PLUMED-NEST

Project ID: plumID:23.027
Source: water-structure-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

# Plumed driver script to calculate ion coordination numbers and identify ion clusters in the EDL and bulk solution regions of CmuMD simulations 
# Aaron R. Finney and Matteo Salvalaglio
# Properties of aqueous electrolyte solutions at carbon electrodes: 
# effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer
# June 2023

#LOAD FILE=PairEntropies.cpp
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

The UNITS action with label  calculates somethingwox: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-12000:3

# Q3
The GROUP action with label wox calculates somethingq3: 
Q3
Calculate 3rd order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=wox 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
The Q3 action with label q3 calculates somethinglq3: 
LOCAL_Q3
Calculate the local degree of order around an atoms by taking the average dot product between the q_3 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. More details
 
SPECIES
=q3 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}
The LOCAL_Q3 action with label lq3 calculates somethinglaq3: 
LOCAL_AVERAGE
Calculate averages over spherical regions centered on atoms More details
 
SPECIES
this keyword is used for colvars such as coordination number
=q3 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100}

The LOCAL_AVERAGE action with label laq3 calculates somethinghhq3: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
DATA
an alternative to the ARG keyword
=q3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100
The HISTOGRAM action with label hhq3 calculates somethinghhlq3: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
DATA
an alternative to the ARG keyword
=lq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100
The HISTOGRAM action with label hhlq3 calculates somethinghhlaq3: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 
DATA
an alternative to the ARG keyword
=laq3 
GRID_MIN
 the lower bounds for the grid
=-1.5 
GRID_MAX
 the upper bounds for the grid
=1.5 
GRID_BIN
the number of bins for the grid
=200 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
STRIDE
 the frequency with which to store data for averaging
=100

The HISTOGRAM action with label hhlaq3 calculates something
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hhq3 
FILE
 the file on which to write the grid
=histo_q3 
STRIDE
 the frequency with which the grid should be output to the file
=1000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hhlq3 
FILE
 the file on which to write the grid
=histo_lq3 
STRIDE
 the frequency with which the grid should be output to the file
=1000
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hhlaq3 
FILE
 the file on which to write the grid
=histo_laq3 
STRIDE
 the frequency with which the grid should be output to the file
=1000

# Pair entropies
#PAIRENTROPIES LABEL=s2 SPECIES=wox MAXR=5 SIGMA=0.15 LOCAL_DENSITY SWITCH={RATIONAL R_0=5.0 D_MAX=7.0 NN=50 MM=100} LOWMEM
#sa: LOCAL_AVERAGE SPECIES=s2 SWITCH={RATIONAL R_0=3.5 D_MAX=4.0 NN=50 MM=100} LOWMEM 

#hhe: HISTOGRAM DATA=s2 GRID_MIN=-6 GRID_MAX=0 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100
#hhle: HISTOGRAM DATA=sa GRID_MIN=-6 GRID_MAX=0 GRID_BIN=200 BANDWIDTH=0.015 STRIDE=100

#DUMPMULTICOLVAR FILE=entropy.xyz STRIDE=1 DATA=s2
#DUMPMULTICOLVAR FILE=localentropy.xyz STRIDE=1 DATA=sa

#DUMPGRID GRID=hhe FILE=histo_e STRIDE=1000
#DUMPGRID GRID=hhle FILE=histo_le STRIDE=1000