Shortcut: LOCAL_Q1

Module	symfunc
Description	Usage
Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere.
output value	type
the values of the local steinhardt parameters for the input atoms	vector

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

Further details and examples

Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere.

The Q1 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere around a particular atom. The difficulty with these vectors comes when combining the order parameters from all of the individual atoms/molecules so as to get a measure of the global degree of order for the system. The simplest way of doing this - calculating the average Steinhardt parameter - can be problematic. If one is examining nucleation say only the order parameters for those atoms in the nucleus will change significantly when the nucleus forms. The order parameters for the atoms in the surrounding liquid will remain pretty much the same. As such if one models a small nucleus embedded in a very large amount of solution/melt any change in the average order parameter will be negligible. Substantial changes in the value of this average can be observed in simulations of nucleation but only because the number of atoms is relatively small.

When the average Q1 parameter is used to bias the dynamics a problems can occur. These averaged coordinates cannot distinguish between the correct, single-nucleus pathway and a concerted pathway in which all the atoms rearrange themselves into their solid-like configuration simultaneously. This second type of pathway would be impossible in reality because there is a large entropic barrier that prevents concerted processes like this from happening. However, in the finite sized systems that are commonly simulated this barrier is reduced substantially. As a result in simulations where average Steinhardt parameters are biased there are often quite dramatic system size effects

If one wants to simulate nucleation using some form on biased dynamics what is really required is an order parameter that measures:

Whether or not the coordination spheres around atoms are ordered
Whether or not the atoms that are ordered are clustered together in a crystalline nucleus

As discussed on this page a variety of variations on the Steinhardt parameters have been introduced to better describe nucleation. That page also shows how PLUMED provides you with flexibility that you can use to implement new combinations of the Steinhardt parameters. However, the inputs that you would need to write to implement common symmetry functions are rather complex so we also provide shortcuts like this one to help you compute CVs that have been widely used in the literature easily.

This particular shortcut allows you to compute the LOCAL_Q1 parameter for a particular atom, which is a number that measures the extent to which the orientation of the atoms in the first coordination sphere of an atom match the orientation of the central atom. It does this by calculating the following quantity for each of the atoms in the system:

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

where $q_{1m}(i)$ and $q_{1m}(j)$ are the 1st order Steinhardt vectors calculated for atom $i$ and atom $j$ respectively and the asterisk denotes complex conjugation. 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. The sum in the numerator of this expression is the dot product of the Steinhardt parameters for atoms $i$ and $j$ and thus measures the degree to which the orientations of these adjacent atoms are correlated.

The following input shows how this works in practice. This input calculates the average value of the LOCAL_Q1 parameter for the 64 Lennard Jones atoms in the system under study and prints this quantity 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 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 vectors 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 compbination 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 --- lq1The LOCAL_Q1 action with label lq1 calculates the following quantities: Quantity    Type    Description  
lq1 vector the values of the local steinhardt parameters for the input atoms
lq1_mean scalar the mean of the colvars: LOCAL_Q1Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. This action is a shortcut. More details SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL D_0=1.3 R_0=0.2} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# lq1: LOCAL_Q1 SPECIES=q1 SWITCH={RATIONAL 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):
lq1_uvecThe CONSTANT action with label lq1_uvec calculates the following quantities: Quantity    Type    Description  
lq1_uvec 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=6
lq1_grpThe GROUP action with label lq1_grp calculates the following quantities: Quantity    Type    Description  
lq1_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=q1
lq1_nmatThe OUTER_PRODUCT action with label lq1_nmat calculates the following quantities: Quantity    Type    Description  
lq1_nmat matrix a matrix containing the outer product of the two input vectors that was obtained using the function that was input: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=q1_norm,lq1_uvec
lq1_uvecsThe VSTACK action with label lq1_uvecs calculates the following quantities: Quantity    Type    Description  
lq1_uvecs matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
lq1_vecsThe CUSTOM action with label lq1_vecs calculates the following quantities: Quantity    Type    Description  
lq1_vecs matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq1_uvecs,lq1_nmat 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
lq1_vecsTThe TRANSPOSE action with label lq1_vecsT calculates the following quantities: Quantity    Type    Description  
lq1_vecsT matrix the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=lq1_vecs
lq1_cmapThe CONTACT_MATRIX action with label lq1_cmap calculates the following quantities: Quantity    Type    Description  
lq1_cmap matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=q1 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}
lq1_dpmatThe MATRIX_PRODUCT action with label lq1_dpmat calculates the following quantities: Quantity    Type    Description  
lq1_dpmat matrix the product of the two input matrices: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=lq1_vecs,lq1_vecsT
lq1_prodThe CUSTOM action with label lq1_prod calculates the following quantities: Quantity    Type    Description  
lq1_prod matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq1_cmap,lq1_dpmat 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
lq1_onesThe CONSTANT action with label lq1_ones calculates the following quantities: Quantity    Type    Description  
lq1_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
lq1The MATRIX_VECTOR_PRODUCT action with label lq1 calculates the following quantities: Quantity    Type    Description  
lq1 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=lq1_prod,lq1_ones
lq1_denomThe MATRIX_VECTOR_PRODUCT action with label lq1_denom calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_cmap,lq1_ones
lq1_avThe CUSTOM action with label lq1_av calculates the following quantities: Quantity    Type    Description  
lq1_av 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=lq1,lq1_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
lq1_meanThe MEAN action with label lq1_mean calculates the following quantities: Quantity    Type    Description  
lq1_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=lq1_av 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=lq1.mean FILEthe name of the file on which to output these quantities=colvar

The following input calculates the distribution of LOCAL_Q1 parameters at any given time and outputs this information to a file.

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 vectors 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 compbination 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 --- lq1The LOCAL_Q1 action with label lq1 calculates the following quantities: Quantity    Type    Description  
lq1 vector the values of the local steinhardt parameters for the input atoms
lq1_between-1 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-2 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-3 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-4 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-5 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-6 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-7 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-8 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-9 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-10 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-11 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-12 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-13 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-14 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-15 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-16 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-17 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-18 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-19 scalar the number of colvars that have a value that lies in a particular interval
lq1_between-20 scalar the number of colvars that have a value that lies in a particular interval: LOCAL_Q1Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. This action is a shortcut. More details SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1}
# PLUMED interprets the command:
# lq1: LOCAL_Q1 SPECIES=q1 SWITCH={RATIONAL 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):
lq1_uvecThe CONSTANT action with label lq1_uvec calculates the following quantities: Quantity    Type    Description  
lq1_uvec 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=6
lq1_grpThe GROUP action with label lq1_grp calculates the following quantities: Quantity    Type    Description  
lq1_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=q1
lq1_nmatThe OUTER_PRODUCT action with label lq1_nmat calculates the following quantities: Quantity    Type    Description  
lq1_nmat matrix a matrix containing the outer product of the two input vectors that was obtained using the function that was input: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=q1_norm,lq1_uvec
lq1_uvecsThe VSTACK action with label lq1_uvecs calculates the following quantities: Quantity    Type    Description  
lq1_uvecs matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1
lq1_vecsThe CUSTOM action with label lq1_vecs calculates the following quantities: Quantity    Type    Description  
lq1_vecs matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq1_uvecs,lq1_nmat 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
lq1_vecsTThe TRANSPOSE action with label lq1_vecsT calculates the following quantities: Quantity    Type    Description  
lq1_vecsT matrix the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=lq1_vecs
lq1_cmapThe CONTACT_MATRIX action with label lq1_cmap calculates the following quantities: Quantity    Type    Description  
lq1_cmap matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=q1 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}
lq1_dpmatThe MATRIX_PRODUCT action with label lq1_dpmat calculates the following quantities: Quantity    Type    Description  
lq1_dpmat matrix the product of the two input matrices: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=lq1_vecs,lq1_vecsT
lq1_prodThe CUSTOM action with label lq1_prod calculates the following quantities: Quantity    Type    Description  
lq1_prod matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=lq1_cmap,lq1_dpmat 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
lq1_onesThe CONSTANT action with label lq1_ones calculates the following quantities: Quantity    Type    Description  
lq1_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
lq1The MATRIX_VECTOR_PRODUCT action with label lq1 calculates the following quantities: Quantity    Type    Description  
lq1 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=lq1_prod,lq1_ones
lq1_denomThe MATRIX_VECTOR_PRODUCT action with label lq1_denom calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_cmap,lq1_ones
lq1_avThe CUSTOM action with label lq1_av calculates the following quantities: Quantity    Type    Description  
lq1_av 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=lq1,lq1_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
lq1_bt1The BETWEEN action with label lq1_bt1 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-1The SUM action with label lq1_between-1 calculates the following quantities: Quantity    Type    Description  
lq1_between-1 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt2The BETWEEN action with label lq1_bt2 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-2The SUM action with label lq1_between-2 calculates the following quantities: Quantity    Type    Description  
lq1_between-2 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt3The BETWEEN action with label lq1_bt3 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-3The SUM action with label lq1_between-3 calculates the following quantities: Quantity    Type    Description  
lq1_between-3 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt4The BETWEEN action with label lq1_bt4 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-4The SUM action with label lq1_between-4 calculates the following quantities: Quantity    Type    Description  
lq1_between-4 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt5The BETWEEN action with label lq1_bt5 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-5The SUM action with label lq1_between-5 calculates the following quantities: Quantity    Type    Description  
lq1_between-5 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt6The BETWEEN action with label lq1_bt6 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-6The SUM action with label lq1_between-6 calculates the following quantities: Quantity    Type    Description  
lq1_between-6 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt7The BETWEEN action with label lq1_bt7 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-7The SUM action with label lq1_between-7 calculates the following quantities: Quantity    Type    Description  
lq1_between-7 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt8The BETWEEN action with label lq1_bt8 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-8The SUM action with label lq1_between-8 calculates the following quantities: Quantity    Type    Description  
lq1_between-8 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt9The BETWEEN action with label lq1_bt9 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-9The SUM action with label lq1_between-9 calculates the following quantities: Quantity    Type    Description  
lq1_between-9 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt9 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt10The BETWEEN action with label lq1_bt10 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-10The SUM action with label lq1_between-10 calculates the following quantities: Quantity    Type    Description  
lq1_between-10 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt10 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt11The BETWEEN action with label lq1_bt11 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-11The SUM action with label lq1_between-11 calculates the following quantities: Quantity    Type    Description  
lq1_between-11 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt12The BETWEEN action with label lq1_bt12 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-12The SUM action with label lq1_between-12 calculates the following quantities: Quantity    Type    Description  
lq1_between-12 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt13The BETWEEN action with label lq1_bt13 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-13The SUM action with label lq1_between-13 calculates the following quantities: Quantity    Type    Description  
lq1_between-13 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt13 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt14The BETWEEN action with label lq1_bt14 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-14The SUM action with label lq1_between-14 calculates the following quantities: Quantity    Type    Description  
lq1_between-14 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt14 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt15The BETWEEN action with label lq1_bt15 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-15The SUM action with label lq1_between-15 calculates the following quantities: Quantity    Type    Description  
lq1_between-15 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt15 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt16The BETWEEN action with label lq1_bt16 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-16The SUM action with label lq1_between-16 calculates the following quantities: Quantity    Type    Description  
lq1_between-16 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt16 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt17The BETWEEN action with label lq1_bt17 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-17The SUM action with label lq1_between-17 calculates the following quantities: Quantity    Type    Description  
lq1_between-17 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt17 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt18The BETWEEN action with label lq1_bt18 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-18The SUM action with label lq1_between-18 calculates the following quantities: Quantity    Type    Description  
lq1_between-18 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt18 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt19The BETWEEN action with label lq1_bt19 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-19The SUM action with label lq1_between-19 calculates the following quantities: Quantity    Type    Description  
lq1_between-19 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_bt19 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq1_bt20The BETWEEN action with label lq1_bt20 calculates the following quantities: Quantity    Type    Description  
lq1_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=lq1_av 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}
lq1_between-20The SUM action with label lq1_between-20 calculates the following quantities: Quantity    Type    Description  
lq1_between-20 scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lq1_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=lq1.* FILEthe name of the file on which to output these quantities=colvar

The following calculates the LOCAL_Q1 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file

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

q1aThe Q1 action with label q1a calculates the following quantities: Quantity    Type    Description  
q1a 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=1-5 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2
q1a: 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=1-5 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-64 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:
# q1a: Q1 SPECIESA=1-5 SPECIESB=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):
q1a_grpThe GROUP action with label q1a_grp calculates the following quantities: Quantity    Type    Description  
q1a_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-5
q1a_matThe CONTACT_MATRIX action with label q1a_mat calculates the following quantities: Quantity    Type    Description  
q1a_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1a_mat.x matrix the projection of the bond on the x axis
q1a_mat.y matrix the projection of the bond on the y axis
q1a_mat.z matrix the projection of the bond on the z axis: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-5 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=1-64 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 vectors connecting the atoms in the contact matrix
q1a_shThe SPHERICAL_HARMONIC action with label q1a_sh calculates the following quantities: Quantity    Type    Description  
q1a_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1a_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1a_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1a_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1a_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1a_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=q1a_mat.x,q1a_mat.y,q1a_mat.z,q1a_mat.w Lthe value of the angular momentum=1
q1a_denom_onesThe CONSTANT action with label q1a_denom_ones calculates the following quantities: Quantity    Type    Description  
q1a_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
q1a_denomThe MATRIX_VECTOR_PRODUCT action with label q1a_denom calculates the following quantities: Quantity    Type    Description  
q1a_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=q1a_mat.w,q1a_denom_ones
q1a_spThe MATRIX_VECTOR_PRODUCT action with label q1a_sp calculates the following quantities: Quantity    Type    Description  
q1a_sp.rm-n1 vector the product of the matrix q1a_sh.rm-n1 and the vector q1a_denom_ones
q1a_sp.rm-0 vector the product of the matrix q1a_sh.rm-0 and the vector q1a_denom_ones
q1a_sp.rm-p1 vector the product of the matrix q1a_sh.rm-p1 and the vector q1a_denom_ones
q1a_sp.im-n1 vector the product of the matrix q1a_sh.im-n1 and the vector q1a_denom_ones
q1a_sp.im-0 vector the product of the matrix q1a_sh.im-0 and the vector q1a_denom_ones
q1a_sp.im-p1 vector the product of the matrix q1a_sh.im-p1 and the vector q1a_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=q1a_sh.*,q1a_denom_ones
q1a_norm2The COMBINE action with label q1a_norm2 calculates the following quantities: Quantity    Type    Description  
q1a_norm2 vector the vector obtained by doing an element-wise application of a linear compbination 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=q1a_sp.rm-n1,q1a_sp.im-n1,q1a_sp.rm-0,q1a_sp.im-0,q1a_sp.rm-p1,q1a_sp.im-p1
q1a_normThe CUSTOM action with label q1a_norm calculates the following quantities: Quantity    Type    Description  
q1a_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=q1a_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
q1aThe CUSTOM action with label q1a calculates the following quantities: Quantity    Type    Description  
q1a 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=q1a_norm,q1a_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 --- q1bThe Q1 action with label q1b calculates the following quantities: Quantity    Type    Description  
q1b 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=6-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2
q1b: 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=6-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-64 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:
# q1b: Q1 SPECIESA=6-64 SPECIESB=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):
q1b_grpThe GROUP action with label q1b_grp calculates the following quantities: Quantity    Type    Description  
q1b_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=6-64
q1b_matThe CONTACT_MATRIX action with label q1b_mat calculates the following quantities: Quantity    Type    Description  
q1b_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q1b_mat.x matrix the projection of the bond on the x axis
q1b_mat.y matrix the projection of the bond on the y axis
q1b_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=6-64 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=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 vectors connecting the atoms in the contact matrix
q1b_shThe SPHERICAL_HARMONIC action with label q1b_sh calculates the following quantities: Quantity    Type    Description  
q1b_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1b_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1b_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q1b_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q1b_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q1b_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=q1b_mat.x,q1b_mat.y,q1b_mat.z,q1b_mat.w Lthe value of the angular momentum=1
q1b_denom_onesThe CONSTANT action with label q1b_denom_ones calculates the following quantities: Quantity    Type    Description  
q1b_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
q1b_denomThe MATRIX_VECTOR_PRODUCT action with label q1b_denom calculates the following quantities: Quantity    Type    Description  
q1b_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=q1b_mat.w,q1b_denom_ones
q1b_spThe MATRIX_VECTOR_PRODUCT action with label q1b_sp calculates the following quantities: Quantity    Type    Description  
q1b_sp.rm-n1 vector the product of the matrix q1b_sh.rm-n1 and the vector q1b_denom_ones
q1b_sp.rm-0 vector the product of the matrix q1b_sh.rm-0 and the vector q1b_denom_ones
q1b_sp.rm-p1 vector the product of the matrix q1b_sh.rm-p1 and the vector q1b_denom_ones
q1b_sp.im-n1 vector the product of the matrix q1b_sh.im-n1 and the vector q1b_denom_ones
q1b_sp.im-0 vector the product of the matrix q1b_sh.im-0 and the vector q1b_denom_ones
q1b_sp.im-p1 vector the product of the matrix q1b_sh.im-p1 and the vector q1b_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=q1b_sh.*,q1b_denom_ones
q1b_norm2The COMBINE action with label q1b_norm2 calculates the following quantities: Quantity    Type    Description  
q1b_norm2 vector the vector obtained by doing an element-wise application of a linear compbination 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=q1b_sp.rm-n1,q1b_sp.im-n1,q1b_sp.rm-0,q1b_sp.im-0,q1b_sp.rm-p1,q1b_sp.im-p1
q1b_normThe CUSTOM action with label q1b_norm calculates the following quantities: Quantity    Type    Description  
q1b_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=q1b_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
q1bThe CUSTOM action with label q1b calculates the following quantities: Quantity    Type    Description  
q1b 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=q1b_norm,q1b_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 --- w1The LOCAL_Q1 action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 vector the values of the local steinhardt parameters for the input atoms
w1_mean scalar the mean of the colvars: LOCAL_Q1Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. This action is a shortcut. More details SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q1a,q1b SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL D_0=1.3 R_0=0.2} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# w1: LOCAL_Q1 SPECIES=q1a,q1b SWITCH={RATIONAL 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):
w1_uvecThe CONSTANT action with label w1_uvec calculates the following quantities: Quantity    Type    Description  
w1_uvec 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=6
w1_grpThe GROUP action with label w1_grp calculates the following quantities: Quantity    Type    Description  
w1_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=q1a,q1b
w1_magsThe CONCATENATE action with label w1_mags calculates the following quantities: Quantity    Type    Description  
w1_mags vector the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=q1a_norm,q1b_norm
w1_uvecs1The VSTACK action with label w1_uvecs1 calculates the following quantities: Quantity    Type    Description  
w1_uvecs1 matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=q1a_sp.rm-n1,q1a_sp.im-n1,q1a_sp.rm-0,q1a_sp.im-0,q1a_sp.rm-p1,q1a_sp.im-p1
w1_uvecs2The VSTACK action with label w1_uvecs2 calculates the following quantities: Quantity    Type    Description  
w1_uvecs2 matrix a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=q1b_sp.rm-n1,q1b_sp.im-n1,q1b_sp.rm-0,q1b_sp.im-0,q1b_sp.rm-p1,q1b_sp.im-p1
w1_nmatThe OUTER_PRODUCT action with label w1_nmat calculates the following quantities: Quantity    Type    Description  
w1_nmat matrix a matrix containing the outer product of the two input vectors that was obtained using the function that was input: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=w1_mags,w1_uvec
w1_uvecsThe CONCATENATE action with label w1_uvecs calculates the following quantities: Quantity    Type    Description  
w1_uvecs matrix the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details MATRIX11specify the matrices that you wish to join together into a single matrix=w1_uvecs1 MATRIX21specify the matrices that you wish to join together into a single matrix=w1_uvecs2
w1_vecsThe CUSTOM action with label w1_vecs calculates the following quantities: Quantity    Type    Description  
w1_vecs matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=w1_uvecs,w1_nmat 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
w1_vecsTThe TRANSPOSE action with label w1_vecsT calculates the following quantities: Quantity    Type    Description  
w1_vecsT matrix the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=w1_vecs
w1_cmapThe CONTACT_MATRIX action with label w1_cmap calculates the following quantities: Quantity    Type    Description  
w1_cmap matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=q1a,q1b 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}
w1_dpmatThe MATRIX_PRODUCT action with label w1_dpmat calculates the following quantities: Quantity    Type    Description  
w1_dpmat matrix the product of the two input matrices: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=w1_vecs,w1_vecsT
w1_prodThe CUSTOM action with label w1_prod calculates the following quantities: Quantity    Type    Description  
w1_prod matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=w1_cmap,w1_dpmat 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
w1_onesThe CONSTANT action with label w1_ones calculates the following quantities: Quantity    Type    Description  
w1_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
w1The MATRIX_VECTOR_PRODUCT action with label w1 calculates the following quantities: Quantity    Type    Description  
w1 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=w1_prod,w1_ones
w1_denomThe MATRIX_VECTOR_PRODUCT action with label w1_denom calculates the following quantities: Quantity    Type    Description  
w1_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=w1_cmap,w1_ones
w1_avThe CUSTOM action with label w1_av calculates the following quantities: Quantity    Type    Description  
w1_av 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=w1,w1_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
w1_meanThe MEAN action with label w1_mean calculates the following quantities: Quantity    Type    Description  
w1_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=w1_av 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=w1.* FILEthe name of the file on which to output these quantities=colvar

Syntax

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

Keyword	Type	Default	Description
SPECIES	optional	not used	the label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters
SPECIESA	optional	not used	the label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters
SPECIESB	optional	not used	the label of the action that computes the Steinhardt parameters that you would like to use when calculating the loal steinhardt parameters
SWITCH	optional	not used	This keyword is used if you want to employ an alternative to the continuous swiching function defined above
LOWMEM	optional	false	this flag does nothing and is present only to ensure back-compatibility
LESS_THAN	optional	not used	calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.
MORE_THAN	optional	not used	calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.
ALT_MIN	optional	not used	calculate the minimum value
MIN	optional	not used	calculate the minimum value
MAX	optional	not used	calculate the maximum value
BETWEEN	optional	not used	calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.
HIGHEST	optional	false	this flag allows you to recover the highest of these variables
HISTOGRAM	optional	not used	calculate a discretized histogram of the distribution of values
LOWEST	optional	false	this flag allows you to recover the lowest of these variables
SUM	optional	false	calculate the sum of all the quantities
MEAN	optional	false	calculate the mean of all the quantities

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