Project ID: plumID:19.081
Source: Al/02_FCC/plumed.start.dat
Originally used with PLUMED version: 2.6-dev
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.LOADLoads a library, possibly defining new actions. More detailsFILE=../../RefCV.cppfile to be loaded
energy:ENERGYCalculate the total potential energy of the simulation box. More details
vol:VOLUMECalculate the volume of the simulation box. More detailsREFCV... SPECIES=1-256 SIGMA=0.04 LATTICE_CONSTANTS=0.38 CRYSTAL_STRUCTURE=FCC LABEL=refcv MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24} MEAN ... REFCVThis action is not part of PLUMED and was included by using a LOAD command More details
# Construct a bias potential using VES # # Basis functions
bf1:BF_LEGENDRELegendre polynomials basis functions. More detailsORDER=8The order of the basis function expansionMINIMUM=-80000The minimum of the interval on which the basis functions are definedMAXIMUM=-51000 bf2:The maximum of the interval on which the basis functions are definedBF_LEGENDRELegendre polynomials basis functions. More detailsORDER=8The order of the basis function expansionMINIMUM=2.9The minimum of the interval on which the basis functions are definedMAXIMUM=4.3 bf3:The maximum of the interval on which the basis functions are definedBF_LEGENDRELegendre polynomials basis functions. More detailsORDER=8The order of the basis function expansionMINIMUM=0.0The minimum of the interval on which the basis functions are definedMAXIMUM=256.0The maximum of the interval on which the basis functions are defined
# Target distributionTD_MULTITHERMAL_MULTIBARIC...Multithermal-multibaric target distribution (dynamic). More detailsLABEL=td_multitpa label for the action so that its output can be referenced in the input to other actionsMIN_PRESSURE=12044.281714Minimum pressureMAX_PRESSURE=24088.563428Maximum pressureMIN_TEMP=1800.0Minimum energyMAX_TEMP=2400.0Maximum energyPRESSURE=18066.422571Target pressure of the barostat used in the MD engineSIGMA=500.0,0.05,10.0The standard deviation parameters of the Gaussian kernels used for smoothing the target distributionTHRESHOLD=20Maximum exploration free energy in kTSTEPS_TEMP=20Number of temperature stepsSTEPS_PRESSURE=20 ... TD_MULTITHERMAL_MULTIBARICNumber of pressure steps
# ExpansionVES_LINEAR_EXPANSION...Linear basis set expansion bias. More detailsARG=energy,vol,refcv.morethanthe input for this action is the scalar output from one or more other actionsBASIS_FUNCTIONS=bf1,bf2,bf3the label of the one dimensional basis functions that should be usedTEMP=2000.0the system temperature - this is needed if the MD code does not pass the temperature to PLUMEDGRID_BINS=40,40,40the number of bins used for the gridTARGET_DISTRIBUTION=td_multitpthe label of the target distribution to be usedLABEL=b1 ... VES_LINEAR_EXPANSIONa label for the action so that its output can be referenced in the input to other actions
# 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=50the step size used for the optimizationFES_OUTPUT=500how often the FES(s) should be written out to fileBIAS_OUTPUT=500how often the bias(es) should be written out to fileTARGETDIST_OUTPUT=500how often the dynamic target distribution(s) should be written out to fileCOEFFS_OUTPUT=100how often the coefficients should be written to fileTARGETDIST_STRIDE=500 #MULTIPLE_WALKERS # Commented out to pass plumed nest's test, uncomment for calculation ... OPT_AVERAGED_SGDstride for updating a target distribution that is iteratively updated during the optimizationQ6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-256this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=0.25 D_MAX=0.35}the switching function that it used in the construction of the contact matrixVMEANcalculate the norm of the mean vectorLABEL=q6 diff:a label for the action so that its output can be referenced in the input to other actionsMATHEVALAn alias to the ef CUSTOM function. More detailsARG=q6.vmean,refcv.meanthe input to this functionFUNC=(x-0.064)/(0.461-0.064)-(y-0.251)/(0.752-0.251the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=diffthe arguments on which the bias is actingAT=0.05the positions of the wallKAPPA=500000the force constant for the wallEXP=2the powers for the wallsLABEL=uwalla label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be output