Shortcut: LOCAL_CRYSTALINITY

Module	symfunc
Description	Usage
Calculate the local crystalinity symmetry function
output value	type
the value of the local crystalinity for each of the input atoms	vector

Details and examples

Calculate the local crystalinity symmetry function

This shortcut provides an implementation of the local crystalinity order parameter that is described in the paper in the bibliography. To use this CV you define a series of unit vectors, $g_k$ , using multiple instances of the GVECTOR keyword. This allows you to define a symmetry function for the $i$ th atom as:

$s_i = \sum_k \left| \frac{\sum_j \sigma(|r_{ij}|) e^{ig_k r_{ij}}}{\sum_j \sigma(|r_{ij}|)} \right|^2$

In this expression $r_{ij}$ is the vector connecting atom $i$ to atom $j$ and $\sigma$ is a switching function that acts upon the magnidue of this vector, $|r_{ij}|$ . The following input is an example that shows how this symmetry function can be used in practice.

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

lcThe LOCAL_CRYSTALINITY action with label lc calculates the following quantities: Quantity    Type    Description  
lc vector the value of the local crystalinity for each of the input atoms
lc_sum scalar the sum of the colvars: LOCAL_CRYSTALINITYCalculate the local crystalinity symmetry function 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 D_0 The d_0 parameter of the switching function=3.0 R_0The r_0 parameter of the switching function=1.5
   GVECTOR1the coefficients of the linear combinations to compute for the CV=1,1,1 GVECTOR2the coefficients of the linear combinations to compute for the CV=1,0.5,0.5 GVECTOR3the coefficients of the linear combinations to compute for the CV=0.5,1.0,1.0 SUM calculate the sum of all the quantities
...
lc: LOCAL_CRYSTALINITYCalculate the local crystalinity symmetry function 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 D_0 The d_0 parameter of the switching function=3.0 R_0The r_0 parameter of the switching function=1.5
   GVECTOR1the coefficients of the linear combinations to compute for the CV=1,1,1 GVECTOR2the coefficients of the linear combinations to compute for the CV=1,0.5,0.5 GVECTOR3the coefficients of the linear combinations to compute for the CV=0.5,1.0,1.0 SUM calculate the sum of all the quantities
 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
...
# PLUMED interprets the command:
# lc: LOCAL_CRYSTALINITY ...
#    SPECIES=1-64 D_0=3.0 R_0=1.5
#    GVECTOR1=1,1,1 GVECTOR2=1,0.5,0.5 GVECTOR3=0.5,1.0,1.0 SUM
# ...
# as follows (Click the red comment above to revert to the short version of the input):
lc_grpThe GROUP action with label lc_grp calculates the following quantities: Quantity    Type    Description  
lc_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
lc_matThe CONTACT_MATRIX action with label lc_mat calculates the following quantities: Quantity    Type    Description  
lc_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
lc_mat.x matrix the projection of the bond on the x axis
lc_mat.y matrix the projection of the bond on the y axis
lc_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 R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=3.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
lc_onesThe CONSTANT action with label lc_ones calculates the following quantities: Quantity    Type    Description  
lc_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
lc_denomThe MATRIX_VECTOR_PRODUCT action with label lc_denom calculates the following quantities: Quantity    Type    Description  
lc_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=lc_mat.w,lc_ones
lc_dot1The COMBINE action with label lc_dot1 calculates the following quantities: Quantity    Type    Description  
lc_dot1 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,1,1
lc_cos1The CUSTOM action with label lc_cos1 calculates the following quantities: Quantity    Type    Description  
lc_cos1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin1The CUSTOM action with label lc_sin1 calculates the following quantities: Quantity    Type    Description  
lc_sin1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum1The MATRIX_VECTOR_PRODUCT action with label lc_cossum1 calculates the following quantities: Quantity    Type    Description  
lc_cossum1 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=lc_cos1,lc_ones
lc_sinsum1The MATRIX_VECTOR_PRODUCT action with label lc_sinsum1 calculates the following quantities: Quantity    Type    Description  
lc_sinsum1 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=lc_sin1,lc_ones
lc_cosmean1The CUSTOM action with label lc_cosmean1 calculates the following quantities: Quantity    Type    Description  
lc_cosmean1 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 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 ARGthe values input to this function=lc_cossum1,lc_denom
lc_sinmean1The CUSTOM action with label lc_sinmean1 calculates the following quantities: Quantity    Type    Description  
lc_sinmean1 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 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 ARGthe values input to this function=lc_sinsum1,lc_denom
lc_1The CUSTOM action with label lc_1 calculates the following quantities: Quantity    Type    Description  
lc_1 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean1,lc_sinmean1
lc_dot2The COMBINE action with label lc_dot2 calculates the following quantities: Quantity    Type    Description  
lc_dot2 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,0.5,0.5
lc_cos2The CUSTOM action with label lc_cos2 calculates the following quantities: Quantity    Type    Description  
lc_cos2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin2The CUSTOM action with label lc_sin2 calculates the following quantities: Quantity    Type    Description  
lc_sin2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum2The MATRIX_VECTOR_PRODUCT action with label lc_cossum2 calculates the following quantities: Quantity    Type    Description  
lc_cossum2 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=lc_cos2,lc_ones
lc_sinsum2The MATRIX_VECTOR_PRODUCT action with label lc_sinsum2 calculates the following quantities: Quantity    Type    Description  
lc_sinsum2 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=lc_sin2,lc_ones
lc_cosmean2The CUSTOM action with label lc_cosmean2 calculates the following quantities: Quantity    Type    Description  
lc_cosmean2 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 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 ARGthe values input to this function=lc_cossum2,lc_denom
lc_sinmean2The CUSTOM action with label lc_sinmean2 calculates the following quantities: Quantity    Type    Description  
lc_sinmean2 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 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 ARGthe values input to this function=lc_sinsum2,lc_denom
lc_2The CUSTOM action with label lc_2 calculates the following quantities: Quantity    Type    Description  
lc_2 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean2,lc_sinmean2
lc_dot3The COMBINE action with label lc_dot3 calculates the following quantities: Quantity    Type    Description  
lc_dot3 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=0.5,1.0,1.0
lc_cos3The CUSTOM action with label lc_cos3 calculates the following quantities: Quantity    Type    Description  
lc_cos3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin3The CUSTOM action with label lc_sin3 calculates the following quantities: Quantity    Type    Description  
lc_sin3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum3The MATRIX_VECTOR_PRODUCT action with label lc_cossum3 calculates the following quantities: Quantity    Type    Description  
lc_cossum3 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=lc_cos3,lc_ones
lc_sinsum3The MATRIX_VECTOR_PRODUCT action with label lc_sinsum3 calculates the following quantities: Quantity    Type    Description  
lc_sinsum3 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=lc_sin3,lc_ones
lc_cosmean3The CUSTOM action with label lc_cosmean3 calculates the following quantities: Quantity    Type    Description  
lc_cosmean3 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 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 ARGthe values input to this function=lc_cossum3,lc_denom
lc_sinmean3The CUSTOM action with label lc_sinmean3 calculates the following quantities: Quantity    Type    Description  
lc_sinmean3 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 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 ARGthe values input to this function=lc_sinsum3,lc_denom
lc_3The CUSTOM action with label lc_3 calculates the following quantities: Quantity    Type    Description  
lc_3 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean3,lc_sinmean3
lcThe COMBINE action with label lc calculates the following quantities: Quantity    Type    Description  
lc 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 NORMALIZE normalize all the coefficients so that in total they are equal to one PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_1,lc_2,lc_3
lc_sumThe SUM action with label lc_sum calculates the following quantities: Quantity    Type    Description  
lc_sum 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=lc 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=lc_sum FILEthe name of the file on which to output these quantities=colvar

As you can see if you expand the shortcut in this input, the sum over $k$ in the above expression has three terms in this input as 3 GVECTORS are specified. Sixty four values for the expression above are computed. These sixty four numbers are then added together in order to give a global mesuare of the crystallinity for the simulated system.

In the input above $\sigma(|r_{ij}|)$ is 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

lcThe LOCAL_CRYSTALINITY action with label lc calculates the following quantities: Quantity    Type    Description  
lc vector the value of the local crystalinity for each of the input atoms
lc_sum scalar the sum of the colvars: LOCAL_CRYSTALINITYCalculate the local crystalinity symmetry function 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=3.0 R_0=1.5 D_MAX=3.0}
   GVECTOR1the coefficients of the linear combinations to compute for the CV=1,1,1 GVECTOR2the coefficients of the linear combinations to compute for the CV=1,0.5,0.5 GVECTOR3the coefficients of the linear combinations to compute for the CV=0.5,1.0,1.0 SUM calculate the sum of all the quantities
...
# PLUMED interprets the command:
# lc: LOCAL_CRYSTALINITY ...
#    SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5 D_MAX=3.0}
#    GVECTOR1=1,1,1 GVECTOR2=1,0.5,0.5 GVECTOR3=0.5,1.0,1.0 SUM
# ...
# as follows (Click the red comment above to revert to the short version of the input):
lc_grpThe GROUP action with label lc_grp calculates the following quantities: Quantity    Type    Description  
lc_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
lc_matThe CONTACT_MATRIX action with label lc_mat calculates the following quantities: Quantity    Type    Description  
lc_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
lc_mat.x matrix the projection of the bond on the x axis
lc_mat.y matrix the projection of the bond on the y axis
lc_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 D_MAX=3.0} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
lc_onesThe CONSTANT action with label lc_ones calculates the following quantities: Quantity    Type    Description  
lc_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
lc_denomThe MATRIX_VECTOR_PRODUCT action with label lc_denom calculates the following quantities: Quantity    Type    Description  
lc_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=lc_mat.w,lc_ones
lc_dot1The COMBINE action with label lc_dot1 calculates the following quantities: Quantity    Type    Description  
lc_dot1 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,1,1
lc_cos1The CUSTOM action with label lc_cos1 calculates the following quantities: Quantity    Type    Description  
lc_cos1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin1The CUSTOM action with label lc_sin1 calculates the following quantities: Quantity    Type    Description  
lc_sin1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum1The MATRIX_VECTOR_PRODUCT action with label lc_cossum1 calculates the following quantities: Quantity    Type    Description  
lc_cossum1 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=lc_cos1,lc_ones
lc_sinsum1The MATRIX_VECTOR_PRODUCT action with label lc_sinsum1 calculates the following quantities: Quantity    Type    Description  
lc_sinsum1 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=lc_sin1,lc_ones
lc_cosmean1The CUSTOM action with label lc_cosmean1 calculates the following quantities: Quantity    Type    Description  
lc_cosmean1 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 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 ARGthe values input to this function=lc_cossum1,lc_denom
lc_sinmean1The CUSTOM action with label lc_sinmean1 calculates the following quantities: Quantity    Type    Description  
lc_sinmean1 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 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 ARGthe values input to this function=lc_sinsum1,lc_denom
lc_1The CUSTOM action with label lc_1 calculates the following quantities: Quantity    Type    Description  
lc_1 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean1,lc_sinmean1
lc_dot2The COMBINE action with label lc_dot2 calculates the following quantities: Quantity    Type    Description  
lc_dot2 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,0.5,0.5
lc_cos2The CUSTOM action with label lc_cos2 calculates the following quantities: Quantity    Type    Description  
lc_cos2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin2The CUSTOM action with label lc_sin2 calculates the following quantities: Quantity    Type    Description  
lc_sin2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum2The MATRIX_VECTOR_PRODUCT action with label lc_cossum2 calculates the following quantities: Quantity    Type    Description  
lc_cossum2 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=lc_cos2,lc_ones
lc_sinsum2The MATRIX_VECTOR_PRODUCT action with label lc_sinsum2 calculates the following quantities: Quantity    Type    Description  
lc_sinsum2 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=lc_sin2,lc_ones
lc_cosmean2The CUSTOM action with label lc_cosmean2 calculates the following quantities: Quantity    Type    Description  
lc_cosmean2 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 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 ARGthe values input to this function=lc_cossum2,lc_denom
lc_sinmean2The CUSTOM action with label lc_sinmean2 calculates the following quantities: Quantity    Type    Description  
lc_sinmean2 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 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 ARGthe values input to this function=lc_sinsum2,lc_denom
lc_2The CUSTOM action with label lc_2 calculates the following quantities: Quantity    Type    Description  
lc_2 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean2,lc_sinmean2
lc_dot3The COMBINE action with label lc_dot3 calculates the following quantities: Quantity    Type    Description  
lc_dot3 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=0.5,1.0,1.0
lc_cos3The CUSTOM action with label lc_cos3 calculates the following quantities: Quantity    Type    Description  
lc_cos3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin3The CUSTOM action with label lc_sin3 calculates the following quantities: Quantity    Type    Description  
lc_sin3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum3The MATRIX_VECTOR_PRODUCT action with label lc_cossum3 calculates the following quantities: Quantity    Type    Description  
lc_cossum3 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=lc_cos3,lc_ones
lc_sinsum3The MATRIX_VECTOR_PRODUCT action with label lc_sinsum3 calculates the following quantities: Quantity    Type    Description  
lc_sinsum3 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=lc_sin3,lc_ones
lc_cosmean3The CUSTOM action with label lc_cosmean3 calculates the following quantities: Quantity    Type    Description  
lc_cosmean3 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 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 ARGthe values input to this function=lc_cossum3,lc_denom
lc_sinmean3The CUSTOM action with label lc_sinmean3 calculates the following quantities: Quantity    Type    Description  
lc_sinmean3 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 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 ARGthe values input to this function=lc_sinsum3,lc_denom
lc_3The CUSTOM action with label lc_3 calculates the following quantities: Quantity    Type    Description  
lc_3 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean3,lc_sinmean3
lcThe COMBINE action with label lc calculates the following quantities: Quantity    Type    Description  
lc 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 NORMALIZE normalize all the coefficients so that in total they are equal to one PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_1,lc_2,lc_3
lc_sumThe SUM action with label lc_sum calculates the following quantities: Quantity    Type    Description  
lc_sum 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=lc 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=lc_sum FILEthe name of the file on which to output these quantities=colvar

Working with two types of atom

If you would like to calculate the function above for the bonds connecting the atoms in GROUPA to the atoms in GROUPB you can use an input like the one shown below:

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

lcThe LOCAL_CRYSTALINITY action with label lc calculates the following quantities: Quantity    Type    Description  
lc vector the value of the local crystalinity for each of the input atoms
lc_sum scalar the sum of the colvars: LOCAL_CRYSTALINITYCalculate the local crystalinity symmetry function This action is a shortcut. More details ...
   SPECIESAthe list of atoms for which the symmetry function is being calculated=1-5 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=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 D_MAX=3.0}
   GVECTOR1the coefficients of the linear combinations to compute for the CV=1,1,1 GVECTOR2the coefficients of the linear combinations to compute for the CV=1,0.5,0.5 GVECTOR3the coefficients of the linear combinations to compute for the CV=0.5,1.0,1.0 SUM calculate the sum of all the quantities
...
# PLUMED interprets the command:
# lc: LOCAL_CRYSTALINITY ...
#    SPECIESA=1-5 SPECIESB=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5 D_MAX=3.0}
#    GVECTOR1=1,1,1 GVECTOR2=1,0.5,0.5 GVECTOR3=0.5,1.0,1.0 SUM
# ...
# as follows (Click the red comment above to revert to the short version of the input):
lc_grpThe GROUP action with label lc_grp calculates the following quantities: Quantity    Type    Description  
lc_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
lc_matThe CONTACT_MATRIX action with label lc_mat calculates the following quantities: Quantity    Type    Description  
lc_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
lc_mat.x matrix the projection of the bond on the x axis
lc_mat.y matrix the projection of the bond on the y axis
lc_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 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=1-5 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=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 D_MAX=3.0} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
lc_onesThe CONSTANT action with label lc_ones calculates the following quantities: Quantity    Type    Description  
lc_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
lc_denomThe MATRIX_VECTOR_PRODUCT action with label lc_denom calculates the following quantities: Quantity    Type    Description  
lc_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=lc_mat.w,lc_ones
lc_dot1The COMBINE action with label lc_dot1 calculates the following quantities: Quantity    Type    Description  
lc_dot1 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,1,1
lc_cos1The CUSTOM action with label lc_cos1 calculates the following quantities: Quantity    Type    Description  
lc_cos1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin1The CUSTOM action with label lc_sin1 calculates the following quantities: Quantity    Type    Description  
lc_sin1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum1The MATRIX_VECTOR_PRODUCT action with label lc_cossum1 calculates the following quantities: Quantity    Type    Description  
lc_cossum1 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=lc_cos1,lc_ones
lc_sinsum1The MATRIX_VECTOR_PRODUCT action with label lc_sinsum1 calculates the following quantities: Quantity    Type    Description  
lc_sinsum1 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=lc_sin1,lc_ones
lc_cosmean1The CUSTOM action with label lc_cosmean1 calculates the following quantities: Quantity    Type    Description  
lc_cosmean1 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 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 ARGthe values input to this function=lc_cossum1,lc_denom
lc_sinmean1The CUSTOM action with label lc_sinmean1 calculates the following quantities: Quantity    Type    Description  
lc_sinmean1 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 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 ARGthe values input to this function=lc_sinsum1,lc_denom
lc_1The CUSTOM action with label lc_1 calculates the following quantities: Quantity    Type    Description  
lc_1 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean1,lc_sinmean1
lc_dot2The COMBINE action with label lc_dot2 calculates the following quantities: Quantity    Type    Description  
lc_dot2 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,0.5,0.5
lc_cos2The CUSTOM action with label lc_cos2 calculates the following quantities: Quantity    Type    Description  
lc_cos2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin2The CUSTOM action with label lc_sin2 calculates the following quantities: Quantity    Type    Description  
lc_sin2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum2The MATRIX_VECTOR_PRODUCT action with label lc_cossum2 calculates the following quantities: Quantity    Type    Description  
lc_cossum2 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=lc_cos2,lc_ones
lc_sinsum2The MATRIX_VECTOR_PRODUCT action with label lc_sinsum2 calculates the following quantities: Quantity    Type    Description  
lc_sinsum2 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=lc_sin2,lc_ones
lc_cosmean2The CUSTOM action with label lc_cosmean2 calculates the following quantities: Quantity    Type    Description  
lc_cosmean2 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 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 ARGthe values input to this function=lc_cossum2,lc_denom
lc_sinmean2The CUSTOM action with label lc_sinmean2 calculates the following quantities: Quantity    Type    Description  
lc_sinmean2 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 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 ARGthe values input to this function=lc_sinsum2,lc_denom
lc_2The CUSTOM action with label lc_2 calculates the following quantities: Quantity    Type    Description  
lc_2 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean2,lc_sinmean2
lc_dot3The COMBINE action with label lc_dot3 calculates the following quantities: Quantity    Type    Description  
lc_dot3 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=0.5,1.0,1.0
lc_cos3The CUSTOM action with label lc_cos3 calculates the following quantities: Quantity    Type    Description  
lc_cos3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin3The CUSTOM action with label lc_sin3 calculates the following quantities: Quantity    Type    Description  
lc_sin3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum3The MATRIX_VECTOR_PRODUCT action with label lc_cossum3 calculates the following quantities: Quantity    Type    Description  
lc_cossum3 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=lc_cos3,lc_ones
lc_sinsum3The MATRIX_VECTOR_PRODUCT action with label lc_sinsum3 calculates the following quantities: Quantity    Type    Description  
lc_sinsum3 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=lc_sin3,lc_ones
lc_cosmean3The CUSTOM action with label lc_cosmean3 calculates the following quantities: Quantity    Type    Description  
lc_cosmean3 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 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 ARGthe values input to this function=lc_cossum3,lc_denom
lc_sinmean3The CUSTOM action with label lc_sinmean3 calculates the following quantities: Quantity    Type    Description  
lc_sinmean3 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 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 ARGthe values input to this function=lc_sinsum3,lc_denom
lc_3The CUSTOM action with label lc_3 calculates the following quantities: Quantity    Type    Description  
lc_3 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean3,lc_sinmean3
lcThe COMBINE action with label lc calculates the following quantities: Quantity    Type    Description  
lc 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 NORMALIZE normalize all the coefficients so that in total they are equal to one PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_1,lc_2,lc_3
lc_sumThe SUM action with label lc_sum calculates the following quantities: Quantity    Type    Description  
lc_sum 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=lc 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=lc_sum FILEthe name of the file on which to output these quantities=colvar

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 TETRAHEDRAL parameter 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

# 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=1-64 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 crystallinity parameters
lcThe LOCAL_CRYSTALINITY action with label lc calculates the following quantities: Quantity    Type    Description  
lc vector the value of the local crystalinity for each of the input atoms: LOCAL_CRYSTALINITYCalculate the local crystalinity symmetry function 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=3.0 R_0=1.5 D_MAX=3.0}
   GVECTOR1the coefficients of the linear combinations to compute for the CV=1,1,1 GVECTOR2the coefficients of the linear combinations to compute for the CV=1,0.5,0.5 GVECTOR3the coefficients of the linear combinations to compute for the CV=0.5,1.0,1.0 MASKthe label for a vector that is used to determine which rows of the matrix are computed=sphere
...
# PLUMED interprets the command:
# lc: LOCAL_CRYSTALINITY ...
#    SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5 D_MAX=3.0}
#    GVECTOR1=1,1,1 GVECTOR2=1,0.5,0.5 GVECTOR3=0.5,1.0,1.0 MASK=sphere
# ...
# as follows (Click the red comment above to revert to the short version of the input):
lc_grpThe GROUP action with label lc_grp calculates the following quantities: Quantity    Type    Description  
lc_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
lc_matThe CONTACT_MATRIX action with label lc_mat calculates the following quantities: Quantity    Type    Description  
lc_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
lc_mat.x matrix the projection of the bond on the x axis
lc_mat.y matrix the projection of the bond on the y axis
lc_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 D_MAX=3.0} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
lc_onesThe CONSTANT action with label lc_ones calculates the following quantities: Quantity    Type    Description  
lc_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
lc_denomThe MATRIX_VECTOR_PRODUCT action with label lc_denom calculates the following quantities: Quantity    Type    Description  
lc_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=lc_mat.w,lc_ones
lc_dot1The COMBINE action with label lc_dot1 calculates the following quantities: Quantity    Type    Description  
lc_dot1 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,1,1
lc_cos1The CUSTOM action with label lc_cos1 calculates the following quantities: Quantity    Type    Description  
lc_cos1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin1The CUSTOM action with label lc_sin1 calculates the following quantities: Quantity    Type    Description  
lc_sin1 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=lc_mat.w,lc_dot1 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum1The MATRIX_VECTOR_PRODUCT action with label lc_cossum1 calculates the following quantities: Quantity    Type    Description  
lc_cossum1 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=lc_cos1,lc_ones
lc_sinsum1The MATRIX_VECTOR_PRODUCT action with label lc_sinsum1 calculates the following quantities: Quantity    Type    Description  
lc_sinsum1 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=lc_sin1,lc_ones
lc_cosmean1The CUSTOM action with label lc_cosmean1 calculates the following quantities: Quantity    Type    Description  
lc_cosmean1 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 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 ARGthe values input to this function=lc_cossum1,lc_denom
lc_sinmean1The CUSTOM action with label lc_sinmean1 calculates the following quantities: Quantity    Type    Description  
lc_sinmean1 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 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 ARGthe values input to this function=lc_sinsum1,lc_denom
lc_1The CUSTOM action with label lc_1 calculates the following quantities: Quantity    Type    Description  
lc_1 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean1,lc_sinmean1
lc_dot2The COMBINE action with label lc_dot2 calculates the following quantities: Quantity    Type    Description  
lc_dot2 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=1,0.5,0.5
lc_cos2The CUSTOM action with label lc_cos2 calculates the following quantities: Quantity    Type    Description  
lc_cos2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin2The CUSTOM action with label lc_sin2 calculates the following quantities: Quantity    Type    Description  
lc_sin2 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=lc_mat.w,lc_dot2 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum2The MATRIX_VECTOR_PRODUCT action with label lc_cossum2 calculates the following quantities: Quantity    Type    Description  
lc_cossum2 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=lc_cos2,lc_ones
lc_sinsum2The MATRIX_VECTOR_PRODUCT action with label lc_sinsum2 calculates the following quantities: Quantity    Type    Description  
lc_sinsum2 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=lc_sin2,lc_ones
lc_cosmean2The CUSTOM action with label lc_cosmean2 calculates the following quantities: Quantity    Type    Description  
lc_cosmean2 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 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 ARGthe values input to this function=lc_cossum2,lc_denom
lc_sinmean2The CUSTOM action with label lc_sinmean2 calculates the following quantities: Quantity    Type    Description  
lc_sinmean2 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 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 ARGthe values input to this function=lc_sinsum2,lc_denom
lc_2The CUSTOM action with label lc_2 calculates the following quantities: Quantity    Type    Description  
lc_2 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean2,lc_sinmean2
lc_dot3The COMBINE action with label lc_dot3 calculates the following quantities: Quantity    Type    Description  
lc_dot3 matrix the matrix obtained by doing an element-wise application of a linear combination to the input matrix: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lc_mat.x,lc_mat.y,lc_mat.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COEFFICIENTS the coefficients of the arguments in your function=0.5,1.0,1.0
lc_cos3The CUSTOM action with label lc_cos3 calculates the following quantities: Quantity    Type    Description  
lc_cos3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*cos(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_sin3The CUSTOM action with label lc_sin3 calculates the following quantities: Quantity    Type    Description  
lc_sin3 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=lc_mat.w,lc_dot3 FUNCthe function you wish to evaluate=x*sin(y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lc_cossum3The MATRIX_VECTOR_PRODUCT action with label lc_cossum3 calculates the following quantities: Quantity    Type    Description  
lc_cossum3 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=lc_cos3,lc_ones
lc_sinsum3The MATRIX_VECTOR_PRODUCT action with label lc_sinsum3 calculates the following quantities: Quantity    Type    Description  
lc_sinsum3 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=lc_sin3,lc_ones
lc_cosmean3The CUSTOM action with label lc_cosmean3 calculates the following quantities: Quantity    Type    Description  
lc_cosmean3 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 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 ARGthe values input to this function=lc_cossum3,lc_denom
lc_sinmean3The CUSTOM action with label lc_sinmean3 calculates the following quantities: Quantity    Type    Description  
lc_sinmean3 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 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 ARGthe values input to this function=lc_sinsum3,lc_denom
lc_3The CUSTOM action with label lc_3 calculates the following quantities: Quantity    Type    Description  
lc_3 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 FUNCthe function you wish to evaluate=x*x+y*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_cosmean3,lc_sinmean3
lcThe COMBINE action with label lc calculates the following quantities: Quantity    Type    Description  
lc 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 NORMALIZE normalize all the coefficients so that in total they are equal to one PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lc_1,lc_2,lc_3
# --- End of included input --- # Multiply local crystallinity 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=lc,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 calculate the average local crystallinity parameter for only those atoms that are within a spherical region that is centered on the point $(2.5,2.5,2.5)$ .

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
GVECTOR	optional	not used	the coefficients of the linear combinations to compute for the CV

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:

Quantity	Type	Description
lc	vector	the value of the local crystalinity for each of the input atoms
lc_sum	scalar	the sum of the colvars