Project ID: plumID:21.047
Source: Sodium/350K-VES/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
tested onv2.9
tested onmaster
tested on master
RESTART
Activate restart. More details

LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../../PairEntropy.cpp
PAIRENTROPY
Calculate the KL Entropy from the radial distribution function More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=s2 ATOMS=1-256
MAXR
the maximum distance to use for the rdf
=0.7 SIGMA=0.0125 ... PAIRENTROPY
ENERGY
Calculate the total potential energy of the simulation box. More details
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ene
VOLUME
Calculate the volume of the simulation box. More details
LABEL
a label for the action so that its output can be referenced in the input to other actions
=vol
COMBINE
Calculate a polynomial combination of a set of other variables. More details
...
ARG
the input to this function
=ene,vol
POWERS
the powers to which you are raising each of the arguments in your function
=1,1
COEFFICIENTS
the coefficients of the arguments in your function
=1.,0.0060221409
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=enthalpy ... COMBINE
COMBINE
Calculate a polynomial combination of a set of other variables. More details
...
ARG
the input to this function
=enthalpy
POWERS
the powers to which you are raising each of the arguments in your function
=1
COEFFICIENTS
the coefficients of the arguments in your function
=0.004
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=enthalpyPerAtom ... COMBINE
# Construct a bias potential using VES # # Basis functions
bf1:
BF_LEGENDRE
Legendre polynomials basis functions. More details
ORDER
The order of the basis function expansion
=40
MINIMUM
The minimum of the interval on which the basis functions are defined
=-108
MAXIMUM
The maximum of the interval on which the basis functions are defined
=-92 bf2:
BF_LEGENDRE
Legendre polynomials basis functions. More details
ORDER
The order of the basis function expansion
=40
MINIMUM
The minimum of the interval on which the basis functions are defined
=-6.5
MAXIMUM
The maximum of the interval on which the basis functions are defined
=-1
# Target dsitribution td_welltemp:
TD_WELLTEMPERED
Well-tempered target distribution (dynamic). More details
BIASFACTOR
The bias factor used for the well-tempered distribution
=50 # Expansion
VES_LINEAR_EXPANSION
Linear basis set expansion bias. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=enthalpyPerAtom,s2
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
=b1
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=350.0
GRID_BINS
the number of bins used for the grid
=300,300
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_welltemp ... VES_LINEAR_EXPANSION
# Optimization algorithm
OPT_AVERAGED_SGD
Averaged stochastic gradient decent with fixed step size. 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
=5
FES_OUTPUT
how often the FES(s) should be written out to file
=1000
BIAS_OUTPUT
how often the bias(es) should be written out to file
=1000
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=500 #MULTIPLE_WALKERS ... OPT_AVERAGED_SGD
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
ARG
the input for this action is the scalar output from one or more other actions
FILE
the name of the file on which to output these quantities
=COLVAR