Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/3-production/IceIII-260.0-2500.0/plumed.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.
RESTARTActivate restart. More details NO switch off restart - can be used to override the behavior of the MD engine
The RESTART action with label calculates somethingENVIRONMENTSIMILARITYMeasure 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={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={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
# ENVIRONMENTSIMILARITY ...
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 More details COMPONENTS also calculate the components of the vector 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 ---
umb1The ECV_UMBRELLAS_LINE action with label umb1 calculates the following quantities: Quantity | Type | Description |
umb1.refcv_morethan | scalar | the value of the argument named refcv_morethan |
: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details ARGthe labels of the scalar values that are input to this action=refcv.morethan TEMP temperature=290 CV_MINthe minimum of the CV range to be explored=324.0 CV_MAXthe maximum of the CV range to be explored=378.0 SIGMAsigma of the umbrella Gaussians=1 BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=100
umb1: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details ARGthe labels of the scalar values that are input to this action=refcv.morethan TEMP temperature=290 CV_MINthe minimum of the CV range to be explored=324.0 CV_MAXthe maximum of the CV range to be explored=378.0 SIGMAsigma of the umbrella Gaussians=1 BARRIERa guess of the free energy barrier to be overcome (better to stay higher than lower)=100 SPACING the distance between umbrellas, in units of SIGMA=1
opesThe OPES_EXPANDED action with label opes calculates the following quantities: Quantity | Type | Description |
opes.bias | scalar | the instantaneous value of the bias potential |
: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe label of the ECVs that define the expansion=umb1.* PACEhow often the bias is updated=500 STRIDEthe frequency with which the forces due to the bias should be calculated=3 WALKERS_MPI switch on MPI version of multiple walkers
opes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe label of the ECVs that define the expansion=umb1.* PACEhow often the bias is updated=500 STRIDEthe frequency with which the forces due to the bias should be calculated=3 WALKERS_MPI switch on MPI version of multiple walkers OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DELTAFS PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100
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={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={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
# ENVIRONMENTSIMILARITY ...
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 More details COMPONENTS also calculate the components of the vector 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