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Research data supporting "The Potential Energy Landscape for Crystallisation of a Lennard-Jones Fluid"


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Authors

de Souza, Vanessa K.  ORCID logo  https://orcid.org/0000-0002-1995-7027
Wales, David J. 

Description

Databases containing minima and transition states for two different bulk systems in periodic boundary conditions, LJ864 and BLJ60, connecting liquid to crystalline regions. LJ864. This directory (./pathsample.LJ864/) contains the files needed to rerun the PATHSAMPLE analysis and recreate the database for the LJ864 system. The analysis is done in 3 stages. In the subdirectory ./1.start/, we include an initial pathsample database containing the two starting structures, the FCC crystal and a liquid structure. The subdirectory contains the following files: (1) min.data -> database of minima (2) odata.connect -> Input file for running OPTIM connections (3) pathdata -> PATHSAMPLE input file (4) points.min -> binary coordinates file for the 2 minima in the database (5) min.A -> file specifying the database entry for one end-point, the liquid (6) min.B -> file specifying the database entry for one end-point, the crystal We have also included coordinates for the minima in a readable format: (7) points.min.1 (8) points.min.2 Files 1-6 are required for PATHSAMPLE to run and once PATHSAMPLE has run and transition states have been found, two further database files will be produced: (9) ts.data (10) points.ts The database produced and the files numbered 1-6, 9 and 10 are then required for subsequent steps of the analysis unless specified otherwise. In ./1.start/ the pathdata input file directs PATHSAMPLE to run on one core to populate the database with enough minima to run on multiple cores in subsequent connection attempts. In ./2.continue/, we provide a pathdata input file (replacing (3)) to continue the analysis on multiple cores. In ./3.untrap/, we provide a new pathdata file and a new min.B file, the new min.B file now includes all 4 perfect crystals. There are 3 further files: (1) metric -> Example file giving lattice angle and %FCC for our minima (2) metric.ordered -> Reordered version of the metric file (3) getmetricordered.f90 -> Code to redorder the metric file These files are specific to the database produced in our analysis and would need to be recreated for any new database created following steps 1 and 2. For sampling specific keywords please refer to the PATHSAMPLE and OPTIM user manuals. (See http://www-wales.ch.cam.ac.uk/PATHSAMPLE/ and http://www-wales.ch.cam.ac.uk/OPTIM/). For further queries please email Prof David J. Wales (dw34@cam.ac.uk). BLJ60. This directory (./pathsample.BLJ60/) contains the full database studied for BLJ60 and contains the following files: (1) min.data -> database of minima (2) ts.data -> database of transition states (3) points.min -> binary coordinates file for the minima in the database (4) points.ts -> binary coordinates file for the transition states in the database (5) min.A -> file specifying the database entry for one end-point, a liquid (6) min.B -> file specifying the database entry for one end-point, the crystal (7) odata.connect -> Input file for running OPTIM connections (8) perm.allow -> input file for OPTIM and PATHSAMPLE, showing which atoms can be permuted. The binary files were produced with OPTIM and PATHSAMPLE compiled with PGI version 7.1 (64 bit) fortran compilers.


This record contains research data supporting "The Potential Energy Landscape for Crystallisation of a Lennard-Jones Fluid" pending publication in J. Stat. Mech:Theory and Experiment. This record will be updated with publication details.

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Publisher

University of Cambridge
Sponsorship
This work was supported by the EPSRC [grant number EP/I001352/1].