**Project ID:** plumID:22.001

**Source:** lammps/CaCO3/sym10/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

#SETTINGS NREPLICAS=2# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsENERGY=eVthe units of energy

# CVsdist:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7345,7346the pair of atom that we are calculating the distance betweenCOORDINATION...Calculate coordination numbers. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionscoordGROUPA=7345First list of atomsGROUPB=2-7343:3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL R_0=1.0 D_0=2.1 NN=4 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=10The cutoff for the neighbor listNL_STRIDE=10 ... COORDINATIONThe frequency with which we are updating the atoms in the neighbor list

# Target distributiontd_wt:TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More detailsBIASFACTOR=5The bias factor used for the well-tempered distribution

# BasissetBF_WAVELETS...Daubechies Wavelets basis functions. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsbfdistORDER=10The order of the basis function expansionMINIMUM=2The minimum of the interval on which the basis functions are definedMAXIMUM=12The maximum of the interval on which the basis functions are definedFUNCTION_LENGTH=3.65The domain size of the individual basis functionsTYPE=SYMLETSSpecify the wavelet typeTAILS_THRESHOLD=0.01 ... BF_WAVELETSThe threshold for cutting off tail wavelets as a fraction of the maximum valueBF_WAVELETS...Daubechies Wavelets basis functions. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsbfcoordORDER=10The order of the basis function expansionMINIMUM=5The minimum of the interval on which the basis functions are definedMAXIMUM=9The maximum of the interval on which the basis functions are definedFUNCTION_LENGTH=3.5The domain size of the individual basis functionsTYPE=SYMLETSSpecify the wavelet typeTAILS_THRESHOLD=0.01 ... BF_WAVELETSThe threshold for cutting off tail wavelets as a fraction of the maximum valueVES_LINEAR_EXPANSION...Linear basis set expansion bias. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsb1ARG=the input for this action is the scalar output from one or more other actionsdist,coordBASIS_FUNCTIONS=the label of the one dimensional basis functions that should be usedbfdist,bfcoordTEMP=300.0the 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 gridOPTIMIZATION_THRESHOLD=0.000001Threshold value to turn off optimization of localized basis functionsTARGET_DISTRIBUTION=the label of the target distribution to be usedtd_wt... VES_LINEAR_EXPANSIONOPT_AVERAGED_SGD...Averaged stochastic gradient decent with fixed step size. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionso1BIAS=the label of the VES bias to be optimizedb1STRIDE=10the frequency of updating the coefficients given in the number of MD stepsSTEPSIZE=0.001the step size used for the optimizationFES_OUTPUT=100how often the FES(s) should be written out to fileBIAS_OUTPUT=100how often the bias(es) should be written out to fileCOEFFS_OUTPUT=10how often the coefficients should be written to fileTARGETDIST_STRIDE=100stride for updating a target distribution that is iteratively updated during the optimizationTARGETDIST_OUTPUT=100how often the dynamic target distribution(s) should be written out to fileMULTIPLE_WALKERS... OPT_AVERAGED_SGDif optimization is to be performed using multiple walkers connected via MPIUPPER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingdistAT=12the positions of the wallKAPPA=12.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0the offset for the start of the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswall... UPPER_WALLSFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=100the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities