PLUMED-NEST-TEST-SITE

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

Click on the labels of the actions for more information on what each action computes

#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 More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-100 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.={CUBIC D_0=0.45  D_MAX=0.55} LOWMEM this flag does nothing and is present only to ensure back-compatibility
# Construct a contact matrix between the atoms in the system   
The COORDINATIONNUMBER action with label lq calculates the following quantities:
 Quantity   
 Description  
lq.value
the coordination numbers of the specified atomscm: 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=lq  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.={CUBIC D_0=0.45  D_MAX=0.55} 
# Use depth first clustering to identify the sizes of the clusters                     
The CONTACT_MATRIX action with label cm calculates the following quantities:
 Quantity   
 Description  
cm.value
a matrix containing the weights for the bonds between each pair of atomsdfs: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=cm 
# Compute the sum of the coordination numbers for the atoms in the largest cluster                                                         
The DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Description  
dfs.value
vector with length that is equal to the number of rows in the input matrixclust1: CLUSTER_PROPERTIESCalculate properties of the distribution of some quantities that are part of a connected component More details CLUSTERSthe label of the action that does the clustering=dfs ARGcalculate the sum of the arguments calculated by this action for the cluster=lq 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 SUM calculate the sum of all the quantities  
# 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 evaporate 
The CLUSTER_PROPERTIES action with label clust1 calculates the following quantities:
 Quantity   
 Description  
clust1.value
a vector that is one if the atom is part of the cluster or interest and zero otherwise
clust1.sum
the sum of the colvarsmt: METADUsed to performed metadynamics on one or more collective variables. More details ...
 ARGthe labels of the scalars on which the bias will act=clust1.sum SIGMAthe widths of the Gaussian hills=10. HEIGHTthe heights of the Gaussian hills=2. PACEthe frequency for hill addition=500 
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=80.7 BIASFACTORuse well tempered metadynamics and use this bias factor=50 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=6000
... 
# Calculate the number of atoms in the largest cluster 
The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potentialss: 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
# Output the number of atoms in the largest cluster to a file
The CLUSTER_NATOMS action with label ss calculates the following quantities:
 Quantity   
 Description  
ss.value
the number of atoms in the clusterPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ss FILEthe name of the file on which to output these quantities=colvar