**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 somethingwoxThe GROUP action with labelwoxcalculates the following quantities::

QuantityTypeDescriptionwox atoms indices of atoms specified in GROUP 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

# Q3q3The Q3 action with labelq3calculates the following quantities::

QuantityTypeDescriptionq3 vector the value calculated by this action Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut. More detailsSPECIES=this keyword is used for colvars such as coordination numberwoxSWITCH={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 switching function that it used in the construction of the contact matrixq3_grpThe GROUP action with labelq3_grpcalculates the following quantities::

QuantityTypeDescriptionq3_grp atoms indices of atoms specified in GROUP 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=the numerical indexes for the set of atoms in the groupwoxq3_matThe CONTACT_MATRIX action with labelq3_matcalculates the following quantities::

QuantityTypeDescriptionq3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=specifies the list of atoms that should be assumed indistinguishablewoxSWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}specify the switching function to use between two sets of indistinguishable atomsCOMPONENTSalso calculate the components of the vector connecting the atoms in the contact matrixq3_shThe SPHERICAL_HARMONIC action with labelq3_shcalculates the following quantities::

QuantityTypeDescriptionq3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More detailsARG=the input to this functionq3_mat.x,q3_mat.y,q3_mat.z,q3_mat.wL=3the value of the angular momentumq3_denom_onesThe CONSTANT action with labelq3_denom_onescalculates the following quantities::

QuantityTypeDescriptionq3_denom_ones vector the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=4000the number of ones that you would like to createq3_denomThe MATRIX_VECTOR_PRODUCT action with labelq3_denomcalculates the following quantities::

QuantityTypeDescriptionq3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionsq3_mat.w,q3_denom_onesq3_spThe MATRIX_VECTOR_PRODUCT action with labelq3_spcalculates the following quantities::

QuantityTypeDescriptionq3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionsq3_sh.*,q3_denom_onesq3_norm2The COMBINE action with labelq3_norm2calculates the following quantities::

QuantityTypeDescriptionq3_norm2 vector the vector obtained by doing an element-wise application of a linear compbination to the input vectors 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=the input to this functionq3_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-p3q3_normThe CUSTOM action with labelq3_normcalculates the following quantities::

QuantityTypeDescriptionq3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_norm2FUNC=sqrt(xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionq3The CUSTOM action with labelq3calculates the following quantities::

QuantityTypeDescriptionq3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_norm,q3_denomFUNC=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 functionlq3The LOCAL_Q3 action with labellq3calculates the following quantities::

QuantityTypeDescriptionlq3 vector the value calculated by this action LOCAL_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):This keyword is used if you want to employ an alternative to the continuous swiching function defined abovelq3_uvecThe CONSTANT action with labellq3_uveccalculates the following quantities::

QuantityTypeDescriptionlq3_uvec vector the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=14the number of ones that you would like to createlq3_grpThe GROUP action with labellq3_grpcalculates the following quantities::

QuantityTypeDescriptionlq3_grp atoms indices of atoms specified in GROUP 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=the numerical indexes for the set of atoms in the groupq3lq3_nmatThe OUTER_PRODUCT action with labellq3_nmatcalculates the following quantities::

QuantityTypeDescriptionlq3_nmat matrix a matrix containing the outer product of the two input vectors that was obtained using the function that was input OUTER_PRODUCTCalculate the outer product matrix of two vectors More detailsARG=the input for this action is the scalar output from one or more other actionsq3_norm,lq3_uveclq3_uvecsThe VSTACK action with labellq3_uvecscalculates the following quantities::

QuantityTypeDescriptionlq3_uvecs matrix a matrix that contains the input vectors in its columns VSTACKCreate a matrix by stacking vectors together More detailsARG=the input for this action is the scalar output from one or more other actionsq3_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-p3lq3_vecsThe CUSTOM action with labellq3_vecscalculates the following quantities::

QuantityTypeDescriptionlq3_vecs matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionlq3_uvecs,lq3_nmatFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionlq3_vecsTThe TRANSPOSE action with labellq3_vecsTcalculates the following quantities::

QuantityTypeDescriptionlq3_vecsT matrix the transpose of the input matrix TRANSPOSECalculate the transpose of a matrix More detailsARG=the input for this action is the scalar output from one or more other actionslq3_vecslq3_cmapThe CONTACT_MATRIX action with labellq3_cmapcalculates the following quantities::

QuantityTypeDescriptionlq3_cmap matrix a matrix containing the weights for the bonds between each pair of atoms CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=specifies the list of atoms that should be assumed indistinguishableq3SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}specify the switching function to use between two sets of indistinguishable atomslq3_dpmatThe MATRIX_PRODUCT action with labellq3_dpmatcalculates the following quantities::

QuantityTypeDescriptionlq3_dpmat matrix the product of the two input matrices MATRIX_PRODUCTCalculate the product of two matrices More detailsARG=the input for this action is the scalar output from one or more other actionslq3_vecs,lq3_vecsTlq3_prodThe CUSTOM action with labellq3_prodcalculates the following quantities::

QuantityTypeDescriptionlq3_prod matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionlq3_cmap,lq3_dpmatFUNC=x*ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionlq3_onesThe CONSTANT action with labellq3_onescalculates the following quantities::

QuantityTypeDescriptionlq3_ones vector the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=4000the number of ones that you would like to createlq3The MATRIX_VECTOR_PRODUCT action with labellq3calculates the following quantities::

QuantityTypeDescriptionlq3 vector the vector that is obtained by taking the product between the matrix and the vector that were input MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionslq3_prod,lq3_oneslq3_denomThe MATRIX_VECTOR_PRODUCT action with labellq3_denomcalculates the following quantities::

QuantityTypeDescriptionlq3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionslq3_cmap,lq3_oneslq3_avThe CUSTOM action with labellq3_avcalculates the following quantities::

QuantityTypeDescriptionlq3_av vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionlq3,lq3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionlaq3The LOCAL_AVERAGE action with labellaq3calculates the following quantities::

QuantityTypeDescriptionlaq3 vector the value calculated by this action LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More detailsSPECIES=this keyword is used for colvars such as coordination numberq3SWITCH={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 switching function that it used in the construction of the contact matrixlaq3_grpThe GROUP action with labellaq3_grpcalculates the following quantities::

QuantityTypeDescriptionlaq3_grp atoms indices of atoms specified in GROUP ATOMS=the numerical indexes for the set of atoms in the groupq3laq3_matThe CONTACT_MATRIX action with labellaq3_matcalculates the following quantities::

QuantityTypeDescriptionlaq3_mat matrix a matrix containing the weights for the bonds between each pair of atoms CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=specifies the list of atoms that should be assumed indistinguishableq3SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}specify the switching function to use between two sets of indistinguishable atomslaq3_onesThe CONSTANT action with labellaq3_onescalculates the following quantities::

QuantityTypeDescriptionlaq3_ones vector the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=4000the number of ones that you would like to createlaq3_coordThe MATRIX_VECTOR_PRODUCT action with labellaq3_coordcalculates the following quantities::

QuantityTypeDescriptionlaq3_coord vector the vector that is obtained by taking the product between the matrix and the vector that were input MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionslaq3_mat,laq3_onesq3_rmn-n3The CUSTOM action with labelq3_rmn-n3calculates the following quantities::

QuantityTypeDescriptionq3_rmn-n3 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-n3,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-n3The CUSTOM action with labelq3_imn-n3calculates the following quantities::

QuantityTypeDescriptionq3_imn-n3 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-n3,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-n2The CUSTOM action with labelq3_rmn-n2calculates the following quantities::

QuantityTypeDescriptionq3_rmn-n2 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-n2,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-n2The CUSTOM action with labelq3_imn-n2calculates the following quantities::

QuantityTypeDescriptionq3_imn-n2 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-n2,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-n1The CUSTOM action with labelq3_rmn-n1calculates the following quantities::

QuantityTypeDescriptionq3_rmn-n1 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-n1,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-n1The CUSTOM action with labelq3_imn-n1calculates the following quantities::

QuantityTypeDescriptionq3_imn-n1 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-n1,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-0The CUSTOM action with labelq3_rmn-0calculates the following quantities::

QuantityTypeDescriptionq3_rmn-0 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-0,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-0The CUSTOM action with labelq3_imn-0calculates the following quantities::

QuantityTypeDescriptionq3_imn-0 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-0,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-p1The CUSTOM action with labelq3_rmn-p1calculates the following quantities::

QuantityTypeDescriptionq3_rmn-p1 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-p1,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-p1The CUSTOM action with labelq3_imn-p1calculates the following quantities::

QuantityTypeDescriptionq3_imn-p1 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-p1,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-p2The CUSTOM action with labelq3_rmn-p2calculates the following quantities::

QuantityTypeDescriptionq3_rmn-p2 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-p2,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-p2The CUSTOM action with labelq3_imn-p2calculates the following quantities::

QuantityTypeDescriptionq3_imn-p2 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-p2,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_rmn-p3The CUSTOM action with labelq3_rmn-p3calculates the following quantities::

QuantityTypeDescriptionq3_rmn-p3 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.rm-p3,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionq3_imn-p3The CUSTOM action with labelq3_imn-p3calculates the following quantities::

QuantityTypeDescriptionq3_imn-p3 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionq3_sp.im-p3,q3_denomFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionlaq3_vstackThe VSTACK action with labellaq3_vstackcalculates the following quantities::

QuantityTypeDescriptionlaq3_vstack matrix a matrix that contains the input vectors in its columns VSTACKCreate a matrix by stacking vectors together More detailsARG=the input for this action is the scalar output from one or more other actionsq3_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-p3laq3_prodThe MATRIX_VECTOR_PRODUCT action with labellaq3_prodcalculates the following quantities::

QuantityTypeDescriptionlaq3_prod.q3_rmn-n3 vector the product of the matrix laq3_mat and the vector q3_rmn-n3 laq3_prod.q3_imn-n3 vector the product of the matrix laq3_mat and the vector q3_imn-n3 laq3_prod.q3_rmn-n2 vector the product of the matrix laq3_mat and the vector q3_rmn-n2 laq3_prod.q3_imn-n2 vector the product of the matrix laq3_mat and the vector q3_imn-n2 laq3_prod.q3_rmn-n1 vector the product of the matrix laq3_mat and the vector q3_rmn-n1 laq3_prod.q3_imn-n1 vector the product of the matrix laq3_mat and the vector q3_imn-n1 laq3_prod.q3_rmn-0 vector the product of the matrix laq3_mat and the vector q3_rmn-0 laq3_prod.q3_imn-0 vector the product of the matrix laq3_mat and the vector q3_imn-0 laq3_prod.q3_rmn-p1 vector the product of the matrix laq3_mat and the vector q3_rmn-p1 laq3_prod.q3_imn-p1 vector the product of the matrix laq3_mat and the vector q3_imn-p1 laq3_prod.q3_rmn-p2 vector the product of the matrix laq3_mat and the vector q3_rmn-p2 laq3_prod.q3_imn-p2 vector the product of the matrix laq3_mat and the vector q3_imn-p2 laq3_prod.q3_rmn-p3 vector the product of the matrix laq3_mat and the vector q3_rmn-p3 laq3_prod.q3_imn-p3 vector the product of the matrix laq3_mat and the vector q3_imn-p3 MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionslaq3_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-p3laq3_vpstackThe VSTACK action with labellaq3_vpstackcalculates the following quantities::

QuantityTypeDescriptionlaq3_vpstack matrix a matrix that contains the input vectors in its columns VSTACKCreate a matrix by stacking vectors together More detailsARG=the input for this action is the scalar output from one or more other actionslaq3_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-p3laq3_lonesThe CONSTANT action with labellaq3_lonescalculates the following quantities::

QuantityTypeDescriptionlaq3_lones vector the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=14the number of ones that you would like to createlaq3_unormThe OUTER_PRODUCT action with labellaq3_unormcalculates the following quantities::

QuantityTypeDescriptionlaq3_unorm matrix a matrix containing the outer product of the two input vectors that was obtained using the function that was input OUTER_PRODUCTCalculate the outer product matrix of two vectors More detailsARG=the input for this action is the scalar output from one or more other actionslaq3_coord,laq3_loneslaq3_avThe CUSTOM action with labellaq3_avcalculates the following quantities::

QuantityTypeDescriptionlaq3_av matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionlaq3_vpstack,laq3_vstack,laq3_unormFUNC=(x+y)/(1+zthe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionlaq3_av2The CUSTOM action with labellaq3_av2calculates the following quantities::

QuantityTypeDescriptionlaq3_av2 matrix CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionlaq3_avFUNC=x*xthe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionlaq3_2The MATRIX_VECTOR_PRODUCT action with labellaq3_2calculates the following quantities::

QuantityTypeDescriptionlaq3_2 vector the vector that is obtained by taking the product between the matrix and the vector that were input MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=the input for this action is the scalar output from one or more other actionslaq3_av2,laq3_loneslaq3The CUSTOM action with labellaq3calculates the following quantities::

QuantityTypeDescriptionlaq3 vector CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionlaq3_2FUNC=sqrt(xthe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionhhq3The HISTOGRAM action with labelhhq3calculates the following quantities::

QuantityTypeDescriptionhhq3 grid 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 it has hidden defaults. More detailsDATA=an alternative to the ARG keywordq3GRID_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 averaginghhq3: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=an alternative to the ARG keywordq3GRID_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):the frequency with whihc to clear the data that is being averagedhhq3_weightThe CONSTANT action with labelhhq3_weightcalculates the following quantities::

QuantityTypeDescriptionhhq3_weight scalar the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=1the number of ones that you would like to createhhq3_kde_uThe KDE action with labelhhq3_kde_ucalculates the following quantities::

QuantityTypeDescriptionhhq3_kde_u grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG=the input for this action is the scalar output from one or more other actionsq3GRID_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 esimtationhhq3_kdeThe CUSTOM action with labelhhq3_kdecalculates the following quantities::

QuantityTypeDescriptionhhq3_kde grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhq3_kde_uif the output of your function is periodic then you should specify the periodicity of the functionFUNC=x/4000the function you wish to evaluatehhq3_kdepThe CUSTOM action with labelhhq3_kdepcalculates the following quantities::

QuantityTypeDescriptionhhq3_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhq3_kde,hhq3_weightFUNC=x*ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionhhq3_uThe ACCUMULATE action with labelhhq3_ucalculates the following quantities::

QuantityTypeDescriptionhhq3_u grid 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=the input for this action is the scalar output from one or more other actionshhq3_kdepSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0the frequency with which to clear all the accumulated datahhq3_nsumThe ACCUMULATE action with labelhhq3_nsumcalculates the following quantities::

QuantityTypeDescriptionhhq3_nsum scalar 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=the input for this action is the scalar output from one or more other actionshhq3_weightSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0the frequency with which to clear all the accumulated datahhq3The CUSTOM action with labelhhq3calculates the following quantities::

QuantityTypeDescriptionhhq3 grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhq3_u,hhq3_nsumFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionhhlq3The HISTOGRAM action with labelhhlq3calculates the following quantities::

QuantityTypeDescriptionhhlq3 grid 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 it has hidden defaults. More detailsDATA=an alternative to the ARG keywordlq3GRID_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 averaginghhlq3: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=an alternative to the ARG keywordlq3GRID_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):the frequency with whihc to clear the data that is being averagedhhlq3_weightThe CONSTANT action with labelhhlq3_weightcalculates the following quantities::

QuantityTypeDescriptionhhlq3_weight scalar the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=1the number of ones that you would like to createhhlq3_kde_uThe KDE action with labelhhlq3_kde_ucalculates the following quantities::

QuantityTypeDescriptionhhlq3_kde_u grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG=the input for this action is the scalar output from one or more other actionslq3GRID_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 esimtationhhlq3_kdeThe CUSTOM action with labelhhlq3_kdecalculates the following quantities::

QuantityTypeDescriptionhhlq3_kde grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhlq3_kde_uif the output of your function is periodic then you should specify the periodicity of the functionFUNC=x/4000the function you wish to evaluatehhlq3_kdepThe CUSTOM action with labelhhlq3_kdepcalculates the following quantities::

QuantityTypeDescriptionhhlq3_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhlq3_kde,hhlq3_weightFUNC=x*ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionhhlq3_uThe ACCUMULATE action with labelhhlq3_ucalculates the following quantities::

QuantityTypeDescriptionhhlq3_u grid 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=the input for this action is the scalar output from one or more other actionshhlq3_kdepSTRIDE=100the frequency with which the data should be collected and added to the quantity being averagedCLEAR=0the frequency with which to clear all the accumulated datahhlq3_nsumThe ACCUMULATE action with labelhhlq3_nsumcalculates the following quantities::

QuantityTypeDescriptionhhlq3_nsum scalar 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=the input for this action is the scalar output from one or more other actionshhlq3_weightthe frequency with which the data should be collected and added to the quantity being averagedCLEAR=0the frequency with which to clear all the accumulated datahhlq3The CUSTOM action with labelhhlq3calculates the following quantities::

QuantityTypeDescriptionhhlq3 grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhlq3_u,hhlq3_nsumFUNC=x/ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionhhlaq3The HISTOGRAM action with labelhhlaq3calculates the following quantities::

QuantityTypeDescriptionhhlaq3 grid 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 it has hidden defaults. More detailsDATA=an alternative to the ARG keywordlaq3GRID_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 averaginghhlaq3: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=an alternative to the ARG keywordlaq3GRID_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):the frequency with whihc to clear the data that is being averagedhhlaq3_weightThe CONSTANT action with labelhhlaq3_weightcalculates the following quantities::

QuantityTypeDescriptionhhlaq3_weight scalar the constant value that was read from the plumed input ONESCreate a constant vector with all elements equal to one More detailsSIZE=1the number of ones that you would like to createhhlaq3_kde_uThe KDE action with labelhhlaq3_kde_ucalculates the following quantities::

QuantityTypeDescriptionhhlaq3_kde_u grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG=the input for this action is the scalar output from one or more other actionslaq3GRID_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 esimtationhhlaq3_kdeThe CUSTOM action with labelhhlaq3_kdecalculates the following quantities::

QuantityTypeDescriptionhhlaq3_kde grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhlaq3_kde_uif the output of your function is periodic then you should specify the periodicity of the functionFUNC=x/4000the function you wish to evaluatehhlaq3_kdepThe CUSTOM action with labelhhlaq3_kdepcalculates the following quantities::

QuantityTypeDescriptionhhlaq3_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhlaq3_kde,hhlaq3_weightFUNC=x*ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionhhlaq3_uThe ACCUMULATE action with labelhhlaq3_ucalculates the following quantities::

QuantityTypeDescriptionhhlaq3_u grid 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=the input for this action is the scalar output from one or more other actionshhlaq3_kdepthe frequency with which the data should be collected and added to the quantity being averagedCLEAR=0the frequency with which to clear all the accumulated datahhlaq3_nsumThe ACCUMULATE action with labelhhlaq3_nsumcalculates the following quantities::

QuantityTypeDescriptionhhlaq3_nsum scalar 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=the input for this action is the scalar output from one or more other actionshhlaq3_weightthe frequency with which the data should be collected and added to the quantity being averagedCLEAR=0the frequency with which to clear all the accumulated datahhlaq3The CUSTOM action with labelhhlaq3calculates the following quantities::

QuantityTypeDescriptionhhlaq3 grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input to this functionhhlaq3_u,hhlaq3_nsumFUNC=x/ythe function you wish to evaluateif 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=the grid you would like to print (can also use ARG for specifying what is being printed)hhq3FILE=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=the grid you would like to print (can also use ARG for specifying what is being printed)hhlq3FILE=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=the grid you would like to print (can also use ARG for specifying what is being printed)hhlaq3FILE=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