Project ID: plumID:21.002
Source: Crystallization/IceIc/216molecules/340K/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
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#SETTINGS NREPLICAS=2# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
#RESTART
volThe VOLUME action with label vol calculates the following quantities::
Quantity Type Description vol scalar the volume of simulation box VOLUMECalculate the volume of the simulation box. More detailsENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More detailsSPECIES=1-648:3this keyword is used for colvars such as coordination numberSIGMA=0.050the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcvThe ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions
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 REFERENCE_1=env1c.pdbPDB files with relative distances from central atomREFERENCE_2=env2c.pdbPDB files with relative distances from central atomMORE_THAN={RATIONAL R_0=0.5 NN=8 MM=16}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantitiesENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More detailsSPECIES=1-648:3this keyword is used for colvars such as coordination numberSIGMA=0.050the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcva label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=env1c.pdbPDB files with relative distances from central atomREFERENCE_2=env2c.pdbPDB files with relative distances from central atomMORE_THAN={RATIONAL R_0=0.5 NN=8 MM=16}calculate the number of variables that are more than a certain target valueMEANcalculate the mean of all the quantitiesCUTOFF=3how many multiples of sigma would you like to consider beyond the maximum distance in the environmentLCUTOFF=0.0001any atoms separated by less than this tolerance should be ignoredLAMBDA=100 ... ENVIRONMENTSIMILARITY # PLUMED interprets the command: # ENVIRONMENTSIMILARITY ... # SPECIES=1-648:3 # SIGMA=0.050 # CRYSTAL_STRUCTURE=CUSTOM # LABEL=refcv # REFERENCE_1=env1c.pdb # REFERENCE_2=env2c.pdb # MORE_THAN={RATIONAL R_0=0.5 NN=8 MM=16} # MEAN # ... ENVIRONMENTSIMILARITY # as follows (Click the red comment above to revert to the short version of the input): refcv_cmatThe DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities:Lambda parameter:
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 detailsCOMPONENTSalso calculate the components of the vector connecting the atoms in the contact matrixGROUP=1-648:3the atoms for which you would like to calculate the adjacency matrixCUTOFF=0.608629 refcv_grpThe GROUP action with label refcv_grp calculates the following quantities:ignore distances that have a value larger than this cutoff:
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 detailsATOMS=1-648:3 refcv_onesThe CONSTANT action with label refcv_ones calculates the following quantities:the numerical indexes for the set of atoms in the group:
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 detailsSIZE=216 refcv_matenv1The CUSTOM action with label refcv_matenv1 calculates the following quantities:the number of ones that you would like to create:
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 detailsARG=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.wthe values input to this functionVAR=x,y,z,wthe names to give each of the arguments in the functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionFUNC=(step(w-0.0001)*step(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y--0.1622)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y-0.1621)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1622)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1621)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025 refcv_env1The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities:the function you wish to evaluate:
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 detailsARG=refcv_matenv1,refcv_ones refcv_matenv2The CUSTOM action with label refcv_matenv2 calculates the following quantities:the label for the matrix and the vector/scalar that are being multiplied:
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 detailsARG=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.wthe values input to this functionVAR=x,y,z,wthe names to give each of the arguments in the functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionFUNC=(step(w-0.0001)*step(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y--0.1621)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y-0.1622)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1621)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1622)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025 refcv_env2The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities:the function you wish to evaluate:
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 detailsARG=refcv_matenv2,refcv_ones refcvThe CUSTOM action with label refcv calculates the following quantities:the label for the matrix and the vector/scalar that are being multiplied:
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 detailsARG=refcv_env1,refcv_env2the values input to this functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionVAR=v1,v2the names to give each of the arguments in the functionFUNC=(1/100)*log(exp(100*v1)+exp(100*v2 refcv_mtThe MORE_THAN action with label refcv_mt calculates the following quantities:the function you wish to evaluate:
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 detailsARG=refcvthe values input to this functionSWITCH={RATIONAL R_0=0.5 NN=8 MM=16} refcv_morethanThe SUM action with label refcv_morethan calculates the following quantities:This keyword is used if you want to employ an alternative to the continuous swiching function defined above:
Quantity Type Description refcv_morethan scalar the sum of all the elements in the input vector SUMCalculate the sum of the arguments More detailsARG=refcv_mtthe values input to this functionPERIODIC=NO refcv_meanThe MEAN action with label refcv_mean calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=refcvthe values input to this functionPERIODIC=NO # --- End of included input ---if the output of your function is periodic then you should specify the periodicity of the function
# Construct a bias potential using VES # # Basis functions
bf1:BF_LEGENDRELegendre polynomials basis functions. More detailsORDER=40The order of the basis function expansionMINIMUM=0.0The minimum of the interval on which the basis functions are definedMAXIMUM=216.0The maximum of the interval on which the basis functions are defined
# Target distribution
The BF_LEGENDRE action with label bf1 calculates somethingtd_uni:TD_UNIFORMUniform target distribution (static). More details
# Expansion
The TD_UNIFORM action with label td_uni calculates somethingVES_LINEAR_EXPANSION...Linear basis set expansion bias. More detailsARG=refcv.morethanthe labels of the scalars on which the bias will actBASIS_FUNCTIONS=bf1the label of the one dimensional basis functions that should be usedTEMP=340.0the system temperature - this is needed if the MD code does not pass the temperature to PLUMEDGRID_BINS=300the number of bins used for the gridTARGET_DISTRIBUTION=td_unithe label of the target distribution to be usedLABEL=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions... VES_LINEAR_EXPANSION
Quantity Type Description b1.bias scalar the instantaneous value of the bias potential b1.force2 scalar the instantaneous value of the squared force due to this bias potential.
# Optimization algorithmOPT_AVERAGED_SGD...Averaged stochastic gradient decent with fixed step size. This action has hidden defaults. More detailsBIAS=b1the label of the VES bias to be optimizedSTRIDE=500the frequency of updating the coefficients given in the number of MD stepsLABEL=o1a label for the action so that its output can be referenced in the input to other actionsSTEPSIZE=5the step size used for the optimizationFES_OUTPUT=500how often the FES(s) should be written out to fileBIAS_OUTPUT=500how often the bias(es) should be written out to fileCOEFFS_OUTPUT=100 #MULTIPLE_WALKERS ... OPT_AVERAGED_SGD The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:how often the coefficients should be written to file
Quantity Description o1.value a scalar OPT_AVERAGED_SGD...Averaged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More detailsBIAS=b1the label of the VES bias to be optimizedSTRIDE=500the frequency of updating the coefficients given in the number of MD stepsLABEL=o1a label for the action so that its output can be referenced in the input to other actionsSTEPSIZE=5the step size used for the optimizationFES_OUTPUT=500how often the FES(s) should be written out to fileBIAS_OUTPUT=500how often the bias(es) should be written out to fileCOEFFS_OUTPUT=100 #MULTIPLE_WALKERShow often the coefficients should be written to fileCOEFFS_FILE=coeffs.data ... OPT_AVERAGED_SGDthe name of output file for the coefficientsQ6Calculate sixth order Steinhardt parameters. This action is a shortcut. More detailsSPECIES=1-648:3this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=0.3 D_MAX=0.35}the switching function that it used in the construction of the contact matrixVMEANcalculate the norm of the mean vectorLABEL=q6The Q6 action with label q6 calculates the following quantities:a label for the action so that its output can be referenced in the input to other actions# PLUMED interprets the command: # Q6 SPECIES=1-648:3 SWITCH={CUBIC D_0=0.3 D_MAX=0.35} VMEAN LABEL=q6 # as follows (Click the red comment above to revert to the short version of the input): q6_grpThe GROUP action with label q6_grp calculates the following quantities:
Quantity Type Description q6 vector the norms of the vectors of spherical harmonic coefficients :
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 detailsATOMS=1-648:3 q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:the numerical indexes for the set of atoms in the group:
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 detailsGROUP=1-648:3specifies the list of atoms that should be assumed indistinguishableSWITCH={CUBIC D_0=0.3 D_MAX=0.35}specify the switching function to use between two sets of indistinguishable atomsCOMPONENTSq6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:also calculate the components of the vector connecting the atoms in the contact matrix:
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 detailsARG=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.wthe values input to this functionL=6 q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities:the value of the angular momentum:
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 detailsSIZE=216 q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:the number of ones that you would like to create:
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 detailsARG=q6_mat.w,q6_denom_ones q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:the label for the matrix and the vector/scalar that are being multiplied:
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 detailsARG=q6_sh.*,q6_denom_ones q6_rmn-n6The CUSTOM action with label q6_rmn-n6 calculates the following quantities:the label for the matrix and the vector/scalar that are being multiplied:
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 detailsARG=q6_sp.rm-n6,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-n6The CUSTOM action with label q6_imn-n6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-n6,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-n5The CUSTOM action with label q6_rmn-n5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-n5,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-n5The CUSTOM action with label q6_imn-n5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-n5,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-n4The CUSTOM action with label q6_rmn-n4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-n4,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-n4The CUSTOM action with label q6_imn-n4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-n4,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-n3The CUSTOM action with label q6_rmn-n3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-n3,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-n3The CUSTOM action with label q6_imn-n3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-n3,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-n2The CUSTOM action with label q6_rmn-n2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-n2,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-n2The CUSTOM action with label q6_imn-n2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-n2,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-n1The CUSTOM action with label q6_rmn-n1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-n1,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-n1The CUSTOM action with label q6_imn-n1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-n1,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-0The CUSTOM action with label q6_rmn-0 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-0,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-0The CUSTOM action with label q6_imn-0 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-0,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-p1The CUSTOM action with label q6_rmn-p1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-p1,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-p1The CUSTOM action with label q6_imn-p1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-p1,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-p2The CUSTOM action with label q6_rmn-p2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-p2,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-p2The CUSTOM action with label q6_imn-p2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-p2,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-p3The CUSTOM action with label q6_rmn-p3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-p3,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-p3The CUSTOM action with label q6_imn-p3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-p3,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-p4The CUSTOM action with label q6_rmn-p4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-p4,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-p4The CUSTOM action with label q6_imn-p4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-p4,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-p5The CUSTOM action with label q6_rmn-p5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-p5,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-p5The CUSTOM action with label q6_imn-p5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-p5,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rmn-p6The CUSTOM action with label q6_rmn-p6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.rm-p6,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_imn-p6The CUSTOM action with label q6_imn-p6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_sp.im-p6,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO q6_rms-n6The MEAN action with label q6_rms-n6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-n6the values input to this functionPERIODIC=NO q6_ims-n6The MEAN action with label q6_ims-n6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-n6the values input to this functionPERIODIC=NO q6_rms-n5The MEAN action with label q6_rms-n5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-n5the values input to this functionPERIODIC=NO q6_ims-n5The MEAN action with label q6_ims-n5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-n5the values input to this functionPERIODIC=NO q6_rms-n4The MEAN action with label q6_rms-n4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-n4the values input to this functionPERIODIC=NO q6_ims-n4The MEAN action with label q6_ims-n4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-n4the values input to this functionPERIODIC=NO q6_rms-n3The MEAN action with label q6_rms-n3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-n3the values input to this functionPERIODIC=NO q6_ims-n3The MEAN action with label q6_ims-n3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-n3the values input to this functionPERIODIC=NO q6_rms-n2The MEAN action with label q6_rms-n2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-n2the values input to this functionPERIODIC=NO q6_ims-n2The MEAN action with label q6_ims-n2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-n2the values input to this functionPERIODIC=NO q6_rms-n1The MEAN action with label q6_rms-n1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-n1the values input to this functionPERIODIC=NO q6_ims-n1The MEAN action with label q6_ims-n1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-n1the values input to this functionPERIODIC=NO q6_rms-0The MEAN action with label q6_rms-0 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-0the values input to this functionPERIODIC=NO q6_ims-0The MEAN action with label q6_ims-0 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-0the values input to this functionPERIODIC=NO q6_rms-p1The MEAN action with label q6_rms-p1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-p1the values input to this functionPERIODIC=NO q6_ims-p1The MEAN action with label q6_ims-p1 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-p1the values input to this functionPERIODIC=NO q6_rms-p2The MEAN action with label q6_rms-p2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-p2the values input to this functionPERIODIC=NO q6_ims-p2The MEAN action with label q6_ims-p2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-p2the values input to this functionPERIODIC=NO q6_rms-p3The MEAN action with label q6_rms-p3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-p3the values input to this functionPERIODIC=NO q6_ims-p3The MEAN action with label q6_ims-p3 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-p3the values input to this functionPERIODIC=NO q6_rms-p4The MEAN action with label q6_rms-p4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-p4the values input to this functionPERIODIC=NO q6_ims-p4The MEAN action with label q6_ims-p4 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-p4the values input to this functionPERIODIC=NO q6_rms-p5The MEAN action with label q6_rms-p5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-p5the values input to this functionPERIODIC=NO q6_ims-p5The MEAN action with label q6_ims-p5 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-p5the values input to this functionPERIODIC=NO q6_rms-p6The MEAN action with label q6_rms-p6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_rmn-p6the values input to this functionPERIODIC=NO q6_ims-p6The MEAN action with label q6_ims-p6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_imn-p6the values input to this functionPERIODIC=NO q6_vmean2The COMBINE action with label q6_vmean2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
Quantity Type Description q6_vmean2 scalar a linear compbination COMBINECalculate a polynomial combination of a set of other variables. More detailsPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPOWERS=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2the powers to which you are raising each of the arguments in your functionARG=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:the values input to this function:
Quantity Type Description q6_vmean scalar an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_vmean2the values input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NO q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPOWERS=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2the powers to which you are raising each of the arguments in your functionARG=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:the values input to this function:
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 detailsARG=q6_norm2the values input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NO q6The CUSTOM action with label q6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the function:
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 detailsARG=q6_norm,q6_denomthe values input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO # --- End of included input ---if the output of your function is periodic then you should specify the periodicity of the functionPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe labels of the values that you would like to print to the fileFILE=COLVARthe name of the file on which to output these quantities