Shortcut: FCCUBIC_FUNC

Module	symfunc
Description	Usage
Measure how similar the environment around atoms is to that found in a FCC structure.
output value	type
a function that measures the similarity with an fcc environment	matrix

Details and examples

Measure how similar the environment around atoms is to that found in a FCC structure.

This is the function that is used in the FCCUBIC shortcut. You can see an example that shows how it is used if you expand the FCCUBIC shortcut in the following example input:

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

dThe FCCUBIC action with label d calculates the following quantities: Quantity    Type    Description  
d vector the symmetry function for each of the specified atoms
d_mean scalar the mean of the colvars: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut and it has hidden defaults. 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=3.0 R_0=1.5} MEAN calculate the mean of all the quantities
d: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut and uses the defaults shown here. 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=3.0 R_0=1.5} MEAN calculate the mean of all the quantities  PHI The Euler rotational angle phi=0.0 THETA The Euler rotational angle theta=0.0 PSI The Euler rotational angle psi=0.0 ALPHA The alpha parameter of the angular function that is used for FCCUBIC=3.0
# PLUMED interprets the command:
# d: FCCUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN
# as follows (Click the red comment above to revert to the short version of the input):
d_grpThe GROUP action with label d_grp calculates the following quantities: Quantity    Type    Description  
d_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
d_matThe CONTACT_MATRIX action with label d_mat calculates the following quantities: Quantity    Type    Description  
d_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
d_mat.x matrix the projection of the bond on the x axis
d_mat.y matrix the projection of the bond on the y axis
d_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=3.0 R_0=1.5} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
d_vfuncThe FCCUBIC_FUNC action with label d_vfunc calculates the following quantities: Quantity    Type    Description  
d_vfunc matrix the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=d_mat.x,d_mat.y,d_mat.z ALPHA The alpha parameter of the angular function=3.0
d_wvfuncThe CUSTOM action with label d_wvfunc calculates the following quantities: Quantity    Type    Description  
d_wvfunc 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=d_vfunc,d_mat.w 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
d_onesThe CONSTANT action with label d_ones calculates the following quantities: Quantity    Type    Description  
d_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
dThe MATRIX_VECTOR_PRODUCT action with label d calculates the following quantities: Quantity    Type    Description  
d 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=d_wvfunc,d_ones
d_denomThe MATRIX_VECTOR_PRODUCT action with label d_denom calculates the following quantities: Quantity    Type    Description  
d_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=d_mat.w,d_ones
d_nThe CUSTOM action with label d_n calculates the following quantities: Quantity    Type    Description  
d_n 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=d,d_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
d_meanThe MEAN action with label d_mean calculates the following quantities: Quantity    Type    Description  
d_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=d_n PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d.* FILEthe name of the file on which to output these quantities=colv

Notice that the decomposition of the function that is illustrated above allows you to do things like the calculation in the following input:

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

# Calculate the distances between atoms
d_matThe DISTANCE_MATRIX action with label d_mat calculates the following quantities: Quantity    Type    Description  
d_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
d_mat.x matrix the projection of the bond on the x axis
d_mat.y matrix the projection of the bond on the y axis
d_mat.z matrix the projection of the bond on the z axis: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action has hidden defaults. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-64 CUTOFF ignore distances that have a value larger than this cutoff=4.5 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
d_mat: DISTANCE_MATRIXCalculate a matrix of distances between atoms. This action uses the defaults shown here. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-64 CUTOFF ignore distances that have a value larger than this cutoff=4.5 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix  NL_CUTOFF The cutoff for the neighbor list=0.0 NL_STRIDE The frequency with which we are updating the atoms in the neighbor list=1
# Find the six nearest atom to each of the coordinates
nnThe NEIGHBORS action with label nn calculates the following quantities: Quantity    Type    Description  
nn matrix a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action has hidden defaults. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=d_mat.w NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=6
nn: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom This action uses the defaults shown here. More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=d_mat.w NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=6  NHIGHEST in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one=0
# Evalulate the FCC function
d_vfuncThe FCCUBIC_FUNC action with label d_vfunc calculates the following quantities: Quantity    Type    Description  
d_vfunc matrix the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=d_mat.x,d_mat.y,d_mat.z MASKthe label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed=nn ALPHA The alpha parameter of the angular function=3.0
# Take the product of the weights with the fcc function evaluations
d_wvfuncThe CUSTOM action with label d_wvfunc calculates the following quantities: Quantity    Type    Description  
d_wvfunc 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=d_vfunc,nn 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 sum of fcc cubic function values for each atom
d_onesThe ONES action with label d_ones calculates the following quantities: Quantity    Type    Description  
d_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=64
# PLUMED interprets the command:
# d_ones: ONES SIZE=64
# as follows (Click the red comment above to revert to the short version of the input):
d_onesThe CONSTANT action with label d_ones calculates the following quantities: Quantity    Type    Description  
d_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
# --- End of included input --- dThe MATRIX_VECTOR_PRODUCT action with label d calculates the following quantities: Quantity    Type    Description  
d 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=d_wvfunc,d_ones
# Calculate the number of neighbours
d_denomThe MATRIX_VECTOR_PRODUCT action with label d_denom calculates the following quantities: Quantity    Type    Description  
d_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=nn,d_ones
# Calculate the average value of the fcc cubic function per bonds
d_nThe CUSTOM action with label d_n calculates the following quantities: Quantity    Type    Description  
d_n 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=d,d_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
d_meanThe MEAN action with label d_mean calculates the following quantities: Quantity    Type    Description  
d_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=d_n 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=d_mean FILEthe name of the file on which to output these quantities=colv

In this input we evaluate the FCCUBIC function for the six nearest neighbours to each atom rather than the atoms that are within a certain cutoff. By using the MASK keyword in the input to FCCUBIC_FUNC we ensure that the FCCUBIC function is only evaluated for the six nearest neighbors.

Input

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

Keyword	Type	Description
ARG	scalar/vector/matrix	the values input to this function
MASK	vector/matrix	the label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed

Full list of keywords

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

Keyword	Type	Default	Description
ARG	input	none	the values input to this function
MASK	input	none	the label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed
ALPHA	compulsory	3.0	The alpha parameter of the angular function

Quantity	Type	Description
d	vector	the symmetry function for each of the specified atoms
d_mean	scalar	the mean of the colvars