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

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.

Further 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 vectors 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 compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 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_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 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} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# lq4: LOCAL_Q4 SPECIES=q4 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):
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
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_meanThe MEAN action with label lq4_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
lq4_mean
scalar
the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=lq4_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=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 vectors 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 compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 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
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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=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 vectors 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 compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 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 vectors 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 compbination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q4a,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 SPECIES=q4a,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,q4b
w4_magsThe CONCATENATE action with label w4_mags calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_mags
vector
the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=q4a_norm,q4b_norm
w4_uvecs1The VSTACK action with label w4_uvecs1 calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_uvecs1
matrix
a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=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_uvecs2The VSTACK action with label w4_uvecs2 calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_uvecs2
matrix
a matrix that contains the input vectors in its columns: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=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_nmatThe OUTER_PRODUCT action with label w4_nmat calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_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=w4_mags,w4_uvec
w4_uvecsThe CONCATENATE action with label w4_uvecs calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_uvecs
matrix
the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details MATRIX11specify the matrices that you wish to join together into a single matrix=w4_uvecs1 MATRIX21specify the matrices that you wish to join together into a single matrix=w4_uvecs2
w4_vecsThe CUSTOM action with label w4_vecs calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_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=w4_uvecs,w4_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
w4_vecsTThe TRANSPOSE action with label w4_vecsT calculates the following quantities:
 Quantity   
 Type   
 Description  
w4_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=w4_vecs
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 GROUPspecifies the list of atoms that should be assumed indistinguishable=q4a,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_vecs,w4_vecsT
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=64
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 all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=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

Syntax

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