Project ID: plumID:20.022
Source: sodium/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.
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
volThe VOLUME action with label vol calculates the following quantities:| Quantity | Type | Description |
| vol | scalar | the volume of simulation box |
: VOLUMECalculate the volume the simulation box. 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 ...
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 |
| refcv_mean | scalar | the mean of the colvars |
SPECIESthis keyword is used for colvars such as coordination number=1-250
SIGMA the width to use for the gaussian kernels=0.065
LATTICE_CONSTANTSLattice constants=0.423
CRYSTAL_STRUCTURE Targeted crystal structure=BCC
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.={RATIONAL R_0=0.5 NN=12 MM=24}
MEAN calculate the mean of all the quantities
... 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 ...
LABELa label for the action so that its output can be referenced in the input to other actions=refcv
SPECIESthis keyword is used for colvars such as coordination number=1-250
SIGMA the width to use for the gaussian kernels=0.065
LATTICE_CONSTANTSLattice constants=0.423
CRYSTAL_STRUCTURE Targeted crystal structure=BCC
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.={RATIONAL R_0=0.5 NN=12 MM=24}
MEAN calculate the mean of all the quantities
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
... 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 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=1-250 CUTOFF ignore distances that have a value larger than this cutoff=0.618
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=1-250
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=250
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(0.618-w)/14)*(exp(-((x-0.2115)^2+(y-0.2115)^2+(z-0.2115)^2)/(4*0.004225))+exp(-((x--0.2115)^2+(y--0.2115)^2+(z--0.2115)^2)/(4*0.004225))+exp(-((x--0.2115)^2+(y-0.2115)^2+(z-0.2115)^2)/(4*0.004225))+exp(-((x-0.2115)^2+(y--0.2115)^2+(z-0.2115)^2)/(4*0.004225))+exp(-((x-0.2115)^2+(y-0.2115)^2+(z--0.2115)^2)/(4*0.004225))+exp(-((x--0.2115)^2+(y--0.2115)^2+(z-0.2115)^2)/(4*0.004225))+exp(-((x-0.2115)^2+(y--0.2115)^2+(z--0.2115)^2)/(4*0.004225))+exp(-((x--0.2115)^2+(y-0.2115)^2+(z--0.2115)^2)/(4*0.004225))+exp(-((x-0.423)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.423)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.423)^2)/(4*0.004225))+exp(-((x--0.423)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.423)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.423)^2)/(4*0.004225)))
refcvThe MATRIX_VECTOR_PRODUCT action with label refcv calculates the following quantities:| Quantity | Type | Description |
| refcv | 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_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={RATIONAL R_0=0.5 NN=12 MM=24}
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
refcv_meanThe MEAN action with label refcv_mean calculates the following quantities:| Quantity | Type | Description |
| refcv_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=refcv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
mtpThe ECV_MULTITHERMAL_MULTIBARIC action with label mtp calculates the following quantities:| Quantity | Type | Description |
| mtp.ene | scalar | the value of the argument named ene |
| mtp.vol | scalar | the value of the argument named vol |
: ECV_MULTITHERMAL_MULTIBARICExpand a simulation to sample multiple temperatures and pressures. More details ...
ARGthe labels of the potential energy and of the volume of the system=ene,vol
TEMP temperature=400
TEMP_MINthe minimum of the temperature range=350
TEMP_MAXthe maximum of the temperature range=450
PRESSUREpressure=0.06022140857*5000
PRESSURE_MINthe minimum of the pressure range=0
PRESSURE_MAXthe maximum of the pressure range=0.06022140857*10000
...
umbThe ECV_UMBRELLAS_LINE action with label umb calculates the following quantities:| Quantity | Type | Description |
| umb.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=400
SIGMAsigma of the umbrella Gaussians=10
CV_MINthe minimum of the CV range to be explored=0
CV_MAXthe maximum of the CV range to be explored=250
...
umb: 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=400
SIGMAsigma of the umbrella Gaussians=10
CV_MINthe minimum of the CV range to be explored=0
CV_MAXthe maximum of the CV range to be explored=250
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=mtp.*,umb.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=500 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=mtp.*,umb.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=500 WALKERS_MPI switch on MPI version of multiple walkers OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100
Q6Calculate sixth order Steinhardt parameters. This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-250 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.4 D_MAX=0.5} VMEAN calculate the norm of the mean vector LABELa label for the action so that its output can be referenced in the input to other actions=q6The Q6 action with label q6 calculates the following quantities:| Quantity | Type | Description |
| q6 | vector | the norms of the vectors of spherical harmonic coefficients |
# Q6 SPECIES=1-250 SWITCH={CUBIC D_0=0.4 D_MAX=0.5} VMEAN LABEL=q6
q6_grpThe GROUP action with label q6_grp calculates the following quantities:| Quantity | Type | Description |
| q6_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=1-250
q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:| Quantity | Type | Description |
| q6_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| q6_mat.x | matrix | the projection of the bond on the x axis |
| q6_mat.y | matrix | the projection of the bond on the y axis |
| q6_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-250 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.4 D_MAX=0.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
q6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:| Quantity | Type | Description |
| q6_sh.rm-n6 | matrix | the real parts of the spherical harmonic values with the m value given This is the n6th of these quantities |
| q6_sh.rm-n5 | matrix | the real parts of the spherical harmonic values with the m value given This is the n5th of these quantities |
| q6_sh.rm-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q6_sh.rm-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q6_sh.rm-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q6_sh.rm-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q6_sh.rm-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q6_sh.rm-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q6_sh.rm-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q6_sh.rm-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q6_sh.rm-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q6_sh.rm-p5 | matrix | the real parts of the spherical harmonic values with the m value given This is the p5th of these quantities |
| q6_sh.rm-p6 | matrix | the real parts of the spherical harmonic values with the m value given This is the p6th of these quantities |
| q6_sh.im-n6 | matrix | the real parts of the spherical harmonic values with the m value given This is the n6th of these quantities |
| q6_sh.im-n5 | matrix | the real parts of the spherical harmonic values with the m value given This is the n5th of these quantities |
| q6_sh.im-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q6_sh.im-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q6_sh.im-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q6_sh.im-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q6_sh.im-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q6_sh.im-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q6_sh.im-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q6_sh.im-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q6_sh.im-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q6_sh.im-p5 | matrix | the real parts of the spherical harmonic values with the m value given This is the p5th of these quantities |
| q6_sh.im-p6 | matrix | the real parts of the spherical harmonic values with the m value given This is the p6th of these quantities |
: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.w Lthe value of the angular momentum=6
q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities:| Quantity | Type | Description |
| q6_denom_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=250
q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:| Quantity | Type | Description |
| q6_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q6_mat.w,q6_denom_ones
q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:| Quantity | Type | Description |
| q6_sp.rm-n6 | vector | the product of the matrix q6_sh.rm-n6 and the vector q6_denom_ones |
| q6_sp.rm-n5 | vector | the product of the matrix q6_sh.rm-n5 and the vector q6_denom_ones |
| q6_sp.rm-n4 | vector | the product of the matrix q6_sh.rm-n4 and the vector q6_denom_ones |
| q6_sp.rm-n3 | vector | the product of the matrix q6_sh.rm-n3 and the vector q6_denom_ones |
| q6_sp.rm-n2 | vector | the product of the matrix q6_sh.rm-n2 and the vector q6_denom_ones |
| q6_sp.rm-n1 | vector | the product of the matrix q6_sh.rm-n1 and the vector q6_denom_ones |
| q6_sp.rm-0 | vector | the product of the matrix q6_sh.rm-0 and the vector q6_denom_ones |
| q6_sp.rm-p1 | vector | the product of the matrix q6_sh.rm-p1 and the vector q6_denom_ones |
| q6_sp.rm-p2 | vector | the product of the matrix q6_sh.rm-p2 and the vector q6_denom_ones |
| q6_sp.rm-p3 | vector | the product of the matrix q6_sh.rm-p3 and the vector q6_denom_ones |
| q6_sp.rm-p4 | vector | the product of the matrix q6_sh.rm-p4 and the vector q6_denom_ones |
| q6_sp.rm-p5 | vector | the product of the matrix q6_sh.rm-p5 and the vector q6_denom_ones |
| q6_sp.rm-p6 | vector | the product of the matrix q6_sh.rm-p6 and the vector q6_denom_ones |
| q6_sp.im-n6 | vector | the product of the matrix q6_sh.im-n6 and the vector q6_denom_ones |
| q6_sp.im-n5 | vector | the product of the matrix q6_sh.im-n5 and the vector q6_denom_ones |
| q6_sp.im-n4 | vector | the product of the matrix q6_sh.im-n4 and the vector q6_denom_ones |
| q6_sp.im-n3 | vector | the product of the matrix q6_sh.im-n3 and the vector q6_denom_ones |
| q6_sp.im-n2 | vector | the product of the matrix q6_sh.im-n2 and the vector q6_denom_ones |
| q6_sp.im-n1 | vector | the product of the matrix q6_sh.im-n1 and the vector q6_denom_ones |
| q6_sp.im-0 | vector | the product of the matrix q6_sh.im-0 and the vector q6_denom_ones |
| q6_sp.im-p1 | vector | the product of the matrix q6_sh.im-p1 and the vector q6_denom_ones |
| q6_sp.im-p2 | vector | the product of the matrix q6_sh.im-p2 and the vector q6_denom_ones |
| q6_sp.im-p3 | vector | the product of the matrix q6_sh.im-p3 and the vector q6_denom_ones |
| q6_sp.im-p4 | vector | the product of the matrix q6_sh.im-p4 and the vector q6_denom_ones |
| q6_sp.im-p5 | vector | the product of the matrix q6_sh.im-p5 and the vector q6_denom_ones |
| q6_sp.im-p6 | vector | the product of the matrix q6_sh.im-p6 and the vector q6_denom_ones |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q6_sh.*,q6_denom_ones
q6_rmn-n6The CUSTOM action with label q6_rmn-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n6 | 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=q6_sp.rm-n6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n6The CUSTOM action with label q6_imn-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n6 | 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=q6_sp.im-n6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n5The CUSTOM action with label q6_rmn-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n5 | 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=q6_sp.rm-n5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n5The CUSTOM action with label q6_imn-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n5 | 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=q6_sp.im-n5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n4The CUSTOM action with label q6_rmn-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n4 | 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=q6_sp.rm-n4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n4The CUSTOM action with label q6_imn-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n4 | 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=q6_sp.im-n4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n3The CUSTOM action with label q6_rmn-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n3 | 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=q6_sp.rm-n3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n3The CUSTOM action with label q6_imn-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n3 | 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=q6_sp.im-n3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n2The CUSTOM action with label q6_rmn-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n2 | 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=q6_sp.rm-n2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n2The CUSTOM action with label q6_imn-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n2 | 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=q6_sp.im-n2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n1The CUSTOM action with label q6_rmn-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n1 | 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=q6_sp.rm-n1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n1The CUSTOM action with label q6_imn-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n1 | 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=q6_sp.im-n1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-0The CUSTOM action with label q6_rmn-0 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-0 | 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=q6_sp.rm-0,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-0The CUSTOM action with label q6_imn-0 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-0 | 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=q6_sp.im-0,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p1The CUSTOM action with label q6_rmn-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p1 | 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=q6_sp.rm-p1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p1The CUSTOM action with label q6_imn-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p1 | 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=q6_sp.im-p1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p2The CUSTOM action with label q6_rmn-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p2 | 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=q6_sp.rm-p2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p2The CUSTOM action with label q6_imn-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p2 | 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=q6_sp.im-p2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p3The CUSTOM action with label q6_rmn-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p3 | 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=q6_sp.rm-p3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p3The CUSTOM action with label q6_imn-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p3 | 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=q6_sp.im-p3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p4The CUSTOM action with label q6_rmn-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p4 | 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=q6_sp.rm-p4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p4The CUSTOM action with label q6_imn-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p4 | 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=q6_sp.im-p4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p5The CUSTOM action with label q6_rmn-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p5 | 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=q6_sp.rm-p5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p5The CUSTOM action with label q6_imn-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p5 | 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=q6_sp.im-p5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p6The CUSTOM action with label q6_rmn-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p6 | 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=q6_sp.rm-p6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p6The CUSTOM action with label q6_imn-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p6 | 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=q6_sp.im-p6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n6The MEAN action with label q6_rms-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n6 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-n6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n6The MEAN action with label q6_ims-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n6 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-n6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n5The MEAN action with label q6_rms-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n5 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-n5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n5The MEAN action with label q6_ims-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n5 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-n5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n4The MEAN action with label q6_rms-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n4 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-n4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n4The MEAN action with label q6_ims-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n4 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-n4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n3The MEAN action with label q6_rms-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n3 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n3The MEAN action with label q6_ims-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n3 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n2The MEAN action with label q6_rms-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n2 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n2The MEAN action with label q6_ims-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n2 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n1The MEAN action with label q6_rms-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n1 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n1The MEAN action with label q6_ims-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n1 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-0The MEAN action with label q6_rms-0 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-0 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-0The MEAN action with label q6_ims-0 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-0 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p1The MEAN action with label q6_rms-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p1 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p1The MEAN action with label q6_ims-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p1 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p2The MEAN action with label q6_rms-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p2 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p2The MEAN action with label q6_ims-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p2 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p3The MEAN action with label q6_rms-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p3 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p3The MEAN action with label q6_ims-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p3 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p4The MEAN action with label q6_rms-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p4 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-p4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p4The MEAN action with label q6_ims-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p4 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-p4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p5The MEAN action with label q6_rms-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p5 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-p5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p5The MEAN action with label q6_ims-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p5 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-p5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p6The MEAN action with label q6_rms-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p6 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_rmn-p6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p6The MEAN action with label q6_ims-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p6 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6_imn-p6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_vmean2The COMBINE action with label q6_vmean2 calculates the following quantities:| Quantity | Type | Description |
| q6_vmean2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q6_rms-n6,q6_ims-n6,q6_rms-n5,q6_ims-n5,q6_rms-n4,q6_ims-n4,q6_rms-n3,q6_ims-n3,q6_rms-n2,q6_ims-n2,q6_rms-n1,q6_ims-n1,q6_rms-0,q6_ims-0,q6_rms-p1,q6_ims-p1,q6_rms-p2,q6_ims-p2,q6_rms-p3,q6_ims-p3,q6_rms-p4,q6_ims-p4,q6_rms-p5,q6_ims-p5,q6_rms-p6,q6_ims-p6
q6_vmeanThe CUSTOM action with label q6_vmean calculates the following quantities:| Quantity | Type | Description |
| q6_vmean | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_vmean2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities:| Quantity | Type | Description |
| q6_norm2 | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
q6_normThe CUSTOM action with label q6_norm calculates the following quantities:| Quantity | Type | Description |
| q6_norm | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6The CUSTOM action with label q6 calculates the following quantities:| Quantity | Type | Description |
| q6 | 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=q6_norm,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- diffThe MATHEVAL action with label diff calculates the following quantities:| Quantity | Type | Description |
| diff | scalar | an arbitrary function |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=q6.vmean,refcv.mean FUNCthe function you wish to evaluate=(x-0.06540)/(0.4035-0.06540)-(y-0.33023)/(0.745086-0.33023) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=0.1 KAPPAthe force constant for the wall=100000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=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 |
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=ene,vol,refcv.*,opes.*,q6.*,diff,uwall.bias FILEthe name of the file on which to output these quantities=Colvar.data
The PRINT action with label calculates somethingENDPLUMEDTerminate plumed input. More details
