PLUMED-NEST

Project ID: plumID:21.047
Source: Sodium/350K-VES/plumed.dat
Originally used with PLUMED version: 2.8
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

RESTARTActivate restart. More details

The RESTART action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../PairEntropy.cpp

PAIRENTROPYCalculate the KL Entropy from the radial distribution function More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=s2The PAIRENTROPY action with label s2 calculates the following quantities:
 Quantity   
 Type   
 Description  
s2
scalar
the value calculated by this action
 ATOMSthe atoms that are being used to calculate the RDF=1-256
 MAXRthe maximum distance to use for the rdf=0.7
 SIGMA an alternative method for specifying the bandwidth instead of using the BANDWIDTH keyword=0.0125
... PAIRENTROPY

ENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy

VOLUMECalculate the volume the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box

COMBINECalculate a polynomial combination of a set of other variables. More details ...
 ARGthe values input to this function=ene,vol
 POWERS the powers to which you are raising each of the arguments in your function=1,1
 COEFFICIENTS the coefficients of the arguments in your function=1.,0.0060221409
 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=enthalpyThe COMBINE action with label enthalpy calculates the following quantities:
 Quantity   
 Type   
 Description  
enthalpy
scalar
a linear compbination
... COMBINE

COMBINECalculate a polynomial combination of a set of other variables. More details ...
 ARGthe values input to this function=enthalpy
 POWERS the powers to which you are raising each of the arguments in your function=1
 COEFFICIENTS the coefficients of the arguments in your function=0.004
 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=enthalpyPerAtomThe COMBINE action with label enthalpyPerAtom calculates the following quantities:
 Quantity   
 Type   
 Description  
enthalpyPerAtom
scalar
a linear compbination
... COMBINE

# Construct a bias potential using VES
#
# Basis functions

bf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=40 MINIMUMThe minimum of the interval on which the basis functions are defined=-108. MAXIMUMThe maximum of the interval on which the basis functions are defined=-92.
The BF_LEGENDRE action with label bf1 calculates somethingbf2: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=40 MINIMUMThe minimum of the interval on which the basis functions are defined=-6.5 MAXIMUMThe maximum of the interval on which the basis functions are defined=-1.

# Target dsitribution
The BF_LEGENDRE action with label bf2 calculates somethingtd_welltemp: TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details BIASFACTORThe bias factor used for the well-tempered distribution=50
# Expansion

The TD_WELLTEMPERED action with label td_welltemp 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=enthalpyPerAtom,s2
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1,bf2
 LABELa label for the action so that its output can be referenced in the input to other actions=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
the instantaneous value of the bias potential
b1.force2
scalar
the instantaneous value of the squared force due to this bias potential.
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=350.0
 GRID_BINSthe number of bins used for the grid=300,300
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_welltemp
... 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=enthalpyPerAtom,s2
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1,bf2
 LABELa label for the action so that its output can be referenced in the input to other actions=b1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=350.0
 GRID_BINSthe number of bins used for the grid=300,300
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_welltemp
 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=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
  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=5.
  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=1000
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=500
  #MULTIPLE_WALKERS
... 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=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
  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=5.
  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=1000
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=500
  #MULTIPLE_WALKERS
 COEFFS_FILE the name of output file for the coefficients=coeffs.data COEFFS_OUTPUT how often the coefficients should be written to file=100
... OPT_AVERAGED_SGD

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR