PLUMED-NEST-TEST-SITE

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=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=../codes/StructureFactor_descriptor.test.cpp
#RESTART

The LOAD action with label  calculates somethingGROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-108 LABELa label for the action so that its output can be referenced in the input to other actions=na
The GROUP action with label na calculates somethingGROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=109-216 LABELa label for the action so that its output can be referenced in the input to other actions=cl
The GROUP action with label cl calculates somethingGROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-216 LABELa label for the action so that its output can be referenced in the input to other actions=nacl


The GROUP action with label nacl calculates somethings1: STRUCTURE_FACTOR_DESCRIPTOR_TESTThis 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_TESTThis 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_MODELLoad a PyTorch model compiled with TorchScript. More details MODEL=nacl_sfNa_ct1.pt ARGthe labels of the values from which the function is calculated=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: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=auto1.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label NNcube1 calculates the following quantities:
 Quantity   
 Description  
NNcube1.value
an arbitrary functionauto2: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details MODEL=nacl_sfCl_ct1.pt ARGthe labels of the values from which the function is calculated=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: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=auto2.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label NNcube2 calculates the following quantities:
 Quantity   
 Description  
NNcube2.value
an arbitrary functions12: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=NNcube1,NNcube2 FUNCthe function you wish to evaluate=0.5*(x+y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


The MATHEVAL action with label s12 calculates the following quantities:
 Quantity   
 Description  
s12.value
an arbitrary functionOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=s12
  PACEthe frequency for kernel deposition=1000
  BARRIERthe free energy barrier to be overcome=600
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_KernelsR.data
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed_KernelsW.data
  STATE_WSTRIDEnumber 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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=NNcube1 ATthe positions of the wall=2.9 KAPPAthe force constant for the wall=5000
The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potentiallwall1: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=NNcube1 ATthe positions of the wall=-2.9 KAPPAthe force constant for the wall=5000

The LOWER_WALLS action with label lwall1 calculates the following quantities:
 Quantity   
 Description  
lwall1.bias
the instantaneous value of the bias potential
lwall1.force2
the instantaneous value of the squared force due to this bias potentialFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500
PRINTPrint 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-na ARGthe labels of the values that you would like to print to the file=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 
PRINTPrint 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-cl ARGthe labels of the values that you would like to print to the file=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
PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g 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-nn ARGthe labels of the values that you would like to print to the file=NNcube1,NNcube2
PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g 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=s12,opes.*,uwall1.*,lwall1.*