Project ID: plumID:22.014
Source: plumed-order-parameters.dat
Originally used with PLUMED version: 2.5.1
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
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LOADLoads a library, possibly defining new actions. More detailsFILE=PairEntropies.cppfile to be loadedUNITSThis command sets the internal units for the code. More detailsLENGTH=A #This is input file for bulkIh-250K. #This is calculation of Q3s.(3 types) q3:the units of lengthsQ3Calculate 3rd order Steinhardt parameters. More detailsSPECIES=1-2880this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} lq3:the switching function that it used in the construction of the contact matrixLOCAL_Q3SPECIES=q3Calculate the local degree of order around an atoms by taking the average dot product between the $q_3 $ vector on the central atom and the $q_3 $ vector on the atoms in the first coordination sphere. More detailsSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} laq3:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=q3this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}the switching function that it used in the construction of the contact matrix
hhq3:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=q3an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhlq3:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=lq3an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhlaq3:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=laq3an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1the frequency with which to store data for averagingDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_q3.xyz STRIDE=1the file that you would like to output the data toDATA=q3the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_lq3.xyz STRIDE=1the file that you would like to output the data toDATA=lq3the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_laq3.xyz STRIDE=1the file that you would like to output the data toDATA=laq3the vector you wish to transformDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhq3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_q3the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlq3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_lq3the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlaq3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_laq3the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the file
#This is calculation of Q4s.(3 types) q4:Q4Calculate fourth order Steinhardt parameters. More detailsSPECIES=1-2880this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} lq4:the switching function that it used in the construction of the contact matrixLOCAL_Q4SPECIES=q4Calculate the local degree of order around an atoms by taking the average dot product between the $q_4 $ vector on the central atom and the $q_4 $ vector on the atoms in the first coordination sphere. More detailsSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} laq4:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=q4this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}the switching function that it used in the construction of the contact matrix
hhq4:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=q4an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhlq4:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=lq4an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhlaq4:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=laq4an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1the frequency with which to store data for averagingDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_q4.xyz STRIDE=1the file that you would like to output the data toDATA=q4the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_lq4.xyz STRIDE=1the file that you would like to output the data toDATA=lq4the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_laq4.xyz STRIDE=1the file that you would like to output the data toDATA=laq4the vector you wish to transformDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhq4the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_q4the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlq4the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_lq4the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlaq4the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_laq4the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the file
#This is calculation of Q6s.(3 types) q6:Q6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-2880this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} lq6:the switching function that it used in the construction of the contact matrixLOCAL_Q6SPECIES=q6Calculate the local degree of order around an atoms by taking the average dot product between the $q_6 $ vector on the central atom and the $q_6 $ vector on the atoms in the first coordination sphere. More detailsSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} laq6:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=q6this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}the switching function that it used in the construction of the contact matrix
hhq6:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=q6an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhlq6:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=lq6an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhlaq6:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=laq6an alternative to the ARG keywordGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1the frequency with which to store data for averagingDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_q6.xyz STRIDE=1the file that you would like to output the data toDATA=q6the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_lq6.xyz STRIDE=1the file that you would like to output the data toDATA=lq6the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_laq6.xyz STRIDE=1the file that you would like to output the data toDATA=laq6the vector you wish to transformDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhq6the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_q6the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlq6the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_lq6the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlaq6the grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_laq6the file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the file
#This is calculation of entropy(2 types)PAIRENTROPIESCalculate the KL entropy from the RDF around each of the atoms More detailsLABEL=s2 SPECIES=1-2880a label for the action so that its output can be referenced in the input to other actionsMAXR=5 SIGMA=0.15 LOCAL_DENSITY SWITCH={RATIONAL R_0=5.0 D_MAX=7.0 NN=50 MM=100} LOWMEMthe maximum distance to use for the rdfLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=s2this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} LOWMEMthe switching function that it used in the construction of the contact matrixLABEL=saa label for the action so that its output can be referenced in the input to other actionsDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_entropy.xyz STRIDE=1the file that you would like to output the data toDATA=s2the vector you wish to transformDUMPMULTICOLVARBasically equivalent to DUMPATOMS More detailsFILE=bulkIh_250K_localentropy.xyz STRIDE=1the file that you would like to output the data toDATA=sathe vector you wish to transform
hhe:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=s2an alternative to the ARG keywordGRID_MIN=-6the lower bounds for the gridGRID_MAX=0the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1 hhle:the frequency with which to store data for averagingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsDATA=saan alternative to the ARG keywordGRID_MIN=-6the lower bounds for the gridGRID_MAX=0the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015the bandwidths for kernel density esimtationSTRIDE=1the frequency with which to store data for averagingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhethe grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_ethe file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=hhlethe grid you would like to print (can also use ARG for specifying what is being printed)FILE=bulkIh_250K_histo_lethe file on which to write the gridSTRIDE=1the frequency with which the grid should be output to the fileENDPLUMEDTerminate plumed input. More details