README

About

These codes are used to analyze bulk systems and calculate Kirkwood-Buff integrals (KBIs) for these systems. rdf.f calculates radial distribution functions (RDFs) and coordination numbers. kb.f calculates KBIs, using the coordination numbers output from the rdf.f code as input. While below we reference a paper about electrolyte systems, these codes can also be used for non-electrolyte systems as well. The example input files are setup for the system 1M NaCl + 1M KBr (aq). In this example, only the (distinguishable) ion-ion RDFs and KBIs would be calculated, not those involving water. This code could also be used to calculate indistinguishable ion-ion RDFs & KBIs if the input files were setup accordingly.

Usage

These codes require a Fortran compiler and an input trajectory file in PDB format. The codes are setup to analyze four components. If you wish to analyze more components, change the ngroup parameter in the .f files and adjust the .dat files accordingly.

RDF Code

To compile the code:

gfortran rdf.f -o rdf

Setup the rdf.dat file for the system you wish to analyze. To run the code:

nohup ./rdf >& myrdf &

KB Code

To compile the code:

gfortran kb.f -o kb

Setup the kb.dat file for the system you wish to analyze. To run the code:

nohup ./kb >& mykb &

Reference

E.A. Ploetz, N.D. Smyers, and P.E. Smith, "Ion-Ion Association in Bulk Mixed Electrolytes Using Global and Local Electroneutrality Constraints" Journal of Physical Chemistry B, 2025, 129, 4, 1387–1398. (Editors' Choice)

Maintainer

@FluctuationSolutionTheory

License

AGPL-v3.0 © 2024 [Elizabeth A. Ploetz and Paul E. Smith]

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published
by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program (see LICENSE file).