Project ID: plumID:19.049
Source: plumed_GeTe.dat
Originally used with PLUMED version: not specified
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# Calculate the Steinhardt Q6 vector for each of the atoms in the system
# N.B. Fewer atoms are used here than were used in the paper for technical reasons
q6: Q6 SPECIES=1-200 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
# Calculate the local Steinhardt parameter for each of the atoms in the system 
# in the manner described by ten Wolde and Frenkel.
lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
# Now select only those atoms that have a local q6 parameter that is larger than a certain threshold
flq6: MFILTER_MORE DATA=lq6 SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
# Calculate the coordination number for those atoms that have a local q6 parameter that is larger than a certain threshold
cc: COORDINATIONNUMBER SPECIES=flq6 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
# Now select those atoms that are coordinated to six or more atoms that have a value for the local q6 parameter that is larger than 
# a certain threshold
fcc: MFILTER_MORE DATA=cc SWITCH={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}
# Compute a contact matrix for the atoms that were selected using the previous command
mat: CONTACT_MATRIX ATOMS=fcc SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
# Perform a depth first search clustering on this matrix
dfs: DFSCLUSTERING MATRIX=mat
# Output the atoms in the largest cluster that was identified
OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=cluster1.xyz
# Calculate the number of clusters that contain 27 or more atoms that have ordered neighbors. 
nclust: CLUSTER_DISTRIBUTION ... 
  CLUSTERS=dfs 
  TRANSFORM={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0} 
  MORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
... 
# Output the number of clusters to a file
PRINT ARG=nclust.* FILE=colvar