PLUMED-NEST

Project ID: plumID:20.022
Source: sodium/plumed.dat
Originally used with PLUMED version: 2.8
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. 

#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#                                                                   #
#  This input generates a multithermal-multibaric simulation that   #
#  samples a whole range of temperatures and pressures, while also  #
#  enhancing the sampling of a crystallinity order parameter        #
#                                                                   #
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#

ene: 
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
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv
  
SPECIES
this keyword is used for colvars such as coordination number
=1-250
  
SIGMA
 the width to use for the gaussian kernels
=0.065
  
LATTICE_CONSTANTS
Lattice constants
=0.423
  
CRYSTAL_STRUCTURE
 Targeted crystal structure
=BCC
  
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=12 MM=24}
  
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

mtp: 
ECV_MULTITHERMAL_MULTIBARIC
Expand a simulation to sample multiple temperatures and pressures. More details
 ...
  
ARG
the labels of the potential energy and of the volume of the system
=ene,vol
  
TEMP
 temperature
=400
  
TEMP_MIN
the minimum of the temperature range
=350
  
TEMP_MAX
the maximum of the temperature range
=450
  
PRESSURE
pressure
=0.06022140857*5000 #0.5 GPa
  
PRESSURE_MIN
the minimum of the pressure range
=0
  
PRESSURE_MAX
the maximum of the pressure range
=0.06022140857*10000
...
The ECV_MULTITHERMAL_MULTIBARIC action with label mtp calculates a scalar quantityumb: 
ECV_UMBRELLAS_LINE
Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan
  
TEMP
 temperature
=400
  
SIGMA
sigma of the umbrella Gaussians
=10
  
CV_MIN
the minimum of the CV range to be explored
=0
  
CV_MAX
the maximum of the CV range to be explored
=250
...
The ECV_UMBRELLAS_LINE action with label umb calculates a scalar quantityopes: 
OPES_EXPANDED
On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details
 
ARG
the label of the ECVs that define the expansion
=mtp.*,umb 
FILE
 a file with the estimate of the relative Delta F for each component of the target and of the global c(t)
=DeltaFs.data 
PACE
how often the bias is updated
=500 
WALKERS_MPI
 switch on MPI version of multiple walkers

The OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
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
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the input for this action is the scalar output from one or more other actions
=ene,vol,refcv.*,opes.*,q6.*,diff,uwall.bias 
FILE
the name of the file on which to output these quantities
=Colvar.data

ENDPLUMED
Terminate plumed input. More details


All walkers have been combined:
 sort -gsk1 Colvar.* > all_Colvar.data

The provided file DeltaFs.data has only few first and last lines