Shortcut: Q1

Module	symfunc
Description	Usage
Calculate 1st order Steinhardt parameters
output value	type
the norms of the vectors of spherical harmonic coefficients	vector

Details and examples

Calculate 1st order Steinhardt parameters

The 1st order Steinhardt parameters allow us to measure the degree to which the first coordination shell around an atom is ordered with the atoms aranged on a line. The Steinhardt parameter for atom, $i$ is complex vector whose components are calculated using the following formula:

$q_{1m}(i) = \sum_j \sigma( r_{ij} ) Y_{1m}(\mathbf{r}_{ij})$

where $Y_{1m}$ is one of the 1st order spherical harmonics so $m$ is a number that runs from $-1$ to $+1$ . The function $\sigma( r_{ij} )$ is a switching function that acts on the distance between atoms $i$ and $j$ . The parameters of this function should be set so that it the function is equal to one when atom $j$ is in the first coordination sphere of atom $i$ and is zero otherwise.

As discussed on this page, the Steinhardt parameters can be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.

$Q_1(i) = \frac{1}{\sum_j \sigma(r_{ij}) } \sqrt{ \sum_{m=-1}^1 q_{1m}(i)^{*} q_{1m}(i) }$

This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. The following input illustrates how by averaging the value of this norm over all the atoms in the system you can measure the global degree of order in the system:

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

q1The Q1 action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 vector the norms of the vectors of spherical harmonic coefficients: Q1Calculate 1st order Steinhardt parameters 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=1.3 R_0The r_0 parameter of the switching function=0.2
q1: Q1Calculate 1st order Steinhardt parameters 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=1.3 R_0The r_0 parameter of the switching function=0.2  NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# PLUMED interprets the command:
# q1: Q1 SPECIES=1-64 D_0=1.3 R_0=0.2
# as follows (Click the red comment above to revert to the short version of the input):
q1_grpThe GROUP action with label q1_grp calculates the following quantities: Quantity    Type    Description  
q1_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
q1_matThe CONTACT_MATRIX action with label q1_mat calculates the following quantities: Quantity    Type    Description  
q1_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1_mat.x matrix the projection of the bond on the x axis
q1_mat.y matrix the projection of the bond on the y axis
q1_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=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q1_shThe SPHERICAL_HARMONIC action with label q1_sh calculates the following quantities: Quantity    Type    Description  
q1_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q1_mat.x,q1_mat.y,q1_mat.z,q1_mat.w Lthe value of the angular momentum=1
q1_denom_onesThe CONSTANT action with label q1_denom_ones calculates the following quantities: Quantity    Type    Description  
q1_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q1_denomThe MATRIX_VECTOR_PRODUCT action with label q1_denom calculates the following quantities: Quantity    Type    Description  
q1_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=q1_mat.w,q1_denom_ones
q1_spThe MATRIX_VECTOR_PRODUCT action with label q1_sp calculates the following quantities: Quantity    Type    Description  
q1_sp.rm-n1 vector the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones
q1_sp.rm-0 vector the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones
q1_sp.rm-p1 vector the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones
q1_sp.im-n1 vector the product of the matrix q1_sh.im-n1 and the vector q1_denom_ones
q1_sp.im-0 vector the product of the matrix q1_sh.im-0 and the vector q1_denom_ones
q1_sp.im-p1 vector the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q1_sh.*,q1_denom_ones
q1_norm2The COMBINE action with label q1_norm2 calculates the following quantities: Quantity    Type    Description  
q1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
q1_normThe CUSTOM action with label q1_norm calculates the following quantities: Quantity    Type    Description  
q1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1The CUSTOM action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 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=q1_norm,q1_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- q1_meanThe MEAN action with label q1_mean calculates the following quantities: Quantity    Type    Description  
q1_mean scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q1_mean FILEthe name of the file on which to output these quantities=colvar

In the above input the 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

q1The Q1 action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 vector the norms of the vectors of spherical harmonic coefficients: Q1Calculate 1st order Steinhardt parameters This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# PLUMED interprets the command:
# q1: Q1 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0}
# as follows (Click the red comment above to revert to the short version of the input):
q1_grpThe GROUP action with label q1_grp calculates the following quantities: Quantity    Type    Description  
q1_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
q1_matThe CONTACT_MATRIX action with label q1_mat calculates the following quantities: Quantity    Type    Description  
q1_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1_mat.x matrix the projection of the bond on the x axis
q1_mat.y matrix the projection of the bond on the y axis
q1_mat.z matrix the projection of the bond on the z axis: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q1_shThe SPHERICAL_HARMONIC action with label q1_sh calculates the following quantities: Quantity    Type    Description  
q1_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q1_mat.x,q1_mat.y,q1_mat.z,q1_mat.w Lthe value of the angular momentum=1
q1_denom_onesThe CONSTANT action with label q1_denom_ones calculates the following quantities: Quantity    Type    Description  
q1_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q1_denomThe MATRIX_VECTOR_PRODUCT action with label q1_denom calculates the following quantities: Quantity    Type    Description  
q1_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=q1_mat.w,q1_denom_ones
q1_spThe MATRIX_VECTOR_PRODUCT action with label q1_sp calculates the following quantities: Quantity    Type    Description  
q1_sp.rm-n1 vector the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones
q1_sp.rm-0 vector the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones
q1_sp.rm-p1 vector the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones
q1_sp.im-n1 vector the product of the matrix q1_sh.im-n1 and the vector q1_denom_ones
q1_sp.im-0 vector the product of the matrix q1_sh.im-0 and the vector q1_denom_ones
q1_sp.im-p1 vector the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q1_sh.*,q1_denom_ones
q1_norm2The COMBINE action with label q1_norm2 calculates the following quantities: Quantity    Type    Description  
q1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
q1_normThe CUSTOM action with label q1_norm calculates the following quantities: Quantity    Type    Description  
q1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1The CUSTOM action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 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=q1_norm,q1_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- q1_meanThe MEAN action with label q1_mean calculates the following quantities: Quantity    Type    Description  
q1_mean scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q1_mean FILEthe name of the file on which to output these quantities=colvar

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

Working with two types of atoms

The command below could be used to measure the Q1 parameters that describe the arrangement of chlorine ions around the sodium atoms in sodium chloride. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input with the 64 Na $^+$ ions followed by the 64 Cl $-$ ions. Once again the average Q1 parameter is calculated and output to a file called colvar

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

q1The Q1 action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 vector the norms of the vectors of spherical harmonic coefficients: Q1Calculate 1st order Steinhardt parameters This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2
q1: Q1Calculate 1st order Steinhardt parameters This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2  NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# PLUMED interprets the command:
# q1: Q1 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2
# as follows (Click the red comment above to revert to the short version of the input):
q1_grpThe GROUP action with label q1_grp calculates the following quantities: Quantity    Type    Description  
q1_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
q1_matThe CONTACT_MATRIX action with label q1_mat calculates the following quantities: Quantity    Type    Description  
q1_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1_mat.x matrix the projection of the bond on the x axis
q1_mat.y matrix the projection of the bond on the y axis
q1_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=1-64 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=65-128 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q1_shThe SPHERICAL_HARMONIC action with label q1_sh calculates the following quantities: Quantity    Type    Description  
q1_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q1_mat.x,q1_mat.y,q1_mat.z,q1_mat.w Lthe value of the angular momentum=1
q1_denom_onesThe CONSTANT action with label q1_denom_ones calculates the following quantities: Quantity    Type    Description  
q1_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q1_denomThe MATRIX_VECTOR_PRODUCT action with label q1_denom calculates the following quantities: Quantity    Type    Description  
q1_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=q1_mat.w,q1_denom_ones
q1_spThe MATRIX_VECTOR_PRODUCT action with label q1_sp calculates the following quantities: Quantity    Type    Description  
q1_sp.rm-n1 vector the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones
q1_sp.rm-0 vector the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones
q1_sp.rm-p1 vector the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones
q1_sp.im-n1 vector the product of the matrix q1_sh.im-n1 and the vector q1_denom_ones
q1_sp.im-0 vector the product of the matrix q1_sh.im-0 and the vector q1_denom_ones
q1_sp.im-p1 vector the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q1_sh.*,q1_denom_ones
q1_norm2The COMBINE action with label q1_norm2 calculates the following quantities: Quantity    Type    Description  
q1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
q1_normThe CUSTOM action with label q1_norm calculates the following quantities: Quantity    Type    Description  
q1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1The CUSTOM action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 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=q1_norm,q1_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- q1_meanThe MEAN action with label q1_mean calculates the following quantities: Quantity    Type    Description  
q1_mean scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q1_mean FILEthe name of the file on which to output these quantities=colvar

If you simply want to examine the values of the Q1 parameters for each of the atoms in your system you can do so by exploiting the command DUMPATOMS as shown in the example below. The following output file will output a file in an extended xyz format called q1.xyz for each frame of the analyzed MD trajectory. The first column in this file will contain a dummy name for each of the atoms, columns 2-4 will then contain the x, y and z positions of the atoms, column 5 will contain the value of the Q1 parameter, columns 6-8 will contain the real parts of the director of the $q_{1m}$ vector while columns 9-11 will contain the imaginary parts of this director.

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

q1The Q1 action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 vector the norms of the vectors of spherical harmonic coefficients
q1_mean scalar the mean of the colvars: Q1Calculate 1st order Steinhardt parameters This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 MEAN calculate the mean of all the quantities
q1: Q1Calculate 1st order Steinhardt parameters This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 MEAN calculate the mean 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:
# q1: Q1 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN
# as follows (Click the red comment above to revert to the short version of the input):
q1_grpThe GROUP action with label q1_grp calculates the following quantities: Quantity    Type    Description  
q1_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
q1_matThe CONTACT_MATRIX action with label q1_mat calculates the following quantities: Quantity    Type    Description  
q1_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1_mat.x matrix the projection of the bond on the x axis
q1_mat.y matrix the projection of the bond on the y axis
q1_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=1-64 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=65-128 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q1_shThe SPHERICAL_HARMONIC action with label q1_sh calculates the following quantities: Quantity    Type    Description  
q1_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q1_mat.x,q1_mat.y,q1_mat.z,q1_mat.w Lthe value of the angular momentum=1
q1_denom_onesThe CONSTANT action with label q1_denom_ones calculates the following quantities: Quantity    Type    Description  
q1_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q1_denomThe MATRIX_VECTOR_PRODUCT action with label q1_denom calculates the following quantities: Quantity    Type    Description  
q1_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=q1_mat.w,q1_denom_ones
q1_spThe MATRIX_VECTOR_PRODUCT action with label q1_sp calculates the following quantities: Quantity    Type    Description  
q1_sp.rm-n1 vector the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones
q1_sp.rm-0 vector the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones
q1_sp.rm-p1 vector the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones
q1_sp.im-n1 vector the product of the matrix q1_sh.im-n1 and the vector q1_denom_ones
q1_sp.im-0 vector the product of the matrix q1_sh.im-0 and the vector q1_denom_ones
q1_sp.im-p1 vector the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q1_sh.*,q1_denom_ones
q1_norm2The COMBINE action with label q1_norm2 calculates the following quantities: Quantity    Type    Description  
q1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
q1_normThe CUSTOM action with label q1_norm calculates the following quantities: Quantity    Type    Description  
q1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1The CUSTOM action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 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=q1_norm,q1_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
q1_meanThe MEAN action with label q1_mean calculates the following quantities: Quantity    Type    Description  
q1_mean scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- DUMPATOMSDump selected atoms on a file. More details ATOMSthe atom indices whose positions you would like to print out=q1 ARGthe labels of vectors that should be output in the xyz file=q1 FILEfile on which to output coordinates; extension is automatically detected=q1.xyz

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 Q1 that it is safe not to calculate the Q1 parameter for some of the atoms. As illustrated below, this is useful if you are using functionality from the volumes module to calculate the average value of the Q1 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=1-400 CENTERthe atom whose vicinity we are interested in examining=center RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52}
# Calculate the fccubic parameter of the atoms
ccThe Q1 action with label cc calculates the following quantities: Quantity    Type    Description  
cc vector the norms of the vectors of spherical harmonic coefficients: Q1Calculate 1st order Steinhardt parameters This action is a shortcut. More details ...
  SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-400 MASKthe label for a vector that is used to determine which rows of the matrix are computed=sphere
  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=6.0}
...
# PLUMED interprets the command:
# cc: Q1 ...
#   SPECIES=1-400 MASK=sphere
#   SWITCH={RATIONAL D_0=3.0 R_0=1.5 D_MAX=6.0}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
cc_grpThe GROUP action with label cc_grp calculates the following quantities: Quantity    Type    Description  
cc_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-400
cc_matThe CONTACT_MATRIX action with label cc_mat calculates the following quantities: Quantity    Type    Description  
cc_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
cc_mat.x matrix the projection of the bond on the x axis
cc_mat.y matrix the projection of the bond on the y axis
cc_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=1-400 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=3.0 R_0=1.5 D_MAX=6.0} 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
cc_shThe SPHERICAL_HARMONIC action with label cc_sh calculates the following quantities: Quantity    Type    Description  
cc_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
cc_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
cc_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
cc_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
cc_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
cc_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=cc_mat.x,cc_mat.y,cc_mat.z,cc_mat.w Lthe value of the angular momentum=1
cc_denom_onesThe CONSTANT action with label cc_denom_ones calculates the following quantities: Quantity    Type    Description  
cc_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=400
cc_denomThe MATRIX_VECTOR_PRODUCT action with label cc_denom calculates the following quantities: Quantity    Type    Description  
cc_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=cc_mat.w,cc_denom_ones
cc_spThe MATRIX_VECTOR_PRODUCT action with label cc_sp calculates the following quantities: Quantity    Type    Description  
cc_sp.rm-n1 vector the product of the matrix cc_sh.rm-n1 and the vector cc_denom_ones
cc_sp.rm-0 vector the product of the matrix cc_sh.rm-0 and the vector cc_denom_ones
cc_sp.rm-p1 vector the product of the matrix cc_sh.rm-p1 and the vector cc_denom_ones
cc_sp.im-n1 vector the product of the matrix cc_sh.im-n1 and the vector cc_denom_ones
cc_sp.im-0 vector the product of the matrix cc_sh.im-0 and the vector cc_denom_ones
cc_sp.im-p1 vector the product of the matrix cc_sh.im-p1 and the vector cc_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cc_sh.*,cc_denom_ones
cc_norm2The COMBINE action with label cc_norm2 calculates the following quantities: Quantity    Type    Description  
cc_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=cc_sp.rm-n1,cc_sp.im-n1,cc_sp.rm-0,cc_sp.im-0,cc_sp.rm-p1,cc_sp.im-p1
cc_normThe CUSTOM action with label cc_norm calculates the following quantities: Quantity    Type    Description  
cc_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cc_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ccThe CUSTOM action with label cc calculates the following quantities: Quantity    Type    Description  
cc 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=cc_norm,cc_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- # Multiply fccubic 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=cc,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 value of the Q1 parameter for only those atoms that are within a spherical region that is centered on the point $(2.5,2.5,2.5)$ .

Deprecated syntax

More information on the deprecated keywords that are given below is available in the documentation for the DISTANCES command. Below is an example where these deprecated keywords are used to calculate the histogram of Q1 parameters for the 64 atoms in a box of Lennard Jones print them to a file called colvar:

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

q1The Q1 action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 vector the norms of the vectors of spherical harmonic coefficients
q1_between-1 scalar the number of colvars that have a value that lies in a particular interval
q1_between-2 scalar the number of colvars that have a value that lies in a particular interval
q1_between-3 scalar the number of colvars that have a value that lies in a particular interval
q1_between-4 scalar the number of colvars that have a value that lies in a particular interval
q1_between-5 scalar the number of colvars that have a value that lies in a particular interval
q1_between-6 scalar the number of colvars that have a value that lies in a particular interval
q1_between-7 scalar the number of colvars that have a value that lies in a particular interval
q1_between-8 scalar the number of colvars that have a value that lies in a particular interval
q1_between-9 scalar the number of colvars that have a value that lies in a particular interval
q1_between-10 scalar the number of colvars that have a value that lies in a particular interval
q1_between-11 scalar the number of colvars that have a value that lies in a particular interval
q1_between-12 scalar the number of colvars that have a value that lies in a particular interval
q1_between-13 scalar the number of colvars that have a value that lies in a particular interval
q1_between-14 scalar the number of colvars that have a value that lies in a particular interval
q1_between-15 scalar the number of colvars that have a value that lies in a particular interval
q1_between-16 scalar the number of colvars that have a value that lies in a particular interval
q1_between-17 scalar the number of colvars that have a value that lies in a particular interval
q1_between-18 scalar the number of colvars that have a value that lies in a particular interval
q1_between-19 scalar the number of colvars that have a value that lies in a particular interval
q1_between-20 scalar the number of colvars that have a value that lies in a particular interval: Q1Calculate 1st order Steinhardt parameters 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=1.3 R_0The r_0 parameter of the switching function=0.2 HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1}
q1: Q1Calculate 1st order Steinhardt parameters 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=1.3 R_0The r_0 parameter of the switching function=0.2 HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1}  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:
# q1: Q1 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1}
# as follows (Click the red comment above to revert to the short version of the input):
q1_grpThe GROUP action with label q1_grp calculates the following quantities: Quantity    Type    Description  
q1_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
q1_matThe CONTACT_MATRIX action with label q1_mat calculates the following quantities: Quantity    Type    Description  
q1_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1_mat.x matrix the projection of the bond on the x axis
q1_mat.y matrix the projection of the bond on the y axis
q1_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=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q1_shThe SPHERICAL_HARMONIC action with label q1_sh calculates the following quantities: Quantity    Type    Description  
q1_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q1_mat.x,q1_mat.y,q1_mat.z,q1_mat.w Lthe value of the angular momentum=1
q1_denom_onesThe CONSTANT action with label q1_denom_ones calculates the following quantities: Quantity    Type    Description  
q1_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q1_denomThe MATRIX_VECTOR_PRODUCT action with label q1_denom calculates the following quantities: Quantity    Type    Description  
q1_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=q1_mat.w,q1_denom_ones
q1_spThe MATRIX_VECTOR_PRODUCT action with label q1_sp calculates the following quantities: Quantity    Type    Description  
q1_sp.rm-n1 vector the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones
q1_sp.rm-0 vector the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones
q1_sp.rm-p1 vector the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones
q1_sp.im-n1 vector the product of the matrix q1_sh.im-n1 and the vector q1_denom_ones
q1_sp.im-0 vector the product of the matrix q1_sh.im-0 and the vector q1_denom_ones
q1_sp.im-p1 vector the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q1_sh.*,q1_denom_ones
q1_norm2The COMBINE action with label q1_norm2 calculates the following quantities: Quantity    Type    Description  
q1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
q1_normThe CUSTOM action with label q1_norm calculates the following quantities: Quantity    Type    Description  
q1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1The CUSTOM action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 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=q1_norm,q1_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
q1_bt1The BETWEEN action with label q1_bt1 calculates the following quantities: Quantity    Type    Description  
q1_bt1 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0 UPPER=0.05 SMEAR=0.1}
q1_between-1The SUM action with label q1_between-1 calculates the following quantities: Quantity    Type    Description  
q1_between-1 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=q1_bt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt2The BETWEEN action with label q1_bt2 calculates the following quantities: Quantity    Type    Description  
q1_bt2 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.05 UPPER=0.1 SMEAR=0.1}
q1_between-2The SUM action with label q1_between-2 calculates the following quantities: Quantity    Type    Description  
q1_between-2 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=q1_bt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt3The BETWEEN action with label q1_bt3 calculates the following quantities: Quantity    Type    Description  
q1_bt3 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.1 UPPER=0.15 SMEAR=0.1}
q1_between-3The SUM action with label q1_between-3 calculates the following quantities: Quantity    Type    Description  
q1_between-3 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=q1_bt3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt4The BETWEEN action with label q1_bt4 calculates the following quantities: Quantity    Type    Description  
q1_bt4 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.15 UPPER=0.2 SMEAR=0.1}
q1_between-4The SUM action with label q1_between-4 calculates the following quantities: Quantity    Type    Description  
q1_between-4 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=q1_bt4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt5The BETWEEN action with label q1_bt5 calculates the following quantities: Quantity    Type    Description  
q1_bt5 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.2 UPPER=0.25 SMEAR=0.1}
q1_between-5The SUM action with label q1_between-5 calculates the following quantities: Quantity    Type    Description  
q1_between-5 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=q1_bt5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt6The BETWEEN action with label q1_bt6 calculates the following quantities: Quantity    Type    Description  
q1_bt6 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.25 UPPER=0.3 SMEAR=0.1}
q1_between-6The SUM action with label q1_between-6 calculates the following quantities: Quantity    Type    Description  
q1_between-6 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=q1_bt6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt7The BETWEEN action with label q1_bt7 calculates the following quantities: Quantity    Type    Description  
q1_bt7 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.3 UPPER=0.35 SMEAR=0.1}
q1_between-7The SUM action with label q1_between-7 calculates the following quantities: Quantity    Type    Description  
q1_between-7 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=q1_bt7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt8The BETWEEN action with label q1_bt8 calculates the following quantities: Quantity    Type    Description  
q1_bt8 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.35 UPPER=0.4 SMEAR=0.1}
q1_between-8The SUM action with label q1_between-8 calculates the following quantities: Quantity    Type    Description  
q1_between-8 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=q1_bt8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt9The BETWEEN action with label q1_bt9 calculates the following quantities: Quantity    Type    Description  
q1_bt9 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.4 UPPER=0.45 SMEAR=0.1}
q1_between-9The SUM action with label q1_between-9 calculates the following quantities: Quantity    Type    Description  
q1_between-9 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=q1_bt9 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt10The BETWEEN action with label q1_bt10 calculates the following quantities: Quantity    Type    Description  
q1_bt10 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.45 UPPER=0.5 SMEAR=0.1}
q1_between-10The SUM action with label q1_between-10 calculates the following quantities: Quantity    Type    Description  
q1_between-10 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=q1_bt10 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt11The BETWEEN action with label q1_bt11 calculates the following quantities: Quantity    Type    Description  
q1_bt11 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.5 UPPER=0.55 SMEAR=0.1}
q1_between-11The SUM action with label q1_between-11 calculates the following quantities: Quantity    Type    Description  
q1_between-11 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=q1_bt11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt12The BETWEEN action with label q1_bt12 calculates the following quantities: Quantity    Type    Description  
q1_bt12 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.55 UPPER=0.6 SMEAR=0.1}
q1_between-12The SUM action with label q1_between-12 calculates the following quantities: Quantity    Type    Description  
q1_between-12 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=q1_bt12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt13The BETWEEN action with label q1_bt13 calculates the following quantities: Quantity    Type    Description  
q1_bt13 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.6 UPPER=0.65 SMEAR=0.1}
q1_between-13The SUM action with label q1_between-13 calculates the following quantities: Quantity    Type    Description  
q1_between-13 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=q1_bt13 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt14The BETWEEN action with label q1_bt14 calculates the following quantities: Quantity    Type    Description  
q1_bt14 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.65 UPPER=0.7 SMEAR=0.1}
q1_between-14The SUM action with label q1_between-14 calculates the following quantities: Quantity    Type    Description  
q1_between-14 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=q1_bt14 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt15The BETWEEN action with label q1_bt15 calculates the following quantities: Quantity    Type    Description  
q1_bt15 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.7 UPPER=0.75 SMEAR=0.1}
q1_between-15The SUM action with label q1_between-15 calculates the following quantities: Quantity    Type    Description  
q1_between-15 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=q1_bt15 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt16The BETWEEN action with label q1_bt16 calculates the following quantities: Quantity    Type    Description  
q1_bt16 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.75 UPPER=0.8 SMEAR=0.1}
q1_between-16The SUM action with label q1_between-16 calculates the following quantities: Quantity    Type    Description  
q1_between-16 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=q1_bt16 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt17The BETWEEN action with label q1_bt17 calculates the following quantities: Quantity    Type    Description  
q1_bt17 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.8 UPPER=0.85 SMEAR=0.1}
q1_between-17The SUM action with label q1_between-17 calculates the following quantities: Quantity    Type    Description  
q1_between-17 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=q1_bt17 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt18The BETWEEN action with label q1_bt18 calculates the following quantities: Quantity    Type    Description  
q1_bt18 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.85 UPPER=0.9 SMEAR=0.1}
q1_between-18The SUM action with label q1_between-18 calculates the following quantities: Quantity    Type    Description  
q1_between-18 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=q1_bt18 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt19The BETWEEN action with label q1_bt19 calculates the following quantities: Quantity    Type    Description  
q1_bt19 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.9 UPPER=0.95 SMEAR=0.1}
q1_between-19The SUM action with label q1_between-19 calculates the following quantities: Quantity    Type    Description  
q1_between-19 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=q1_bt19 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_bt20The BETWEEN action with label q1_bt20 calculates the following quantities: Quantity    Type    Description  
q1_bt20 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.95 UPPER=1 SMEAR=0.1}
q1_between-20The SUM action with label q1_between-20 calculates the following quantities: Quantity    Type    Description  
q1_between-20 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=q1_bt20 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=q1.* FILEthe name of the file on which to output these quantities=colvar

The following example illustrates how you can use VSUM to calculate a global vector of $Q_{1m}$ values as follows:

$Q_{1m} = \sum_i \frac{q_{1m}(i)}{\sum_j \sigma(r_{ij})}$

where the sum runs over all the atoms. You can then take these $Q_{1m}$ values and compute the following norm:

$s = \sqrt{ \sum_{m=-1}^1 Q_{1m}^{*} Q_{1m} }$

The VMEAN command that is also used in the input below performs a similar operations. The only difference is that we divide the sums in the first expression above by the number of atoms.

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

q1The Q1 action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 vector the norms of the vectors of spherical harmonic coefficients: Q1Calculate 1st order Steinhardt parameters 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=1.3 R_0The r_0 parameter of the switching function=0.2 VMEAN calculate the norm of the mean vector VSUM calculate the norm of the sum of all the vectors
q1: Q1Calculate 1st order Steinhardt parameters 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=1.3 R_0The r_0 parameter of the switching function=0.2 VMEAN calculate the norm of the mean vector VSUM calculate the norm of the sum of all the vectors  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:
# q1: Q1 SPECIES=1-64 D_0=1.3 R_0=0.2 VMEAN VSUM
# as follows (Click the red comment above to revert to the short version of the input):
q1_grpThe GROUP action with label q1_grp calculates the following quantities: Quantity    Type    Description  
q1_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
q1_matThe CONTACT_MATRIX action with label q1_mat calculates the following quantities: Quantity    Type    Description  
q1_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1_mat.x matrix the projection of the bond on the x axis
q1_mat.y matrix the projection of the bond on the y axis
q1_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=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q1_shThe SPHERICAL_HARMONIC action with label q1_sh calculates the following quantities: Quantity    Type    Description  
q1_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q1_mat.x,q1_mat.y,q1_mat.z,q1_mat.w Lthe value of the angular momentum=1
q1_denom_onesThe CONSTANT action with label q1_denom_ones calculates the following quantities: Quantity    Type    Description  
q1_denom_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64
q1_denomThe MATRIX_VECTOR_PRODUCT action with label q1_denom calculates the following quantities: Quantity    Type    Description  
q1_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=q1_mat.w,q1_denom_ones
q1_spThe MATRIX_VECTOR_PRODUCT action with label q1_sp calculates the following quantities: Quantity    Type    Description  
q1_sp.rm-n1 vector the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones
q1_sp.rm-0 vector the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones
q1_sp.rm-p1 vector the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones
q1_sp.im-n1 vector the product of the matrix q1_sh.im-n1 and the vector q1_denom_ones
q1_sp.im-0 vector the product of the matrix q1_sh.im-0 and the vector q1_denom_ones
q1_sp.im-p1 vector the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q1_sh.*,q1_denom_ones
q1_rmn-n1The CUSTOM action with label q1_rmn-n1 calculates the following quantities: Quantity    Type    Description  
q1_rmn-n1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_sp.rm-n1,q1_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
q1_imn-n1The CUSTOM action with label q1_imn-n1 calculates the following quantities: Quantity    Type    Description  
q1_imn-n1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_sp.im-n1,q1_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
q1_rmn-0The CUSTOM action with label q1_rmn-0 calculates the following quantities: Quantity    Type    Description  
q1_rmn-0 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_sp.rm-0,q1_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
q1_imn-0The CUSTOM action with label q1_imn-0 calculates the following quantities: Quantity    Type    Description  
q1_imn-0 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_sp.im-0,q1_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
q1_rmn-p1The CUSTOM action with label q1_rmn-p1 calculates the following quantities: Quantity    Type    Description  
q1_rmn-p1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_sp.rm-p1,q1_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
q1_imn-p1The CUSTOM action with label q1_imn-p1 calculates the following quantities: Quantity    Type    Description  
q1_imn-p1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_sp.im-p1,q1_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
q1_rms-n1The MEAN action with label q1_rms-n1 calculates the following quantities: Quantity    Type    Description  
q1_rms-n1 scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1_rmn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_ims-n1The MEAN action with label q1_ims-n1 calculates the following quantities: Quantity    Type    Description  
q1_ims-n1 scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1_imn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_rms-0The MEAN action with label q1_rms-0 calculates the following quantities: Quantity    Type    Description  
q1_rms-0 scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1_rmn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_ims-0The MEAN action with label q1_ims-0 calculates the following quantities: Quantity    Type    Description  
q1_ims-0 scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1_imn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_rms-p1The MEAN action with label q1_rms-p1 calculates the following quantities: Quantity    Type    Description  
q1_rms-p1 scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1_rmn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_ims-p1The MEAN action with label q1_ims-p1 calculates the following quantities: Quantity    Type    Description  
q1_ims-p1 scalar the MEAN of the elements in the input value: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q1_imn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_vmean2The COMBINE action with label q1_vmean2 calculates the following quantities: Quantity    Type    Description  
q1_vmean2 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_rms-n1,q1_ims-n1,q1_rms-0,q1_ims-0,q1_rms-p1,q1_ims-p1
q1_vmeanThe CUSTOM action with label q1_vmean calculates the following quantities: Quantity    Type    Description  
q1_vmean scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_vmean2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_rmz-n1The SUM action with label q1_rmz-n1 calculates the following quantities: Quantity    Type    Description  
q1_rmz-n1 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=q1_rmn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_imz-n1The SUM action with label q1_imz-n1 calculates the following quantities: Quantity    Type    Description  
q1_imz-n1 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=q1_imn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_rmz-0The SUM action with label q1_rmz-0 calculates the following quantities: Quantity    Type    Description  
q1_rmz-0 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=q1_rmn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_imz-0The SUM action with label q1_imz-0 calculates the following quantities: Quantity    Type    Description  
q1_imz-0 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=q1_imn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_rmz-p1The SUM action with label q1_rmz-p1 calculates the following quantities: Quantity    Type    Description  
q1_rmz-p1 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=q1_rmn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_imz-p1The SUM action with label q1_imz-p1 calculates the following quantities: Quantity    Type    Description  
q1_imz-p1 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=q1_imn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_vsum2The COMBINE action with label q1_vsum2 calculates the following quantities: Quantity    Type    Description  
q1_vsum2 scalar a linear combination: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_rmz-n1,q1_imz-n1,q1_rmz-0,q1_imz-0,q1_rmz-p1,q1_imz-p1
q1_vsumThe CUSTOM action with label q1_vsum calculates the following quantities: Quantity    Type    Description  
q1_vsum scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_vsum2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1_norm2The COMBINE action with label q1_norm2 calculates the following quantities: Quantity    Type    Description  
q1_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2 ARGthe values input to this function=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
q1_normThe CUSTOM action with label q1_norm calculates the following quantities: Quantity    Type    Description  
q1_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q1_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q1The CUSTOM action with label q1 calculates the following quantities: Quantity    Type    Description  
q1 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=q1_norm,q1_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q1.* FILEthe name of the file on which to output these quantities=colvar

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
_vmean	scalar	VMEAN	the norm of the mean vector
_vsum	scalar	VSUM	the norm of the mean vector

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
VMEAN	optional	false	calculate the norm of the mean vector
VSUM	optional	false	calculate the norm of the sum of all the vectors
USEGPUThis keyword do not have examples	optional	false	run part of this calculation on the GPU

deprecated keywords

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

Keyword	Description
LESS_THAN	calculate the number of variables that are less than a certain target value
MORE_THAN	calculate the number of variables that are more than a certain target value
ALT_MIN	calculate the minimum value
MIN	calculate the minimum value
MAX	calculate the maximum value
BETWEEN	calculate the number of values that are within a certain range
HIGHEST	this flag allows you to recover the highest of these variables
HISTOGRAM	calculate a discretized histogram of the distribution of values
LOWEST	this flag allows you to recover the lowest of these variables
SUM	calculate the sum of all the quantities
MEAN	calculate the mean of all the quantities
LOWMEM	Including this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only

References

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

A. D. White, G. A. Voth, Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. Journal of Chemical Theory and Computation. 10, 3023–3030 (2014)

Quantity	Type	Description
q1	vector	the norms of the vectors of spherical harmonic coefficients