Project ID: plumID:21.047
Source: Sodium/350K-VES/plumed.start.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
LOADLoads a library, possibly defining new actions. More detailsFILE=../../PairEntropy.cppfile to be loadedPAIRENTROPY...Calculate the KL Entropy from the radial distribution function More detailsLABEL=s2 ATOMS=1-256a label for the action so that its output can be referenced in the input to other actionsMAXR=0.7 SIGMA=0.0125 ... PAIRENTROPYthe maximum distance to use for the rdfENERGYCalculate the total potential energy of the simulation box. More detailsLABEL=enea label for the action so that its output can be referenced in the input to other actionsVOLUMECalculate the volume of the simulation box. More detailsLABEL=vola label for the action so that its output can be referenced in the input to other actionsCOMBINE...Calculate a polynomial combination of a set of other variables. More detailsARG=ene,volthe input to this functionPOWERS=1,1the powers to which you are raising each of the arguments in your functionCOEFFICIENTS=1.,0.0060221409the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=enthalpy ... COMBINEa label for the action so that its output can be referenced in the input to other actionsCOMBINE...Calculate a polynomial combination of a set of other variables. More detailsARG=enthalpythe input to this functionPOWERS=1the powers to which you are raising each of the arguments in your functionCOEFFICIENTS=0.004the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=enthalpyPerAtom ... COMBINEa label for the action so that its output can be referenced in the input to other actions
# Construct a bias potential using VES # # Basis functions
bf1:BF_LEGENDRELegendre polynomials basis functions. More detailsORDER=40The order of the basis function expansionMINIMUM=-108The minimum of the interval on which the basis functions are definedMAXIMUM=-92 bf2:The maximum of the interval on which the basis functions are definedBF_LEGENDRELegendre polynomials basis functions. More detailsORDER=40The order of the basis function expansionMINIMUM=-6.5The minimum of the interval on which the basis functions are definedMAXIMUM=-1The maximum of the interval on which the basis functions are defined
# Target dsitribution td_welltemp:TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More detailsBIASFACTOR=50 # ExpansionThe bias factor used for the well-tempered distributionVES_LINEAR_EXPANSION...Linear basis set expansion bias. More detailsARG=enthalpyPerAtom,s2the input for this action is the scalar output from one or more other actionsBASIS_FUNCTIONS=bf1,bf2the label of the one dimensional basis functions that should be usedLABEL=b1a label for the action so that its output can be referenced in the input to other actionsTEMP=350.0the system temperature - this is needed if the MD code does not pass the temperature to PLUMEDGRID_BINS=300,300the number of bins used for the gridTARGET_DISTRIBUTION=td_welltemp ... VES_LINEAR_EXPANSIONthe label of the target distribution to be used
# Optimization algorithmOPT_AVERAGED_SGD...Averaged stochastic gradient decent with fixed step size. More detailsBIAS=b1the label of the VES bias to be optimizedSTRIDE=500the frequency of updating the coefficients given in the number of MD stepsLABEL=o1a label for the action so that its output can be referenced in the input to other actionsSTEPSIZE=5the step size used for the optimizationFES_OUTPUT=1000how often the FES(s) should be written out to fileBIAS_OUTPUT=1000how often the bias(es) should be written out to fileTARGETDIST_STRIDE=500 #MULTIPLE_WALKERS ... OPT_AVERAGED_SGDstride for updating a target distribution that is iteratively updated during the optimizationPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities