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 details LENGTHthe units of lengths=A ENERGYthe units of energy=eV # CVs dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7345,7346 COORDINATIONCalculate coordination numbers. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=coord GROUPAFirst list of atoms=7345 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2-7343:3 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 D_0=2.1 NN=4 MM=8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=10 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 ... COORDINATION
# Target distribution td_wt: TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details BIASFACTORThe bias factor used for the well-tempered distribution=5 # Basisset BF_WAVELETSDaubechies Wavelets basis functions. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=bfdist ORDERThe order of the basis function expansion=10 MINIMUMThe minimum of the interval on which the basis functions are defined=2 MAXIMUMThe maximum of the interval on which the basis functions are defined=12 FUNCTION_LENGTHThe domain size of the individual basis functions=3.65 TYPESpecify the wavelet type=SYMLETS TAILS_THRESHOLDThe threshold for cutting off tail wavelets as a fraction of the maximum value=0.01 ... BF_WAVELETS
BF_WAVELETSDaubechies Wavelets basis functions. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=bfcoord ORDERThe order of the basis function expansion=10 MINIMUMThe minimum of the interval on which the basis functions are defined=5 MAXIMUMThe maximum of the interval on which the basis functions are defined=9 FUNCTION_LENGTHThe domain size of the individual basis functions=3.5 TYPESpecify the wavelet type=SYMLETS TAILS_THRESHOLDThe threshold for cutting off tail wavelets as a fraction of the maximum value=0.01 ... BF_WAVELETS
VES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=b1 ARGthe labels of the scalars on which the bias will act=dist,coord BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bfdist,bfcoord TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300.0 GRID_BINSthe number of bins used for the grid=300,300 OPTIMIZATION_THRESHOLDThreshold value to turn off optimization of localized basis functions=0.000001 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_wt ... VES_LINEAR_EXPANSION
OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=o1 BIASthe label of the VES bias to be optimized=b1 STRIDEthe frequency of updating the coefficients given in the number of MD steps=10 STEPSIZEthe step size used for the optimization=0.001 FES_OUTPUThow often the FES(s) should be written out to file=100 BIAS_OUTPUThow often the bias(es) should be written out to file=100 COEFFS_OUTPUT how often the coefficients should be written to file=10 TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=100 TARGETDIST_OUTPUThow often the dynamic target distribution(s) should be written out to file=100 MULTIPLE_WALKERS if optimization is to be performed using multiple walkers connected via MPI ... OPT_AVERAGED_SGD
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=dist ATthe positions of the wall=12 KAPPAthe force constant for the wall=12.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0. LABELa label for the action so that its output can be referenced in the input to other actions=wall ... UPPER_WALLS
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=100 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR