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
 |
 |
# 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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gna SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gcl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gcl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gna SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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. Options for this keyword are explained in the documentation for LESS_THAN.={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. Options for this keyword are explained in the documentation for LESS_THAN.={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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gna SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gcl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0} cn3: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=gcl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gna SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gna SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gcl SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gcl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gna SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=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_MOREApply one minus a switching function to the input vector. 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_MOREApply one minus a switching function to the input vector. 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 SPECIESAthe list of atoms for which the symmetry function is being calculated=flq60s SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=flq61s SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 SPECIESAthe list of atoms for which the symmetry function is being calculated=flq61s SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=flq60s SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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. Options for this keyword are explained in the documentation for LESS_THAN.={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. Options for this keyword are explained in the documentation for LESS_THAN.={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 SPECIESAthe list of atoms for which the symmetry function is being calculated=flq60s SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=flq61s SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0} cn7: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=flq61s SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=flq60s SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.38 D_MAX=1.0} MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=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 SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=gions SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={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. Options for this keyword are explained in the documentation for MORE_THAN.={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. Options for this keyword are explained in the documentation for MORE_THAN.={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. Options for this keyword are explained in the documentation for LESS_THAN.={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