PLUMED-NEST

Project ID: plumID:19.081
Source: Al/02_FCC/plumed.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

# 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

RESTART
Activate restart. More details

energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details

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

The VOLUME action with label vol calculates a scalar quantity
REFCV
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 SPECIES=1-256
 SIGMA=0.04
 LATTICE_CONSTANTS=0.38
 CRYSTAL_STRUCTURE=FCC
 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
=8 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-80000 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=-51000
bf2: 
BF_LEGENDRE
Legendre polynomials basis functions. More details
 
ORDER
The order of the basis function expansion
=8 
MINIMUM
The minimum of the interval on which the basis functions are defined
=2.9 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=4.3
bf3: 
BF_LEGENDRE
Legendre polynomials basis functions. More details
 
ORDER
The order of the basis function expansion
=8 
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
=256.0

# Target distribution

TD_MULTITHERMAL_MULTIBARIC
Multithermal-multibaric target distribution (dynamic). More details
 ... 
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=td_multitp
 
MIN_PRESSURE
Minimum pressure
=12044.281714
 
MAX_PRESSURE
Maximum pressure
=24088.563428
 
MIN_TEMP
Minimum energy
=1800.0
 
MAX_TEMP
Maximum energy
=2400.0
 
PRESSURE
Target pressure of the barostat used in the MD engine
=18066.422571
 
SIGMA
The standard deviation parameters of the Gaussian kernels used for smoothing the target distribution
=500.0,0.05,10.0
 
THRESHOLD
 Maximum exploration free energy in kT
=20
 
STEPS_TEMP
 Number of temperature steps
=20
 
STEPS_PRESSURE
 Number of pressure steps
=20
... TD_MULTITHERMAL_MULTIBARIC

# 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
=energy,vol,refcv.morethan
 
BASIS_FUNCTIONS
the label of the one dimensional basis functions that should be used
=bf1,bf2,bf3
 
TEMP
the system temperature - this is needed if the MD code does not pass the temperature to PLUMED
=2000.0
 
GRID_BINS
the number of bins used for the grid
=40,40,40
 
TARGET_DISTRIBUTION
the label of the target distribution to be used
=td_multitp
 
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

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 potential
OPT_DUMMY
Dummy optimizer for debugging. 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
  
COEFFS_OUTPUT
 how often the coefficients should be written to file
=10
... OPT_DUMMY

The OPT_DUMMY action with label o1 calculates a scalar quantity
Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-256 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=0.25 D_MAX=0.35} 
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-0.064)/(0.461-0.064)-(y-0.251)/(0.752-0.251 
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
=0.05 
KAPPA
the force constant for the wall
=500000 
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