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
tested onv2.9
tested onmaster
tested on master
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.

LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../0_code/NeuralNetworkVes.cpp
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
=0.04
LATTICE_CONSTANTS
Lattice constants
=0.5431
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

q6:
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=0.235 D_MAX=0.3}
LOWMEM
this flag does nothing and is present only to ensure back-compatibility
VMEAN
calculate the norm of the mean vector

# nn bias
NN_VES
This 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
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
FILE
the name of the file on which to output these quantities
=COLVAR
ENDPLUMED
Terminate 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