Command line version of softBV 1.2 (1 Oct 2020)

Download executable version 1.2 for Windows

"Download softBV 1.2 for Windows command line"

Installation for Windows

It is sufficient to unzip the folder anywhere on your computer. No further installation is required if you keep all files in the same (bin) folder.
The programme can be run from the cmd window
The basic format of the formats of softBV is:
(path)\bin\softBV.exe --command-name [compulsory arguments] | {optional arguments}

Download executable version 1.2 for Linux (64bit)

"Download softBV 1.2 for Linux command line"

Installation for Linux

It is sufficient to unzip the folder anywhere on your computer. No further installation is required if you keep all files in the same folder.
Note that the Linux version will only occasionally be updated and has no user interface. The programme can be run from the cmd window
The basic format of the formats of softBV is:
(path)/bin/softBV.x --command-name [compulsory arguments] | {optional arguments}

License for academic use of command line version of softBV 1.0 - 1.2 (21 Dec 2018)

This software and data are provided as a service to the scientific community and may be used free of charge for research and educational purposes.The incorporation of any part of this software into other academic software is permitted as long as this software is equally distributed free of charge and the source is properly cited. Any publications making use of this software should cite the following papers
(1) H. Chen, L.L. Wong, S.Adams; SoftBV - a software tool for screening the materials genome of inorganic fast ion conductors. Acta Crystallogr. B 75 (2019), 18-33. https://doi.org/10.1107/S2052520618015718 (as the source of the code)
(2) H. Chen, S. Adams; Bond softness sensitive bond-valence parameters for crystal structure plausibility tests. IUCrJ 4 (2017) 614-625. https://doi.org/10.1107/S2052520618015718 (as the source of the BV parameters)
Users are also encouraged to register by sending an Email to mseasn@nus.edu.sg. In this case they will be notified of updates or corrections.

License for non-academic use

License agreements for non-academic use are available on request. Please contact the author. This software may not be sold,licensed, transferred, copied or reproduced in whole or in part or in any manner of form other than in accordance with the license conditions shown above or otherwise without the prior written consent of the copyright owner.

WARRANTY DISCLAIMER

THE softBV SOFTWARE AND THE PARAMETERS USED THEREIN HAVE BEEN CAREFULLY DETERMINED. NEVERTHELESS THE AUTHOR OR HIS EMPLOYER CANNOT GRANT FOR THE ACCURACY OF ALL PARTS OF THE SOFTWARE OR THE SUITABILITY OF THIS SOFTWARE OR DATA FOR ANY PURPOSE, AND MAKE NO WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING THE WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THIS SOFTWARE OR DATA WILL NOT INFRINGE ANY THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OF OTHER RIGHTS. IT IS PROVIDED "AS IS".

softBV Commands

List of available commands. More detailed help with each command can be found by typing the command without argument:

--gen-cif : write the loaded cell to file in cif format.

--gen-cif-reduced : write the loaded cell reduced by symmetry to file in cif format.

--gen-cif-p1 : write the loaded cell to file in cif format without symmetry.

--gen-cif-assign : write the loaded cell to file in cif format with partially occupied sites of conducting species assigned occupancy = 1.0 randomly.

--gen-cif-assign-all : write the loaded cell to file in cif format with all partially occupied sites assigned occupancy = 1.0 randomly.

--gen-gin-lib : generate a forcefield file in .lib format for calculation with software GULP.

--gen-gin : generate an overall input file in .gin format for performing molecular dynamics calculaiton with software GULP.

--gen-cube: calculate the static energy landscape for ionic conduction and write the result to file in Gaussian cube format.

--cal-bv : calculate bond valences of the loaded cell.

--cal-gii : calculate the global instability index of the loaded cell.

--cal-cn-bv : calculate coordination numbers of the loaded cell using a BV-based algorithm.

--cal-cn : calculate coordination numbers of the loaded cell using a geometric algorithm (superseded by --cal-cn-bv).

--cal-sym : calculate symmetry of the loaded cell.

--cal-tot-en : calculate the total BVSE energy of the loaded cell.

--help : display this help text.

--print-cell : print the loaded cell.

--print-ppt : print the property corresponding to the loaded cell.

--print-sym : print the symmetry corresponding to the loaded cell.

--print-cube : print a summary of the loaded cube.

--rx-sd : perform a relaxation of loaded cell with steepest descend algorithm and write the result to file in cif format.

--rx-neb: perform a simple nudged elastic bend calculation with input of two end images.

--rx-neb-images : perform a simple nudged elastic bend calculation with input of a series of images.

--fft : perform a fourier transform analysis to determine critical points and eigenvalues/vectors at these points.

--fft-cubes : perform a fourier transform analysis and generate cubes corresponding to force, force constant, laplacian and slope.

--fp-map: generates a cif file representing conduction path in the given cube file.

--gh : generates cif files and csv file representing the characteristic conduction pathway in the given cube file.

--sites: output a summary of sites based on graph analysis.

--md: perform a simple "molecular dynamics" simulation allowing only conducting ions to move.

--kmc: conduct a kinetic monte carlo simulation to estimate the ionic conductivity given the cif and cube files. It should be noted that this implementation has significant limitations and depending on the actual ion transport mechanism may only roughly correlate with the true ionic conductivity.

Pathway analyser

The distributions also contain an alternative pathway analysis algorithm (that works best with the GUI version of softBV). In command line mode the pathway analyser is invoked by

(path)\bin\BVPA.exe --cube [cube file name] --cif [cif file name] [conducting ion identifier] --path --gui --vesta .
Here, [conducting ion identifier] has e.g. the format "Ag1+" for an Ag⁺ ion. This entry has to match the conducting ion specified in the header of the cube file.

The command --path creates two output files in the working folder:
- The text file BVPA_events.txt summarising the changes of the pathway topology as a function of the bond valence site energy relative to the lowest enegy site in the cube file.
- the csv file BVPA_rp.csv showing the reaction path. This file can be used to plot the pathway in the compound.

Adding the command --gui creates the additional file "BVPA_gui.csv" in the working folder, which lists the positions of the occupied sites, interstitial sites and saddle points for the specified conducting ion.

Adding the command --vesta creates the file "BVPA.vesta" in the working folder. This file is an input file suitable for visualising structure and pathways in the free-for-academic-use 3D visualisation programme VESTA. The authors of softBV have no relationship to the authors of VESTA.