PLUMED-NEST

Project ID: plumID:21.039
Source: data/silicon/1_opes_dlda/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

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#  >> Silicon <<
#  OPES simulation biasing Deep-LDA
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# Load structure factor code
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../StructureFactor_descriptor.test.cpp

The LOAD action with label  calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

# Define CVs
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
 SPECIESthis keyword is used for colvars such as coordination number=1-216
 SIGMA the width to use for the gaussian kernels=0.4
 LATTICE_CONSTANTSLattice constants=5.431
 CRYSTAL_STRUCTURE Targeted crystal structure=DIAMOND
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=12 MM=24}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Description  
refcv.value
the environmental similar parameter for each of the input atoms
refcv.morethan
the number of colvars that have a value more than a threshold
refcv.mean
the mean of the colvarsene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingvol: VOLUMECalculate the volume the simulation box. More details
The VOLUME action with label vol calculates the volume of simulation boxepv: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=ene,vol

The COMBINE action with label epv calculates the following quantities:
 Quantity   
 Description  
epv.value
a linear compbinationQ6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-216 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 LABELa label for the action so that its output can be referenced in the input to other actions=q6

# Define descriptors
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6._vmean
the norm of the mean vector
q6.value
the norms of the vectors of spherical harmonic coefficientscv: STRUCTURE_FACTOR_DESCRIPTOR_TESTThis 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-LDA CV
deep: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=model_lda.pt ARGthe labels of the values from which the function is calculated=cv.*

# Define Bias
The PYTORCH_MODEL action with label deep calculates the following quantities:
 Quantity   
 Description  
deep.node
Model outputsopes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ARGthe labels of the scalars on which the bias will act=deep.node-0 BARRIERthe free energy barrier to be overcome=1100 PACEthe frequency for kernel deposition=500 TEMP temperature=1700 FILE a file in which the list of all deposited kernels is stored=KERNELS_LDA

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 biasPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=refcv.*,deep.*,q6.*,ene,vol,opes.*

ENDPLUMEDTerminate plumed input. More details