PLUMED-NEST

Project ID: plumID:19.080
Source: ohco2/symm-param/plumed.inp
Originally used with PLUMED version: 2.4.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=d1The COORDINATION action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=d1  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=d2The COORDINATION action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=d2  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0

COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=nmThe COMBINE action with label nm calculates the following quantities:
 Quantity   
 Type   
 Description  
nm
scalar
a linear compbination

bf1: BF_CHEBYSHEVChebyshev polynomial basis functions. More details MINIMUMThe minimum of the interval on which the basis functions are defined=0.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=1.0 ORDERThe order of the basis function expansion=48

The BF_CHEBYSHEV action with label bf1 calculates somethingtd: TD_GRIDTarget distribution from an external grid file (static). More details FILEThe name of the external grid file to be used as a target distribution=histo

# Expansion

The TD_GRID action with label td calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. This action has hidden defaults. More details ...
 ARGthe labels of the scalars on which the bias will act=nm
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300
 GRID_BINSthe number of bins used for the grid=500
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
 LABELa label for the action so that its output can be referenced in the input to other actions=externalThe VES_LINEAR_EXPANSION action with label external calculates the following quantities:
 Quantity   
 Type   
 Description  
external.bias
scalar
the instantaneous value of the bias potential
external.force2
scalar
the instantaneous value of the squared force due to this bias potential.
... VES_LINEAR_EXPANSION
VES_LINEAR_EXPANSIONLinear basis set expansion bias. This action uses the defaults shown here. More details ...
 ARGthe labels of the scalars on which the bias will act=nm
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300
 GRID_BINSthe number of bins used for the grid=500
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
 LABELa label for the action so that its output can be referenced in the input to other actions=external
 GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION

# Optimization algorithm

OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action has hidden defaults. More details ...
  BIASthe label of the VES bias to be optimized=external
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=2000
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=0.25
  FES_OUTPUThow often the FES(s) should be written out to file=1000
  BIAS_OUTPUThow often the bias(es) should be written out to file=10
  FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=20
  COEFFS_OUTPUT how often the coefficients should be written to file=1
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details ...
  BIASthe label of the VES bias to be optimized=external
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=2000
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=0.25
  FES_OUTPUThow often the FES(s) should be written out to file=1000
  BIAS_OUTPUThow often the bias(es) should be written out to file=10
  FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=20
  COEFFS_OUTPUT how often the coefficients should be written to file=1
 COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD

FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=200
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nm,external.bias STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar