Project ID: plumID:23.027
Source: water-structure-driver.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
# Plumed driver script to calculate ion coordination numbers and identify ion clusters in the EDL and bulk solution regions of CmuMD simulations # Aaron R. Finney and Matteo Salvalaglio # Properties of aqueous electrolyte solutions at carbon electrodes: # effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer # June 2023
#LOAD FILE=PairEntropies.cppUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
The UNITS action with label calculates somethingwox:GROUPDefine 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=1-12000:3the numerical indexes for the set of atoms in the group
# Q3 The GROUP action with label wox calculates somethingq3:Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut. More detailsSPECIES=woxthis keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} # PLUMED interprets the command: # q3: Q3 SPECIES=wox SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} # as follows (Click the red comment above to revert to the short version of the input): The Q3 action with label q3 calculates the following quantities:the switching function that it used in the construction of the contact matrixq3_grp:
Quantity Description GROUPDefine 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=wox The GROUP action with label q3_grp calculates somethingq3_mat:the numerical indexes for the set of atoms in the groupCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=woxspecifies the list of atoms that should be assumed indistinguishableSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}specify the switching function to use between two sets of indistinguishable atomsCOMPONENTSThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:also calculate the components of the vector connecting the atoms in the contact matrixq3_sh:
Quantity Description q3_mat.w a matrix containing the weights for the bonds between each pair of atoms q3_mat.x the projection of the bond on the x axis q3_mat.y the projection of the bond on the y axis q3_mat.z the projection of the bond on the z axis q3_mat.value a matrix containing the weights for the bonds between each pair of atoms SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More detailsARG=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.wthe input to this functionL=3 The SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:the value of the angular momentumq3_denom_ones:
Quantity Description q3_sh.rm the real parts of the spherical harmonic values with the m value given q3_sh.im the real parts of the spherical harmonic values with the m value given ONESCreate a constant vector with all elements equal to one More detailsSIZE=4000 The ONES action with label q3_denom_ones calculates the following quantities:the number of ones that you would like to createq3_denom:
Quantity Description q3_denom_ones.value a vector of ones with the required number of elements MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=q3_mat.w,q3_denom_ones The MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:the input for this action is the scalar output from one or more other actionsq3_sp:
Quantity Description q3_denom.value the vector that is obtained by taking the product between the matrix and the vector that were input q3_denom..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=q3_sh.*,q3_denom_ones The MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:the input for this action is the scalar output from one or more other actionsq3_norm2:
Quantity Description q3_sp.value the vector that is obtained by taking the product between the matrix and the vector that were input q3_sp..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details COMBINECalculate a polynomial combination of a set of other variables. More detailsPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPOWERS=2,2,2,2,2,2,2,2,2,2,2,2,2,2the powers to which you are raising each of the arguments in your functionARG=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 The COMBINE action with label q3_norm2 calculates the following quantities:the input to this functionq3_norm:
Quantity Description q3_norm2.value a linear compbination CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_norm2the input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_norm calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3:
Quantity Description q3_norm.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_norm,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO # --- End of included input --- lq3:if the output of your function is periodic then you should specify the periodicity of the functionLOCAL_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. This action is a shortcut. More detailsSPECIES=q3SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} # PLUMED interprets the command: # lq3: LOCAL_Q3 SPECIES=q3 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} # as follows (Click the red comment above to revert to the short version of the input): The LOCAL_Q3 action with label lq3 calculates the following quantities:This keyword is used if you want to employ an alternative to the continuous swiching function defined abovelq3_uvec:
Quantity Description ONESCreate a constant vector with all elements equal to one More detailsSIZE=14 The ONES action with label lq3_uvec calculates the following quantities:the number of ones that you would like to createlq3_grp:
Quantity Description lq3_uvec.value a vector of ones with the required number of elements GROUPDefine 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=q3 The GROUP action with label lq3_grp calculates somethinglq3_nmat:the numerical indexes for the set of atoms in the groupOUTER_PRODUCTCalculate the outer product matrix of two vectors More detailsARG=q3_norm,lq3_uvec The OUTER_PRODUCT action with label lq3_nmat calculates the following quantities:the input for this action is the scalar output from one or more other actionslq3_uvecs:
Quantity Description lq3_nmat.value a matrix containing the outer product of the two input vectors that was obtained using the function that was input VSTACKCreate a matrix by stacking vectors together More detailsARG=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 The VSTACK action with label lq3_uvecs calculates the following quantities:the input for this action is the scalar output from one or more other actionslq3_vecs:
Quantity Description lq3_uvecs.value a matrix that contains the input vectors in its columns CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=lq3_uvecs,lq3_nmatthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label lq3_vecs calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionlq3_vecsT:
Quantity Description lq3_vecs.value an arbitrary function TRANSPOSECalculate the transpose of a matrix More detailsARG=lq3_vecs The TRANSPOSE action with label lq3_vecsT calculates the following quantities:the input for this action is the scalar output from one or more other actionslq3_cmap:
Quantity Description lq3_vecsT.value the transpose of the input matrix CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=q3specifies the list of atoms that should be assumed indistinguishableSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} The CONTACT_MATRIX action with label lq3_cmap calculates the following quantities:specify the switching function to use between two sets of indistinguishable atomslq3_dpmat:
Quantity Description lq3_cmap.value a matrix containing the weights for the bonds between each pair of atoms MATRIX_PRODUCTCalculate the product of two matrices More detailsARG=lq3_vecs,lq3_vecsT The MATRIX_PRODUCT action with label lq3_dpmat calculates the following quantities:the input for this action is the scalar output from one or more other actionslq3_prod:
Quantity Description lq3_dpmat.value the product of the two input matrices CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=lq3_cmap,lq3_dpmatthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label lq3_prod calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionlq3_ones:
Quantity Description lq3_prod.value an arbitrary function ONESCreate a constant vector with all elements equal to one More detailsSIZE=4000 The ONES action with label lq3_ones calculates the following quantities:the number of ones that you would like to createlq3:
Quantity Description lq3_ones.value a vector of ones with the required number of elements MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=lq3_prod,lq3_ones lq3_denom:the input for this action is the scalar output from one or more other actionsMATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=lq3_cmap,lq3_ones The MATRIX_VECTOR_PRODUCT action with label lq3_denom calculates the following quantities:the input for this action is the scalar output from one or more other actionslq3_av:
Quantity Description lq3_denom.value the vector that is obtained by taking the product between the matrix and the vector that were input lq3_denom..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=lq3,lq3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO # --- End of included input --- The CUSTOM action with label lq3_av calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionlaq3:
Quantity Description lq3_av.value an arbitrary function LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. 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} # PLUMED interprets the command: # laq3: LOCAL_AVERAGE SPECIES=q3 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} # as follows (Click the red comment above to revert to the short version of the input): The LOCAL_AVERAGE action with label laq3 calculates the following quantities:the switching function that it used in the construction of the contact matrixlaq3_grp:
Quantity Description GROUPDefine 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=q3 The GROUP action with label laq3_grp calculates somethinglaq3_mat:the numerical indexes for the set of atoms in the groupCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=q3specifies the list of atoms that should be assumed indistinguishableSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} The CONTACT_MATRIX action with label laq3_mat calculates the following quantities:specify the switching function to use between two sets of indistinguishable atomslaq3_ones:
Quantity Description laq3_mat.value a matrix containing the weights for the bonds between each pair of atoms ONESCreate a constant vector with all elements equal to one More detailsSIZE=4000 The ONES action with label laq3_ones calculates the following quantities:the number of ones that you would like to createlaq3_coord:
Quantity Description laq3_ones.value a vector of ones with the required number of elements MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=laq3_mat,laq3_ones The MATRIX_VECTOR_PRODUCT action with label laq3_coord calculates the following quantities:the input for this action is the scalar output from one or more other actionsq3_rmn-n3:
Quantity Description laq3_coord.value the vector that is obtained by taking the product between the matrix and the vector that were input laq3_coord..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-n3,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-n3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-n3:
Quantity Description q3_rmn-n3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-n3,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-n3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-n2:
Quantity Description q3_imn-n3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-n2,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-n2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-n2:
Quantity Description q3_rmn-n2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-n2,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-n2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-n1:
Quantity Description q3_imn-n2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-n1,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-n1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-n1:
Quantity Description q3_rmn-n1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-n1,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-n1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-0:
Quantity Description q3_imn-n1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-0,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-0 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-0:
Quantity Description q3_rmn-0.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-0,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-0 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-p1:
Quantity Description q3_imn-0.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-p1,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-p1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-p1:
Quantity Description q3_rmn-p1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-p1,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-p1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-p2:
Quantity Description q3_imn-p1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-p2,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-p2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-p2:
Quantity Description q3_rmn-p2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-p2,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-p2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-p3:
Quantity Description q3_imn-p2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.rm-p3,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_rmn-p3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq3_imn-p3:
Quantity Description q3_rmn-p3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q3_sp.im-p3,q3_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q3_imn-p3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionlaq3_vstack:
Quantity Description q3_imn-p3.value an arbitrary function VSTACKCreate a matrix by stacking vectors together More detailsARG=q3_rmn-n3,q3_imn-n3,q3_rmn-n2,q3_imn-n2,q3_rmn-n1,q3_imn-n1,q3_rmn-0,q3_imn-0,q3_rmn-p1,q3_imn-p1,q3_rmn-p2,q3_imn-p2,q3_rmn-p3,q3_imn-p3 The VSTACK action with label laq3_vstack calculates the following quantities:the input for this action is the scalar output from one or more other actionslaq3_prod:
Quantity Description laq3_vstack.value a matrix that contains the input vectors in its columns MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=laq3_mat,q3_rmn-n3,q3_imn-n3,q3_rmn-n2,q3_imn-n2,q3_rmn-n1,q3_imn-n1,q3_rmn-0,q3_imn-0,q3_rmn-p1,q3_imn-p1,q3_rmn-p2,q3_imn-p2,q3_rmn-p3,q3_imn-p3 The MATRIX_VECTOR_PRODUCT action with label laq3_prod calculates the following quantities:the input for this action is the scalar output from one or more other actionslaq3_vpstack:
Quantity Description laq3_prod.value the vector that is obtained by taking the product between the matrix and the vector that were input laq3_prod..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details VSTACKCreate a matrix by stacking vectors together More detailsARG=laq3_prod.q3_rmn-n3,laq3_prod.q3_imn-n3,laq3_prod.q3_rmn-n2,laq3_prod.q3_imn-n2,laq3_prod.q3_rmn-n1,laq3_prod.q3_imn-n1,laq3_prod.q3_rmn-0,laq3_prod.q3_imn-0,laq3_prod.q3_rmn-p1,laq3_prod.q3_imn-p1,laq3_prod.q3_rmn-p2,laq3_prod.q3_imn-p2,laq3_prod.q3_rmn-p3,laq3_prod.q3_imn-p3 The VSTACK action with label laq3_vpstack calculates the following quantities:the input for this action is the scalar output from one or more other actionslaq3_lones:
Quantity Description laq3_vpstack.value a matrix that contains the input vectors in its columns ONESCreate a constant vector with all elements equal to one More detailsSIZE=14 The ONES action with label laq3_lones calculates the following quantities:the number of ones that you would like to createlaq3_unorm:
Quantity Description laq3_lones.value a vector of ones with the required number of elements OUTER_PRODUCTCalculate the outer product matrix of two vectors More detailsARG=laq3_coord,laq3_lones The OUTER_PRODUCT action with label laq3_unorm calculates the following quantities:the input for this action is the scalar output from one or more other actionslaq3_av:
Quantity Description laq3_unorm.value a matrix containing the outer product of the two input vectors that was obtained using the function that was input CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=laq3_vpstack,laq3_vstack,laq3_unormthe input to this functionFUNC=(x+y)/(1+zthe function you wish to evaluatePERIODIC=NO The CUSTOM action with label laq3_av calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionlaq3_av2:
Quantity Description laq3_av.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=laq3_avthe input to this functionFUNC=x*xthe function you wish to evaluatePERIODIC=NO The CUSTOM action with label laq3_av2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionlaq3_2:
Quantity Description laq3_av2.value an arbitrary function MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=laq3_av2,laq3_lones The MATRIX_VECTOR_PRODUCT action with label laq3_2 calculates the following quantities:the input for this action is the scalar output from one or more other actionslaq3:
Quantity Description laq3_2.value the vector that is obtained by taking the product between the matrix and the vector that were input laq3_2..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=laq3_2the input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NO # --- End of included input ---if the output of your function is periodic then you should specify the periodicity of the function
hhq3:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. 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=100 The HISTOGRAM action with label hhq3 calculates the following quantities:the frequency with which to store data for averaginghhq3:
Quantity Description hhq3.value the estimate of the histogram as a function of the argument that was obtained HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. 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=100the frequency with which to store data for averagingNORMALIZATION=ndataThis controls how the data is normalized it can be set equal to true, false or ndataCLEAR=0 # PLUMED interprets the command: # hhq3: HISTOGRAM DATA=q3 GRID_MIN=-1.5 GRID_MAX=1.5 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100 # as follows (Click the red comment above to revert to the short version of the input): hhq3_weight:the frequency with whihc to clear the data that is being averagedONESCreate a constant vector with all elements equal to one More detailsSIZE=1 The ONES action with label hhq3_weight calculates the following quantities:the number of ones that you would like to createhhq3_kde_u:
Quantity Description hhq3_weight.value a vector of ones with the required number of elements KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG=q3the input for this action is the scalar output from one or more other actionsGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015 The KDE action with label hhq3_kde_u calculates the following quantities:the bandwidths for kernel density esimtationhhq3_kde:
Quantity Description hhq3_kde_u.value a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhq3_kde_uthe input to this functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionFUNC=x/4000 The CUSTOM action with label hhq3_kde calculates the following quantities:the function you wish to evaluatehhq3_kdep:
Quantity Description hhq3_kde.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhq3_kde,hhq3_weightthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label hhq3_kdep calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionhhq3_u:
Quantity Description hhq3_kdep.value an arbitrary function ACCUMULATESum the elements of this value over the course of the trajectory More detailsARG=hhq3_kdepthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0 The ACCUMULATE action with label hhq3_u calculates the following quantities:the frequency with which to clear all the accumulated datahhq3_nsum:
Quantity Description hhq3_u.value a sum calculated from the time series of the input quantity ACCUMULATESum the elements of this value over the course of the trajectory More detailsARG=hhq3_weightthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0 The ACCUMULATE action with label hhq3_nsum calculates the following quantities:the frequency with which to clear all the accumulated datahhq3:
Quantity Description hhq3_nsum.value a sum calculated from the time series of the input quantity CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhq3_u,hhq3_nsumthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO # --- End of included input --- hhlq3:if the output of your function is periodic then you should specify the periodicity of the functionHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. 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=100 The HISTOGRAM action with label hhlq3 calculates the following quantities:the frequency with which to store data for averaginghhlq3:
Quantity Description hhlq3.value the estimate of the histogram as a function of the argument that was obtained HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. 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=100the frequency with which to store data for averagingNORMALIZATION=ndataThis controls how the data is normalized it can be set equal to true, false or ndataCLEAR=0 # PLUMED interprets the command: # hhlq3: HISTOGRAM DATA=lq3 GRID_MIN=-1.5 GRID_MAX=1.5 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100 # as follows (Click the red comment above to revert to the short version of the input): hhlq3_weight:the frequency with whihc to clear the data that is being averagedONESCreate a constant vector with all elements equal to one More detailsSIZE=1 The ONES action with label hhlq3_weight calculates the following quantities:the number of ones that you would like to createhhlq3_kde_u:
Quantity Description hhlq3_weight.value a vector of ones with the required number of elements KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG=lq3the input for this action is the scalar output from one or more other actionsGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015 The KDE action with label hhlq3_kde_u calculates the following quantities:the bandwidths for kernel density esimtationhhlq3_kde:
Quantity Description hhlq3_kde_u.value a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhlq3_kde_uthe input to this functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionFUNC=x/4000 The CUSTOM action with label hhlq3_kde calculates the following quantities:the function you wish to evaluatehhlq3_kdep:
Quantity Description hhlq3_kde.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhlq3_kde,hhlq3_weightthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label hhlq3_kdep calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionhhlq3_u:
Quantity Description hhlq3_kdep.value an arbitrary function ACCUMULATESum the elements of this value over the course of the trajectory More detailsARG=hhlq3_kdepthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0 The ACCUMULATE action with label hhlq3_u calculates the following quantities:the frequency with which to clear all the accumulated datahhlq3_nsum:
Quantity Description hhlq3_u.value a sum calculated from the time series of the input quantity ACCUMULATESum the elements of this value over the course of the trajectory More detailsARG=hhlq3_weightthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0 The ACCUMULATE action with label hhlq3_nsum calculates the following quantities:the frequency with which to clear all the accumulated datahhlq3:
Quantity Description hhlq3_nsum.value a sum calculated from the time series of the input quantity CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhlq3_u,hhlq3_nsumthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO # --- End of included input --- hhlaq3:if the output of your function is periodic then you should specify the periodicity of the functionHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. 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=100 The HISTOGRAM action with label hhlaq3 calculates the following quantities:the frequency with which to store data for averaginghhlaq3:
Quantity Description hhlaq3.value the estimate of the histogram as a function of the argument that was obtained HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. 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=100the frequency with which to store data for averagingNORMALIZATION=ndataThis controls how the data is normalized it can be set equal to true, false or ndataCLEAR=0 # PLUMED interprets the command: # hhlaq3: HISTOGRAM DATA=laq3 GRID_MIN=-1.5 GRID_MAX=1.5 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100 # as follows (Click the red comment above to revert to the short version of the input): hhlaq3_weight:the frequency with whihc to clear the data that is being averagedONESCreate a constant vector with all elements equal to one More detailsSIZE=1 The ONES action with label hhlaq3_weight calculates the following quantities:the number of ones that you would like to createhhlaq3_kde_u:
Quantity Description hhlaq3_weight.value a vector of ones with the required number of elements KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG=laq3the input for this action is the scalar output from one or more other actionsGRID_MIN=-1.5the lower bounds for the gridGRID_MAX=1.5the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.015 The KDE action with label hhlaq3_kde_u calculates the following quantities:the bandwidths for kernel density esimtationhhlaq3_kde:
Quantity Description hhlaq3_kde_u.value a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhlaq3_kde_uthe input to this functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionFUNC=x/4000 The CUSTOM action with label hhlaq3_kde calculates the following quantities:the function you wish to evaluatehhlaq3_kdep:
Quantity Description hhlaq3_kde.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhlaq3_kde,hhlaq3_weightthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label hhlaq3_kdep calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionhhlaq3_u:
Quantity Description hhlaq3_kdep.value an arbitrary function ACCUMULATESum the elements of this value over the course of the trajectory More detailsARG=hhlaq3_kdepthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0 The ACCUMULATE action with label hhlaq3_u calculates the following quantities:the frequency with which to clear all the accumulated datahhlaq3_nsum:
Quantity Description hhlaq3_u.value a sum calculated from the time series of the input quantity ACCUMULATESum the elements of this value over the course of the trajectory More detailsARG=hhlaq3_weightthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0 The ACCUMULATE action with label hhlaq3_nsum calculates the following quantities:the frequency with which to clear all the accumulated datahhlaq3:
Quantity Description hhlaq3_nsum.value a sum calculated from the time series of the input quantity CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=hhlaq3_u,hhlaq3_nsumthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO # --- End of included input ---if the output of your function is periodic then you should specify the periodicity of the functionDUMPGRIDOutput 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=histo_q3the file on which to write the gridSTRIDE=1000the 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=histo_lq3the file on which to write the gridSTRIDE=1000the 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=histo_laq3the file on which to write the gridSTRIDE=1000the frequency with which the grid should be output to the file
# Pair entropies #PAIRENTROPIES LABEL=s2 SPECIES=wox MAXR=5 SIGMA=0.15 LOCAL_DENSITY SWITCH={RATIONAL R_0=5.0 D_MAX=7.0 NN=50 MM=100} LOWMEM #sa: LOCAL_AVERAGE SPECIES=s2 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} LOWMEM
#hhe: HISTOGRAM DATA=s2 GRID_MIN=-6 GRID_MAX=0 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100 #hhle: HISTOGRAM DATA=sa GRID_MIN=-6 GRID_MAX=0 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100
#DUMPMULTICOLVAR FILE=entropy.xyz STRIDE=1 DATA=s2 #DUMPMULTICOLVAR FILE=localentropy.xyz STRIDE=1 DATA=sa
#DUMPGRID GRID=hhe FILE=histo_e STRIDE=1000 #DUMPGRID GRID=hhle FILE=histo_le STRIDE=1000