PLUMED-NEST

Project ID: plumID:19.081
Source: Al/01_References/Bcc-Fcc/BainTransformation/Example/1500K-30GPa/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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for 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 quantitycell: 
CELL
Calculate the components of the simulation cell More details

The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrixlambda1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cell.cz 
FUNC
the function you wish to evaluate
=(x/4-0.378810046139)/(0.296244982844-0.378810046139 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
lambda2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cell.ax 
FUNC
the function you wish to evaluate
=(x/4-0.378810046139)/(sqrt(2)*0.296244982844-0.378810046139 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

diff: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=lambda1,lambda2 
FUNC
the function you wish to evaluate
=(x-y)*(x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# 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
=20 
MINIMUM
The minimum of the interval on which the basis functions are defined
=-0.5 
MAXIMUM
The maximum of the interval on which the basis functions are defined
=1.5

# Target distribution
td_welltemp: 
TD_WELLTEMPERED
Well-tempered target distribution (dynamic). More details
 
BIASFACTOR
The bias factor used for the well-tempered distribution
=15

# 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
=lambda1
 
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
=1500.0
 
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

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_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
=10
  
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
  #MULTIPLE_WALKERS # Commented out to pass plumed nest's test, uncomment for calculation
... OPT_AVERAGED_SGD

The OPT_AVERAGED_SGD action with label o1 calculates a scalar quantitywall1: 
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
=lambda1 
AT
the positions of the wall
=1 
EXP
 the powers for the walls
=2 
KAPPA
the force constant for the wall
=10000 
wall2: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=lambda1 
AT
the positions of the wall
=0 
EXP
 the powers for the walls
=2 
KAPPA
the force constant for the wall
=10000 
wall3: 
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 
EXP
 the powers for the walls
=2 
KAPPA
the force constant for the wall
=10000 

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