PLUMED-NEST

Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/3-production/IceIII-270.0-3000.0/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

ENVIRONMENTSIMILARITYMeasure 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 ...
 SPECIESthis 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
 LABELa 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_1PDB files with relative distances from central atom=env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4.pdb
 REFERENCE_5PDB files with relative distances from central atom=env5.pdb
 REFERENCE_6PDB files with relative distances from central atom=env6.pdb
 REFERENCE_7PDB files with relative distances from central atom=env7.pdb
 REFERENCE_8PDB files with relative distances from central atom=env8.pdb
 REFERENCE_9PDB files with relative distances from central atom=env9.pdb
 REFERENCE_10PDB files with relative distances from central atom=env10.pdb
 REFERENCE_11PDB files with relative distances from central atom=env11.pdb
 REFERENCE_12PDB files with relative distances from central atom=env12.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.604 D_MAX=0.972}
... ENVIRONMENTSIMILARITY
ENVIRONMENTSIMILARITYMeasure 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 ...
 SPECIESthis 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
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv
 REFERENCE_1PDB files with relative distances from central atom=env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4.pdb
 REFERENCE_5PDB files with relative distances from central atom=env5.pdb
 REFERENCE_6PDB files with relative distances from central atom=env6.pdb
 REFERENCE_7PDB files with relative distances from central atom=env7.pdb
 REFERENCE_8PDB files with relative distances from central atom=env8.pdb
 REFERENCE_9PDB files with relative distances from central atom=env9.pdb
 REFERENCE_10PDB files with relative distances from central atom=env10.pdb
 REFERENCE_11PDB files with relative distances from central atom=env11.pdb
 REFERENCE_12PDB files with relative distances from central atom=env12.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={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_MATRIXCalculate a matrix of distances between atoms. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPthe 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: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-1944:3
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: ONESCreate a constant vector with all elements equal to one More details SIZEthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO VARthe names to give each of the arguments in the function=v1,v2,v3,v4,v5,v6,v7,v8,v9,v10,v11,v12 FUNCthe 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_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=refcv SWITCHThis 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: SUMCalculate the sum of the arguments More details ARGthe values input to this function=refcv_mt PERIODICif 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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=refcv.morethan ATthe positions of the wall=324. KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=2 STRIDEthe 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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=refcv.morethan ATthe positions of the wall=378. KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=2 STRIDEthe frequency with which the forces due to the bias should be calculated=5

ENVIRONMENTSIMILARITYMeasure 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 ...
 SPECIESthis 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
 LABELa 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_1PDB files with relative distances from central atom=env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4.pdb
 REFERENCE_5PDB files with relative distances from central atom=env5.pdb
 REFERENCE_6PDB files with relative distances from central atom=env6.pdb
 REFERENCE_7PDB files with relative distances from central atom=env7.pdb
 REFERENCE_8PDB files with relative distances from central atom=env8.pdb
 REFERENCE_9PDB files with relative distances from central atom=env9.pdb
 REFERENCE_10PDB files with relative distances from central atom=env10.pdb
 REFERENCE_11PDB files with relative distances from central atom=env11.pdb
 REFERENCE_12PDB files with relative distances from central atom=env12.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.763000 D_MAX=0.763001}
... ENVIRONMENTSIMILARITY
ENVIRONMENTSIMILARITYMeasure 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 ...
 SPECIESthis 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
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv2
 REFERENCE_1PDB files with relative distances from central atom=env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4.pdb
 REFERENCE_5PDB files with relative distances from central atom=env5.pdb
 REFERENCE_6PDB files with relative distances from central atom=env6.pdb
 REFERENCE_7PDB files with relative distances from central atom=env7.pdb
 REFERENCE_8PDB files with relative distances from central atom=env8.pdb
 REFERENCE_9PDB files with relative distances from central atom=env9.pdb
 REFERENCE_10PDB files with relative distances from central atom=env10.pdb
 REFERENCE_11PDB files with relative distances from central atom=env11.pdb
 REFERENCE_12PDB files with relative distances from central atom=env12.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={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_MATRIXCalculate a matrix of distances between atoms. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPthe 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: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-1944:3
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: ONESCreate a constant vector with all elements equal to one More details SIZEthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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_PRODUCTCalculate the product of the matrix and the vector More details ARGthe 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: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO VARthe names to give each of the arguments in the function=v1,v2,v3,v4,v5,v6,v7,v8,v9,v10,v11,v12 FUNCthe 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_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=refcv2 SWITCHThis 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: SUMCalculate the sum of the arguments More details ARGthe values input to this function=refcv2_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR.EQUIL