MD++ Commands and variables
Documentation entries (926 results found)
Name | Description | Source | Data type | Default value |
---|---|---|---|---|
dope_Yttria | If input = [ yttriaconc ] is set before calling the command, then
relabel certain (randomly chosen) Zr atoms as Y atoms and remove certain (randomly chosen) Oxygen atoms (creating vacancies) to achieve the specified Yttria doping concentration (yttriaconc). |
bmb | COMMAND | N/A |
eamgrid | The length of the table to be read for the arrays rho, rhop, phi, phip, …. | eam | INT | 6000 |
pottype | 1 for EAM, 2 for MEAM (not implemented in this program). | eam | INT | 1 |
eamfiletype | If eamfiletype = 2 then the EAM potential file also contains the cross potential data (phix and phipx) between two elements. | eam | INT | 0 |
readeam | Read parameters for the EAM potential contained in the potfile.
Usage: potfile = filename eamgrid = n readeam Example: MD++/scripts/Examples/example05-au.tcl |
eam | COMMAND | N/A |
readMEAM | Empty function. Do not use. | eam | COMMAND | N/A |
Broadcast_EAM_Param | CPU 0 (master) broadcast EAM potential parameters to other CPUs (slaves).
Needed before eval_parallel. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
eam | COMMAND | N/A |
F_Ewald | Array containing Ewald contribution to the force on each atom. | ewald | DOUBLE | N/A |
F_Ewald_Real | Array containing the real space part of the Ewald contribution to the force on each atom. | ewald | DOUBLE | N/A |
F_Ewald_Rec | Array containing the reciprocal space part of the Ewald contribution to the force on each atom. | ewald | DOUBLE | N/A |
EPOT_IND_Ewald | Array containing Ewald contribution to the local energy of each atom. | ewald | DOUBLE | N/A |
EPOT_IND_Ewald_Real | Array containing the real space part of the Ewald contribution to the local energy of each atom. | ewald | DOUBLE | N/A |
EPOT_IND_Ewald_Rec | Array containing the reciprocal space part of the Ewald contribution to the local energy of each atom. | ewald | DOUBLE | N/A |
A | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
d | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
beta | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
c | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
c0 | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
c1 | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
c2 | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
alpha | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
b0 | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
B | Parameters in the FS potential.
It will be specified by the readpot command. |
fs | DOUBLE | N/A |
readpot | Read parameters for the FS potential specified in the potfile. | fs | COMMAND | N/A |
Broadcast_FS_Param | CPU 0 (master) broadcast FS potential parameters to other CPUs (slaves).
Needed before eval_parallel. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
fs | COMMAND | N/A |
rhoh | Array containing electron density at each atom.
For diagnostic purposes. |
fs | DOUBLE | N/A |
af | Array containing the square root of the electron density at each atom.
For diagnostic purposes. |
fs | DOUBLE | N/A |
myname | Empty variable. Do not use. | ising | STRING | N/A |
command | Has similar meaning as the same variable in md | ising | STRING | N/A |
input | Has similar meaning as the same variable in md | ising | DOUBLE | N/A |
NX | NX, NY, NZ specify the size of the Ising model. | ising | INT | 100 |
NY | NX, NY, NZ specify the size of the Ising model. | ising | INT | 100 |
NZ | NX, NY, NZ specify the size of the Ising model. | ising | INT | 1 |
nsample | Number of samples (i.e. tests) for command ComputeSuccessRate. | ising | INT | 100 |
nsuccess | Number of successful outcomes in ComputeSuccessRate.
Also see nsample. |
ising | INT | 0 |
kBT | kBT is the temperature in the Ising model | ising | DOUBLE | N/A |
J | J and H are two parameters in the Hamiltonian of the Ising model | ising | DOUBLE | N/A |
H | J and H are two parameters in the Hamiltonian of the Ising model | ising | DOUBLE | N/A |
totalsteps | Has similar meaning as the same variable in md | ising | INT | N/A |
savepropfreq | Has similar meaning as the same variable in md | ising | INT | N/A |
randseed | Has similar meaning as the same variable in md | ising | INT | N/A |
curstep | Has similar meaning as the same variable in md | ising | INT | N/A |
continue_curstep | Has similar meaning as the same variable in md | ising | INT | N/A |
N_lgst_cluster | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | ising | INT | N/A |
N_lgst_avg | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | ising | INT | N/A |
saveFFScn | Has similar meaning as the same variable in md | ising | INT | N/A |
FFSoption | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
FFSpruning | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
FFScn_weight | Parameter in Forward Flux Sampling (FFS) simulations | ising | DOUBLE | N/A |
FFS_Pp | Parameter in Forward Flux Sampling (FFS) simulations | ising | DOUBLE | N/A |
FFS0_check | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
lambda_A | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
lambda_B | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
FFScurstep | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
FFSautoend | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
YES_UMB | Umbrella Sampling parameter | ising | INT | N/A |
UMB_K | Umbrella Sampling parameter | ising | DOUBLE | N/A |
UMB_equilstep | Umbrella Sampling parameter | ising | INT | N/A |
UMB_curstep | Umbrella Sampling parameter | ising | INT | N/A |
n_center | Umbrella Sampling parameter | ising | INT | 0 |
delta_n | Umbrella Sampling parameter | ising | INT | 0 |
Kinetic | Has similar meaning as the same variable in md | ising | INT | N/A |
Kinetic_Time | Has similar meaning as the same variable in md | ising | DOUBLE | N/A |
Kinetic_Swip | Has similar meaning as the same variable in md | ising | INT | N/A |
savecn | Has similar meaning as the same variable in md | ising | INT | N/A |
saveprop | Has similar meaning as the same variable in md | ising | INT | N/A |
savecnfreq | Has similar meaning as the same variable in md | ising | INT | N/A |
savepropfreq | Has similar meaning as the same variable in md | ising | INT | N/A |
printfreq | Has similar meaning as the same variable in md | ising | INT | N/A |
calcryfreq | During Monte Carlo simulations, the command calcrystalorder is called
when curstep is a multiple of calcryfreq and when
iter is a multiple of calcryfreq1.
For details, see Seunghwa Ryu. |
ising | INT | 100 |
calcryfreq1 | During Monte Carlo simulations, the command calcrystalorder is called
when curstep is a multiple of calcryfreq and when
iter is a multiple of calcryfreq1.
For details, see Seunghwa Ryu. |
ising | INT | 1 |
filecounter | Has similar meaning as the same variable in md | ising | INT | N/A |
FFSfilecounter | Parameter in Forward Flux Sampling (FFS) simulations | ising | INT | N/A |
incnfile | Has similar meaning as the same variable in md | ising | STRING | N/A |
finalcnfile | Has similar meaning as the same variable in md | ising | STRING | N/A |
outpropfile | Has similar meaning as the same variable in md | ising | STRING | N/A |
intercnfile | Has similar meaning as the same variable in md | ising | STRING | N/A |
FFScnfile | Parameter in Forward Flux Sampling (FFS) simulations | ising | STRING | N/A |
zipfiles | Has similar meaning as the same variable in md | ising | INT | N/A |
win_width | Has similar meaning as the same variable in md | ising | INT | N/A |
win_height | Has similar meaning as the same variable in md | ising | INT | N/A |
plotfreq | Has similar meaning as the same variable in md | ising | INT | N/A |
atomradius | Has similar meaning as the same variable in md | ising | DOUBLE | N/A |
backgroundcolor | Has similar meaning as the same variable in md | ising | STRING | N/A |
rotateangles | Has similar meaning as the same variable in md | ising | DOUBLE | N/A |
rotateangles | Has similar meaning as the same variable in md | ising | STRING | N/A |
atomcolor | Has similar meaning as the same variable in md | ising | STRING | N/A |
atomcolor | Has similar meaning as the same variable in md | ising | STRING | N/A |
runcommand | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
initspin | Initialize the spin matrix S.
Usage: input = style initspin
If style = -1, then the entire matrix S is set to -1.
|
ising | COMMAND | N/A |
initpath | Usage: input = pn initpath
Initialize the path to be a random path going from all spin down (-1) to all spin up (+1). The path will be used in future path sampling simulations. There are three paths in the MD++/ising model: pathA, pathB, pathC. Which one gets initialized by initpath depends on the value of pn (1 for pathA, 2 for pathB, 3 for pathC). Also see copyPathtoS. |
ising | COMMAND | N/A |
MCrun | Perform Monte Carlo (MC) simulation.
Variables totalsteps, saveprop, savecn, … etc. should be set before calling this command. |
ising | COMMAND | N/A |
srand | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
srand48 | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
srandbytime | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
srand48bytime | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
copyPathtoS | Usage: input = [ pn id ] copyPathtoS
Copy the spin configuration from the path to array S. There are three paths in the MD++/ising model: pathA, pathB, pathC. Which one gets chosen by copyPathtoS depends on the value of pn (1 for pathA, 2 for pathB, 3 for pathC). id specifies which configuration along the chosen path will be copied. Also see initpath, copyRchaintoCN. |
ising | COMMAND | N/A |
SampleMCpath | Usage: input = [ smin smax nmax pn ] SampleMCpath
Generate a new path by performing Monte Carlo simulation from an initial condition stored in array S. The Monte Carlo simulation continues until the average spin value drops below smin, or exceeds smax, or if the average number of MC steps exceeds nmax. The resulting path is stored in one of the three paths: pathA, pathB, pathC, depending on the value of pn (1 for pathA, 2 for pathB, 3 for pathC). Also see ComputeSuccessRate. |
ising | COMMAND | N/A |
WalkonChain | Usage: input = [ smin smax nmax ] WalkonChain
Sample transition paths connecting two states (most spins down v.s. most spins up) by randomly picking a point on the existing path and generate a trajectory (by SampleMCpath) with this point as the initial condition. The trajectory is then used to replace half of the original path to generate a new path. The parameters smin smax nmax are passed to SampleMCpath. Also see ComputeSuccessRate. |
ising | COMMAND | N/A |
ComputeSuccessRate | Usage: nsample = NS input = [ smin smax nmax ] ComputeSuccessRate
Compute the success rate of a given spin configuration stored in array S.
by generating paths all starting from S via SampleMCpath.
The result is stored in the nsuccess variable. |
ising | COMMAND | N/A |
AnalyzeConfigs | Usage: nsample = NS input = [ nstart nend smin smax nmax ] WalkonChain
Read in intermediate .cn files "inter####.cn" (in the current directory specified by dirname), whose numbers run from nstart to nend, and compute the energy, total spin, and success rate. The success rate is the probability of reaching state with most spins up in Monte Carlo simulations starting from this configuration as the initical condition. It is computed by calling ComputeSuccessRate. |
ising | COMMAND | N/A |
FFSprocess | Implements the Forward Flux Sampling (FFS) algorithm. Called within MCrun. | ising | COMMAND | N/A |
calcrystalorder | Group spins into clusters and determine the size of the largest cluster.
For details, ask Seunghwa Ryu. |
ising | COMMAND | N/A |
allocDFS | Allocate arrays needed to analyze the size distribution of clusters (islands of opposite spin) in the spin configuration S generated by the Monte Carlo simulation. | ising | COMMAND | N/A |
assign_Lam | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
writecn | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
readcn | Read spin configurations from incnfile. | ising | COMMAND | N/A |
openintercnfile | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
openFFScnfile | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
writeintercn | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
writeFFScn | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
setfilecounter | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
setFFSfilecounter | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
openpropfile | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
writepath | Usage: input = pn finalcnfile = fname writepath
Write the path into file. There are three paths in the MD++/ising model: pathA, pathB, pathC. Which one gets written depends on the value of pn (1 for pathA, 2 for pathB, 3 for pathC). Also see readpath. |
ising | COMMAND | N/A |
readpath | Usage: input = pn incnfile = fname readpath
Read path from file. There are three paths in the MD++/ising model: pathA, pathB, pathC. Which one gets written depends on the value of pn (1 for pathA, 2 for pathB, 3 for pathC). Also see writepath. |
ising | COMMAND | N/A |
openwin | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
plot | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
alloccolors | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
alloccolorsX | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
rotate | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
saverot | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
reversergb | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
wintogglepause | Has similar meaning as the same command in md. | ising | COMMAND | N/A |
C12_00 | Parameter in the LJ potential between species 0 and 0.
Φ(r) = C12 / r12 - C6 / r6 |
lj2 | DOUBLE | N/A |
C6_00 | Parameter in the LJ potential between species 0 and 0.
Φ(r) = C12 / r12 - C6 / r6 |
lj2 | DOUBLE | N/A |
C12_11 | Parameter in the LJ potential between species 1 and 1.
Φ(r) = C12 / r12 - C6 / r6 |
lj2 | DOUBLE | N/A |
C6_11 | Parameter in the LJ potential between species 1 and 1.
Φ(r) = C12 / r12 - C6 / r6 |
lj2 | DOUBLE | N/A |
C12_01 | Parameter in the LJ potential between species 0 and 1.
Φ(r) = C12 / r12 - C6 / r6 |
lj2 | DOUBLE | N/A |
C6_01 | Parameter in the LJ potential between species 0 and 1.
Φ(r) = C12 / r12 - C6 / r6 |
lj2 | DOUBLE | N/A |
initLJ | Initialize the parameters in the LJ potential. | lj2 | COMMAND | N/A |
C12_ij | Parameter in the LJ potential between species i and j.
The actual parameters to set in MD++ are: C12_00, C12_01, …
Φ(r) = C12 / r12 - C6 / r6 |
ljbond | DOUBLE | N/A |
C6_ij | Parameter in the LJ potential between species i and j.
The actual parameters to set in MD++ are: C6_00, C6_01, …
Φ(r) = C12 / r12 - C6 / r6 |
ljbond | DOUBLE | N/A |
BOND_R0 | Equilibrium length of the bonds between nearest neighbor atoms in a lipid molecule.
Also see BOND_K. |
ljbond | DOUBLE | N/A |
BOND_K | Stiffness of the bond between nearest neighbor atoms in a lipid molecule modeled as a harmonic spring.
Also see BOND_R0. |
ljbond | DOUBLE | 0 |
WALL_X0 | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
WALL_K | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
ATTRAC_R0 | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
ATTRAC_K | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
WALL2_X0 | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
WALL2_K | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
ATTRAC2_Y0 | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
ATTRAC2_K | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
LMAX | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
LAMBDA | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
dUdLAM_WALL | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
dUdLAM_ATT | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
dUdLAM_WALL2 | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
dUdLAM_ATT2 | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
dUdLAM_L | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
dUdLAM | Parameter in wall potentials to compute free energy of lipid bilayer. Still under development. | ljbond | DOUBLE | N/A |
Rcut | Cut-off radius of the LJ potential. | ljbond | DOUBLE | N/A |
usrfile | Name of the atomic configuration file in Atomeye .usr format, which is created
when command writeatomeyeusr is called.
The .usr file instructs Atomeye to draw bonds between which atomic pairs, and may also contain information about the atom color/radius and bond color/radius. |
ljbond | STRING | N/A |
initLJ | Initialize the parameters in the LJ potential. | ljbond | COMMAND | N/A |
makelipids | When the array input = [ nsolvent nlipid chainlen headid bond_len nalkane alkanelen ] is set before calling this command, then
create an initial configuration containing solvent, lipid and alkane molecules. Lipid and alkane molecules are chain-like molecules formed by linking a series of atoms by covalent bonds. |
ljbond | COMMAND | N/A |
linklipids | After a configuration has been read from a file, make covalent bonds between nearest neighbor atoms in lipid and alkane molecules.
Requires the input array to be set before calling this command, in the same way as makelipids. |
ljbond | COMMAND | N/A |
writeatomeyeusr | Write Atomeye .usr file from the current atomic configuration.
Before calling this function, the filename must be specified in variable usrfile. |
ljbond | COMMAND | N/A |
myname | Empty variable. Do not use. | md | STRING | N/A |
command | A string containing a shell command for MD++ to call by runcommand.
For example: command = "ls" runcommand |
md | STRING | echo Hello World |
input | A generic input array that is used by many commands. The corresponding input parameters
need to be set before the command is called.
Also see makedipole, makedislpolygon, makecylinder, scaleVel, extendbox. |
md | DOUBLE | N/A |
output_dat | (For debugging purposes. Not for general use.) | md | DOUBLE | N/A |
output_str | For debugging purposes. output_str is the string that contains the numerical values
of the variables specified in output_fmt. During MD simulation (run), every
savepropfreq steps the output_str string is evaluated and gets written
into the property file.
Also see saveprop, outpropfile. |
md | STRING | N/A |
output_fmt | A string instructing MD++ what variables to write to the property file. Any variable
recognized by MD++ can included, e.g. output_fmt = "curstep EPOT KATOM Tinst" Example: MD++/scripts/Examples/example05-au.tcl Also see saveprop, outpropfile. |
md | STRING | N/A |
NP | Total number of atoms (particles). This variable is usually not set manually
by the user, but is set automatically when commands such as makecrystal
and readcn is called. In Tcl the value of this variable can be printed
out by, e.g.
puts "Number of atoms = [MD++_Get NP]" |
md | INT | 0 |
NP0 | Empty variable. Do not use. | md | INT | 0 |
NIMAGES | A parameter for the implementation of torsional Periodic Boundary Conditions (tPBC)
or bending Periodic Boundary Conditions (bPBC).
Also see bendspec. |
md | INT | 0 |
NPfree | Number of atoms i whose fixed[i] == 0.
Also see NP, NPfixed. |
md | INT | 0 |
NPfixed | Number of atoms i whose fixed[i] == 1.
Also see NP, NPfree. |
md | INT | 0 |
H | The 3x3 matrix H consists of three column vectors
[c1 | c2 | c3 ],
which are the repeat vector of the simulation cell (under periodic boundary
conditions).
See wiki page for more details. |
md | DOUBLE | 0 |
H0 | A copy of the H matrix.
Also see saveH, restoreH. |
md | DOUBLE | 0 |
OMEGA | Volume of the simulation cell, OMEGA = det ( H ). | md | DOUBLE | N/A |
VIRIAL | VIRIAL (in unit of eV) is a Rank 2 tensor (force times distance),
which is an intermediate result for computing the total Virial stress
TSTRESS (in unit of eV/Å3).
TSTRESS = (VIRIAL + PSTRESS) / OMEGA Also see PSTRESS, TSTRESS, TSTRESSinMPa. |
md | DOUBLE | N/A |
DVIRIALDexx | A 3x3 matrix containing the derivative of the VIRIAL matrix
with respect to strain e_xx = e_11.
DVIRIALDexx_ij = d(VIRIAL_ij) / (de_11) VIRIAL is the Virial stress tensor and e is the strain tensor. Also see Dexx. |
md | DOUBLE | N/A |
DVIRIAL_1111 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2222 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3333 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1122 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2211 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2233 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3322 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3311 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1133 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1112 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1121 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1123 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1132 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1131 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1113 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2212 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2221 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2223 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2232 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2231 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2213 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3312 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3321 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3323 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3332 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3331 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3313 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1211 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1222 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1233 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1212 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1221 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1223 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1232 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1231 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1213 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2111 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2122 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2133 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2112 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2121 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2123 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2132 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2131 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2113 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2311 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2322 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2333 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2312 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2321 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2323 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2332 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2331 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_2313 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3211 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3222 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3233 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3212 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3221 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3223 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3232 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3231 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3213 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3111 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3122 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3133 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3112 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3121 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3123 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3132 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3131 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_3113 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1311 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1322 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1333 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1312 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1321 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1323 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1332 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1331 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
DVIRIAL_1313 | A component of the DVIRIAL (rank 4) tensor.
DVIRIAL_ijkl = d(VIRIAL_ij) / (de_kl) VIRIAL is the Virial stress tensor and e is the strain tensor. |
md | DOUBLE | N/A |
Dexx | The step size used to compute the DVIRIAL tensor by centered finite difference.
Also see DVIRIALDexx, DVIRIAL_ijkl. |
md | DOUBLE | 0 |
VH | A 3x3 matrix containing the velocity of the box matrix H times timestep. | md | DOUBLE | N/A |
EPOT | The potential energy of the simulation cell in eV.
Also see EPOT_IND, KATOM, eval. |
md | DOUBLE | 0 |
EPBOX | Potential energy of the box in Parrinello-Raman dynamics.
Also see EPBOX. |
md | DOUBLE | 0 |
EPOT0 | The potential energy just before the trial move in Monte Carlo simulation.
Also see EPOT, runMC. |
md | DOUBLE | 0 |
ESTRAIN | Empty variable. Do not use. | md | DOUBLE | N/A |
KATOM | The kinetic energy of the simulation cell in eV.
Also see EPOT. |
md | DOUBLE | 0 |
KBOX | Kinetic energy of the box in Parrinello-Raman dynamics.
Also see EPBOX. |
md | DOUBLE | 0 |
Tinst | The instantaneous temperature (in K) computed from the kinetic energy of all atoms.
Tinst = KATOM / (1.5 * KB * NPfree) Also see KATOM, NPfree. |
md | DOUBLE | 0 |
zeta | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
zetav | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | N/A |
zetaa | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
zeta2 | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
zeta3 | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
zeta4 | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
zeta5 | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
zetaNHC | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
zetaNHCv | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
zetaNHCa | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
zetaNHC2 | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
zetaNHC3 | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
zetaNHC4 | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
zetaNHC5 | Parameter for the Nose-Hoover chain thermostat. | md | DOUBLE | N/A |
HELM | HELM = EPOT + KATOM in NVE ensemble, where EPOT is
the potential energy and KATOM is the kinetic energy of the atoms. In other ensembles,
the energies of the thermo-stat and bario-stat are added to HELM as well.
Also see HELMP. |
md | DOUBLE | N/A |
HELMP | HELMP equals HELM plus additional terms to make HELMP
a conserved quantity in various ensembles, including NVE, NVT, NPH,
NPT, … It is useful to include HELMP in output_fmt
so that we can check whether this quantity is conserved in the property file.
Also see HELM, saveprop. |
md | DOUBLE | N/A |
PSTRESS | PSTRESS (in unit of eV) is a Rank 2 tensor (mass times velocity times velocity),
which is an intermediate result for computing the total Virial stress
TSTRESS (in unit of eV/Å3).
TSTRESS = (VIRIAL + PSTRESS) / OMEGA Also see VIRIAL, TSTRESS, TSTRESSinMPa. |
md | DOUBLE | N/A |
TSTRESS | Total stress in the simulation cell in unit of in eV/Å3.
Sign convention: a hydrostatic pressure corresponds to a positive value in TSTRESS. A tensile stress corresponds to negative value in TSTRES. Also see TSTRESSinMPa. |
md | DOUBLE | N/A |
TSTRESSinMPa | Total stress in the simulation cell in MPa, converted from TSTRESS (in eV/Å3).
TSTRESSinMPa = TSTRESS ∗ 160.2e3 Also see TSTRESS. |
md | DOUBLE | N/A |
PRESSURE | Average of the diagnoal components of the total stress
TSTRESS matrix (in unit of eV/Å3).
Also see TSTRESS, TSTRESSinMPa. |
md | DOUBLE | N/A |
SIGMA | A 3x3 matrix (Σ) that is needed to compute GH in Parrinello-Rahman barostat.
Reference: Parrinello and Rahman, J. Appl. Phys. 52, 7182 (1981), Eq.(2.24). Also see GH, relax_freebox. |
md | DOUBLE | 0 |
GH | A 3x3 matrix containing the gradient of the potential energy
with respect to the box matrix H.
Also see relax_freebox. |
md | DOUBLE | N/A |
curstep | Current step number in MD simulation run.
It is used to determine when whether the X-window needs to be refreshed, or intermediate .cn file needs to be saved, at the current simulation step. Also see plotfreq, savecnfreq, continue_curstep, conj_step. |
md | INT | N/A |
conj_step | Current step number in conjugate gradient relaxation relax,
equivalent to curstep in MD simulation run.
It is used to determine when whether the X-window needs to be refreshed, or intermediate .cn file needs to be saved, at the current simulation step. Also see plotfreq, savecnfreq. |
md | INT | 0 |
continue_curstep | If continue_curstep = 1, then at the beginning of MD simulation by command run, the variable curstep will not be reset to zero. Instead, it will keep its current value and the simulation will continue for another totalsteps number of steps. In this case, the curstep entry in the property file will be monotonically increasing, when the command run is called several times in the input (script or tcl) file. | md | INT | 0 |
MC_accept_ratio | The average acceptance ratio in Monte Carlo simulations. For maximum efficiency the timestep parameter should be adjusted so that MC_accept_ratio is around 0.5. | md | DOUBLE | 0 |
MC_dr | A vector containing the random trial displacement in the current Monte Carlo simulation step.
In Monte Carlo simulation, the maximum displacement in x, y, z directions is specified by variable timestep (here in unit of Å). |
md | DOUBLE | N/A |
dH | A 3x3 matrix containing the change of H matrix introduced in makedipole to accomodate the plastic strain of the dislocation dipole. | md | DOUBLE | N/A |
dEdlambda | The derivative of the potential function with respect to the switching parameter λ
(that goes between lambda0 and lambda1) in free energy calculations.
Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
dlambdadt | The switching rate (dλ/dt) in free energy calculations.
Also see dEdlambda, runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
Wtot | The total work done during adiabatic switching simulation.
Wtot += dEdlambda * dlambdadt * (lambda1 - lambda0) at each time step.
Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
Wavg | The average work done per time step during adiabatic switching simulation.
Wavg = Wtot / totalsteps.
Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
RLIST | The cut-off radius of the Verlet neighbor list. It equals the cut-off radius of the
potential plus SKIN. This variable is usually not set manually, but is
set automatically by the command that reads and initializes the potential.
Also see refreshnnlist, SKIN. |
md | DOUBLE | 0 |
SKIN | The cut-off radius of the Verlet neighbor list RLIST minus the cut-off radius of the
potential. SKIN is usually 0.1 times the cut-off radius of the potential.
This variable is usually not set manually, but is set automatically by the command that
reads and initializes the potential.
Also see refreshnnlist, RLIST. |
md | DOUBLE | 0 |
enable_Fext | If enable_Fext = 1, then the external force vector Fext[i] is added to the total force F[i] for every atom i. | md | INT | 0 |
applyFext | Same as enable_Fext. | md | INT | 0 |
indentor_Z | Empty variable. Do not use. | md | DOUBLE | N/A |
indentor_Z0 | Empty variable. Do not use. | md | DOUBLE | N/A |
indentor_Vz | Empty variable. Do not use. | md | DOUBLE | N/A |
indentor_K | Empty variable. Do not use. | md | DOUBLE | N/A |
indentor_Fz | Empty variable. Do not use. | md | DOUBLE | N/A |
enable_FlatIndentor | Empty variable. Do not use. | md | INT | N/A |
TSTRESS_xx | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_xy | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_xz | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_yx | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_yy | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_yz | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_zx | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_zy | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESS_zz | A component of the TSTRESS (total stress) tensor (in eV/Å3). | md | DOUBLE | N/A |
TSTRESSinMPa_xx | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_xy | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_xz | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_yx | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_yy | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_yz | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_zx | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_zy | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
TSTRESSinMPa_zz | A component of the TSTRESSinMPa (total stress) tensor (in MPa). | md | DOUBLE | N/A |
H_11 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_12 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_13 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_21 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_22 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_23 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_31 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_32 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
H_33 | A component of the H (3x3) matrix. | md | DOUBLE | N/A |
relaxation_algorithm | The name of the different variations of the conjugate gradient relaxation algorithms.
The options are ZXCGR and PRPLUS.
Also see relax. |
md | STRING | ZXCGR |
conj_itmax | Maximum number of search iterations in conjugate gradient relaxation.
Also see relax. |
md | INT | 1000 |
conj_fevalmax | Maximum number of times the potential function can be called during
conjugate gradient relaxation.
Also see relax. |
md | INT | 10000 |
conj_step | Current step number in conjugate gradient relaxation relax,
equivalent to curstep in MD simulation run.
It is used to determine when whether the X-window needs to be refreshed, or intermediate .cn file needs to be saved, at the current simulation step. Also see plotfreq, savecnfreq. |
md | INT | 0 |
conj_fixbox | If conj_fixbox = 1 then in the conjugate gradient relaxation
(invoked by the relax command), the box matrix H is not
allowed to change.
If conj_fixbox = 0 then the box matrix H is allowed to change during relaxation. Also see conj_fixboxvec. |
md | INT | 1 |
conj_fixboxvec | If conj_fixbox = 0, we may still fix individual components of
the box matrix H during the conjugate gradient relaxation
(invoked by the relax command).
Format: conj_fixboxvec = [
If fij == 1 , then Hij is fixed. |
md | DOUBLE | 0 |
conj_g2res | Residual gradient in the conjugate gradient relaxation. More precisely, it is the sum of the square of the gradient for each degree of freedom. | md | DOUBLE | 0 |
fixbox | Same as conj_fix_box.
Also see fixboxvec. |
md | INT | 1 |
fixboxvec | Same as conj_fixboxvec. | md | DOUBLE | 0 |
conj_fixdir | Empty variable. Do not use. | md | INT | 0 |
conj_fixshape | Option not yet working. | md | INT | 0 |
conj_fixatoms | If conj_fixatoms = 1 then in the conjugate gradient relaxation
(invoked by the relax command), all scaled coordinates of the atoms
will be fixed. Only the box matrix H is allowed to change.
Also see conj_fixbox. |
md | INT | 0 |
conj_etol | The tolerance in the energy. If the variation becomes lower than
this value, the conjugate gradient relaxation will declare convergence and exit.
This option is only used if relaxation_algorithm = PRPLUS (not the default).
Also see relax. |
md | DOUBLE | 1e-8 |
conj_ftol | The tolerance in the residual gradient. If the residual gradient becomes lower than
this value, the conjugate gradient relaxation will declare convergence and exit.
Also see relax. |
md | DOUBLE | 1e-8 |
conj_dfpred | The anticipated reduction of potential energy in the first trial step of the conjugate gradient relaxation. There is usually no need to change it from the default value. | md | DOUBLE | 1e-3 |
H | The 3x3 matrix H consists of three column vectors
[c1 | c2 | c3 ],
which are the repeat vector of the simulation cell (under periodic boundary
conditions).
See wiki page for more details. |
md | DOUBLE | 0 |
H0 | A copy of the H matrix.
Also see saveH, restoreH. |
md | DOUBLE | 0 |
stress | A 3x3 matrix specifying the external stress (in MPa) applied to the simulation cell. This
affects relax if conj_fixbox = 0, as well as run if
ensemble_type = NPT or NPH.
The sign convention of MD++ is such that a hydrostatic pressure corresponds to a positive value in stress, while tensile loading corresponds to a negative value. We need to make sure stress is set to a symmetric matrix. |
md | DOUBLE | N/A |
stressmul | A multiplicative factor in front of the stress matrix. This allows us to easily vary the magnitude of stress without changing its orientation. | md | DOUBLE | 1 |
extforce | extforce = [ n fx1 fy1 fz1
fx2 fy2 fz2 … fxn fyn fzn ] n is the number of groups affected by this setting. If n > 0, then atoms beloning to group k will experience an additional external force fxk fyk fzk . |
md | DOUBLE | 0 |
forcemul | A multiplication factor to the external forces specified in the extforce array. | md | DOUBLE | N/A |
pressureadd | Empty variable. Do not use. | md | DOUBLE | N/A |
vacuumratio | A value between 0 and 1 describing the fraction of the space in the simulation
cell occupied by vacuum. This instructs MD++ to subtract off the vacuum volume
when computing the stress.
TSTRESS = (VIRIAL + PSTRESS) / (OMEGA * (1-vacuumratio)) |
md | DOUBLE | 0 |
hprecond | Preconditioning parameters for conjugate gradient relaxation. Perhaps useful when simulation box is highly different from a cube. | md | DOUBLE | 1 |
xprecond | Preconditioning parameters for conjugate gradient relaxation. Perhaps useful when simulation box is highly different from a cube. | md | DOUBLE | 1 |
yprecond | Preconditioning parameters for conjugate gradient relaxation. Perhaps useful when simulation box is highly different from a cube. | md | DOUBLE | 1 |
zprecond | Preconditioning parameters for conjugate gradient relaxation. Perhaps useful when simulation box is highly different from a cube. | md | DOUBLE | 1 |
constrainS | The imposed constraint value during constrained relaxation.
Also see constrainS_INST, constrainatoms. |
md | DOUBLE | N/A |
constrainS_INST | The instantaneous (actual) value of the constraint, during constrained relaxation. It is supposed to
match the imposed constrain value constrainS.
Also see constrainS. |
md | DOUBLE | N/A |
constrainF | The force against the constraint in constrained relaxation.
Also see constrainS, constrainatoms. |
md | DOUBLE | N/A |
constrainatoms | constrainatoms = [ n i1 i2 … in ]
When n > 0, then atoms i1 i2 … in will be constrained in the hyperplane perpendicular to SR2 - SR1, which are two configurations set by setconfig1 and setconfig2. Also see constrainedMD, constrainedrelax. |
md | INT | 0 |
ensemble_type | Specify the ensemble type of MD simulation, such as NVE,
NVT, NPH or NPT.
Must be set before MD simulation (run). |
md | STRING | NVE |
integrator_type | The name of the integrator to be used in MD simulation (run). Choices are:
Gear6 and VVerlet.
Also see ensemble_type, implementation_type. |
md | STRING | Gear6 |
implementation_type | Select which implementation of the time integrator to use. For certain
ensemble_type and integrator_type, multiple versions of
the integrators have been implemented to choose from.
See integrators.cpp to find how many implementations are available. |
md | INT | 0 |
initvelocity_type | A string specifying the probability distribution of velocities to be assigned by command initvelocity. Choices are Uniform and Gaussian. | md | STRING | Uniform |
zerorot | A string specifying which component(s) of the angular momentum need to be zeroed out
in initvelocity.
For example, for a nanowire under PBC along z axis but subjected to free surface boundary conditions in x and y directions, we need to set zerorot = z. For a nanoparticle under free surface boundary conditions in x, y, and z directions, we need to set zerorot = all. |
md | STRING | none |
SAVEMEMORY | A parameter instructing which arrays to allocate (or not) when creating a new configuration
(e.g. makecrystal) or reading one from file (e.g. readcn).
When SAVEMEMORY = 9, only arrays SR and fixed are allocated. This allows a crystal to be created and written to a file. When SAVEMEMORY = 8, arrays R and R0 are allocated, in addition to the above. When SAVEMEMORY = 7, arrays F, EPOT_IND and species are allocated, in addition to the above. This allows the structure to be relaxed (e.g. relax). When SAVEMEMORY = 6, arrays VR and VSR are allocated, in addition to the above. This allows simple MD simulation (e.g. run). When SAVEMEMORY = 5, arrays image, TOPOL and group are allocated, in addition to the above. This allows the analysis and visualization of the structure by central symmetry parameter (e.g. calcentralsymmetry). When SAVEMEMORY = 4, arrays F0 and Fext are allocated, in addition to the above. This allows external forces to be applied (e.g. enable_Fext). When SAVEMEMORY = 1 (default), all the remaining arrays, EPOT_RMV, VIRIAL_IND, TORQUE_IND and BENDMOMENT_IND are allocated, in addition to the above. |
md | INT | 0 |
nspecies | Total number of atomic species in the simulation.
Also see species. |
md | INT | 1 |
totalsteps | Total number of steps for Molecular dynamics simulation.
Also see timestep, run. |
md | INT | N/A |
equilsteps | The number of equilibration steps in MD simulation. The property file only
gets written to after the simulation has passed equilstep number of steps.
Also see run, totalsteps, saveprop. |
md | INT | 0 |
atommass | An array containing the atomic mass of each species (in g/mol).
Must be set before performing MD simulation (run).
Example: MD++/scripts/Example/example02a-si-md.script |
md | DOUBLE | N/A |
atomcharge | An array storing the electric charge of each atomic species in unit of the fundamental
charge unit (e).
Also see species, ewald. |
md | DOUBLE | N/A |
wallmass | Effective mass of the box matrix H in Parrinello-Rahman dynamics. Reference: Parrinello and Rahman, J. Appl. Phys. 52, 7182 (1981). Also see KBOX. | md | DOUBLE | 1 |
NHMass | Parameter for the Nose-Hoover thermostat. | md | DOUBLE | 0 |
NHChainLen | Parameter for the Nose-Hoover chain thermostat. | md | INT | N/A |
T_OBJ | The target temperature (in K) used by initvelocity.
It is also used for the thermostat in MD simulation (run) when
ensemble_type = NVT or NPT.
Also see DOUBLE_T. |
md | DOUBLE | 0 |
DOUBLE_T | If DOUBLE_T = 1, then initvelocity will set the instantaneous temperature to twice the value specified in T_OBJ (in K). | md | INT | 0 |
allocmultiple | If allocmultiple = n is set before
readcn or makecrystal, then the memory for NP ∗
n atoms is allocated, where NP is the actual number of atoms.
Useful for extendbox. |
md | INT | 1 |
vt2 | Obsolete variable for controlling the Nose-Hoover thermostat. Do not use. Use NHMass instead. | md | DOUBLE | 0.25 |
boxdamp | A damping coefficient on the box matrix H in MD simulations in the NPH
or NPT ensemble to damp out the oscillations so that the box can be equilibrated
faster.
run, ensemble_type. |
md | DOUBLE | 0 |
timestep | Molecular dynamics simulation time step in picoseconds.
Also see totalsteps, run. |
md | DOUBLE | N/A |
RLIST | The cut-off radius of the Verlet neighbor list. It equals the cut-off radius of the
potential plus SKIN. This variable is usually not set manually, but is
set automatically by the command that reads and initializes the potential.
Also see refreshnnlist, SKIN. |
md | DOUBLE | 0 |
NIC | Empty variable. Do not use. | md | INT | N/A |
NNM | The maximum number of neighbors in the neighbor list. You may need to enlarge this value if you use a large cut off radius RLIST. | md | INT | 60 |
nl_skip_pairs | An array specifying the atom pairs that will be skipped when constructing the neighbor
list. This effectively remove the interaction between the atom pairs, and is one way
to prepare a crack.
Format: nl_skip_pairs = [ n i1 j1 i2 j2
… in jn ]
This array is usually not set manually, but is set automatically by commands cutbonds and cutbonds_by_ellipse. |
md | INT | 0 |
current_NIC | The maximum number of atoms in one cell after the construction of the cell list. | md | INT | 0 |
current_NNM | The maximum number of neighbors in the neighbor list of all atoms after the construction of the cell list. | md | INT | 0 |
shearrate | shearrate is a 3x3 matrix. When applyshear = 1,
then at every time step the simulation box matrix H is updated by,
H += H * shearrate * timestep . Also see applyshear. |
md | DOUBLE | N/A |
applyshear | When applyshear = 1,
then at every time step the simulation box matrix H is updated by,
H += H * shearrate * timestep . Also see shearrate. |
md | INT | 0 |
constrainedMD | If constrainedMD = 1, then during MD simulation, the scaled coordinates of the atoms specified in array constrainatoms will be constrained in the hyperplane perpendicular to SR2 - SR1. | md | INT | 0 |
runavgCN | Empty variable. Do not use. | md | INT | N/A |
enable_DPD | Dissipative Particle Dynamics (stochastic thermostat) parameter | md | INT | 0 |
DPD_friction_const | Dissipative Particle Dynamics (stochastic thermostat) parameter | md | DOUBLE | 0 |
DPD_ratio | Dissipative Particle Dynamics (stochastic thermostat) parameter | md | DOUBLE | 1 |
DPD_rcut | Dissipative Particle Dynamics (stochastic thermostat) parameter | md | DOUBLE | 100 |
enable_ANDERSON | If enable_ANDERSON = 1, then the Anderson thermostat is activated, so that the atomic
velocities will be randomly reassigned during MD simulations.
Also see ANDERSON_ratio. |
md | INT | N/A |
ANDERSON_ratio | A value between 0 and 1, specifying the probability of randomly reassigning the velocities
for each atom at every MD step.
Also see enable_ANDERSON. |
md | DOUBLE | N/A |
mcatom | If mcatom >= 0, then at each step of the Monte Carlo simulation, an atoms will be selected
at random to be displaced by a small random vector (trial move). mcatom then stores the
index of this selected atoms.
If mcatom = -1, then all atoms will be displaced by random vectors in the trial move. This generally leads to very low acceptance ratio unless the simulation cell is very small. |
md | INT | 0 |
lambda0 | The beginning value λ0 of thermodynamic integration (i.e. λ-integration).
Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
lambda1 | The final value λ1 of thermodynamic integration (i.e. λ-integration).
Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 1 |
Ecoh | A parameter used to adjust the zero point of potential energy in free energy calculations using the Adiabatic Switching method. | md | DOUBLE | 0 |
switchfreq | Parameter for adiabatic switching simulation for free energy calculation | md | INT | N/A |
switchoffatoms | Parameter for adiabatic switching simulation for free energy calculation
switchoffatoms = [ n i1 i2 … in ]
When n > 0, then atoms i1 i2 … in will be gradually switched on or off during the adiabatic switching simulation. |
md | INT | N/A |
switchfunc | Parameter for adiabatic switching simulation for free energy calculation | md | INT | N/A |
refpotential | Specifies the reference potential in adiabatic switching simulations to compute free energy. Options are:
0: Einstein crystal (not implemented yet). Also see I12_epsilon, Gauss_epsilon, runMDSWITCH, runMCSWITCH. |
md | INT | 0 |
enableswitch | Parameter for adiabatic switching simulation for free energy calculation | md | INT | N/A |
ecspring | Spring constant in the Einstein crystal model, which is a reference system for free energy calculations
by adiabatic switching.
Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
I12_rc | Cut-off radius in the inverse-12 (I12) purely repulsive potential, which can be used
as a reference model for adiabatic switching simulations.
Φ(r) = I12_epsilon ⋅ (I12_sigma / r)12 (if r < I12_rc) Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
I12_sigma | A parameter in the inverse-12 (I12) purely repulsive potential, which can be used
as a reference model for adiabatic switching simulations.
Φ(r) = I12_epsilon ⋅ (I12_sigma / r)12 (if r < I12_rc) Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
I12_epsilon | A parameter in the inverse-12 (I12) purely repulsive potential, which can be used
as a reference model for adiabatic switching simulations.
Φ(r) = I12_epsilon ⋅ (I12_sigma / r)12 (if r < I12_rc) Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
Gauss_rc | Cut-off radius in the Gaussian potential, which can be used
as a reference model for adiabatic switching simulations.
Φ(r) = Gauss_epsilon ⋅ exp(- r2 / (2 * Gauss_sigma2 ) (if r < Gauss_rc) Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
Gauss_sigma | A parameter in the Gaussian potential, which can be used
as a reference model for adiabatic switching simulations.
Φ(r) = Gauss_epsilon ⋅ exp(- r2 / (2 * Gauss_sigma2 ) (if r < Gauss_rc) Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
Gauss_epsilon | A parameter in the Gaussian potential, which can be used
as a reference model for adiabatic switching simulations.
Φ(r) = Gauss_epsilon ⋅ exp(- r2 / (2 * Gauss_sigma2 ) (if r < Gauss_rc) Also see runMDSWITCH, runMCSWITCH. |
md | DOUBLE | 0 |
randseed | The seed to randomize the random number generator. Must be set before calling srand48 or srand. | md | INT | 12345 |
MC_dV_freq | In Monte Carlo simulation under the NPT ensemble, a volume change is
attempted every MC_dV_freq steps.
Also see runMC, ensemble_type, MC_dVmax. |
md | INT | 1 |
MC_dN_freq | In Monte Carlo simulation under the uVT ensemble, a change of number of atoms is
attempted every MC_dN_freq steps.
Also see runMC, ensemble_type. |
md | INT | 1 |
MC_dVmax | The maximum allowed change of simulation cell volume in one trial step of MC simulation in
the NPT ensemble. The actual trial volume change is MC_dVmax * (2*drand48() - 1).
Also see runMC. |
md | DOUBLE | 0.1 |
MC_dfrac | In Monte Carlo simulations under the uVT ensemble, an atom is allowed to take
fractional occupancy. MC_dfrac is the change of the fractional
occupancy of the atom in a trial move.
Also see runMC. |
md | DOUBLE | 0.1 |
MC_P_ext | The external pressure applied to the simulation cell Monte Carlo simulations in which the volume is allowed to fluctuate (when ensemble_type = NPT). | md | DOUBLE | 0 |
MC_mu_ext | The external chemical potential for an atom that will be gradually switched on or off during
Monte Carlo switching simulations.
Also see runMCSWITCH. |
md | DOUBLE | N/A |
nebspec | Parameter for relaxation by the Nudged Elastic Band (NEB) method
(nebrelax) or the string method (stringrelax).
When used by nebrelax, nebspec has the following meaning. nebspec = [ relax_surround k moveleftend moverightend yesclimbimage ] If relax_surround = 1, then relaxing the surrounding atoms of the constrained atoms during nebrelax. We usually use relax_surround = 0, then the surrounding atoms will be a linear interpolation between SR1 and SR2. When all atoms are included in constrainatoms, then this option has no effect. relax_surround = 1 does not work for parallel version of nebrelax. k is the spring constant of the nudged elastic band. If k = 0, then the spring constant will be automatically chosen as the maximum force magnitude times the number of chains.
If moveleftend = 0, then the left end replica of the chain does not move
during NEB relaxation. This is the correct setting if the left end is already at
an energy minimum. moverightend has similar meaning for the right end. If yesclimbimage = 1, then the image (or replica) of the highest energy starts to climb up the hill when curstep > equilsteps. This means that if yesclimbimage = 1, we need to set equilsteps to a non-zero value, e.g. 1000, and set totalsteps > equilsteps. Otherwise, equilstep = 0 by default and running with yesclimbimage = 1 from the beginning makes nebrelax more unstable. Typically, we can set totalsteps to be equilsteps + 500, which means that the climbing image method will be applied to the last 500 steps of nebrelax. (In the future, we may want to use a different variable to replace equilsteps.) When used by stringrelax, nebspec (or, equivalently stringspec) has the following meaning. nebspec = [ relax_surround redistr_freq moveleftend moverightend yesclimbimage islengthconstant ] The main difference from above is in redistrib_freq (instead of k) and in islengthconstant. In the string method, there is no need to specify a spring constant. Instead, redistr_freq specifies how often the path gets reparameterized. We recommend redistrib_freq = 1, which means reparameterization at every step of stringrelax. If islengthconstant = 1, the total length of the string will be kept constant duringn stringrelax. This option is neglected if both ends are fixed. This option only works for parallel version of stringrelax. Note that if yesclimbimage = 1, equilsteps need to be set to a non-zero value (e.g. 1000) to avoid instability. Also see nebrelax, stringrelax. |
md | INT | N/A |
stringspec | The same as (i.e. an alias of) nebspec. | md | INT | N/A |
readrchainspec | Setting for command readRchain. | md | INT | -1 |
annealspec | Parameter for simulated annealing. | md | DOUBLE | N/A |
chainlength | The number of replicas in chain-of-state relaxation methods (nebrelax
and stringrelax) to find the minimum energy path between two states.
Also see nebrelax, stringrelax, allocchain. |
md | INT | 0 |
YES_SURFTEN | Parameter for surface tension calculation | md | INT | 0 |
surftensionspec | Parameter for surface tension calculation | md | INT | N/A |
YES_SURFTEN1 | Parameter for surface tension calculation | md | INT | N/A |
ST_step | Parameter for surface tension calculation | md | INT | N/A |
ST_orien | Parameter for surface tension calculation | md | INT | N/A |
ST_Kmax | Parameter for surface tension calculation | md | DOUBLE | 0 |
ST_LAMBDA | Parameter for surface tension calculation | md | DOUBLE | 0 |
ST_LMAX | Parameter for surface tension calculation | md | DOUBLE | 0 |
ST_dUdLAM_L | Parameter for surface tension calculation | md | DOUBLE | 0 |
ST_dUdLAM_POT | Parameter for surface tension calculation | md | DOUBLE | 0 |
ST_dUdLAM_TOT | Parameter for surface tension calculation | md | DOUBLE | 0 |
YES_FFS | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
L_for_QLM | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | INT | 0 |
l_for_qlm | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | INT | 0 |
N_solid_P | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | 0 |
Principal_Inertia | Variables describing the shape of a cluster of (defect) atoms identified by findcore.
Printcipal_Inertia = [ I1 I2 I3 ] |
md | DOUBLE | N/A |
N_lgst_index | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | md | DOUBLE | 0 |
N_lgst_skin | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | md | DOUBLE | 0 |
N_lgst_skin_index | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | md | DOUBLE | 0 |
qlm_type | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | STRING | N/A |
wSKIN | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
DLxyz | Empty variable. Do not use. | md | INT | N/A |
DLNdiv | Empty variable. Do not use. | md | INT | N/A |
N_lgst_cluster | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | md | INT | 0 |
Rc_for_QLM | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
QLM_cutoff | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
saveFFScn | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFSoption | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFSpruning | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFScn_weight | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
FFS_Pp | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
FFS0_check | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
lambda_A | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
lambda_B | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFScurstep | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFSautoend | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFShist | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
Delta_LAM | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MIN_LAM | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MAX_LAM | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFSbackward | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
B_lambda_cut | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
B_lambda_B | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
B_lambda_0 | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
FFScommitor | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
YES_UMB | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | 0 |
UMB_order_param | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
UMB_order_group | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
KinkDmax | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
printUMBorder | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
UMB_noslipdirection | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
HETERO_DN | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | 0 |
MCequilstep | Parameter in Umbrella Sampling by Monte Carlo simulation.
For details, as Seunghwa Ryu. |
md | INT | N/A |
UMB_K | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
UMB_equilstep | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
UMB_curstep | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
UMB_tryrate | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
UMB_continue | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MC_UMB_cal_period | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MC_UMB_log_period | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MC_UMB_accept_tot | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MC_UMB_accept_ratio | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
MC_UMB_num_of_trials | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
n_center | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | 0 |
delta_n | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | 0 |
acc_UMB | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | N/A |
MC_RC_cal_period | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
Kinetic | A parameter controlling the Molecular Dynamics and Monte Carlo simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
Kinetic_Time | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | 10 |
Kinetic_Swip | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | 0 |
N_lgst_temp | Parameter for largest cluster sampled in Forward-Flus Sampling (FFS) and Umbrella Sampling (US) simulations. | md | INT | 0 |
KN_Center | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | 0 |
YES_HMC | Parameter for Hybrid Monte Carlo
For details, ask Seunghwa Ryu. |
md | INT | 0 |
Ns_HMC | Parameter for Hybrid Monte Carlo
For details, ask Seunghwa Ryu. |
md | INT | N/A |
YES_SEP | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | 0 |
CLUSTER_CM | Center of mass position of a cluster identified in the Forward Flux Sampling (FFS) simulation.
For details, ask Seunghwa Ryu. |
md | DOUBLE | N/A |
SEPA_ORDER | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
SEPA_TARGET | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
SEPA_RATIO | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
NORM_REACTION | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
NC_TIMES_SEPA | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
IMP_INDEX | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | INT | 0 |
IMP_TOPOL_INDEX | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
IMP_R_EXP | Umbrella Sampling parameter
For details, ask Seunghwa Ryu. |
md | DOUBLE | 2.5 |
VIRIAL_Ewald | Ewald contribution to the VIRIAL tensor. | md | DOUBLE | N/A |
VIRIAL_Ewald_Real | Real space part of the Ewald contribution to the VIRIAL tensor. | md | DOUBLE | N/A |
VIRIAL_Ewald_Rec | Reciprocal space part of the Ewald contribution to the VIRIAL tensor. | md | DOUBLE | N/A |
EPOT_Ewald | Ewald contribution to the potential energy of the entire simulation cell. | md | DOUBLE | N/A |
EPOT_Ewald_Real | The real space part of the Ewald contribution to the potential energy of the entire simulation cell. | md | DOUBLE | N/A |
EPOT_Ewald_Rec | The reciprocal space part of the Ewald contribution to the potential energy of the entire simulation cell. | md | DOUBLE | N/A |
EPOT_Ewald_Self | The self-energy part of the Ewald contribution to the potential energy of the entire simulation cell. | md | DOUBLE | N/A |
Ewald_CE_or_PME | 0 to choose the classical Ewald (CE) method
1 to choose the particle mesh Ewald (PME) method |
md | INT | 0 |
Ewald_option_Alpha | Specifies whether or not the value for Alpha in the Ewald method is to be determined
automatically or specified manually.
If Ewald_option_Alpha = 0, then Ewald_Alpha is determined automatically, and Ewald_Rcut = Ewald_precision / Ewald_Alpha. If Ewald_option_Alpha = 1, then Ewald_precision and Ewald_Rcut are specified manually, and Ewald_Alpha = Ewald_precision / Ewald_Rcut. |
md | INT | 0 |
Ewald_Alpha | A parameter in the Ewald method.
Also see Ewald_option_Alpha, Ewald_precision. |
md | DOUBLE | 0 |
Ewald_precision | A parameter in the Ewald method.
For details, ask Hark Lee. Also see Ewald_Alpha, Ewald_option_Alpha. |
md | DOUBLE | N/A |
Ewald_time_ratio | A parameter in the Ewald method.
For details, ask Hark Lee. Also see Ewald_option_Alpha, Ewald_precision. |
md | DOUBLE | N/A |
Ewald_Rcut | Real space cut-off radius in Ewald method.
Also see Ewald_precision, Ewald_option_Alpha. |
md | DOUBLE | 9 |
CE_Kc | Cut off in the reciprocal space for the classical Ewald (CE) method. | md | DOUBLE | 0 |
PME_K1 | Parameter for Particle Mesh Ewald method | md | INT | N/A |
PME_K2 | Parameter for Particle Mesh Ewald method | md | INT | N/A |
PME_K3 | Parameter for Particle Mesh Ewald method | md | INT | N/A |
PME_bsp_n | Parameter for Particle Mesh Ewald method | md | INT | N/A |
crystalstructure | The crystal structure to be created by command makecrystal.
Example: MD++/scripts/Example/example00-makecrystal.script |
md | STRING | N/A |
latticeconst | The lattice constant (in Å) of the crystal to be created by command makecrystal.
Example: MD++/scripts/Example/example00-makecrystal.script |
md | DOUBLE | N/A |
latticesize | latticesize = [ a_1 a_2 a_3 repeat_a b_1 b_2 b_3 repeat_b c_1 c_2 c_3 repeat_c ] where [a_1 a_2 a_3] specifies the first repeat vector of the simulation supercell in Miller indices, and repeat_a is the number of the repeats in that direction. [b_1 b_2 b_3] specifies the first repeat vector of the simulation supercell in Miller indices, and repeat_b is the number of the repeats in that direction. [c_1 c_2 c_3] specifies the first repeat vector of the simulation supercell in Miller indices, and repeat_c is the number of the repeats in that direction. Also see crystalstructure, latticeconst, makecrystal. Example: MD++/scripts/Example/example00-makecrystal.script |
md | DOUBLE | N/A |
torsionsim | If torsionsim = 1, it activates the torsional Periodic Boundary Condition (tPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). |
md | INT | 0 |
torquespec | Simulation settings pertaining to torsional Periodic Boundary Condition (tPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). |
md | DOUBLE | 0 |
Torque | Total torque in torsional Periodic Boundary Condition (tPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). |
md | DOUBLE | 0 |
bendsim | If bendsim = 1, it activates the bending Periodic Boundary Condition (bPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). |
md | INT | 0 |
bendspec | Simulation settings pertaining to bending Periodic Boundary Condition (bPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). |
md | DOUBLE | 0 |
BendMoment | Total bending moment in bending Periodic Boundary Condition (bPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). |
md | DOUBLE | 0 |
P_com | A vector specifying the total linear momentum of the simulation cell (i.e. its center of mass).
This quantity is conserved in Molecular Dynamics simulations without an external potential.
The command initvelocity is supposed to make sure this quantity is zero. |
md | DOUBLE | N/A |
F_com | A (3x1) vector containing total force on all the atoms (i.e. the center-of-mass) of the simulation cell.
Usually this vector should be zero during the MD simulation unless an external potential is applied. |
md | DOUBLE | N/A |
L_com | A vector specifying the total angular momentum of the simulation cell (i.e. its center of mass).
For a nano-particle or nano-wire simulation, this quantity is conserved along certain direction
when PBC is not applied in the perpendicular directions.
The command initvelocity is supposed to make sure this quantity is zero in such cases. |
md | DOUBLE | N/A |
Ptheta_com | The momentum for the generalized coordinate Θ of the center of mass of the simulation cell under
torsional periodic boundary condition (tPBC) or bending periodic boundary condition (bPBC).
For details, see J. Mech. Phys. Solids 56, 3242, (2008). Also see P_com, L_com. |
md | DOUBLE | 0 |
latticestructure | Same as crystalstructure. | md | STRING | N/A |
makecnspec | Same as latticesize. | md | DOUBLE | N/A |
mkdipole | Same as input. | md | DOUBLE | N/A |
mkdislspec | Same as input. | md | DOUBLE | N/A |
mkcylinderspec | Same as input. | md | DOUBLE | N/A |
savecn | If savecn = 1 and savecnfreq != 0, then during MD simulation (invoked by the run command), an intermediate .cn file is saved every savecnfreq steps. | md | INT | 0 |
saveprop | If saveprop = 1 and savepropfreq != 0, then during MD simulation (invoked by the run command), a line is written in the property file (named by variable outpropfile) every savepropfreq steps. The content of the property file is specified by the outputfmt variable. | md | INT | 0 |
savecfg | If savecfg = 1 and savecfgfreq != 0, then during MD simulation (invoked by the run command), an intermediate Atomeye .cfg file is saved every savecfgfreq steps. | md | INT | 0 |
savecnfreq | If savecn = 1 and savecnfreq != 0, then during MD simulation (invoked by the run command), an intermediate .cn file is saved every savecnfreq steps. | md | INT | 100 |
savecontinuecnfreq | If savecontinuecnfreq > 0, then the atomic configuration will be saved
in a .cn file specified by continuecnfile every savecontinuecnfreq
steps during MD simulation (run).
Unlike intercnfile, the file name specified by continuecnfile does not automatically increase. This means that a new continuecnfile will overwrite the old file (unless the file name continuecnfile is changed intentionally). This allows the hard disk to always hold a copy of the latest configuration for restarting purposes, without requiring a huge disk space. If you want to record the configurations during MD simulations all in different files, use savecnfreq instead. Also see readcontinuecn, continuecnfile, intercnfile. |
md | INT | 0 |
savepropfreq | If saveprop = 1 and savepropfreq != 0, then during MD simulation (invoked by the run command), a line is written in the property file (named by variable outpropfile) every savepropfreq steps. The content of the property file is specified by the outputfmt variable. | md | INT | 100 |
savecfgfreq | If savecfg = 1 and savecfgfreq != 0, then during MD simulation (invoked by the run command), an intermediate Atomeye .cfg file is saved every savecfgfreq steps. | md | INT | 100 |
printfreq | If printfreq > 0, then the current time step information curstep is printed to the terminal (if setnolog has been set) or the A.log file (if setnolog has not bee set) during the MD simulation every printfreq steps. In Monte Carlo simulations other diagnostic information, such as acceptance ratio, is also printed. | md | INT | 100 |
filecounter | The number added to the base name of intermediate .cn files. It is automatically
incremented by one when a previous intermediate .cn file is closed and a new one is
to be opened.
Also see setfilecounter, intercnfile, savecn. |
md | INT | 1 |
FFSfilecounter | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | INT | N/A |
incnfile | Name of the file containing atomic positions and other information (optional) that command readcn will read from. Other commands, such as readMDCASK and readPOSCAR also use incnfile to specify the input configuration file name. | md | STRING | con.cn |
finalcnfile | Name of the file containing atomic positions and other information (optional) that command writecn will write to. Other commands, such as writeMDCASK, writePOSCAR, and writeatomeyecfg also use finalcnfile to specify the output configuration file name. | md | STRING | final.cn |
continuecnfile | The name of the file that the latest configuration gets saved to (for restarting purposes)
during MD simulation if savecontinuecnfreq > 0.
It is also the name of the file that readcontinuecn reads from. Also see intercnfile. ~ |
md | STRING | continue.cn |
outpropfile | The name of the file in which thermal properties (such as EPOT, Tinst) are saved
periodically during MD simulation.
Also see saveprop, output_fmt. |
md | STRING | prop.out |
intercnfile | The base name of the intermediate .cn files that will be saved periodically
during MD simulation. The actual file names will have numbers added to them,
e.g. inter0001.cn, inter0002.cn, …
Also see savecn, savecnfreq. |
md | STRING | inter.cn |
FFScnfile | Parameter in Forward Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | STRING | FFS.cn |
intercfgfile | The base name of the intermediate .cfg files that will be saved periodically
during MD simulation. The actual file names will have numbers added to them,
e.g. auto0001.cfg, auto0002.cfg, …
Also see savecfg, savecfgfreq. |
md | STRING | auto.cfg |
potfile | Name of the file that contains the information on the interatomic potential model.
Also see readpot, readeam. |
md | STRING | ../Mo.pot |
writevelocity | If writevelocity = 1, then subsequent saving of .cn files
by writecn will contain the following information for each atom:
SR.x SR.y SR.z VSR.x VSR.y VSR.z See wiki page for more details. |
md | INT | 0 |
writeall | If writeall = 1, then subsequent saving of .cn files
by writecn will contain much more information than the default,
i.e. each atomic line will contain:
SR.x SR.y SR.z VSR.x VSR.y VSR.z EPOT_IND fixed TOPOL species group image See wiki page for more details. |
md | INT | 0 |
zipfiles | If zipfiles = 1, then the .cn, .cfg and property files that MD++ creates
will be automatically zipped to save space. MD++ will automatically unzip zipped
.cn files when reading them, so you don't have to unzip them manually.
Also see writecn, writeatomeyecfg. |
md | INT | 0 |
fortranpath | A string containing the path that holds a Fortran compiled executable. Must be set before calling fortranrelax. | md | STRING | N/A |
fortranexe | A string containing the name of a Fortran compiled executable. Must be set before calling fortranrelax. | md | STRING | N/A |
atomeyepath | A string containing the path that holds the Atomeye executable.
Must be set before calling atomeye. |
md | STRING | N/A |
atomeyerepeat | atomeyerepeat = [ activate n_1 n_2 n_3 ]
If activate = 1, then the atomic configuration exported to the Atomeye cfg format will be repeated by n_1, n_2, and n_3 times along the first, second and third repeat direction of the simulation supercell. Also see H, writeatomeyecfg. |
md | INT | N/A |
atomeyeexe | A string containing the name of the Atomeye executable, e.g.
A.i686, A.exe.
Must be set before calling atomeye. |
md | STRING | N/A |
MDCASKpot | Specify the potential model used in MDCASK. Choices are SW, TERSOFF, ROCKETT, ZBL, EAM, EDIP, MEAM. It needs to be set before calling readMDCASK. | md | STRING | SW |
win_width | The initial width of the X-window. The window size can be adjusted using mouse after it is opened.
Also see win_height, openwin. |
md | INT | 350 |
win_height | The initial height of the X-window. The window size can be adjusted using mouse after it is opened.
Also see win_width, openwin. |
md | INT | 350 |
plotfreq | If the X-window is opened, then during MD simulation (invoked by the run command)
or conjugate gradient relaxation (invoked by the relax command), the atomic
positions will be refreshed in the X-window every plotfreq steps.
Also see openwin, plot |
md | INT | 1 |
atomradius | An array specifying the size of each atomic species in the X-window.
Also see atomcolor, plot. |
md | DOUBLE | 0.1 |
bondradius | The width of the line representing bonds between atoms in the X-window.
Also see bondcolor, bondlength. |
md | DOUBLE | 0.1 |
bondlength | In the X-window, two atoms whose distance is less than bondlength (in Å) will have a bond drawn between them. | md | DOUBLE | 0 |
bondcolor | The color names for drawing bonds between atoms in the X-window.
Also see bondradius, bondlength. |
md | STRING | red |
highlightcolor | The color names for atoms that are highlighted. These atoms are specified by plot_highlight_atoms. | md | STRING | purple |
fixatomcolor | The color names for atoms that are marked as fixed (fixed[i] = 1). This variable need to be set before calling alloccolor. | md | STRING | N/A |
backgroundcolor | The color name for the background of the X-window to be allocated by alloccolor.
Also see highlightcolor. |
md | STRING | N/A |
rotateangles | Specify the HOME viewing orientation of the X-window. This is the viewing orientation
when the X-window is first opened, and is also the viewing orientation the X-winndow
returns to whenever the HOME key is pressed.
The default HOME orientation is such that the x axis points from left to right, and the y axis points points from bottom to top, and the z axis points out of the screen. But this can be changed by setting rotateangle and then call rotate and saverot.
rotateangle = [ h_rot v_rot s_rot scale ]
Also see openwin, plot. |
md | DOUBLE | N/A |
coloratoms | If coloratoms = 0 (default), then atoms are colored according to their species.
If coloratoms = 1 (default), then atoms are colored according to their group ID.
Also see color00, color01, color02, alloccolors. |
md | INT | 0 |
plot_limits | Limits which atoms will be plotted in the X-window by their scaled coordinates.
Also affects which atoms will be exported to the Atomeye .cfg file.
Format: plot_limits = [ enable sxmin sxmax symin symax szmin szmax ] If enable == 1, the only atoms whose scaled coordinates falls within the limits defined by the subsequent parameters are plotted (or exported). |
md | DOUBLE | 0 |
plot_atom_info | A flag indicating what information will be printed to the screen (or A.log file)
when an atom in the X-window is clicked.
1: print scaled coordinates of the atom Example: MD++/scripts/CSD-book/chap3/sect3.3/al-fr-eng.script Also see plot_color_windows, plot_color_axis. |
md | INT | 1 |
plot_map_pbc | If plot_map_pbc = 1, atoms will be mapped to the primary domain, i.e. with scaled
coordinates in the domain [-0.5, 0.5), when plotting in the X-window. Note that this is only
for visualization purposes. The actual (scaled or real) coordinates are not changed.
By default, the actual coordinates of the atoms are used in the plotting, so atoms can appear outside the primary domain (i.e. the purple-colored simulation box). |
md | INT | 0 |
plot_color_windows | plot_color_window = [ n fmin_1 fmax_1 cw_1 fmin_2 fmax_2 cw_2 … fmin_n fmax_n cw_n ] When n > 0, this option is activated. It specifies that there will be n windows. An atom i falls into window k if fmin_k < = color_ind[i] <= fmax_k. cw_k specifies the color to be used for window k. For example, if cw_k = 6, then atoms in window k will be plotted with color06. By default, color_ind[i] is the same as EPOT_IND[i] (the potential energy contribution from atom i). But it can be changed to TOPOL[i] (the central symmetry parameter) if plot_color_axis = 2. Example: MD++/scripts/CSD-book/chap3/sect3.3/al-fr-eng.script For more information, see Computer Simulations of Dislocations Chapter 3, Section 3.3. |
md | DOUBLE | 0 |
plot_color_bar | plot_color_bar = [ enable fmin fmax ]
If enable == 1, then the atoms will be colored using a continuous color bar according to their color_ind[i] values. When color_ind[i] reaches fmin or fmax, the color on the end of the color bar is used. color_ind is either EPOT_IND or TOPOL depending on the value of plot_color_axis. |
md | DOUBLE | N/A |
plot_highlight_atoms | plot_highlight_atoms = [ n i1 i2 … in ]
When n > 0, then atoms i1 i2 … in ] will be highlighted. Also see highlightcolor. |
md | INT | N/A |
energycolorbar | Same as plot_color_bar. | md | DOUBLE | N/A |
plot_color_axis | When plot_color_axis = 0, the array color_ind[i] is the same as
EPOT_IND[i]. This means that the potential energy contribution of each atom
is used to determine the color of atoms (when plot_color_windows is activated).
When plot_color_axis = 2, the array color_ind[i] is the same as TOPOL[i]. This means that the central symmetry parameter is used to determine the color of atoms (when plot_color_windows is activated). Also see plot_color_windows. |
md | INT | 0 |
NCS | Number of nearest neighbors for each atom in the perfect crystal in central symmetry deviation (CSD)
analysis. Use NCS = 12 for FCC crystal, and NCS = 8 for BCC crystal.
Also see TOPOL, calcentralsymmetry. |
md | INT | 12 |
autowritegiffreq | If autowritegiffreq != 0 and if an X-window is open during an MD simulation (i.e. interactive run), then a screen snapshot (.gif) is taken every autowritegiffreq steps. | md | INT | 0 |
NNM_plot | Maximum number of neighbors for each atom in the plot-neighbor-list, i.e. the neighbor list
used for plotting and geometric analysis purposes. If this neighbor list is constructed for
a reference configuration, and is not updated when a newer configuration is loaded, it allows
us to compute the change of bond lengths between atoms and their original neighbors.
Also see construct_plot_nnlist, caldisregistry. |
md | INT | 4 |
rc_plot | Cut-off radius for each atom in the plot-neighbor-list, i.e. the neighbor list
used for plotting and geometric analysis purposes. If this neighbor list is constructed for
a reference configuration, and is not updated when a newer configuration is loaded, it allows
us to compute the change of bond lengths between atoms and their original neighbors.
Also see construct_plot_nnlist, caldisregistry. |
md | DOUBLE | N/A |
L_for_QLM | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | INT | 0 |
Rc_for_QLM | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | DOUBLE | 0 |
Rc_for_QLM | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | STRING | 0 |
Rc_for_QLM | Setting for computing the crystalline order parameter.
Also see calcrystalorder, allocQLM. For details, ask Seunghwa Ryu. |
md | STRING | 0 |
atomcolor | The color names for atoms of different species to be allocated by alloccolor.
atomcolor0, atomcolor1, … are for species 0, 1,
….
atomcolor is the same as atomcolor0. |
md | STRING | orange |
atomcolor | The color names for atoms of different species to be allocated by alloccolor.
atomcolor0, atomcolor1, … are for species 0, 1,
….
atomcolor is the same as atomcolor0. |
md | STRING | orange |
opendir | Create the directory specified by dirname (if it does not exist) and enter
this directory.
Note: This command is usually not called directly in the input file. It is automatically called when the dirname variable is set. |
md | COMMAND | N/A |
print_randseed | Print the value of randseed to the screen or the A.log file. | md | COMMAND | N/A |
runcommand | Execute a shell command specified in command.
For example: command = "ls" runcommand |
md | COMMAND | N/A |
relax | Conjugate gradient relaxation.
Variables conj_ftol, conj_itmax, conj_fevalmax, conj_fixbox, conj_fixboxvec (optional) should be set before calling this command. |
md | COMMAND | N/A |
relax_by_group | Usage: input = [ ng group_1 group_2 … group_ng ] relax_by_group
If ng > 0, then all atoms i whose group[i] value matches any of the group_1 group_2 … group_ng will be relaxed, while other atoms remain fixed. Redundant function. Can be reproduced by fixatoms_by_group and relax. |
md | COMMAND | N/A |
steepest_descent_relax | Usage: input = [etol ignoreE] totalsteps = N timestep = Δ steepest_descent_relax
Perform steepest descent relaxation for a maximum of N steps with step size Δ. The relaxation will exit if the reduction of EPOT is less than etol. The EPOT will not be monitored if ignoreE = 1. For debugging/testing purposes. Much slower than relax, which uses the conjugate gradient algorithm. |
md | COMMAND | N/A |
step | Perform one (integration) step of the Molecular Dynamics simulation. This function is usually not called directly by the user, but is automatically called within the run command. For debugging purposes. | md | COMMAND | N/A |
run | Perform molecular dynamics (MD) simulation.
Variables totalsteps, timestep, ensemble_type, integrator_type, saveprop, savecn, … etc. should be set before calling this command. |
md | COMMAND | N/A |
runMDSWITCH | Run Molecular Dynamics simulations in which the Hamiltonian changes
graduately from one model to another, in order to compute free energy
difference.
Also see refpotential, lambda0, lambda1, dEdlambda, dlambdadt. |
md | COMMAND | N/A |
eval | Call the potential function and compute total potential energy, force, kinetic energy, temperature and Virial stress for the current configuration. The total potential energy and stress are printed to the screen or to the A.log file (depending on whether or not setnolog is set). | md | COMMAND | N/A |
multieval | Usage: totalsteps = N multeval
Call the potential function N times. For debugging and speed benchmark purposes. |
md | COMMAND | N/A |
eval_insertparticle | Evaluate the potential energy change if a new particle is randomly inserted into the simulation cell.
Repeated calls to this function generate statistics that can be used to evaluate the chemical
potential. Since the number of atoms will need to increase, make sure to
set allocmultiple to be greater than 1 when calling makecrystal or
readcn above.
Reference: Frenkel and Smit, Understanding Molecular Simulation, 2nd ed., Section 7.2, Chemical Potentials. Also see eval_removeparticle. |
md | COMMAND | N/A |
eval_removeparticle | Evaluate the potential energy change if a randomly chosen particle is removed the simulation cell
(by setting fixed[i] = -1).
Also see eval_insertparticle. |
md | COMMAND | N/A |
refreshnnlist | Reconstruct the Verlet neighborlist (by first constructing the cell list) if necessary.
If the maximum displacement among all atoms since the last neighbor list construction
(i.e. maxi |R(i) - R0(i)|) is less than SKIN / 2, then there is
no need to reconstruct the neighbor list.
Also see R0, SKIN. |
md | COMMAND | N/A |
construct_plot_nnlist | Construct the plot-neighbor-list, i.e. the neighbor list
used for plotting and geometric analysis purposes. If this neighbor list is constructed for
a reference configuration, and is not updated when a newer configuration is loaded, it allows
us to compute the change of bond lengths between atoms and their original neighbors.
Also see rc_plot, caldisregistry. |
md | COMMAND | N/A |
printnnlist | Print the neighbor list information to the screen (or to the A.log file) for debugging purposes. | md | COMMAND | N/A |
calphonondisp | Function under development. Do not use.
Intended to compute the phonon dispersion relation based on the Hessian matrix. Also see calHessian. |
md | COMMAND | N/A |
calHessian | Compute Hessian matrix by numerical differentiation.
The step size in (Å) for numerical differentiation is specified by timestep. Result saved in hessian.out in the current directory. Note that the results are actually the negative of the Hessian matrix, i.e. it is the first derivative of the forces that are computed. To compute the free energy based on Harmonic Approximation, use MD++/Tools/matlab/free_eng_ha.m as a starting point. If input[0]=0, then the entire Hessian matrix is computed. If input[0] ≠ 0, then input[0] = n specifies the number of atoms whose corresponding (3) columns in the Hessian matrix will be computed. The atom indices are specified in input[1], … , input[n]. Also see: Computer Simulations of Dislocations web site Chapter 6, Section 6.2. |
md | COMMAND | N/A |
readHessian | Read the Hessian matrix (the second derivative of the potential function with respect to real coordinates)
from file whose name is specified by incnfile.
Also see calHessian. |
md | COMMAND | N/A |
calModeHessian | Function under development. Do not use. | md | COMMAND | N/A |
calmisfit | Compute the misfit potential of a crystal by tilting the simulation box H.
Usage: input = [ surfacenormal x0 dx x1 y0 dy y1 z0 dz z1 ] calmisfit For more details, see wiki page on ideal strength calculation. Also see calmisfit2. |
md | COMMAND | N/A |
calmisfit2 | Compute the misfit potential of a crystal without tilting the simulation box H.
Usage: input = [ surfacenormal x0 dx x1 y0 dy y1 z0 dz z1 xmin xmax ymin ymax zmin zmax ] calmisfit2 For more details, see wiki page on ideal strength calculation. Also see calmisfit. |
md | COMMAND | N/A |
testpotential | For testing a newly implemented potential. Print out the maximum force experienced by the atoms and check the self-consistency between force and potential energy (by taking numerical derivatives of the potential energy). | md | COMMAND | N/A |
calcentralsymmetry | Computes central symmetry deviation (CSD) parameter for each
atom and store them in the TOPOL array.
Requires NCS to be set (number of nearest neighbors in CSD calculation). For FCC crystal, use NCS = 12. For BCC crystal, use NCS = 8. Also see GnuPlotHistogram. |
md | COMMAND | N/A |
caldisregistry | Calculate the distance between atoms and their original neighbors (in the reference
configuration in which the plot-neighbor-list was constructed).
This allows us to identify slip events.
Also see construct_plot_nnlist. |
md | COMMAND | N/A |
findcore | Usage: input = [ tmin tmax cal_shape ] findcore
Determine the average position of defect atoms whose central symmetry deviation (CSD) parameter TOPOL is within the range of [tmin, tmax). The atoms included in the analysis can be further limited by setting plot_limits. If cal_shape = 1 then the Principal_Inertia of the defect cluster is also computed. Assumes that all defect atoms for a single cluster. |
md | COMMAND | N/A |
initvelocity | Initialize the atomic velocities according to desired temperature TOBJ.
Also see initvelocity_type. |
md | COMMAND | N/A |
perturbevelocity | Implementation not complete. Do not use.
Also see MCperturbvelocity, initvelocity. |
md | COMMAND | N/A |
MCperturbevelocity | Implementation not complete. Do not use.
Also see perturbvelocity, initvelocity. |
md | COMMAND | N/A |
multiplyvelocity | Usage: input = vratio multiplyvelocity
The velocity VSR of all atoms is multiplied by vratio. If a thermostat is used, the velocity of the thermostat variable (zetav) is multiplied by vratio as well. If a barostat is used, the velocity of the box matrix VH is also multiplied by vratio. Also see scaleVel. |
md | COMMAND | N/A |
randomposition | Set the scaled coordinates of all atoms to be random numbers uniformly distributed
in [-0.5, 0.5). This can be used to initialize the configuration for gas or liquid
simulation. Because some atoms may accidentally get too close to each other (leading
to very high energy and repulsive forces), relax usually is necessary before
MD simulation (run).
Also see initvelocity. |
md | COMMAND | N/A |
zerorotation | Add rigid body rotation velocity field to the simulation cell so that
its total angular momentum around a given axis is zero. The axis is
specified by zerorot which can be "x", or "y",
or "z".
There is usually no need to call this command manually. initvelocity is supposed to accomplish that after randomizing the velocities. Also see L_com. |
md | COMMAND | N/A |
zerototmom | Add a constant velocity to all atoms so that the center of mass velocity of the entire
simulation cell is zero.
There is usually no need to call this command manually. initvelocity is supposed to accomplish that after randomizing the velocities. Also see P_com. |
md | COMMAND | N/A |
applyconstraint | Move the current configuration to the hyperplane perpendicular to SR2 - SR1
specified by the parameter constrainS.
Also see constrainedMD, constrainedrelax. |
md | COMMAND | N/A |
runMC | Perform Monte Carlo (MC) simulation.
Variables totalsteps, timestep, ensemble_type, saveprop, savecn, … etc. should be set before calling this command. |
md | COMMAND | N/A |
runMCSWITCH | Run Monte Carlo simulations in which the Hamiltonian changes
graduately from one model to another, in order to compute free energy
difference.
Also see refpotential, lambda0, lambda1, dEdlambda, dlambdadt. |
md | COMMAND | N/A |
runTAMC | Temperature accelerated Monte Carlo simulation to find transition pathways.
Simulation only performed for atoms specified by constrainatoms.
During the simulation (at high temperature), the configuration is periodically
checked (by relax) to see whether a transition has occured.
If a transition has occurred, the command will exit. The transition path thus
identified can be saved by calling writeRchain.
Example: MD++/scripts/CSD-book/chap7/sect7.5/si-kink-tas.script For details, see Computer Simulations of Dislocations, Chapter 7, Section 7.5. Also see constrainatoms. |
md | COMMAND | N/A |
srand | Do not use. Use srand48 instead.
Randomize random number generator using randseed, which must be set before calling this command. This affects future calls to drand(). Notice that by default MD++ uses drand48() (which should be initialized by srand48) as random number generators (e.g. in initvelocity). Only use this command if drand48 is not available from the compiler, in which case you need to use rand() instead. In this case you need to modify the MD++ source code. Also see srandbytime. |
md | COMMAND | N/A |
srand48 | Randomize random number generator using randseed, which must be set before calling this command. This affects future calls to drand48(). | md | COMMAND | N/A |
srandbytime | Do not use. Use srand48bytime instead.
Randomize random number generator using current CPU time as the seed. This affects future calls to rand(). Notice that by default MD++ uses drand48() (which should be initialized by srand48) as random number generators (e.g. in initvelocity). Only use this command if drand48 is not available from the compiler, in which case you need to use rand() instead. In this case you need to modify the MD++ source code. Also see srand. |
md | COMMAND | N/A |
srand48bytime | Randomize random number generator using current CPU time as the seed. This affects future calls to drand48(). | md | COMMAND | N/A |
stringrelax | Finding the minimum energy path and the energy barrier using the
string method.
stringrelax is more stable than nebrelax (in which we need to choose the spring constant carefully). However, the parallel version of nebrelax is faster than the parallel version of stringrelax (because reparametrization requires communication between all CPUs). Also see nebrelax, nebspec. |
md | COMMAND | N/A |
runstringmethod | Alternative implementation. Do not use. Use stringrelax instead.
Reference: J. Chem. Phys. vol.126, 164103 (2007). For details, ask Keonwook Kang. |
md | COMMAND | N/A |
nebrelax | Finding the minimum energy path and the energy barrier using the
Nudged Elastic Band (NEB) method.
For details, ask Keonwook Kang. Reference: Journal of Chemical Physics Vol.113 9978-9985, 2000 Example: MD++/scripts/CSD-book/chap7/sect7.3/si-kink-nebmep.script For details, see Computer Simulations of Dislocations, Chapter 7, Section 7.3. Also see stringrelax, nebspec. |
md | COMMAND | N/A |
constrainedrelax | Conjugate gradient relaxation with a selected set of atoms constrained in the
hyperplane perpendicular to SR2 - SR1.
Example: MD++/scripts/CSD-book/chap7/sect7.3/si-kink-cstmep.script For details, see Computer Simulations of Dislocations, Chapter 7, Section 7.3. Also see relax, constrainatoms. |
md | COMMAND | N/A |
annealpath | Simulated annealing of transition path between two states by Monte Carlo.
Usage: annealspec = [ rmax T0 λ alg ] annealpath
rmax is the maximum allowed distance between neighboring states during the
Monte Carlo (annealing) simulation.
Example: MD++/scripts/CSD-book/chap7/sect7.4/si-kink-pathmc.script For details, see Computer Simulations of Dislocations, Chapter 7, Section 7.4. Also see runTAMC. |
md | COMMAND | N/A |
statedistance | Compute the distance (sqrt of two-norm) between SR1 and SR2.
If constrainedatoms[0] = 0, then all atoms are included in computing this
distance.
If constrainedatoms[0] > 0, then only constrained atoms are included in
computing this distance.
Also see setconfig1, setconfig2. |
md | COMMAND | N/A |
cutpath | Usage: annealspec = [ step n0 n1 ] cutpath
Select a subset of configurations along the chain Rc, with id n0, n0+step, n0+2*step, …, n1, and make that the new chain. Also see chainlength. |
md | COMMAND | N/A |
initRchain | Initialize the array Rc as a linear chain connecting
SR1 and SR2.
Also see setconfig1, setconfig2, nebrelax, stringrelax. |
md | COMMAND | N/A |
allocchain | Allocate replicas for the chain-of-state relaxation methods (nebrelax
and stringrelax) to find the minimum energy path between two states.
Also see chainlength, nebrelax, stringrelax. |
md | COMMAND | N/A |
interpCN | Usage: input = s interpCN
Make the current configuration SR a linear interpolation between SR1 and SR2. SR[i] = (1-s)*SR1[i] + s*SR2[i]. The center of mass difference between SR1 and SR2 is removed from SR. Also see setconfig1, setconfig2, constrainedrelax. |
md | COMMAND | N/A |
copyRchaintoCN | Usage: input = j copyRchaintoCN
Copy the scaled coordinates of its constrained atoms (specified by constrainedatoms) from replica j (Rc0[j]) to SR. |
md | COMMAND | N/A |
copyCNtoRchain | Usage: input = j copyCNtoRchain
Copy the scaled coordinates of its constrained atoms (specified by constrainedatoms) from SR to replica j (Rc0[j]). |
md | COMMAND | N/A |
moveRchain | Usage: input = [ j_des j_src ] moveRchain
Copy atomic positions in replica j_src to replica j_des in array Rc. Also see initRchain, copyCNtoRchain. |
md | COMMAND | N/A |
Fold_into_Unitcell | Same as maptoprimarycell. | md | COMMAND | N/A |
allocUMBorder | Umbrella Sampling utility
For details, ask Seunghwa Ryu. |
md | COMMAND | N/A |
assignUMBslipvec | Umbrella Sampling utility
For details, ask Seunghwa Ryu. |
md | COMMAND | N/A |
calcrystalorder | Compute the crystalline order parameter.
For details, ask Seunghw Ryu. Also see calqlml. |
md | COMMAND | N/A |
calqlwl | Compute the crystalline order parameter using GSL functions.
For details, ask Seunghw Ryu. Also see calcrystalorder. |
md | COMMAND | N/A |
allocqlm | Allocate the qlm array and other arrays needed for calqlwl.
For details, ask Seunghwa Ryu. Also see allocQLM. |
md | COMMAND | N/A |
caldislocationorder | Calculate the order parameter for Umbrella Sampling of dislocation nucleation.
Not a general purpose utility.
Reference: Proc. Natl. Acad. Sci. 108, 5174 (2011), J. Mater. Res. 26, 2335 (2011). For details, ask Seunghwa Ryu. |
md | COMMAND | N/A |
allocQLM | Allocate the QLM array and other arrays needed for calcrystalorder.
For details, ask Seunghwa Ryu. Also see allocqlm. |
md | COMMAND | N/A |
assign_Lam | Allocate and assign the Lam_array for Forward-Flux Sampling (FFS) simulations.
For details, ask Seunghwa Ryu. |
md | COMMAND | N/A |
Ewald_init | Initialize parameters in the Ewald method.
For details, ask Hark Lee. Also see Ewald_Alpha, Ewald_option_Alpha, Ewald_precision. |
md | COMMAND | N/A |
CE | Calculates the electrostatic potential energy and forces using the classical Ewald (CE) method.
Also see Ewald_CE_or_PME. |
md | COMMAND | N/A |
CE_clear | Free variables used in the classical Ewald (CE) calculation.
Also see CE. |
md | COMMAND | N/A |
PME | Calculates the electrostatic potential energy and forces using the particle-mesh Ewald (PME) method.
Also see Ewald_CE_or_PME. |
md | COMMAND | N/A |
PME_clear | Free variables used in the particle mesh Ewald (PME) calculation.
Also see PME. |
md | COMMAND | N/A |
makecrystal | Create a perfect crystal structure specified by crystalstructure,
latticeconst and latticesize.
Also see allocmultiple. |
md | COMMAND | N/A |
makecn | Same as makecrystal. | md | COMMAND | N/A |
makecut | Fix all atoms that are on one side of a plane specified in crystal coordinate system,
i.e. by Miller indices.
This command allows one to expose crystallograhic planes for visualization.
Usage: input = [ ind nx ny nz x0 y0 z0 ] makecut
ind = 1 or -1 allows one to easily flip the positive direction
of the plane.
Also see removefixedatoms. |
md | COMMAND | N/A |
makedipole | Create a dislocation dipole in a crystal. The dislocation line and dipole
direction must be parallel to one of the repeat vectors of the simulation box.
Usage: input = [ zind yind sbx sby sbz sx0 sy0 sy1 nu nimg_xmin nimg_xmax nimg_ymin nimg_ymax tilt_box limit_sz sz_min sz_max store ] makedipole
zind = 1, 2 or 3 specifies the direction of the dislocation line
(to be parallel to c1, c2,
or c3).
Note: atoms may need to be removed or inserted when executing this command. If atoms need to be inserted, you will need to set allocmultiple to be greater than 1 when calling makecrystal or readcn above. Also see makedislocation. Example: MD++/scripts/CSD-book/chap5/sect5.1/mo-screw-dipole.script For details, see Computer Simulations of Dislocations, Chapter 5, Section 5.1. |
md | COMMAND | N/A |
makedislcylinder | Outdated function. Use makecylinder and makedislocation instead. | md | COMMAND | N/A |
makecylinder | Cut a cylinder out of the current configuration.
Usage: input = [ zind yind sx0 sy0 rrem flag szmin szmax ] makecylinder
zind = 1, 2 or 3 specifies the direction of the cylinder axis (to be
parallel to c1, c2,
or c3).
Example: MD++/scripts/CSD-book/chap3/sect3.1/ta-screw.script For details, see Computer Simulations of Dislocations, Chapter 3, Section 3.1. |
md | COMMAND | N/A |
makedislocation | Create an arbitrarily oriented straight dislocation line.
Usage: input = [ enable a bx by bz lx ly lz nx ny nz x0 y0 z0 nu store ] makedislocation
enable = 1 activates this command. Note: vectors b, l, n are all expressed in the lab coordinate system, not the crystal coordinate system. Note: This cannot work if the simulation cell is subjected to periodic boundary condition (PBC) in all three directions. Use makedipole instead in such conditions. Also see makecylinder. Example: MD++/scripts/CSD-book/chap3/sect3.1/ta-screw.script For details, see Computer Simulations of Dislocations, Chapter 3, Section 3.1. |
md | COMMAND | N/A |
makedislpolygon | Introduce an arbitrarily shaped dislocation polygon (loop) into the crystal.
Usage: input = [ enable store nu a bx by bz n x_1 y_1 z_1 x_2 y_2 z_2 … x_n y_n z_n ] makedislellipse
enable = 1 activates this command.
Note: all cut planes go through the first node x_1 y_1 z_1. References: D. M. Barnett, The displacement field of a triangular dislocation loop, Phil. Mag. A. (1985) vol.51 383--387; D. M. Barnett and R. W. Balluffi, The displacement field of a triangular dislocation loop -- a correction with commentary, Phil. Mag. Lett. (2007) vol.87 943--944; A. Van Oosterom and J. Strackee, The Solid angle of a plane trangle, IEEE transactions on biomedical engr. (1983) vol.bme-30 125--126. For more information, ask Keonwook Kang. Also see makedislellipse. |
md | COMMAND | N/A |
makedislellipse | Introduce an elliptical shaped dislocation loop into the crystal.
Usage: input = [ enable Ra Rb a bx by bz lx ly lz nx ny nz x0 y0 z0 store ] makedislellipse
enable = 1 activates this command. Note: the displacement field used in this function is only an approximation. It is simply proportional to the solid angle of the ellipse viewed from the field point. The actual displacement field must contain a term that depends on the Poisson's ratio. Also see makedislpolygon. |
md | COMMAND | N/A |
makegrainboundary | Make a grain boundary by rotating the current crystal in two different
orientations and put the two copies of the crystal together. Can be
used to create certain types of grain boundaries. Not a general utility.
Usage: input = [ gb_type sx0 sy0 p q shift_x shift_y shift_z ] makegrainboundary
gb_type has to be non-zero. The two crystals are rotated from the parent crystal around the z-axis by angle α and -α, respectively, where arctan(α) = p/q. sx0, sy0 specify the center of the rotation. The plane sx = sx0 is also the boundary between the two crystals. So the grain boundary thus created is a pure tilt boundary. WARNING: the values of shift_x, shift_y, shift_z are currently ignored? For details, ask Hark Lee. |
md | COMMAND | N/A |
makegb | Same as makegrainboundary. | md | COMMAND | N/A |
makewave | Usage: input = [ enable A dx dy dz skx sky skz ] makewave
Assign a displacement field to the atoms in the form of a plane wave. A is the amplitude of the wave. dr = (dx,dy,dz) is a unit vector (it is automatically normalized at the beginning of this command). sk = (skx,sky,skz) is the wave vector for scaled coordinates. The displacement field in real coordinates is du[i] = A * dr * exp( sk · SR[i] * 2π ) Be ware of the use of real and scaled coordinates in this expression. Note that the velocity is not assigned, so that the configuration corresponds to a superposition of two plane waves travelling in opposite directions. Note that this only works for a simple crystal structure (with one atom basis). The displacement field of a complex lattice (with more than one atom basis) is not known a priori. |
md | COMMAND | N/A |
cutbonds | Create a slit-like atomically sharp crack by removing the interaction between two
sides of a cut-plane. All atomic pairs that reside on two sides of the cut plane
are registered in the nl_skip_pairs array, so that they will not appear
on each other's neighbor list, effectively removing their interactions.
Usage: input = [ enable zind yind sx0 sy0 sy1 sz0 sz1 ] The input parameters are similar to those of makedipole. Also see cutbonds_by_ellipse. |
md | COMMAND | N/A |
cutbonds_by_ellipse | Create an elliptic atomically sharp crack by removing the interaction between two
sides of a cut-plane. All atomic pairs that reside on two sides of the cut plane
are registered in the nl_skip_pairs array, so that they will not appear
on each other's neighbor list, effectively removing their interactions.
Usage: input = [ enable zind yind sx0 sy0 sy1 sz0 sz1 ] Also see cutbonds. |
md | COMMAND | N/A |
scaleH | Usage: input = s scaleH
Multiply the H matrix by scalar s. |
md | COMMAND | N/A |
setH | Obsolete command. Do no use. Instead, assign a value to a given
component of H by, for example,
H_23 = value |
md | COMMAND | N/A |
saveH | Copy H to H0.
Also see restoreH. |
md | COMMAND | N/A |
restoreH | Copy H0 to H.
Also see saveH. |
md | COMMAND | N/A |
reorientH | Rotate the simulation box H = [c1 |
c2 | c3 ] so that
H is an upper triangle matrix. This means that
c1 is parallel to the x-axis, and c2
is on the x-y plane.
The scaled coordinates are not changed so that the real coordinates are rotated by this operation. |
md | COMMAND | N/A |
changeH_keepR | When input = [ i j α ] is set before calling this command, then
change the supercell H while keeping the real coordinates of the atoms rk constant. The scaled coordinates sk change because rk = H ⋅ sk. The matrix H consists of three column vectors [c1 | c2 | c3 ], and will be changed by ci = ci + α cj. Same as redefinepbc. Also see changeH_keepS. |
md | COMMAND | N/A |
changeH_keepS | When input = [ i j α ] is set before calling this command, then
change the supercell H while keeping the scaled coordinates of the atoms sk constant. The real coordinates rk change because rk = H ⋅ sk. The matrix H consists of three column vectors [c1 | c2 | c3 ], and will be changed by ci = ci + α cj. Same as shiftbox. Also see changeH_keepR. |
md | COMMAND | N/A |
shiftbox | Same as changeH_keepS. | md | COMMAND | N/A |
redefinepbc | Same as changeH_keepR. | md | COMMAND | N/A |
switchindex | Usage: input = [ i_dir j_dir ] switchindex
Switch the two indices for every atom's scaled coordinates. i_dir, j_dir = 1, 2, 3 for x, y, z. Vector arrays SR, R, R0, VSR, VR and box matrix H are changed. WARNING: There seems to be a bug. The real coordinate should not change if both scaled coordinate and H matrix have changed. |
md | COMMAND | N/A |
maptoprimarycell | Map every component of the scaled coordinate of all atoms SR to the
domain of [-0.5, 0.5) by subtracting the closest integer.
Also see pbcshiftatom. |
md | COMMAND | N/A |
RHtoS | For every atom k, update its scaled coordinates from its real coordinates.
sk = inv(H) ⋅ rk. This command must be called if you have changed the real coordinates R manually, because MD++ always computes the real coordinates from the scaled coordinate inside the potential function. Also see SHtoR. |
md | COMMAND | N/A |
SHtoR | For every atom k, update its real coordinates from its scaled coordinates.
rk = H ⋅ sk. Usually we don't need to call this command, because always computes the real coordinates from the scaled coordinate inside the potential function. Also see RHtoS. |
md | COMMAND | N/A |
RtoR0 | Make a copy of the R array to R0, i.e. for all i, do
R0[i] = R[i] Also see R0toR. |
md | COMMAND | N/A |
R0toR | Copy the R0 array back to R, i.e. for all i, do
R[i] = R0[i] and then call RHtoS. Also see RtoR0. |
md | COMMAND | N/A |
clearR0 | Set vector R0[i] = (0, 0, 0) for all atoms i. This has the consequence that the neighbor list will certainly be constructed again the next time command refreshnnlist is called. | md | COMMAND | N/A |
applystrain | Usage: input = [ M11 M12 M13 M21 M22 M23 M31 M32 M33 s11 s12 s13 s21 s22 s23 s31 s32 s33 eps ] Apply a strain to box matrix H while keeping the scaled coordinates of the atoms fixed. The first nine components of the input array specify the transformation matrix M, the next nine components specify the strain matrix EPSILON in a rotated coordinate system. The row vectors of matrix M are normalized by MD++ if they were not already normalized in the input. H += M * EPSILON * MT * eps The box matrix prior to applying the strain is saved into H0. |
md | COMMAND | N/A |
extendbox | Usage: input = [ dir n ] extendbox
Extend the current configuration along the dir-th direction (1, 2, 3 for x, y, z) by replicating it n times. allocmultiple = n must be set when calling readcn or makecrystal if command extendbox will be called later. Also see cutslice. |
md | COMMAND | N/A |
scaleVel | Usage: input = vratio scaleVel
The velocity VSR of all atoms whose fixed[i] != 0 is multiplied by vratio. A more complete implementation is multiplyvelocity. |
md | COMMAND | N/A |
cutslice | Usage: input = [ dir n ] cutslice
Cut an 1/n slice of the configuration along the dir-th direction (1, 2, 3 for x, y, z). This operation is the inverse of extendbox. For this to work well, the current configuration better be created by a previous call to command extendbox. |
md | COMMAND | N/A |
splicecn | Usage: input = [ dir ] splicecn
Put the configuration stored in incnfile next to the configuration in memory (in array SR) along the direction dir (1, 2, 3 for x, y, z). The dir-th column of the H matrix is incremented by the amount specified in incnfile. Also see cutslice. |
md | COMMAND | N/A |
cutpastecn | Usage: input = [ dir s0 s1 ds ] cutpastecn
Replace all atoms whose dir-th scaled coordinates falls within [s0,s1] to those given in the incnfile, and then displace these atoms by ds in the dir-th direction. (dir = 1, 2, 3 for x, y, z.) |
md | COMMAND | N/A |
setconfig1 | Copy the current configuration SR (scaled coordinate) to SR1 for all atoms.
Also see setconfig2, constrainatoms. |
md | COMMAND | N/A |
setconfig2 | Copy the current configuration SR (scaled coordinate) to SR2 for all atoms.
Also see setconfig1, constrainatoms. |
md | COMMAND | N/A |
copytoconfig1 | Usage: input = i copytoconfig1
Copy the current configuration SR (scaled coordinate) to SR1 only for atom
i.
Also see setconfig1. |
md | COMMAND | N/A |
copytoconfig2 | Usage: input = i copytoconfig2
Copy the current configuration SR (scaled coordinate) to SR2 only for atom
i.
Also see setconfig2. |
md | COMMAND | N/A |
switchconfig | Change the scaled coordinates SR[i] of all atoms i to
SR[i] - SR1[i] + SR2[i] Also see setconfig1, setconfig2, runMDSWITCH, nebrelax. |
md | COMMAND | N/A |
replacefreeatom | Replace the scaled coordinates of atoms whose fixed[i] == 0 by those
given in the .cn file incnfile. The scaled coordinates of other atoms
as well as the H matrix are not changed. At the end of replacefreeatom
the real coordinates are updated by a call to SHtoR.
Also see readcn. |
md | COMMAND | N/A |
relabelatom | Usage: input = [ n0 n1 ] relabelatom
Switch the scaled coordinates (SR) between atom n0 and n1. Note that other properties, such as velocity, force, etc. are not switched by this command. |
md | COMMAND | N/A |
moveatom | Usage: input = [ n dx dy dz i_1 i_2 … i_n ] moveatom
Move real coordinates of all atoms whose indices are given in i_1, i_2, … i_n by dx, dy, dz (in Å). Also see movegroup. |
md | COMMAND | N/A |
movegroup | Usage: input = [ ng dx dy dz gID_1 gID_2 … gID_ng ] movegroup
Move real coordinates of all atoms belonging to groups with ID gID_1, gID_2, … gID_ng by dx, dy, dz (in Å). Also see setfixedatomsgroup, moveatom. |
md | COMMAND | N/A |
setgroupcomvel | Usage: input = [ ng vx vy vz gID_1 gID_2 … gID_ng ] setgroupcomvel
Set the center of mass velocity (times timestep) of all groups with ID gID_1, gID_2, … gID_ng to vx, vy, vz (in Å). Also see P_com. |
md | COMMAND | N/A |
printatoms_in_sphere | Usage: input = [ x0 y0 z0 r ] printatoms_in_sphere
Print the indices of all atoms whose real coordinates fall within a sphere centered at x0 y0 z0 with radius r. These atoms can then be fixed by fixatoms_by_ID. |
md | COMMAND | N/A |
pbcshiftatom | Usage: input = [ dsx dsy dsz ] pbcshiftatom
Add dsx, dsy, dsz to the scaled coordinates of all atoms and then map the scaled coordinates to the domain [-0.5, 0.5). |
md | COMMAND | N/A |
maketorquehandle | Utility function pertaining to torsional Periodic Boundary Condition (tPBC).
Also see torsionsim, torquespec. |
md | COMMAND | N/A |
addtorque | Utility function pertaining to torsional Periodic Boundary Condition (tPBC).
Also see torsionsim, torquespec. |
md | COMMAND | N/A |
copytorqueatoms | Utility function pertaining to torsional Periodic Boundary Condition (tPBC).
Also see torsionsim, torquespec. |
md | COMMAND | N/A |
makebendhandle | Utility function pertaining to bending Periodic Boundary Condition (bPBC).
Also see bendsim, bendspec. |
md | COMMAND | N/A |
addbend | Utility function pertaining to bending Periodic Boundary Condition (bPBC).
Also see bendsim, bendspec. |
md | COMMAND | N/A |
copybendatoms | Utility function pertaining to bending Periodic Boundary Condition (bPBC).
Also see bendsim, bendspec. |
md | COMMAND | N/A |
writeimagefile | Empty function. Do not use. | md | COMMAND | N/A |
readimagefile | Empty function. Do not use. | md | COMMAND | N/A |
fixatoms_by_ID | When input = [ n i1 … in ] is set before
calling this command, then
mark all atoms i = i1, … , in$ with fixed[i] = 1. |
md | COMMAND | N/A |
fixatoms_by_position | Fix all atoms whose position falls within a specified domain.
Usage: input = [ enable sx_min sx_max sy_min sy_max sz_min sz_max ]
If, however, enable = 2, then all atoms whose real coordiantes fall
within a cylindrical (tube) region will be fixed. In this case, the input array
will be interpreted differently. Also see fixatoms_by_pos_topol. |
md | COMMAND | N/A |
fixatoms_by_group | Usage: input = [ ng group_1 group_2 … group_ng ] fixatoms_by_group
If ng > 0, then all atoms i whose group[i] value matches any of the group_1 group_2 … group_ng will have fixed[i] = 1 set. Also see setfixedatomsgroup. |
md | COMMAND | N/A |
RtoR0_by_group | Usage: input = [ ng gID_1 gID_2 … gID_ng ] RtoR0_by_group
Make a copy of the R array to R0 for all atoms whose group id (group[i]) matches one of those specified by input. Also see RtoR0. |
md | COMMAND | N/A |
R0toR_by_group | Usage: input = [ ng gID_1 gID_2 … gID_ng ] R0toR_by_group
Copy R0 array back to R for all atoms whose group id (group[i]) matches one of those specified by input. Also see R0toR. |
md | COMMAND | N/A |
fixatoms_by_species | Usage: input = [ ns species_1 species_2 … species_ns ] fixatoms_by_species
If ns > 0, then all atoms i whose species[i] value matches any of the species_1 species_2 … species_ns will have fixed[i] = 1 set. Also see setfixedatomsspecies. |
md | COMMAND | N/A |
fixatoms_by_pos_topol | Fix all atoms whose position falls within a specified domain and whose TOPOL[i] value
falls within a range.
Usage: input = [ enable sx_min sx_max sy_min sy_max sz_min sz_max t_min t_max ]
Also see fixatoms_by_position. |
md | COMMAND | N/A |
fixallatoms | Mark all atoms with fixed[i] = 1, for i = 0, … NP-1. | md | COMMAND | N/A |
freeallatoms | Mark all atoms with fixed[i] = 0, for i = 0, … NP-1. | md | COMMAND | N/A |
reversefixedatoms | For all atoms i = 0, …, NP, set species[i] to 1 if it was 0,
set species[i] to 0 if it was 1.
Also see setfixedatomsspecies. |
md | COMMAND | N/A |
constrain_fixedatoms | Set constrainedatoms array to include all fixed atoms. This is usually used as
fixatoms_by_position constrain_fixedatoms freeallatoms Also see fixatoms_by_pos_topol, fixatoms_by_ID. |
md | COMMAND | N/A |
fix_constrainedatoms | Set all atoms specified in the constrainatoms array to have be fixed
(i.e. fixed[i] = 1).
This is the inverse of the command constrain_fixedatoms. This command is useful to visualize which atoms are included in the constrainatoms because fixed atoms are usually plotted in yellow. Also see fixatomcolor. |
md | COMMAND | N/A |
fix_imageatoms | All atoms i whose image[i] value is >= 0 will have fixed[i] set to 1.
Also see fixatoms_by_group. |
md | COMMAND | N/A |
setfixedatomsspecies | Usage: input = id setfixedatomsspecies
Set species[i] = id for all atoms i whose fixed[i] == 1. Also see fixatoms_by_pos_topol, fixatoms_by_ID, fixatoms_by_species. |
md | COMMAND | N/A |
setfixedatomsgroup | Usage: input = id setfixedatomsgroup
Set group[i] = id for all atoms i whose fixed[i] == 1. Also see fixatoms_by_pos_topol, fixatoms_by_ID, fixatoms_by_group. |
md | COMMAND | N/A |
reversespecies | For all atoms i = 0, …, NP, set fixed[i] to 1 if it was 0, set fixed[i] to 0 if it was 1. | md | COMMAND | N/A |
movefixedatoms | Usage: input = [ dsx dsy dsz ] movefixedatoms
Add dsx, dsy, dsz to the scaled coordinates SR[i] of all atoms i whose fixed[i] == 1. Also see fixatoms_by_pos_topol, fixatoms_by_ID, removefixedatoms. |
md | COMMAND | N/A |
removefixedatoms | Remove all atoms i whose fixed[i] == 1.
Also see markremovefixedatoms. |
md | COMMAND | N/A |
markremovefixedatoms | Mark all atoms i whose fixed[i] == 1 as removed, i.e. set fixed[i] = -1.
An atom i with fixed[i] == -1 will be ignored in potential function / force evaluations.
So they are effectively removed, but can be quickly restored without changing the indices of other
atoms.
Also see removefixedatoms. |
md | COMMAND | N/A |
removeellipsoid | Usage: input = [ enable x0 y0 z0 a b c ] removeellipsoid
If enable = 1 then this command is activated. x0 y0 z0 specify the center of the ellipsoid (in real coordinates) and a b c specify the semi-axes of the ellipsoid (in real coordinates). All atoms falling within the ellipsoid are removed. |
md | COMMAND | N/A |
removerectbox | Usage: input = [ ax ay az La bx by bz Lb cx cy cz Lc x0 y0 z0 plotonly outside ]
removerectbox
The regions to be removed are specified in the crystal coordinate system (so coordinate transformation is involved). Sorry this one is too complicated to explain. Please read the source code (md.cpp) or find an example that uses this command. This function is useful for creating a prismatic dislocation loop by removing atoms. |
md | COMMAND | N/A |
removeoverlapatoms | Usage: input = [ rc ] removeoverlapatoms
For every pair of atoms that are closer to each other than rc remove one of them, until no two atoms are closer to each other than rc. |
md | COMMAND | N/A |
find_com | Apply rigid-body rotation around the center of mass (COM) so that the current configuration
best matches that stored in SR1.
Requires input = 1 or 2 or 3 to be set before calling this command, to specify whether rotation is around x or y or z axis. Currently only rotation around z axis has been implemented. Also see setconfig1, translate_com. |
md | COMMAND | N/A |
translate_com | Compute the the center of mass (COM) of the current configuration (stored in SR). The result (although not accessible from the user) will be used in subsequent calls of functions translate_com, rotate_com. | md | COMMAND | N/A |
rotate_com | Apply rigid-body translation so that the center of mass (COM) of the current configuration
matches that stored in SR1.
Also see setconfig1, rotate_com. |
md | COMMAND | N/A |
clearFext | Reset the Fext vector array, Fext[i] = 0 for all i from 0 to NP.
Also see Fext, addFext_to_group. |
md | COMMAND | N/A |
addFext_to_group | When input = [ g_id fx fy fz ] is set before
calling this command, then atoms with group[i] == g_id will have
their Fext[i] vector set to (fx, fy, fz).
If enable_Fext is set to 1, then Fext[i] will be added to the force experienced by atom i for all atoms. |
md | COMMAND | N/A |
writecn | Requires finalcnfile = file to be set before calling
this command. Write atomic positions of the current configuration to file.
If write_all = 1 is also set, the atomic velocities and other information are written in file as well. See wiki page for more details. Also see zipfiles. |
md | COMMAND | N/A |
writeavgcn | Write array SRA into file whose name is specified by finalcnfile.
SRA contains a running average of atomic configurations during MD simulation. For details, ask Keonwook Kang. |
md | COMMAND | N/A |
readcn | When incnfile = file is set before calling this command, then
read atomic positions, velocities (optional) and other information from file to the current configuration. See wiki page for more details. |
md | COMMAND | N/A |
readcontinuecn | Read atomic configuration from the file speficied by continuecnfile.
Also see savecontinuecnfreq, readcn. |
md | COMMAND | N/A |
readPOSCAR | Read atomic position from incnfile written in POSCAR (VASP) format. | md | COMMAND | N/A |
readOUTCAR | Read atomic force from
VASP OUTCAR file.
The file name has to be OUTCAR and must be in the current directory
(specified by dirname).
Also see readPOSCAR. |
md | COMMAND | N/A |
readMDCASK | Read atomic position and EPOT_IND array
from incnfile written in MDCASK format.
Also see writeMDCASK. |
md | COMMAND | N/A |
readMDCASKJAIME | Read atomic position from incnfile written in MDCASK format. | md | COMMAND | N/A |
readXYZ | Read atomic position from incnfile written in XYZ format. | md | COMMAND | N/A |
writeMDCASKXYZ | Write atomic position (in real coordinates)
into MDCASK format with file name specified
by finalcnfile.
Also see readMDCASK. |
md | COMMAND | N/A |
readLAMMPS | Read atomic position and velocity from a file in LAMMPS format with file name specified
by incnfile.
Also see writeLAMMPS. |
md | COMMAND | N/A |
readRchain | Read a chain of configurations Rc from file incnfile.
Also see readrchainspec, initRchain, writeRchain. |
md | COMMAND | N/A |
convertXDATCAR | Convert a series of atomic configurations stored in a single file (in XDATCAR format of VASP) into a series of .cn files using writeintercn. | md | COMMAND | N/A |
openintercnfile | Open the first intermediate .cn file so that they can be written subsequently
either by calling writeintercn or during MD simulation run
if savecn = 1.
Also see intercnfile |
md | COMMAND | N/A |
openFFScnfile | Open the first intermediate cn file so that they can be written to during FFS simulations.
Similar to openintercnfile.
Also see FFScnfile. |
md | COMMAND | N/A |
writeintercn | Write the current atomic configuration in the intermediate .cn file whose
name is specified by intercnfile and filecounter. Usually
this is command is not called directly by the user. Instead, it is called periodically
in MD simulation run if savecn = 1.
Also see openintercnfile. |
md | COMMAND | N/A |
writeFFScn | Write the current configuration in FFS simulation into a file whose base name is specified by FFScnfile
and increment the counter by 1.
Similar to writeintercn.
Also see FFSfilecounter. |
md | COMMAND | N/A |
setfilecounter | Usage: filecounter = n setfilecounter
Set the counter in the file name of intercnfile to n. |
md | COMMAND | N/A |
setFFSfilecounter | Usage: FFSfilecounter = n setFFSfilecounter
Set the counter in the file name of FFScnfile to n. Also see openFFScnfile. |
md | COMMAND | N/A |
openpropfile | Open the property file whose name is specified by outpropfile and
in which thermal properties (such as EPOT, Tinst) are saved periodically during MD simulation.
Also see savepropfreq, output_fmt. |
md | COMMAND | N/A |
closepropfile | Close the property file in which thermal properties (such as EPOT, Tinst) have been
saved periodically during MD simulation, to ensure the file on disk is up to date
before exiting the program.
Also see openpropfile. |
md | COMMAND | N/A |
writePOSCAR | Write atomic position and velocity
into VASP POSCAR format
with file name specified by finalcnfile.
Also see readPOSCAR. |
md | COMMAND | N/A |
writeMDCASK | Write atomic position (in scaled coordinates)
into MDCASK format with file name specified
by finalcnfile.
Also see readMDCASK. |
md | COMMAND | N/A |
writePINYMD | Write atomic position (in real coordinates) and velocity into PINYMD format with file name specified by finalcnfile. | md | COMMAND | N/A |
writeLAMMPS | Write atomic position (in real coordinates) and velocity
into LAMMPS format with file name specified
by finalcnfile.
Also see readLAMMPS. |
md | COMMAND | N/A |
writeRchain | Save the vector array Rc[j][i] into file specified by finalcnfile.
Rc contains the real coordinates of the atoms specified by constrainatoms.
Note that the file format created by writeRchain is different from that of the .cn file. Also see readRchain, chainlength. |
md | COMMAND | N/A |
fortranrelax | Call an external program (compiled by Fortran) to relax the atomistic configuration.
Also see fortranpath, fortranexe. |
md | COMMAND | N/A |
atomeye | Call Atomeye to visualize atomic structure.
Atomeye is an external visualization tool developed by Dr. Ju Li. Requires variables atomeyepath and atomeyeexe to be set before calling this command. MD++ saves the atomic configuration into file atomeye.cfg in the current directory before calling Atomeye. |
md | COMMAND | N/A |
writeatomeyecfg | Write Atomeye .cfg file from the current atomic configuration.
Before calling this function, the filename must be specified in variable finalcnfile.
Also see zipfiles. |
md | COMMAND | N/A |
convertCNtoCFG | Usage: input = [ istart iend ] convertCNtoCFG
Read several files named inter####.cn from the current folder (specified by dirname) and write them into Atomeye cfg files inter####.cfg, where the index number goes from istart to iend. This functionality can be reproduced in Tcl by calling readcn and writeatomeyecfg in a for loop. |
md | COMMAND | N/A |
writepovray | Write atomic position into POVRAY
format with file name specified by finalcnfile.
By default all atoms are exported, but a subset of atoms can be selected by the plot_color_windows and plot_limits variables. |
md | COMMAND | N/A |
writeRASMOLXYZ | Write atomic position into RASMOL-XYZ format with file name specified
by finalcnfile. Each ine of the file contains
element[0] R[i].x R[i].y R[i].z EPOT_IND[i] TOPOL[i] |
md | COMMAND | N/A |
readRASMOLXYZ | Read atomic position from incnfile written in RASMOL-XYZ format. | md | COMMAND | N/A |
writeatomtv | Write atomic position into atomtv format with file name specified
by finalcnfile. Each ine of the file contains
R[i].x R[i].y R[i].z EPOT_IND[i] TOPOL[i] By default all atoms are exported, but a subset of atoms can be selected by the plot_color_windows and plot_limits variables. |
md | COMMAND | N/A |
writeENERGY | Write a single columned file containing the color_ind array
for all atoms. The file name is specified by finalcnfile.
The content of the color_ind array depends on the value of plot_color_axis. When plot_color_axis = 0 or 1, color_ind is the same as the potential energy contribution from each atom (EPOT_IND). When plot_color_axis = 2, color_ind is the same as the central symmetry deviation parameter (TOPOL). |
md | COMMAND | N/A |
writeFORCE | Write force F on all atoms into a text file with filename specified by finalcnfile.
Each line of the file contains i _F[i].x _F[i].y _F[i].z fixed[i]. If input = 1 is set before calling this command, then only atoms with fixed[i] == 1 have their information written into the file. In this case, each line of the file contains i _F0[i].x _F0[i].y _F0[i].z fixed[i]. |
md | COMMAND | N/A |
writePOSITION | Write the real coordinates of atoms into a file whose name is specified by finalcnfile.
Each line of the file has the format of:
i R[i].x R[i].y R[i].z fixed[i] If input = 1 is set before calling this command, only atoms whose fixed[i] value is nonzero are written. |
md | COMMAND | N/A |
GnuPlotHistogram | Call gnuplot
to plot the histogram of atom energy
i.e. EPOT_IND (by default).
If plot_color_axis = 2 then the histogram of TOPOL is plotted instead. The array TOPOL stores the computes the central symmetry deviation (CSD) parameters for each atom computed by calcentralsymmetry. |
md | COMMAND | N/A |
openwin | Open X-window to display current atom position in 3D.
Click and drag in the X-window to rotate. Press F1 for help. Usually used as openwin alloccolors rotate saverot eval plot |
md | COMMAND | N/A |
plot | Plot atoms in the X-window in an interactive run. This command can be called manually
in the input file to visualize the current configuration. It is also called periodically
within run and relax according to plotfreq.
Also see openwin, alloccolors. |
md | COMMAND | N/A |
alloccolors | Allocate colors for the X-window display.
Use after openwin and before plot. Variables atomcolor, backgroundcolor, bondcolor, color00, …, color10 may be set before calling this command. |
md | COMMAND | N/A |
alloccolorsX | Allocate colors for the X-window display. Use this only on computers where command alloccolors does not work. | md | COMMAND | N/A |
testcolor | (For debugging purposes. Not for general use.) | md | COMMAND | N/A |
reversergb | On some computers, you may find that an atom that is supposed to be red appears blue, while an
atom that is supposed to be blue appears red. These computers uses the opposite RGB convention
to indicate colors than most others. Use reversergb to fix this problem.
Also see alloccolors. |
md | COMMAND | N/A |
writeps | Export the current view in the X-window as a post script file named Yshot####.ps,
where the number automatically increases by 1 when the function is called again. Pressing
the F10 key in the X-window has the same effect.
Also see openwin, plot. |
md | COMMAND | N/A |
rotate | Rotate the viewing orientation and scale the size of the plot for the X-window as
specified in rotateangles.
Also see saverot. |
md | COMMAND | N/A |
saverot | Save the current viewing orientation and scaling parameter for the X-window as
the HOME value, which will be returned to when the HOME key is pressed in the X-window.
Also see rotate. |
md | COMMAND | N/A |
wintogglepause | When the X-window is open, toggle between the pause and continue state for the MD simulation
(run). The same effect is produced whe pressing "p" in the X-window.
Also see openwin. |
md | COMMAND | N/A |
SR | A vector array containing the scaled coordinates of atoms (dimensionless).
The real coordinates rk and scaled coordinats sk of atom k is related to each other by rk = H ⋅ sk. Also see R, H, SHtoR, RHtoS, changeH_keepS, changeH_keepR. |
md | DOUBLE | N/A |
fixed | An integer array specifying whether atom i is fixed (fixed[i] = 1)
or is free (fixed[i] = 0). The atom is considered to be removed (i.e. not
included in the calculation of potential energy and forces) if fixed[i] = -1.
Also see species, group, fixatoms_by_ID, fixatoms_by_position. |
md | INT | N/A |
R | A vector array containing the real coordinates of atoms (in Å).
The real coordinates rk and scaled coordinats sk of atom k is related to each other by rk = H ⋅ sk. Also see SR, H, SHtoR, RHtoS, changeH_keepS, changeH_keepR. |
md | DOUBLE | N/A |
R0 | A vector array to hold a copy of the R vector array (containing real coordinates of atoms) to assist configuration manipulations. | md | DOUBLE | N/A |
F | A vector array containing the forces on each atom (in eV/Å).
Also see EPOT_IND. |
md | DOUBLE | N/A |
EPOT_IND | An array containing the contributions to the potential energy EPOT
from each atom (in eV).
Also see F. |
md | DOUBLE | N/A |
species | An integer array specifying the chemical species of each atom.
Also see group. |
md | INT | 0 |
VR | A vector array containing the velocity multiplied by timestep
of atoms in real coordinates (in Å).
Also see VSR, H. |
md | DOUBLE | N/A |
VSR | A vector array containing the velocity multiplied by timestep
of atoms in scaled coordinates (dimensionless).
Also see VR, H. |
md | DOUBLE | N/A |
image | Empty variable. Do not use. | md | INT | N/A |
TOPOL | An array storing the geometric information of each atom, such as the central symmetry deviation (CSD)
parameter.
Also see plot_color_axis. |
md | DOUBLE | N/A |
group | An integer array specifying the group ID of each atom.
Also see species. |
md | INT | 0 |
F0 | A vector array to store the forces on atoms. It is an intermediate variable when the potential
is a linear combination of two existing potentials, as in adiabatic switching.
Also see runMDSWITCH, runMCSWITCH, refpotential. |
md | DOUBLE | N/A |
Fext | A vector array containing the external forces on each atom (in eV/Å). They will be added to the vector array F if enable_Fext = 1. The Fext array can be set manually, but is more convenient to use command addFext_to_group. | md | DOUBLE | 0 |
EPOT_RMV | An array. EPOT_RMV[i] is the change of the potential energy of the entire simulation cell
if atom i were removed. For a pair potential, it is twice of EPOT_IND.
Also see EPOT_IND. |
md | DOUBLE | 0 |
VIRIAL_IND | A (3x3) matrix array containing the contributions to the VIRIAL
matrix from each atom (in eV).
Also see EPOT_IND. |
md | DOUBLE | 0 |
TORQUE_IND | An array storing the contribution from each atom to the Virial Torque of the simulation
cell subjected to torsional Periodic Boundary Condition.
Also see torquespec, EPOT_IND. |
md | DOUBLE | 0 |
BENDMOMENT_IND | An array storing the contribution from each atom to the Virial Bending Moment of the simulation
cell subjected to bending Periodic Boundary Condition.
Also see bendspec, EPOT_IND. |
md | DOUBLE | 0 |
storedr | For debugging purposes.
In many configuration manipulation tools, such as makedipole, the displacement field of one dislocation is not immediately applied to the atomic positions. Instead, there is an option to accumulate the displacement fields in the vector array storedr when multipole dislocations are to be introduced. The displacement field is applied to the atomic positions after the displacement field of the last dislocation has been included in the sum. |
md | DOUBLE | N/A |
myIX | ID of this CPU in x direction. Values range from 0, …, nXdoms. | mdparallel | INT | 0 |
myIY | ID of this CPU in y direction. Values range from 0, …, nYdoms. | mdparallel | INT | 0 |
myIZ | ID of this CPU in z direction. Values range from 0, …, nZdoms. | mdparallel | INT | 0 |
nXdoms | Numer of divisions in x direction in spatial domain decomposition for parallel MD simulation
or relaxation.
Note: parallel simulation not implemented except nebrelax_parallel and stringrelax_parallel, which do not require spatial domain decomposition. Also see nYdoms, nZdoms. |
mdparallel | INT | 1 |
nYdoms | Numer of divisions in y direction in spatial domain decomposition for parallel MD simulation
or relaxation.
Note: parallel simulation not implemented except nebrelax_parallel and stringrelax_parallel, which do not require spatial domain decomposition. Also see nXdoms, nZdoms. |
mdparallel | INT | 1 |
nZdoms | Numer of divisions in z direction in spatial domain decomposition for parallel MD simulation
or relaxation.
Note: parallel simulation not implemented except nebrelax_parallel and stringrelax_parallel, which do not require spatial domain decomposition. Also see nXdoms, nYdoms. |
mdparallel | INT | 1 |
myDomain | The ID of current domain (i.e. CPU) in a parallel run.
myDomain == 0 for the master domain. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | INT | 0 |
numDomains | Total number of domains (i.e. CPUs) in a parallel run.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | INT | 1 |
myXmin | Boundary in x axis (in scaled coordinates) for spatial domain decomposition. Not fully implemented. | mdparallel | DOUBLE | -10 |
myYmin | Boundary in y axis (in scaled coordinates) for spatial domain decomposition. Not fully implemented. | mdparallel | DOUBLE | -10 |
myZmin | Boundary in z axis (in scaled coordinates) for spatial domain decomposition. Not fully implemented. | mdparallel | DOUBLE | -10 |
myXmax | Boundary in x axis (in scaled coordinates) for spatial domain decomposition. Not fully implemented. | mdparallel | DOUBLE | 10 |
myYmax | Boundary in y axis (in scaled coordinates) for spatial domain decomposition. Not fully implemented. | mdparallel | DOUBLE | 10 |
myZmax | Boundary in z axis (in scaled coordinates) for spatial domain decomposition. Not fully implemented. | mdparallel | DOUBLE | 10 |
Master_to_Slave | When command = cmd is set before calling this command, then
CPU 0 (master) request other CPUs (slaves) to execute cmd, Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. which can be any MD++ command or variable assignment. |
mdparallel | COMMAND | N/A |
Broadcast_Atoms | CPU 0 (master) broadcast all atom positions to other CPUs (slaves).
Needed before eval_parallel. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
Slave_to_Master_Atoms | Slave CPUs send its atom position SR and velocity VSR (in scaled coordinates)
to Master CPU (whose myDomain == 0).
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
Slave_chdir | Slave CPUs change the directory to that specified by dirname.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
Partition_Domains | Decide the boundary of spatial domain decomposition.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
Mark_Local_Atoms | Each CPU marks atoms i outside the domain boundary (by more than a skin distance)
as fixed[i] = -1.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
eval_parallel | CPU 0 (Master) calls eval with the help of all other CPUs (slaves).
Broadcast_Atoms must be called before calling this command. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
run_parallel | Parallel version of run (MD simulation). (Not fully tested)
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
alloc_all | Every processor (master and slave) allocate memory
for arrays such as SR, F, … according to the number
of atoms NP.
Needed before calling eval_parallel. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
quit_all | All processes (master and slavev) call quit.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
nebrelax_parallel | Running nebrelax in parallel mode. Each replica occupies one CPU.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
stringrelax_parallel | Running stringrelax in parallel mode. Each replica occupies one CPU.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
allocchain_parallel | Running allocchain in parallel mode. Each replica occupies one CPU.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc
or SYS = mpigpp.
Also see nebrelax_parallel, stringrelax_parallel. |
mdparallel | COMMAND | N/A |
initRchain_parallel | Parallel version of initRchain.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. Also see nebrelax_parallel, stringrelax_parallel. |
mdparallel | COMMAND | N/A |
readRchain_parallel | Parallel version of readRchain. If incnfile = fname,
each CPU writes the file named fname.cpu00, fname.cpu01,
…, where the integer is the value of myDomain.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
writeRchain_parallel | Parallel version of writeRchain. If finalcnfile = fname,
each CPU writes the file named fname.cpu00, fname.cpu01,
…, where the integer is the value of myDomain.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
copyRchaintoCN_parallel | Parallel version of copyCNtoRchain, with the difference that the input
variable is no longer needed. Each CPU copy the scaled coordinates of its constrained atoms
(specified by constrainedatoms) from Rc0 to SR.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
copyCNtoRchain_parallel | Parallel version of copyRchaintoCN, with the difference that the input
variable is no longer needed. Each CPU copy the scaled coordinates of its constrained atoms
(specified by constrainedatoms) from SR to Rc0.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
readcnfile_parallel | Parallel version of readcn. If incnfile = fname,
each CPU reads the file named fname.cpu00, fname.cpu01,
…, where the integer is the value of myDomain.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
writefinalcnfile_parallel | Parallel version of writecn. If finalcnfile = fname,
each CPU writes the file named fname.cpu00, fname.cpu01,
…, where the integer is the value of myDomain.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
writeatomeyecfg_parallel | Parallel version of writeatomeyecfg.
Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
mdparallel | COMMAND | N/A |
domainID | An array containing the information of which domain (i.e. CPU) does each atom belong to.
Also see myDomain. |
mdparallel | INT | N/A |
rho | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
rho0 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
rho1 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
rho2 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
rho3 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
frhop | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
gamma | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
dgamma1 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
dgamma2 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
dgamma3 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
arho2b | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
arho1 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
arho2 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
arho3 | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
arho3b | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
t_ave | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
tsq_ave | Internal array when computing the MEAM-LAMMPS potential.
For diagnostic purposes. |
meam-lammps | DOUBLE | N/A |
meamfile | Name of the file containing parameters for the MEAM-LAMMPS potential.
Also see meafile. |
meam-lammps | STRING | N/A |
meafile | Name of the file containing parameters for the MEAM-LAMMPS potential.
Also see meamfile. |
meam-lammps | STRING | N/A |
rcut | Cut off radius of the MEAM-LAMMPS potential. | meam-lammps | DOUBLE | N/A |
readMEAM | Read parameters for the MEAM-LAMMPS potential contained in the meamfile and meafile. | meam-lammps | COMMAND | N/A |
printpairpot | (For debugging purposes. Not for general use.) | meam-lammps | COMMAND | N/A |
Broadcast_MEAM_Param | CPU 0 (master) broadcast MEAM-LAMMPS potential parameters to other CPUs (slaves).
Needed before eval_parallel. Effective only when MD++ is compiled for parallel runs, e.g. with SYS = mpicc or SYS = mpigpp. |
meam-lammps | COMMAND | N/A |
setoverwrite | By default, MD++ will abort if the directory specified by dirname already exists, to avoid overwriting previous simulation data. Use this command before assigning dirname if you want to remove this protection and allow overwriting the data in the existing directory. | organizer | COMMAND | N/A |
setnolog | This command tells MD++ not to open the A.log file in the directory
specified by dirname. Instead, the output is directed to the screen.
Use this command before assigning variable dirname. |
organizer | COMMAND | N/A |
quit | Quit MD++. Print total CPU time. | organizer | COMMAND | N/A |
sleep | Put MD++ to sleep for the number of seconds specified in sleepseconds. The X-window (if opened) remain responsive to mouse and keyboard. This allows you to visually examine the final structure of your simulation before it exits. | organizer | COMMAND | N/A |
dirname | MD++ immediately opens a directory specified by this variable and enters (i.e. cd into) this directory. This becomes the working directory for all future operations and the place for all output files. Output to screen is redirected to the A.log file in this directory if setnolog is not set beforehand. | organizer | STRING | N/A |
sleepseconds | Number of seconds used by command sleep. | organizer | INT | 600 |
intval | (For debugging purposes. Not for general use.) | organizer | INT | N/A |
x | (For debugging purposes. Not for general use.) | organizer | DOUBLE | N/A |
y | (For debugging purposes. Not for general use.) | organizer | DOUBLE | N/A |
z | (For debugging purposes. Not for general use.) | organizer | DOUBLE | N/A |
str | (For debugging purposes. Not for general use.) | organizer | STRING | N/A |
printall | (For debugging purposes. Not for general use.) | organizer | COMMAND | N/A |
openfile | (For debugging purposes. Not for general use.) | organizer | COMMAND | N/A |
closefile | (For debugging purposes. Not for general use.) | organizer | COMMAND | N/A |
rebofile | Name of the file containing parameters for the REBO potential. | rebo | STRING | N/A |
rcut | Cut-off radius for the REBO potential. | rebo | DOUBLE | N/A |
readREBO | Read parameters for the REBO potential contained in the rebofile. | rebo | COMMAND | N/A |
C12_ij | Parameter in the LJ potential between species i and j.
The actual parameters to set in MD++ are: C12_00, C12_01, …
Φ(r) = C12 / r12 - C6 / r6 |
rebolj | DOUBLE | 0 |
C6_ij | Parameter in the LJ potential between species i and j.
The actual parameters to set in MD++ are: C6_00, C6_01, …
Φ(r) = C12 / r12 - C6 / r6 |
rebolj | DOUBLE | 0 |
LJ_Rcut | Cut-off radius of the LJ potential. | rebolj | DOUBLE | N/A |
NUM_REBO_GROUPS | Number of groups of atoms that are treated separately in the REBOLJ potential.
Atoms within the same group interact with the REBO potential. Atoms in different group interact with the LJ potential. The atomic configuration need to have the group array (in addition to the species array, if both Carbon and Hydrogen are present) set up accordingly for this to work properly. |
rebolj | INT | N/A |
substrate_Z | Parameter for an external potential mimicing the substrate. | rebolj | DOUBLE | N/A |
substrate_REP | Parameter for an external potential mimicing the substrate. | rebolj | DOUBLE | N/A |
substrate_ATR | Parameter for an external potential mimicing the substrate. | rebolj | DOUBLE | N/A |
initLJ | Initialize the parameters in the LJ potential. | rebolj | COMMAND | N/A |
ncpu | (For debugging purposes. Not for general use.) | scparser | INT | N/A |
shmsize | (For debugging purposes. Not for general use.) | scparser | INT | N/A |
abort | Abort the parser program, i.e. stop reading the input file. | scparser | COMMAND | N/A |
a | (For debugging purposes. Not for general use.) | scparser | DOUBLE | N/A |
I | (For debugging purposes. Not for general use.) | scparser | INT | N/A |
L | (For debugging purposes. Not for general use.) | scparser | LONG | N/A |
s | (For debugging purposes. Not for general use.) | scparser | STRING | N/A |
help | Print out a short message on the available commands and variables for this parser. | scparser | COMMAND | N/A |
printall | Print the values of all variables (a, I, L, s) defined in this test parser program. | scparser | COMMAND | N/A |
quit | Exit the entire program.
In the source code: exit(2); |
scparser | COMMAND | N/A |
ALPHA_BKS | Parameters in the SILICA-BKSMOD potential.
The potential parameters are set by the initBKS command. |
silica-bksmod | DOUBLE | N/A |
initBKS | Initialize the parameters in the the SILICA-BKSMOD potential. | silica-bksmod | COMMAND | N/A |
sw3b_multiply | Ad hoc multiplication factor to the three-body term of the original Stillinger-Weber potential.
For details, see Philosophical Magazine, 87, 2169, (2007). |
sw | DOUBLE | 1 |
sw2b_multiply | Ad hoc multiplication factor to the two-body term of the original Stillinger-Weber potential.
For details, see Philosophical Magazine, 87, 2169, (2007). |
sw | DOUBLE | 1 |
tote2 | Two-body term contribution to the potential energy.
EPOT = tote2 + tote3. |
sw | DOUBLE | 0 |
tote3 | Three-body term contribution to the potential energy.
EPOT = tote2 + tote3. |
sw | DOUBLE | 0 |
C12 | Parameter in the LJ potential.
Φ(r) = C12 / r12 - C6 / r6 |
swlj | DOUBLE | N/A |
C6 | Parameter in the LJ potential.
Φ(r) = C12 / r12 - C6 / r6 |
swlj | DOUBLE | N/A |
tipforce | This is an output array of length 3. It contains the total force felt by atoms
in group = 0 and group = 4.
When the simulation is set up such that an indentor consisting of these two groups of atoms is pressing against a substrate (consisting of other groups of atoms), then tipforce measures the total force on the indentor tip from the substrate. |
swlj | DOUBLE | N/A |
initLJ | Initialize the parameters in the LJ potential. | swlj | COMMAND | N/A |