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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.LOADLoads a library, possibly defining new actions. More detailsFILE=../codes/StructureFactor_descriptor.test.cpp #RESTARTfile to be loadedGROUPDefine 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 detailsATOMS=1-108the numerical indexes for the set of atoms in the groupLABEL=naa label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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 detailsATOMS=109-216the numerical indexes for the set of atoms in the groupLABEL=cla label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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 detailsATOMS=1-216the numerical indexes for the set of atoms in the groupLABEL=nacla label for the action so that its output can be referenced in the input to other actions
s1:STRUCTURE_FACTOR_DESCRIPTOR_TESTACTIVE_SHELLS=27,36,72,99 ATOMS=na s2:This action is not part of PLUMED and was included by using a LOAD command More detailsSTRUCTURE_FACTOR_DESCRIPTOR_TESTACTIVE_SHELLS=27,36,72,99 ATOMS=clThis action is not part of PLUMED and was included by using a LOAD command More details
auto1:PYTORCH_MODELMODEL=nacl_sfNa_ct1.ptLoad a PyTorch model compiled with TorchScript. More detailsARG=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 NNcube1:the input for this action is the scalar output from one or more other actionsMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=auto1.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
auto2:PYTORCH_MODELMODEL=nacl_sfCl_ct1.ptLoad a PyTorch model compiled with TorchScript. More detailsARG=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 NNcube2:the input for this action is the scalar output from one or more other actionsMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=auto2.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
s12:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=NNcube1,NNcube2the input to this functionFUNC=0.5*(x+ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionOPES_METAD...On-the-fly probability enhanced sampling with metadynamics-like target distribution. More detailsLABEL=opesa label for the action so that its output can be referenced in the input to other actionsARG=s12the input for this action is the scalar output from one or more other actionsPACE=1000the frequency for kernel depositionBARRIER=600the free energy barrier to be overcomeFILE=Kernels.dataa file in which the list of all deposited kernels is storedSTATE_RFILE=compressed_KernelsR.dataread from this file the compressed kernels and all the info needed to RESTART the simulationSTATE_WFILE=compressed_KernelsW.datawrite to this file the compressed kernels and all the info needed to RESTART the simulationSTATE_WSTRIDE=5000 ...number of MD steps between writing the STATE_WFILE
uwall1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=NNcube1the arguments on which the bias is actingAT=2.9the positions of the wallKAPPA=5000 lwall1:the force constant for the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=NNcube1the arguments on which the bias is actingAT=-2.9the positions of the wallKAPPA=5000the force constant for the wallFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=500the frequency with which all the open files should be flushedPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVAR-nathe name of the file on which to output these quantitiesARG=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_3the input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVAR-clthe name of the file on which to output these quantitiesARG=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_3the input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsFMT=%gthe format that should be used to output real numbersSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVAR-nnthe name of the file on which to output these quantitiesARG=NNcube1,NNcube2the input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsFMT=%gthe format that should be used to output real numbersSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesARG=s12,opes.*,uwall1.*,lwall1the input for this action is the scalar output from one or more other actions