# Qbox User Guide

Qbox User Guide version 1.63.2 2016-01-28 http://qboxcode.org 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 constantpressure simulations. 1.1 New features As of release 1.63.2, Qbox includes the implementation of the following new features: – the partial_charge command computes the amount of electronic charge located inside a sphere of a given radius centered on an arbitrary atom. – the iter_cmd variable can be used to specify the name of a command or a script that will be executed periodically during a simulation. The iter_cmd_period variable defines the interval between executions of the iter_cmd script, i.e. the iter_cmd script is executed every iter_cmd_period iterations. This can be used to generate plot files for animations. – The Harris-Foulkes functional is used to compute the value of etotal_int during self-consistent iterations. This provides more accurate values of etotal_int when a combination of selfconsistent and non self-consistent iterations is used (e.g. nitscf > 0 and nite>0). Qbox can use the SG15 library of Optimized Norm-Conserving Vanderbilt (ONCV) pseudopotentials available at http://www.quantum-simulation.org . ONCV potentials were built to reproduce all-electron calculations with high accuracy. Note: using ONCV potentials requires the updated XML Schema file species.xsd provided in the xml directory of the distribution. 2 Qbox distribution Qbox is distributed in source form under the GPL license. For source distribution see http://eslab.ucdavis.edu/software/qbox . Qbox has been built on several Linux platforms including CentOS-7, CentOS-6, Fedora, Ubuntu, BlueGene/P, BlueGene/Q, Cray XE6, Cray XC30, Dell PowerEdge C8220 (TACC stampede). Information on how to build Qbox is available at http://eslab.ucdavis.edu/software/qbox/build.htm . 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 <ntasks> qbox_exec input_file > output_file Depending on your installation of MPI, the arguments of the mpirun command may differ. 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 atom bisection compute_mlwf constraint distance extforce fold_in_ws help kpoint list_atoms list_species load move partial_charge plot print quit randomize_r randomize_v randomize_wf rescale_v reset_vcm rseed run save set species status strain torsion !(shell escape) compute the angle formed by three atoms define an atom apply recursive subspace bisection to wave functions compute maximally localized Wannier functions manage constraints on atomic positions compute the distance between two atoms add external forces on atoms fold atoms into the Wigner-Seitz cell print a short message about the use of a command add or remove k-points print a list of currently defined atoms print a list of currently defined atomic species load a sample from a file previously saved move atoms compute the amount of charge in atom-centered spheres. generate a plot file with atoms and/or charge density print the value of a Qbox variable exit Qbox add random noise to the atomic positions add random noise to the atomic velocities add random noise to the wavefunction coefficients rescale atomic velocities set the velocity of the center of mass to zero initialize the random number generator run MD or electronic optimization steps save a sample on a file for later use assign a value to a Qbox variable define a new atomic species print a summary of the current state impose a strain on the sample compute the dihedral angle defined by four atoms 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 [qbox] list_atoms # get a list of all atoms 3.3 Qbox variables 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 alpha_PBE0 atoms_dyn blHF btHF cell cell_dyn cell_lock cell_mass charge_mix_coeff charge_mix_ndim charge_mix_rcut debug dt ecut ecutprec ecuts e_field emass ext_stress fermi_temp iter_cmd iter_cmd_period nempty net_charge nrowmax nspin coefficient of HF exchange in PBE0 ionic dynamics control variable bisection levels in Hartree-Fock exchange bisection threshold in Hartree-Fock exchange dimensions of the unit cell unit cell dynamics control variable control of allowed unit cell motions fictitious mass of the unit cell mixing coefficient for charge density update Anderson dimension for charge density mixing Kerker screening for charge density update debug parameters (not for normal use) time step (a.u.) plane wave energy cutoff (Ry) energy cutoff of the preconditioner (Ry) energy cutoff of the confinement potential applied electric field fictitious electronic mass (for CP dynamics) externally applied stress (GPa) Fermi temperature (K) script executed every iter_cmd_period steps number of steps between iter_cmd executions number of empty states net charge of the system maximum size of process grid columns number of spin degrees of freedom polarization ref_cell scf_tol stress thermostat th_temp th_time th_width wf_diag wf_dyn xc algorithm used to compute dipole and quadrupole dimensions of the reference unit cell tolerance criterion for SCF iterations stress control variable thermostat control variable thermostat temperature (K) thermostat time constant (a.u.) thermostat width (K) wavefunction diagonalization control variable wavefunction dynamics control variable 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 0 0 0 20 0 0 0 20 species silicon silicon.xml atom Si1 silicon 3.000 0.000 atom Si2 silicon 0.000 2.000 atom Si3 silicon -3.000 0.000 atom Si4 silicon 0.000 -2.000 0.000 0.000 0.000 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://fpmd.ucdavis.edu/potentials/C/C_HSCV_PBE-1.0.xml When a URI is used to define a species, Qbox downloads the species definition from the corresponding web site. Note that this requires web access from the computer on which Qbox is running. This access may not be available on the compute nodes of some clusters. If web access is not available on compute nodes, the species definition file must be downloaded before starting Qbox using e.g. the wget command wget http://fpmd.ucdavis.edu/potentials/C/C_HSCV_PBE-1.0.xml which creates a local copy of the file C_HSCV_PBE-1.0.xml. The species command can then be invoked in a Qbox script using the local file species carbon C_HSCV_PBE-1.0.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 The test directory of the Qbox distribution contains examples of electronic structure calculations and molecular dynamics simulations. 4.1 Electronic structure of a Si4 cluster The following example shows how to use Qbox to compute the electronic ground state of a silicon 4atom 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 set cell 20 0 0 0 20 0 0 0 20 species silicon silicon.xml atom Si1 silicon 3.500 0.000 atom Si2 silicon 0.000 2.000 atom Si3 silicon -3.000 0.000 atom Si4 silicon 0.500 -2.000 set ecut 12 set wf_dyn PSDA set ecutprec 4 randomize_wf run 0 200 of si4 0.000 0.000 0.000 0.000 4.2 Structure optimization The following example shows how to optimize the structure of a Si4 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 20 0 0 0 20 0 0 0 20 species silicon silicon.xml atom Si1 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 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 ground 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 20 0 0 0 20 0 0 0 20 species silicon silicon.xml atom Si1 silicon 3.500 0.000 0.000 atom Si2 silicon 0.000 2.000 0.000 atom Si3 silicon -3.500 0.000 atom Si4 silicon 0.000 -2.000 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 0.000 0.000 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 20 0 0 0 20 0 0 0 20 species silicon silicon.xml atom Si1 silicon 3.500 0.000 atom Si2 silicon 0.000 2.000 atom Si3 silicon -3.500 0.000 atom Si4 silicon 0.000 -2.000 set ecut 12 set wf_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 0.000 0.000 0.000 0.000 # 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 the plane wave 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 compared 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 <ntasks> 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 output on output_file. After executing the last command in input_file, close output_file and create a file named input_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) Go to 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 <ntasks> qbox_exec -server in0 out0 & mpirun -np <ntasks> qbox_exec -server in1 out1 & mpirun -np <ntasks> qbox_exec -server in2 out2 & The client must then write on the files in0, in1, in2, and read output from the files out0, out1, out2. This allows for simulations involving multiple samples, 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 [-pbc] atom1 atom2 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. If the -pbc option is used, the positions of the atoms are interpreted as those of the nearest atom replica, taking into account periodic boundary conditions. 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 bisection NAME bisection –perform recursive subspace bisection of the wave functions SYNOPSIS bisection lx ly lz threshold DESCRIPTION The bisection command transform electronic wave functions according to recursive subspace bisection, as described in [F. Gygi, Phys. Rev. Lett. 102, 166406 (2009)]. The resulting wave functions are maximally localized in rectangular domains defined by recursively subdividing the unit cell lx, ly, and lz times in the x, y, and z directions respectively. The lx, ly, lz arguments define the level of recursion used in the x, y, z directions. The threshold argument is used to print information about the bisected wave functions. For each wave function, the bisection command prints the value of the localization vector, the size of the wave function and the number of non-zero overlaps with other functions (for the given value of the threshold). The localization vector is a binary vector in which a pair of bits is associated with each of the bisecting planes of the recursive bisection process, starting at the least significant bit. Within each pair of bits, a value of 1 signifies that the wave function has significant amplitude on one side of the corresponding bisecting plane. Thus the bit pattern “11” signifies that the wave function is extended across the corresponding bisecting plane, while the bit patterns “01” and “10” signify that the wave function is localized on one side only of the bisecting plane. The bit values are defined by the amount of electronic charge located on either side of the bisecting plane. The value is 1 if the amount of charge is larger than the threshold. At the end of the bisection command, wave functions are transformed so as to be maximally localized in the subdomains defined by the bisection planes. The effect of recursive bisection can then be inspected using the plot command. RELATED INFORMATION compute_mlwf NAME compute_mlwf –compute maximally localized Wannier functions SYNOPSIS compute_mlwf DESCRIPTION The compute_mlwf command transforms the current wave functions into maximally localized Wannier functions following the algorithm in Computer Physics 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 wave functions 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 atom2 distance [velocity] constraint define angle constraint_name atom1 atom2 atom3 angle [velocity] constraint define torsion constraint_name atom1 atom2 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 constraints 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 atom2 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 atom2 atom3 angle [velocity] Define an angle constraint on atoms atom1, atom2 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 atom2 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 step 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 [-pbc] --print the distance between two atoms SYNOPSIS distance atom1 atom2 DESCRIPTION The distance command prints the value of the distance separating two atoms. If the -pbc option is used, the positions of the atoms are interpreted as those of the nearest atom replica, taking into account periodic boundary conditions. RELATED INFORMATION angle, torsion extforce NAME extforce –add, modify or delete external forces on atoms SYNOPSIS extforce define atomic extforce_name atom fx fy fz extforce define pair extforce_name atom1 atom2 f extforce define global extforce_name fx fy fz extforce set extforce_name fx fy fz extforce set extforce_name f extforce list extforce delete extforce_name DESCRIPTION The extforce command is used to define, modify or delete external forces acting on specific atoms. The “define”, “set”, “list” and “delete” subcommands modiy the set of external forces as detailed below for each choice of parameters. extforce define atomic extforce_name atom fx fy fz This command defines an external force named extforce_name acting on atom atom. The force has components fx,fy,fz. The force components must be given in atomic units (Hartree/Bohr). extforce define pair extforce_name atom1 atom2 f This command defines a pair force named extforce_name acting only on the atoms atom1 and atom2. The magnitude of the pair force is f and must be given in atomic units (Hartree/Bohr). A positive value of f defines an attractive force between atom1 and atom2. extforce define global extforce_name fx fy fz This command defines a global external force named extforce_name acting on all atoms. The force has components fx,fy,fz. The force components must be given in atomic units (Hartree/Bohr). extforce set extforce_name fx fy fz This command modifies the components of the force associated with the external force extforce_name. This syntax applies to the “atomic” and “global” forces only. extforce set extforce_name f This command modifies the magnitude of the force associated with the external force extforce_name. This syntax applies to the “pair” force only. extforce list This command prints a list of all external forces. extforce delete extforce_name This command removes the external force extforce_name from the set of external forces. RELATED INFORMATION 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 within 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 an 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 b1 b2 and b3 the k-point defined by the numbers (kx, ky, kz) on the command line is kx * b1 + ky * b2 + kz * b3. 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 Γ point) with a weight of 1.0. When defining a k-point set, it is necessary to first delete the Γ point before defining other k-points. This is due to two possible reasons: 1) The desired k-point set does not contain the Γ point. 2) The desired k-point set contains the Γ point, but with a weight different from 1.0. In this case, the Γ 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 kpoints currently defined. Since comparisons of floating point numbers are unreliable, the kpoint delete command will delete any k-point located within a radius of 10-6 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 10-6 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 # X point kpoint add 0.5 0.0 0.0 0.125 0.0 0.125 kpoint add kpoint add # R point kpoint add # M point kpoint add kpoint add kpoint add 0.0 0.0 0.5 0.0 0.0 0.5 0.125 0.125 0.5 0.5 0.5 0.125 0.5 0.5 0.0 0.5 0.0 0.5 0.0 0.5 0.5 0.125 0.125 0.125 Define the X and L points in the Brillouin Zone of a FCC lattice, with zero weight: # a1 = (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) # X point # X = (2*pi/a) ( 1.0, 0.0, 0.0 ) = 0.5 * ( b1 + b3 ) kpoint 0.5 0.0 0.5 0.0000 # L point # L = (2*pi/a) ( 0.5, 0.5, 0.5 ) = 0.5 * ( b1 + b2 + b3 ) kpoint add 0.5 0.5 0.5 0.0000 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.org/examples/samples/ch4.xml) Qbox will download the document from the corresponding web site. Note that loading a URL remotely only works if the nodes on which Qbox is running have web access. This may not be the case on some parallel computers in which compute nodes do not have web access. 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, orbitals or local potential SYNOPSIS plot filename plot -density filename plot -wf n filename plot -wfs nmin nmax [-spin {1|2}] filename plot -vlocal [-spin {1|2}]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. ● plot filename This command generates an xyz file containing atomic positions only. ● plot -density [-spin {1|2}] filename This command generates a file in cube format containing the atomic positions and the total charge density. If the -spin option is used, the density of the first (1) or second (2) spin is used. ● plot -wf n [-spin {1|2}] filename This command generates a file in cube format containing the n-th wave function. If the -spin option is used, the wave function of the first (1) or second (2) spin is used. ● plot -wfs nmin nmax [-spin {1|2}] filename Generate a file in cube format containing the sum of the squares of the amplitudes of the wavefunctions nmin to nmax inclusive. If the -spin option is used, the wave functions of the first (1) or second (2) spin are used. ● plot -vlocal [-spin {1|2}] filename This command generates a file in cube format containing the local potential (Vlocal+VHartree+Vxc). If the -spin option is used, the potential for the first (1) or second (2) spin is used. The plot command is currently only working for wave functions at the Γ point. RELATED INFORMATION partial_charge NAME partial_charge –compute the amount of electronic charge in a sphere centered on an atom SYNOPSIS partial_charge [-spin {1|2}] name radius DESCRIPTION The partial_charge command computes the amount of electronic charge contained in a sphere of radius radius centered on atom name. The radius value must be specified in atomic units (Bohr). When using the -spin option, the charge density of the given spin is computed. If nspin=2 and the -spin option is not used, the total charge is computed. 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_r NAME randomize_r --add a random perturbation to atomic positions SYNOPSIS randomize_r amplitude DESCRIPTION The randomize_r command adds random numbers to the coordinates of the atomic positions. The random displacements are drawn from a normal distribution scaled by the amplitude argument. RELATED INFORMATION randomize_v randomize_v NAME randomize_v –initialize atomic velocities with random values from a Maxwell Boltzmann distribution SYNOPSIS randomize_v temperature DESCRIPTION The randomize_v command initializes atomic velocities with random numbers drawn from a Maxwell-Boltzmann distribution. The temperature argument determines the temperature of the distribution. RELATED INFORMATION randomize_r 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 wave function. 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 rescale_v NAME rescale_v –rescale atomic velocities SYNOPSIS rescale_v scaling_factor DESCRIPTION The rescale_v command rescales the velocity of all atoms by a common factor defined by the scaling_factor argument. 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 modifies 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 rseed NAME rseed –initialize the random number generator SYNOPSIS rseed [seed] DESCRIPTION The rseed command initializes the random number generator. Qbox uses random numbers in the implementation of the randomize_wf command and in stochastic thermostats (LOWE, ANDERSON, BDP). If a seed argument is provided, it is used to initialize the random number generator. If no seed is provided the time function is used to generate a seed. Note: when running multiple instances of Qbox in client-server mode, and if the rseed command is not used, all instances may be initialized with the same seed if they are started at the same time. This problem can be avoided by using the rseed command for each instance with a different argument, or by starting all instances in a staggered way using a delay of a few seconds. run NAME run --update electronic wavefunctions and/or atomic positions and/or unit cell 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 ● -atomic_density The first self-consistent iteration is started using a charge density made of a superposition of atomic charge densities. ● 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. ● nitscf The maximum number of self-consistent electronic iterations. The charge density is updated at the beginning of each self-consistent iteration. Iterations may be skipped if the energy has reached convergence within the scf_tol tolerance criterion. ● nite The number of electronic iterations performed between updates of the charge density The run command can be used in the following ways ● run niter 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 1). Using “run 0” computes the total energy without modifying the electronic wavefunction. ● 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. ● 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 0 100 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 states 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, scf_tol save NAME save --save the current sample into a file SYNOPSIS save [-serial] [-text] [-atomsonly] [-no_wfv] 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 wave function, and optionally the time derivative of the wave function. If the -serial option is used, the data is saved from task 0 only and no attempt is made to use optimized I/O functionality. If the -text option is used, the wave function coefficients are written in formatted text form rather than encoded in base64 format in the sample file. If the -atomsonly option is used, only the <atomset> element is written. If the -no_wfv option is used, wave function velocities are not saved. 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 from the corresponding web site. The species definition document must conform to the species XML Schema definition given at http://www.quantum-simulation.org If the species name is already defined, the definition is replaced with that of the URI argument. 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 components 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 (dihedral) defined by the positions of four atoms SYNOPSIS torsion [-pbc] atom1 atom2 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. If the -pbc option is used, the positions of the atoms are interpreted as those of the nearest atom replica, taking into account periodic boundary conditions. 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 an argument in a Unix shell. RELATED INFORMATION 6 Qbox variables alpha_PBE0 NAME alpha_PBE0 –coefficient of Hartree-Fock exchange in the PBE0 xc functional DESCRIPTION The alpha_PBE0 variable defines the coefficient multiplying the Hartree-Fock exchange energy in the PBE0 exchange-correlation functional. The default value is 0.25. ALLOWED VALUES non-negative real numbers RELATED INFORMATION xc 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 2 t dt = R t dt F t R 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 > 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 > 1 in the run command. Using this algorithm requires a full calculation of the electronic ground state at each ionic step, i.e. nitscf > 1 in the run command. ● MD: Molecular dynamics. Ionic forces are computed and ionic positions are updated using the Verlet algorithm 2 t− R t −dt dt R tdt =2 R F t m ● This algorithm can be used to perform either Born-Oppenheimer molecular dynamics (using nitscf > 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 > 1 in the run command. ALLOWED VALUES LOCKED, SD, SDA, CG, MD, BMD RELATED INFORMATION dt blHF NAME blHF –bisection levels for Hartree-Fock exchange computation DESCRIPTION The blHF variable consists of three integer values lx ly lz that specify the number of recursive levels of bisection that must be perfomed on wave functions in the x, y, and z directions when computing the Hartree-Fock exchange energy. The values of blHF are only used if the variable btHF is nonzero. ALLOWED VALUES positive integers RELATED INFORMATION btHF, bisection btHF NAME btHF –bisection threshold for Hartree-Fock exchange computation DESCRIPTION The btHF variable defines the threshold used in the recursive bisection perfomed on wave functions when computing the Hartree-Fock exchange energy. If btHF is zero, no bisection is performed during Hartree-Fock exchange calculations. The default value of btHF is zero. ALLOWED VALUES floating point numbers in [0,1] RELATED INFORMATION blHF, bisection cell NAME cell --unit cell parameters DESCRIPTION The cell variable contains the coordinates of the three lattice vectors a⃗1, a⃗2, a⃗3 defining the unit cell. The unit cell is defined using the set command with the following arguments set cell a1x a1y a1z a2x a2y a2z a3x a3y a3z The lattice vectors a⃗1, a⃗2, a⃗3 form the columns of the 3x3 lattice parameter matrix A a 11 a12 a 13 A= a 21 a22 a 32 a 31 a32 a 33 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: ● LOCKED: The unit cell is not updated. This is the default. ● SD: Steepest Descent. The unit cell is updated using the computed stress tensor and the steepest descent algorithm dt 2 a ij ( t+dt )=a ij (t )+ Ω ( σ ( t )−σ ext (t ) ) A( t ) mΩ where σ (t ) is the stress tensor, σ ext (t ) is the externally applied stress (variable ext_stress), Ω is the volume of the unit cell, mΩ 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). ● CG: Conjugate Gradient. The unit cell and the atomic positions are updated using the computed stress tensor and the atomic forces using a conjugate gradient algorithm. Note that both the unit cell and atomic positions are optmized simultaneously independently of the value of atoms_dyn. ALLOWED VALUES LOCKED, SD, CG 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 ● OFF: No restriction on the unit cell parameters are enforced. This is the default. ● A: The lattice vector a⃗1 is fixed. ● B: The lattice vector a⃗2 is fixed. ● C: The lattice vector a3 is fixed. ● AB: The lattice vectors a1 and a2 are fixed. ● AC: The lattice vectors a1 and a3 are fixed. ● BC: The lattice vectors a2 and a3 are fixed. ● ABC: All lattice vectors are fixed. This is equivalent to cell_dyn = LOCKED. ● S: The shape of the unit cell is preserved. Lattice vectors can change length but not direction. ● AS: The lattice vector a1 is fixed and the shape of the unit cell is preserved. ● BS: The lattice vector a2 is fixed and the shape of the unit cell is preserved. ● CS: The lattice vector a3 is fixed and the shape of the unit cell is preserved. ● ABS: The lattice vectors a1 and a2 are fixed and the shape of the unit cell is preserved. 3 are fixed and the shape of the unit cell is preserved. ● ACS: The lattice vectors a1 and a a a ● BCS: The lattice vectors 2 and 3 are fixed and the shape of the unit cell is preserved. ● 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 selfconsistent 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 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 ink1 = f 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 n f = ∑ i k i=1 k k−i k k k − where =out −in is the difference between the output and input charge density of the self- consistent iteration k, and n =in ∑ i in −in k k−i k i=1 2 The coefficients i are chosen so as to minimize ∥f ∥2 in a row-weighted least squares sense. The weight used in the LS calculation is the Kerker screening function 2 2 G q0 w G = 2 G where q0=2 / r c and r c is the charge mixing cutoff radius (charge_mix_rcut). The default value of n is 3. SPECIAL VALUES k 1 Using n=0 leads to simple mixing: in k k k =in out −in 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_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 cut . 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 cut . 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 defined by k ij= ij k G { 1 1 2 prec G E cut prec 2 E cut 2 k G= 1 1 prec E E≥E cut 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 PSDA or JD. If ecutprec = 0, an automatic preconditioner is used. The default value of ecutprec is zero (automatic preconditioning). ALLOWED VALUES non-negative 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 E conf = ∑∣cn G∣2 G 2 f G 2 n, G where 1 f g=f s 1− 2 s 1expG / 2−E cut / s 1 f s=2 and s= . 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 1StPrinciples Simulation, Europhys. Lett. 26 (5): 345-351 (1994). 2. M. Bernasconi, G. L. Chiarotti, P. Focher, et al. First-Principle Constant-Pressure MolecularDynamics, Journal 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 e_field NAME e_field --applied electric field (displacement field) DESCRIPTION The e_field variable consists of three numbers that define the applied electric field (displacement ⃗ =( D x , D y , D z ) . The field must be given in atomic units (1 Hartree/(electron field, or induction) D Bohr) = 5.1422×1011 V/m. The polarization variable must be set to define the algorithm used to compute the electric dipole and quadrupole in the presence of the applied field. The default value is zero. ALLOWED VALUES real numbers RELATED INFORMATION polarization 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 2 me =2 E cut dt . The value of emass is only relevant if the variable wf_dyn is set to MD (i.e. if the wave function 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 set ext_stress σ xx σ yy σ zz σ xy σ yz σ xz 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. ALLOWED VALUES non-negative real numbers RELATED INFORMATION nempty iter_cmd NAME iter_cmd --command or script to be executed every iter_cmd_period ionic steps DESCRIPTION The iter_cmd variable defines a command or script that is executed every iter_cmd_period ionic steps. If a single command must be executed, the full command (with arguments) can be used as the value of iter_cmd. If multiple commands are used, they must be written in a local script file, and the name of the script is used as the value of iter_cmd. ALLOWED VALUES string RELATED INFORMATION iter_cmd_period iter_cmd_period NAME iter_cmd_period --number of ionic steps between executions of iter_cmd DESCRIPTION The iter_cmd_period variable defines the number of ionic steps that separate successive executions of the command (or script) defined by iter_cmd. The default value is 1. ALLOWED VALUES positive integers RELATED INFORMATION iter_cmd 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. ALLOWED VALUES positive integers RELATED INFORMATION nspin NAME nspin --number of spin degrees of freedom DESCRIPTION The nspin variable is used to determine the number of spin components of the wave function. The default value is 1. ALLOWED VALUES 1 or 2 RELATED INFORMATION polarization NAME polarization --algorithm used to compute the dipole and quadrupole moments DESCRIPTION The polarization variable is used to determine the algorithm used to compute the electric dipole and quadrupole. The allowed values are ● ● OFF MLWF ● MLWF_REF ● MLWF_REF_Q ● BERRY The dipole and quadrupole are not computed. This is the default. The electronic dipole is defined as the center of charge of maximally localized Wannier functions (MLWF) centers. The electronic dipole is defined as the center of charge of maximally localized Wannier functions (MLWF) centers with the refinement correction proposed by M. Stengel and N. Spaldin, Phys. Rev. B73, 075121 (2006). The electronic dipole is defined as for MLWF_REF and the quadrupole moment is computed. The electronic dipole is computed using the definition based on the Berry phase as defined by I. Souza et al, Phys. Rev. Lett. 89, 117602 (2002). The ionic, electronic and total dipole ⃗ d are computed and printed in units of (electron Bohr). Note that the total dipole is only defined modulo an additive constant multiple of the lattice vectors in a periodic system. A dipole expressed in (electron Bohr) can be converted to (Debye) using the relation 1 (electron Bohr) = 2.5417462 (Debye). Conversely, dipoles expressed in (Debye) can be converted to (electron Bohr) using the relation 1 (Debye) = 0.39343031 (electron Bohr). ⃗ =( D x , D y , D z ) defined by the e_field If an external field is applied, i.e. the displacement field D variable is non-zero, the calculation of the electronic ground state takes into account the presence of the external field. The electric enthalpy is included in the total enthalpy. The polarizability tensor αij of a molecule is defined as αij = δ di δ Dj and is defined in units of (Bohr3), δ d i in (electron Bohr), and δ D j in (Hartree/(electron Bohr)). The polarizability tensor αij of a molecule can be computed using calculations of the total dipole ⃗ =0 . induced by small changes δ D j around D The change in dipole δ d i due to a small change in applied field δ D j is computed using the centered finite difference expression 1 [ d (+δ D j )−d i (−δ D j ) ] 2 i The polarizability tensor can then be expressed as δ d i= αij = d i (+δ D j )−d i (−δ D j ) 2δ D j The full polarization tensor can be obtained using 6 calculations of the dipole (2 evaluations of δ d i (δ D j ) in 3 directions). Note that since the polarization due to a finite field includes linear and higher order terms, this calculation must be repeated with decreasing values of δ D j in order to obtain an accurate value of the linear polarizability. In solids, the average polarization (dipole per unit volume) is defined as d⃗ ⃗ P= Ω where Ω is the unit cell volume. The susceptibility tensor χ ij and the dielectric tensor ϵ ij are related by ϵ=I +χ and the polarization is ⃗ ⃗ =χ ϵ−1 D=( ⃗ I −ϵ−1 ) D ⃗ P=χ E A small change in applied field δ D induces a change of polarization δ ⃗ P ⃗ δ⃗ P=( I −ϵ−1)δ D If a sufficiently large unit cell is used, an estimate of the inverse dielectric tensor can be computed using the finite-difference expression δ P i (+δ D j )−δ P i (−δ D j ) 2δDj or, in terms of the dipole moment, (ϵ−1 )ij =δij − (ϵ−1 )ij =δij − δ d i (+δ D j )−δ d i (−δ D j ) . 2Ω δ D j The quadrupole moment tensor is computed if the MLWF_REF_Q value is used. It is defined as Q ij =e ∫Ω x i x j ρ( x)d 3 x in units of (e Bohr2). Note that this may differ from other definitions used in the literature, which may include a factor 1/2 in the above definition. The traceless quadrupole 1 tensor defined as Q −( Tr Q) I is also computed and printed. Some definitions used in the 3 literature include an extra multiplicative factor of 3, or 3/2. The quadrupole moment is sometimes expressed in units of (Debye Å), related to (e Bohr2) by the expressions 1 (Debye Å) = 0.743476 (e Bohr2) and 1(e Bohr2) = 1.3450336 (Debye Å) . The NIST Computational Chemistry Database http://cccbdb.nist.gov provides quadrupole moments of molecules in (Debye Å). A comparison of Qbox results with NIST values can be made using the relation: QNIST (Debye Å) = (3/2) 1.3450336 QQbox (e Bohr2). Born effective charges are defined as the derivatives of ionic forces with respect to the applied field δ F αi Z = δDj α where F i is the ith component of the force on atom α . Born effective charges can be similarly computed using finite difference expressions. α ij As of release 1.62.3 the calculation of the polarization is only implemented at the Γ point of the Brillouin zone, for systems having no spin polarization. ALLOWED VALUES OFF, MLWF, MLWF_REF, MLWF_REF_Q, BERRY RELATED INFORMATION e_field 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 scf_tol NAME scf_tol –tolerance for convergence of SCF iterations DESCRIPTION The scf_tol variable determines the energy tolerance criterion for convergence of SCF iterations. The unit is (a.u.) (Hartree). The default value is zero. The maximum number of SCF iterations is determined by the second argument of the run command: “run niter nitscf nite”. If scf_tol is set to a non-zero value and if the energy changes by less than scf_tol in three successive SCF iterations, the remaining SCF iterations are skipped. If scf_tol is zero, the number of SCF iterations is nitscf. ALLOWED VALUES non-negative real numbers RELATED INFORMATION run 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 ● OFF: No thermostat is used. This is the default. ● SCALING: Scaling of velocities. At each MD step, the velocities of all atoms are rescaled as v i =v i 1− dt where T −T ref 1 = tanh is the thermostat time constant (variable th_time), T is the instantaneous temperature computed from the ionic kinetic energy, Tref is the thermostat reference temperature (variable th_temp), and is the thermostat temperature width (variable th_width). ● ANDERSEN: Andersen thermostat. The atoms are subjected to random collisions with particles drawn from a Maxwell distribution of velocities with temperature Tref. The collision frequency is 1/ where is given by the variable th_time (see H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)). ● LOWE: Lowe thermostat. Pairs of atoms are subjected to random collisions with a particle drawn from a Maxwell distribution of velocities with temperature Tref. The collision frequency is 1/ where 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)). ● BDP: Bussi-Donadio-Parrinello thermostat. The stochastic thermostat described by Bussi, Donadio and Parrinello in J. Chem. Phys. 126, 014101 (2007) is used. The parameter used in the BDP paper is the value of the variable th_time. The value of the variable th_width is ignored. When using the BDP thermostat, the value of <econst> printed on output corresponds to the conserved energy described in the above paper. ALLOWED VALUES OFF, SCALING, ANDERSON, LOWE, BDP 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_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 ● T: True. Eigenvalues and eigenvectors are computed. Eigenvalues are printed on output in eV units. ● F: False. Eigenvalues and eigenvectors are not computed. This is the default. ● EIGVAL: Eigenvalues only. The eigenvalues are computed and printed, but eigenvectors are not computed. ● MLWF: Maximally localized Wannier Functions (MLWFs) are computed. ● MLWFC: The position of MLWF centers is computed and printed but MLWFs are not computed. If empty states are added to the calculation (variable nempty > 0) the eigenvalues and eigenvectors are always computed. ALLOWED VALUES T, F, EIGVAL,MLWF,MLWFC RELATED INFORMATION wf_dyn NAME wf_dyn –wave function dynamics control variable DESCRIPTION The wf_dyn variable determines which algorithm is used to update the wave functions during electronic structure optimization. The choices are ● SD: Steepest Descent. This the default. Wavefunctions are updated as follows: = k − H k k 1 where { 1 2 E cut = dt 2 me me=0 me0 and me is the fictitious electronic mass (variable emass). By default, me=0. (Note that the SD algorithm is very inefficient and is not used in practice. It is provided for debugging purposes). ● PSD: Preconditioned Steepest Descent. Wavefunctions are updated as follows: k 1 = k − K P ⊥ H k where K is a preconditioning matrix k ij= ij k G { 1 1 2 G E prec cut prec 2 E cut 2 k G= 1 1 prec E E≥ E cut 2 2 and P ⊥ =I −∑i ∣ i 〉〈 i∣ is a projector on the orthogonal complement of the subspace spanned by prec all wavefunctions. The preconditioning matrix depends on the value of E cut (variable ecutprec). ● 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)). ● JD: Jacobi-Davidson. Wavefunctions are updated using a preconditioned Jacobi-Davidson algorithm. ● MD: Molecular Dynamics. Wavefunctions are updated using the Car-Parrinello scheme dt 2 ki 1 =2 ki − k−1 − H ki ∑ j ij k i j me where holonomic constraints are used to enforce orthogonality. ● LOCKED. Wavefunctions are not updated. ALLOWED VALUES SD, PSD, PSDA, JD, MD, LOCKED RELATED INFORMATION ecutprec 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 choices are ● LDA: Local Density Approximation, Ceperley-Alder data. This is the default. ● ● ● ● VWN: Local Density Approximation, parameterized by Vosko, Wilk and Nusair. PBE: Perdew-Burke-Ernzerhof GGA functional. PBE0: Hybrid density functional [C. Adamo and V. Barone, JCP 110, 6158 (1999)]. B3LYP: Three-parameter Becke-Lee-Yang-Parr hybrid density functional. ALLOWED VALUES LDA, VWN, PBE, PBE0, B3LYP RELATED INFORMATION

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