Qbox commands

angle - compute the angle formed by three atoms
atom - define an atom
bisection - apply recursive bisection to wave functions
compute_mlwf - compute maximally localized Wannier functions
constraint - manage constraints on atomic positions
distance - compute the distance between two atoms
extforce - add external forces on atoms
fold_in_ws - fold atoms into the Wigner-Seitz cell
help - print a short message about the use of a command
kpoint - manage the set of 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 previously saved restart file
move - move atoms
partial_charge - compute the electronic charge in atom-centered spheres
plot - generate a plot file with atoms and/or charge density
print - print the value of a Qbox variable
quit - exit Qbox
randomize_r - add random noise to the atomic positions
randomize_v - add random noise to the atomic velocities
randomize_wf - add random noise to the wave function coefficients
rescale_v - rescale all atomic velocities
reset_rotation - reset atomic velocities to cancel global rotations
reset_vcm - set the velocity of the center of mass to zero
response - compute the polarizability or response to a potential
rseed - initialize the random number generator
run - run MD or electronic optimization steps
save - save a sample on a restart file for later use
set - assign a value to a Qbox variable
set_velocity - set the velocity of an atom
species - define a new atomic species
spectrum - compute the optical absorption spectrum
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)_cmd - execute a shell command

angle

NAME

angle – compute the angle defined by 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.

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 transforms electronic wave functions according to the recursive subspace bisection algorithm, 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.

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 described in Computer Physics Communications 155 , p. 1 (2003), using 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 method stops when the decrease of the spread is sufficiently small between two iterations, or when a maximum number of iterations is reached. In the 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 (i.e. have minimum spread).

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. The list of currently defined 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 value.

constraint define position constraint_name atom1

Define a position constraint on atom atom1. This locks the atom atom1 into its current position.

constraint define distance constraint_name atom1 atom2 dist [velocity]

Define a distance constraint between atoms atom1 and atom2. If the optional 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 argument dist must be given in (bohr). 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 the optional 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 argument angle must be given in (degree). 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 the optional 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 argument angle must be given in (degree). 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 named 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 command only applies to the distance, angle and torsion constraints.

Note

Defining constraints does not move atoms. Atomic positions are only modified when running ionic steps (i.e. with atoms_dyn not equal to LOCKED), or if the constraint enforce command is used explicitly.

Note

If multiple constraints are defined, it may not be possible to enforce all constraints simultaneously.

Note

The set of constraints is not saved in a restart file.

RELATED INFORMATION

list_atoms, angle, distance, torsion

distance

NAME

distance - print the distance between two atoms

SYNOPSIS

distance [-pbc] 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 - manage external forces on atoms

SYNOPSIS

extforce define atomic extforce_name atom1 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 atom1 fx fy fz

This command defines an external force named extforce_name acting on atom atom1. The force has components fx, fy, fz. The force components must be given in atomic units (hartree/bohr). [ 1 (hartree/bohr) = 82.3886 nN ]

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 a repulsive 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 the list of currently defined external forces.

extforce delete extforce_name

This command removes the external force extforce_name from the set of external forces.

Note

The set of external forces is not saved in a restart file.

Note

1 (hartree/bohr) = 82.3886 nN

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 located within the Wigner-Seitz cell.

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.

kpoint

NAME

kpoint – manage the set of k-points used in the electronic structure calculation

SYNOPSIS

kpoint add kx ky kz weight

kpoint move kx ky kz kx’ ky’ kz’

kpoint delete kx ky kz

kpoint list

DESCRIPTION

The kpoint command is used to manage the set of k-points used in the electronic structure calculation. k-points can be added, moved and deleted.

kpoint add kx ky kz weight

This command adds a k-point to the k-point set. The weight of the k-point must be in [0,1] and is used to weigh the contribution of the k-point to the charge density.

kpoint move kx ky kz kx’ ky’ kz’

This command moves a k-point located at kx ky kz to kx’ ky’ kz’ while preserving wave functions amplitudes. This command can be used to explore details of the band structure using small displacements in k-space.

kpoint list

This command lists all currently defined k-points.

kpoint delete kx ky kz

This command deletes the k-point located at kx ky kz.

A k-point is defined by its coefficients kx ky kz on the basis of the reciprocal lattice vectors. If reciprocal lattice vectors are \(\vec{b_1},\, \vec{b_2},\, \vec{b_3}\), the k-point defined by the numbers kx, ky, kz is \(\vec{k} = kx\, \vec{b_1} + ky\, \vec{b_2} + kz\, \vec{b_3}\). 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 sum of the weights of all k-points must add up to 1.0. This is currently not checked by Qbox.

A k-point can be defined with zero weight, in which case the wave functions and eigenvalues are computed at that k-point, 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: \(\vec k =(0,0,0)\) (the \(\Gamma\) point) with a weight of 1.0. When defining a k-point set, it is necessary to first delete the \(\Gamma\) point before defining other k-points. This is due to two possible reasons:

The desired k-point set does not contain the \(\Gamma\) point.

The desired k-point set contains the \(\Gamma\) point, but with a weight different from 1.0. In this case, the \(\Gamma\) point must be first deleted and then added again with the appropriate 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).

Adding or removing k-points erases all wave functions. It is not possible to modify the k-point set after running a calculation or after loading a sample without resetting the wave functions.

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^-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 k-point.

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 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
EXAMPLE
Define the X and L points in the Brillouin Zone of an 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

list_atoms

NAME

list_atoms - print a list of all atoms 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 a restart file

SYNOPSIS

load URI

DESCRIPTION

The load command loads a simulation sample defined in an XML document previously generated using the save command.

The URI argument 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_name to x y z

move atom_name 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).

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 filename

DESCRIPTION

The plot command creates a plot file to be viewed with another rendering program such as VMD (http://www.ks.uiuc.edu/Research/vmd/) or XCrySDen (http://www.xcrysden.org/). 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. The “cube” file can be visualized using the VMD program.

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

This command generates a file in “cube” format containing the sum of the squares of the amplitudes of the wave functions 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 filename

This command generates a file in “cube” format containing the potential \(V_{\rm local}+V_{\rm Hartree}\).

Note

The -wf and -wfs options currently only work for wave functions at the \(\Gamma\) point.

partial_charge

NAME

partial_charge – compute the amount of electronic charge in a sphere centered on an atom

SYNOPSIS

partial_charge [-spin {1|2}] atom_name r

DESCRIPTION

The partial_charge command computes the amount of electronic charge contained in a sphere of radius r centered on atom atom_name. The radius r 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.

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 Qbox commands page.

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 to a restart file, 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 all 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 wave functions

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 may 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.

rescale_v

NAME

rescale_v – rescale atomic velocities

SYNOPSIS

rescale_v f

DESCRIPTION

The rescale_v command rescales the velocity of all atoms by a factor f.

reset_rotation

NAME

reset_rotation - reset atomic velocities so as to cancel global rotations.

SYNOPSIS

reset_rotation

DESCRIPTION

The reset_rotation command modifies the velocity of all atoms so as to ensure that the total angular momentum of the system is zero. This command is used periodically during molecular dynamics simulations of isolated molecules to prevent a global rotation.

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.

response

NAME

response - compute the polarizability or the response to an external potential

SYNOPSIS

response amplitude [-RPA|-IPA] nitscf [nite]

response -vext filename [-cube] [-RPA|-IPA] [-amplitude a ] nitscf [nite]

DESCRIPTION

The response command computes the polarizability of the system, or the density response to a specific external potential. The response command uses a series of self-consistent calculations in finite electric field (or finite potential). The nitscf and nite values are used to control the number of iterations performed in each of the finite field calculations. Finite-field calculations are performed in three possible ways depending on the use of the options -RPA and -IPA. By default, the Hartree and exchange-correlation potentials are updated self-consistently during the finite-field calculations. If the -RPA option is used, only the Hartree potential is updated (Random Phase Approximation). If the -IPA option is used, neither the Hartree potential nor the exchange-correlation potential are updated (Independent Particle Approximation).

response amplitude nitscf [nite]

This command computes the response of the system to a constant electric field in the x, y, and z directions. The resulting polarizability tensor is printed. The unit of polarizability is (bohr) \(^3\)

response -vext filename [-cube] [-RPA|-IPA] [-amplitude a ] nitscf [nite]

This command computes the density response to an external potential defined in the file filename. The default format of the external potential file is XML, as described for the vext variable. If the -cube option is used, the format of the external potential file is the cube format. If the -amplitude option is used, the external potential is multiplied by the given value, and the density response is then divided by the same value. The density response if written to a file having the same format as the external potential file (XML or cube). The density response file name is formed by appending “.response” to the name of the external potential file.

Note

The polarization variable must be set before using the response command.

Note

The response command can only be used for wave functions defined at the \(\Gamma\) point of the Brillouin zone, for systems having no spin polarization.

RELATED INFORMATION

polarization

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 an integer seed argument is provided, it is used to initialize the random number generator. If no seed is provided the Unix 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 wave functions 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, electronic wave functions, and/or unit cell are updated. The algorithms used to update the atomic positions, electronic states and/or unit cell are determined by the variables atoms_dyn, wf_dyn and cell_dyn.

If the -atomic_density option is used, the first self-consistent iteration is started using a charge density made of a superposition of atomic charge densities.

The parameters are defined as follows

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 wave function updates are desired.

nitscf

The maximum number of self-consistent iterations. The charge density is updated at the beginning of each self-consistent iteration. Iterations are 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. These iterations are needed in metallic systems, in systems exhibiting a small HOMO-LUMO gap, or if empty states are included in the calculation (see nempty).

TYPICAL USES

run 0 nitscf

Perform nitscf self-consistent iterations without moving ions. This is the most common way to compute the electronic ground state in insulators.

run 0 nitscf nite

Perform nitscf self-consistent iterations with nite updates of the wave functions between charge density updates, without moving ions. This is the most common way to compute the electronic ground state in metals and small band gap semiconductors.

run niter nitscf

Perform niter ionic steps with nitscf updates of the charge density between ionic steps. This is the most common way to perform geometry optimization or first-principles molecular dynamics (FPMD) in insulators.

run niter nitscf nite

Perform niter ionic steps, with nitscf updates of the charge density between ionic steps, and nite updates of the wave functions between charge density updates. This is the most common way to perform geometry optimization or FPMD in metals.

EXAMPLE
Electronic ground state calculation:
set wf_dyn JD
run 0 100
Perform 100 scf iterations with atoms locked, using the Jacobi-Davidson algorithm to update wave functions.
EXAMPLE
Geometry optimization in insulators:
set wf_dyn JD
set atoms_dyn CG
run 50 10
Perform 50 steps of geometry optimization using the conjugate gradient algorithm to update atomic positions. Use 10 scf iterations before each ionic step. Wave functions are updated using the Jacobi-Davidson algorithm.
EXAMPLE
Molecular dynamics in insulators:
set wf_dyn JD
set atoms_dyn MD
run 50 10
Perform 50 steps molecular dynamics (MD) using the Verlet algorithm to update atomic positions. Use 10 scf iterations before each ionic step. Wave functions are updated using the Jacobi-Davidson algorithm.
EXAMPLE
Geometry optimization in metals:
set wf_dyn JD
set atoms_dyn CG
run 50 10 10
Perform 50 steps of geometry optmization. The charge density is updated 5 times before each ionic step. The wave functions are updated 10 times before each charge density update.
EXAMPLE
Optimization of geometry and cell parameters:
set wf_dyn JD
set stress ON
set cell_dyn CG
run 50 10 10
Perform 50 steps of joint optimization of atomic positions and cell parameters. Note: see also the ecuts and ref_cell variables for more details on cell parameter optimization.
RELATED INFORMATION

atoms_dyn, wf_dyn, scf_tol

save

NAME

save - save the current sample into a restart file for later use

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 functions, and optionally the time derivative of the wave functions. If the -serial option is used, the data is saved from task 0 only and no attempt is made to use optimized parallel I/O functionality. If the -text option is used, the wave function values 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 and wave functions are not included. 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 value(s) to a Qbox variable. Some variables (e.g. cell) are multivalued, in which case the set command requires multiple arguments.

RELATED INFORMATION

print

set_velocity

NAME

set_velocity - set the velocity of an atom

SYNOPSIS

set_velocity atom_name {vx|*|-} {vy|*|-} {vz|*|-}

DESCRIPTION

The set_velocity command sets the velocity of atom atom_name to (vx,vy,vz). If one or more of the arguments is ‘*’, the corresponding component of the velocity is unchanged. If an argument is ‘-’, the corresponding component of the velocity changes sign.

EXAMPLE
Set the component x of the velocity of atom C18 to 0.01, leave the component y unchanged and change the sign of the component z.
set_velocity C18 0.01 * -
RELATED INFORMATION

move, list_atoms

species

NAME

species - define a new atomic species and add it to the list of currently defined species

SYNOPSIS

species species_name URI

DESCRIPTION

The species command defines a new atomic species under the name species_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

spectrum

NAME

spectrum - compute the optical absorption spectrum

SYNOPSIS

spectrum filename

spectrum width filename

spectrum emin emax width filename

DESCRIPTION

The spectrum command computes the dipole transition strengths between occupied and empty orbitals. It computes Kohn-Sham eigenvalues and eigenfunctions of the current wave function using the the current value of the xc variable. The corresponding absorption spectrum is written on an output file after convolution with a gaussian function of width width.

The parameters are defined as follows

emin, emax

energy range of plot (optional)

width

width of the gaussian used in the convolution (optional) (default 0.05 eV)

filename

output file name

If emin and emax are not given, the energy range includes all possible transitions between occupied and empty orbitals. All energy parameters must be given in eV.

RELATED INFORMATION

xc

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.

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

ext_stress

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, 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 within Qbox

SYNOPSIS

! [cmd]

DESCRIPTION

The ! command executes the cmd command in a Unix shell.