PLUMED-NEST

Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/3-production/IceIII-260.0-2500.0/plumed.equil.dat
Originally used with PLUMED version: 2.8
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1944:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcvThe ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv
vector
the environmental similar parameter for each of the input atoms
refcv_morethan
scalar
the number of colvars that have a value more than a threshold
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
REFERENCE_11
PDB files with relative distances from central atom
=env11.pdb
 
REFERENCE_12
PDB files with relative distances from central atom
=env12.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.604 D_MAX=0.972}
... ENVIRONMENTSIMILARITY
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1944:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
REFERENCE_11
PDB files with relative distances from central atom
=env11.pdb
 
REFERENCE_12
PDB files with relative distances from central atom
=env12.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.604 D_MAX=0.972}
 
CUTOFF
 how many multiples of sigma would you like to consider beyond the maximum distance in the environment
=3 
LCUTOFF
 any atoms separated by less than this tolerance should be ignored
=0.0001 
LAMBDA
 Lambda parameter
=100
... ENVIRONMENTSIMILARITY
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIES=1-1944:3
#  SIGMA=0.0675
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv
#  REFERENCE_1=env1.pdb
#  REFERENCE_2=env2.pdb
#  REFERENCE_3=env3.pdb
#  REFERENCE_4=env4.pdb
#  REFERENCE_5=env5.pdb
#  REFERENCE_6=env6.pdb
#  REFERENCE_7=env7.pdb
#  REFERENCE_8=env8.pdb
#  REFERENCE_9=env9.pdb
#  REFERENCE_10=env10.pdb
#  REFERENCE_11=env11.pdb
#  REFERENCE_12=env12.pdb
#  MORE_THAN={CUBIC D_0=0.604 D_MAX=0.972}
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv_cmatThe DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_cmat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
refcv_cmat.x
matrix
the projection of the bond on the x axis
refcv_cmat.y
matrix
the projection of the bond on the y axis
refcv_cmat.z
matrix
the projection of the bond on the z axis: 
DISTANCE_MATRIX
Calculate a matrix of distances More details
 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
 
GROUP
the atoms for which you would like to calculate the adjacency matrix
=1-1944:3 
CUTOFF
 ignore distances that have a value larger than this cutoff
=0.62126
refcv_grpThe GROUP action with label refcv_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_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
=1-1944:3
refcv_onesThe CONSTANT action with label refcv_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_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
=648
refcv_matenv1The CUSTOM action with label refcv_matenv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv1
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.271)^2+(y--0.009)^2+(z-0.013)^2)/(4*0.00455625))+exp(-((x-0.152)^2+(y--0.128)^2+(z-0.313)^2)/(4*0.00455625))+exp(-((x--0.189)^2+(y--0.069)^2+(z-0.189)^2)/(4*0.00455625))+exp(-((x-0.205)^2+(y-0.331)^2+(z-0.142)^2)/(4*0.00455625))+exp(-((x--0.188)^2+(y-0.328)^2+(z-0.157)^2)/(4*0.00455625))+exp(-((x--0.128)^2+(y-0.139)^2+(z-0.359)^2)/(4*0.00455625))+exp(-((x-0.145)^2+(y-0.142)^2+(z-0.345)^2)/(4*0.00455625))+exp(-((x-0.339)^2+(y-0.196)^2+(z--0.1484)^2)/(4*0.00455625))+exp(-((x--0.3274)^2+(y-0.196)^2+(z--0.1484)^2)/(4*0.00455625))+exp(-((x--0.128)^2+(y-0.139)^2+(z--0.3344)^2)/(4*0.00455625))+exp(-((x-0.205)^2+(y--0.3354)^2+(z-0.142)^2)/(4*0.00455625))+exp(-((x-0.145)^2+(y-0.142)^2+(z--0.3484)^2)/(4*0.00455625))+exp(-((x--0.188)^2+(y--0.3384)^2+(z-0.157)^2)/(4*0.00455625))+exp(-((x--0.053)^2+(y--0.189)^2+(z--0.2084)^2)/(4*0.00455625))+exp(-((x-0.006)^2+(y-0.273)^2+(z--0.0334)^2)/(4*0.00455625))+exp(-((x-0.006)^2+(y--0.3934)^2+(z--0.0334)^2)/(4*0.00455625))+exp(-((x--0.3954)^2+(y--0.009)^2+(z-0.013)^2)/(4*0.00455625
refcv_env1The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env1
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv1,refcv_ones
refcv_matenv2The CUSTOM action with label refcv_matenv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv2
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.119)^2+(y-0.119)^2+(z--0.3)^2)/(4*0.00455625))+exp(-((x--0.341)^2+(y-0.059)^2+(z--0.124)^2)/(4*0.00455625))+exp(-((x--0.205)^2+(y--0.061)^2+(z-0.172)^2)/(4*0.00455625))+exp(-((x-0.19)^2+(y--0.071)^2+(z-0.202)^2)/(4*0.00455625))+exp(-((x--0.28)^2+(y-0.267)^2+(z-0.046)^2)/(4*0.00455625))+exp(-((x--0.007)^2+(y-0.27)^2+(z-0.032)^2)/(4*0.00455625))+exp(-((x-0.3264)^2+(y--0.2104)^2+(z--0.156)^2)/(4*0.00455625))+exp(-((x-0.3254)^2+(y-0.059)^2+(z--0.124)^2)/(4*0.00455625))+exp(-((x--0.152)^2+(y-0.128)^2+(z--0.313)^2)/(4*0.00455625))+exp(-((x-0.053)^2+(y--0.2074)^2+(z--0.171)^2)/(4*0.00455625))+exp(-((x--0.007)^2+(y--0.3964)^2+(z-0.032)^2)/(4*0.00455625
refcv_env2The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env2
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv2,refcv_ones
refcv_matenv3The CUSTOM action with label refcv_matenv3 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv3
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.003)^2+(y--0.395)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x--0.194)^2+(y--0.054)^2+(z--0.2)^2)/(4*0.00455625))+exp(-((x--0.333)^2+(y-0.077)^2+(z-0.115)^2)/(4*0.00455625))+exp(-((x--0.068)^2+(y--0.205)^2+(z-0.1614)^2)/(4*0.00455625))+exp(-((x--0.339)^2+(y--0.196)^2+(z-0.1484)^2)/(4*0.00455625))+exp(-((x--0.134)^2+(y-0.135)^2+(z-0.2904)^2)/(4*0.00455625))+exp(-((x-0.003)^2+(y-0.2714)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x-0.1994)^2+(y--0.057)^2+(z--0.186)^2)/(4*0.00455625))+exp(-((x-0.3334)^2+(y-0.077)^2+(z-0.115)^2)/(4*0.00455625))+exp(-((x-0.3274)^2+(y--0.196)^2+(z-0.1484)^2)/(4*0.00455625))+exp(-((x-0.1394)^2+(y-0.132)^2+(z-0.3054)^2)/(4*0.00455625))+exp(-((x-0.2744)^2+(y-0.2814)^2+(z--0.06)^2)/(4*0.00455625
refcv_env3The MATRIX_VECTOR_PRODUCT action with label refcv_env3 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env3
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv3,refcv_ones
refcv_matenv4The CUSTOM action with label refcv_matenv4 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv4
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.061)^2+(y--0.208)^2+(z--0.17)^2)/(4*0.00455625))+exp(-((x--0.06)^2+(y-0.189)^2+(z--0.202)^2)/(4*0.00455625))+exp(-((x-0.075)^2+(y--0.328)^2+(z-0.126)^2)/(4*0.00455625))+exp(-((x-0.273)^2+(y-0.003)^2+(z--0.014)^2)/(4*0.00455625))+exp(-((x-0.134)^2+(y-0.134)^2+(z-0.301)^2)/(4*0.00455625))+exp(-((x-0.128)^2+(y--0.139)^2+(z-0.3344)^2)/(4*0.00455625))+exp(-((x-0.075)^2+(y-0.3384)^2+(z-0.126)^2)/(4*0.00455625))+exp(-((x-0.128)^2+(y--0.139)^2+(z--0.359)^2)/(4*0.00455625))+exp(-((x-0.28)^2+(y--0.267)^2+(z--0.046)^2)/(4*0.00455625))+exp(-((x--0.1994)^2+(y-0.057)^2+(z-0.186)^2)/(4*0.00455625))+exp(-((x--0.3934)^2+(y-0.003)^2+(z--0.014)^2)/(4*0.00455625))+exp(-((x--0.1964)^2+(y-0.3284)^2+(z-0.156)^2)/(4*0.00455625
refcv_env4The MATRIX_VECTOR_PRODUCT action with label refcv_env4 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env4
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv4,refcv_ones
refcv_matenv5The CUSTOM action with label refcv_matenv5 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv5
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.066)^2+(y--0.34)^2+(z--0.129)^2)/(4*0.00455625))+exp(-((x--0.393)^2+(y--0.003)^2+(z-0.015)^2)/(4*0.00455625))+exp(-((x--0.06)^2+(y--0.189)^2+(z-0.203)^2)/(4*0.00455625))+exp(-((x-0.137)^2+(y-0.1364)^2+(z--0.3204)^2)/(4*0.00455625))+exp(-((x-0.066)^2+(y-0.3264)^2+(z--0.129)^2)/(4*0.00455625))+exp(-((x--0.053)^2+(y-0.2074)^2+(z-0.171)^2)/(4*0.00455625))+exp(-((x--0.205)^2+(y-0.3354)^2+(z--0.142)^2)/(4*0.00455625))+exp(-((x-0.2734)^2+(y--0.003)^2+(z-0.015)^2)/(4*0.00455625))+exp(-((x-0.2724)^2+(y-0.2664)^2+(z-0.047)^2)/(4*0.00455625))+exp(-((x--0.205)^2+(y--0.331)^2+(z--0.142)^2)/(4*0.00455625))+exp(-((x-0.134)^2+(y--0.135)^2+(z--0.2904)^2)/(4*0.00455625))+exp(-((x--0.199)^2+(y--0.058)^2+(z--0.1754)^2)/(4*0.00455625
refcv_env5The MATRIX_VECTOR_PRODUCT action with label refcv_env5 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env5
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv5,refcv_ones
refcv_matenv6The CUSTOM action with label refcv_matenv6 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv6
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.126)^2+(y--0.151)^2+(z--0.332)^2)/(4*0.00455625))+exp(-((x--0.198)^2+(y--0.331)^2+(z-0.14)^2)/(4*0.00455625))+exp(-((x--0.139)^2+(y-0.131)^2+(z-0.315)^2)/(4*0.00455625))+exp(-((x-0.126)^2+(y--0.151)^2+(z-0.3614)^2)/(4*0.00455625))+exp(-((x--0.145)^2+(y--0.142)^2+(z-0.3484)^2)/(4*0.00455625))+exp(-((x-0.007)^2+(y-0.3964)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x--0.198)^2+(y-0.3354)^2+(z-0.14)^2)/(4*0.00455625))+exp(-((x-0.197)^2+(y-0.3254)^2+(z-0.17)^2)/(4*0.00455625))+exp(-((x-0.3934)^2+(y--0.003)^2+(z-0.014)^2)/(4*0.00455625))+exp(-((x--0.145)^2+(y--0.142)^2+(z--0.345)^2)/(4*0.00455625))+exp(-((x-0.007)^2+(y--0.27)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x-0.194)^2+(y-0.054)^2+(z-0.2)^2)/(4*0.00455625))+exp(-((x--0.273)^2+(y--0.003)^2+(z-0.014)^2)/(4*0.00455625))+exp(-((x-0.06)^2+(y-0.189)^2+(z--0.203)^2)/(4*0.00455625
refcv_env6The MATRIX_VECTOR_PRODUCT action with label refcv_env6 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env6
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv6,refcv_ones
refcv_matenv7The CUSTOM action with label refcv_matenv7 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv7
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.001)^2+(y--0.397)^2+(z-0.032)^2)/(4*0.00455625))+exp(-((x-0.135)^2+(y-0.1494)^2+(z--0.3654)^2)/(4*0.00455625))+exp(-((x--0.001)^2+(y-0.2694)^2+(z-0.032)^2)/(4*0.00455625))+exp(-((x-0.188)^2+(y-0.3384)^2+(z--0.157)^2)/(4*0.00455625))+exp(-((x-0.135)^2+(y-0.1494)^2+(z-0.328)^2)/(4*0.00455625))+exp(-((x-0.188)^2+(y--0.328)^2+(z--0.157)^2)/(4*0.00455625))+exp(-((x--0.3264)^2+(y-0.2104)^2+(z-0.156)^2)/(4*0.00455625))+exp(-((x--0.1394)^2+(y--0.132)^2+(z--0.3054)^2)/(4*0.00455625))+exp(-((x-0.06)^2+(y--0.189)^2+(z-0.202)^2)/(4*0.00455625))+exp(-((x-0.393)^2+(y-0.003)^2+(z--0.015)^2)/(4*0.00455625))+exp(-((x--0.2734)^2+(y-0.003)^2+(z--0.015)^2)/(4*0.00455625))+exp(-((x-0.194)^2+(y--0.055)^2+(z--0.1904)^2)/(4*0.00455625))+exp(-((x--0.1364)^2+(y-0.1394)^2+(z-0.358)^2)/(4*0.00455625))+exp(-((x--0.1364)^2+(y-0.1394)^2+(z--0.3354)^2)/(4*0.00455625))+exp(-((x--0.2074)^2+(y-0.3294)^2+(z--0.144)^2)/(4*0.00455625
refcv_env7The MATRIX_VECTOR_PRODUCT action with label refcv_env7 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env7
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv7,refcv_ones
refcv_matenv8The CUSTOM action with label refcv_matenv8 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv8
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.136)^2+(y-0.12)^2+(z--0.296)^2)/(4*0.00455625))+exp(-((x-0.395)^2+(y--0.01)^2+(z-0.03)^2)/(4*0.00455625))+exp(-((x-0.053)^2+(y-0.189)^2+(z-0.2084)^2)/(4*0.00455625))+exp(-((x-0.205)^2+(y-0.061)^2+(z--0.172)^2)/(4*0.00455625))+exp(-((x--0.2744)^2+(y--0.2814)^2+(z-0.06)^2)/(4*0.00455625))+exp(-((x--0.075)^2+(y-0.328)^2+(z--0.126)^2)/(4*0.00455625))+exp(-((x--0.075)^2+(y--0.3384)^2+(z--0.126)^2)/(4*0.00455625))+exp(-((x-0.198)^2+(y-0.331)^2+(z--0.14)^2)/(4*0.00455625))+exp(-((x-0.198)^2+(y--0.3354)^2+(z--0.14)^2)/(4*0.00455625))+exp(-((x--0.135)^2+(y--0.1494)^2+(z-0.3654)^2)/(4*0.00455625))+exp(-((x--0.135)^2+(y--0.1494)^2+(z--0.328)^2)/(4*0.00455625))+exp(-((x-0.059)^2+(y--0.2044)^2+(z-0.175)^2)/(4*0.00455625))+exp(-((x--0.2714)^2+(y--0.01)^2+(z-0.03)^2)/(4*0.00455625
refcv_env8The MATRIX_VECTOR_PRODUCT action with label refcv_env8 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env8
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv8,refcv_ones
refcv_matenv9The CUSTOM action with label refcv_matenv9 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv9
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.265)^2+(y--0.282)^2+(z-0.0464)^2)/(4*0.00455625))+exp(-((x--0.006)^2+(y--0.273)^2+(z-0.0334)^2)/(4*0.00455625))+exp(-((x-0.199)^2+(y-0.058)^2+(z-0.1754)^2)/(4*0.00455625))+exp(-((x--0.194)^2+(y-0.055)^2+(z-0.1904)^2)/(4*0.00455625))+exp(-((x--0.059)^2+(y-0.2044)^2+(z--0.175)^2)/(4*0.00455625))+exp(-((x-0.336)^2+(y-0.1944)^2+(z--0.145)^2)/(4*0.00455625))+exp(-((x--0.006)^2+(y-0.3934)^2+(z-0.0334)^2)/(4*0.00455625))+exp(-((x-0.333)^2+(y--0.077)^2+(z--0.115)^2)/(4*0.00455625))+exp(-((x--0.3334)^2+(y--0.077)^2+(z--0.115)^2)/(4*0.00455625))+exp(-((x--0.134)^2+(y--0.134)^2+(z--0.301)^2)/(4*0.00455625))+exp(-((x-0.139)^2+(y--0.131)^2+(z--0.315)^2)/(4*0.00455625))+exp(-((x--0.3304)^2+(y-0.1944)^2+(z--0.145)^2)/(4*0.00455625
refcv_env9The MATRIX_VECTOR_PRODUCT action with label refcv_env9 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env9
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv9,refcv_ones
refcv_matenv10The CUSTOM action with label refcv_matenv10 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv10
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.071)^2+(y-0.19)^2+(z-0.1914)^2)/(4*0.00455625))+exp(-((x-0.1364)^2+(y--0.1394)^2+(z--0.358)^2)/(4*0.00455625))+exp(-((x-0.1964)^2+(y--0.3284)^2+(z--0.156)^2)/(4*0.00455625))+exp(-((x-0.3304)^2+(y--0.1944)^2+(z-0.145)^2)/(4*0.00455625))+exp(-((x-0.1364)^2+(y--0.1394)^2+(z-0.3354)^2)/(4*0.00455625))+exp(-((x-0.1354)^2+(y-0.13)^2+(z--0.326)^2)/(4*0.00455625))+exp(-((x-0.2714)^2+(y-0.01)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x-0.1354)^2+(y-0.13)^2+(z-0.3674)^2)/(4*0.00455625))+exp(-((x--0.19)^2+(y-0.071)^2+(z--0.202)^2)/(4*0.00455625))+exp(-((x--0.003)^2+(y-0.395)^2+(z-0.03)^2)/(4*0.00455625))+exp(-((x--0.003)^2+(y--0.2714)^2+(z-0.03)^2)/(4*0.00455625))+exp(-((x--0.137)^2+(y--0.1364)^2+(z-0.3204)^2)/(4*0.00455625))+exp(-((x--0.197)^2+(y--0.3254)^2+(z--0.17)^2)/(4*0.00455625))+exp(-((x--0.395)^2+(y-0.01)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x--0.336)^2+(y--0.1944)^2+(z-0.145)^2)/(4*0.00455625
refcv_env10The MATRIX_VECTOR_PRODUCT action with label refcv_env10 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env10
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv10,refcv_ones
refcv_matenv11The CUSTOM action with label refcv_matenv11 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv11
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.189)^2+(y-0.069)^2+(z--0.189)^2)/(4*0.00455625))+exp(-((x-0.341)^2+(y--0.059)^2+(z-0.124)^2)/(4*0.00455625))+exp(-((x--0.3254)^2+(y--0.059)^2+(z-0.124)^2)/(4*0.00455625))+exp(-((x-0.061)^2+(y-0.208)^2+(z-0.17)^2)/(4*0.00455625))+exp(-((x--0.2724)^2+(y--0.2664)^2+(z--0.047)^2)/(4*0.00455625))+exp(-((x-0.001)^2+(y-0.397)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x-0.001)^2+(y--0.2694)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x-0.136)^2+(y--0.12)^2+(z-0.296)^2)/(4*0.00455625))+exp(-((x--0.1354)^2+(y--0.13)^2+(z-0.326)^2)/(4*0.00455625))+exp(-((x--0.1354)^2+(y--0.13)^2+(z--0.3674)^2)/(4*0.00455625))+exp(-((x--0.2064)^2+(y-0.06)^2+(z--0.176)^2)/(4*0.00455625
refcv_env11The MATRIX_VECTOR_PRODUCT action with label refcv_env11 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env11
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv11,refcv_ones
refcv_matenv12The CUSTOM action with label refcv_matenv12 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_matenv12
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 values input to this function
=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.2074)^2+(y--0.3294)^2+(z-0.144)^2)/(4*0.00455625))+exp(-((x-0.2064)^2+(y--0.06)^2+(z-0.176)^2)/(4*0.00455625))+exp(-((x-0.3954)^2+(y-0.009)^2+(z--0.013)^2)/(4*0.00455625))+exp(-((x--0.271)^2+(y-0.009)^2+(z--0.013)^2)/(4*0.00455625))+exp(-((x--0.119)^2+(y--0.119)^2+(z-0.3)^2)/(4*0.00455625))+exp(-((x-0.068)^2+(y-0.205)^2+(z--0.1614)^2)/(4*0.00455625))+exp(-((x--0.066)^2+(y-0.34)^2+(z-0.129)^2)/(4*0.00455625))+exp(-((x--0.066)^2+(y--0.3264)^2+(z-0.129)^2)/(4*0.00455625))+exp(-((x--0.126)^2+(y-0.151)^2+(z-0.332)^2)/(4*0.00455625))+exp(-((x--0.126)^2+(y-0.151)^2+(z--0.3614)^2)/(4*0.00455625))+exp(-((x--0.265)^2+(y-0.282)^2+(z--0.0464)^2)/(4*0.00455625))+exp(-((x-0.071)^2+(y--0.19)^2+(z--0.1914)^2)/(4*0.00455625
refcv_env12The MATRIX_VECTOR_PRODUCT action with label refcv_env12 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_env12
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 label for the matrix and the vector/scalar that are being multiplied
=refcv_matenv12,refcv_ones
refcvThe CUSTOM action with label refcv calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv
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 values input to this function
=refcv_env1,refcv_env2,refcv_env3,refcv_env4,refcv_env5,refcv_env6,refcv_env7,refcv_env8,refcv_env9,refcv_env10,refcv_env11,refcv_env12 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
VAR
the names to give each of the arguments in the function
=v1,v2,v3,v4,v5,v6,v7,v8,v9,v10,v11,v12 
FUNC
the function you wish to evaluate
=(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4)+exp(100*v5)+exp(100*v6)+exp(100*v7)+exp(100*v8)+exp(100*v9)+exp(100*v10)+exp(100*v11)+exp(100*v12
refcv_mtThe MORE_THAN action with label refcv_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_mt
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the values input to this function
=refcv 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={CUBIC D_0=0.604 D_MAX=0.972}
refcv_morethanThe SUM action with label refcv_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv_morethan
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=refcv_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
# Restraint
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=refcv.morethan 
AT
the positions of the wall
=324 
KAPPA
the force constant for the wall
=1.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=5
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=refcv.morethan 
AT
the positions of the wall
=378 
KAPPA
the force constant for the wall
=1.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=5

ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1944:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv2The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2
vector
the environmental similar parameter for each of the input atoms
refcv2_morethan
scalar
the number of colvars that have a value more than a threshold
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
REFERENCE_11
PDB files with relative distances from central atom
=env11.pdb
 
REFERENCE_12
PDB files with relative distances from central atom
=env12.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.763000 D_MAX=0.763001}
... ENVIRONMENTSIMILARITY
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1944:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv2
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
REFERENCE_11
PDB files with relative distances from central atom
=env11.pdb
 
REFERENCE_12
PDB files with relative distances from central atom
=env12.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.763000 D_MAX=0.763001}
 
CUTOFF
 how many multiples of sigma would you like to consider beyond the maximum distance in the environment
=3 
LCUTOFF
 any atoms separated by less than this tolerance should be ignored
=0.0001 
LAMBDA
 Lambda parameter
=100
... ENVIRONMENTSIMILARITY
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIES=1-1944:3
#  SIGMA=0.0675
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv2
#  REFERENCE_1=env1.pdb
#  REFERENCE_2=env2.pdb
#  REFERENCE_3=env3.pdb
#  REFERENCE_4=env4.pdb
#  REFERENCE_5=env5.pdb
#  REFERENCE_6=env6.pdb
#  REFERENCE_7=env7.pdb
#  REFERENCE_8=env8.pdb
#  REFERENCE_9=env9.pdb
#  REFERENCE_10=env10.pdb
#  REFERENCE_11=env11.pdb
#  REFERENCE_12=env12.pdb
#  MORE_THAN={CUBIC D_0=0.763000 D_MAX=0.763001}
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv2_cmatThe DISTANCE_MATRIX action with label refcv2_cmat calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_cmat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
refcv2_cmat.x
matrix
the projection of the bond on the x axis
refcv2_cmat.y
matrix
the projection of the bond on the y axis
refcv2_cmat.z
matrix
the projection of the bond on the z axis: 
DISTANCE_MATRIX
Calculate a matrix of distances More details
 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
 
GROUP
the atoms for which you would like to calculate the adjacency matrix
=1-1944:3 
CUTOFF
 ignore distances that have a value larger than this cutoff
=0.62126
refcv2_grpThe GROUP action with label refcv2_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_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
=1-1944:3
refcv2_onesThe CONSTANT action with label refcv2_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_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
=648
refcv2_matenv1The CUSTOM action with label refcv2_matenv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv1
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.271)^2+(y--0.009)^2+(z-0.013)^2)/(4*0.00455625))+exp(-((x-0.152)^2+(y--0.128)^2+(z-0.313)^2)/(4*0.00455625))+exp(-((x--0.189)^2+(y--0.069)^2+(z-0.189)^2)/(4*0.00455625))+exp(-((x-0.205)^2+(y-0.331)^2+(z-0.142)^2)/(4*0.00455625))+exp(-((x--0.188)^2+(y-0.328)^2+(z-0.157)^2)/(4*0.00455625))+exp(-((x--0.128)^2+(y-0.139)^2+(z-0.359)^2)/(4*0.00455625))+exp(-((x-0.145)^2+(y-0.142)^2+(z-0.345)^2)/(4*0.00455625))+exp(-((x-0.339)^2+(y-0.196)^2+(z--0.1484)^2)/(4*0.00455625))+exp(-((x--0.3274)^2+(y-0.196)^2+(z--0.1484)^2)/(4*0.00455625))+exp(-((x--0.128)^2+(y-0.139)^2+(z--0.3344)^2)/(4*0.00455625))+exp(-((x-0.205)^2+(y--0.3354)^2+(z-0.142)^2)/(4*0.00455625))+exp(-((x-0.145)^2+(y-0.142)^2+(z--0.3484)^2)/(4*0.00455625))+exp(-((x--0.188)^2+(y--0.3384)^2+(z-0.157)^2)/(4*0.00455625))+exp(-((x--0.053)^2+(y--0.189)^2+(z--0.2084)^2)/(4*0.00455625))+exp(-((x-0.006)^2+(y-0.273)^2+(z--0.0334)^2)/(4*0.00455625))+exp(-((x-0.006)^2+(y--0.3934)^2+(z--0.0334)^2)/(4*0.00455625))+exp(-((x--0.3954)^2+(y--0.009)^2+(z-0.013)^2)/(4*0.00455625
refcv2_env1The MATRIX_VECTOR_PRODUCT action with label refcv2_env1 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env1
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv1,refcv2_ones
refcv2_matenv2The CUSTOM action with label refcv2_matenv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv2
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.119)^2+(y-0.119)^2+(z--0.3)^2)/(4*0.00455625))+exp(-((x--0.341)^2+(y-0.059)^2+(z--0.124)^2)/(4*0.00455625))+exp(-((x--0.205)^2+(y--0.061)^2+(z-0.172)^2)/(4*0.00455625))+exp(-((x-0.19)^2+(y--0.071)^2+(z-0.202)^2)/(4*0.00455625))+exp(-((x--0.28)^2+(y-0.267)^2+(z-0.046)^2)/(4*0.00455625))+exp(-((x--0.007)^2+(y-0.27)^2+(z-0.032)^2)/(4*0.00455625))+exp(-((x-0.3264)^2+(y--0.2104)^2+(z--0.156)^2)/(4*0.00455625))+exp(-((x-0.3254)^2+(y-0.059)^2+(z--0.124)^2)/(4*0.00455625))+exp(-((x--0.152)^2+(y-0.128)^2+(z--0.313)^2)/(4*0.00455625))+exp(-((x-0.053)^2+(y--0.2074)^2+(z--0.171)^2)/(4*0.00455625))+exp(-((x--0.007)^2+(y--0.3964)^2+(z-0.032)^2)/(4*0.00455625
refcv2_env2The MATRIX_VECTOR_PRODUCT action with label refcv2_env2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env2
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv2,refcv2_ones
refcv2_matenv3The CUSTOM action with label refcv2_matenv3 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv3
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.003)^2+(y--0.395)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x--0.194)^2+(y--0.054)^2+(z--0.2)^2)/(4*0.00455625))+exp(-((x--0.333)^2+(y-0.077)^2+(z-0.115)^2)/(4*0.00455625))+exp(-((x--0.068)^2+(y--0.205)^2+(z-0.1614)^2)/(4*0.00455625))+exp(-((x--0.339)^2+(y--0.196)^2+(z-0.1484)^2)/(4*0.00455625))+exp(-((x--0.134)^2+(y-0.135)^2+(z-0.2904)^2)/(4*0.00455625))+exp(-((x-0.003)^2+(y-0.2714)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x-0.1994)^2+(y--0.057)^2+(z--0.186)^2)/(4*0.00455625))+exp(-((x-0.3334)^2+(y-0.077)^2+(z-0.115)^2)/(4*0.00455625))+exp(-((x-0.3274)^2+(y--0.196)^2+(z-0.1484)^2)/(4*0.00455625))+exp(-((x-0.1394)^2+(y-0.132)^2+(z-0.3054)^2)/(4*0.00455625))+exp(-((x-0.2744)^2+(y-0.2814)^2+(z--0.06)^2)/(4*0.00455625
refcv2_env3The MATRIX_VECTOR_PRODUCT action with label refcv2_env3 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env3
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv3,refcv2_ones
refcv2_matenv4The CUSTOM action with label refcv2_matenv4 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv4
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.061)^2+(y--0.208)^2+(z--0.17)^2)/(4*0.00455625))+exp(-((x--0.06)^2+(y-0.189)^2+(z--0.202)^2)/(4*0.00455625))+exp(-((x-0.075)^2+(y--0.328)^2+(z-0.126)^2)/(4*0.00455625))+exp(-((x-0.273)^2+(y-0.003)^2+(z--0.014)^2)/(4*0.00455625))+exp(-((x-0.134)^2+(y-0.134)^2+(z-0.301)^2)/(4*0.00455625))+exp(-((x-0.128)^2+(y--0.139)^2+(z-0.3344)^2)/(4*0.00455625))+exp(-((x-0.075)^2+(y-0.3384)^2+(z-0.126)^2)/(4*0.00455625))+exp(-((x-0.128)^2+(y--0.139)^2+(z--0.359)^2)/(4*0.00455625))+exp(-((x-0.28)^2+(y--0.267)^2+(z--0.046)^2)/(4*0.00455625))+exp(-((x--0.1994)^2+(y-0.057)^2+(z-0.186)^2)/(4*0.00455625))+exp(-((x--0.3934)^2+(y-0.003)^2+(z--0.014)^2)/(4*0.00455625))+exp(-((x--0.1964)^2+(y-0.3284)^2+(z-0.156)^2)/(4*0.00455625
refcv2_env4The MATRIX_VECTOR_PRODUCT action with label refcv2_env4 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env4
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv4,refcv2_ones
refcv2_matenv5The CUSTOM action with label refcv2_matenv5 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv5
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.066)^2+(y--0.34)^2+(z--0.129)^2)/(4*0.00455625))+exp(-((x--0.393)^2+(y--0.003)^2+(z-0.015)^2)/(4*0.00455625))+exp(-((x--0.06)^2+(y--0.189)^2+(z-0.203)^2)/(4*0.00455625))+exp(-((x-0.137)^2+(y-0.1364)^2+(z--0.3204)^2)/(4*0.00455625))+exp(-((x-0.066)^2+(y-0.3264)^2+(z--0.129)^2)/(4*0.00455625))+exp(-((x--0.053)^2+(y-0.2074)^2+(z-0.171)^2)/(4*0.00455625))+exp(-((x--0.205)^2+(y-0.3354)^2+(z--0.142)^2)/(4*0.00455625))+exp(-((x-0.2734)^2+(y--0.003)^2+(z-0.015)^2)/(4*0.00455625))+exp(-((x-0.2724)^2+(y-0.2664)^2+(z-0.047)^2)/(4*0.00455625))+exp(-((x--0.205)^2+(y--0.331)^2+(z--0.142)^2)/(4*0.00455625))+exp(-((x-0.134)^2+(y--0.135)^2+(z--0.2904)^2)/(4*0.00455625))+exp(-((x--0.199)^2+(y--0.058)^2+(z--0.1754)^2)/(4*0.00455625
refcv2_env5The MATRIX_VECTOR_PRODUCT action with label refcv2_env5 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env5
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv5,refcv2_ones
refcv2_matenv6The CUSTOM action with label refcv2_matenv6 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv6
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.126)^2+(y--0.151)^2+(z--0.332)^2)/(4*0.00455625))+exp(-((x--0.198)^2+(y--0.331)^2+(z-0.14)^2)/(4*0.00455625))+exp(-((x--0.139)^2+(y-0.131)^2+(z-0.315)^2)/(4*0.00455625))+exp(-((x-0.126)^2+(y--0.151)^2+(z-0.3614)^2)/(4*0.00455625))+exp(-((x--0.145)^2+(y--0.142)^2+(z-0.3484)^2)/(4*0.00455625))+exp(-((x-0.007)^2+(y-0.3964)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x--0.198)^2+(y-0.3354)^2+(z-0.14)^2)/(4*0.00455625))+exp(-((x-0.197)^2+(y-0.3254)^2+(z-0.17)^2)/(4*0.00455625))+exp(-((x-0.3934)^2+(y--0.003)^2+(z-0.014)^2)/(4*0.00455625))+exp(-((x--0.145)^2+(y--0.142)^2+(z--0.345)^2)/(4*0.00455625))+exp(-((x-0.007)^2+(y--0.27)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x-0.194)^2+(y-0.054)^2+(z-0.2)^2)/(4*0.00455625))+exp(-((x--0.273)^2+(y--0.003)^2+(z-0.014)^2)/(4*0.00455625))+exp(-((x-0.06)^2+(y-0.189)^2+(z--0.203)^2)/(4*0.00455625
refcv2_env6The MATRIX_VECTOR_PRODUCT action with label refcv2_env6 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env6
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv6,refcv2_ones
refcv2_matenv7The CUSTOM action with label refcv2_matenv7 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv7
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.001)^2+(y--0.397)^2+(z-0.032)^2)/(4*0.00455625))+exp(-((x-0.135)^2+(y-0.1494)^2+(z--0.3654)^2)/(4*0.00455625))+exp(-((x--0.001)^2+(y-0.2694)^2+(z-0.032)^2)/(4*0.00455625))+exp(-((x-0.188)^2+(y-0.3384)^2+(z--0.157)^2)/(4*0.00455625))+exp(-((x-0.135)^2+(y-0.1494)^2+(z-0.328)^2)/(4*0.00455625))+exp(-((x-0.188)^2+(y--0.328)^2+(z--0.157)^2)/(4*0.00455625))+exp(-((x--0.3264)^2+(y-0.2104)^2+(z-0.156)^2)/(4*0.00455625))+exp(-((x--0.1394)^2+(y--0.132)^2+(z--0.3054)^2)/(4*0.00455625))+exp(-((x-0.06)^2+(y--0.189)^2+(z-0.202)^2)/(4*0.00455625))+exp(-((x-0.393)^2+(y-0.003)^2+(z--0.015)^2)/(4*0.00455625))+exp(-((x--0.2734)^2+(y-0.003)^2+(z--0.015)^2)/(4*0.00455625))+exp(-((x-0.194)^2+(y--0.055)^2+(z--0.1904)^2)/(4*0.00455625))+exp(-((x--0.1364)^2+(y-0.1394)^2+(z-0.358)^2)/(4*0.00455625))+exp(-((x--0.1364)^2+(y-0.1394)^2+(z--0.3354)^2)/(4*0.00455625))+exp(-((x--0.2074)^2+(y-0.3294)^2+(z--0.144)^2)/(4*0.00455625
refcv2_env7The MATRIX_VECTOR_PRODUCT action with label refcv2_env7 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env7
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv7,refcv2_ones
refcv2_matenv8The CUSTOM action with label refcv2_matenv8 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv8
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.136)^2+(y-0.12)^2+(z--0.296)^2)/(4*0.00455625))+exp(-((x-0.395)^2+(y--0.01)^2+(z-0.03)^2)/(4*0.00455625))+exp(-((x-0.053)^2+(y-0.189)^2+(z-0.2084)^2)/(4*0.00455625))+exp(-((x-0.205)^2+(y-0.061)^2+(z--0.172)^2)/(4*0.00455625))+exp(-((x--0.2744)^2+(y--0.2814)^2+(z-0.06)^2)/(4*0.00455625))+exp(-((x--0.075)^2+(y-0.328)^2+(z--0.126)^2)/(4*0.00455625))+exp(-((x--0.075)^2+(y--0.3384)^2+(z--0.126)^2)/(4*0.00455625))+exp(-((x-0.198)^2+(y-0.331)^2+(z--0.14)^2)/(4*0.00455625))+exp(-((x-0.198)^2+(y--0.3354)^2+(z--0.14)^2)/(4*0.00455625))+exp(-((x--0.135)^2+(y--0.1494)^2+(z-0.3654)^2)/(4*0.00455625))+exp(-((x--0.135)^2+(y--0.1494)^2+(z--0.328)^2)/(4*0.00455625))+exp(-((x-0.059)^2+(y--0.2044)^2+(z-0.175)^2)/(4*0.00455625))+exp(-((x--0.2714)^2+(y--0.01)^2+(z-0.03)^2)/(4*0.00455625
refcv2_env8The MATRIX_VECTOR_PRODUCT action with label refcv2_env8 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env8
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv8,refcv2_ones
refcv2_matenv9The CUSTOM action with label refcv2_matenv9 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv9
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.265)^2+(y--0.282)^2+(z-0.0464)^2)/(4*0.00455625))+exp(-((x--0.006)^2+(y--0.273)^2+(z-0.0334)^2)/(4*0.00455625))+exp(-((x-0.199)^2+(y-0.058)^2+(z-0.1754)^2)/(4*0.00455625))+exp(-((x--0.194)^2+(y-0.055)^2+(z-0.1904)^2)/(4*0.00455625))+exp(-((x--0.059)^2+(y-0.2044)^2+(z--0.175)^2)/(4*0.00455625))+exp(-((x-0.336)^2+(y-0.1944)^2+(z--0.145)^2)/(4*0.00455625))+exp(-((x--0.006)^2+(y-0.3934)^2+(z-0.0334)^2)/(4*0.00455625))+exp(-((x-0.333)^2+(y--0.077)^2+(z--0.115)^2)/(4*0.00455625))+exp(-((x--0.3334)^2+(y--0.077)^2+(z--0.115)^2)/(4*0.00455625))+exp(-((x--0.134)^2+(y--0.134)^2+(z--0.301)^2)/(4*0.00455625))+exp(-((x-0.139)^2+(y--0.131)^2+(z--0.315)^2)/(4*0.00455625))+exp(-((x--0.3304)^2+(y-0.1944)^2+(z--0.145)^2)/(4*0.00455625
refcv2_env9The MATRIX_VECTOR_PRODUCT action with label refcv2_env9 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env9
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv9,refcv2_ones
refcv2_matenv10The CUSTOM action with label refcv2_matenv10 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv10
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x--0.071)^2+(y-0.19)^2+(z-0.1914)^2)/(4*0.00455625))+exp(-((x-0.1364)^2+(y--0.1394)^2+(z--0.358)^2)/(4*0.00455625))+exp(-((x-0.1964)^2+(y--0.3284)^2+(z--0.156)^2)/(4*0.00455625))+exp(-((x-0.3304)^2+(y--0.1944)^2+(z-0.145)^2)/(4*0.00455625))+exp(-((x-0.1364)^2+(y--0.1394)^2+(z-0.3354)^2)/(4*0.00455625))+exp(-((x-0.1354)^2+(y-0.13)^2+(z--0.326)^2)/(4*0.00455625))+exp(-((x-0.2714)^2+(y-0.01)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x-0.1354)^2+(y-0.13)^2+(z-0.3674)^2)/(4*0.00455625))+exp(-((x--0.19)^2+(y-0.071)^2+(z--0.202)^2)/(4*0.00455625))+exp(-((x--0.003)^2+(y-0.395)^2+(z-0.03)^2)/(4*0.00455625))+exp(-((x--0.003)^2+(y--0.2714)^2+(z-0.03)^2)/(4*0.00455625))+exp(-((x--0.137)^2+(y--0.1364)^2+(z-0.3204)^2)/(4*0.00455625))+exp(-((x--0.197)^2+(y--0.3254)^2+(z--0.17)^2)/(4*0.00455625))+exp(-((x--0.395)^2+(y-0.01)^2+(z--0.03)^2)/(4*0.00455625))+exp(-((x--0.336)^2+(y--0.1944)^2+(z-0.145)^2)/(4*0.00455625
refcv2_env10The MATRIX_VECTOR_PRODUCT action with label refcv2_env10 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env10
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv10,refcv2_ones
refcv2_matenv11The CUSTOM action with label refcv2_matenv11 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv11
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.189)^2+(y-0.069)^2+(z--0.189)^2)/(4*0.00455625))+exp(-((x-0.341)^2+(y--0.059)^2+(z-0.124)^2)/(4*0.00455625))+exp(-((x--0.3254)^2+(y--0.059)^2+(z-0.124)^2)/(4*0.00455625))+exp(-((x-0.061)^2+(y-0.208)^2+(z-0.17)^2)/(4*0.00455625))+exp(-((x--0.2724)^2+(y--0.2664)^2+(z--0.047)^2)/(4*0.00455625))+exp(-((x-0.001)^2+(y-0.397)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x-0.001)^2+(y--0.2694)^2+(z--0.032)^2)/(4*0.00455625))+exp(-((x-0.136)^2+(y--0.12)^2+(z-0.296)^2)/(4*0.00455625))+exp(-((x--0.1354)^2+(y--0.13)^2+(z-0.326)^2)/(4*0.00455625))+exp(-((x--0.1354)^2+(y--0.13)^2+(z--0.3674)^2)/(4*0.00455625))+exp(-((x--0.2064)^2+(y-0.06)^2+(z--0.176)^2)/(4*0.00455625
refcv2_env11The MATRIX_VECTOR_PRODUCT action with label refcv2_env11 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env11
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv11,refcv2_ones
refcv2_matenv12The CUSTOM action with label refcv2_matenv12 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_matenv12
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 values input to this function
=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w 
VAR
the names to give each of the arguments in the function
=x,y,z,w 
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
=(step(w-0.0001)*step(0.62126-w)/17)*(exp(-((x-0.2074)^2+(y--0.3294)^2+(z-0.144)^2)/(4*0.00455625))+exp(-((x-0.2064)^2+(y--0.06)^2+(z-0.176)^2)/(4*0.00455625))+exp(-((x-0.3954)^2+(y-0.009)^2+(z--0.013)^2)/(4*0.00455625))+exp(-((x--0.271)^2+(y-0.009)^2+(z--0.013)^2)/(4*0.00455625))+exp(-((x--0.119)^2+(y--0.119)^2+(z-0.3)^2)/(4*0.00455625))+exp(-((x-0.068)^2+(y-0.205)^2+(z--0.1614)^2)/(4*0.00455625))+exp(-((x--0.066)^2+(y-0.34)^2+(z-0.129)^2)/(4*0.00455625))+exp(-((x--0.066)^2+(y--0.3264)^2+(z-0.129)^2)/(4*0.00455625))+exp(-((x--0.126)^2+(y-0.151)^2+(z-0.332)^2)/(4*0.00455625))+exp(-((x--0.126)^2+(y-0.151)^2+(z--0.3614)^2)/(4*0.00455625))+exp(-((x--0.265)^2+(y-0.282)^2+(z--0.0464)^2)/(4*0.00455625))+exp(-((x-0.071)^2+(y--0.19)^2+(z--0.1914)^2)/(4*0.00455625
refcv2_env12The MATRIX_VECTOR_PRODUCT action with label refcv2_env12 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_env12
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 label for the matrix and the vector/scalar that are being multiplied
=refcv2_matenv12,refcv2_ones
refcv2The CUSTOM action with label refcv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2
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 values input to this function
=refcv2_env1,refcv2_env2,refcv2_env3,refcv2_env4,refcv2_env5,refcv2_env6,refcv2_env7,refcv2_env8,refcv2_env9,refcv2_env10,refcv2_env11,refcv2_env12 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
VAR
the names to give each of the arguments in the function
=v1,v2,v3,v4,v5,v6,v7,v8,v9,v10,v11,v12 
FUNC
the function you wish to evaluate
=(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4)+exp(100*v5)+exp(100*v6)+exp(100*v7)+exp(100*v8)+exp(100*v9)+exp(100*v10)+exp(100*v11)+exp(100*v12
refcv2_mtThe MORE_THAN action with label refcv2_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_mt
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the values input to this function
=refcv2 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={CUBIC D_0=0.763000 D_MAX=0.763001}
refcv2_morethanThe SUM action with label refcv2_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv2_morethan
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=refcv2_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the labels of the values that you would like to print to the file
 
FILE
the name of the file on which to output these quantities
=COLVAR.EQUIL