PLUMED-NEST

Project ID: plumID:21.039
Source: data/silicon/3_opes_dlda_dtica/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. 

####################################
#  >> Silicon <<
#  OPES Deep-LDA (static) + Deep-TICA
####################################

# Load structure factor code
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../StructureFactor_descriptor.test.cpp

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

# Define CVs
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-216
 
SIGMA
 the width to use for the gaussian kernels
=0.4
 
LATTICE_CONSTANTS
Lattice constants
=5.431
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=DIAMOND
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv
 
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

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 quantityepv: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
COEFFICIENTS
 the coefficients of the arguments in your function
=1,0.06022140857 
ARG
the input to this function
=ene,vol

Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-216 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=2.35 D_MAX=3} 
VMEAN
 calculate the norm of the mean vector
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6

# Define Descriptors
cv: 
STRUCTURE_FACTOR_DESCRIPTOR_TEST
This action is not part of PLUMED and was included by using a LOAD command More details
 STRUCTURE=DIAMOND UNIT_CELLS=3 ACTIVE_SHELLS=27,72,99,144,171,216,243,288,315

# Deep-TICA and Deep-LDA CVs
deep: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=../2_training_cvs/model_1.pt 
ARG
the input for this action is the scalar output from one or more other actions
=cv
The PYTORCH_MODEL action with label deep calculates the following quantities:
 Quantity   
 Description  
deep.node
Model outputslda: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=model_lda.pt 
ARG
the input for this action is the scalar output from one or more other actions
=cv

# Define Bias
# uncomment to enable the static bias (requires to first perform a OPES simulation)
#static: OPES_METAD ARG=lda.node-0 BARRIER=1100 PACE=100000000 TEMP=1700 RESTART=YES FILE=../1_opes_dlda/KERNELS_LDA
The PYTORCH_MODEL action with label lda calculates the following quantities:
 Quantity   
 Description  
lda.node
Model outputsopes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=deep.node-0 
BARRIER
the free energy barrier to be overcome
=700 
PACE
the frequency for kernel deposition
=500 
TEMP
 temperature
=1700

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
 
ENDPLUMED
Terminate plumed input. More details