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PLUMED manual

Shortcut: LOCAL_AVERAGE

Shortcut: LOCAL_AVERAGE

Module	symfunc
Description	Usage
Calculate averages over spherical regions centered on atoms
output value	type
the values of the local averages	vector

Details and examples

Calculate averages over spherical regions centered on atoms

As is explained in this video certain PLUMED actions calculate one scalar quantity or one vector for each of the atoms in the system. For example COORDINATIONNUMBER measures the coordination number of each of the atoms in the system and Q4 measures the 4th order Steinhardt parameter for each of the atoms in the system. These quantities provide tell us something about the disposition of the atoms in the first coordination sphere of each of the atoms of interest. In the paper in the bibliography Lechner and Dellago have suggested that one can probe local order in a system by taking the average value of such symmetry functions over the atoms within a spherical cutoff of each of these atoms in the systems. When this is done with Steinhardt parameters they claim this gives a coordinate that is better able to distinguish solid and liquid configurations of Lennard-Jones atoms.

You can calculate such locally averaged quantities within plumed by using the LOCAL_AVERAGE command. This command calculates the following atom-centered quantities:

$s_i = \frac{ c_i + \sum_j \sigma(r_{ij})c_j }{ 1 + \sum_j \sigma(r_{ij}) }$

where the $c_i$ and $c_j$ values can be any vector of symmetry functions that can be calculated using plumed multicolvars. The function $\sigma( r_{ij} )$ is a switching function that acts on the distance between atoms $i$ and $j$ . Lechner and Dellago suggest that the parameters of this function should be set so that it the function is equal to one when atom $j$ is in the first coordination sphere of atom $i$ and is zero otherwise.

To see how this works in practice consider the following example input.

Click on the labels of the actions for more information on what each action computes

d1The COORDINATIONNUMBER action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# d1: COORDINATIONNUMBER SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
d1_grpThe GROUP action with label d1_grp calculates the following quantities: Quantity    Type    Description  
d1_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-64
d1_matThe CONTACT_MATRIX action with label d1_mat calculates the following quantities: Quantity    Type    Description  
d1_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
d1_onesThe CONSTANT action with label d1_ones calculates the following quantities: Quantity    Type    Description  
d1_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
d1The MATRIX_VECTOR_PRODUCT action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 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 details  ARGthe label for the matrix and the vector/scalar that are being multiplied=d1_mat,d1_ones
# --- End of included input --- laThe LOCAL_AVERAGE action with label la calculates the following quantities: Quantity    Type    Description  
la vector the values of the local averages: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=d1 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
# PLUMED interprets the command:
# la: LOCAL_AVERAGE SPECIES=d1 D_0=1.3 R_0=0.2 NN=6 MM=12
# as follows (Click the red comment above to revert to the short version of the input):
la_grpThe GROUP action with label la_grp calculates the following quantities: Quantity    Type    Description  
la_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 details ATOMSthe numerical indexes for the set of atoms in the group=d1
la_matThe CONTACT_MATRIX action with label la_mat calculates the following quantities: Quantity    Type    Description  
la_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=d1 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
la_onesThe CONSTANT action with label la_ones calculates the following quantities: Quantity    Type    Description  
la_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
la_coordThe MATRIX_VECTOR_PRODUCT action with label la_coord calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,la_ones
la_prodThe MATRIX_VECTOR_PRODUCT action with label la_prod calculates the following quantities: Quantity    Type    Description  
la_prod 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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,d1
laThe CUSTOM action with label la calculates the following quantities: Quantity    Type    Description  
la 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 details ARGthe values input to this function=la_prod,d1,la_coord FUNCthe function you wish to evaluate=(x+y)/(1+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- mtfThe MORE_THAN action with label mtf calculates the following quantities: Quantity    Type    Description  
mtf vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=la SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=4}
la_morethanThe SUM action with label la_morethan calculates the following quantities: Quantity    Type    Description  
la_morethan scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=mtf PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=la_morethan FILEthe name of the file on which to output these quantities=colvar

This input calculates the coordination numbers for all the atoms in the system. These coordination numbers are then averaged over spherical regions. The number of averaged coordination numbers that are greater than 4 is then output to a file. Furthermore, if you expand the input above you can see how the LOCAL_AVERAGE command is a shortcut action that expands to a longer input that you should be able to interpret.

In the input above we use a rational switching function with the parameters above. We would recommend using SWITCH syntax rather than the syntax above when giving the parameters for the switching function as you can then use any of the switching functions described in the documentation for LESS_THAN. More importantly, however, using this syntax allows you to set the D_MAX parameter for the switching function as demonstrated below:

Click on the labels of the actions for more information on what each action computes

d1The COORDINATIONNUMBER action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# d1: COORDINATIONNUMBER SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
d1_grpThe GROUP action with label d1_grp calculates the following quantities: Quantity    Type    Description  
d1_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-64
d1_matThe CONTACT_MATRIX action with label d1_mat calculates the following quantities: Quantity    Type    Description  
d1_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
d1_onesThe CONSTANT action with label d1_ones calculates the following quantities: Quantity    Type    Description  
d1_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
d1The MATRIX_VECTOR_PRODUCT action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 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 details  ARGthe label for the matrix and the vector/scalar that are being multiplied=d1_mat,d1_ones
# --- End of included input --- laThe LOCAL_AVERAGE action with label la calculates the following quantities: Quantity    Type    Description  
la vector the values of the local averages: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=d1 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# la: LOCAL_AVERAGE SPECIES=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
la_grpThe GROUP action with label la_grp calculates the following quantities: Quantity    Type    Description  
la_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 details ATOMSthe numerical indexes for the set of atoms in the group=d1
la_matThe CONTACT_MATRIX action with label la_mat calculates the following quantities: Quantity    Type    Description  
la_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=d1 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
la_onesThe CONSTANT action with label la_ones calculates the following quantities: Quantity    Type    Description  
la_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
la_coordThe MATRIX_VECTOR_PRODUCT action with label la_coord calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,la_ones
la_prodThe MATRIX_VECTOR_PRODUCT action with label la_prod calculates the following quantities: Quantity    Type    Description  
la_prod 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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,d1
laThe CUSTOM action with label la calculates the following quantities: Quantity    Type    Description  
la 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 details ARGthe values input to this function=la_prod,d1,la_coord FUNCthe function you wish to evaluate=(x+y)/(1+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- mtfThe MORE_THAN action with label mtf calculates the following quantities: Quantity    Type    Description  
mtf vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=la SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=4}
la_morethanThe SUM action with label la_morethan calculates the following quantities: Quantity    Type    Description  
la_morethan scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=mtf PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=la_morethan FILEthe name of the file on which to output these quantities=colvar

Setting the D_MAX can substantially improve PLUMED performance as it turns on the linked list algorithm that is discussed in the optimisation details part of the documentation for CONTACT_MATRIX.

Locally averaged Steinhardt Parameters

What Lechner and Dellago did in their paper was a little more complicated than the example in the previous section. To reproduce what they did you would use an input something like this:

Click on the labels of the actions for more information on what each action computes

q4The Q4 action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 vector the norms of the vectors of spherical harmonic coefficients: Q4Calculate fourth order Steinhardt parameters. This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2}
# PLUMED interprets the command:
# q4: Q4 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2}
# as follows (Click the red comment above to revert to the short version of the input):
q4_grpThe GROUP action with label q4_grp calculates the following quantities: Quantity    Type    Description  
q4_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-64
q4_matThe CONTACT_MATRIX action with label q4_mat calculates the following quantities: Quantity    Type    Description  
q4_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q4_mat.x matrix the projection of the bond on the x axis
q4_mat.y matrix the projection of the bond on the y axis
q4_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q4_shThe SPHERICAL_HARMONIC action with label q4_sh calculates the following quantities: Quantity    Type    Description  
q4_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q4_mat.x,q4_mat.y,q4_mat.z,q4_mat.w Lthe value of the angular momentum=4
q4_denom_onesThe CONSTANT action with label q4_denom_ones calculates the following quantities: Quantity    Type    Description  
q4_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q4_denomThe MATRIX_VECTOR_PRODUCT action with label q4_denom calculates the following quantities: Quantity    Type    Description  
q4_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=q4_mat.w,q4_denom_ones
q4_spThe MATRIX_VECTOR_PRODUCT action with label q4_sp calculates the following quantities: Quantity    Type    Description  
q4_sp.rm-n4 vector the product of the matrix q4_sh.rm-n4 and the vector q4_denom_ones
q4_sp.rm-n3 vector the product of the matrix q4_sh.rm-n3 and the vector q4_denom_ones
q4_sp.rm-n2 vector the product of the matrix q4_sh.rm-n2 and the vector q4_denom_ones
q4_sp.rm-n1 vector the product of the matrix q4_sh.rm-n1 and the vector q4_denom_ones
q4_sp.rm-0 vector the product of the matrix q4_sh.rm-0 and the vector q4_denom_ones
q4_sp.rm-p1 vector the product of the matrix q4_sh.rm-p1 and the vector q4_denom_ones
q4_sp.rm-p2 vector the product of the matrix q4_sh.rm-p2 and the vector q4_denom_ones
q4_sp.rm-p3 vector the product of the matrix q4_sh.rm-p3 and the vector q4_denom_ones
q4_sp.rm-p4 vector the product of the matrix q4_sh.rm-p4 and the vector q4_denom_ones
q4_sp.im-n4 vector the product of the matrix q4_sh.im-n4 and the vector q4_denom_ones
q4_sp.im-n3 vector the product of the matrix q4_sh.im-n3 and the vector q4_denom_ones
q4_sp.im-n2 vector the product of the matrix q4_sh.im-n2 and the vector q4_denom_ones
q4_sp.im-n1 vector the product of the matrix q4_sh.im-n1 and the vector q4_denom_ones
q4_sp.im-0 vector the product of the matrix q4_sh.im-0 and the vector q4_denom_ones
q4_sp.im-p1 vector the product of the matrix q4_sh.im-p1 and the vector q4_denom_ones
q4_sp.im-p2 vector the product of the matrix q4_sh.im-p2 and the vector q4_denom_ones
q4_sp.im-p3 vector the product of the matrix q4_sh.im-p3 and the vector q4_denom_ones
q4_sp.im-p4 vector the product of the matrix q4_sh.im-p4 and the vector q4_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q4_sh.*,q4_denom_ones
q4_norm2The COMBINE action with label q4_norm2 calculates the following quantities: Quantity    Type    Description  
q4_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
q4_normThe CUSTOM action with label q4_norm calculates the following quantities: Quantity    Type    Description  
q4_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 details ARGthe values input to this function=q4_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4The CUSTOM action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 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 details ARGthe values input to this function=q4_norm,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- laThe LOCAL_AVERAGE action with label la calculates the following quantities: Quantity    Type    Description  
la vector the values of the local averages: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=q4 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2}
# PLUMED interprets the command:
# la: LOCAL_AVERAGE SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2}
# as follows (Click the red comment above to revert to the short version of the input):
la_grpThe GROUP action with label la_grp calculates the following quantities: Quantity    Type    Description  
la_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 details ATOMSthe numerical indexes for the set of atoms in the group=q4
la_matThe CONTACT_MATRIX action with label la_mat calculates the following quantities: Quantity    Type    Description  
la_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=q4 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2}
la_onesThe CONSTANT action with label la_ones calculates the following quantities: Quantity    Type    Description  
la_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
la_coordThe MATRIX_VECTOR_PRODUCT action with label la_coord calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,la_ones
q4_rmn-n4The CUSTOM action with label q4_rmn-n4 calculates the following quantities: Quantity    Type    Description  
q4_rmn-n4 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 details ARGthe values input to this function=q4_sp.rm-n4,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-n4The CUSTOM action with label q4_imn-n4 calculates the following quantities: Quantity    Type    Description  
q4_imn-n4 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 details ARGthe values input to this function=q4_sp.im-n4,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-n3The CUSTOM action with label q4_rmn-n3 calculates the following quantities: Quantity    Type    Description  
q4_rmn-n3 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 details ARGthe values input to this function=q4_sp.rm-n3,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-n3The CUSTOM action with label q4_imn-n3 calculates the following quantities: Quantity    Type    Description  
q4_imn-n3 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 details ARGthe values input to this function=q4_sp.im-n3,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-n2The CUSTOM action with label q4_rmn-n2 calculates the following quantities: Quantity    Type    Description  
q4_rmn-n2 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 details ARGthe values input to this function=q4_sp.rm-n2,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-n2The CUSTOM action with label q4_imn-n2 calculates the following quantities: Quantity    Type    Description  
q4_imn-n2 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 details ARGthe values input to this function=q4_sp.im-n2,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-n1The CUSTOM action with label q4_rmn-n1 calculates the following quantities: Quantity    Type    Description  
q4_rmn-n1 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 details ARGthe values input to this function=q4_sp.rm-n1,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-n1The CUSTOM action with label q4_imn-n1 calculates the following quantities: Quantity    Type    Description  
q4_imn-n1 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 details ARGthe values input to this function=q4_sp.im-n1,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-0The CUSTOM action with label q4_rmn-0 calculates the following quantities: Quantity    Type    Description  
q4_rmn-0 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 details ARGthe values input to this function=q4_sp.rm-0,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-0The CUSTOM action with label q4_imn-0 calculates the following quantities: Quantity    Type    Description  
q4_imn-0 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 details ARGthe values input to this function=q4_sp.im-0,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-p1The CUSTOM action with label q4_rmn-p1 calculates the following quantities: Quantity    Type    Description  
q4_rmn-p1 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 details ARGthe values input to this function=q4_sp.rm-p1,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-p1The CUSTOM action with label q4_imn-p1 calculates the following quantities: Quantity    Type    Description  
q4_imn-p1 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 details ARGthe values input to this function=q4_sp.im-p1,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-p2The CUSTOM action with label q4_rmn-p2 calculates the following quantities: Quantity    Type    Description  
q4_rmn-p2 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 details ARGthe values input to this function=q4_sp.rm-p2,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-p2The CUSTOM action with label q4_imn-p2 calculates the following quantities: Quantity    Type    Description  
q4_imn-p2 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 details ARGthe values input to this function=q4_sp.im-p2,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-p3The CUSTOM action with label q4_rmn-p3 calculates the following quantities: Quantity    Type    Description  
q4_rmn-p3 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 details ARGthe values input to this function=q4_sp.rm-p3,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-p3The CUSTOM action with label q4_imn-p3 calculates the following quantities: Quantity    Type    Description  
q4_imn-p3 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 details ARGthe values input to this function=q4_sp.im-p3,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_rmn-p4The CUSTOM action with label q4_rmn-p4 calculates the following quantities: Quantity    Type    Description  
q4_rmn-p4 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 details ARGthe values input to this function=q4_sp.rm-p4,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q4_imn-p4The CUSTOM action with label q4_imn-p4 calculates the following quantities: Quantity    Type    Description  
q4_imn-p4 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 details ARGthe values input to this function=q4_sp.im-p4,q4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
la_vstackThe VSTACK action with label la_vstack calculates the following quantities: Quantity    Type    Description  
la_vstack matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=q4_rmn-n4,q4_imn-n4,q4_rmn-n3,q4_imn-n3,q4_rmn-n2,q4_imn-n2,q4_rmn-n1,q4_imn-n1,q4_rmn-0,q4_imn-0,q4_rmn-p1,q4_imn-p1,q4_rmn-p2,q4_imn-p2,q4_rmn-p3,q4_imn-p3,q4_rmn-p4,q4_imn-p4
la_prodThe MATRIX_VECTOR_PRODUCT action with label la_prod calculates the following quantities: Quantity    Type    Description  
la_prod.q4_rmn-n4 vector the product of the matrix la_mat and the vector q4_rmn-n4
la_prod.q4_imn-n4 vector the product of the matrix la_mat and the vector q4_imn-n4
la_prod.q4_rmn-n3 vector the product of the matrix la_mat and the vector q4_rmn-n3
la_prod.q4_imn-n3 vector the product of the matrix la_mat and the vector q4_imn-n3
la_prod.q4_rmn-n2 vector the product of the matrix la_mat and the vector q4_rmn-n2
la_prod.q4_imn-n2 vector the product of the matrix la_mat and the vector q4_imn-n2
la_prod.q4_rmn-n1 vector the product of the matrix la_mat and the vector q4_rmn-n1
la_prod.q4_imn-n1 vector the product of the matrix la_mat and the vector q4_imn-n1
la_prod.q4_rmn-0 vector the product of the matrix la_mat and the vector q4_rmn-0
la_prod.q4_imn-0 vector the product of the matrix la_mat and the vector q4_imn-0
la_prod.q4_rmn-p1 vector the product of the matrix la_mat and the vector q4_rmn-p1
la_prod.q4_imn-p1 vector the product of the matrix la_mat and the vector q4_imn-p1
la_prod.q4_rmn-p2 vector the product of the matrix la_mat and the vector q4_rmn-p2
la_prod.q4_imn-p2 vector the product of the matrix la_mat and the vector q4_imn-p2
la_prod.q4_rmn-p3 vector the product of the matrix la_mat and the vector q4_rmn-p3
la_prod.q4_imn-p3 vector the product of the matrix la_mat and the vector q4_imn-p3
la_prod.q4_rmn-p4 vector the product of the matrix la_mat and the vector q4_rmn-p4
la_prod.q4_imn-p4 vector the product of the matrix la_mat and the vector q4_imn-p4: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,q4_rmn-n4,q4_imn-n4,q4_rmn-n3,q4_imn-n3,q4_rmn-n2,q4_imn-n2,q4_rmn-n1,q4_imn-n1,q4_rmn-0,q4_imn-0,q4_rmn-p1,q4_imn-p1,q4_rmn-p2,q4_imn-p2,q4_rmn-p3,q4_imn-p3,q4_rmn-p4,q4_imn-p4
la_vpstackThe VSTACK action with label la_vpstack calculates the following quantities: Quantity    Type    Description  
la_vpstack matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=la_prod.q4_rmn-n4,la_prod.q4_imn-n4,la_prod.q4_rmn-n3,la_prod.q4_imn-n3,la_prod.q4_rmn-n2,la_prod.q4_imn-n2,la_prod.q4_rmn-n1,la_prod.q4_imn-n1,la_prod.q4_rmn-0,la_prod.q4_imn-0,la_prod.q4_rmn-p1,la_prod.q4_imn-p1,la_prod.q4_rmn-p2,la_prod.q4_imn-p2,la_prod.q4_rmn-p3,la_prod.q4_imn-p3,la_prod.q4_rmn-p4,la_prod.q4_imn-p4
la_lonesThe CONSTANT action with label la_lones calculates the following quantities: Quantity    Type    Description  
la_lones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=18
la_unormThe OUTER_PRODUCT action with label la_unorm calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe labels of the two vectors from which the outer product is being computed=la_coord,la_lones
la_avThe CUSTOM action with label la_av calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe values input to this function=la_vpstack,la_vstack,la_unorm FUNCthe function you wish to evaluate=(x+y)/(1+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
la_av2The CUSTOM action with label la_av2 calculates the following quantities: Quantity    Type    Description  
la_av2 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 details ARGthe values input to this function=la_av FUNCthe function you wish to evaluate=x*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
la_2The MATRIX_VECTOR_PRODUCT action with label la_2 calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_av2,la_lones
laThe CUSTOM action with label la calculates the following quantities: Quantity    Type    Description  
la 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 details ARGthe values input to this function=la_2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- la_meanThe MEAN action with label la_mean calculates the following quantities: Quantity    Type    Description  
la_mean scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=la PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=la_mean FILEthe name of the file on which to output these quantities=colvar

This example input calculates the Q4 vectors for each of the atoms in the system. These vectors are then averaged component by component over a spherical region. The average value for this quantity is then outputeed to a file. If you want to understand more about the shortcut that is used here you can read this page.

Using SPECIESA/SPECIESB

If you only want to calculate the local averages for a subset of the atoms you might use an input like the one shown below:

Click on the labels of the actions for more information on what each action computes

# Calculate the coordination numbers for the two types of atom
d1aThe COORDINATIONNUMBER action with label d1a calculates the following quantities: Quantity    Type    Description  
d1a vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-5 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# d1a: COORDINATIONNUMBER SPECIES=1-5 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
d1a_grpThe GROUP action with label d1a_grp calculates the following quantities: Quantity    Type    Description  
d1a_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-5
d1a_matThe CONTACT_MATRIX action with label d1a_mat calculates the following quantities: Quantity    Type    Description  
d1a_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-5 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
d1a_onesThe CONSTANT action with label d1a_ones calculates the following quantities: Quantity    Type    Description  
d1a_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=5
d1aThe MATRIX_VECTOR_PRODUCT action with label d1a calculates the following quantities: Quantity    Type    Description  
d1a 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 details  ARGthe label for the matrix and the vector/scalar that are being multiplied=d1a_mat,d1a_ones
# --- End of included input --- d1bThe COORDINATIONNUMBER action with label d1b calculates the following quantities: Quantity    Type    Description  
d1b vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# d1b: COORDINATIONNUMBER SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
d1b_grpThe GROUP action with label d1b_grp calculates the following quantities: Quantity    Type    Description  
d1b_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-64
d1b_matThe CONTACT_MATRIX action with label d1b_mat calculates the following quantities: Quantity    Type    Description  
d1b_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
d1b_onesThe CONSTANT action with label d1b_ones calculates the following quantities: Quantity    Type    Description  
d1b_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
d1bThe MATRIX_VECTOR_PRODUCT action with label d1b calculates the following quantities: Quantity    Type    Description  
d1b 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 details  ARGthe label for the matrix and the vector/scalar that are being multiplied=d1b_mat,d1b_ones
# --- End of included input --- # Now compute the local average
laThe LOCAL_AVERAGE action with label la calculates the following quantities: Quantity    Type    Description  
la vector the values of the local averages: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=d1a SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=d1b SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# la: LOCAL_AVERAGE SPECIESA=d1a SPECIESB=d1b SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
la_grpThe GROUP action with label la_grp calculates the following quantities: Quantity    Type    Description  
la_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 details ATOMSthe numerical indexes for the set of atoms in the group=d1a
la_matThe CONTACT_MATRIX action with label la_mat calculates the following quantities: Quantity    Type    Description  
la_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 details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=d1a GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=d1b SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
la_onesThe CONSTANT action with label la_ones calculates the following quantities: Quantity    Type    Description  
la_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
la_coordThe MATRIX_VECTOR_PRODUCT action with label la_coord calculates the following quantities: Quantity    Type    Description  
la_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,la_ones
la_prodThe MATRIX_VECTOR_PRODUCT action with label la_prod calculates the following quantities: Quantity    Type    Description  
la_prod 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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=la_mat,d1b
laThe CUSTOM action with label la calculates the following quantities: Quantity    Type    Description  
la 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 details ARGthe values input to this function=la_prod,d1a,la_coord FUNCthe function you wish to evaluate=(x+y)/(1+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- DUMPATOMSDump selected atoms on a file. More details ARGthe labels of vectors that should be output in the xyz file=la ATOMSthe atom indices whose positions you would like to print out=1-5 FILEfile on which to output coordinates; extension is automatically detected=atoms.xyz

In the input above the local averages are computed for atoms 1-5 only. However, to calculate these local averages we still need to calculate the coordination numbers of all the atoms in the system.

The MASK keyword

You can use the MASK keyword with this action in the same way that it is used with COORDINATIONNUMBER. This keyword thus expects a vector in input, which tells PLUMED the atoms for which you do not need to calculate the function. As illustrated below, this is useful if you are using functionality from the volumes module to calculate the average value of the local averages for only those atoms that lie in a certain part of the simulation box.

Click on the labels of the actions for more information on what each action computes

# Calculate the coordination number for all the atoms
ccThe COORDINATIONNUMBER action with label cc calculates the following quantities: Quantity    Type    Description  
cc vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-400 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# cc: COORDINATIONNUMBER SPECIES=1-400 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
cc_grpThe GROUP action with label cc_grp calculates the following quantities: Quantity    Type    Description  
cc_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-400
cc_matThe CONTACT_MATRIX action with label cc_mat calculates the following quantities: Quantity    Type    Description  
cc_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-400 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
cc_onesThe CONSTANT action with label cc_ones calculates the following quantities: Quantity    Type    Description  
cc_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=400
ccThe MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities: Quantity    Type    Description  
cc 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 details  ARGthe label for the matrix and the vector/scalar that are being multiplied=cc_mat,cc_ones
# --- End of included input --- # Fixed virtual atom which serves as the probe volume's center (pos. in nm)
centerThe FIXEDATOM action with label center calculates the following quantities: Quantity    Type    Description  
center atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.5,2.5,2.5
center: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.5,2.5,2.5  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
# Vector in which element i is one if atom i is in sphere of interest and zero otherwise
sphereThe INSPHERE action with label sphere calculates the following quantities: Quantity    Type    Description  
sphere vector vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details ATOMSthe group of atoms that you would like to investigate=1-400 CENTERthe atom whose vicinity we are interested in examining=center RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52}
# Calculate the local average
lccThe LOCAL_AVERAGE action with label lcc calculates the following quantities: Quantity    Type    Description  
lcc vector the values of the local averages: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=cc SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKthe label for a vector that is used to determine which rows of the matrix are computed=sphere
# PLUMED interprets the command:
# lcc: LOCAL_AVERAGE SPECIES=cc SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASK=sphere
# as follows (Click the red comment above to revert to the short version of the input):
lcc_grpThe GROUP action with label lcc_grp calculates the following quantities: Quantity    Type    Description  
lcc_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 details ATOMSthe numerical indexes for the set of atoms in the group=cc
lcc_matThe CONTACT_MATRIX action with label lcc_mat calculates the following quantities: Quantity    Type    Description  
lcc_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=cc SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
lcc_onesThe CONSTANT action with label lcc_ones calculates the following quantities: Quantity    Type    Description  
lcc_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=400
lcc_coordThe MATRIX_VECTOR_PRODUCT action with label lcc_coord calculates the following quantities: Quantity    Type    Description  
lcc_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=lcc_mat,lcc_ones
lcc_prodThe MATRIX_VECTOR_PRODUCT action with label lcc_prod calculates the following quantities: Quantity    Type    Description  
lcc_prod 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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=lcc_mat,cc
lccThe CUSTOM action with label lcc calculates the following quantities: Quantity    Type    Description  
lcc 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 details ARGthe values input to this function=lcc_prod,cc,lcc_coord FUNCthe function you wish to evaluate=(x+y)/(1+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- # Multiply local averages parameters numbers by sphere vector
prodThe CUSTOM action with label prod calculates the following quantities: Quantity    Type    Description  
prod 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 details ARGthe values input to this function=lcc,sphere FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Sum of coordination numbers for atoms that are in the sphere of interest
numerThe SUM action with label numer calculates the following quantities: Quantity    Type    Description  
numer scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=prod PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Number of atoms that are in sphere of interest
denomThe SUM action with label denom calculates the following quantities: Quantity    Type    Description  
denom scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=sphere PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Average coordination number for atoms in sphere of interest
avThe CUSTOM action with label av calculates the following quantities: Quantity    Type    Description  
av scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=numer,denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And print out final CV to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=av FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

This input calculates the average value of the local average for those atoms that are within a spherical region that is centered on the point $(2.5,2.5,2.5)$ . By including the MASK keyword in the LOCAL_AVERAGE line we reduce the number of local averages that are computed. These quantities are only calculated for those atoms that are within the spherical region of interest. However, we are still asking PLUMED to calculate the coordination numbers for many atoms that will not contribute to the final averaged quantity in the COORDINATIONNUMBER commmand with label cc. If you use an input like the one shown below you can ensure that only those coordiantion numbers that compute to the final average are computed.

Click on the labels of the actions for more information on what each action computes

# Fixed virtual atom which serves as the probe volume's center (pos. in nm)
centerThe FIXEDATOM action with label center calculates the following quantities: Quantity    Type    Description  
center atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.5,2.5,2.5
center: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.5,2.5,2.5  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
# Vector in which element i is one if atom i is in sphere of interest and zero otherwise
sphereThe INSPHERE action with label sphere calculates the following quantities: Quantity    Type    Description  
sphere vector vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details ATOMSthe group of atoms that you would like to investigate=1-400 CENTERthe atom whose vicinity we are interested in examining=center RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52}
onesThe ONES action with label ones calculates the following quantities: Quantity    Type    Description  
ones vector a vector of ones with the required number of elements: ONESCreate a constant vector with all elements equal to one This action is a shortcut. More details SIZEthe number of ones that you would like to create=400
# PLUMED interprets the command:
# ones: ONES SIZE=400
# as follows (Click the red comment above to revert to the short version of the input):
onesThe CONSTANT action with label ones calculates the following quantities: Quantity    Type    Description  
ones vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details NOLOG do not report all the read in scalars in the log VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
# --- End of included input --- # Calculate a elements of adjacency matrix for those elements that are inside the sphere
vol_cmapThe CONTACT_MATRIX action with label vol_cmap calculates the following quantities: Quantity    Type    Description  
vol_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-400 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
# Create a matrix that for the sphere stuff
sphere_matThe OUTER_PRODUCT action with label sphere_mat calculates the following quantities: Quantity    Type    Description  
sphere_mat 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 This action has hidden defaults. More details ARGthe labels of the two vectors from which the outer product is being computed=sphere,ones MASKa matrix that is used to used to determine which elements of the output matrix to compute=vol_cmap
sphere_mat: OUTER_PRODUCTCalculate the outer product matrix of two vectors This action uses the defaults shown here. More details ARGthe labels of the two vectors from which the outer product is being computed=sphere,ones MASKa matrix that is used to used to determine which elements of the output matrix to compute=vol_cmap  FUNC the function of the input vectors that should be put in the elements of the outer product=x*y
# Multiply this contact matrix by the map
bonds_matThe CUSTOM action with label bonds_mat calculates the following quantities: Quantity    Type    Description  
bonds_mat 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 details ARGthe values input to this function=vol_cmap,sphere_mat FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Transpose the above matrix
bonds_matTThe TRANSPOSE action with label bonds_matT calculates the following quantities: Quantity    Type    Description  
bonds_matT matrix the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=bonds_mat
# And multiply by the volume
bondsThe MATRIX_VECTOR_PRODUCT action with label bonds calculates the following quantities: Quantity    Type    Description  
bonds 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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=bonds_matT,sphere
#  And make sure we calculate the coordination numbers for the atoms in the volume too
maskThe CUSTOM action with label mask calculates the following quantities: Quantity    Type    Description  
mask 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 details ARGthe values input to this function=bonds,sphere FUNCthe function you wish to evaluate=x+y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Calculate the coordination number for all the atoms
ccThe COORDINATIONNUMBER action with label cc calculates the following quantities: Quantity    Type    Description  
cc vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-400 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKthe label for a vector that is used to determine which rows of the matrix are computed=mask
# PLUMED interprets the command:
# cc: COORDINATIONNUMBER SPECIES=1-400 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASK=mask
# as follows (Click the red comment above to revert to the short version of the input):
cc_grpThe GROUP action with label cc_grp calculates the following quantities: Quantity    Type    Description  
cc_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 details ATOMSthe numerical indexes for the set of atoms in the group=1-400
cc_matThe CONTACT_MATRIX action with label cc_mat calculates the following quantities: Quantity    Type    Description  
cc_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-400 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=mask
cc_onesThe CONSTANT action with label cc_ones calculates the following quantities: Quantity    Type    Description  
cc_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=400
ccThe MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities: Quantity    Type    Description  
cc 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 details  ARGthe label for the matrix and the vector/scalar that are being multiplied=cc_mat,cc_ones
# --- End of included input --- # Calculate the local average
lccThe LOCAL_AVERAGE action with label lcc calculates the following quantities: Quantity    Type    Description  
lcc vector the values of the local averages: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=cc SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKthe label for a vector that is used to determine which rows of the matrix are computed=sphere
# PLUMED interprets the command:
# lcc: LOCAL_AVERAGE SPECIES=cc SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASK=sphere
# as follows (Click the red comment above to revert to the short version of the input):
lcc_grpThe GROUP action with label lcc_grp calculates the following quantities: Quantity    Type    Description  
lcc_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 details ATOMSthe numerical indexes for the set of atoms in the group=cc
lcc_matThe CONTACT_MATRIX action with label lcc_mat calculates the following quantities: Quantity    Type    Description  
lcc_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 details GROUPspecifies the list of atoms that should be assumed indistinguishable=cc SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
lcc_onesThe CONSTANT action with label lcc_ones calculates the following quantities: Quantity    Type    Description  
lcc_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=400
lcc_coordThe MATRIX_VECTOR_PRODUCT action with label lcc_coord calculates the following quantities: Quantity    Type    Description  
lcc_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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=lcc_mat,lcc_ones
lcc_prodThe MATRIX_VECTOR_PRODUCT action with label lcc_prod calculates the following quantities: Quantity    Type    Description  
lcc_prod 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 details ARGthe label for the matrix and the vector/scalar that are being multiplied=lcc_mat,cc
lccThe CUSTOM action with label lcc calculates the following quantities: Quantity    Type    Description  
lcc 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 details ARGthe values input to this function=lcc_prod,cc,lcc_coord FUNCthe function you wish to evaluate=(x+y)/(1+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- # Multiply local averages parameters numbers by sphere vector
prodThe CUSTOM action with label prod calculates the following quantities: Quantity    Type    Description  
prod 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 details ARGthe values input to this function=lcc,sphere FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Sum of coordination numbers for atoms that are in the sphere of interest
numerThe SUM action with label numer calculates the following quantities: Quantity    Type    Description  
numer scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=prod PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Number of atoms that are in sphere of interest
denomThe SUM action with label denom calculates the following quantities: Quantity    Type    Description  
denom scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=sphere PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Average coordination number for atoms in sphere of interest
avThe CUSTOM action with label av calculates the following quantities: Quantity    Type    Description  
av scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=numer,denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And print out final CV to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=av FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1

In the above input the only elements of the CONTACT_MATRIX with label vol_cmap that are non-zero are those that are bonded to one of the atoms in the sphere of interest. By transposing this matrix and multiplying by a vector of ones we thus get a vector with a length equal to total number of coordination numbers in the system. The only elements in this vector that are non-zero are those that are bonded to atoms that are within the sphere of interest. Consequently, if we add the vector sphere to this we can a vector in which element $i$ is only non-zero if we have to calculate that coordination number to evaluate the final quantity of interest.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
SPECIES	atoms	the list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments
SPECIESA	atoms	the list of atoms for which the symmetry function is being calculated
SPECIESB	atoms	the list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
lessthan	scalar	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	scalar	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	scalar	ALT_MIN	the minimum value of the cv
min	scalar	MIN	the minimum colvar
max	scalar	MAX	the maximum colvar
between	scalar	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	scalar	HIGHEST	the largest of the colvars
lowest	scalar	LOWEST	the smallest of the colvars
sum	scalar	SUM	the sum of the colvars
mean	scalar	MEAN	the mean of the colvars

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
SPECIES	input	none	the list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments
SPECIESA	input	none	the list of atoms for which the symmetry function is being calculated
SPECIESB	input	none	the list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated
NN	compulsory	6	The n parameter of the switching function
MM	compulsory	0	The m parameter of the switching function; 0 implies 2*NN
D_0	compulsory	0.0	The d_0 parameter of the switching function
R_0	compulsory	none	The r_0 parameter of the switching function
SWITCH	optional	not used	the switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.
MASK	optional	not used	the label for a vector that is used to determine which rows of the matrix are computed
USEGPUThis keyword do not have examples	optional	false	run part of this calculation on the GPU

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
LESS_THAN	calculate the number of variables that are less than a certain target value
MORE_THAN	calculate the number of variables that are more than a certain target value
ALT_MIN	calculate the minimum value
MIN	calculate the minimum value
MAX	calculate the maximum value
BETWEEN	calculate the number of values that are within a certain range
HIGHEST	this flag allows you to recover the highest of these variables
HISTOGRAM	calculate a discretized histogram of the distribution of values
LOWEST	this flag allows you to recover the lowest of these variables
SUM	calculate the sum of all the quantities
MEAN	calculate the mean of all the quantities

References

More information about how this action can be used is available in the following articles:

W. Lechner, C. Dellago, Accurate determination of crystal structures based on averaged local bond order parameters. The Journal of Chemical Physics 129 (2008)