PLUMED-NEST

Project ID: plumID:19.081
Source: Al/03_BCC/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. 

RESTART
Activate restart. More details

The RESTART action with label  calculates something
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

The ENERGY action with label energy calculates somethingvol: 
VOLUME
Calculate the volume of the simulation box. More details

The VOLUME action with label vol calculates the volume of simulation box
REFCV
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 SPECIES=1-250
 SIGMA=0.045
 LATTICE_CONSTANTS=0.3
 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
=8 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-76000 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=-50000
The BF_LEGENDRE action with label bf1 calculates somethingbf2: 
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
=2.8 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=4.2
The BF_LEGENDRE action with label bf2 calculates somethingbf3: 
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
=250.0

# Target distribution

The BF_LEGENDRE action with label bf3 calculates something
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

The TD_MULTITHERMAL_MULTIBARIC action with label td_multitp calculates something
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 the following quantities:
 Quantity   
 Description  
o1.value
a scalar
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=0.25 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
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6._vmean
the norm of the mean vectordiff: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=q6.vmean,refcv.mean 
FUNC
the function you wish to evaluate
=(x-0.0652)/(0.4167-0.0652)-(y-0.3232)/(0.7579-0.3232 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label diff calculates the following quantities:
 Quantity   
 Description  
diff.value
an arbitrary function
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

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potential
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