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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

The UNITS action with label  calculates somethingwox: 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=1-12000:3

# Q3
The GROUP action with label wox calculates somethingq3: Q3Calculate 3rd order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=wox 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=3.5 D_MAX=4.0 NN=50 MM=100}
The Q3 action with label q3 calculates the following quantities:
 Quantity   
 Description  
q3.value
the norms of the vectors of spherical harmonic coefficientslq3: LOCAL_Q3Calculate 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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q3 SWITCHThis 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 the following quantities:
 Quantity   
 Description  
lq3.value
the values of the local steinhardt parameters for the input atomslaq3: LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=q3 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=3.5 D_MAX=4.0 NN=50 MM=100}

The LOCAL_AVERAGE action with label laq3 calculates the following quantities:
 Quantity   
 Description  
laq3.value
the values of the local averageshhq3: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details DATAan 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_BINthe number of bins for the grid=200 BANDWIDTHthe 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 the following quantities:
 Quantity   
 Description  
hhq3.value
the estimate of the histogram as a function of the argument that was obtainedhhlq3: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details DATAan 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_BINthe number of bins for the grid=200 BANDWIDTHthe 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 the following quantities:
 Quantity   
 Description  
hhlq3.value
the estimate of the histogram as a function of the argument that was obtainedhhlaq3: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details DATAan 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_BINthe number of bins for the grid=200 BANDWIDTHthe 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 the following quantities:
 Quantity   
 Description  
hhlaq3.value
the estimate of the histogram as a function of the argument that was obtainedDUMPGRIDOutput 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)=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
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)=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
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)=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