PLUMED-NEST

Project ID: plumID:23.027
Source: water-structure-driver.dat
Originally used with PLUMED version: 2.5.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

# Plumed driver script to calculate ion coordination numbers and identify ion clusters in the EDL and bulk solution regions of CmuMD simulations 
# Aaron R. Finney and Matteo Salvalaglio
# Properties of aqueous electrolyte solutions at carbon electrodes: 
# effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer
# June 2023

#LOAD FILE=PairEntropies.cpp
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

The UNITS action with label  calculates somethingwoxThe GROUP action with label wox calculates the following quantities:
 Quantity   
 Type   
 Description  
wox
atoms
indices of atoms specified in GROUP: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-12000:3

# Q3
q3The Q3 action with label q3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3
vector
the value calculated by this action: 
Q3
Calculate 3rd order Steinhardt parameters. This action is a shortcut. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=wox 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
# PLUMED interprets the command:
# q3: Q3 SPECIES=wox SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
# as follows (Click the red comment above to revert to the short version of the input):
q3_grpThe GROUP action with label q3_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_grp
atoms
indices of atoms specified in GROUP: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=wox 
q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_mat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
q3_mat.x
matrix
the projection of the bond on the x axis
q3_mat.y
matrix
the projection of the bond on the y axis
q3_mat.z
matrix
the projection of the bond on the z axis: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUP
specifies the list of atoms that should be assumed indistinguishable
=wox 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
 
q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_sh.rm-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q3_sh.rm-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q3_sh.rm-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q3_sh.rm-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q3_sh.rm-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q3_sh.rm-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q3_sh.rm-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q3_sh.im-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q3_sh.im-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q3_sh.im-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q3_sh.im-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q3_sh.im-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q3_sh.im-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q3_sh.im-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities: 
SPHERICAL_HARMONIC
Calculate the values of all the spherical harmonic funtions for a particular value of l. More details
 
ARG
the input to this function
=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w 
L
the value of the angular momentum
=3 
q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_denom_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=4000
q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_denom
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=q3_mat.w,q3_denom_ones 
q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_sp.rm-n3
vector
the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones
q3_sp.rm-n2
vector
the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones
q3_sp.rm-n1
vector
the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones
q3_sp.rm-0
vector
the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones
q3_sp.rm-p1
vector
the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones
q3_sp.rm-p2
vector
the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones
q3_sp.rm-p3
vector
the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones
q3_sp.im-n3
vector
the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones
q3_sp.im-n2
vector
the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones
q3_sp.im-n1
vector
the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones
q3_sp.im-0
vector
the product of the matrix q3_sh.im-0 and the vector q3_denom_ones
q3_sp.im-p1
vector
the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones
q3_sp.im-p2
vector
the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones
q3_sp.im-p3
vector
the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=q3_sh.*,q3_denom_ones 
q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_norm2
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
PERIODIC
if 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 
ARG
the input to this function
=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 
q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_norm
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_norm2 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3The CUSTOM action with label q3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_norm,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- lq3The LOCAL_Q3 action with label lq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3
vector
the value calculated by this action: 
LOCAL_Q3
Calculate the local degree of order around an atoms by taking the average dot product between the q_3 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. This action is a shortcut. More details
 
SPECIES
=q3 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
# PLUMED interprets the command:
# lq3: LOCAL_Q3 SPECIES=q3 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
# as follows (Click the red comment above to revert to the short version of the input):
lq3_uvecThe CONSTANT action with label lq3_uvec calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_uvec
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=14
lq3_grpThe GROUP action with label lq3_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_grp
atoms
indices of atoms specified in GROUP: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=q3 
lq3_nmatThe OUTER_PRODUCT action with label lq3_nmat calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_nmat
matrix
a matrix containing the outer product of the two input vectors that was obtained using the function that was input: 
OUTER_PRODUCT
Calculate the outer product matrix of two vectors More details
 
ARG
the input for this action is the scalar output from one or more other actions
=q3_norm,lq3_uvec 
lq3_uvecsThe VSTACK action with label lq3_uvecs calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_uvecs
matrix
a matrix that contains the input vectors in its columns: 
VSTACK
Create a matrix by stacking vectors together More details
 
ARG
the input for this action is the scalar output from one or more other actions
=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 
lq3_vecsThe CUSTOM action with label lq3_vecs calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_vecs
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=lq3_uvecs,lq3_nmat 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
lq3_vecsTThe TRANSPOSE action with label lq3_vecsT calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_vecsT
matrix
the transpose of the input matrix: 
TRANSPOSE
Calculate the transpose of a matrix More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lq3_vecs 
lq3_cmapThe CONTACT_MATRIX action with label lq3_cmap calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_cmap
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUP
specifies the list of atoms that should be assumed indistinguishable
=q3 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} 
lq3_dpmatThe MATRIX_PRODUCT action with label lq3_dpmat calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_dpmat
matrix
the product of the two input matrices: 
MATRIX_PRODUCT
Calculate the product of two matrices More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lq3_vecs,lq3_vecsT 
lq3_prodThe CUSTOM action with label lq3_prod calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_prod
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=lq3_cmap,lq3_dpmat 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
lq3_onesThe CONSTANT action with label lq3_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=4000
lq3The MATRIX_VECTOR_PRODUCT action with label lq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lq3_prod,lq3_ones 
lq3_denomThe MATRIX_VECTOR_PRODUCT action with label lq3_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_denom
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lq3_cmap,lq3_ones 
lq3_avThe CUSTOM action with label lq3_av calculates the following quantities:
 Quantity   
 Type   
 Description  
lq3_av
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=lq3,lq3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- laq3The LOCAL_AVERAGE action with label laq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3
vector
the value calculated by this action: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms This action is a shortcut. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=q3 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
# PLUMED interprets the command:
# laq3: LOCAL_AVERAGE SPECIES=q3 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
# as follows (Click the red comment above to revert to the short version of the input):
laq3_grpThe GROUP action with label laq3_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_grp
atoms
indices of atoms specified in GROUP: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=q3 
laq3_matThe CONTACT_MATRIX action with label laq3_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUP
specifies the list of atoms that should be assumed indistinguishable
=q3 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} 
laq3_onesThe CONSTANT action with label laq3_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=4000
laq3_coordThe MATRIX_VECTOR_PRODUCT action with label laq3_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_coord
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=laq3_mat,laq3_ones 
q3_rmn-n3The CUSTOM action with label q3_rmn-n3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-n3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-n3,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-n3The CUSTOM action with label q3_imn-n3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-n3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-n3,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_rmn-n2The CUSTOM action with label q3_rmn-n2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-n2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-n2,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-n2The CUSTOM action with label q3_imn-n2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-n2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-n2,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_rmn-n1The CUSTOM action with label q3_rmn-n1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-n1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-n1,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-n1The CUSTOM action with label q3_imn-n1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-n1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-n1,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_rmn-0The CUSTOM action with label q3_rmn-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-0
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-0,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-0The CUSTOM action with label q3_imn-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-0
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-0,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_rmn-p1The CUSTOM action with label q3_rmn-p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-p1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-p1,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-p1The CUSTOM action with label q3_imn-p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-p1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-p1,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_rmn-p2The CUSTOM action with label q3_rmn-p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-p2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-p2,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-p2The CUSTOM action with label q3_imn-p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-p2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-p2,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_rmn-p3The CUSTOM action with label q3_rmn-p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_rmn-p3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.rm-p3,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
q3_imn-p3The CUSTOM action with label q3_imn-p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
q3_imn-p3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=q3_sp.im-p3,q3_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
laq3_vstackThe VSTACK action with label laq3_vstack calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_vstack
matrix
a matrix that contains the input vectors in its columns: 
VSTACK
Create a matrix by stacking vectors together More details
 
ARG
the input for this action is the scalar output from one or more other actions
=q3_rmn-n3,q3_imn-n3,q3_rmn-n2,q3_imn-n2,q3_rmn-n1,q3_imn-n1,q3_rmn-0,q3_imn-0,q3_rmn-p1,q3_imn-p1,q3_rmn-p2,q3_imn-p2,q3_rmn-p3,q3_imn-p3 
laq3_prodThe MATRIX_VECTOR_PRODUCT action with label laq3_prod calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_prod.q3_rmn-n3
vector
the product of the matrix laq3_mat and the vector q3_rmn-n3
laq3_prod.q3_imn-n3
vector
the product of the matrix laq3_mat and the vector q3_imn-n3
laq3_prod.q3_rmn-n2
vector
the product of the matrix laq3_mat and the vector q3_rmn-n2
laq3_prod.q3_imn-n2
vector
the product of the matrix laq3_mat and the vector q3_imn-n2
laq3_prod.q3_rmn-n1
vector
the product of the matrix laq3_mat and the vector q3_rmn-n1
laq3_prod.q3_imn-n1
vector
the product of the matrix laq3_mat and the vector q3_imn-n1
laq3_prod.q3_rmn-0
vector
the product of the matrix laq3_mat and the vector q3_rmn-0
laq3_prod.q3_imn-0
vector
the product of the matrix laq3_mat and the vector q3_imn-0
laq3_prod.q3_rmn-p1
vector
the product of the matrix laq3_mat and the vector q3_rmn-p1
laq3_prod.q3_imn-p1
vector
the product of the matrix laq3_mat and the vector q3_imn-p1
laq3_prod.q3_rmn-p2
vector
the product of the matrix laq3_mat and the vector q3_rmn-p2
laq3_prod.q3_imn-p2
vector
the product of the matrix laq3_mat and the vector q3_imn-p2
laq3_prod.q3_rmn-p3
vector
the product of the matrix laq3_mat and the vector q3_rmn-p3
laq3_prod.q3_imn-p3
vector
the product of the matrix laq3_mat and the vector q3_imn-p3: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=laq3_mat,q3_rmn-n3,q3_imn-n3,q3_rmn-n2,q3_imn-n2,q3_rmn-n1,q3_imn-n1,q3_rmn-0,q3_imn-0,q3_rmn-p1,q3_imn-p1,q3_rmn-p2,q3_imn-p2,q3_rmn-p3,q3_imn-p3 
laq3_vpstackThe VSTACK action with label laq3_vpstack calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_vpstack
matrix
a matrix that contains the input vectors in its columns: 
VSTACK
Create a matrix by stacking vectors together More details
 
ARG
the input for this action is the scalar output from one or more other actions
=laq3_prod.q3_rmn-n3,laq3_prod.q3_imn-n3,laq3_prod.q3_rmn-n2,laq3_prod.q3_imn-n2,laq3_prod.q3_rmn-n1,laq3_prod.q3_imn-n1,laq3_prod.q3_rmn-0,laq3_prod.q3_imn-0,laq3_prod.q3_rmn-p1,laq3_prod.q3_imn-p1,laq3_prod.q3_rmn-p2,laq3_prod.q3_imn-p2,laq3_prod.q3_rmn-p3,laq3_prod.q3_imn-p3 
laq3_lonesThe CONSTANT action with label laq3_lones calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_lones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=14
laq3_unormThe OUTER_PRODUCT action with label laq3_unorm calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_unorm
matrix
a matrix containing the outer product of the two input vectors that was obtained using the function that was input: 
OUTER_PRODUCT
Calculate the outer product matrix of two vectors More details
 
ARG
the input for this action is the scalar output from one or more other actions
=laq3_coord,laq3_lones 
laq3_avThe CUSTOM action with label laq3_av calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_av
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=laq3_vpstack,laq3_vstack,laq3_unorm 
FUNC
the function you wish to evaluate
=(x+y)/(1+z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
laq3_av2The CUSTOM action with label laq3_av2 calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_av2
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=laq3_av 
FUNC
the function you wish to evaluate
=x*x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
laq3_2The MATRIX_VECTOR_PRODUCT action with label laq3_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3_2
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=laq3_av2,laq3_lones 
laq3The CUSTOM action with label laq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
laq3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=laq3_2 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
hhq3The HISTOGRAM action with label hhq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3
grid
the estimate of the histogram as a function of the argument that was obtained: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 
DATA
an alternative to the ARG keyword
=q3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100
hhq3: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 
DATA
an alternative to the ARG keyword
=q3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
# PLUMED interprets the command:
# hhq3: HISTOGRAM DATA=q3 GRID_MIN=-1.5 GRID_MAX=1.5 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100
# as follows (Click the red comment above to revert to the short version of the input):
hhq3_weightThe CONSTANT action with label hhq3_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
hhq3_kde_uThe KDE action with label hhq3_kde_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3_kde_u
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=q3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
hhq3_kdeThe CUSTOM action with label hhq3_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3_kde
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhq3_kde_u 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=x/4000 
hhq3_kdepThe CUSTOM action with label hhq3_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhq3_kde,hhq3_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hhq3_uThe ACCUMULATE action with label hhq3_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hhq3_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=100 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hhq3_nsumThe ACCUMULATE action with label hhq3_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hhq3_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=100 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hhq3The CUSTOM action with label hhq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
hhq3
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhq3_u,hhq3_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- hhlq3The HISTOGRAM action with label hhlq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3
grid
the estimate of the histogram as a function of the argument that was obtained: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 
DATA
an alternative to the ARG keyword
=lq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100
hhlq3: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 
DATA
an alternative to the ARG keyword
=lq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
# PLUMED interprets the command:
# hhlq3: HISTOGRAM DATA=lq3 GRID_MIN=-1.5 GRID_MAX=1.5 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100
# as follows (Click the red comment above to revert to the short version of the input):
hhlq3_weightThe CONSTANT action with label hhlq3_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
hhlq3_kde_uThe KDE action with label hhlq3_kde_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3_kde_u
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
hhlq3_kdeThe CUSTOM action with label hhlq3_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3_kde
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhlq3_kde_u 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=x/4000 
hhlq3_kdepThe CUSTOM action with label hhlq3_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhlq3_kde,hhlq3_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hhlq3_uThe ACCUMULATE action with label hhlq3_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hhlq3_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=100 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hhlq3_nsumThe ACCUMULATE action with label hhlq3_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hhlq3_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=100 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hhlq3The CUSTOM action with label hhlq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlq3
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhlq3_u,hhlq3_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- hhlaq3The HISTOGRAM action with label hhlaq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3
grid
the estimate of the histogram as a function of the argument that was obtained: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 
DATA
an alternative to the ARG keyword
=laq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100
hhlaq3: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 
DATA
an alternative to the ARG keyword
=laq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
# PLUMED interprets the command:
# hhlaq3: HISTOGRAM DATA=laq3 GRID_MIN=-1.5 GRID_MAX=1.5 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100
# as follows (Click the red comment above to revert to the short version of the input):
hhlaq3_weightThe CONSTANT action with label hhlaq3_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
hhlaq3_kde_uThe KDE action with label hhlaq3_kde_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3_kde_u
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=laq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
hhlaq3_kdeThe CUSTOM action with label hhlaq3_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3_kde
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhlaq3_kde_u 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=x/4000 
hhlaq3_kdepThe CUSTOM action with label hhlaq3_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhlaq3_kde,hhlaq3_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hhlaq3_uThe ACCUMULATE action with label hhlaq3_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hhlaq3_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=100 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hhlaq3_nsumThe ACCUMULATE action with label hhlaq3_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hhlaq3_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=100 
CLEAR
 the frequency with which to clear all the accumulated data
=0 
hhlaq3The CUSTOM action with label hhlaq3 calculates the following quantities:
 Quantity   
 Type   
 Description  
hhlaq3
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hhlaq3_u,hhlaq3_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hhq3 
FILE
 the file on which to write the grid
=histo_q3 
STRIDE
 the frequency with which the grid should be output to the file
=1000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hhlq3 
FILE
 the file on which to write the grid
=histo_lq3 
STRIDE
 the frequency with which the grid should be output to the file
=1000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hhlaq3 
FILE
 the file on which to write the grid
=histo_laq3 
STRIDE
 the frequency with which the grid should be output to the file
=1000

# Pair entropies
#PAIRENTROPIES LABEL=s2 SPECIES=wox MAXR=5 SIGMA=0.15 LOCAL_DENSITY SWITCH={RATIONAL R_0=5.0 D_MAX=7.0 NN=50 MM=100} LOWMEM
#sa: LOCAL_AVERAGE SPECIES=s2 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} LOWMEM 

#hhe: HISTOGRAM DATA=s2 GRID_MIN=-6 GRID_MAX=0 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100
#hhle: HISTOGRAM DATA=sa GRID_MIN=-6 GRID_MAX=0 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100

#DUMPMULTICOLVAR FILE=entropy.xyz STRIDE=1 DATA=s2
#DUMPMULTICOLVAR FILE=localentropy.xyz STRIDE=1 DATA=sa

#DUMPGRID GRID=hhe FILE=histo_e STRIDE=1000
#DUMPGRID GRID=hhle FILE=histo_le STRIDE=1000