PLUMED-NEST

Project ID: plumID:21.005
Source: NaCl/plumed.dat
Originally used with PLUMED version: 2.7-mod
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. 
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../codes/StructureFactor_descriptor.test.cpp
#RESTART

GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-108 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=na
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=109-216 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cl
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-216 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=nacl


s1: 
STRUCTURE_FACTOR_DESCRIPTOR_TEST
This action is not part of PLUMED and was included by using a LOAD command More details
 ACTIVE_SHELLS=27,36,72,99 ATOMS=na
s2: 
STRUCTURE_FACTOR_DESCRIPTOR_TEST
This action is not part of PLUMED and was included by using a LOAD command More details
 ACTIVE_SHELLS=27,36,72,99 ATOMS=cl

auto1: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 MODEL=nacl_sfNa_ct1.pt 
ARG
the input for this action is the scalar output from one or more other actions
=s1.Sk3_-3_-3,s1.Sk3_-3_3,s1.Sk3_3_-3,s1.Sk3_3_3,s1.Sk6_0_0,s1.Sk0_6_-6,s1.Sk0_6_6,s1.Sk6_-6_0,s1.Sk6_0_-6,s1.Sk6_0_6,s1.Sk6_6_0,s1.Sk9_-3_-3,s1.Sk9_-3_3,s1.Sk9_3_-3,s1.Sk9_3_3
The PYTORCH_MODEL action with label auto1 calculates the following quantities:
 Quantity   
 Description  
auto1.node
Model outputsNNcube1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=auto1.node-0 
FUNC
the function you wish to evaluate
=x+x^3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

auto2: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 MODEL=nacl_sfCl_ct1.pt 
ARG
the input for this action is the scalar output from one or more other actions
=s2.Sk3_-3_-3,s2.Sk3_-3_3,s2.Sk3_3_-3,s2.Sk3_3_3,s2.Sk6_0_0,s2.Sk0_6_-6,s2.Sk0_6_6,s2.Sk6_-6_0,s2.Sk6_0_-6,s2.Sk6_0_6,s2.Sk6_6_0,s1.Sk9_-3_-3,s2.Sk9_-3_3,s2.Sk9_3_-3,s2.Sk9_3_3
The PYTORCH_MODEL action with label auto2 calculates the following quantities:
 Quantity   
 Description  
auto2.node
Model outputsNNcube2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=auto2.node-0 
FUNC
the function you wish to evaluate
=x+x^3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

s12: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=NNcube1,NNcube2 
FUNC
the function you wish to evaluate
=0.5*(x+y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO


OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opes
  
ARG
the input for this action is the scalar output from one or more other actions
=s12
  
PACE
the frequency for kernel deposition
=1000
  
BARRIER
the free energy barrier to be overcome
=600
  
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
  
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=compressed_KernelsR.data
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=compressed_KernelsW.data
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=5000 
...

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 biasuwall1: 
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
=NNcube1 
AT
the positions of the wall
=2.9 
KAPPA
the force constant for the wall
=5000
lwall1: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=NNcube1 
AT
the positions of the wall
=-2.9 
KAPPA
the force constant for the wall
=5000

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=500
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-na 
ARG
the input for this action is the scalar output from one or more other actions
=s1.Sk3_-3_-3,s1.Sk3_-3_3,s1.Sk3_3_-3,s1.Sk3_3_3,s1.Sk6_0_0,s1.Sk0_6_-6,s1.Sk0_6_6,s1.Sk6_-6_0,s1.Sk6_0_-6,s1.Sk6_0_6,s1.Sk6_6_0,s1.Sk9_-3_-3,s1.Sk9_-3_3,s1.Sk9_3_-3,s1.Sk9_3_3 
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-cl 
ARG
the input for this action is the scalar output from one or more other actions
=s2.Sk3_-3_-3,s2.Sk3_-3_3,s2.Sk3_3_-3,s2.Sk3_3_3,s2.Sk6_0_0,s2.Sk0_6_-6,s2.Sk0_6_6,s2.Sk6_-6_0,s2.Sk6_0_-6,s2.Sk6_0_6,s2.Sk6_6_0,s1.Sk9_-3_-3,s2.Sk9_-3_3,s2.Sk9_3_-3,s2.Sk9_3_3
PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
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-nn 
ARG
the input for this action is the scalar output from one or more other actions
=NNcube1,NNcube2
PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
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
=s12,opes.*,uwall1.*,lwall1