Qbox User Guide
Contents
1. gt output file The input file contains a list of commands that are read and executed by Qbox The output file created by Qbox is a valid and well formed XML document It can be used to extract various diagnostic information after the run is completed During a Qbox run the output file can be used to track the progress of the simulation 3 2 Qbox commands When used in interactive mode Qbox prints a prompt qbox and waits for the user to type a command When used in batch mode Qbox reads input from an input file Output is written on standard output stdout and can be redirected to a file A Qbox input file consists of a sequence of Qbox commands with one command per line Qbox commands are angle compute the angle formed by three atoms atom define an atom compute mlwf compute maximally localized Wannier functions constraint manage constraints on atomic positions distance compute the distance between two atoms fold in ws fold atoms into the Wigner Seitz cell help print a short message about the use of a command kpoint add or remove k points list atoms print a list of currently defined atoms list species print a list of currently defined atomic species load load a sample from a file previously saved move move atoms plot generate a plot file with atoms and or charge density rint print the value of a Qbox variable quit exit Qbox randomize wf add random noise to the wavefunction coefficients reset vcm set the velocity of2. K th time thermostat time constant a u th width thermostat width K wf diag wavefunction diagonalization control variable wf dyn wavefunction dynamics control variable XC exchange correlation control variable Qbox variables have a default value Refer to the Section Qbox variables for details 3 4 Structure of a Qbox script A Qbox script starts with commands defining the sample being simulated For example the sequence of commands set cell 20 00 0200 0020 species silicon silicon xml atom Sil silicon 3 000 0 000 0 000 atom Si2 silicon 0 000 2 000 0 000 atom Si3 silicon 3 000 0 000 0 000 atom Si4 silicon 0 000 2 000 0 000 defines a sample in a cubic unit cell of size 20 a u Bohr radii The sample consists of a 4 atom silicon cluster The definition of the species silicon is given in the file silicon xml A species definition document contains all the information needed to describe an atomic species including the pseudopotential used to represent the electron ion interaction Species can also be defined by a URI as in the following command species carbon http www example org species carbon xml Species definition documents are XML documents that follow the syntax defined by the http www quantum simulation org XML Schema definition 4 Examples of use of Qbox 4 1 Electronic structure of a Si cluster The following example shows how to use Qbox to compute the electronic ground state of a silicon 4
3. atom cluster Approximate input atomic coordinates are used The electronic ground state is computed using 200 iterations of the preconditioned steepest descent algorithm with Anderson acceleration PSDA example electronic structure of si4 set cell 2000 0200 0020 species silicon silicon xml atom Sil silicon 3 500 0 000 0 000 atom Si2 silicon 0 000 2 000 0 000 atom Si3 silicon 3 000 0 000 0 000 atom Si4 silicon 0 500 2 000 0 000 set ecut 12 set wf dyn PSDA set ecutprec 4 randomize wf run O 200 4 2 Structure optimization The following example shows how to optimize the structure of a Si cluster The electronic ground state is computed using 200 iterations of the preconditioned steepest descent algorithm PSDA The structure is then optimized using 50 steps of the steepest descent with Anderson acceleration SDA algorithm Five steps of electronic optimization are performed before each ionic step example structure optimization of Si4 set cell 2000 0200 00 20 species silicon silicon xml atom Sil silicon 3 500 0 000 0 000 atom Si2 silicon 0 000 2 000 0 000 atom Si3 silicon 3 500 0 000 0 000 atom Si4 silicon 0 000 2 000 0 000 set ecut 12 set wf_dyn PSDA set ecutprec 4 randomize_wf run O 200 start structure optimization set atoms_dyn SDA set dt 100 run 50 5 4 3 Molecular dynamics simulation The following example shows how to perform a Born Oppenheimer molecular dynamics simulation The electronic grou
4. file lock to signal that Qbox is ready for more commands 3 Wait for the file input file lock to be removed by the driver 4 Goto 1 Client 1 Wait for the file input file lock to appear 2 Open the file output file and read its contents 3 Analyze the contents and decide what course of action to take 4 Open the file input file and overwrite it with new commands 5 Close input file 6 Remove input file lock to signal that the file input file is ready 7 Go to 1 Note that in server mode Qbox only exits when it reads the quit command When reaching the end of file in input Qbox does not exit but creates the lock file and then waits for the client to remove it It then starts reading the input file again The contents of output_file form a valid XML document i e The XML header is repeated every time the output file is rewritten This allows one to process each output file using XML tools such as e g XSLT scripts A client can manage multiple copies of Qbox running in server mode In that case multiple copies of Qbox must be launched with different input and output file names For example mpirun np lt ntasks gt qbox_exec server inO out0 amp mpirun np lt ntasks gt qbox_exec server ini out1 amp mpirun np lt ntasks gt qbox_exec server in2 out2 amp The client must then write on the files in ini in2 and read output from the files outO out1 out2 This allows for simulations involving multiple samples
5. many previous charge density corrections are used in the Anderson acceleration of the charge mixing scheme The new input charge density is computed according to k 1 _ 7 Pin TP af where is the charge mixing coefficient charge mix coeff and f is the least squares residual in the subspace spanned by the n previous charge density corrections f 5p 0 8 p p i 1 k _ k k where p P Pin consistent iteration k and p 06 2 Ook pi i 1 is the difference between the output and input charge density of the self The coefficients 9 are chosen so as to minimize f in a row weighted least squares sense The weight used in the LS calculation is the Kerker screening function Gra w G g where qo 27 r and r is the charge mixing cutoff radius charge mix rcut The default value of n is 3 SPECIAL VALUES Using n 0 leads to simple mixing p p a p p ALLOWED VALUES non negative integers RELATED INFORMATION charge mix rcut charge mix coeff charge mix rcut NAME charge mix rcut charge mixing cutoff radius DESCRIPTION The charge mix rcut variable is used to define the range of the Coulomb interaction in the Kerker screening function used in the charge density mixing scheme see charge mix ndim The default value of charge mix rcut is 10 a u If charge mix rcut is set to zero no screening is used ALLOWED VALUES positive real numbers RELATED INFORMATION charge mix ndim charge mix
6. org examples samples ch4 xml Qbox will download the document from the corresponding web site Qbox sample documents must conform to the XML Schema definition provided at http www quantum simulation org RELATED INFORMATION Save move NAME move change the position of an atom SYNOPSIS move atom to X y Z move atom by dx dy dz DESCRIPTION The move command moves an atom to an absolute position specified by x y z or by a relative displacement specified by dx dy dz Positions or displacements must be given in atomic units Bohr RELATED INFORMATION plot NAME plot generate a plot file with atoms and or charge density or orbitals SYNOPSIS plot filename plot density filename plot wf n filename plot wf nmin nmax filename DESCRIPTION The plot command creates a plot file to be viewed with another rendering program such as VMD or XcrysDen The type of output file generated depends on the arguments given to the plot command e plot filename This command generates an xyz file containing atomic positions only e plot density filename This command generates a file in cube format containing the atomic positions and the total charge density e plot wf n filename This command generates a file in cube format containing the n th wavefunction e plot wf nmin nmax filename Generate a file in cube format containing the sum of the squares of the amplitudes of the wavefunctions nmin to nmax inclusive The plot comman
7. point kpoint add 0 5 0 0 0 0 0 125 kpoint add 0 0 0 5 0 0 0 125 kpoint add 0 0 0 0 0 5 0 125 R point kpoint add 0 5 0 5 0 5 0 125 M point kpoint add 0 5 0 5 0 0 0 125 kpoint add 0 5 0 0 0 5 0 125 kpoint add 0 0 0 5 0 5 0 125 Define the X and L points in the Brillouin Zone of a FCC lattice with zero weight al a 2 a 2 0 a2 0 a 2 a 2 a3 a 2 0 a 2 b1 2 pi a 1 0 1 0 1 0 b2 2 pi a 1 0 1 0 1 0 b3 2 pi a 1 0 1 0 1 0 0 0 0 0 0 0 5 bi b3 0 5 0 5 0 5 bi b2 b3 RELATED INFORMATION list atoms NAME list atoms print a list of atoms currently defined in the sample SYNOPSIS list atoms DESCRIPTION The list atoms command prints a list of all atoms currently defined RELATED INFORMATION list species atom list species NAME list species print a list of all species currently defined SYNOPSIS list species DESCRIPTION The list species command prints a list of all species currently defined For each species the parameters of the corresponding pseudopotential are printed RELATED INFORMATION list atoms species load NAME load load a sample from an XML sample document SYNOPSIS load URI DESCRIPTION The load command loads a simulation sample defined in an XML document provided by the URI argument The URI can be a local file in which case Qbox will open and read the file If URI is a URL e g http www quantum simulation
8. width thermostat temperature window DESCRIPTION The th width determines the value of the thermostat temperature width See thermostat details The value of th width must be given in Kelvin units The default value is 100 K ALLOWED VALUES positive real numbers RELATED INFORMATION th temp th time thermostat wf diag NAME wf diag diagonalization control variable DESCRIPTION The wf diag variable determines whether eigenvectors and or eigenvalues of the hamiltonian are computed after each optimization of the electronic structure The choices are e T True Eigenvalues and eigenvectors are computed Eigenvalues are printed on output in eV units e F False Eigenvalues and eigenvectors are not computed This is the default e EIGVAL Eigenvalues only The eigenvalues are computed and printed but eigenvectors are not computed e MLWE Maximally localized Wannier Functions MLWFSs are computed e MLWEC The position of MLWF centers is computed and printed but MLWFs are not computed If empty states are added to the calculation variable nempty gt 0 the eigenvalues and eigenvectors are always computed ALLOWED VALUES T F EIGVAL MLWF MLWFC RELATED INFORMATION wf_dyn NAME wf_dyn wavefunction dynamics control variable DESCRIPTION The wf dyn variable determines which algorithm is used to update the wavefunctions during electronic structure optimization The choices are e SD Steepest Descent This the defaul
9. 1 Using run 0 computes the total energy without modifying the electronic wavefunction e run niter nitscf Perform niter ionic steps Before each ionic step the charge density is updated nitscf times Before each update of the charge density the electronic states are updated once i e the parameter nite defaults to 1 e run niter nitscf nite Perform niter ionic steps Before each ionic step the charge density is updated nitscf times Before each charge density update the electronic states are updated nite times Example 1 run O 100 is used to perform 100 self consistent electronic optimization steps Only electronic optimization is performed This the most common way of computing the electronic ground state Example 2 run 50 10 is used to perform 50 ionic steps with 10 charge density updates before each ionic step Before each charge density update the electronic states are updated once Example 3 run 50 5 10 is used to performed 50 ionic steps The charge density is updated 5 times before each ionic step The electronic states are updated 10 times before each charge density update If the variable cell dyn is not set to LOCKED the unit cell parameters are updated each time the atomic positions are updated In that case the stress variable must be set to ON so that the stress tensor is computed before the cell parameters are updated Atomic positions are updated before the charge density and electronic state
10. LOWED VALUES non negative real numbers RELATED INFORMATION nempt nempty NAME nempty number of empty electronic states DESCRIPTION The nempty variable determines the number of electronic states that are included in the calculation in addition to the number of states needed to accomodate the total number of electrons If nempty is non zero the eigenvalues and eigenvectors of the Kohn Sham hamiltonian are computed at each electronic iteration and the charge density is recomputed from the eigenvectors using a Fermi distribution The default value is of nempty is zero ALLOWED VALUES non negative integers RELATED INFORMATION fermi temp net charge NAME net charge net charge of the system DESCRIPTION The net charge variable is used to control the total amount of electronic charge in the calculation If net charge 0 the total number of electrons is determined from the sum of the valence charges given in the species definition files and the system is neutral If net charge 1 an extra electron is added to the system If net charge 1 an electron is removed from the system The default value is Zero ALLOWED VALUES integers RELATED INFORMATION nrowmax NAME nrowmax maximum number of process grid rows DESCRIPTION The nrowmax variable determines the shape of the process grid used in parallel calculations It is used to optimize performance when large numbers of parallel tasks are used The default value is 32 AL
11. LOWED VALUES positive integers RELATED INFORMATION ref_cell NAME ref_cell reference unit cell DESCRIPTION The ref_cell variable determines the size of the reference unit cell The reference unit cell is used in constant pressure calculations to ensure constant resolution of the basis set as the unit cell changes size The unit cell must always be enclosed in the reference unit cell during a constant pressure calculation ALLOWED VALUES positive real numbers RELATED INFORMATION cell stress NAME stress stress calculation control variable DESCRIPTION The stress variable determines whether the stress tensor is calculated The possible values are ON and OFF The default is OFF ALLOWED VALUES ON OFF RELATED INFORMATION ext stress cell dyn thermostat NAME thermostat thermostat control variable DESCRIPTION The thermostat variable determines what type of thermostat is used for constant temperature simulations The choices are e OFF No thermostat is used This is the default e SCALING Scaling of velocities At each MD step the velocities of all atoms are rescaled as v v 1 ndt where L TE ref n tanh A T is the thermostat time constant variable th time T is the instantaneous temperature computed from the ionic kinetic energy Tres is the thermostat reference temperature variable th temp and A is the thermostat temperature width variable th width e ANDERSEN Andersen thermostat The ato
12. Qbox User Guide version 1 50 0 2009 09 10 Fran ois Gygi fgygi ucdavis edu http eslab ucdavis edu 1 Introduction Qbox is a First Principles Molecular Dynamics code It can be used to compute the electronic structure of atoms molecules solids and liquids within the Density Functional Theory DFT formalism It can also be used to perform first principles molecular dynamics FPMD simulations using forces computed within DFT Qbox computes the solutions of the Kohn Sham equations using a plane wave basis set and norm conserving pseudopotentials It can perform constant temperature and or constant pressure simulations 2 Qbox distribution Qbox is distributed in source form under the GPL license and in executable form for specific platforms For source distribution see http eslab ucdavis edu software gbox Qbox has been built and run on the following combinations of platforms and systems 1 AMD Opteron 270 Infinipath CentOS Rocks Intel Xeon x86 64 Fedora8 BlueGene L SDSC LLNL ANL IBM p655 Series Datastar SDSC Teragrid Mercury Teragrid Cobalt Teragrid Tungsten BlueGene P ANL 9 Cray XT4 NERSC franklin Some precompiled executables are available at http eslab ucdavis edu eo ces Som e IM 3 Basic Qbox operation 3 1 Starting Qbox On most platforms Qbox is started using the mpirun command On a Linux platform using the mpich implementation of MPI the command is mpirun np lt ntasks gt qbox exec input file
13. an argument in a Unix shell RELATED INFORMATION 6 Qbox variables atoms dyn NAME atoms dyn atom dynamics control variable DESCRIPTION The atoms dyn variable determines the algorithm used to update atomic positions during a simulation The following values are allowed LOCKED Ionic forces are not computed and atomic positions are not updated This is the default SD Steepest Descent Ionic forces are computed and atomic positions are updated using the steepest descent algorithm R t at R e e Fo m where F is the force m is the ionic mass and dt is the time step see variable dt SDA Steepest Descent with Acceleration A line minimization algorithm is used to find a minimum satisfying the Wolfe conditions before changing the descent direction Using this algorithm requires a full calculation of the electronic ground state at each ionic step i e nitscf gt 1 in the run command CG Conjugate Gradient A line minimization algorithm is used to find a minimum satisfying the Wolfe conditions before changing the descent direction The Polak Ribiere formula is used to update descent directions Using this algorithm requires a full calculation of the electronic ground state at each ionic step i e nitscf gt 1 in the run command Using this algorithm requires a full calculation of the electronic ground state at each ionic step i e nitscf gt 1 in the run command MD Molecular dynamics Ionic forces are computed and ioni
14. c positions are updated using the Verlet algorithm Rit a 2R 0 R ede dE Fe This algorithm can be used to perform either Born Oppenheimer molecular dynamics using nitscf gt 1 in the run command or Car Parrinello molecular dynamics nitscf 1 See also the wf dyn variable BMD Blocked Molecular dynamics This algorithm updates ionic positions according to the MD algorithm Verlet but velocities are reset to zero every time the total energy increases This algorithm is used to optimize geometry It requires a full calculation of the electronic ground state at each ionic step i e nitscf gt 1 in the run command ALLOWED VALUES LOCKED SD SDA CG MD BMD RELATED INFORMATION dt cell NAME cell unit cell parameters DESCRIPTION The cell variable contains the coordinates of the three lattice vectors 4 q a defining the unit cell The unit cell is defined using the set command with the following arguments set cell aj dy Giz A2x A2 A2 A3x A3y A37 The lattice vectors 4 d form the columns of the 3x3 lattice parameter matrix A dy Ay ay A a ap ay der ay a The default value of all cell parameters is zero ALLOWED VALUES positive real numbers RELATED INFORMATION ref cell cell_dyn NAME cell_dyn cell dynamics control variable DESCRIPTION The cell_dyn variable determines the algorithm used to update the unit cell during a simulation The following values are allowed e LOCKED The unit cell is not update
15. d This is the default e SD Steepest Descent The unit cell is updated using the computed stress tensor and the steepest descent algorithm astt di a olol 9 A O where o t isthe stress tensor o t is the externally applied stress variable ext stress Q is the volume of the unit cell mo is the mass of the unit cell variable cell mass A is the 3x3 lattice parameter matrix see cell variable and dt is the time step variable dt ALLOWED VALUES LOCKED SD RELATED INFORMATION cell ref cell cell lock cell lock NAME cell lock cell dynamics constraints control variable DESCRIPTION The cell lock variable is used to restrict the possible changes of the unit cell parameters The allowed values are e OFF No restriction on the unit cell parameters are enforced This is the default e A Thelattice vector d is fixed e B Thelatticevector q is fixed e C The lattice vector is fixed e AB The lattice vectors a and q are fixed e AC Thelatticevectors d and 4d are fixed e BC Thelatticevectors d and are fixed e ABC Alllattice vectors are fixed This is equivalent to cell dyn LOCKED os The shape of the unit cell is preserved Lattice vectors can change length but not direction e AS Thelattice vector d is fixed and the shape of the unit cell is preserved e BS Thelattice vector 4 is fixed and the shape of the unit cell is preserved e CS The lattice vector 4 is fixed and the shape o
16. d is only working for wavefunctions at the F point RELATED INFORMATION print NAME print print the current value of a Qbox variable SYNOPSIS print variable DESCRIPTION The print command prints the current value a Qbox variable For a list of variables see the section Qbox variables RELATED INFORMATION set quit NAME quit exit Qbox SYNOPSIS quit DESCRIPTION The quit command exits Qbox without saving any information about the sample To save the current sample see the save command RELATED INFORMATION save randomize wf NAME randomize wf add a random perturbation to electronic wavefunctions SYNOPSIS randomize wf amplitude DESCRIPTION The randomize wf command adds random numbers to the Fourier coefficients of the electronic wavefunction The amplitude argument can be used to change the intensity of the perturbation The randomize wf command is used at the beginning of an electronic structure calculation when the symmetry of the atomic coordinates is high In such situations the iterative algorithms used to compute the electronic ground state can converge to saddle points of the energy functional instead of true minima Using randomize wf introduces a slight symmetry breaking which is sufficient to avoid high symmetry saddle points RELATED INFORMATION reset vcm NAME reset vcm reset the velocity of the center of mass to zero SYNOPSIS reset vcm DESCRIPTION The reset vcm command mo
17. defined by k 6 k G 1 1 Gta pre opre 2 cu k G cut lg trer 2 2 The value of ecutprec must be given in Rydberg units Preconditioning is only used if the wf dyn variable is set to either PSD or PSDA If ecutprec 0 no preconditioning is used The default value of ecutprec is zero Effective preconditioning is achieved with ecutprec lt ecut 2 or ecutprec lt ecut 4 Small values of ecutprec lt 5 Ry can lead to instabilities ALLOWED VALUES positive real numbers smaller than or equal to ecut RELATED INFORMATION ecut wf dyn ecuts NAME ecuts energy cutoff for stress confinement potential DESCRIPTION The ecuts variable defines the energy cutoff used in a confinement potential in Fourier space The confinement potential is used when computing the stress tensor with variable cell size in order to ensure constant resolution as the unit cell changes size The confinement energy is 1 Beo Se leef G f G n G where 1 1 exp G 2 Ei lo 1 f 2 and o 2 The default value of ecuts is zero in which case the confinement potential is not used For a detailed description of the use of confinement potentials in constant pressure simulations see 1 P Focher G L Chiarotti M Bernasconi et al Structural Phase Transformations Via 1St Principles Simulation Europhys Lett 26 5 345 351 1994 2 M Bernasconi G L Chiarotti P Focher et al First Principle Constant Pressure Molecular Dynamics Journa
18. difies the velocity of all atoms so as to ensure that the velocity of the center of mass is zero The current value of the velocity of the center of mass is printed by the status command RELATED INFORMATION run NAME run update electronic wavefunctions and or atomic positions SYNOPSIS run atomic density niter run atomic density niter nitscf run atomic density niter nitscf nite DESCRIPTION The run command starts a simulation in which atomic positions and or electronic states are updated The algorithms used to update the atomic positions and electronic states are determined by the variables atoms dyn and wf dyn The parameters are defined as follows e atomic density The first self consistent iteration is started using a charge density made of a superposition of atomic charge densities e niter The number of ionic steps to be performed i e steps during which atomic positions are updated This number can be zero if only electronic wavefunction updates are desired e nitscf The number of self consistent electronic iterations The charge density is updated at the beginning of each self consistent iteration e nite The number of electronic iterations performed between updates of the charge density The run command can be used in the following ways e runniter Perform niter ionic steps Before each ionic step the electronic states are updated once and the charge density is updated i e both parameters nitscf and nite default to
19. dyn PSDA set ecutprec 4 randomize_wf run 0 200 perform 10 MD steps set atoms_dyn MD set dt 40 run 50 5 save the sample save si4 xml script 2 restart from saved sample and perform 50 MD steps load si4 xml set wf dyn PSDA set ecutprec 4 set atoms dyn MD run 50 5 save the sample save si4 xml 4 5 Changing energy cutoff on the fly The size of sample files can become large when simulating large systems Although Qbox uses a parallel I O algorithm to save sample data the process of writing data to a file can be slow especially on platforms that do not offer a parallel file system This problem can be alleviated by saving the sample with reduced resolution for wavefunctions The value of the variable ecut can be changed using the set ecut command at any time during the simulation When the value of ecut changes Qbox interpolates wavefunctions onto the plane wave basis defined by the new value The size of the sample file can be reduced by changing the value of ecut to a small value before using the save command When loading a sample that was saved with reduced resolution the original resolution can be restored by first redefining the value of ecut and then reoptimizing the wavefunctions The ability to change energy cutoff on the fly is also useful to accelerate a ground state calculation by starting the calculation at low cutoff and gradually increasing the cutoff to the final desired value This procedure can be c
20. f the unit cell is preserved e ABS The lattice vectors and q are fixed and the shape of the unit cell is preserved e ACS The lattice vectors and 4 are fixed and the shape of the unit cell is preserved e BCS The lattice vectors and q are fixed and the shape of the unit cell is preserved o R The aspect ratio of the unit cell is preserved All lattice vectors are rescaled by the same constant ALLOWED VALUES OFF A B C AB AC BC ABC S AS BS CS ABS ACS BCS R RELATED INFORMATION cell cell dyn cell mass cell mass NAME cell mass mass of the unit cell DESCRIPTION The cell mass variable is the mass of the unit cell in atomic units in which the mass of a carbon atom is 12 0 The default value is 10000 ALLOWED VALUES positive real values RELATED INFORMATION cell cell dyn charge mix coeff NAME charge mix coeff charge density mixing coefficient DESCRIPTION The charge density mixing coefficient is used to update the electronic charge density during self consistent iterations see charge mix ndim The default value is 0 5 Smaller values can be used to accelerate the convergence of self consistent iterations in metallic systems ALLOWED VALUES real values in the interval 0 1 RELATED INFORMATION charge mix rcut charge mix ndim charge mix ndim NAME charge mix ndim dimension of Anderson acceleration of charge mixing DESCRIPTION The charge mix ndim parameter n determines how
21. l Of Physics And Chemistry Of Solids 56 3 4 501 505 1995 ALLOWED VALUES positive real numbers smaller than or equal to ecut RELATED INFORMATION stress cell dyn emass NAME emass fictitious electronic mass for Car Parrinello simulations DESCRIPTION The emass variable defines the fictitious electronic mass used in Car Parrinello simulations The default value is zero in which case the fictitious electronic mass used in the calculation is m 2E dt The value of emass is only relevant if the variable wf dyn is set to MD i e if the wavefunction dynamics is Car Parrinello It is ignored otherwise ALLOWED VALUES positive real values RELATED INFORMATION wf dyn ext stress NAME ext stress external stress DESCRIPTION The ext stress variable determines the value of the externally applied stress The ext stress variable must be set using the following syntax setext stress OO 0 0 0 0 where the values of the elements of the stress tensor must be given in GPa units The external stress can be positive or negative The default value is zero ALLOWED VALUES real numbers RELATED INFORMATION stress fermi temp NAME fermi temp Fermi temperature for fractionally occupied states DESCRIPTION The fermi temp variable determines the value of the Fermi temperature used in the calculation of occupation factors for fractionally occupied states The value must be given in Kelvin The default value is zero AL
22. ms are subjected to random collisions with particles drawn from a Maxwell distribution of velocities with temperature Tet The collision frequency is 1 t where T is given by the variable th time see H C Andersen J Chem Phys 72 2384 1980 e LOWE Lowe thermostat Pairs of atoms are subjected to random collisions with a particle drawn from a Maxwell distribution of velocities with temperature Ter The collision frequency is 1 t where T is given by the variable th time The Lowe thermostat is similar to the Andersen thermostat but conserves total momentum see C P Lowe Europhys Lett 47 145 1999 ALLOWED VALUES OFF SCALING ANDERSON LOWE RELATED INFORMATION th temp th time th width th temp NAME th temp thermostat reference temperature DESCRIPTION The th temp variable determines the thermostat reference temperature The default is zero See thermostat ALLOWED VALUES non negative real numbers RELATED INFORMATION th time th width thermostat th time NAME th time thermostat time constant DESCRIPTION The th time variable determines the thermostat time constant The time constant is a measure of the time over which the thermostat adjusts the temperature See thermostat for details The value of th time must be given in atomic units of time The default value is 5000 a u 120 fs ALLOWED VALUES positive real numbers RELATED INFORMATION th temp th width thermostat th width NAME th
23. n argument When used without arguments prints a list of valid commands RELATED INFORMATION kpoint NAME kpoint define and manage the set of k points used in the calculation of the electronic structure SYNOPSIS kpoint list kpoint add kx ky kz weight kpoint delete kx ky kz DESCRIPTION The kpoint command is used to add and delete k points to the set of k points used in the electronic structure calculation The kpoint is defined by a vector on the basis of the reciprocal lattice vectors If reciprocal lattice vectors are b bz and b the k point defined by the numbers kx ky kz on the command line is kx b ky b2 kz bs For example the X point of the Brillouin Zone for an FCC lattice is specified as kx 0 5 ky 0 5 kz 0 0 The list of all currently defined k points can be printed using the command kpoint list The sum of the weight arguments must add up to 1 0 This is currently not checked by Qbox Some k points can be defined with zero weight In that case the electronic wavefunctions and eigenvalues are computed at these points but they are not included in the calculation of the charge density By default Qbox starts with a k point set containing a single k point k 0 0 0 the T point with a weight of 1 0 When defining a k point set it is necessary to first delete the point before defining other k points This is due to two possible reasons 1 The desired k point set does not contain the F point 2 The de
24. nd state is first computed using 200 iterations of the preconditioned steepest descent algorithm PSDA A Born Oppenheimer MD is then done by running 50 ionic steps with 5 electronic iterations at each ionic step example molecular dynamics of si4 set cell 2000 0200 00 20 species silicon silicon xml atom Sil silicon 3 500 0 000 0 000 atom Si2 silicon 0 000 2 000 0 000 atom Si3 silicon 3 500 0 000 0 000 atom Si4 silicon 0 000 2 000 0 000 set ecut 12 set wf_dyn PSDA set ecutprec 4 randomize_wf run 0 200 start molecular dynamics set atoms_dyn MD set dt 40 run 50 5 4 4 Saving and restarting a simulation The following example shows how to save the simulation sample on a file at the end of a simulation and how to restart from the saved file In the first script the electronic ground state is computed using 200 iterations of the preconditioned steepest descent algorithm PSDA A Born Oppenheimer MD is then done by performing 50 ionic steps with 5 electronic iterations at each ionic step The sample is saved at the end of the first script on file si4 xml In the second script the sample is loaded from the restart file and 50 additional MD steps are performed script 1 electronic ground state and 50 MD steps set cell 2000 0200 0020 species silicon silicon xml atom Sil silicon 3 500 0 000 0 000 atom Si2 silicon 0 000 2 000 0 000 atom Si3 silicon 3 500 0 000 0 000 atom Si4 silicon 0 000 2 000 0 000 set ecut 12 set wf_
25. ndim debug NAME debug debug parameters DESCRIPTION The debug variable is used to pass debug parameters to Qbox It is not intended for normal use ALLOWED VALUES character strings RELATED INFORMATION dt NAME dt simulation time step DESCRIPTION The dt variable is the simulation time step in atomic units of time 1 a u of time 0 02418885 fs The default value is 3 a u ALLOWED VALUES non negative real numbers RELATED INFORMATION atoms dyn wf dyn cell dyn ecut NAME ecut plane wave basis energy cutoff DESCRIPTION The ecut variable defines the size of the plane wave basis used to define the electronic wavefunctions It must given in Rydberg units The wavefunction plane wave basis consists of all plane waves having a kinetic energy smaller than E The charge density and the total potential are described using a larger basis set that includes all plane waves with a kinetic energy smaller than 4 E The default value of ecut is zero in which case the plane wave basis contains one basis function the plane wave of wavevector G 0 ALLOWED VALUES non negative real numbers RELATED INFORMATION ecutprec NAME ecutprec preconditioning energy cutoff DESCRIPTION The ecutprec variable defines the energy cutoff used in the preconditioner for electronic structure optimization Corrections to the electronic wavefunctions are preconditioned in Fourier space using a diagonal preconditioning matrix K whose elements are
26. oices are e LDA Local Density Approximation Ceperley Alder data This is the default e PBE Perdew Burke Ernzerhof GGA functional ALLOWED VALUES LDA PBE RELATED INFORMATION
27. om the corresponding web site The species definition document must conform to the species XML Schema definition given at http www quantum simulation org RELATED INFORMATION list species atom status NAME status print status of the current sample SYNOPSIS status DESCRIPTION The status command prints a brief summary of the characteristics of the current sample RELATED INFORMATION strain NAME strain apply strain on the system SYNOPSIS strain atomsonly inverse uxx uyy uzz uxy uyz uxz DESCRIPTION The strain command modifies the shape of the unit cell and modifies the atomic positions to impose a strain defined by the component of the symmetric strain tensor u Using the inverse flag causes the inverse transformation to be applied Using atomsonly changes the postitions of atoms without affecting the unit cell RELATED INFORMATION torsion NAME torsion print the value of the torsion angle defined by the positions of four atoms SYNOPSIS torsion atom1 atom atom3 atom4 DESCRIPTION The torsion command prints the value of the angle dihedral defined by the four atoms given as arguments The names atom1 atom2 atom3 and atom4 must refer to the names of atoms currently defined in the sample RELATED INFORMATION list_atoms angle distance shell escape NAME shell escape execute a Unix command from withing Qbox SYNOPSIS command arguments DESCRIPTION The command executes the command given as
28. ompared to the full approximation scheme of the multigrid method 4 6 Using Qbox in client server mode Qbox can be used in client server mode This means that Qbox can run on one computer as a server that listens to commands being sent from another computer Commands can be sent by a user but also by another program the client or driver This allows for extensions of the functionality of Qbox in which the client and the server interact to achieve a result that is not easy to get with the conventional approach of submitting a fixed input file to Qbox A Qbox driver or Qbox application program sends commands to Qbox by writing them to a file Qbox reads the commands executes them and produces an output file The client code can then read the output file process it and send the next commands to Qbox Synchronization of this process is implemented through the creation or destruction of a file the lock file that signals that the output or input file is ready for use Qbox is run in client server mode by invoking it as follows mpirun np lt ntasks gt qbox_exec server input_file output_file The sequence of operations in client server mode is described below Qbox 1 Create a new file output file 2 Read commands from input file and execute them until the end of file is reached Write the outputon output file After executing the last command in input file close output file and create a file named input
29. s Calculation parameters such as the plane wave energy cutoff are specified using Qbox variables Qbox variables can be set using the set command Their value can be printed using the print command For example the command set ecut 24 sets the variable ecut to the value 24 This causes the plane wave basis set to be resized to include all plane waves with a kinetic energy not exceeding 24 Rydberg Other Qbox variables can be set similarly The Qbox variables are atoms dyn ionic dynamics control variable cell dimensions of the unit cell cell dyn unit cell dynamics control variable cell lock control of allowed unit cell motions cell mass fictitious mass of the unit cell charge mix coeff mixing coefficient for charge density update charge mix ndim Anderson dimension for charge density mixing charge mix rcut Kerker screening for charge density update debug debug parameters not for normal use dt time step a u ecut plane wave energy cutoff Ry ecutprec energy cutoff of the preconditioner Ry ecuts energy cutoff of the confinement potential emass fictitious electronic mass for CP dynamics ext stress externally applied stress GPa fermi temp Fermi temperature K nempty number of empty states net charge net charge of the system nrowmax maximum size of process grid columns ref cell dimensions of the reference unit cell stress stress control variable thermostat thermostat control variable th temp thermostat temperature
30. s are updated As a consequence the atomic positions and the electronic structure are consistent at the end of a run command RELATED INFORMATION atoms dyn wf dyn save NAME save save the current sample into a file SYNOPSIS save filename DESCRIPTION The save command saves the current sample into a file in XML format The format used conforms to the XML Schema defined at http www quantum simulation org The information saved includes the dimensions of the unit cell atomic positions and velocities the electronic wavefunction and optionally the time derivative of the wavefunction RELATED INFORMATION load set NAME set assign a value to a Qbox variable SYNOPSIS set variable value value DESCRIPTION The set command assigns the value s value to the variable variable Some variables e g cell are multivalued in which case the set command requires multiple arguments RELATED INFORMATION print species NAME species define a new atomic species and add it to the list of currently known species SYNOPSIS species name URI DESCRIPTION The species command defines a new atomic species under the name name The newly defined species is added to the list of currently known species The definition is read from the given URI If the URI is a local file Qbox opens and reads it If the URI is a URL e g http www quantum simulation org examples species hydrogen pbe xml Qbox downloads the species definition fr
31. sics Communications 155 p 1 2003 and a one sided iterative Jacobi algorithm for simultaneous diagonalization The position of Wannier centers and the corresponding spreads are printed on output The value of the electronic ionic and total dipole are printed The iterative methods stops when the decrease of the spread is sufficiently small between two iterations or when a maximum number of iterations is reached In that latter case the compute mlwf command can be issued again to try to improve the convergence of the spread minimization After execution of the compute_mlwf command the wavefunctions are maximally localized RELATED INFORMATION constraint NAME constraint manage constraints on atomic positions SYNOPSIS constraint define position constraint name atom1 constraint define distance constraint name atom1 atom distance velocity constraint define angle constraint name atom1 atom atom3 angle velocity constraint define torsion constraint name atom1 atom atom3 atom4 angle velocity constraint list constraint delete constraint name constraint enforce constraint set constraint name value velocity DESCRIPTION The constraint command is used to manage the constraint set Constraints can be of the following types position distance angle or torsion Constraints are added to the constraint set using the constraint define command They can be removed from the set using the constraint delete command A list of cons
32. sired k point set contains the F point but with a weight different from 1 0 In this case the point must be deleted and then added in order to be defined with the correct weight The only way to change the weight of a k point is to delete it and define it again Qbox does not perform any symmetrization of the charge density to reduce the number of k points to the irreducible wedge of the Brillouin Zone The full set of k points must be defined except for the k k symmetry i e If k is included in the set then k need not be included Modifying the k point set erases all wavefunctions It is not possible to modify the k point set after running a calculation or after loading a sample without resetting the wavefunctions Note When deleting a kpoint the arguments kx ky kz are compared to the coordinates of the k points currently defined Since comparisons of floating point numbers are unreliable the kpoint delete command will delete any k point located within a radius of 10 of the vector kx ky kz Similarly when adding a new k point the kpoint add command will exit without defining the new k point and print a warning message if a previously defined k point is located within a radius of 10 of the new kpoint EXAMPLE Define a set of 8 k points for a simple cubic or orthorhombic cell This k point set is equivalent to doubling the cell in all three directions kpoint delete 0 0 0 Gamma point kpoint add 0 0 0 0 0 0 0 125 X
33. such as replica exchange dynamics nudged elastic band NEB simulations or path integral molecular dynamics 5 Qbox commands angle NAME angle compute the value of the angle defined by the positions of three atoms SYNOPSIS angle atom atom atom3 DESCRIPTION The angle command prints the value of the angle formed by the three atoms given as arguments The names atom1 atom2 and atom3 must refer to the names of atoms currently defined in the sample RELATED INFORMATION list atoms distance torsion atom NAME atom add an atom to the current sample SYNOPSIS atom name species x y z vx vy vz DESCRIPTION The atom command adds an atom to the current sample The name argument can be any character string but must differ from all the other names of atoms in the current sample The species argument must refer to an atomic species previously defined using the species command The position of the atom is specified by its coordinates x y z in atomic units Bohr Optionally the velocity of the atom can be specified by its components vx vy vz in atomic units Bohr atomic unit of time One atomic unit of time is 0 02418885 fs RELATED INFORMATION list atoms species compute mlwf NAME compute mlwf compute maximally localized Wannier functions SYNOPSIS compute mlwf DESCRIPTION The compute mlwf command transforms the current wavefunctions into maximally localized Wannier functions following the algorithm in Computer Phy
34. t Wavefunctions are updated as follows k 1 y y aH y where DE cut de m e a m gt 0 e and m is the fictitious electronic mass variable emass By default m 0 e PSD Preconditioned Steepest Descent Wavefunctions are updated as follows y y aKP Hy where K is a preconditioning matrix k 6 k G ZOEN 2 EP 2 k G cut ig Le pre 2 2 and P 1 gt dv BI w l is a projector on the orthogonal complement of the subspace spanned by prec cut all wavefunctions The preconditioning matrix depends on the value of E variable ecutprec e PSDA Preconditioned Steepest Descent with Anderson acceleration Wavefunctions are updated as with the PSD option and convergence is accelerated by the Anderson scheme D G Anderson JACM 12 No 4 pp 547 560 1965 e JD Jacobi Davidson Wavefunctions are updated using a preconditioned Jacobi Davidson algorithm e MD Molecular Dynamics Wavefunctions are updated using the Car Parrinello scheme 2 k 1 _ k kei dt www e where holonomic constraints are used to enforce orthogonality e LOCKED Wavefunctions are not updated ALLOWED VALUES SD PSD PSDA JD MD LOCKED RELATED INFORMATION other variables or commands XC NAME xc exchange correlation functional control variable DESCRIPTION The xc variable determines which exchange correlation functional is used in the electronic structure calculation The ch
35. tep of the simulation at a rate specified by the velocity argument The velocity must be given in degree a u time constraint list Print a list of all currently defined constraints constraint delete constraint_name Remove the constraint constraint_name from the constraint set constraint enforce Modify atomic positions so as to enforce all constraints using the SHAKE algorithm constraint set constraint_name value velocity Modify the value of a constraint and optionally its velocity This applies to the distance angle and torsion constraints only for which the value is distance angle and angle respectively RELATED INFORMATION list_atoms angle distance torsion distance NAME distance print the distance between two atoms SYNOPSIS distance atom1 atom2 DESCRIPTION The distance command prints the value of the distance separating two atoms In periodic samples the printed distance is not necessarily the minimal distance between the two atoms RELATED INFORMATION angle torsion fold_in_ws NAME fold in ws fold all atoms within the Wigner Seitz cell SYNOPSIS fold in ws DESCRIPTION The fold in ws command moves atoms by multiples of the unit cell lattice vectors so that all atoms are withing the Wigner Seitz cell RELATED INFORMATION help NAME help print a brief help message about a command SYNOPSIS help command DESCRIPTION The help command prints a short description of the command given as a
36. the center of mass to zero run run MD or electronic optimization steps save save a sample on a file for later use set assign a value to a Qbox variable species define a new atomic species status print a summary of the current state strain impose a strain on the sample torsion compute the dihedral angle defined by four atoms shell escape execute a shell command Commands and their syntax are described in detail in the Section Qbox commands If a command is read on input and is not in the above list Qbox interprets it as the name of an input script and attempts to open a file having that name in the current working directory If the file can be opened and is readable Qbox starts interpreting each line of that file as its input Qbox scripts can be nested At the end of a script Qbox returns to the previous script level and continues to read commands At the end of the topmost level script Qbox exits Unix commands can be issued within a Qbox input sequence using a shell escape character at the beginning of a line For example the line qbox date invokes the Unix date command Comments can be inserted in Qbox input by inserting a character at the beginning of each comment line qbox print the list of all atoms qbox list_atoms Comments can also be added at the end of a command line by inserting a character where the comment starts gbox list atoms get a list of all atoms 3 3 Qbox variable
37. traints can be printed using the constraint list command Some constraints have an associated value that can be modified using the constraint set command The atom names used in the constraint command must refer to atoms previously defined using the atom command All constraints have a name which allows for selective removal of constraints and for individual modification of the constraint values constraint define position constraint name atom1 Define a position constraint on atom atom1 This locks the atom into its current position constraint define distance constraint name atom1 atom distance velocity Define a distance constraint on atoms atom1 and atom2 If a velocity argument is given the value of the distance will change at each time step of the simulation at a rate specified by the velocity argument The velocity must be given in Bohr a u time constraint define angle constraint name atom1 atom atom3 angle velocity Define an angle constraint on atoms atom1 atom and atom3 If a velocity argument is given the value of the angle will change at each time step of the simulation at a rate specified by the velocity argument The velocity must be given in degree a u time constraint define torsion constraint name atom1 atom atom3 atom4 angle velocity Define a torsion or dihedral constraint on atoms atom1 atom2 atom3 and atom4 If a velocity argument is given the value of the angle will change at each time s
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