries without conflicts and without missing symbols If they aren t and the compilation fail configure will revert to serial compilation Apart from such problems QUANTUM ESPRESSO compiles and works on all non buggy properly configured hardware and software combinations You may have to recompile MPI libraries not all MPI installations contain support for the fortran 90 compiler of your choice or for any fortran 90 compiler at all Useful step by step instructions for MPI compilation can be found in the following post by Javier Antonio Montoya http www democritos it pipermail pw_forum 2008April 008818 htm If QUANTUM ESPRESSO does not work for some reason on a PC cluster try first if it works in serial execution A frequent problem with parallel execution is that QUANTUM ESPRESSO does not read from standard input due to the configuration of MPI libraries see Sec B 2 If you are dissatisfied with the performances in parallel execution see Sech and in particular Sec 10 4 See also the following post from Axel Kohlmeyer http www democritos it pipermail pw forum 2008 April 008796 html 2 7 7 Intel Mac OS X Newer Mac OS X machines 10 4 and later with Intel CPUs a
63. f the complexity of a plain scf calculation with pw x for NCPP USPP and PAW give raise additional terms to be calculated that may add from a few percent up to 30 40 to execution time For phonon calculations each of the 3N modes requires a time of the same order of magnitude of self consistent calculation in the same system possibly times a small multiple For cp x each time step takes something in the order of Th Torth T oub defined below 57 The time required for the self consistent solution at fixed ionic positions Tsef is Dyer Niter Titer Tini where Nier number of self consistency iterations niter Tirer time for a single iteration Tinit initialization time usually much smaller than the first term The time required for a single self consistency iteration Titer is Titer NT Trho F Tscf where N number of k points Tiag time per Hamiltonian iterative diagonalization Trho time for charge density calculation Ts time for Hartree and XC potential calculation The time for a Hamiltonian iterative diagonalization Tdiag is Tdiag F NT Torth Tsub where N number of Hy products needed by iterative diagonalization Tp time per Hw product Tori CPU time for orthonormalization Tsup CPU time for subspace diagonaliza tion The time T required for a Hw product is Th aMN az MN N2N3log N N2N3 azMPN The first term comes from the kinetic term and is usually much smaller
64. files with the density of states projected on each atomic wavefunction of each atom and a BIG amount of data on the standard output the last few lines of which contain the decomposition of Lowdin charges on angular momentum and spin component of each atom What is the order of Y m components in projected DOS projection of atomic wavefunctions See input data documentation for projwfc x Why is the sum of partial Lowdin charges not equal to the total charge Lowdin charges as well as other conventional atomic charges do not satisfy any sum rule You can easily convince yourself that this is the case because the atomic orbitals that are used to calculate them are arbitrary to some extent If you like you can think that the missing charge is delocalized or bonding charge but this would be another way of naming the conventional to some extent character of L wdin charge Stefano Baroni Sept 2008 See also the definition of spilling parameter Sanchez Portal et al Sol State Commun 95 685 1995 The spilling parameter measures the ability of the basis provided by the pseudo atomic wfc to represent the PW eigenstates by measuring how much of the subspace of the Hamiltonian eigenstates falls outside the subspace spanned by the atomic basis I cannot find the Fermi energy where is it It is printed in the output If not the information on Gaussian smearing needed to calculate a sensible Fermi energy was not p
65. files in memory instead of writing them without changes to the code You have to do a module load iobuf before compiling and then add liobuf at link time If you run a job you set the environment variable IOBUF PARAMS to proper numbers and you can gain a lot Here is one example env IOBUF_PARAMS wfcx noflush count 1 size 15M verbose X dat count 2 size 50M lazyflush lazyclose verbose UPF xml count 8 size 8M verbose pbsyod ch espresso bin pw x npool 4 in si64pw2x2x2 inp gt amp si64pw2x2x232moreiobuf out E This will ignore all flushes on the wfc scratch files using a single i o buffer large enough to contain the whole file 12 Mb here this way they are actually never written to disk The dat files are part of the restart so needed but you can be lazy since they are writeonly xml files have a lot of accesses due to iotk but with a few rather small buffers this can be handled as well You have to pay attention not to make the buffers too large if the code needs a lot of memory too and in this example there is a lot of room for improvement After you have tuned those parameters you can remove the verboses and enjoy the fast execution Apart from the i o issues the cray xt3 is a really nice and fast machine Info by Axel Kohlmeyer maybe obsolete 3 4 Tricks and problems Trouble with input files Some implementations of the MPI library have problems with input redirection in parallel This
66. gorithm is the default since v 3 1 See also examples VCSexample 5 3 Direct interface with CASINO PWscf now supports the Cambridge quantum Monte Carlo program CASINO directly For more information on the CASINO code see http www tcm phy cam ac uk mdt26 casino html CASINO may take the output of PWSCF and improve it giving considerably more accurate total energies and other quantities than DFT is capable of PWscf users wishing to learn how to use CASINO may like to attend one of the annual CASINO summer schools in Mike Towler s Apuan Alps Centre for Physics in Tuscany Italy More information can be found at http www vallico net tti tti html Practicalities The interface between PWscf and CASINO is provided through a file with a standard format containing geometry basis set and orbital coefficients which PWscf will pro duce on demand For SCF calculations the name of this file may be pwfn data bwfn data or bwfn data b1 depending on user requests see below If the files are produced from an MD run the files have a suffix 0001 0002 0003 etc corresponding to the sequence of timesteps CASINO support is implemented by three routines in the PW directory of the espresso distri bution 39 e pw2casino f90 the main routine e pw2casino write f90 writes the CASINO xwfn data file in various formats e pw2blip f90 does the plane wave to blip conversion if requested Relevant behavior of PWscf may be modifie
67. he names of files containing the desired PDOS Type sumpdos x h or look into the source code for more details Code epsilon x calculates RPA frequency dependent complex dielectric function Docu mentation is in Doc eps_man tex The code path_int x is intended to be used in the framework of NEB calculations It is a tool to generate a new path what is actually generated is the restart file starting from an old one through interpolation cubic splines The new path can be discretized with a different number of images this is its main purpose images are equispaced and the interpolation can be also performed on a subsection of the old path The input file needed by path_int x can be easily set up with the help of the self explanatory path_int sh shell script 9 Using CP This section is intended to explain how to perform basic Car Parrinello CP simulations using the CP package It is important to understand that a CP simulation is a sequence of different runs some of them used to prepare the initial state of the system and other performed to collect statistics or to modify the state of the system itself i e modify the temperature or the pressure To prepare and run a CP simulation you should first of all define the system atomic positions system cell pseudopotentials cut offs number of electrons and bands optional FFT grids optional An example of input file Benzene Molecule amp control title Benzene Mole
68. htly coupled and communications are significant This means that Gigabit ethernet typical for cheap PC clusters is ok up to 4 8 processors per pool but fast communication hardware e g Mirynet or comparable is absolutely needed beyond 8 processors per pool Choosing parameters To control the number of processors in each group command line switches nimage npools ntg northo for cp x or ndiag for pw x are used As an example consider the following command line mpirun np 4096 pw x nimage 8 npool 2 ntg 8 ndiag 144 input my input This executes PWscf on 4096 processors to simulate a system with 8 images each of which is distributed across 512 processors k points are distributed across 2 pools of 256 processors each 3D FFT is performed using 8 task groups 64 processors each so the 3D real space grid is cut into 64 slices and the diagonalization of the subspace Hamiltonian is distributed to a square grid of 144 processors 12x12 Default values are nimage 1 npool 1 ntg 1 ndiag is set to 1 if ScaLAPACK is not compiled it is set to the square integer smaller than or equal to half the number of processors of each pool 30 Massively parallel calculations For very large jobs i e O 1000 atoms or so or for very long jobs to be run on massively parallel machines e g IBM BlueGene it is crucial to use in an effective way both the task group and the linear algebra parallelization Without a judicious choice
69. input data Warning negative or imaginary charge or core charge or npt with rhoup lt 0 or rho dw lt 0 These are warning messages that can be safely ignored unless the negative or imaginary charge is sizable let us say of the order of 0 1 If it is something seriously wrong is going on Otherwise the origin of the negative charge is the following When one transforms a positive function in real space to Fourier space and truncates at some finite cutoff the positive function is no longer guaranteed to be positive when transformed back to real space This happens only with core corrections and with USPPs In some cases it may be a source of trouble see next point but it is usually solved by increasing the cutoff for the charge density Structural optimization is slow or does not converge or ends with a mysterious bfgs error Typical structural optimizations based on the BFGS algorithm converge to the default thresholds etot_conv_thr and forc_conv_thr in 15 25 BFGS steps depending on the starting configuration This may not happen when your system is characterized by floppy low energy modes that make very difficult and of little use anyway to reach a well converged structure no matter what Other possible reasons for a problematic convergence are listed below Close to convergence the self consistency error in forces may become large with respect to the value of forces The resulting mismatch between forces a
70. ion contains the following core packages for the cal culation of electronic structure properties within Density Functional Theory DFT using a Plane Wave PW basis set and pseudopotentials PP e PWscf Plane Wave Self Consistent Field e CP Car Parrinello It also includes the following more specialized packages e NEB energy barriers and reaction pathways through the Nudged Elastic Band method e PHonon phonons with Density Functional Perturbation Theory e PostProc various utilities for data postprocessing e PWcond ballistic conductance http people sissa it smogunov PWCOND pwcond htm1 e XSPECTRA K edge X ray adsorption spectra e vdW experimental dynamic polarizability e GWW experimental GW calculation using Wannier functions http gww qe forge org e TD DFPT calculations of spectra using Time Dependent Density Functional Perturbation Theory see TDDFPT README for a list of reference papers The following auxiliary codes are included as well e PWgui a Graphical User Interface producing input data files for PWscf 3 atomic a program for atomic calculations and generation of pseudopotentials QHA utilities for the calculation of projected density of states PDOS and of the free energy in the Quasi Harmonic Approximation to be used in conjunction with PHonon PlotPhon phonon dispersion plotting utility to be used in conjunction with PHonon A copy of required external libraries are included
71. ith so e If you are not running on the same machines on which the code was compiled you need either to have the same shared libraries installed on both machines or to load statically all libraries using appropriate configure or loader options The same applies to Beowulf style parallel machines the needed shared libraries must be present on all PCs errors in examples with parallel execution If you get error messages in the example scripts i e not errors in the codes on a parallel machine such as e g run example n command not found you may have forgotten the in the definitions of PARA_PREFIX and PARA POSTFIX pw x prints the first few lines and then nothing happens parallel execution If the code looks like it is not reading from input maybe it isn t the MPI libraries need to be properly configured to accept input redirection Use pw x inp and the input file name see Sec 3 2 or inquire with your local computer wizard if any Since v 4 2 this is for sure the reason if the code stops at Waiting for input pw x stops with error while reading data There is an error in the input data typically a misspelled namelist variable or an empty input file Unfortunately with most compilers the code just reports Error while reading XXX namelist and no further useful information Here are some more subtle sources of trouble e Out of bound indices in dimensioned variables read in the namelists e Input data file
72. known fields including some that are specific to CP are ignored by PWscf and vice versa CP ignores PWscf specific fields See the files mentioned above for details on the available cards Note about k points The k point grid can be either automatically generated or manually provided as a list of k points and a weight in the Irreducible Brillouin Zone only of the Bravais lattice of the crystal The code will generate unless instructed not to do so see variable nosym all required k point and weights if the symmetry of the system is lower than the symmetry of the Bravais lattice The automatic generation of k points follows the convention of Monkhorst and Pack 4 2 Data files The output data files are written in the directory specified by variable outdir with names specified by variable prefix a string that is prepended to all file names whose default value is prefix pwscf The iotk toolkit is used to write the file in a XML format whose definition can be found in the Developer Manual In order to use the data directory on a different machine you need to convert the binary files to formatted and back using the bin iotk script The execution stops if you create a file prefix EXIT in the working directory NOTA BENE this is the directory where the program is executed NOT the directory outdir defined in input where files are written Note that with some versions of MPI the working directory is the directory where the pw x exec
73. les work but crash with a mysterious iotk error when reading from data files Recent versions should be fine If you experience problems in reading files produced by previous versions of QUANTUM ESPRESSO gfortran used 64 bit record markers to allow writing of records larger than 2 GB Before with 32 bit record markers only records lt 2GB could be written However this caused problems with older files and inter compiler operability This was solved in GCC 4 2 by using 32 bit record markers but such that one can still store gt 2GB records following the implementation of Intel Thus this issue should be gone See 4 2 release notes item Fortran at http gcc gnu org gcc 4 2 changes html Info by Tobias Burnus March 2010 Using gfortran v 4 4 after May 27 2009 and 4 5 after May 5 2009 can produce wrong results unless the environment variable GFORTRAN_UNBUFFERED_ALL 1 is set Newer 4 4 4 5 versions later than April 2010 should be OK See http gcc gnu org bugzilla show_bug cgi id 43551 Info by Tobias Burnus March 2010 Linux PCs with g95 295 v 0 91 and later versions http www g95 org work The exe cutables that produce are however slower let us say 20 or so that those produced by gfortran which in turn are slower by another 20 or so than those produced by ifort Linux PCs with Sun Studio compiler The Sun Studio compiler sunf95 is free web site http developers sun com sunstudio and comes wi
74. lf qsmp omp PGI mp ftn mp nonuma OpenMP parallelization is currently implemented and tested for the following combinations of FFTs and libraries internal FFTW copy D__FFTW ESSL D__ESSL or D__LINUX_ESSL link with lesslsmp ACML D__ACML link with lacml_mp Currently ESSL when available are faster than internal FFTW which in turn are faster than ACML 3 3 1 Understanding parallel I O In parallel execution each processor has its own slice of wavefunctions to be written to tem porary files during the calculation The way wavefunctions are written by pw x is governed by variable wf_collect in namelist CONTROL If wf_collect true the final wavefunctions are collected into a single directory written by a single processor whose format is independent on the number of processors If wf_collect false default each processor writes its own slice of the final wavefunctions to disk in the internal format used by PWscf The former case requires more disk I O and disk space but produces portable data files the latter case requires less I O and disk space but the data so produced can be read only by 31 a job running on the same number of processors and pools and if all files are on a file system that is visible to all processors i e you cannot use local scratch directories there is presently no way to ensure that the distribution of processes on processors will follow the same pattern for different jobs cp x i
75. lf Marenostrum configure ARCH ppc64 bg IBM BG P BlueGene configure Generates the following files 12 install make sys compilation rules and flags used by Makefile install configure msg a report of the configuration run not needed for compilation install config log detailed log of the configuration run may be needed for debugging include fft_defs h defines fortran variable for C pointer used only by FFTW include c defs h defines C to fortran calling convention and a few more definitions used by C files NOTA BENE unlike previous versions configure no longer runs the makedeps sh shell script that updates dependencies If you modify the sources run install makedeps sh or type make depend to update files make depend in the various subdirectories You should always be able to compile the QUANTUM ESPRESSO suite of programs without having to edit any of the generated files However you may have to tune configure by specifying appropriate environment variables and or command line options Usually the tricky part is to get external libraries recognized and used see Sech for details and hints Environment variables may be set in any of these ways export VARIABLE value configure sh bash ksh setenv VARIABLE value configure csh tcsh configure VARIABLE value any shell Some environment variables that are relevant to configure are ARCH label identifying the machine type see below F90 F77 CC names of Fortran 95 Fo
76. libraries are not correctly installed 71 Compilation works but the executable doesn t start because shared libraries not found This is a frequent problem with MKL libraries You need to set some environment variables telling the system where the shared libraries are See the documentation by Intel that comes with MKL libraries 12 3 Pseudopotentials Can I mix USPP NCPP PAW Yes you can if implemented of course a few kinds of calculations are not available with USPP a few more are not for PAW A small restrictions exists in cp x expecting atoms with USPP listed before those with NCPP which in turn are expected before local PP s if any A further restriction that can be overridden is that all PP s should be generated with the same XC Otherwise you can mix and match Note that it is the hardest atom that determines the cutoff Where can I find pseudopotentials for atom X First a general rule when you ask for a pseudopotential you should always specify which kind of PP you need NCPP USPP PAW full or scalar relativistic for which XC functional and for many elements with how many electrons in valence If you do not find anything suitable in the pseudopotential page of the web site or in the links thereof we have bad news for you you have to produce it by yourself See for more Where can I find pseudopotentials for rare earth X Please consider first if DFT is suitable for your system In many cases it isn
77. ling list is a voluntary endeavor nobody is entitled to an answer even less to an immediate answer e Finally please note that the mailing list is not a replacement for your own work nor is it a replacement for your thesis director s work 1 4 Terms of use QUANTUM ESPRESSO is free software released under the GNU General Public License See http www gnu org licenses old licenses gp1 2 0 txt or the file License in the distribution We shall greatly appreciate if scientific work done using this code will contain an explicit acknowledgment and the following reference P Giannozzi S Baroni N Bonini M Calandra R Car C Cavazzoni D Ceresoli G L Chiarotti M Cococcioni I Dabo A Dal Corso S Fabris G Fratesi S de Gironcoli R Gebauer U Gerstmann C Gougoussis A Kokalj M Lazzeri L Martin Samos N Marzari H Mauri R Mazzarello S Paolini A Pasquarello L Paulatto C Sbraccia S Scandolo G Sclauzero A P Seitsonen A Smo gunov P Umari R M Wentzcovitch J Phys Condens Matter 21 395502 2009 http arxiv org abs 0906 2569 Note the form QUANTUM ESPRESSO for textual citations of the code Pseudopotentials should be cited as for instance We used the pseudopotentials C pbe rrjkus UPF and O pbe vbc UPF from http www quantum espresso org 2 Installation 2 1 Download Presently QUANTUM ESPRESSO is only distributed in source form some precompiled exe cutables binary files
78. lips are considerably more efficient in quantum Monte Carlo calculations If blip_convert false a pwfn data file is produced orbitals expanded in plane waves if blip_convert true either a bwfn data file or a bwfn data b1 file is produced depending on the value of blip binary see below blip_binary if true and if blip convert is also true write the blip wave function as an un formatted binary bwfn data b1 file This is much smaller than the formatted bwfn data file but is not generally portable across all machines blip_single_prec if false the orbital coefficients in bwfn data b1 are written out in double precision if the user runs into hardware limits blip_single_prec can be set to true in which case the coefficients are written in single precision reducing the memory and disk requirements at the cost of a small amount of accuracy 40 blip_multiplicity the quality of the blip expansion i e the fineness of the blip grid can be improved by increasing the grid multiplicity parameter given by this keyword Increasing the grid multiplicity results in a greater number of blip coefficients and therefore larger memory requirements and file size but the CPU time should be unchanged For very accurate work one may want to experiment with grid multiplicity larger that 1 0 Note however that it might be more efficient to keep the grid multiplicity to 1 0 and increase the plane wave cutoff instead n points for test if
79. ls Remember that parallelization with respect to k points pools does not distribute memory parallelization with respect to R and G space does e buggy or weird behaving compiler pw x crashes with error in davcio davcio is the routine that performs most of the I O operations read from disk and write to disk in pw x error in davcio means a failure of an I O operation e If the error is reproducible and happens at the beginning of a calculation check if you have read write permission to the scratch directory specified in variable outdir Also check if there is enough free space available on the disk you are writing to and check your disk quota if any e If the error is irreproducible your might have flaky disks if you are writing via the network using NFS which you shouldn t do anyway your network connection might be not so stable or your NFS implementation is unable to work under heavy load e If it happens while restarting from a previous calculation you might be restarting from the wrong place or from wrong data or the files might be corrupted e If you are running two or more instances of pw x at the same time check if you are using the same file names in the same temporary directory For instance if you submit a series of jobs to a batch queue do not use the same outdir and the same prefix unless you are sure that one job doesn t start before a preceding one has finished pw x crashes in parallel execution wi
80. m files produced by pw xfor band structure plotting projwfc x calculates projections of wavefunction over atomic orbitals performs Lowdin population analysis and calculates projected density of states These can be summed using auxiliary code sumpdos x plotrho x produces PostScript 2 d contour plots plotband x reads the output of bands x produces PostScript plots of the band structure average x calculates planar averages of quantities produced by pp x potentials charge magnetization densities dos x calculates electronic Density of States DOS epsilon x calculates RPA frequency dependent complex dielectric function pw2wannier x interface with Wannier90 package wannier_ham x generate a model Hamiltonian in Wannier functions basis pmw x generates Poor Man s Wannier functions to be used in DFT U calculations about Bader s analysis on http theory cm utexas edu bader one can find a soft that performs Bader s analysis starting from charge on a regular grid The required cube format can be produced by QUANTUM ESPRESSO using pp x info by G Lapenna who has successfully used this technique but adds Problems occur with polar X H bonds or in all cases where the zero flux of density comes too close to atoms described with pseudo potentials This code should perform decomposition into Voronoi polyhedra as well in place of obsolete code voronoy x removed from distribution since v 4 2 The utility program
81. m_input and add the IONIC_VELOCITIES card after the ATOMIC_POSITION card with the list of velocities in atomic units NOTA BENE in restarting the dynamics after the first CP run remember to remove or comment the velocities parameters amp electrons emass 400 d0 emass_cutoff 2 5d0 electron_dynamics verlet electron_velocities zero amp ions ion_dynamics verlet jon_velocities zero otherwise you will quench the system interrupting the sampling of the microcanonical ensemble 52 Varying the temperature It is possible to change the temperature of the system or to sample the canonical ensemble fixing the average temperature this is done using the Nos thermostat To activate this thermostat for ions you have to specify in namelist amp IONS amp ions ion_dynamics verlet ion_temperature nose fnosep 60 0 tempw 300 0 where fnosep is the frequency of the thermostat in THz that should be chosen to be comparable with the center of the vibrational spectrum of the system in order to excite as many vibrational modes as possible tempw is the desired average temperature in Kelvin Note to avoid a strong coupling between the Nos thermostat and the system proceed step by step Don t switch on the thermostat from a completely relaxed configuration adding a random displacement is strongly recommended Check which is the average temperature via a few steps of a
82. microcanonical simulation Don t increase the temperature too much Finally switch on the thermostat In the case of molecular system different modes have to be thermalized it is better to use a chain of thermostat or equivalently running different simulations with different frequencies Nose thermostat for electrons It is possible to specify also the thermostat for the electrons This is usually activated in metals or in systems where we have a transfer of energy between ionic and electronic degrees of freedom Beware the usage of electronic thermostats is quite delicate The following information comes from K Kudin The main issue is that there is usually some natural fictitious kinetic energy that electrons gain from the ionic motion drag One could easily quantify how much of the fictitious energy comes from this drag by doing a CP run then a couple of CG same as BO steps and then going back to CP The fictitious electronic energy at the last CP restart will be purely due to the drag effect The thermostat on electrons will either try to overexcite the otherwise cold electrons or it will try to take them down to an unnaturally cold state where their fictitious kinetic energy is even below what would be just due pure drag Neither of this is good I think the only workable regime with an electronic thermostat is a mild overexcitation of the electrons however to do this one will need to know rather p
83. mization stage Use the input of the first run changing restart mode gt from_scratch to restart_mode restart NOTA BENE Unless you are already experienced with the system you are studying or with the internals of the code you will usually need to tune some input parameters like emass dt and cut offs For this purpose a few trial runs could be useful you can perform short minimizations say 10 steps changing and adjusting these parameters to fit your needs You can specify the degree of convergence with these two thresholds etot_conv_thr total energy difference between two consecutive steps ekin_conv_thr value of the fictitious kinetic energy of the electrons Usually we consider the system on the GS when ekin_conv_thr lt 1075 You could check the value of the fictitious kinetic energy on the standard output column EKINC Different strategies are available to minimize electrons but the most used ones are e steepest descent electron dynamics sd e damped dynamics electron_dynamics damp electron_damping a number typ ically ranging from 0 1 and 0 5 See the input description to compute the optimal damping factor 9 2 Relax the system Once your system is in the GS depending on how you have prepared the starting atomic configuration 1 if you have set the atomic positions by hand and or from a classical code check the forces on atoms and if they are large 0 1 1 0 atomic units
84. n CP Mike Towler wrote the PWscf to CASINO subsection 1 3 Contacts The web site for QUANTUM ESPRESSO is http www quantum espresso org Releases and patches can be downloaded from this site or following the links contained in it The main entry point for developers is the QE forge web site http www qe forge org The recommended place where to ask questions about installation and usage of QUANTUM ESPRESSO and to report bugs is the pw_forum mailing list pw forumOpwscf org Here you can receive news about QUANTUM ESPRESSO and obtain help from the developers and from knowledgeable users Please read the guidelines for posting section 1 3 1 You have to be subscribed in order to post to the pw_forum list NOTA BENE only messages that appear to come from the registered user s e mail address in its exact form will be accepted Messages waiting for moderator approval are automatically deleted with no further processing sorry too much spam In case of trouble carefully check that your return e mail is the correct one i e the one you used to subscribe Since pw_forum averages 10 message a day an alternative low traffic mailing list pw_usersOpwscf org is provided for those interested only in QUANTUM ESPRESSO related news such as e g announcements of new versions tutorials etc You can subscribe but not post to this list from the QUANTUM ESPRESSO web site Contacts section If you need to contact the developers
85. n the MPI libraries and sometimes even from flaky hardware Sorry not our fault Why is the code saying Wrong atomic coordinates Because they are two or more atoms in the list of atoms have overlapping or anyway too close positions Can t you see why look better or use XCrySDen see above and remember that the code checks periodic images as well The code stops with an error in davcio Possible reasons disk is full outdir is not writable for any reason you changed some parameter s in the input like wf_collect or the number of processors pools without doing a bit of cleanup in your temporary files you were running more than one instance of pw x in the same temporary directory with the same file names The code stops with a wrong charge error In most cases you are treating a metallic system as if it were insulating The code stops with a mysterious error in IOTK OTK is a toolkit that reads writes XML files There are frequent reports of mysterious errors with IO TK not finding some variable in the XML data file If this error has no obvious explanation e g the file is properly written and read the searched variable is present etc and if it appears to be erratic or irreproducible e g it occurs only with version X of compiler Y it is almost certainly due to a compiler bug Try to reduce optimization level or use a different compiler If you paid real money for your compiler complain with the vendor 12 7 Self Consistency
86. nd energies may confuse the line minimization algorithm which assumes consistency between the two The code reduces the starting self consistency threshold conv thr when approaching the minimum energy configura tion up to a factor defined by upscale Reducing conv_thr or increasing upscale yields a smoother structural optimization but if conv_thr becomes too small electronic self consistency may not converge You may also increase variables etot_conv_thr and forc_conv_thr that determine the threshold for convergence the default values are quite strict A limitation to the accuracy of forces comes from the absence of perfect translational in variance If we had only the Hartree potential our PW calculation would be translationally invariant to machine precision The presence of an XC potential introduces Fourier components in the potential that are not in our basis set This loss of precision more serious for gradient corrected functionals translates into a slight but detectable loss of translational invariance the energy changes if all atoms are displaced by the same quantity not commensurate with the FFT grid This sets a limit to the accuracy of forces The situation improves somewhat by increasing the ecutrho cutoff pw x stops during variable cell optimization in checkallsym with non orthogonal operation error Variable cell optimization may occasionally break the starting symmetry of the cell When this happens the run is stopped beca
87. ng the spin polarized case 8 3 Projection over atomic states DOS The code projwfc x calculates projections of wavefunctions over atomic orbitals The atomic wavefunctions are those contained in the pseudopotential file s The Lowdin population anal ysis similar to Mulliken analysis is presently implemented The projected DOS or PDOS the DOS projected onto atomic orbitals can also be calculated and written to file s More details on the input data are found in file Doc INPUT_PROJWFC The ordering of the various angular momentum components defined in routine flib ylmr2 f90 is as follows Po o t Pi olt Pii t cosd Pyi t sing Poolt Poi t cosd Poi t sing P22 t cos2 P22 t sin2 and so on where P m Legendre Polynomials t cos0 z r atan y z The total electronic DOS is instead calculated by code dos x See Example 08 for total and projected electronic DOS calculations 8 4 Wannier functions There are several Wannier related utilities in PostProc 46 1 The Poor Man Wannier code pmw x to be used in conjunction with DFT U calcula tions see Example 25 2 The interface with Wannier90 code pw2wannier x see the documentation in W90 you have to install the Wannier90 plug in 3 The wannier_ham x code generates a model Hamiltonian in Wannier functions basis see examples WannierHam example 8 5 Other tools Code sumpdos x can be used to sum selected PDOS produced by projwfc x by specifying t
88. nly see the Developer Manual 2 3 1 Manual configuration If configure stops before the end and you don t find a way to fix it you have to write working make sys include fft defs h and include c defs h files For the latter two files follow the explanations in include defs h README If configure has run till the end you should need only to edit make sys A few templates each for a different machine type are provided in the insta11 directory they have names of the form Make system where system is a string identifying the architecture and compiler The template used by configure is also found there as make sys in and contains explanations of the meaning of the various variables The difficult part will be to locate libraries Note that you will need to select appropriate preprocessing flags in conjunction with the desired or available libraries e g you need to add D__FFTW to DFLAGS if you want to link internal FFTW For a correct choice of preprocessing flags refer to the documentation in include defs h README NOTA BENE If you change any settings e g preprocessing compilation flags after a previous successful or failed compilation you must run make clean before recompiling unless you know exactly which routines are affected by the changed settings and how to force their recompilation 14 2 4 Libraries QUANTUM ESPRESSO makes use of the following external libraries e BLAS http www netlib org blas and e LAPACK
89. nput file for non scf calculation See Example 03 Molecular Dynamics Specify calculation md the time step dt and possibly the num ber of MD stops nstep Use variable ion_dynamics in namelist amp IONS for a fine grained control of the kind of dynamics Other options for setting the initial temperature and for thermalization using velocity rescaling are available Remember this is MD on the electronic ground state not Car Parrinello MD See Example 04 Free energy surface calculations Once PWscf is patched with the PLUMED plug in it is possible to use most PLUMED functionalities by running PWscf as pw x plumed plus the 38 other usual PWscf arguments The input file for PLUMED must be found in the specified outdir with fixed name plumed dat Variable cell optimization Since v 4 2 the newer BFGS algorithm covers the case of variable cell optimization as well Note however that variable cell calculations both optimization and dynamics are performed with plane waves and G vectors calculated for the starting cell This means that if you re run a self consistent calculation for the final cell and atomic positions using the same cutoff ecutwfc and or ecutrho if applicable you may not find exactly the same results unless your final and initial cells are very similar or unless your cutoff s are very high In order to provide a further check a last step is performed in which a scf calculation is performed for the converged structu
90. nstead always collects the final wavefunctions into a single directory Files written by pw x can be read by cp x only if wf_collect true and if produced for k 0 case The directory for data is specified in input variables outdir and prefix the former can be specified as well in environment variable ESPRESSO_TMPDIR outdir prefix save A copy of pseudopotential files is also written there If some processor cannot access the data directory the pseudopotential files are read instead from the pseudopotential directory specified in input data Unpredictable results may follow if those files are not the same as those in the data directory IMPORTANT Avoid I O to network mounted disks via NFS as much as you can Ideally the scratch directory outdir should be a modern Parallel File System If you do not have any you can use local scratch disks i e each node is physically connected to a disk and writes to it but you may run into trouble anyway if you need to access your files that are scattered in an unpredictable way across disks residing on different nodes You can use input variable disk_io minimal or even none if you run into trouble or into angry system managers with excessive I O with pw x The code will store wavefunctions into RAM during the calculation Note however that this will increase your memory usage and may limit or prevent restarting from interrupted runs Cray XT3 On the cray xt3 there is a special hack to keep
91. o problems have been encountered so far Sadly as of 11 1 088 the 64 bit binary misbehave under some tests Any attempt to compile 64 bit binary using 11 1 088 will result in very strange compilation errors Like the previous section I would recommend installing macports compiler suite First make sure that you are using the 32 bit version of the compilers i e opt intel Compiler 11 1 088 bin ifortvars sh ia32 opt intel Compiler 11 1 088 bin iccvars sh ia32 will set the environment for 32 bit compilation in my case Then the MPI environment has to be set up for Intel compilers similar to previous section The recommended configuration line for QUANTUM ESPRESSO is configure CC icc CXX icpc F77 ifort F90 ifort FC ifort CPP cpp mp 4 3 MKL libraries will be detected automatically if they are in their default locations Otherwise mklvars32 has to be sourced before the configuration script Security issues MacOs 10 6 comes with a disabled firewall Preparing a ipfw based firewall is recommended Open source and free GUIs such as WaterRoof and NoobProof are available that may help you in the process 2 7 8 SGI Alpha SGI Mips machines e g Origin and HP Compaq Alpha machines are no longer supported since v 4 2 27 3 Parallelism 3 1 Understanding Parallelism Two different parallelization paradigms are currently implemented in QUANTUM ESPRESSO 1 Message Passing MPI A copy of the executable runs on each
92. ode will stop if too small values are required it will waste CPU time and memory for too large values Note that in parallel execution it is very convenient to have FFT grid dimensions along z that are a multiple of the number of processors pw x does not find all the symmetries you expected pw x determines first the symmetry operations rotations of the Bravais lattice then checks which of these are symmetry operations of the system including if needed fractional translations This is done by rotating and translating if needed the atoms in the unit cell and verifying if the rotated unit cell coincides with the original one Assuming that your coordinates are correct please carefully check you may not find all the symmetries you expect because e the number of significant figures in the atomic positions is not large enough In file PW eqvect f90 the variable accep is used to decide whether a rotation is a symmetry operation Its current value 107 is quite strict a rotated atom must coincide with another atom to 5 significant digits You may change the value of accep and recompile e they are not acceptable symmetry operations of the Bravais lattice This is the case for Cen for instance the I icosahedral group of Cen contains 5 fold rotations that are incompatible with translation symmetry e the system is rotated with respect to symmetry axis For instance a Cen molecule in the fcc lattice will have 24 symmetry operations T
93. of all you should verify that the structure is really the same hint compare Ewald energies Also note that that a the modified kinetic energy functional often used in variable cell calculations affects the calculated pressure stress b the PW basis set used in a variable cell calculations is determined by the cutoff and the initial cell gemometry If you make a calculation with the final geometry at the same cutoff you get slightly different results The difference should be small though unless you are using a too low cutoff for your system Since v 4 3 1 a final scf is performed at the end of the vc relax run to check for this Why do I get negative starting charge Self consistency requires an initial guess for the charge density in order to bootstrap the iterative algorithm This first guess is usually built from a superposition of atomic charges constructed from pseudopotential data More often than not this charges are a slightly too hard to be expanded very accurately in PWs hence some aliasing error will be introduced Especially if the unit cell is big and mostly empty some local low negative charge density will be produced This is NOT harmful at all the negative charge density is handled properly by the code and will disappear during the self consistent cycles but if it is very high let s say more than 0 001 number of electrons it may be a symptom that your charge density cutoff is too low L Paulatto November
94. of parameters large jobs will find a stumbling block in either memory or CPU requirements In particular the linear algebra parallelization is used in the diagonalization of matrices in the subspace of Kohn Sham states whose dimension is as a strict minimum equal to the number of occupied states These are stored as block distributed matrices distributed across processors and diagonalized using custom tailored diagonalization algorithms that work on block distributed matrices Since v 4 1 ScaLAPACK can be used to diagonalize block distributed matrices yielding bet ter speed up than the default algorithms for large gt 1000 matrices when using a large number of processors gt 512 If you want to test ScaLAPACK use configure with scalapack This will add D_ SCALAPACK to DFLAGS in make sys and set LAPACK_LIBS to something like LAPACK_LIBS lscalapack lblacs lblacsF77init lblacs llapack The repeated 1blacs is not an error it is needed If configure does not recognize ScaLA PACK inquire with your system manager on the correct way to link them A further possibility to expand scalability especially on machines like IBM BlueGene is to use mixed MPI OpenMP The idea is to have one or more MPI process es per multicore node with OpenMP parallelization inside a same node This option is activated by configure with openmp which adds preprocessing flag D__OPENMP and one of the following compiler options ifort openmp x
95. on as anything changes In particular between serial and parallel execution there are operations that are not performed in the same order As the numerical accuracy of computer numbers is finite this can yield slightly different results It is also normal that the total energy converges to a better accuracy than its terms since only the sum is variational i e has a minimum in correspondence to ground state charge density Thus if the convergence threshold is for instance 1078 you get 8 digit accuracy on the total energy but one or two less on other terms e g XC and Hartree energy It this is a problem for you reduce the convergence threshold for instance to 107 or 107 The differences should go away but it will probably take a few more iterations to converge Execution time is time dependent Yes it is On most machines and on most operating systems depending on machine load on communication load for parallel machines on various other factors including maybe the phase of the moon reported execution times may vary quite a lot for the same job 66 Warning N eigenvectors not converged This is a warning message that can be safely ignored if it is not present in the last steps of self consistency If it is still present in the last steps of self consistency and if the number of unconverged eigenvector is a significant part of the total it may signal serious trouble in self consistency see next point or something badly wrong in
96. ong to their respective owners 1 1 What can QUANTUM ESPRESSO do PWscf can currently perform the following kinds of calculations e ground state energy and one electron Kohn Sham orbitals e atomic forces stresses and structural optimization e molecular dynamics on the ground state Born Oppenheimer surface also with variable cell e macroscopic polarization and finite electric fields via the modern theory of polarization Berry Phases e the modern theory of polarization Berry Phases e free energy surface calculation at fixed cell through meta dynamics if patched with PLUMED All of the above works for both insulators and metals in any crystal structure for many exchange correlation XC functionals including spin polarization DFT U nonlocal VdW functional hybrid functionals for norm conserving Hamann Schluter Chiang PPs NCPPs in separable form or Ultrasoft Vanderbilt PPs USPPs or Projector Augmented Waves PAW method Non collinear magnetism and spin orbit interactions are also implemented An imple mentation of finite electric fields with a sawtooth potential in a supercell is also available NEB calculates reaction pathways and energy barriers using the Nudged Elastic Band NEB and Fourier String Method Dynamics SMD methods Note that these calculations are no longer performed by the pw x executable of PWscf Also note that NEB with Car Parrinello Molecular Dynamics is currently not implemented PHonon c
97. ound 0 05 is good for many systems It is also better to specify to restart with zero ionic and electronic velocities since we have changed the masses Change further the ionic masses to accelerate the minimization ATOMIC_SPECIES C 0 1d0 c_blyp_gia pp H 0 1d0 h ps when the system is really close to the equilibrium the damped dynamics slow down too especially because since we are moving electron and ions together the ionic forces are not properly correct then it is often better to perform a ionic step every N electronic steps or to move ions only when electron are in their GS within the chosen threshold This can be specified by adding in the ionic section the ion nstepe parameter then the amp IONS namelist become as follows 50 amp ions ion_dynamics damp ion_damping 0 2 ion_velocities zero ion_nstepe 10 Then we specify in the amp CONTROL namelist etot_conv_thr 1 d 6 ekin_conv_thr 1 d 5 forc_conv_thr 1 d 3 As aresult the code checks every 10 electronic steps whether the electronic system satisfies the two thresholds etot_conv_thr ekin_conv_thr if it does the ions are advanced by one step The process thus continues until the forces become smaller than forc_conv_thr Note that to fully relax the system you need many runs and different strategies that you should mix and change in order to speed up the convergence The process is not automatic but is strongly based on experience
98. ourse depending on the number of atoms and of images Here is some free advice 42 1 Don t use Climbing Image CI from the beginning It makes convergence slower espe cially if the special image changes during the convergence process this may happen if CI_scheme auto and if it does it may mess up everything Converge your calcula tion then restart from the last configuration with CI option enabled note that this will increase the barrier 2 Carefully choose the initial path Remember that QUANTUM ESPRESSO assumes con tinuity between the first and the last image at the initial condition In other words periodic images are NOT used you may have to manually translate an atom by one or more unit cell base vectors in order to have a meaningful initial path You can visualize NEB input files with XCrySDen as animations take some time to check if any atoms overlap or get very close in the initial path you will have to add intermediate images in this case 3 Try to start the NEB process with most atomic positions fixed in order to converge the more problematic ones before leaving all atoms move 4 Especially for larger systems you can start NEB with lower accuracy less k points lower cutoff and then increase it when it has converged to refine your calculation 5 Use the Broyden algorithm instead of the default one it is a bit more fragile but it removes the problem of oscillations in the calculated ac
99. r else of a less than perfect convergence of the geometry of the molecule Why do I get negative phonon frequencies Negative frequencies actually are imag inary frequencies w lt 0 If these occur for acoustic frequencies at Gamma point or for rotational modes of a molecule see above In all other cases it depends It may be a problem of bad convergence see above or it may signal a real instability Why do I get a message no elec field with metals If you want to calculate the contribution of macroscopic electric fields to phonons a quantity that is well defined in insulators only you cannot use smearing in the scf calculation or else the code will complain How can I calculate Raman IR coefficients in metals You cannot they are well defined only for insulators How can I calculate the electron phonon coefficients in insulators You cannot the current implementation is for metals only 77
100. r in compilation or preprocessing options try make clean recompile The make command should take care of all dependencies but do not rely too heavily on it If the problem persists recompile with reduced optimization level e maybe your input data are weird 64 FFT grid is machine dependent Yes they are The code automatically chooses the small est grid that is compatible with the specified cutoff in the specified cell and is an allowed value for the FFT library used Most FFT libraries are implemented or perform well only with dimensions that factors into products of small numbers 2 3 5 typically sometimes 7 and 11 Different FFT libraries follow different rules and thus different dimensions can result for the same system on different machines or even on the same machine with a different FFT See function allowed in Modules fft_scalar f90 As a consequence the energy may be slightly different on different machines The only piece that explicitly depends on the grid parameters is the XC part of the energy that is computed numerically on the grid The differences should be small though especially for LDA calculations Manually setting the FFT grids to a desired value is possible but slightly tricky using input variables nr1 nr2 nr3 and nris nr2s nr3s The code will still increase them if not acceptable Automatic FFT grid dimensions are slightly overestimated so one may try very carefully to reduce them a little bit The c
101. r interface with CASINO For PHonon we mention in particular e Michele Lazzeri Univ Paris VI for the 2n 1 code and Raman cross section calculation with 2nd order response e Andrea Dal Corso for USPP noncolinear spin orbit extensions to PHonon For PostProc we mention e Andrea Benassi SISSA for the epsilon utility e Dmitry Korotin Inst Met Phys Ekaterinburg for the wannier_ham utility The CP package is based on the original code written by Roberto Car and Michele Parrinello CP was developed by Alfredo Pasquarello IRRMA Lausanne Kari Laasonen Oulu Andrea Trave Roberto Car Princeton Nicola Marzari Univ Oxford Paolo Giannozzi and others FPMD later merged with CP was developed by Carlo Cavazzoni Gerardo Ballabio CINECA Sandro Scandolo ICTP Guido Chiarotti SISSA Paolo Focher and others We quote in particular e Manu Sharma Princeton and Yudong Wu Princeton for maximally localized Wannier functions and dynamics with Wannier functions e Paolo Umari Univ Padua for finite electric fields and conjugate gradients e Paolo Umari and Ismaila Dabo for ensemble DFT e Xiaofei Wang Princeton for META GGA e The Autopilot feature was implemented by Targacept Inc Other packages in QUANTUM ESPRESSO e PWcond was written by Alexander Smogunov CEA and Andrea Dal Corso For an introduction see http people sissa it smogunov PWCOND pwcond html e PWgui was written by Anton Kokalj IJS Ljubljana
102. r which the occupation number is also fractional so the number of band nbnd has to be chosen such as to have some empty states As a rule of thumb start with an initial occupation number of about 1 6 1 8 the more bands you consider the more the calculation is accurate but it also takes longer The CPU time scales almost linearly with the number of bands NOTA3 the parameter emass_cutoff is used in the preconditioning and it has a completely different meaning with respect to plain CP It ranges between 4 and 7 56 All the other parameters have the same meaning in the usual CP input and they are discussed above 9 4 3 Free energy surface calculations Once CP is patched with PLUMED plug in it becomes possible to turn on most of the PLUMED functionalities running CP as cp x plumed plus the other usual CP arguments The PLUMED input file has to be located in the specified outdir with the fixed name plumed dat 9 4 4 Treatment of USPPs The cutoff ecutrho defines the resolution on the real space FFT mesh as expressed by nr1 nr2 and nr3 that the code left on its own sets automatically In the USPP case we refer to this mesh as the hard mesh since it is denser than the smooth mesh that is needed to represent the square of the non norm conserving wavefunctions On this hard fine spaced mesh you need to determine the size of the cube that will encompass the largest of the augmentation charges this is what nr1b nr2b nr3b are
103. re with plane waves and G vectors calculated for the final cell Small differences between the two last steps are thus to be expected and give an estimate of the reliability of the variable cell optimization If you get a large difference you are likely quite far from convergence in the plane wave basis set and you need to increase the cutoff s Variable cell molecular dynamics A common mistake many new users make is to set the time step dt improperly to the same order of magnitude as for CP algorithm or not setting dt at all This will produce a not evolving dynamics Good values for the original RMW RM Wentzcovitch dynamics are dt 50 70 The choice of the cell mass is a delicate matter An off optimal mass will make convergence slower Too small masses as well as too long time steps can make the algorithm unstable A good cell mass will make the oscillation times for internal degrees of freedom comparable to cell degrees of freedom in non damped Variable Cell MD Test calculations are advisable before extensive calculation I have tested the damping algorithm that I have developed and it has worked well so far It allows for a much longer time step dt 100 150 than the RMW one and is much more stable with very small cell masses which is useful when the cell shape not the internal degrees of freedom is far out of equilibrium It also converges in a smaller number of steps than RMW Info from Cesar Da Silva the new damping al
104. re supported by configure with gcc4 g95 gfortran and the Intel compiler ifort with MKL libraries Parallel compilation with OpenMPI also works Intel Mac OS X with ifort Uninstall darwin ports fink and developer tools The presence of all of those at the same time generates many spooky events in the compilation procedure I installed just the developer tools from apple the intel fortran compiler and everything went on great Info by Riccardo Sabatini Nov 2007 25 Intel Mac OS X 10 4 with g95 and gfortran An updated version of Developer Tools XCode 2 4 1 or 2 5 that can be downloaded from Apple may be needed Some tests fails with mysterious errors that disappear if fortran BLAS are linked instead of system Atlas libraries Use BLAS_LIBS_SWITCH internal BLAS_LIBS path to espresso BLAS blas a latlas Info by Paolo Giannozzi jan 2008 updated April 2010 Detailed installation instructions for Mac OS X 10 6 Instructions for 10 6 3 by Osman Baris Malcioglu tested as of May 2010 Summary for the hasty GNU Install macports compilers Install MPI environment Configure QUANTUM ESPRESSO using configure CC gcc mp 4 3 CPP cpp mp 4 3 CXX g mp 4 3 F77 g95 FC g95 Intel Use Version 11 1 088 Use 32 bit compilers Install MPI environment install macports provided cpp optional Configure QUANTUM ESPRESSO using configure CC icc CXX icpc F77 ifort F90 ifort FC ifort CPP cpp mp 4 3 Compilation with GNU compiler
105. real space to processors in reciprocal space it is columns of G vectors that are distributed to processors task groups In order to allow good parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes data can be redistributed to task groups so that each group can process several wavefunctions at the same time linear algebra group A further level of parallelization independent on PW or k point parallelization is the parallelization of subspace diagonalization pw x or iterative orthonor malization cp x Both operations required the diagonalization of arrays whose dimension is the number of Kohn Sham states or a small multiple All such arrays are distributed block like across the linear algebra group a subgroup of the pool of processors organized in a square 2D grid As a consequence the number of processors in the linear algebra group is given by n where n is an integer n must be smaller than the number of processors of a single pool The diagonalization is then performed in parallel using standard linear algebra operations This diagonalization is used by but should not be confused with the iterative Davidson algorithm One can choose to compile ScaLAPACK if available internal built in algorithms otherwise Communications Images and pools are loosely coupled and processors communicate between different images and pools only once in a while whereas processors within each pool are tig
106. recisely what is the fictitious kinetic energy due to the drag 9 4 Advanced usage 9 4 1 Self interaction Correction The self interaction correction SIC included in the CP package is based on the Constrained Local Spin Density approach proposed my F Mauri and coworkers M D Avezac et al PRB 71 205210 2005 It was used for the first time in QUANTUM ESPRESSO by F Baletto C Cavazzoni and S Scandolo PRL 95 176801 2005 This approach is a simple and nice way to treat ONE and only one excess charge It is moreover necessary to check a priori that the spin up and spin down eigenvalues are not 93 too different for the corresponding neutral system working in the Local Spin Density Ap proximation setting nspin 2 If these two conditions are satisfied and you are interest in charged systems you can apply the SIC This approach is a on the fly method to correct the self interaction with the excess charge with itself Briefly both the Hartree and the XC part have been corrected to avoid the interaction of the excess charge with tself For example for the Boron atoms where we have an even number of electrons valence electrons 3 the parameters for working with the SIC are system nbnd 2 total_magnetization 1 sic_alpha 1 d0 sic_epsilon 1 0d0 Sic sic_mac force_pairing true amp ions ion_dynamics none ion_radius 1 0 8d0 sic_rloc 1 0 ATOMIC_POSITIONS bohr B 0 00 0
107. rovided in input In this case pw x prints instead the highest occupied and lowest unoccupied levels If not the number of bands to be calculated was not provided in input and pw x calculates occupied bands only 75 What is the reference level for Kohn Sham energies Why do I get positive values for Kohn Sham levels The reference level is an ill defined quantity in calculations in solids with periodic boundary conditions Absolute values of Kohn Sham eigenvalues are meaningless Why do I get a strange value of the Fermi energy The value of the Fermi energy as well as of any energy for that matter depends of the reference level What you are referring to is probably the Fermi energy referred to the vacuum level i e the work function In order to obtain that you need to know what the vacuum level is which cannot be said from a bulk calculation only Stefano Baroni Sept 2008 Why I don t get zero pressure stress at equilibrium If you make a calculation with fixed cell parameters you will never get exactly zero pressure stress unless you use the cell that yields perfect equilibrium for your pseudopotentials cutoffs k points etc Such cell will anyway be slightly different from the experimental one Note however that pressures stresses in the order of a few KBar correspond to very small differences in terms of lattice parameters Why do I get different results from vc relax and from scf on the same structure First
108. rtran 77 and C compilers MPIF90 name of parallel Fortran 95 compiler using MPI CPP source file preprocessor defaults to CC E LD linker defaults to MPIF90 C F F90 CPP LD FLAGS compilation preprocessor loader flags LIBDIRS extra directories where to search for libraries For example the following command line configure MPIF90 mpf90 FFLAGS 02 assume byterecl CC gcc CFLAGS 03 LDFLAGS static instructs configureto use mpf90 as Fortran 95 compiler with flags 02 assume byterecl gcc as C compiler with flags 03 and to link with flag static Note that the value of FFLAGS must be quoted because it contains spaces NOTA BENE do not pass compiler names with the leading path included F90 f90xyz is ok F90 path to f90xyz is not Do not use environmental variables with configure unless they are needed try configure with no options as a first step If your machine type is unknown to configure you may use the ARCH variable to suggest an architecture among supported ones Some large parallel machines using a front end e g Cray XT will actually need it or else configure will correctly recognize the front end but not the specialized compilation environment of those machines In some cases cross compilation requires to specify the target machine with the host option This feature has not been ex tensively tested but we had at least one successful report compilation for NEC SX6 on a PC Currently supported architectures are
109. s The following instructions use macports version of gnu compilers due to some issues in mixing gnu supplied fortran compilers with apple modified gnu compiler collection For more information regarding macports please refer to http www macports org First install necessary compilers from macports port install gcc43 port install g95 The apple supplied MPI environment has to be overridden since there is a new set of compilers now and Apple provided mpif90 is just an empty placeholder since Apple does not provide fortran compilers I have used OpenMPI for this case Recommended minimum configuration line is configure CC gcc mp 4 3 CPP cpp mp 4 3 CXX g mp 4 3 F77 g95 FC g95 of course installation directory should be set accordingly if a multiple compiler environment is desired The default installation directory of OpenMPI overwrites apple supplied MPI perma nently Next step is QUANTUM ESPRESSO itself Sadly the Apple supplied optimized BLAS LAPACK libraries tend to misbehave under different tests and it is much safer to use internal libraries The minimum recommended configuration line is presuming the environment is set correctly configure CC gcc mp 4 3 CXX g mp 4 3 F77 g95 F90 g95 FC g95 CPP cpp mp 4 3 wi 26 Compilation with Intel compilers Newer versions of Intel compiler 11 1 067 support Mac OS X 10 6 and furthermore they are bundled with intel MKL 32 bit binaries obtained using 11 1 088 are tested and n
110. s also possible see section 2 2 Further documentation beyond what is provided in this guide can be found in the pw_forum mailing list pw_forum pwscf org You can subscribe to this list browse and search its archives links in http www quantum espresso org contacts php See section 1 3 Contacts for more info the Doc directory of the QUANTUM ESPRESSO distribution containing a detailed description of input data for most codes in files INPUT_ txt and INPUT_ html plus and a few additional pdf documents the QUANTUM ESPRESSO web site http www quantum espresso org e the QUANTUM ESPRESSO Wiki http www quantum espresso org wiki index php Main Page People who want to contribute to QUANTUM ESPRESSO should read the Developer Manual Doc developer_man pdf This guide does not explain the basic Unix concepts shell execution path directories etc and utilities needed to run QUANTUM ESPRESSO it does not explain either solid state physics and its computational methods If you want to learn the latter you should read a good textbook such as e g the book by Richard Martin Electronic Structure Basic Theory and Practical Methods Cambridge University Press 2004 or Density functional theory a practical introduction D S Sholl J A Steckel Wiley 2009 See also the Learn section in the QUANTUM ESPRESSO web site the Reference Papers section in the Wiki All trademarks mentioned in this guide bel
111. s containing M Control M characters at the end of lines or non ASCII characters e g non ASCII quotation marks that at a first glance may look the same as the ASCII character Typically this happens with files coming from Windows or produced with smart editors Both may cause the code to crash with rather mysterious error messages If none of the above applies and the code stops at the first namelist CONTROL and you are running in parallel see the previous item pw x mumbles something like cannot recover or error reading recover file You are trying to restart from a previous job that either produced corrupted files or did not do what you think it did No luck you have to restart from scratch 61 pw x stops with inconsistent DFT error As a rule the flavor of DFT used in the calculation should be the same as the one used in the generation of pseudopotentials which should all be generated using the same flavor of DFT This is actually enforced the type of DFT is read from pseudopotential files and it is checked that the same DFT is read from all PPs If this does not hold the code stops with the above error message Use at your own risk input variable input_dft to force the usage of the DFT you like pw x stops with error in cdiaghg or rdiaghg Possible reasons for such behavior are not always clear but they typically fall into one of the following cases e serious error in data such as bad atomic positions or bad cr
112. s in pwtools are dist x calculates distances and angles between atoms in a cell taking into account periodicity ev x fits energy vs volume data to an equation of state kpoints x produces lists of k points pwi2xsf sh pwo2xsf sh process respectively input and output files not data files for pw xand produce an XSF formatted file suitable for plotting with XCrySDen a powerful crystalline and molecular structure visualization program http www xcrysden org BEWARE the pwi2xsf sh shell script requires the pwi2xsf x executables to be located somewhere in your PATH band _plot x undocumented and possibly obsolete bs awk mv awk are scripts that process the output of pw x not data files Usage 18 awk f bs awk lt my pw file gt myfile bs awk f mv awk lt my pw file gt myfile mv The files so produced are suitable for use with xbs a very simple X windows utility to display molecules available at http www ccl net cca software X WINDOW xbsa README shtml e kvecs_FS x bands_FS x utilities for Fermi Surface plotting using XCrySDen Other utilities VdW contains the sources for the calculation of the finite imaginary fre quency molecular polarizability using the approximated Thomas Fermi von Weizacker scheme contributed by H V Nguyen Sissa and Hanoi University Compile with make vdw executa bles in VdW vdw x no documentation yet but an example in examples example34 2 6 Running examples As a fin
113. ses that the two sets are not the same In particular it is often convenient to have nrxi nri 1 to reduce memory conflicts 4 4 Pseudopotential files Pseudopotential files for tests and examples are found in the pseudo subdirectory A much larger set of PP s can be found under the pseudo link of the web site QUANTUM ESPRESSO uses a unified pseudopotential format UPF for all types of pseudopotentials but still accepts a number of older formats If you do not find what you need you may e Convert pseudopotentials written in a different format using the converters listed in upftools UPF compile with make upf e Generate it using atomic See the documentation in atomic_doc and in particular the library of input files in pseudo_library e Generate it using other packages David Vanderbilt s code UltraSoft and Norm Conserving OPIUM Norm Conserving The Fritz Haber code Norm Conserving The first two codes produce pseudopotentials in one of the supported formats the third in a format that can be converted to UPF Remember always test the pseudopotentials on simple test systems before proceeding to serious calculations Note that the type of XC used in the calculation is read from pseudopotential files As a rule you should use only pseudopotentials that have been generated using the same XC that you are using in your simulation You can override this restriction by setting input variable input_dft Th
114. setting the following variables as needed BIN_DIR directory where executables reside PSEUDO_DIR directory where pseudopotential files reside TMP_DIR directory to be used as temporary storage area 19 The default values of BIN DIR and PSEUDO DIR should be fine unless you have in stalled things in nonstandard places TMP_DIR must be a directory where you have read and write access to with enough available space to host the temporary files produced by the example runs and possibly offering high I O performance i e don t use an NFS mounted directory NOTA BENE do not use a directory containing other data the examples will clean it If you have compiled the parallel version of QUANTUM ESPRESSO this is the default if parallel libraries are detected you will usually have to specify a driver program such as mpirun or mpiexec and the number of processors see Sec 3 2 for details In order to do that edit again the environment_variables file and set the PARA_PREFIX and PARA POSTFIX variables as needed Parallel executables will be run by a command like this PARA_PREFIX pw x PARA_POSTFIX lt file in gt file out For example if the command line is like this as for an IBM SP poe pw x procs 4 lt file in gt file out you should set PARA_PREFIX poe PARA_POSTFIX procs 4 Furthermore if your machine does not support interactive use you must run the commands specified below through the batch queuing system
115. sors see below 98 10 2 Memory requirements A typical self consistency or molecular dynamics run requires a maximum memory in the order of O double precision complex numbers where O mMN PN pN N2N3 q4Nr1Nr2 N73 with m p q small factors all other variables have the same meaning as above Note that if the P point only k 0 is used to sample the Brillouin Zone the value of N will be cut into half The memory required by the phonon code follows the same patterns with somewhat larger factors m p q 10 3 File space requirements A typical pw x run will require an amount of temporary disk space in the order of O double precision complex numbers O N MN IN Nr2N 3 where q 2x mixing_ndim number of iterations used in self consistency default value 8 if disk_io is set to high q 0 otherwise 10 4 Parallelization issues pw x and cp x can run in principle on any number of processors The effectiveness of par allelization is ultimately judged by the scaling i e how the time needed to perform a job scales with the number of processors and depends upon e the size and type of the system under study e the judicious choice of the various levels of parallelization detailed in Sec 3 2 e the availability of fast interprocess communications or lack of it Ideally one would like to have linear scaling i e T Tp N for Np processors where To is the estimated time for serial execution In ad
116. t intel mk170 1ib 32 usr lib math If this still fails you may set some or all of the _LIBS variables manually and retry For example configure BLAS_LIBS L usr lib math 1f77blas latlas_sse Beware that in this case configure will blindly accept the specified value and won t do any extra search 2 5 Compilation There are a few adjustable parameters in Modules parameters f90 The present values will work for most cases All other variables are dynamically allocated you do not need to recompile your code for a different system At your option you may compile the complete QUANTUM ESPRESSO suite of programs with make all or only some specific programs make with no arguments yields a list of valid compilation targets Here is a list e make pw produces PW pw x pw x calculates electronic structure structural optimization molecular dynamics e make neb produces the following codes in NEB for NEB calculations neb x calculates reaction barriers and pathways using NEB path_int x used by utility path_int sh that generates starting from a path a set of images a new one with a different number of images The initial and final points of the new path can differ from those in the original one e make ph produces the following codes in PH for phonon calculations ph x Calculates phonon frequencies and displacement patterns dielectric tensors effective charges uses data produced by pw x dynmat
117. t or output files should be the same in the two runs See Examples 01 05 08 NOTA BENE until v 4 0 atomic positions for a non scf calculations were read from input while the scf potential was read from the data file of the scf calculation Since v 4 1 both atomic positions and the scf potential are read from the data file so that consistency is guaranteed Noncolinear magnetization spin orbit interactions The following input variables are relevant for noncolinear and spin orbit calculations noncolin lspinorb starting magnetization one for each type of atoms To make a spin orbit calculation noncolin must be true If starting_ magnetization is set to zero or not given the code makes a spin orbit calculation without spin magnetization it assumes that time reversal symmetry holds and it does not calculate the magnetization The states are still two component spinors but the total magnetization is zero If starting magnetization is different from zero it makes a non collinear spin polarized calculation with spin orbit interaction The final spin magnetization might be zero or different from zero depending on the system Furthermore to make a spin orbit calculation you must use fully relativistic pseudopoten tials at least for the atoms in which you think that spin orbit interaction is large If all the pseudopotentials are scalar relativistic the calculation becomes equivalent to a noncolinear cal culation without spin orbit Andrea
118. tails see Example 06 7 3 Calculation of electron phonon interaction coefficients The calculation of electron phonon coefficients in metals is made difficult by the slow conver gence of the sum at the Fermi energy It is convenient to use a coarse k point grid to calculate 44 phonons on a suitable wavevector grid a dense k point grid to calculate the sum at the Fermi energy The calculation proceeds in this way 1 a scf calculation for the dense k point grid or a scf calculation followed by a non scf one on the dense k point grid specify option la2f true to pw x in order to save a file with the eigenvalues on the dense k point grid The latter MUST contain all k and k q grid points used in the subsequent electron phonon calculation All grids MUST be unshifted i e include k 0 2 a normal scf phonon dispersion calculation on the coarse k point grid specifying op tion elph true and the file name where the self consistent first order variation of the potential is to be stored variable fildvscf The electron phonon coefficients are calculated using several values of Gaussian broadening see PH elphon f90 because this quickly shows whether results are converged or not with respect to the k point grid and Gaussian broadening 3 Finally you can use matdyn x and lambda x input documentation in the header of PH lambda f90 to get the a F w function the electron phonon coefficient A and an estimate of the critical temperat
119. th a set of algebra libraries that can be used in place of the slow built in libraries It also supports OpenMP which g95 does not On the other hand it is a pain to compile MPI with it Furthermore the most recent version has a terrible bug that totally miscompiles the iotk input output library you ll have to compile it with reduced optimization info by Lorenzo Paulatto March 2010 Linux PCs with AMD Open64 suite The AMD Open64 compiler suite openf95 web site http developer amd com cpu open64 pages default aspx can be freely downloaded from the AMD site It is recognized by configure but little tested It sort of works but it fails to pass several tests info by Paolo Giannozzi March 2010 I have configured for Pathscale then switched to the Open64 compiler by editing make sys make pw succeeded and pw x did process my file but with make all I get an internal compiler error in CPV wf f90 info by Cezary Sliwa April 2011 Linux PCs with Intel compiler ifort The Intel compiler ifort is available for free for personal usage http software intel com It seem to produce the faster executables at least on Intel CPUs but not all versions work as expected ifort versions lt 9 1 are not recom mended due to the presence of subtle and insidious bugs In case of trouble update your version with the most recent patches available via Intel Premier support registration free of charge for Linux http soft
120. th an obscure message related to MPI errors Random crashes due to MPI errors have often been reported typically in Linux PC clusters We cannot rule out the possibility that bugs in QUANTUM ESPRESSO cause such behavior but we are quite confident that the most likely explanation is a hardware problem defective RAM for instance or a software bug in MPI libraries compiler operating system Debugging a parallel code may be difficult but you should at least verify if your problem is reproducible on different architectures software configurations input data sets and if there is some particular condition that activates the bug If this doesn t seem to happen the odds are that the problem is not in QUANTUM ESPRESSO You may still report your problem but 63 consider that reports like it crashes with obscure MPI error contain 0 bits of information and are likely to get 0 bits of answers pw x stops with error message the system is metallic specify occupations You did not specify state occupations but you need to since your system appears to have an odd number of electrons The variable controlling how metallicity is treated is occupations in namelist SYSTEM The default occupations fixed occupies the lowest N electrons 2 states and works only for insulators with a gap In all other cases use smearing tetrahedra for DOS calculations See input reference documentation for more details pw x stops with internal error c
121. than the others The second and third terms come respectively from local and nonlocal potential a a2 a3 are prefactors i e small numbers O 1 M number of valence bands nbnd N number of PW basis set dimension npw N1 Na Na dimensions of the FFT grid for wavefunctions nris nr2s nr3s N NN 8N P number of pseudopotential projectors summed on all atoms on all values of the angular momentum l and m 1 2 1 The time Torin required by orthonormalization is Lei b NM and the time Tsup required by subspace diagonalization is EH bo M where b and bz are prefactors A number of trial wavefunctions this will vary between M and 2 4M depending on the algorithm The time TA for the calculation of charge density from wavefunctions is Trho c MN 1N 2N r3log N1 Ny2 N 3 co MN 1 Nr2N 73 ck Tis where C1 C2 c3 are prefactors N 1 Na Na dimensions of the FFT grid for charge density nr1 nr2 nr3 N N 2N 3 8N where N number of G vectors for the charge density ngm and Tas time required by PAW USPPs contribution if any Note that for NCPPs the FFT grids for charge and wavefunctions are the same The time 7 for calculation of potential from charge density is Deaf dGNANaha daNy1 Ny2N 3log Ny1 Ny2 Ny3 where dj da are prefactors The above estimates are for serial execution In parallel execution each contribution may scale in a different manner with the number of proces
122. this is set to a positive integer greater than zero PWscf will sample the wave function the Laplacian and the gradient at a large number of random points in the simulation cell and compute the overlap of the blip orbitals with the original plane wave orbitals a lt BW PW gt y lt BW BW gt lt PW PW gt The closer a is to 1 the better the blip representation By increasing blip_multiplicity or by increasing the plane wave cutoff one ought to be able to make a as close to 1 as desired The number of random points used is given by n_points_for_test Finally note that DFT trial wave functions produced by PWSCF must be generated using the same pseudopotential as in the subsequent QMC calculation This requires the use of tools to switch between the different file formats used by the two codes CASINO uses the CASINO tabulated format PWSCF officially supports the UPFv2 format though it will read other deprecated formats This can be done through the casino2upf and upf2casino tools included in the upftools directory see the upftools README file for instructions An alternative converter casinogon is included in the CASINO distribution which produces the deprecated GON format but which can be useful when using non standard grids 6 NEB calculations Reminder 1 NEB calculations are no longer performed by pw x In order to perform a NEB calculation you should compile NEB neb x command make neb Remin
123. tivation energies If these oscil lations persist and you cannot afford more images focus to a smaller problem decompose it into pieces 6 A gross estimate of the required number of iterations is number of images number of atoms 3 Atoms that do not move should not be counted It may take half that many iterations or twice as many but more or less that s the order of magnitude unless one starts from a very good or very bad initial guess Courtesy of Lorenzo Paulatto 7 Phonon calculations Phonon calculation is presently a two step process First you have to find the ground state atomic and electronic configuration Second you can calculate phonons using Density Functional Perturbation Theory Further processing to calculate Interatomic Force Constants to add macroscopic electric field and impose Acoustic Sum Rules at q 0 may be needed In the following we will indicate by q the phonon wavevectors while k will indicate Bloch vectors used for summing over the Brillouin Zone Since version 4 0 it is possible to safely stop execution of ph x code using the same mecha nism of the pw x code i e by creating a file prefix EXIT in the working directory Execution can be resumed by setting recover true in the subsequent input data 7 1 Single q calculation The phonon code ph x calculates normal modes at a given q vector starting from data files produced by pw xwith a simple SCF calculation NOTE the alternative procedure
124. to write to the screen If this doesn t help move to next point pw x crashes with segmentation fault or similarly obscure messages Possible rea sons e too much RAM memory or stack requested see next item e if you are using highly optimized mathematical libraries verify that they are designed for your hardware e If you are using aggressive optimization in compilation verify that you are using the appropriate options for your machine e The executable was not properly compiled or was compiled on a different and incompat ible environment e buggy compiler or libraries this is the default explanation if you have problems with the provided tests and examples 62 pw x works for simple systems but not for large systems or whenever more RAM is needed Possible solutions e increase the amount of RAM you are authorized to use which may be much smaller than the available RAM Ask your system administrator if you don t know what to do In some cases the stack size can be a source of problems if so increase it with command limits or ulimit e reduce nbnd to the strict minimum or reduce the cutoffs or the cell size or a combination of them e use conjugate gradient diagonalization cg slow but very robust it requires less memory than the default Davidson algorithm If you stick to the latter use diago david_ndim 2 e in parallel execution use more processors or use the same number of processors with less poo
125. ure T For more details see Example 07 7 4 Distributed Phonon calculations A complete phonon dispersion calculation can be quite long and expensive but it can be split into a number of semi independent calculations using options start o last q start_irr last_irr An example on how to distribute the calculations and collect the results can be found in examples GRID_example Reference Calculation of Phonon Dispersions on the GRID using Quantum ESPRESSO R di Meo A Dal Corso P Giannozzi and S Cozzini in Chemistry and Material Science Applications on Grid Infrastructures editors S Cozzini A Lagana ICTP Lecture Notes Series Vol 24 pp 165 183 2009 8 Post processing There are a number of auxiliary codes performing postprocessing tasks such as plotting aver aging and so on on the various quantities calculated by pw x Such quantities are saved by pw x into the output data file s Postprocessing codes are in the PP directory All codes for which input documentation is not explicitly mentioned have documentation in the header of the fortran sources 8 1 Plotting selected quantities The main postprocessing code pp x reads data file s extracts or calculates the selected quan tity writes it into a format that is suitable for plotting Quantities that can be read or calculated are 45 charge density spin polarization various potentials local density of states at Ep local density of electronic entropy S
126. use the number of k points calculated for the starting configuration may no longer be suitable Possible solutions e start with a nonsymmetric cell 67 e use a symmetry conserving algorithm the Wentzcovitch algorithm cell dynamics damp w should not break the symmetry 11 2 Compilation problems with PLUMED xlc compiler If you get an error message like Operation between types char and int is not allowed change in file clib metadyn h define snew ptr nelem ptr nelem 0 NULL typeof ptr calloc melem sizeof define srenew ptr nelem ptr typeof ptr realloc ptr nelem sizeof ptr with define snew ptr nelem ptr nelem 0 NULL void calloc nelem sizeof ptr define srenew ptr nelem ptr void realloc ptr nelem sizeof ptr Calling C from fortran PLUMED assumes that fortran compilers add a single _ at the end of C routines You may get an error message as ERROR Undefined symbol init_metadyn ERROR Undefined symbol meta_force_calculation eliminate the _ from the definition of init_metadyn and meta_force_calculation i e change at line 529 void meta_force_calculation_ real cell int istep real xxx real yyy real zzz with void meta_force_calculation real cell int istep real xxx real yyy real zzz and at line 961 void init_metadyn_ int atoms real ddt real mass void init_metadyn_ int atoms real ddt real mass 11 3 Compilation
127. utable is The advantage of this procedure is that all files are properly closed whereas just killing the process may leave data and output files in unusable state 4 3 Format of arrays containing charge density potential etc The index of arrays used to store functions defined on 3D meshes is actually a shorthand for three indices following the FORTRAN convention leftmost index runs faster An example will explain this better Suppose you have a 3D array psi mrix nr2x nr3x FORTRAN compilers store this array sequentially in the computer RAM in the following way psi 1 1 1 psi 2 1 1 psi nr x 1 E psi 1 2 1 pert 2 2 1 psi nr ix 2 1 psi nrix nr2x 1 psi nrix nr2x nr3x etc Let ind be the position of the i j k element in the above list the following relation ind i j 1 nrix k 1 nr2x nrix 39 holds This should clarify the relation between 1D and 3D indexing In real space the i j k point of the FFT grid with dimensions nr1 lt nr1x nr2 lt nr2x nr3 lt nr3x is 1 1 KEN b kl Tij T T KE T T jk nrl l nr2 nr3 S where the 7 are the basis vectors of the Bravais lattice The latter are stored row wise in the at array 7 at 1 n at 2 T3 at 3 The distinction between the dimensions of the FFT grid nr1 nr2 nr3 and the physical dimensions of the array nr1x nr2x nr3x is done only because it is computationally conve nient in some ca
128. ware intel com en us articles intel software developer support 23 Since each major release of ifort differs a lot from the previous one compiled objects from dif ferent releases may be incompatible and should not be mixed If configure doesn t find the compiler or if you get Error loading shared libraries at run time you may have forgotten to execute the script that sets up the correct PATH and library path Unless your system manager has done this for you you should execute the appropriate script located in the directory containing the compiler executable in your initialization files Consult the documentation provided by Intel The warning feupdateenv is not implemented and will always fail showing up in recent versions can be safely ignored Warnings on bad preprocessing option when compiling iotk should also be ignored ifort v 12 release 12 0 0 miscompiles iotk leading to mysterious errors when reading data files Workaround increase the parameter BLOCKSIZE to e g 131072 1024 when opening files in iotk src iotk_files f90 info by Lorenzo Paulatto Nov 2010 Release 12 0 2 seems to work and to produce faster executables than previous versions on 64 bit CPUs info by P Giannozzi March 2011 ifort v 11 Segmentation faults were reported for the combination ifort 11 0 081 MKL 10 1 1 019 OpenMP 1 3 3 The problem disappeared with ifort 11 1 056 and MKL 10 2 2 025 Carlo Nervi Oct 2009 ifort v 10 On 64 bit
129. was done The maintenance and further development of the QUANTUM ESPRESSO distribution is promoted by the DEMOCRITOS National Simulation Center of IOM CNR under the coor dination of Paolo Giannozzi Univ Udine Italy and Layla Martin Samos Democritos with the strong support of the CINECA National Supercomputing Center in Bologna under the responsibility of Carlo Cavazzoni The PWscf package which included PHonon and PostProc in earlier releases was origi nally developed by Stefano Baroni Stefano de Gironcoli Andrea Dal Corso SISSA Paolo Giannozzi and many others We quote in particular e Matteo Cococcioni Univ Minnesota for DFT U implementation e David Vanderbilt s group at Rutgers for Berry s phase calculations e Ralph Gebauer ICTP Trieste and Adriano Mosca Conte SISSA Trieste for noncolinear magnetism e Andrea Dal Corso for spin orbit interactions e Carlo Sbraccia Princeton for NEB Strings method for improvements to structural optimization and to many other parts Paolo Umari Univ Padua for finite electric fields e Renata Wentzcovitch and collaborators Univ Minnesota for variable cell molecular dynamics Lorenzo Paulatto Univ Paris VI for PAW implementation built upon previous work by Guido Fratesi Univ Milano Bicocca and Riccardo Mazzarello ETHZ USI Lugano Ismaila Dabo INRIA Palaiseau for electrostatics with free boundary conditions e Norbert Nemec and Mike Towler U Cambridge fo
130. which is described in the Appendix A 5 of the QUANTUM ESPRESSO paper mentioned in the Introduction note the reference to the Gygi and Baldereschi paper See also J Comp Chem 29 2098 2008 JACS 129 10402 2007 for examples of applications Dispersion interaction with non local functional vdwDF See example examples example_vw and references quoted in file README therein Polarization via Berry Phase See Example 10 file example10 README and the documen tation in the header of PW bp_c_phase f90 Finite electric fields There are two different implementations of macroscopic electric fields in pw x via an external sawtooth potential input variable tefield true and via the modern theory of polarizability lelfield true The former is useful for surfaces especially in conjunction with dipolar corrections dipfield true see examples dipole_example for an example of application Electric fields via modern theory of polarization are documented in example 31 The exact meaning of the related variables for both cases is explained in the general input documentation 5 2 Optimization and dynamics Structural optimization For fixed cell optimization specify calculation relax and add namelist amp IONS All options for a single SCF calculation apply plus a few others You may follow a structural optimization with a non SCF band structure calculation since v 4 1 you do not need any longer to update the atomic positions in the i
131. will often result in bad scf convergence Please carefully check your structure first e g using XCrySDen Assuming that your input data is sensible 1 Verify if your system is metallic or is close to a metallic state especially if you have few k points If the highest occupied and lowest unoccupied state s keep exchanging place during self consistency forget about reaching convergence A typical sign of such behavior is that the self consistency error goes down down down than all of a sudden up again and so on Usually one can solve the problem by adding a few empty bands and a small broadening 2 Reduce mixing beta to 0 3 0 1 or smaller Try the mixing mode value that is more appropriate for your problem For slab geometries used in surface problems or for elon gated cells mixing_mode local TF should be the better choice dampening charge sloshing You may also try to increase mixing ndim to more than 8 default value Beware this will increase the amount of memory you need 3 Specific to USPP the presence of negative charge density regions due to either the pseudization procedure of the augmentation part or to truncation at finite cutoff may give convergence problems Raising the ecutrho cutoff for charge density will usually help I do not get the same results in different machines If the difference is small do not panic It is quite normal for iterative methods to reach convergence through different paths as so
132. x PWCOND PWcond source files for conductance calculations pwcond x vdW VdW source files for molecular polarizability calculation at finite frequency CPV CP source files for Car Parrinello code cp x atomic atomic source files for the pseudopotential generation package 1d1 x atomic_doc Documentation tests and examples for atomic GUI PWGui Graphical User Interface 11 2 2 Prerequisites To install QUANTUM ESPRESSO from source you need first of all a minimal Unix envi ronment basically a command shell e g bash or tesh and the utilities make awk sed MS Windows users need to have Cygwin a UNIX environment which runs under Windows installed see http www cygwin com Note that the scripts contained in the distribution assume that the local language is set to the standard i e C other settings may break them Use export LC_ALL C sh bash or setenv LC_ALL C csh tcsh to prevent any problem when running scripts including installation scripts Second you need C and Fortran 95 compilers For parallel execution you will also need MPI libraries and a parallel i e MPI aware compiler For massively parallel machines or for simple multicore parallelization an OpenMP aware compiler and libraries are also required Big machines with specialized hardware e g IBM SP CRAY etc typically have a Fortran 95 compiler with MPI and OpenMP libraries bundled with the software Workstations or commodity ma
133. x applies various kinds of Acoustic Sum Rule ASR calculates LO TO splitting at q 0 in insulators IR and Raman cross sections if the coefficients have been properly calculated from the dynamical matrix produced by ph x 16 q2r x calculates Interatomic Force Constants IFC in real space from dynamical matrices produced by ph x on a regular q grid matdyn x produces phonon frequencies at a generic wave vector using the IFC file calculated by q2r x may also calculate phonon DOS the electron phonon coefficient A the function a F w lambda x also calculates A and a F w plus T for superconductivity using the McMillan formula e make d3 produces D3 d3 x calculates anharmonic phonon lifetimes third order deriva tives of the energy using data produced by pw x and ph x USPP and PAW not sup ported e make gamma produces Gamma phcg x a version of ph x that calculates phonons at q 0 using conjugate gradient minimization of the density functional expanded to second order Only the F k 0 point is used for Brillouin zone integration It is faster and takes less memory than ph x but does not support USPP and PAW e make pp produces several codes for data postprocessing in PP see list below e make tools produces several utility programs in pwtools see list below e make pwcond produces PWCOND pwcond x for ballistic conductance calculations e make pwall produces all of the above e make 1d1 produces cod
134. you should perform an ionic minimization otherwise the system could break up during the dynamics 2 if you have taken the positions from a previous run or a previous ab initio simulation check the forces and if they are too small 107 atomic units this means that atoms are already in equilibrium positions and even if left free they will not move Then you need to randomize positions a little bit see below 49 Let us consider case 1 There are different strategies to relax the system but the most used are again steepest descent or damped dynamics for ions and electrons You could also mix electronic and ionic minimization scheme freely i e ions in steepest descent and electron in with damped dynamics or vice versa a suppose we want to perform steepest descent for ions Then we should specify the follow ing section for ions amp ions ion_dynamics sd Change also the ionic masses to accelerate the minimization ATOMIC_SPECIES C 2 0d0 c_blyp_gia pp H 2 00d0 h ps while leaving other input parameters unchanged Note that if the forces are really high gt 1 0 atomic units you should always use steepest descent for the first 100 relaxation steps As the system approaches the equilibrium positions the steepest descent scheme slows down so is better to switch to damped dynamics amp ions ion_dynamics damp ion_damping 0 2 ion_velocities zero A value of ion damping ar
135. ystal structure supercell e a bad pseudopotential typically with a ghost or a USPP giving non positive charge density leading to a violation of positiveness of the S matrix appearing in the USPP formalism e a failure of the algorithm performing subspace diagonalization The LAPACK algorithms used by cdiaghg for generic k points or rdiaghg for only case are very robust and extensively tested Still it may seldom happen that such algorithms fail Try to use conjugate gradient diagonalization diagonalization cg a slower but very robust algorithm and see what happens e buggy libraries Machine optimized mathematical libraries are very fast but sometimes not so robust from a numerical point of view Suspicious behavior you get an error that is not reproducible on other architectures or that disappears if the calculation is repeated with even minimal changes in parameters Known cases HP Compaq alphas with cxml libraries Mac OS X with system BLAS LAPACK Try to use compiled BLAS and LAPACK or better ATLAS instead of machine optimized libraries pw x crashes with no error message at all This happens quite often in parallel execu tion or under a batch queue or if you are writing the output to a file When the program crashes part of the output including the error message may be lost or hidden into error files where nobody looks into It is the fault of the operating system not of the code Try to run interactively and

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