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 SPECIESthis keyword is used for colvars such as coordination number=wox SWITCHthe 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 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 SPECIES=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 SPECIESthis keyword is used for colvars such as coordination number=q3 SWITCHthe 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 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