PLUMED-NEST

Project ID: plumID:19.060
Source: 4_silicon/plumed.dat
Originally used with PLUMED version: 2.5
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. 

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../0_code/NeuralNetworkVes.cpp

The LOAD action with label  calculates somethingENVIRONMENTSIMILARITYMeasure 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=0.04
 LATTICE_CONSTANTSLattice constants=0.5431
 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 somethingq6: Q6Calculate 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=0.235 D_MAX=0.3} LOWMEMIncluding this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only VMEAN calculate the norm of the mean vector

# nn bias
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 coefficientsNN_VESThis action is not part of PLUMED and was included by using a LOAD command More details ...
LABEL=nn
ARG=refcv.morethan
NODES=48,24,12
OPTIM=ADAM
ACTIVATION=RELU
GRID_MIN=0.
GRID_MAX=216.
GRID_BIN=500
TEMP=1700.
AVE_STRIDE=500
PRINT_STRIDE=1000
TARGET_STRIDE=1
GAMMA=70
LRATE=0.001
TAU_KL=5000
DECAY=2000
ADAPTIVE_DECAY=0.5
... NN_VES


PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR


ENDPLUMEDTerminate plumed input. More details

METAD ...
 ARG=refcv.morethan
 BIASFACTOR=50
 GRID_MIN=-5
 GRID_MAX=220.0
 GRID_BIN=1000
 ADAPTIVE=DIFF
 SIGMA=250
 SIGMA_MIN=0.5
 SIGMA_MAX=20.
 TEMP=1600.
 PACE=500
 LABEL=metad
 HEIGHT=60.
 CALC_RCT
... METAD
# to avoid other structures
Q6 SPECIES=1-216 SWITCH={CUBIC D_0=0.235 D_MAX=0.3} VMEAN LABEL=q6
#diff: MATHEVAL ARG=q6.vmean,refcv.mean FUNC=(x-0.035)/(0.42-0.035)-(y-0.34)/(0.85-0.34) PERIODIC=NO
#UPPER_WALLS ARG=diff AT=0.15 KAPPA=50000 EXP=2 LABEL=uwall