Project ID: plumID:21.002
Source: Crystallization/IceIc/216molecules/350K/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
#SETTINGS NREPLICAS=2# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
#RESTART
vol:VOLUMECalculate the volume of the simulation box. More details
The VOLUME action with label vol calculates the volume of simulation boxENVIRONMENTSIMILARITY...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=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 valueMEAN... ENVIRONMENTSIMILARITY The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:calculate the mean of all the quantities
Quantity Description refcv.morethan the number of colvars that have a value more than a threshold refcv.mean the mean of the colvars ENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More 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_cmat:Lambda parameterDISTANCE_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 The DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities:ignore distances that have a value larger than this cutoffrefcv_grp:
Quantity Description refcv_cmat.w a matrix containing the weights for the bonds between each pair of atoms refcv_cmat.x the projection of the bond on the x axis refcv_cmat.y the projection of the bond on the y axis refcv_cmat.z the projection of the bond on the z axis refcv_cmat.value a matrix containing the weights for the bonds between each pair of atoms 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 The GROUP action with label refcv_grp calculates somethingrefcv_ones:the numerical indexes for the set of atoms in the groupONESCreate a constant vector with all elements equal to one More detailsSIZE=216 The ONES action with label refcv_ones calculates the following quantities:the number of ones that you would like to createrefcv_matenv1:
Quantity Description refcv_ones.value a vector of ones with the required number of elements CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.wthe 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 The CUSTOM action with label refcv_matenv1 calculates the following quantities:the function you wish to evaluaterefcv_env1:
Quantity Description refcv_matenv1.value an arbitrary function MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=refcv_matenv1,refcv_ones The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities:the input for this action is the scalar output from one or more other actionsrefcv_matenv2:
Quantity Description refcv_env1.value the vector that is obtained by taking the product between the matrix and the vector that were input refcv_env1..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.wthe 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 The CUSTOM action with label refcv_matenv2 calculates the following quantities:the function you wish to evaluaterefcv_env2:
Quantity Description refcv_matenv2.value an arbitrary function MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=refcv_matenv2,refcv_ones The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities:the input for this action is the scalar output from one or more other actionsrefcv:
Quantity Description refcv_env2.value the vector that is obtained by taking the product between the matrix and the vector that were input refcv_env2..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=refcv_env1,refcv_env2the 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_mt:the function you wish to evaluateMORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More detailsARG=refcvthe input to this functionSWITCH={RATIONAL R_0=0.5 NN=8 MM=16} The MORE_THAN action with label refcv_mt calculates the following quantities:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboverefcv_morethan:
Quantity Description refcv_mt.value a function that is one if the if the input is more than a threshold SUMCalculate the sum of the arguments More detailsARG=refcv_mtthe input to this functionPERIODIC=NO The SUM action with label refcv_morethan calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionrefcv_mean:
Quantity Description refcv_morethan.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=refcvthe 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
The MEAN action with label refcv_mean calculates the following quantities:bf1:
Quantity Description refcv_mean.value the sum 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 input for this action is the scalar output from one or more other actionsBASIS_FUNCTIONS=bf1the label of the one dimensional basis functions that should be usedTEMP=350.0the 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=b1 ... VES_LINEAR_EXPANSIONa label for the action so that its output can be referenced in the input to other actions
# Optimization algorithm
The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
Quantity Description b1.bias the instantaneous value of the bias potential b1.force2 the instantaneous value of the squared force due to this bias potential OPT_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=q6 # 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): The 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 actionsq6_grp:
Quantity Description q6._vmean the norm of the mean vector 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 The GROUP action with label q6_grp calculates somethingq6_mat:the numerical indexes for the set of atoms in the groupCONTACT_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 atomsCOMPONENTSThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:also calculate the components of the vector connecting the atoms in the contact matrixq6_sh:
Quantity Description q6_mat.w a matrix containing the weights for the bonds between each pair of atoms q6_mat.x the projection of the bond on the x axis q6_mat.y the projection of the bond on the y axis q6_mat.z the projection of the bond on the z axis q6_mat.value a matrix containing the weights for the bonds between each pair of atoms 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 input to this functionL=6 The SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:the value of the angular momentumq6_denom_ones:
Quantity Description q6_sh.rm the real parts of the spherical harmonic values with the m value given q6_sh.im the real parts of the spherical harmonic values with the m value given ONESCreate a constant vector with all elements equal to one More detailsSIZE=216 The ONES action with label q6_denom_ones calculates the following quantities:the number of ones that you would like to createq6_denom:
Quantity Description q6_denom_ones.value a vector of ones with the required number of elements MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=q6_mat.w,q6_denom_ones The MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:the input for this action is the scalar output from one or more other actionsq6_sp:
Quantity Description q6_denom.value the vector that is obtained by taking the product between the matrix and the vector that were input q6_denom..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=q6_sh.*,q6_denom_ones The MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:the input for this action is the scalar output from one or more other actionsq6_rmn-n6:
Quantity Description q6_sp.value the vector that is obtained by taking the product between the matrix and the vector that were input q6_sp..#!custom the names of the output components for this action depend on the actions input file see the example inputs below for details CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-n6,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q6_rmn-n6 calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq6_imn-n6:
Quantity Description q6_rmn-n6.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-n6,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-n5:
Quantity Description q6_imn-n6.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-n5,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-n5:
Quantity Description q6_rmn-n5.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-n5,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-n4:
Quantity Description q6_imn-n5.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-n4,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-n4:
Quantity Description q6_rmn-n4.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-n4,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-n3:
Quantity Description q6_imn-n4.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-n3,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-n3:
Quantity Description q6_rmn-n3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-n3,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-n2:
Quantity Description q6_imn-n3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-n2,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-n2:
Quantity Description q6_rmn-n2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-n2,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-n1:
Quantity Description q6_imn-n2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-n1,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-n1:
Quantity Description q6_rmn-n1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-n1,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-0:
Quantity Description q6_imn-n1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-0,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-0:
Quantity Description q6_rmn-0.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-0,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-p1:
Quantity Description q6_imn-0.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-p1,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-p1:
Quantity Description q6_rmn-p1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-p1,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-p2:
Quantity Description q6_imn-p1.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-p2,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-p2:
Quantity Description q6_rmn-p2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-p2,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-p3:
Quantity Description q6_imn-p2.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-p3,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-p3:
Quantity Description q6_rmn-p3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-p3,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-p4:
Quantity Description q6_imn-p3.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-p4,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-p4:
Quantity Description q6_rmn-p4.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-p4,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-p5:
Quantity Description q6_imn-p4.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-p5,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-p5:
Quantity Description q6_rmn-p5.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-p5,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rmn-p6:
Quantity Description q6_imn-p5.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.rm-p6,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_imn-p6:
Quantity Description q6_rmn-p6.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_sp.im-p6,q6_denomthe input to this functionFUNC=x/ythe function you wish to evaluatePERIODIC=NO The 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 functionq6_rms-n6:
Quantity Description q6_imn-p6.value an arbitrary function MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-n6the input to this functionPERIODIC=NO The 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 functionq6_ims-n6:
Quantity Description q6_rms-n6.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-n6the input to this functionPERIODIC=NO The 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 functionq6_rms-n5:
Quantity Description q6_ims-n6.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-n5the input to this functionPERIODIC=NO The 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 functionq6_ims-n5:
Quantity Description q6_rms-n5.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-n5the input to this functionPERIODIC=NO The 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 functionq6_rms-n4:
Quantity Description q6_ims-n5.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-n4the input to this functionPERIODIC=NO The 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 functionq6_ims-n4:
Quantity Description q6_rms-n4.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-n4the input to this functionPERIODIC=NO The 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 functionq6_rms-n3:
Quantity Description q6_ims-n4.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-n3the input to this functionPERIODIC=NO The 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 functionq6_ims-n3:
Quantity Description q6_rms-n3.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-n3the input to this functionPERIODIC=NO The 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 functionq6_rms-n2:
Quantity Description q6_ims-n3.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-n2the input to this functionPERIODIC=NO The 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 functionq6_ims-n2:
Quantity Description q6_rms-n2.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-n2the input to this functionPERIODIC=NO The 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 functionq6_rms-n1:
Quantity Description q6_ims-n2.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-n1the input to this functionPERIODIC=NO The 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 functionq6_ims-n1:
Quantity Description q6_rms-n1.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-n1the input to this functionPERIODIC=NO The 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 functionq6_rms-0:
Quantity Description q6_ims-n1.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-0the input to this functionPERIODIC=NO The 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 functionq6_ims-0:
Quantity Description q6_rms-0.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-0the input to this functionPERIODIC=NO The 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 functionq6_rms-p1:
Quantity Description q6_ims-0.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-p1the input to this functionPERIODIC=NO The 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 functionq6_ims-p1:
Quantity Description q6_rms-p1.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-p1the input to this functionPERIODIC=NO The 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 functionq6_rms-p2:
Quantity Description q6_ims-p1.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-p2the input to this functionPERIODIC=NO The 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 functionq6_ims-p2:
Quantity Description q6_rms-p2.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-p2the input to this functionPERIODIC=NO The 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 functionq6_rms-p3:
Quantity Description q6_ims-p2.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-p3the input to this functionPERIODIC=NO The 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 functionq6_ims-p3:
Quantity Description q6_rms-p3.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-p3the input to this functionPERIODIC=NO The 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 functionq6_rms-p4:
Quantity Description q6_ims-p3.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-p4the input to this functionPERIODIC=NO The 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 functionq6_ims-p4:
Quantity Description q6_rms-p4.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-p4the input to this functionPERIODIC=NO The 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 functionq6_rms-p5:
Quantity Description q6_ims-p4.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-p5the input to this functionPERIODIC=NO The 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 functionq6_ims-p5:
Quantity Description q6_rms-p5.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-p5the input to this functionPERIODIC=NO The 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 functionq6_rms-p6:
Quantity Description q6_ims-p5.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_rmn-p6the input to this functionPERIODIC=NO The 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 functionq6_ims-p6:
Quantity Description q6_rms-p6.value the sum MEANCalculate the arithmetic mean of the elements in a vector More detailsARG=q6_imn-p6the input to this functionPERIODIC=NO The 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 functionq6_vmean2:
Quantity Description q6_ims-p6.value the sum 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 The COMBINE action with label q6_vmean2 calculates the following quantities:the input to this functionq6_vmean:
Quantity Description q6_vmean2.value a linear compbination CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_vmean2the input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q6_vmean calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq6_norm2:
Quantity Description q6_vmean.value an arbitrary function 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 The COMBINE action with label q6_norm2 calculates the following quantities:the input to this functionq6_norm:
Quantity Description q6_norm2.value a linear compbination CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_norm2the input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NO The CUSTOM action with label q6_norm calculates the following quantities:if the output of your function is periodic then you should specify the periodicity of the functionq6:
Quantity Description q6_norm.value an arbitrary function CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=q6_norm,q6_denomthe 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 input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities