Shortcut: LOCAL_Q4

Module	symfunc
Description	Usage
Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 vector on the atoms in the first coordination sphere.
output value	type
the values of the local steinhardt parameters for the input atoms	vector

Details and examples

Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 vector on the atoms in the first coordination sphere.

The Q4 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 Q4 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_Q4 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:

$s_i = \frac{ \sum_j \sigma( r_{ij} ) \sum_{m=-4}^4 q_{4m}^{*}(i)q_{4m}(j) }{ \sum_j \sigma( r_{ij} ) }$

where $q_{4m}(i)$ and $q_{4m}(j)$ are the 4th 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_Q4 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

q4The Q4 action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 vector the norms of the vectors of spherical harmonic coefficients: Q4Calculate fourth 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
q4: Q4Calculate fourth 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:
# q4: Q4 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):
q4_grpThe GROUP action with label q4_grp calculates the following quantities: Quantity    Type    Description  
q4_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
q4_matThe CONTACT_MATRIX action with label q4_mat calculates the following quantities: Quantity    Type    Description  
q4_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q4_mat.x matrix the projection of the bond on the x axis
q4_mat.y matrix the projection of the bond on the y axis
q4_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
q4_shThe SPHERICAL_HARMONIC action with label q4_sh calculates the following quantities: Quantity    Type    Description  
q4_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th 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=q4_mat.x,q4_mat.y,q4_mat.z,q4_mat.w Lthe value of the angular momentum=4
q4_denom_onesThe CONSTANT action with label q4_denom_ones calculates the following quantities: Quantity    Type    Description  
q4_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
q4_denomThe MATRIX_VECTOR_PRODUCT action with label q4_denom calculates the following quantities: Quantity    Type    Description  
q4_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=q4_mat.w,q4_denom_ones
q4_spThe MATRIX_VECTOR_PRODUCT action with label q4_sp calculates the following quantities: Quantity    Type    Description  
q4_sp.rm-n4 vector the product of the matrix q4_sh.rm-n4 and the vector q4_denom_ones
q4_sp.rm-n3 vector the product of the matrix q4_sh.rm-n3 and the vector q4_denom_ones
q4_sp.rm-n2 vector the product of the matrix q4_sh.rm-n2 and the vector q4_denom_ones
q4_sp.rm-n1 vector the product of the matrix q4_sh.rm-n1 and the vector q4_denom_ones
q4_sp.rm-0 vector the product of the matrix q4_sh.rm-0 and the vector q4_denom_ones
q4_sp.rm-p1 vector the product of the matrix q4_sh.rm-p1 and the vector q4_denom_ones
q4_sp.rm-p2 vector the product of the matrix q4_sh.rm-p2 and the vector q4_denom_ones
q4_sp.rm-p3 vector the product of the matrix q4_sh.rm-p3 and the vector q4_denom_ones
q4_sp.rm-p4 vector the product of the matrix q4_sh.rm-p4 and the vector q4_denom_ones
q4_sp.im-n4 vector the product of the matrix q4_sh.im-n4 and the vector q4_denom_ones
q4_sp.im-n3 vector the product of the matrix q4_sh.im-n3 and the vector q4_denom_ones
q4_sp.im-n2 vector the product of the matrix q4_sh.im-n2 and the vector q4_denom_ones
q4_sp.im-n1 vector the product of the matrix q4_sh.im-n1 and the vector q4_denom_ones
q4_sp.im-0 vector the product of the matrix q4_sh.im-0 and the vector q4_denom_ones
q4_sp.im-p1 vector the product of the matrix q4_sh.im-p1 and the vector q4_denom_ones
q4_sp.im-p2 vector the product of the matrix q4_sh.im-p2 and the vector q4_denom_ones
q4_sp.im-p3 vector the product of the matrix q4_sh.im-p3 and the vector q4_denom_ones
q4_sp.im-p4 vector the product of the matrix q4_sh.im-p4 and the vector q4_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=q4_sh.*,q4_denom_ones
q4_norm2The COMBINE action with label q4_norm2 calculates the following quantities: Quantity    Type    Description  
q4_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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
q4_normThe CUSTOM action with label q4_norm calculates the following quantities: Quantity    Type    Description  
q4_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=q4_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
q4The CUSTOM action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 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=q4_norm,q4_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 --- lq4The LOCAL_Q4 action with label lq4 calculates the following quantities: Quantity    Type    Description  
lq4 vector the values of the local steinhardt parameters for the input atoms: LOCAL_Q4Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 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=q4 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}
# PLUMED interprets the command:
# lq4: LOCAL_Q4 SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2}
# as follows (Click the red comment above to revert to the short version of the input):
lq4_uvecThe CONSTANT action with label lq4_uvec calculates the following quantities: Quantity    Type    Description  
lq4_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=18
lq4_grpThe GROUP action with label lq4_grp calculates the following quantities: Quantity    Type    Description  
lq4_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=q4
lq4_nmatThe OUTER_PRODUCT action with label lq4_nmat calculates the following quantities: Quantity    Type    Description  
lq4_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=q4_norm,lq4_uvec
lq4_uvecsThe VSTACK action with label lq4_uvecs calculates the following quantities: Quantity    Type    Description  
lq4_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=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
lq4_vecsThe CUSTOM action with label lq4_vecs calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_uvecs,lq4_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
lq4_vecsTThe TRANSPOSE action with label lq4_vecsT calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_vecs
lq4_cmapThe CONTACT_MATRIX action with label lq4_cmap calculates the following quantities: Quantity    Type    Description  
lq4_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=q4 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}
lq4_dpmatThe MATRIX_PRODUCT action with label lq4_dpmat calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_vecs,lq4_vecsT MASKa matrix that is used to used to determine which elements of the output matrix to compute=lq4_cmap
lq4_prodThe CUSTOM action with label lq4_prod calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_cmap,lq4_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
lq4_onesThe CONSTANT action with label lq4_ones calculates the following quantities: Quantity    Type    Description  
lq4_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
lq4The MATRIX_VECTOR_PRODUCT action with label lq4 calculates the following quantities: Quantity    Type    Description  
lq4 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=lq4_prod,lq4_ones
lq4_denomThe MATRIX_VECTOR_PRODUCT action with label lq4_denom calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_cmap,lq4_ones
lq4_avThe CUSTOM action with label lq4_av calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4,lq4_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 --- lq4_meanThe MEAN action with label lq4_mean calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4 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=lq4_mean FILEthe name of the file on which to output these quantities=colvar

The following input calculates the distribution of LOCAL_Q4 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

q4The Q4 action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 vector the norms of the vectors of spherical harmonic coefficients: Q4Calculate fourth 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
q4: Q4Calculate fourth 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:
# q4: Q4 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):
q4_grpThe GROUP action with label q4_grp calculates the following quantities: Quantity    Type    Description  
q4_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
q4_matThe CONTACT_MATRIX action with label q4_mat calculates the following quantities: Quantity    Type    Description  
q4_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q4_mat.x matrix the projection of the bond on the x axis
q4_mat.y matrix the projection of the bond on the y axis
q4_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
q4_shThe SPHERICAL_HARMONIC action with label q4_sh calculates the following quantities: Quantity    Type    Description  
q4_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th 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=q4_mat.x,q4_mat.y,q4_mat.z,q4_mat.w Lthe value of the angular momentum=4
q4_denom_onesThe CONSTANT action with label q4_denom_ones calculates the following quantities: Quantity    Type    Description  
q4_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
q4_denomThe MATRIX_VECTOR_PRODUCT action with label q4_denom calculates the following quantities: Quantity    Type    Description  
q4_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=q4_mat.w,q4_denom_ones
q4_spThe MATRIX_VECTOR_PRODUCT action with label q4_sp calculates the following quantities: Quantity    Type    Description  
q4_sp.rm-n4 vector the product of the matrix q4_sh.rm-n4 and the vector q4_denom_ones
q4_sp.rm-n3 vector the product of the matrix q4_sh.rm-n3 and the vector q4_denom_ones
q4_sp.rm-n2 vector the product of the matrix q4_sh.rm-n2 and the vector q4_denom_ones
q4_sp.rm-n1 vector the product of the matrix q4_sh.rm-n1 and the vector q4_denom_ones
q4_sp.rm-0 vector the product of the matrix q4_sh.rm-0 and the vector q4_denom_ones
q4_sp.rm-p1 vector the product of the matrix q4_sh.rm-p1 and the vector q4_denom_ones
q4_sp.rm-p2 vector the product of the matrix q4_sh.rm-p2 and the vector q4_denom_ones
q4_sp.rm-p3 vector the product of the matrix q4_sh.rm-p3 and the vector q4_denom_ones
q4_sp.rm-p4 vector the product of the matrix q4_sh.rm-p4 and the vector q4_denom_ones
q4_sp.im-n4 vector the product of the matrix q4_sh.im-n4 and the vector q4_denom_ones
q4_sp.im-n3 vector the product of the matrix q4_sh.im-n3 and the vector q4_denom_ones
q4_sp.im-n2 vector the product of the matrix q4_sh.im-n2 and the vector q4_denom_ones
q4_sp.im-n1 vector the product of the matrix q4_sh.im-n1 and the vector q4_denom_ones
q4_sp.im-0 vector the product of the matrix q4_sh.im-0 and the vector q4_denom_ones
q4_sp.im-p1 vector the product of the matrix q4_sh.im-p1 and the vector q4_denom_ones
q4_sp.im-p2 vector the product of the matrix q4_sh.im-p2 and the vector q4_denom_ones
q4_sp.im-p3 vector the product of the matrix q4_sh.im-p3 and the vector q4_denom_ones
q4_sp.im-p4 vector the product of the matrix q4_sh.im-p4 and the vector q4_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=q4_sh.*,q4_denom_ones
q4_norm2The COMBINE action with label q4_norm2 calculates the following quantities: Quantity    Type    Description  
q4_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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
q4_normThe CUSTOM action with label q4_norm calculates the following quantities: Quantity    Type    Description  
q4_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=q4_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
q4The CUSTOM action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 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=q4_norm,q4_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 --- lq4The LOCAL_Q4 action with label lq4 calculates the following quantities: Quantity    Type    Description  
lq4 vector the values of the local steinhardt parameters for the input atoms
lq4_between-1 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-2 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-3 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-4 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-5 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-6 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-7 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-8 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-9 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-10 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-11 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-12 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-13 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-14 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-15 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-16 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-17 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-18 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-19 scalar the number of colvars that have a value that lies in a particular interval
lq4_between-20 scalar the number of colvars that have a value that lies in a particular interval: LOCAL_Q4Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 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=q4 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:
# lq4: LOCAL_Q4 SPECIES=q4 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):
lq4_uvecThe CONSTANT action with label lq4_uvec calculates the following quantities: Quantity    Type    Description  
lq4_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=18
lq4_grpThe GROUP action with label lq4_grp calculates the following quantities: Quantity    Type    Description  
lq4_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=q4
lq4_nmatThe OUTER_PRODUCT action with label lq4_nmat calculates the following quantities: Quantity    Type    Description  
lq4_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=q4_norm,lq4_uvec
lq4_uvecsThe VSTACK action with label lq4_uvecs calculates the following quantities: Quantity    Type    Description  
lq4_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=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
lq4_vecsThe CUSTOM action with label lq4_vecs calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_uvecs,lq4_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
lq4_vecsTThe TRANSPOSE action with label lq4_vecsT calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_vecs
lq4_cmapThe CONTACT_MATRIX action with label lq4_cmap calculates the following quantities: Quantity    Type    Description  
lq4_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=q4 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}
lq4_dpmatThe MATRIX_PRODUCT action with label lq4_dpmat calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_vecs,lq4_vecsT MASKa matrix that is used to used to determine which elements of the output matrix to compute=lq4_cmap
lq4_prodThe CUSTOM action with label lq4_prod calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_cmap,lq4_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
lq4_onesThe CONSTANT action with label lq4_ones calculates the following quantities: Quantity    Type    Description  
lq4_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
lq4The MATRIX_VECTOR_PRODUCT action with label lq4 calculates the following quantities: Quantity    Type    Description  
lq4 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=lq4_prod,lq4_ones
lq4_denomThe MATRIX_VECTOR_PRODUCT action with label lq4_denom calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_cmap,lq4_ones
lq4_avThe CUSTOM action with label lq4_av calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4,lq4_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
lq4_bt1The BETWEEN action with label lq4_bt1 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-1The SUM action with label lq4_between-1 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt2The BETWEEN action with label lq4_bt2 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-2The SUM action with label lq4_between-2 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt3The BETWEEN action with label lq4_bt3 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-3The SUM action with label lq4_between-3 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt4The BETWEEN action with label lq4_bt4 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-4The SUM action with label lq4_between-4 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt5The BETWEEN action with label lq4_bt5 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-5The SUM action with label lq4_between-5 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt6The BETWEEN action with label lq4_bt6 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-6The SUM action with label lq4_between-6 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt7The BETWEEN action with label lq4_bt7 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-7The SUM action with label lq4_between-7 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt8The BETWEEN action with label lq4_bt8 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-8The SUM action with label lq4_between-8 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt9The BETWEEN action with label lq4_bt9 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-9The SUM action with label lq4_between-9 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt9 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt10The BETWEEN action with label lq4_bt10 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-10The SUM action with label lq4_between-10 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt10 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt11The BETWEEN action with label lq4_bt11 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-11The SUM action with label lq4_between-11 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt12The BETWEEN action with label lq4_bt12 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-12The SUM action with label lq4_between-12 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt13The BETWEEN action with label lq4_bt13 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-13The SUM action with label lq4_between-13 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt13 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt14The BETWEEN action with label lq4_bt14 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-14The SUM action with label lq4_between-14 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt14 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt15The BETWEEN action with label lq4_bt15 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-15The SUM action with label lq4_between-15 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt15 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt16The BETWEEN action with label lq4_bt16 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-16The SUM action with label lq4_between-16 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt16 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt17The BETWEEN action with label lq4_bt17 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-17The SUM action with label lq4_between-17 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt17 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt18The BETWEEN action with label lq4_bt18 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-18The SUM action with label lq4_between-18 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt18 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt19The BETWEEN action with label lq4_bt19 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-19The SUM action with label lq4_between-19 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_bt19 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lq4_bt20The BETWEEN action with label lq4_bt20 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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}
lq4_between-20The SUM action with label lq4_between-20 calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_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=lq4.* FILEthe name of the file on which to output these quantities=colvar

The following calculates the LOCAL_Q4 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

q4aThe Q4 action with label q4a calculates the following quantities: Quantity    Type    Description  
q4a vector the norms of the vectors of spherical harmonic coefficients: Q4Calculate fourth 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
q4a: Q4Calculate fourth 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:
# q4a: Q4 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):
q4a_grpThe GROUP action with label q4a_grp calculates the following quantities: Quantity    Type    Description  
q4a_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
q4a_matThe CONTACT_MATRIX action with label q4a_mat calculates the following quantities: Quantity    Type    Description  
q4a_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q4a_mat.x matrix the projection of the bond on the x axis
q4a_mat.y matrix the projection of the bond on the y axis
q4a_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 vector connecting the atoms in the contact matrix
q4a_shThe SPHERICAL_HARMONIC action with label q4a_sh calculates the following quantities: Quantity    Type    Description  
q4a_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4a_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4a_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4a_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4a_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4a_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4a_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4a_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4a_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4a_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4a_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4a_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4a_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4a_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4a_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4a_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4a_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4a_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th 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=q4a_mat.x,q4a_mat.y,q4a_mat.z,q4a_mat.w Lthe value of the angular momentum=4
q4a_denom_onesThe CONSTANT action with label q4a_denom_ones calculates the following quantities: Quantity    Type    Description  
q4a_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
q4a_denomThe MATRIX_VECTOR_PRODUCT action with label q4a_denom calculates the following quantities: Quantity    Type    Description  
q4a_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=q4a_mat.w,q4a_denom_ones
q4a_spThe MATRIX_VECTOR_PRODUCT action with label q4a_sp calculates the following quantities: Quantity    Type    Description  
q4a_sp.rm-n4 vector the product of the matrix q4a_sh.rm-n4 and the vector q4a_denom_ones
q4a_sp.rm-n3 vector the product of the matrix q4a_sh.rm-n3 and the vector q4a_denom_ones
q4a_sp.rm-n2 vector the product of the matrix q4a_sh.rm-n2 and the vector q4a_denom_ones
q4a_sp.rm-n1 vector the product of the matrix q4a_sh.rm-n1 and the vector q4a_denom_ones
q4a_sp.rm-0 vector the product of the matrix q4a_sh.rm-0 and the vector q4a_denom_ones
q4a_sp.rm-p1 vector the product of the matrix q4a_sh.rm-p1 and the vector q4a_denom_ones
q4a_sp.rm-p2 vector the product of the matrix q4a_sh.rm-p2 and the vector q4a_denom_ones
q4a_sp.rm-p3 vector the product of the matrix q4a_sh.rm-p3 and the vector q4a_denom_ones
q4a_sp.rm-p4 vector the product of the matrix q4a_sh.rm-p4 and the vector q4a_denom_ones
q4a_sp.im-n4 vector the product of the matrix q4a_sh.im-n4 and the vector q4a_denom_ones
q4a_sp.im-n3 vector the product of the matrix q4a_sh.im-n3 and the vector q4a_denom_ones
q4a_sp.im-n2 vector the product of the matrix q4a_sh.im-n2 and the vector q4a_denom_ones
q4a_sp.im-n1 vector the product of the matrix q4a_sh.im-n1 and the vector q4a_denom_ones
q4a_sp.im-0 vector the product of the matrix q4a_sh.im-0 and the vector q4a_denom_ones
q4a_sp.im-p1 vector the product of the matrix q4a_sh.im-p1 and the vector q4a_denom_ones
q4a_sp.im-p2 vector the product of the matrix q4a_sh.im-p2 and the vector q4a_denom_ones
q4a_sp.im-p3 vector the product of the matrix q4a_sh.im-p3 and the vector q4a_denom_ones
q4a_sp.im-p4 vector the product of the matrix q4a_sh.im-p4 and the vector q4a_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=q4a_sh.*,q4a_denom_ones
q4a_norm2The COMBINE action with label q4a_norm2 calculates the following quantities: Quantity    Type    Description  
q4a_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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4a_sp.rm-n4,q4a_sp.im-n4,q4a_sp.rm-n3,q4a_sp.im-n3,q4a_sp.rm-n2,q4a_sp.im-n2,q4a_sp.rm-n1,q4a_sp.im-n1,q4a_sp.rm-0,q4a_sp.im-0,q4a_sp.rm-p1,q4a_sp.im-p1,q4a_sp.rm-p2,q4a_sp.im-p2,q4a_sp.rm-p3,q4a_sp.im-p3,q4a_sp.rm-p4,q4a_sp.im-p4
q4a_normThe CUSTOM action with label q4a_norm calculates the following quantities: Quantity    Type    Description  
q4a_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=q4a_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
q4aThe CUSTOM action with label q4a calculates the following quantities: Quantity    Type    Description  
q4a 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=q4a_norm,q4a_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 --- q4bThe Q4 action with label q4b calculates the following quantities: Quantity    Type    Description  
q4b vector the norms of the vectors of spherical harmonic coefficients: Q4Calculate fourth 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
q4b: Q4Calculate fourth 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:
# q4b: Q4 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):
q4b_grpThe GROUP action with label q4b_grp calculates the following quantities: Quantity    Type    Description  
q4b_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
q4b_matThe CONTACT_MATRIX action with label q4b_mat calculates the following quantities: Quantity    Type    Description  
q4b_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q4b_mat.x matrix the projection of the bond on the x axis
q4b_mat.y matrix the projection of the bond on the y axis
q4b_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 vector connecting the atoms in the contact matrix
q4b_shThe SPHERICAL_HARMONIC action with label q4b_sh calculates the following quantities: Quantity    Type    Description  
q4b_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4b_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4b_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4b_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4b_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4b_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4b_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4b_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4b_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4b_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4b_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4b_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4b_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4b_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4b_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4b_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4b_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4b_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th 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=q4b_mat.x,q4b_mat.y,q4b_mat.z,q4b_mat.w Lthe value of the angular momentum=4
q4b_denom_onesThe CONSTANT action with label q4b_denom_ones calculates the following quantities: Quantity    Type    Description  
q4b_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
q4b_denomThe MATRIX_VECTOR_PRODUCT action with label q4b_denom calculates the following quantities: Quantity    Type    Description  
q4b_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=q4b_mat.w,q4b_denom_ones
q4b_spThe MATRIX_VECTOR_PRODUCT action with label q4b_sp calculates the following quantities: Quantity    Type    Description  
q4b_sp.rm-n4 vector the product of the matrix q4b_sh.rm-n4 and the vector q4b_denom_ones
q4b_sp.rm-n3 vector the product of the matrix q4b_sh.rm-n3 and the vector q4b_denom_ones
q4b_sp.rm-n2 vector the product of the matrix q4b_sh.rm-n2 and the vector q4b_denom_ones
q4b_sp.rm-n1 vector the product of the matrix q4b_sh.rm-n1 and the vector q4b_denom_ones
q4b_sp.rm-0 vector the product of the matrix q4b_sh.rm-0 and the vector q4b_denom_ones
q4b_sp.rm-p1 vector the product of the matrix q4b_sh.rm-p1 and the vector q4b_denom_ones
q4b_sp.rm-p2 vector the product of the matrix q4b_sh.rm-p2 and the vector q4b_denom_ones
q4b_sp.rm-p3 vector the product of the matrix q4b_sh.rm-p3 and the vector q4b_denom_ones
q4b_sp.rm-p4 vector the product of the matrix q4b_sh.rm-p4 and the vector q4b_denom_ones
q4b_sp.im-n4 vector the product of the matrix q4b_sh.im-n4 and the vector q4b_denom_ones
q4b_sp.im-n3 vector the product of the matrix q4b_sh.im-n3 and the vector q4b_denom_ones
q4b_sp.im-n2 vector the product of the matrix q4b_sh.im-n2 and the vector q4b_denom_ones
q4b_sp.im-n1 vector the product of the matrix q4b_sh.im-n1 and the vector q4b_denom_ones
q4b_sp.im-0 vector the product of the matrix q4b_sh.im-0 and the vector q4b_denom_ones
q4b_sp.im-p1 vector the product of the matrix q4b_sh.im-p1 and the vector q4b_denom_ones
q4b_sp.im-p2 vector the product of the matrix q4b_sh.im-p2 and the vector q4b_denom_ones
q4b_sp.im-p3 vector the product of the matrix q4b_sh.im-p3 and the vector q4b_denom_ones
q4b_sp.im-p4 vector the product of the matrix q4b_sh.im-p4 and the vector q4b_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=q4b_sh.*,q4b_denom_ones
q4b_norm2The COMBINE action with label q4b_norm2 calculates the following quantities: Quantity    Type    Description  
q4b_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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4b_sp.rm-n4,q4b_sp.im-n4,q4b_sp.rm-n3,q4b_sp.im-n3,q4b_sp.rm-n2,q4b_sp.im-n2,q4b_sp.rm-n1,q4b_sp.im-n1,q4b_sp.rm-0,q4b_sp.im-0,q4b_sp.rm-p1,q4b_sp.im-p1,q4b_sp.rm-p2,q4b_sp.im-p2,q4b_sp.rm-p3,q4b_sp.im-p3,q4b_sp.rm-p4,q4b_sp.im-p4
q4b_normThe CUSTOM action with label q4b_norm calculates the following quantities: Quantity    Type    Description  
q4b_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=q4b_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
q4bThe CUSTOM action with label q4b calculates the following quantities: Quantity    Type    Description  
q4b 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=q4b_norm,q4b_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 --- w4The LOCAL_Q4 action with label w4 calculates the following quantities: Quantity    Type    Description  
w4 vector the values of the local steinhardt parameters for the input atoms
w4_mean scalar the mean of the colvars: LOCAL_Q4Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 vector on the atoms in the first coordination sphere. This action is a shortcut. More details SPECIESAthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q4a SPECIESBthe label of the action that computes the Steinhardt parameters that you would like to use when calculating the loal steinhardt parameters=q4b 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:
# w4: LOCAL_Q4 SPECIESA=q4a SPECIESB=q4b 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):
w4_uvecThe CONSTANT action with label w4_uvec calculates the following quantities: Quantity    Type    Description  
w4_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=18
w4_grpThe GROUP action with label w4_grp calculates the following quantities: Quantity    Type    Description  
w4_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=q4a
w4_nmatAThe OUTER_PRODUCT action with label w4_nmatA calculates the following quantities: Quantity    Type    Description  
w4_nmatA 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=q4a_norm,w4_uvec
w4_uvecsAThe VSTACK action with label w4_uvecsA calculates the following quantities: Quantity    Type    Description  
w4_uvecsA 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=q4a_sp.rm-n4,q4a_sp.im-n4,q4a_sp.rm-n3,q4a_sp.im-n3,q4a_sp.rm-n2,q4a_sp.im-n2,q4a_sp.rm-n1,q4a_sp.im-n1,q4a_sp.rm-0,q4a_sp.im-0,q4a_sp.rm-p1,q4a_sp.im-p1,q4a_sp.rm-p2,q4a_sp.im-p2,q4a_sp.rm-p3,q4a_sp.im-p3,q4a_sp.rm-p4,q4a_sp.im-p4
w4_vecsAThe CUSTOM action with label w4_vecsA calculates the following quantities: Quantity    Type    Description  
w4_vecsA 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=w4_uvecsA,w4_nmatA 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
w4_nmatBThe OUTER_PRODUCT action with label w4_nmatB calculates the following quantities: Quantity    Type    Description  
w4_nmatB 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=w4_uvec,q4b_norm
w4_uvecsBTThe VSTACK action with label w4_uvecsBT calculates the following quantities: Quantity    Type    Description  
w4_uvecsBT 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=q4b_sp.rm-n4,q4b_sp.im-n4,q4b_sp.rm-n3,q4b_sp.im-n3,q4b_sp.rm-n2,q4b_sp.im-n2,q4b_sp.rm-n1,q4b_sp.im-n1,q4b_sp.rm-0,q4b_sp.im-0,q4b_sp.rm-p1,q4b_sp.im-p1,q4b_sp.rm-p2,q4b_sp.im-p2,q4b_sp.rm-p3,q4b_sp.im-p3,q4b_sp.rm-p4,q4b_sp.im-p4
w4_uvecsBThe TRANSPOSE action with label w4_uvecsB calculates the following quantities: Quantity    Type    Description  
w4_uvecsB 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=w4_uvecsBT
w4_vecsBThe CUSTOM action with label w4_vecsB calculates the following quantities: Quantity    Type    Description  
w4_vecsB 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=w4_uvecsB,w4_nmatB 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
w4_cmapThe CONTACT_MATRIX action with label w4_cmap calculates the following quantities: Quantity    Type    Description  
w4_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 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=q4a 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=q4b 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}
w4_dpmatThe MATRIX_PRODUCT action with label w4_dpmat calculates the following quantities: Quantity    Type    Description  
w4_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=w4_vecsA,w4_vecsB MASKa matrix that is used to used to determine which elements of the output matrix to compute=w4_cmap
w4_prodThe CUSTOM action with label w4_prod calculates the following quantities: Quantity    Type    Description  
w4_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=w4_cmap,w4_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
w4_onesThe CONSTANT action with label w4_ones calculates the following quantities: Quantity    Type    Description  
w4_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=59
w4The MATRIX_VECTOR_PRODUCT action with label w4 calculates the following quantities: Quantity    Type    Description  
w4 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=w4_prod,w4_ones
w4_denomThe MATRIX_VECTOR_PRODUCT action with label w4_denom calculates the following quantities: Quantity    Type    Description  
w4_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=w4_cmap,w4_ones
w4_avThe CUSTOM action with label w4_av calculates the following quantities: Quantity    Type    Description  
w4_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=w4,w4_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
w4_meanThe MEAN action with label w4_mean calculates the following quantities: Quantity    Type    Description  
w4_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=w4_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=w4.* FILEthe name of the file on which to output these quantities=colvar

The MASK keyword

You can use the MASK keyword with this action in the same way that it is used with COORDINATIONNUMBER. This keyword thus expects a vector in input, which tells PLUMED the atoms for which you do not need to calculate the function. As illustrated below, this is useful if you are using functionality from the volumes module to calculate the average value of the $s_i$ parameter that is defined by the equation above 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

# Calculate the Q4 parameters for all the atoms
q4The Q4 action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 vector the norms of the vectors of spherical harmonic coefficients: Q4Calculate fourth 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 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:
# q4: Q4 SPECIES=1-400 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):
q4_grpThe GROUP action with label q4_grp calculates the following quantities: Quantity    Type    Description  
q4_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
q4_matThe CONTACT_MATRIX action with label q4_mat calculates the following quantities: Quantity    Type    Description  
q4_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms
q4_mat.x matrix the projection of the bond on the x axis
q4_mat.y matrix the projection of the bond on the y axis
q4_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=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
q4_shThe SPHERICAL_HARMONIC action with label q4_sh calculates the following quantities: Quantity    Type    Description  
q4_sh.rm-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.rm-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4_sh.im-n4 matrix the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.im-p4 matrix the real parts of the spherical harmonic values with the m value given  This is the p4th 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=q4_mat.x,q4_mat.y,q4_mat.z,q4_mat.w Lthe value of the angular momentum=4
q4_denom_onesThe CONSTANT action with label q4_denom_ones calculates the following quantities: Quantity    Type    Description  
q4_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
q4_denomThe MATRIX_VECTOR_PRODUCT action with label q4_denom calculates the following quantities: Quantity    Type    Description  
q4_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=q4_mat.w,q4_denom_ones
q4_spThe MATRIX_VECTOR_PRODUCT action with label q4_sp calculates the following quantities: Quantity    Type    Description  
q4_sp.rm-n4 vector the product of the matrix q4_sh.rm-n4 and the vector q4_denom_ones
q4_sp.rm-n3 vector the product of the matrix q4_sh.rm-n3 and the vector q4_denom_ones
q4_sp.rm-n2 vector the product of the matrix q4_sh.rm-n2 and the vector q4_denom_ones
q4_sp.rm-n1 vector the product of the matrix q4_sh.rm-n1 and the vector q4_denom_ones
q4_sp.rm-0 vector the product of the matrix q4_sh.rm-0 and the vector q4_denom_ones
q4_sp.rm-p1 vector the product of the matrix q4_sh.rm-p1 and the vector q4_denom_ones
q4_sp.rm-p2 vector the product of the matrix q4_sh.rm-p2 and the vector q4_denom_ones
q4_sp.rm-p3 vector the product of the matrix q4_sh.rm-p3 and the vector q4_denom_ones
q4_sp.rm-p4 vector the product of the matrix q4_sh.rm-p4 and the vector q4_denom_ones
q4_sp.im-n4 vector the product of the matrix q4_sh.im-n4 and the vector q4_denom_ones
q4_sp.im-n3 vector the product of the matrix q4_sh.im-n3 and the vector q4_denom_ones
q4_sp.im-n2 vector the product of the matrix q4_sh.im-n2 and the vector q4_denom_ones
q4_sp.im-n1 vector the product of the matrix q4_sh.im-n1 and the vector q4_denom_ones
q4_sp.im-0 vector the product of the matrix q4_sh.im-0 and the vector q4_denom_ones
q4_sp.im-p1 vector the product of the matrix q4_sh.im-p1 and the vector q4_denom_ones
q4_sp.im-p2 vector the product of the matrix q4_sh.im-p2 and the vector q4_denom_ones
q4_sp.im-p3 vector the product of the matrix q4_sh.im-p3 and the vector q4_denom_ones
q4_sp.im-p4 vector the product of the matrix q4_sh.im-p4 and the vector q4_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=q4_sh.*,q4_denom_ones
q4_norm2The COMBINE action with label q4_norm2 calculates the following quantities: Quantity    Type    Description  
q4_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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
q4_normThe CUSTOM action with label q4_norm calculates the following quantities: Quantity    Type    Description  
q4_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=q4_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
q4The CUSTOM action with label q4 calculates the following quantities: Quantity    Type    Description  
q4 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=q4_norm,q4_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 --- # 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 local_q4 parameters
lq4The LOCAL_Q4 action with label lq4 calculates the following quantities: Quantity    Type    Description  
lq4 vector the values of the local steinhardt parameters for the input atoms: LOCAL_Q4Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 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=q4 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 D_MAX=3.0} MASKthe label/s for vectors that are used to determine which local steinhardt parameters to compute=sphere
# PLUMED interprets the command:
# lq4: LOCAL_Q4 SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} MASK=sphere
# as follows (Click the red comment above to revert to the short version of the input):
lq4_uvecThe CONSTANT action with label lq4_uvec calculates the following quantities: Quantity    Type    Description  
lq4_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=18
lq4_grpThe GROUP action with label lq4_grp calculates the following quantities: Quantity    Type    Description  
lq4_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=q4
lq4_nmatThe OUTER_PRODUCT action with label lq4_nmat calculates the following quantities: Quantity    Type    Description  
lq4_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=q4_norm,lq4_uvec
lq4_uvecsThe VSTACK action with label lq4_uvecs calculates the following quantities: Quantity    Type    Description  
lq4_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=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
lq4_vecsThe CUSTOM action with label lq4_vecs calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_uvecs,lq4_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
lq4_vecsTThe TRANSPOSE action with label lq4_vecsT calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_vecs
lq4_cmapThe CONTACT_MATRIX action with label lq4_cmap calculates the following quantities: Quantity    Type    Description  
lq4_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=q4 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} MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere
lq4_dpmatThe MATRIX_PRODUCT action with label lq4_dpmat calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_vecs,lq4_vecsT MASKa matrix that is used to used to determine which elements of the output matrix to compute=lq4_cmap
lq4_prodThe CUSTOM action with label lq4_prod calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_cmap,lq4_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
lq4_onesThe CONSTANT action with label lq4_ones calculates the following quantities: Quantity    Type    Description  
lq4_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
lq4The MATRIX_VECTOR_PRODUCT action with label lq4 calculates the following quantities: Quantity    Type    Description  
lq4 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=lq4_prod,lq4_ones
lq4_denomThe MATRIX_VECTOR_PRODUCT action with label lq4_denom calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4_cmap,lq4_ones
lq4_avThe CUSTOM action with label lq4_av calculates the following quantities: Quantity    Type    Description  
lq4_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=lq4,lq4_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=lq4,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 calculates the average $s_i$ parameter for those atoms that are within a spherical region that is centered on the point $(2.5,2.5,2.5)$ . By including the MASK keyword in the LOCAL_Q4 line we reduce the number of $s_i$ values we have to compute using the expression above. However, we are still asking PLUMED to calculate the $q_{lm}$ vectors for many atoms that will not contribute to the final averaged quantity. The documentation for LOCAL_AVERAGE discusses how you can create a mask vector that can act upon the Q4 action here that will ensure that you are not calculating $q_{lm}$ vectors that are not required.

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
lessthan	scalar	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	scalar	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	scalar	ALT_MIN	the minimum value of the cv
min	scalar	MIN	the minimum colvar
max	scalar	MAX	the maximum colvar
between	scalar	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	scalar	HIGHEST	the largest of the colvars
lowest	scalar	LOWEST	the smallest of the colvars
sum	scalar	SUM	the sum of the colvars
mean	scalar	MEAN	the mean of the colvars

Full list of keywords

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

Keyword	Type	Default	Description
SPECIES	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
MASK	optional	not used	the label/s for vectors that are used to determine which local steinhardt parameters to compute
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
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
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

Quantity	Type	Description
q4	vector	the norms of the vectors of spherical harmonic coefficients