# 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 atomsSYNOPSIS

angle [-pbc]atom1atom2atom3DESCRIPTION

The

anglecommand prints the value of the angle formed by the three atoms given as arguments. The namesatom1,atom2andatom3must refer to the names of atoms currently defined in the sample. If the-pbcoption 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 sampleSYNOPSIS

atomnamespeciesxyz[vxvyvz]DESCRIPTION

The

atomcommand adds an atom to the current sample. Thenameargument can be any character string but must differ from all the other names of atoms in the current sample. Thespeciesargument must refer to an atomic species previously defined using the species command. The position of the atom is specified by its coordinatesx,y,zin atomic units (bohr). Optionally, the velocity of the atom can be specified by its componentsvx,vy,vzin atomic units (bohr/atomic-unit-of-time). (One atomic-unit-of-time is 0.02418885 fs).RELATED INFORMATION

## bisection

NAME

bisection– perform recursive subspace bisection of the wave functionsSYNOPSIS

bisectionlx ly lz thresholdDESCRIPTION

The

bisectioncommand 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 functionsSYNOPSIS

compute_mlwfDESCRIPTION

The

compute_mlwfcommand 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, thecompute_mlwfcommand 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 positionsSYNOPSIS

constraint define positionconstraint_name atom1constraint define distanceconstraint_name atom1 atom2 distance [velocity]constraint define angleconstraint_name atom1 atom2 atom3 angle [velocity]constraint define torsionconstraint_name atom1 atom2 atom3 atom4 angle [velocity]constraint listconstraint deleteconstraint_nameconstraint enforceconstraint setconstraint_name value [velocity]DESCRIPTION

The

constraintcommand is used to manage the constraint set. Constraints can be of the following types:position,distance,angleortorsion. Constraints are added to the constraint set using theconstraint definecommand. They can be removed from the set using theconstraint deletecommand. The list of currently defined constraints can be printed using theconstraint listcommand. Some constraints have an associated value that can be modified using theconstraint setcommand. 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 positionconstraint_name atom1Define a position constraint on atom

atom1. This locks the atomatom1into its current position.

constraint define distanceconstraint_name atom1 atom2 dist [velocity]Define a distance constraint between atoms

atom1andatom2. If the optionalvelocityargument is given, the value of the distance will change at each time step of the simulation at a rate specified by thevelocityargument. The argumentdistmust be given in (bohr). Thevelocitymust be given in (bohr/(a.u. time)).

constraint define angleconstraint_name atom1 atom2 atom3 angle [velocity]Define an angle constraint on atoms

atom1,atom2andatom3. If the optionalvelocityargument 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 argumentanglemust be given in (degree). Thevelocitymust be given in (degree/(a.u. time)).

constraint define torsionconstraint_name atom1 atom2 atom3 atom4 angle [velocity]Define a torsion (or dihedral) constraint on atoms

atom1,atom2,atom3andatom4. If the optionalvelocityargument 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 argumentanglemust be given in (degree). Thevelocitymust be given in (degree/(a.u. time)).

constraint listPrint a list of all currently defined constraints.

constraint deleteconstraint_nameRemove the constraint named

constraint_namefrom the constraint set.

constraint enforceModify atomic positions so as to enforce all constraints using the SHAKE algorithm.

constraint setconstraint_name value [velocity]Modify the value of a constraint and, optionally, its velocity. This command only applies to the

distance,angleandtorsionconstraints.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 enforcecommand 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

## distance

NAME

distance- print the distance between two atomsSYNOPSIS

distance [-pbc]atom1 atom2DESCRIPTION

The

distancecommand prints the value of the distance separating two atoms. If the-pbcoption is used, the positions of the atoms are interpreted as those of the nearest atom replica, taking into account periodic boundary conditions.RELATED INFORMATION

## extforce

NAME

extforce- manage external forces on atomsSYNOPSIS

extforce define atomicextforce_name atom1 fx fy fzextforce define pairextforce_name atom1 atom2 fextforce define globalextforce_name fx fy fzextforce setextforce_name fx fy fzextforce setextforce_name fextforce listextforce deleteextforce_nameDESCRIPTION

The

extforcecommand is used to define, modify or delete external forces acting on specific atoms. Thedefine,set,listanddeletesubcommands modiy the set of external forces as detailed below for each choice of parameters.

extforce define atomicextforce_name atom1 fx fy fzThis command defines an external force named

extforce_nameacting on atomatom1. The force has componentsfx, fy, fz. The force components must be given in atomic units (hartree/bohr). [ 1 (hartree/bohr) = 82.3886 nN ]

extforce define pairextforce_name atom1 atom2 fThis command defines a pair force named

extforce_nameacting only on the atomsatom1andatom2. The magnitude of the pair force isfand must be given in atomic units (hartree/bohr). A positive value offdefines a repulsive force betweenatom1andatom2.

extforce define globalextforce_name fx fy fzThis command defines a global external force named

extforce_nameacting on all atoms. The force has componentsfx,fy,fz. The force components must be given in atomic units (hartree/bohr).

extforce setextforce_name fx fy fzThis 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 setextforce_name fThis command modifies the magnitude of the force associated with the external force

extforce_name. This syntax applies to the “pair” force only.

extforce listThis command prints the list of currently defined external forces.

extforce deleteextforce_nameThis command removes the external force

extforce_namefrom 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 cellSYNOPSIS

fold_in_wsDESCRIPTION

The

fold_in_wscommand 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 commandSYNOPSIS

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 calculationSYNOPSIS

kpoint addkx ky kz weightkpoint movekx ky kz kx’ ky’ kz’kpoint deletekx ky kzkpoint listDESCRIPTION

The

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

kpoint addkx ky kz weightThis command adds a k-point to the k-point set. The

weightof the k-point must be in [0,1] and is used to weigh the contribution of the k-point to the charge density.

kpoint movekx ky kz kx’ ky’ kz’This command moves a k-point located at

kx ky kztokx’ 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 listThis command lists all currently defined k-points.

kpoint deletekx ky kzThis command deletes the k-point located at

kx ky kz.A k-point is defined by its coefficients

kx ky kzon 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 numberskx, ky, kzis \(\vec{k} = kx\, \vec{b_1} + ky\, \vec{b_2} + kz\, \vec{b_3}\). 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, kzare compared to the coordinates of the k-points currently defined. Since comparisons of floating point numbers are unreliable, thekpoint deletecommand 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, thekpoint addcommand 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 0.125EXAMPLE

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 sampleSYNOPSIS

list_atomsDESCRIPTION

The

list_atomscommand prints a list of all atoms currently defined.RELATED INFORMATION

## list_species

NAME

list_species- print a list of all species currently definedSYNOPSIS

list_speciesDESCRIPTION

The

list_speciescommand prints a list of all species currently defined. For each species, the parameters of the corresponding pseudopotential are printed.RELATED INFORMATION

## load

NAME

load- load a sample from a restart fileSYNOPSIS

loadURIDESCRIPTION

The

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

URIargument can be a local file, in which case Qbox will open and read the file. IfURIis 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.orgRELATED INFORMATION

## move

NAME

move- change the position of an atomSYNOPSIS

moveatom_nametox y zmoveatom_namebydx dy dzDESCRIPTION

The

movecommand moves an atom to an absolute position specified byx, y, zor by a relative displacement specified bydx, 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 potentialSYNOPSIS

plotfilenameplot -densityfilenameplot -wfn filenameplot -wfsnmin nmax[-spin {1|2}]filenameplot -vlocalfilenameDESCRIPTION

The

plotcommand 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.

plotfilenameThis command generates an xyz file containing atomic positions only.

plot -density [-spin {1|2}]filenameThis command generates a file in “cube” format containing the atomic positions and the total charge density. If the

-spinoption 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 -wfn[-spin {1|2}]filenameThis command generates a file in “cube” format containing the n-th wave function. If the

-spinoption is used, the wave function of the first (1) or second (2) spin is used.

plot -wfsnmin nmax[-spin {1|2}]filenameThis command generates a file in “cube” format containing the sum of the squares of the amplitudes of the wave functions

nmintonmaxinclusive. If the-spinoption is used, the wave functions of the first (1) or second (2) spin are used.

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

Note

The

-wfand-wfsoptions 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 atomSYNOPSIS

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

The

partial_chargecommand computes the amount of electronic charge contained in a sphere of radiusrcentered on atomatom_name. The radiusrmust be specified in atomic units (bohr). When using the-spinoption, the charge density of the given spin is computed. If nspin=2 and the-spinoption is not used, the total charge is computed.

## print

NAME

SYNOPSIS

variableDESCRIPTION

The

RELATED INFORMATION

## quit

## randomize_r

NAME

randomize_r- add a random perturbation to atomic positionsSYNOPSIS

randomize_ramplitudeDESCRIPTION

The

randomize_rcommand adds random numbers to the coordinates of all atomic positions. The random displacements are drawn from a normal distribution scaled by theamplitudeargument.RELATED INFORMATION

## randomize_v

NAME

randomize_v– initialize atomic velocities with random values from a Maxwell-Boltzmann distributionSYNOPSIS

randomize_vtemperatureDESCRIPTION

The

randomize_vcommand initializes atomic velocities with random numbers drawn from a Maxwell-Boltzmann distribution. Thetemperatureargument determines the temperature of the distribution.RELATED INFORMATION

## randomize_wf

NAME

randomize_wf- add a random perturbation to electronic wave functionsSYNOPSIS

randomize_wf[amplitude]DESCRIPTION

The

randomize_wfcommand 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. Therandomize_wfcommand 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. Usingrandomize_wfintroduces a slight symmetry breaking which is sufficient to avoid high-symmetry saddle points.

## rescale_v

NAME

rescale_v– rescale atomic velocitiesSYNOPSIS

rescale_vfDESCRIPTION

The

rescale_vcommand rescales the velocity of all atoms by a factorf.

## reset_rotation

NAME

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

reset_rotationDESCRIPTION

The

reset_rotationcommand 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 zeroSYNOPSIS

reset_vcmDESCRIPTION

The

reset_vcmcommand 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 potentialSYNOPSIS

responseamplitude[-RPA|-IPA]nitscf[nite]response -vextfilename[-cube][-RPA|-IPA][-amplitudea]nitscf[nite]DESCRIPTION

The

responsecommand computes the polarizability of the system, or the density response to a specific external potential. Theresponsecommand uses a series of self-consistent calculations in finite electric field (or finite potential). Thenitscfandnitevalues 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-RPAand-IPA. By default, the Hartree and exchange-correlation potentials are updated self-consistently during the finite-field calculations. If the-RPAoption is used, only the Hartree potential is updated (Random Phase Approximation). If the-IPAoption is used, neither the Hartree potential nor the exchange-correlation potential are updated (Independent Particle Approximation).

responseamplitudenitscf[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 -vextfilename[-cube][-RPA|-IPA][-amplitudea]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-cubeoption is used, the format of the external potential file is the cube format. If the-amplitudeoption 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

responsecommand.Note

The

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

## rseed

NAME

rseed– initialize the random number generatorSYNOPSIS

rseed[seed]DESCRIPTION

The

rseedcommand initializes the random number generator. Qbox uses random numbers in the implementation of therandomize_wfcommand and in stochastic thermostats (LOWE, ANDERSON, BDP). If an integerseedargument 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 therseedcommand 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 cellSYNOPSIS

run [-atomic_density]niterrun [-atomic_density]niter nitscfrun [-atomic_density]niter nitscf niteDESCRIPTION

The

runcommand 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_densityoption 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

niterThe 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.

nitscfThe 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.

niteThe 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

run0 nitscfPerform

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

run0 nitscf nitePerform

nitscfself-consistent iterations withniteupdates 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.

runniternitscfPerform

niterionic steps withnitscfupdates 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.

runniternitscfnitePerform

niterionic steps, withnitscfupdates of the charge density between ionic steps, andniteupdates 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 100Perform 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 10Perform 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 10Perform 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 10Perform 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

RELATED INFORMATION

## save

NAME

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

save [-serial] [-text] [-atomsonly] [-no_wfv]filenameDESCRIPTION

The

savecommand 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-serialoption is used, the data is saved from task 0 only and no attempt is made to use optimized parallel I/O functionality. If the-textoption is used, the wave function values are written in formatted text form rather than encoded in base64 format in the sample file. If the-atomsonlyoption is used, only the <atomset> element is written and wave functions are not included. If the-no_wfvoption is used, wave function velocities are not saved.RELATED INFORMATION

## set

## set_velocity

NAME

set_velocity- set the velocity of an atomSYNOPSIS

set_velocityatom_name {vx|*|-} {vy|*|-} {vz|*|-}DESCRIPTION

The

set_velocitycommand sets the velocity of atomatom_nameto(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

## species

NAME

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

speciesspecies_name URIDESCRIPTION

The

speciescommand defines a new atomic species under the namespecies_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

## spectrum

NAME

spectrum- compute the optical absorption spectrumSYNOPSIS

spectrumfilenamespectrumwidth filenamespectrumemin emax width filenameDESCRIPTION

The

spectrumcommand 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 widthwidth.The parameters are defined as follows

emin,emaxenergy range of plot (optional)

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

filenameoutput file name

If

eminandemaxare not given, the energy range includes all possible transitions between occupied and empty orbitals. All energy parameters must be given in eV.RELATED INFORMATION

## status

NAME

status- print status of the current sampleSYNOPSIS

statusDESCRIPTION

The

statuscommand prints a brief summary of the characteristics of the current sample.

## strain

NAME

strain– apply strain on the systemSYNOPSIS

strain [-atomsonly] [-inverse]uxx uyy uzz uxy uyz uxzDESCRIPTION

The

straincommand modifies the shape of the unit cell and modifies the atomic positions to impose a strain defined by the components of the symmetric strain tensoru. Using the-inverseflag causes the inverse transformation to be applied. Using-atomsonlychanges 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 atomsSYNOPSIS

torsion [-pbc]atom1 atom2 atom3 atom4DESCRIPTION

The

torsioncommand prints the value of the angle (dihedral) defined by the four atoms given as arguments. The namesatom1, atom2, atom3, atom4must refer to the names of atoms currently defined in the sample. If the-pbcoption is used, the positions of the atoms are interpreted as those of the nearest atom replica, taking into account periodic boundary conditions.RELATED INFORMATION

## ! (shell escape)

NAME

! (shell escape)- execute a Unix command from within QboxSYNOPSIS

![cmd]DESCRIPTION

The

!command executes thecmdcommand in a Unix shell.