Shortcut: XSPRINT

Module	xsprint
Description	Usage
Calculate eXtended SPRINT (xSPRINT) topological variables from adjacency matrices over multiple shells.

Details and examples

Calculate eXtended SPRINT (xSPRINT) topological variables from adjacency matrices over multiple shells.

The xSPRINT coordinates, introduced in \cite ketkaew2022, extend the standard SPRINT coordinates by incorporating structural information from multiple concentric spherical shells around each atom. For a system divided into $N$ shells, the xSPRINT coordinate of atom $i$ is defined as:

$S_i^x = \begin{cases} S_i, & \text{if } r_{ij} < r_0 \\ \frac{1}{\omega} \sum_{n=1}^{N} r_n\, S_i^{(n)}, & \text{otherwise} \end{cases}$

where $S_i^{(n)}$ is the SPRINT coordinate computed from the adjacency matrix of the $n$ -th shell, $r_n = n\,r_0$ is the shell radius, $r_0$ is the user-defined cutoff for the first shell, and $\omega = \left(\sum_{n=1}^{N} r_n\right)^2$ is a normalization weight. Adjacency matrix elements from inner shells are zeroed out before computing each shell's SPRINT to avoid redundancy.

When NSHELLS=1 the xSPRINT coordinate reduces to the standard SPRINT coordinate.

The following example computes the xSPRINT coordinates for a 7-atom cluster using 3 shells with a shell radius of 0.1:

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

xs: XSPRINTCalculate eXtended SPRINT (xSPRINT) topological variables from adjacency matrices over multiple shells. This action is a shortcut. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-7 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=0.1} R0the radius of the first shell for xSPRINT (shell n has radius n*R0)=0.1 NSHELLS the number of concentric shells to use for the xSPRINT calculation=3
# PLUMED interprets the command:
# xs: XSPRINT GROUP=1-7 SWITCH={RATIONAL R_0=0.1} R0=0.1 NSHELLS=3
# as follows (Click the red comment above to revert to the short version of the input):
The XSPRINT action with label xs calculates the following quantities: Quantity    Description  
xs.coord the xsprint coordinatesxs_shell1_matThe CONTACT_MATRIX action with label xs_shell1_mat calculates the following quantities: Quantity    Type    Description  
xs_shell1_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details  GROUPspecifies the list of atoms that should be assumed indistinguishable=1-7 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 R_0=0.1}
xs_shell1_sprint: SPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=xs_shell1_mat
The SPRINT action with label xs_shell1_sprint calculates the following quantities: Quantity    Description  
xs_shell1_sprint.coord the sprint coordinatesxs_shell2_matThe CONTACT_MATRIX action with label xs_shell2_mat calculates the following quantities: Quantity    Type    Description  
xs_shell2_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details  GROUPspecifies the list of atoms that should be assumed indistinguishable=1-7 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 R_0=0.2}
xs_shell2_diffThe CUSTOM action with label xs_shell2_diff calculates the following quantities: Quantity    Type    Description  
xs_shell2_diff 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=xs_shell2_mat,xs_shell1_mat FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_shell2_sprint: SPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=xs_shell2_diff
The SPRINT action with label xs_shell2_sprint calculates the following quantities: Quantity    Description  
xs_shell2_sprint.coord the sprint coordinatesxs_shell3_matThe CONTACT_MATRIX action with label xs_shell3_mat calculates the following quantities: Quantity    Type    Description  
xs_shell3_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details  GROUPspecifies the list of atoms that should be assumed indistinguishable=1-7 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 R_0=0.3}
xs_shell3_diffThe CUSTOM action with label xs_shell3_diff calculates the following quantities: Quantity    Type    Description  
xs_shell3_diff 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=xs_shell3_mat,xs_shell2_mat FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_shell3_sprint: SPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=xs_shell3_diff
The SPRINT action with label xs_shell3_sprint calculates the following quantities: Quantity    Description  
xs_shell3_sprint.coord the sprint coordinatesxs_xspThe COMBINE action with label xs_xsp calculates the following quantities: Quantity    Type    Description  
xs_xsp 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 ARGthe values input to this function=xs_shell1_sprint_sp,xs_shell2_sprint_sp,xs_shell3_sprint_sp COEFFICIENTS the coefficients of the arguments in your function=0.277778,0.555556,0.833333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_selection1The SELECT_WITH_MASK action with label xs_selection1 calculates the following quantities: Quantity    Type    Description  
xs_selection1 vector a vector/matrix of values that is obtained using a mask to select elements of interest: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=xs_xsp COMPONENTSthe components in the input value that you woul like to build a new vector from=1,2,3,4,5,6,7
xs1The SORT action with label xs1 calculates the following quantities: Quantity    Type    Description  
xs1.1 scalar the 1th largest element in the input vector
xs1.2 scalar the 2th largest element in the input vector
xs1.3 scalar the 3th largest element in the input vector
xs1.4 scalar the 4th largest element in the input vector
xs1.5 scalar the 5th largest element in the input vector
xs1.6 scalar the 6th largest element in the input vector
xs1.7 scalar the 7th largest element in the input vector: SORTThis function can be used to sort colvars according to their magnitudes. More details ARGthe values input to this function=xs_selection1
xs_coord-0The COMBINE action with label xs_coord-0 calculates the following quantities: Quantity    Type    Description  
xs_coord-0 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-1The COMBINE action with label xs_coord-1 calculates the following quantities: Quantity    Type    Description  
xs_coord-1 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-2The COMBINE action with label xs_coord-2 calculates the following quantities: Quantity    Type    Description  
xs_coord-2 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-3The COMBINE action with label xs_coord-3 calculates the following quantities: Quantity    Type    Description  
xs_coord-3 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-4The COMBINE action with label xs_coord-4 calculates the following quantities: Quantity    Type    Description  
xs_coord-4 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-5The COMBINE action with label xs_coord-5 calculates the following quantities: Quantity    Type    Description  
xs_coord-5 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-6The COMBINE action with label xs_coord-6 calculates the following quantities: Quantity    Type    Description  
xs_coord-6 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.7 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=xs.* FILEthe name of the file on which to output these quantities=colvar

Note that R0 defines the xSPRINT shell radius ( $r_0$ in the equation) and is independent of R_0 inside SWITCH, which controls the shape of the switching function. For shell $n$ , the switching function R_0 is automatically set to $n \times$ R0.

This example computes xSPRINT with 2 shells for two groups of atoms:

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

xs: XSPRINTCalculate eXtended SPRINT (xSPRINT) topological variables from adjacency matrices over multiple shells. This action is a shortcut. More details ...
  GROUP1specifies the list of atoms that should be assumed indistinguishable=1-7 GROUP2specifies the list of atoms that should be assumed indistinguishable=8-14
  SWITCH11specify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=2.6 NN=6 MM=12}
  SWITCH12specify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=2.2 NN=6 MM=12}
  SWITCH22specify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=2.2 NN=6 MM=12}
  R0the radius of the first shell for xSPRINT (shell n has radius n*R0)=2.0
  NSHELLS the number of concentric shells to use for the xSPRINT calculation=2
...
# PLUMED interprets the command:
# xs: XSPRINT ...
#   GROUP1=1-7 GROUP2=8-14
#   SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
#   SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
#   SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
#   R0=2.0
#   NSHELLS=2
# ...
# as follows (Click the red comment above to revert to the short version of the input):
The XSPRINT action with label xs calculates the following quantities: Quantity    Description  
xs.coord the xsprint coordinatesxs_shell1_matThe CONCATENATE action with label xs_shell1_mat calculates the following quantities: Quantity    Type    Description  
xs_shell1_mat matrix the concatenated vector/matrix that was constructed from the input values: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details  GROUP1specifies the list of atoms that should be assumed indistinguishable=1-7 GROUP2specifies the list of atoms that should be assumed indistinguishable=8-14 SWITCH11the 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 R_0=2 NN=6 MM=12} SWITCH12the 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 R_0=2 NN=6 MM=12} SWITCH22the 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 R_0=2 NN=6 MM=12}
xs_shell1_sprint: SPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=xs_shell1_mat
The SPRINT action with label xs_shell1_sprint calculates the following quantities: Quantity    Description  
xs_shell1_sprint.coord the sprint coordinatesxs_shell2_matThe CONCATENATE action with label xs_shell2_mat calculates the following quantities: Quantity    Type    Description  
xs_shell2_mat matrix the concatenated vector/matrix that was constructed from the input values: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details  GROUP1specifies the list of atoms that should be assumed indistinguishable=1-7 GROUP2specifies the list of atoms that should be assumed indistinguishable=8-14 SWITCH11the 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 R_0=4 NN=6 MM=12} SWITCH12the 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 R_0=4 NN=6 MM=12} SWITCH22the 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 R_0=4 NN=6 MM=12}
xs_shell2_diffThe CUSTOM action with label xs_shell2_diff calculates the following quantities: Quantity    Type    Description  
xs_shell2_diff 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=xs_shell2_mat,xs_shell1_mat FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_shell2_sprint: SPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=xs_shell2_diff
The SPRINT action with label xs_shell2_sprint calculates the following quantities: Quantity    Description  
xs_shell2_sprint.coord the sprint coordinatesxs_xspThe COMBINE action with label xs_xsp calculates the following quantities: Quantity    Type    Description  
xs_xsp 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 ARGthe values input to this function=xs_shell1_sprint_sp,xs_shell2_sprint_sp COEFFICIENTS the coefficients of the arguments in your function=0.0555556,0.111111 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_selection1The SELECT_WITH_MASK action with label xs_selection1 calculates the following quantities: Quantity    Type    Description  
xs_selection1 vector a vector/matrix of values that is obtained using a mask to select elements of interest: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=xs_xsp COMPONENTSthe components in the input value that you woul like to build a new vector from=1,2,3,4,5,6,7
xs1The SORT action with label xs1 calculates the following quantities: Quantity    Type    Description  
xs1.1 scalar the 1th largest element in the input vector
xs1.2 scalar the 2th largest element in the input vector
xs1.3 scalar the 3th largest element in the input vector
xs1.4 scalar the 4th largest element in the input vector
xs1.5 scalar the 5th largest element in the input vector
xs1.6 scalar the 6th largest element in the input vector
xs1.7 scalar the 7th largest element in the input vector: SORTThis function can be used to sort colvars according to their magnitudes. More details ARGthe values input to this function=xs_selection1
xs_coord-0The COMBINE action with label xs_coord-0 calculates the following quantities: Quantity    Type    Description  
xs_coord-0 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-1The COMBINE action with label xs_coord-1 calculates the following quantities: Quantity    Type    Description  
xs_coord-1 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-2The COMBINE action with label xs_coord-2 calculates the following quantities: Quantity    Type    Description  
xs_coord-2 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-3The COMBINE action with label xs_coord-3 calculates the following quantities: Quantity    Type    Description  
xs_coord-3 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-4The COMBINE action with label xs_coord-4 calculates the following quantities: Quantity    Type    Description  
xs_coord-4 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-5The COMBINE action with label xs_coord-5 calculates the following quantities: Quantity    Type    Description  
xs_coord-5 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-6The COMBINE action with label xs_coord-6 calculates the following quantities: Quantity    Type    Description  
xs_coord-6 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs1.7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_selection2The SELECT_WITH_MASK action with label xs_selection2 calculates the following quantities: Quantity    Type    Description  
xs_selection2 vector a vector/matrix of values that is obtained using a mask to select elements of interest: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=xs_xsp COMPONENTSthe components in the input value that you woul like to build a new vector from=8,9,10,11,12,13,14
xs2The SORT action with label xs2 calculates the following quantities: Quantity    Type    Description  
xs2.1 scalar the 1th largest element in the input vector
xs2.2 scalar the 2th largest element in the input vector
xs2.3 scalar the 3th largest element in the input vector
xs2.4 scalar the 4th largest element in the input vector
xs2.5 scalar the 5th largest element in the input vector
xs2.6 scalar the 6th largest element in the input vector
xs2.7 scalar the 7th largest element in the input vector: SORTThis function can be used to sort colvars according to their magnitudes. More details ARGthe values input to this function=xs_selection2
xs_coord-7The COMBINE action with label xs_coord-7 calculates the following quantities: Quantity    Type    Description  
xs_coord-7 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-8The COMBINE action with label xs_coord-8 calculates the following quantities: Quantity    Type    Description  
xs_coord-8 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-9The COMBINE action with label xs_coord-9 calculates the following quantities: Quantity    Type    Description  
xs_coord-9 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-10The COMBINE action with label xs_coord-10 calculates the following quantities: Quantity    Type    Description  
xs_coord-10 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-11The COMBINE action with label xs_coord-11 calculates the following quantities: Quantity    Type    Description  
xs_coord-11 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-12The COMBINE action with label xs_coord-12 calculates the following quantities: Quantity    Type    Description  
xs_coord-12 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-13The COMBINE action with label xs_coord-13 calculates the following quantities: Quantity    Type    Description  
xs_coord-13 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs2.7 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=xs.* FILEthe name of the file on which to output these quantities=colvar

You can also provide a pre-built matrix (for a single-shell case this is equivalent to SPRINT):

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

bThe BRIDGE_MATRIX action with label b calculates the following quantities: Quantity    Type    Description  
b matrix a matrix containing the weights for the bonds between each pair of atoms: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action has hidden defaults. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-7 BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=8-100 SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}
b: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure This action uses the defaults shown here. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-7 BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=8-100 SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.2}  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
xs: XSPRINTCalculate eXtended SPRINT (xSPRINT) topological variables from adjacency matrices over multiple shells. This action is a shortcut. More details MATRIXthe matrix that you would like to perform xSPRINT on (used only when NSHELLS=1)=b NSHELLS the number of concentric shells to use for the xSPRINT calculation=1
# PLUMED interprets the command:
# xs: XSPRINT MATRIX=b NSHELLS=1
# as follows (Click the red comment above to revert to the short version of the input):
The XSPRINT action with label xs calculates the following quantities: Quantity    Description  
xs.coord the xsprint coordinatesxs_sprint: SPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=b
The SPRINT action with label xs_sprint calculates the following quantities: Quantity    Description  
xs_sprint.coord the sprint coordinatesxs_coord-0The COMBINE action with label xs_coord-0 calculates the following quantities: Quantity    Type    Description  
xs_coord-0 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-1The COMBINE action with label xs_coord-1 calculates the following quantities: Quantity    Type    Description  
xs_coord-1 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-2The COMBINE action with label xs_coord-2 calculates the following quantities: Quantity    Type    Description  
xs_coord-2 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-3The COMBINE action with label xs_coord-3 calculates the following quantities: Quantity    Type    Description  
xs_coord-3 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-4The COMBINE action with label xs_coord-4 calculates the following quantities: Quantity    Type    Description  
xs_coord-4 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-5The COMBINE action with label xs_coord-5 calculates the following quantities: Quantity    Type    Description  
xs_coord-5 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
xs_coord-6The COMBINE action with label xs_coord-6 calculates the following quantities: Quantity    Type    Description  
xs_coord-6 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=xs_sprint_coord-6 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=xs.* FILEthe name of the file on which to output these quantities=colvar

Full list of keywords

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

Keyword	Type	Default	Description
NSHELLS	compulsory	1	the number of concentric shells to use for the xSPRINT calculation
MATRIX	optional	not used	the matrix that you would like to perform xSPRINT on (used only when NSHELLS=1)
GROUP	optional	not used	specifies the list of atoms that should be assumed indistinguishable
SWITCH	optional	not used	specify the switching function to use between two sets of indistinguishable atoms
R0	optional	not used	the radius of the first shell for xSPRINT (shell n has radius n*R0)

References

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

R. Ketkaew, F. Creazzo, S. Luber, Machine Learning-Assisted Discovery of Hidden States in Expanded Free Energy Space. The Journal of Physical Chemistry Letters 13, 1797–1805 (2022)

Quantity	Type	Description
xs_shell1_mat	matrix	a matrix containing the weights for the bonds between each pair of atoms

Quantity	Description
xs_shell1_sprint.coord	the sprint coordinates

Quantity	Description
xs_shell2_sprint.coord	the sprint coordinates

Quantity	Description
xs_shell3_sprint.coord	the sprint coordinates

Quantity	Description
xs_sprint.coord	the sprint coordinates