PLUMED-NEST

Project ID: plumID:22.001
Source: ves_md_linearexpansion/2d-wolfe_quapp/plumed_gaussians.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
UNITS
This 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: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details

td_uni: 
TD_UNIFORM
Uniform target distribution (static). More details

The TD_UNIFORM action with label td_uni calculates something
BF_GAUSSIANS
Gaussian basis functions. More details
 ...
  
ORDER
The order of the basis function expansion
=18
  
MINIMUM
The minimum of the interval on which the basis functions are defined
=-3
  
MAXIMUM
The maximum of the interval on which the basis functions are defined
=+3
  
WIDTH
The width (i
=0.25
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bf1
... BF_GAUSSIANS

The BF_GAUSSIANS action with label bf1 calculates something
BF_GAUSSIANS
Gaussian basis functions. More details
 ...
  
ORDER
The order of the basis function expansion
=18
  
MINIMUM
The minimum of the interval on which the basis functions are defined
=-3
  
MAXIMUM
The maximum of the interval on which the basis functions are defined
=+3
  
WIDTH
The width (i
=0.25
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bf2
... BF_GAUSSIANS

The BF_GAUSSIANS action with label bf2 calculates something
VES_LINEAR_EXPANSION
Linear basis set expansion bias. More details
 ...
 
ARG
the labels of the scalars on which the bias will act
=p.x,p.y
 
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1,bf2
 
LABEL
a 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.
 
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=1
 
GRID_BINS
the number of bins used for the grid
=300,300
 
OPTIMIZATION_THRESHOLD
Threshold value to turn off optimization of localized basis functions
=0.000001
 
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_uni
... VES_LINEAR_EXPANSION

OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. This action has hidden defaults. More details
 ...
  
BIAS
the label of the VES bias to be optimized
=b1
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=500
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=o1
  
STEPSIZE
the step size used for the optimization
=0.5
  
FES_OUTPUT
how often the FES(s) should be written out to file
=100
  
BIAS_OUTPUT
how 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 scalar
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details
 ...
  
BIAS
the label of the VES bias to be optimized
=b1
  
STRIDE
the frequency of updating the coefficients given in the number of MD steps
=500
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=o1
  
STEPSIZE
the step size used for the optimization
=0.5
  
FES_OUTPUT
how often the FES(s) should be written out to file
=100
  
BIAS_OUTPUT
how 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


PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
 
FILE
the name of the file on which to output these quantities
=colvar.data 
FMT
the format that should be used to output real numbers
=%8.4f