Project ID: plumID:19.049
Source: plumed_lj_gas_liquid.dat
Originally used with PLUMED version: not specified
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#SETTINGS NATOMS=32768 # Calculate the coordination numbers of the 100 atoms in the system lq:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More detailsSPECIES=1-100this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=0.45 D_MAX=0.55}the switching function that it used in the construction of the contact matrixLOWMEM# Construct a contact matrix between the atoms in the system cm:this flag does nothing and is present only to ensure back-compatibilityCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsATOMS=lqthe atoms for which you would like to calculate the adjacency matrixSWITCH={CUBIC D_0=0.45 D_MAX=0.55} # Use depth first clustering to identify the sizes of the clusters 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=cm # Compute the sum of the coordination numbers for the atoms in the largest cluster clust1:the input matrix (can use ARG instead)CLUSTER_PROPERTIESCalculate properties of the distribution of some quantities that are part of a connected component This action is a shortcut. More detailsCLUSTERS=dfsthe label of the action that does the clusteringARG=lqcalculate the sum of the arguments calculated by this action for the clusterCLUSTER=1which 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 onSUM# Apply a metadynamics bias on the sum of the coordination number for the atoms # in the largest cluster so as to force droplets of liquid to condense and evaporatecalculate the sum of all the quantitiesMETAD...Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More detailsARG=clust1.sumthe input for this action is the scalar output from one or more other actionsSIGMA=10the widths of the Gaussian hillsHEIGHT=2the heights of the Gaussian hillsPACE=500the frequency for hill additionTEMP=80.7the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=50use well tempered metadynamics and use this bias factorGRID_MIN=0the lower bounds for the gridGRID_MAX=6000 ... mt: # Calculate the number of atoms in the largest cluster ss:the upper bounds for the gridCLUSTER_NATOMSCalculate the number of atoms in the cluster of interest This action is a shortcut. More detailsCLUSTERS=dfsthe label of the action that does the clusteringCLUSTER=1 # Output the number of atoms in the largest cluster to a filewhich 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 onPrint quantities to a file. More detailsARG=ssthe 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