PLUMED-NEST

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

Click on the labels of the actions for more information on what each action computes

#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
The UNITS action with label  calculates somethingdist:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7345,7346

The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atomsCOORDINATIONCalculate 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
The COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.value
the value of the coordinationtd_wt: TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details BIASFACTORThe bias factor used for the well-tempered distribution=5


# Basisset
The TD_WELLTEMPERED action with label td_wt calculates somethingBF_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

The BF_WAVELETS action with label bfdist calculates somethingBF_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


The BF_WAVELETS action with label bfcoord calculates somethingVES_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

The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.force2
the instantaneous value of the squared force due to this bias potentialOPT_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

The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarUPPER_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

The UPPER_WALLS action with label wall calculates the following quantities:
 Quantity   
 Description  
wall.bias
the instantaneous value of the bias potential
wall.force2
the instantaneous value of the squared force due to this bias potentialFLUSHThis 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