PLUMED-NEST

Project ID: plumID:22.001
Source: ves_md_linearexpansion/1d-double_well/plumed_sym8.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
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label  calculates somethingpThe POSITION action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the atom position
p.y
scalar
the y-component of the atom position
p.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

td_uni: TD_UNIFORMUniform target distribution (static). More details

# Basisset
The TD_UNIFORM action with label td_uni calculates somethingBF_WAVELETSDaubechies Wavelets basis functions. More details ...
  ORDERThe order of the basis function expansion=8
  MINIMUMThe minimum of the interval on which the basis functions are defined=-3.0
  MAXIMUMThe maximum of the interval on which the basis functions are defined=+3.0
  TYPESpecify the wavelet type=SYMLETS
  FUNCTION_LENGTHThe domain size of the individual basis functions=6
  TAILS_THRESHOLDThe threshold for cutting off tail wavelets as a fraction of the maximum value=0.01
  LABELa label for the action so that its output can be referenced in the input to other actions=bf1
... BF_WAVELETS

The BF_WAVELETS action with label bf1 calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. This action has hidden defaults. More details ...
 ARGthe labels of the scalars on which the bias will act=p.x
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 LABELa label for the action so that its output can be referenced in the input to other actions=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
the instantaneous value of the bias potential
b1.force2
scalar
the instantaneous value of the squared force due to this bias potential.
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=0.5
 GRID_BINSthe number of bins used for the grid=300
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_uni
 OPTIMIZATION_THRESHOLDThreshold value to turn off optimization of localized basis functions=0.000001
... VES_LINEAR_EXPANSION
VES_LINEAR_EXPANSIONLinear basis set expansion bias. This action uses the defaults shown here. More details ...
 ARGthe labels of the scalars on which the bias will act=p.x
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 LABELa label for the action so that its output can be referenced in the input to other actions=b1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=0.5
 GRID_BINSthe number of bins used for the grid=300
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_uni
 OPTIMIZATION_THRESHOLDThreshold value to turn off optimization of localized basis functions=0.000001
 GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION

OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action has hidden defaults. More details ...
  BIASthe label of the VES bias to be optimized=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=0.5
  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=500
  COEFFS_OUTPUT how often the coefficients should be written to file=10
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details ...
  BIASthe label of the VES bias to be optimized=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=0.5
  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=500
  COEFFS_OUTPUT how often the coefficients should be written to file=10
 COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=colvar.data STRIDE the frequency with which the quantities of interest should be output=100