PLUMED-NEST

Project ID: plumID:19.081
Source: Al/01_References/Bcc-Fcc/BainTransformation/Example/1500K-30GPa/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 somethingenergyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the value calculated by this action: 
ENERGY
Calculate the total potential energy of the simulation box. More details

volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: 
VOLUME
Calculate the volume of the simulation box. More details

cellThe CELL action with label cell calculates the following quantities:
 Quantity   
 Type   
 Description  
cell.ax
scalar
the ax component of the cell matrix
cell.ay
scalar
the ay component of the cell matrix
cell.az
scalar
the az component of the cell matrix
cell.bx
scalar
the bx component of the cell matrix
cell.by
scalar
the by component of the cell matrix
cell.bz
scalar
the bz component of the cell matrix
cell.cx
scalar
the cx component of the cell matrix
cell.cy
scalar
the cy component of the cell matrix
cell.cz
scalar
the cz component of the cell matrix: 
CELL
Calculate the components of the simulation cell More details

lambda1The MATHEVAL action with label lambda1 calculates the following quantities:
 Quantity   
 Type   
 Description  
lambda1
scalar
an arbitrary function: 
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
=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
lambda2The MATHEVAL action with label lambda2 calculates the following quantities:
 Quantity   
 Type   
 Description  
lambda2
scalar
an arbitrary function: 
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
=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

diffThe MATHEVAL action with label diff calculates the following quantities:
 Quantity   
 Type   
 Description  
diff
scalar
an arbitrary function: 
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
=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
The BF_LEGENDRE action with label bf1 calculates somethingtd_welltemp: 
TD_WELLTEMPERED
Well-tempered target distribution (dynamic). More details
 
BIASFACTOR
The bias factor used for the well-tempered distribution
=15

# Expansion

The TD_WELLTEMPERED action with label td_welltemp 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
=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
=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
the instantaneous value of the bias potential
b1.force2
scalar
the instantaneous value of the squared force due to this bias potential.
... VES_LINEAR_EXPANSION

# Optimization algorithm

OPT_DUMMY
Dummy optimizer for debugging. This action has hidden defaults. 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
OPT_DUMMY
Dummy optimizer for debugging. This action uses the defaults shown here. 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
 
COEFFS_FILE
 the name of output file for the coefficients
=coeffs.data
... OPT_DUMMY

wall1The UPPER_WALLS action with label wall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
wall1.bias
scalar
the instantaneous value of the bias potential
wall1.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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 
wall2The LOWER_WALLS action with label wall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
wall2.bias
scalar
the instantaneous value of the bias potential
wall2.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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 
wall3The UPPER_WALLS action with label wall3 calculates the following quantities:
 Quantity   
 Type   
 Description  
wall3.bias
scalar
the instantaneous value of the bias potential
wall3.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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