Project ID: plumID:19.081
Source: Na/02_References/Example/plumed.start.dat
Originally used with PLUMED version: 2.6-dev
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
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.

LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../../../RefCV.cpp
energy:
ENERGY
Calculate the total potential energy of the simulation box. More details

vol:
VOLUME
Calculate the volume of the simulation box. More details

REFCV
This action is not part of PLUMED and was included by using a LOAD command More details
... SPECIES=1-250 SIGMA=0.065 LATTICE_CONSTANTS=0.432 CRYSTAL_STRUCTURE=BCC LABEL=refcv MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24} MEAN ... REFCV
# 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
=10
MINIMUM
The minimum of the interval on which the basis functions are defined
=0.0
MAXIMUM
The maximum of the interval on which the basis functions are defined
=250.0
# Target distribution
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
=refcv.morethan
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1
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
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_welltemp
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b1 ... 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
=1
FES_OUTPUT
how often the FES(s) should be written out to file
=500
BIAS_OUTPUT
how often the bias(es) should be written out to file
=500
TARGETDIST_OUTPUT
how often the dynamic target distribution(s) should be written out to file
=500
COEFFS_OUTPUT
how often the coefficients should be written to file
=100
TARGETDIST_STRIDE
stride for updating a target distribution that is iteratively updated during the optimization
=500 ... OPT_AVERAGED_SGD
Q6
Calculate sixth order Steinhardt parameters. More details
SPECIES
this keyword is used for colvars such as coordination number
=1-250
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=0.4 D_MAX=0.5}
VMEAN
calculate the norm of the mean vector
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6 diff:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=q6.vmean,refcv.mean
FUNC
the function you wish to evaluate
=(x-0.06540)/(0.4035-0.06540)-(y-0.33023)/(0.745086-0.33023
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=diff
AT
the positions of the wall
=0.1
KAPPA
the force constant for the wall
=100000
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
PRINT
Print quantities to a file. More details
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
STRIDE
the frequency with which the quantities of interest should be output
=500