Project ID: plumID:21.044
Source: driver.dat
Originally used with PLUMED version: 2.5.1
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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# From NaCl Crystallisation Pathways; Aaron R. Finney and Matteo Salvalaglio # Plumed driver file to post-process MD and well-tempered metadynamics simulations
# Fixed atom at the centre of the simulation box p:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.,2.,2coordinates of the virtual atom
# DEfine the ion groups gna: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=6151-6520 gcl:the numerical indexes for the set of atoms in the groupGROUPDefine 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=6521-6890 gions:the numerical indexes for the set of atoms in the groupGROUPDefine 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=6151-6890the numerical indexes for the set of atoms in the group
# Measure coordination in the biased sphere cn0:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=gnathis keyword is used for colvars such as the coordination numberSPECIESB=gclthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0} cn1:the switching function that it used in the construction of the contact matrixCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=gclthis keyword is used for colvars such as the coordination numberSPECIESB=gnathis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrix
sphere0:INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More detailsATOM=pthe atom whose vicinity we are interested in examiningDATA=cn0the label of an action that calculates multicolvarsRADIUS={TANH R_0=1.5}the switching function that tells us the extent of the sphereical region of interestMORE_THAN={RATIONAL R_0=5.0} sphere1:calcualte the number of colvars that are inside the region of interest and that are greater that a certain thresholdINSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More detailsATOM=pthe atom whose vicinity we are interested in examiningDATA=cn1the label of an action that calculates multicolvarsRADIUS={TANH R_0=1.5}the switching function that tells us the extent of the sphereical region of interestMORE_THAN={RATIONAL R_0=5.0}calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
ncrysts:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=sphere0.morethan,sphere1.morethanthe input to this functionPOWERS=1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NO vcrysts:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=ncryststhe input to this functionPOWERS=0.333the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Measure coordination throughout the box cn2:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=gnathis keyword is used for colvars such as the coordination numberSPECIESB=gclthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrixMORE_THAN={RATIONAL R_0=5.0} cn3:calculate the number of variables that are more than a certain target valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=gclthis keyword is used for colvars such as the coordination numberSPECIESB=gnathis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrixMORE_THAN={RATIONAL R_0=5.0}calculate the number of variables that are more than a certain target value
ncrysta:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=cn2.morethan,cn3.morethanthe input to this functionPOWERS=1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NO vcrysta:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=ncrystathe input to this functionPOWERS=0.333the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Measure coordination of crystalline ions in the biased sphere q60s:Q6Calculate sixth order Steinhardt parameters. More detailsSPECIESA=gnathis keyword is used for colvars such as the coordination numberSPECIESB=gclthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrixLOWMEMq61s:this flag does nothing and is present only to ensure back-compatibilityQ6Calculate sixth order Steinhardt parameters. More detailsSPECIESA=gclthis keyword is used for colvars such as the coordination numberSPECIESB=gnathis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrixLOWMEMthis flag does nothing and is present only to ensure back-compatibility
lq60s:LOCAL_Q6Calculate the local degree of order around an atoms by taking the average dot product between the $q_6 $ vector on the central atom and the $q_6 $ vector on the atoms in the first coordination sphere. More detailsSPECIES=q60sSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveLOWMEMlq61s:this flag does nothing and is present only to ensure back-compatibilityLOCAL_Q6Calculate the local degree of order around an atoms by taking the average dot product between the $q_6 $ vector on the central atom and the $q_6 $ vector on the atoms in the first coordination sphere. More detailsSPECIES=q61sSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveLOWMEMthis flag does nothing and is present only to ensure back-compatibility
flq60s:MFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=lq60sthe vector you wish to transformSWITCH={GAUSSIAN R_0=0.55 D_MAX=0.56} flq61s:the switching function that transformMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=lq61sthe vector you wish to transformSWITCH={GAUSSIAN R_0=0.55 D_MAX=0.56}the switching function that transform
cn4:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=flq60sthis keyword is used for colvars such as the coordination numberSPECIESB=flq61sthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0} cn5:the switching function that it used in the construction of the contact matrixCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=flq61sthis keyword is used for colvars such as the coordination numberSPECIESB=flq60sthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrix
sphere2:INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More detailsATOM=pthe atom whose vicinity we are interested in examiningDATA=cn4the label of an action that calculates multicolvarsRADIUS={TANH R_0=1.5}the switching function that tells us the extent of the sphereical region of interestMORE_THAN={RATIONAL R_0=5.0} sphere3:calcualte the number of colvars that are inside the region of interest and that are greater that a certain thresholdINSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More detailsATOM=pthe atom whose vicinity we are interested in examiningDATA=cn5the label of an action that calculates multicolvarsRADIUS={TANH R_0=1.5}the switching function that tells us the extent of the sphereical region of interestMORE_THAN={RATIONAL R_0=5.0}calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
qncrysts:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=sphere2.morethan,sphere3.morethanthe input to this functionPOWERS=1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NO qvcrysts:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=qncryststhe input to this functionPOWERS=0.333the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Measure coordination of crystalline ions in the box cn6:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=flq60sthis keyword is used for colvars such as the coordination numberSPECIESB=flq61sthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrixMORE_THAN={RATIONAL R_0=5.0} cn7:calculate the number of variables that are more than a certain target valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=flq61sthis keyword is used for colvars such as the coordination numberSPECIESB=flq60sthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=0.38 D_MAX=1.0}the switching function that it used in the construction of the contact matrixMORE_THAN={RATIONAL R_0=5.0}calculate the number of variables that are more than a certain target value
qncrysta:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=cn6.morethan,cn7.morethanthe input to this functionPOWERS=1,1the powers to which you are raising each of the arguments in your functionPERIODIC=NO qvcrysta:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=qncrystathe input to this functionPOWERS=0.333the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPrint quantities to a file. More detailsARG=ncrysts,vcrysts,qncrysts,qvcrysts,ncrysta,vcrysta,qncrysta,qvcrystathe input for this action is the scalar output from one or more other actionsFILE=q6-sphere-and-all.datthe name of the file on which to output these quantities
# histograms for the rxn coordinate variables histcv1:HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=vcrystathe quantity that is being averagedGRID_MIN=-1the lower bounds for the gridGRID_MAX=10the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.01 histcv2:the bandwidths for kernel density esimtationHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=qvcrystathe quantity that is being averagedGRID_MIN=-1the lower bounds for the gridGRID_MAX=10the upper bounds for the gridGRID_BIN=200the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=histcv1the grid you would like to print (can also use ARG for specifying what is being printed)FILE=histn.datthe file on which to write the gridFMT=%8.4fthe format that should be used to output real numbersDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=histcv2the grid you would like to print (can also use ARG for specifying what is being printed)FILE=histnq6.datthe file on which to write the gridFMT=%8.4fthe format that should be used to output real numbers
# Get the Na-Cl coordination number cnint:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIES=gionsthis keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=0.355 D_MAX=0.36}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesHIGHESTthis flag allows you to recover the highest of these variables
# Report the mean and highest coordination numbersPrint quantities to a file. More detailsARG=cnintthe input for this action is the scalar output from one or more other actionsFILE=cn-regions.datthe name of the file on which to output these quantities
# DFS on ion clusters built according to simple cut-off criterion mat:CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsATOMS=cnintthe atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)SWITCH={RATIONAL R_0=0.355 D_MAX=0.36} dfs:specify the switching function to use between two sets of indistinguishable atomsDFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More detailsMATRIX=matthe input matrix (can use ARG instead)
# Cluster size distribution and number of ion clusters/monomers nhist:CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More detailsCLUSTERS=dfsthe label of the action that does the clusteringHISTOGRAM={GAUSSIAN LOWER=-1.5 UPPER=499.5 NBINS=501 NORM} nclust1:calculate a discretized histogram of the distribution of valuesCLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More detailsCLUSTERS=dfsthe label of the action that does the clusteringMORE_THAN={GAUSSIAN D_0=0.95 R_0=0.01 D_MAX=0.96} nclust2:calculate the number of variables that are more than a certain target valueCLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More detailsCLUSTERS=dfsthe label of the action that does the clusteringMORE_THAN={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.96} nfree:calculate the number of variables that are more than a certain target valueCLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More detailsCLUSTERS=dfsthe label of the action that does the clusteringLESS_THAN={GAUSSIAN D_0=0.55 R_0=0.01 D_MAX=0.96}calculate the number of variables that are less than a certain target value
# Largest cluster at the interface clust0nat:CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More detailsCLUSTERS=dfsthe label of the action that does the clusteringCLUSTER=1 clust1nat:which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so onCLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More detailsCLUSTERS=dfsthe label of the action that does the clusteringCLUSTER=2 clust2nat:which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so onCLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More detailsCLUSTERS=dfsthe label of the action that does the clusteringCLUSTER=3which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
# Report the cluster informationPrint quantities to a file. More detailsARG=nfree.*,nclust1.*,nclust2.*,clust0nat.*,clust1nat.*,clust2natthe input for this action is the scalar output from one or more other actionsFILE=cluster.datthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=nhistthe input for this action is the scalar output from one or more other actionsFILE=csd.datthe name of the file on which to output these quantities