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 details ATcoordinates of the virtual atom=2.,2.,2. # 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 details ATOMSthe numerical indexes for the set of atoms in the group=6151-6520 gcl: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6521-6890 gions: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=6151-6890 # 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 details SPECIESAthis keyword is used for colvars such as the coordination number=gna SPECIESBthis keyword is used for colvars such as the coordination number=gcl SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} cn1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=gcl SPECIESBthis keyword is used for colvars such as the coordination number=gna SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0}
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 details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn0 RADIUSthe switching function that tells us the extent of the sphereical region of interest={TANH R_0=1.5} MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0} sphere1: 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 details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn1 RADIUSthe switching function that tells us the extent of the sphereical region of interest={TANH R_0=1.5} MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0}
ncrysts: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=sphere0.morethan,sphere1.morethan POWERS the powers to which you are raising each of the arguments in your function=1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vcrysts: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ncrysts POWERS the powers to which you are raising each of the arguments in your function=0.333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # Measure coordination throughout the box cn2: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=gna SPECIESBthis keyword is used for colvars such as the coordination number=gcl SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=5.0} cn3: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=gcl SPECIESBthis keyword is used for colvars such as the coordination number=gna SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=5.0}
ncrysta: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn2.morethan,cn3.morethan POWERS the powers to which you are raising each of the arguments in your function=1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vcrysta: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ncrysta POWERS the powers to which you are raising each of the arguments in your function=0.333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # Measure coordination of crystalline ions in the biased sphere q60s: Q6Calculate sixth order Steinhardt parameters. More details SPECIESAthis keyword is used for colvars such as the coordination number=gna SPECIESBthis keyword is used for colvars such as the coordination number=gcl SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility q61s: Q6Calculate sixth order Steinhardt parameters. More details SPECIESAthis keyword is used for colvars such as the coordination number=gcl SPECIESBthis keyword is used for colvars such as the coordination number=gna SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} LOWMEM this 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 details SPECIES=q60s SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.38 D_MAX=1.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility lq61s: 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 details SPECIES=q61s SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.38 D_MAX=1.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility
flq60s: MFILTER_MOREBasically equivalent to MORE_THAN. More details DATAthe vector you wish to transform=lq60s SWITCHthe switching function that transform={GAUSSIAN R_0=0.55 D_MAX=0.56} flq61s: MFILTER_MOREBasically equivalent to MORE_THAN. More details DATAthe vector you wish to transform=lq61s SWITCHthe switching function that transform={GAUSSIAN R_0=0.55 D_MAX=0.56}
cn4: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=flq60s SPECIESBthis keyword is used for colvars such as the coordination number=flq61s SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} cn5: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=flq61s SPECIESBthis keyword is used for colvars such as the coordination number=flq60s SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0}
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 details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn4 RADIUSthe switching function that tells us the extent of the sphereical region of interest={TANH R_0=1.5} MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0} sphere3: 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 details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn5 RADIUSthe switching function that tells us the extent of the sphereical region of interest={TANH R_0=1.5} MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0}
qncrysts: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=sphere2.morethan,sphere3.morethan POWERS the powers to which you are raising each of the arguments in your function=1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO qvcrysts: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=qncrysts POWERS the powers to which you are raising each of the arguments in your function=0.333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # 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 details SPECIESAthis keyword is used for colvars such as the coordination number=flq60s SPECIESBthis keyword is used for colvars such as the coordination number=flq61s SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=5.0} cn7: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=flq61s SPECIESBthis keyword is used for colvars such as the coordination number=flq60s SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=5.0}
qncrysta: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn6.morethan,cn7.morethan POWERS the powers to which you are raising each of the arguments in your function=1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO qvcrysta: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=qncrysta POWERS the powers to which you are raising each of the arguments in your function=0.333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # Print PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ncrysts,vcrysts,qncrysts,qvcrysts,ncrysta,vcrysta,qncrysta,qvcrysta FILEthe name of the file on which to output these quantities=q6-sphere-and-all.dat # histograms for the rxn coordinate variables histcv1: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=vcrysta GRID_MIN the lower bounds for the grid=-1. GRID_MAX the upper bounds for the grid=10. GRID_BINthe number of bins for the grid=200 BANDWIDTHthe bandwidths for kernel density esimtation=0.01 histcv2: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=qvcrysta GRID_MIN the lower bounds for the grid=-1. GRID_MAX the upper bounds for the grid=10. GRID_BINthe number of bins for the grid=200 BANDWIDTHthe bandwidths for kernel density esimtation=0.01 DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=histcv1 FILE the file on which to write the grid=histn.dat FMTthe format that should be used to output real numbers=%8.4f DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=histcv2 FILE the file on which to write the grid=histnq6.dat FMTthe format that should be used to output real numbers=%8.4f # 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 details SPECIESthis keyword is used for colvars such as coordination number=gions SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.355 D_MAX=0.36} MEAN calculate the mean of all the quantities HIGHEST this flag allows you to recover the highest of these variables
# Report the mean and highest coordination numbers PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cnint.* FILEthe name of the file on which to output these quantities=cn-regions.dat # 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 details ATOMSthe atoms for which you would like to calculate the adjacency matrix=cnint SWITCHspecify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=0.355 D_MAX=0.36} dfs: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat # Cluster size distribution and number of ion clusters/monomers nhist: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=-1.5 UPPER=499.5 NBINS=501 NORM} nclust1: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs MORE_THANcalculate the number of variables that are more than a certain target value={GAUSSIAN D_0=0.95 R_0=0.01 D_MAX=0.96} nclust2: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs MORE_THANcalculate the number of variables that are more than a certain target value={GAUSSIAN D_0=1.95 R_0=0.01 D_MAX=1.96} nfree: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details CLUSTERSthe label of the action that does the clustering=dfs LESS_THANcalculate the number of variables that are less than a certain target value={GAUSSIAN D_0=0.55 R_0=0.01 D_MAX=0.96}
# Largest cluster at the interface clust0nat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe label of the action that does the clustering=dfs CLUSTER 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 on=1 clust1nat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe label of the action that does the clustering=dfs CLUSTER 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 on=2 clust2nat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe label of the action that does the clustering=dfs CLUSTER 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 on=3 # Report the cluster information PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nfree.*,nclust1.*,nclust2.*,clust0nat.*,clust1nat.*,clust2nat.* FILEthe name of the file on which to output these quantities=cluster.dat PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nhist.* FILEthe name of the file on which to output these quantities=csd.dat