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

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 ([e-mail]). 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.

包含两种不同大块体系的最低能量点和过渡态数据库，分别为LJ864和BLJ60，它们连接了液态与晶态区域。LJ864目录（./pathsample.LJ864/）包含重运行PATHSAMPLE分析和重建LJ864体系数据库所需的文件。分析分为三个阶段进行。在子目录./1.start/中，我们包含了一个初始的PATHSAMPLE数据库，其中包含两个起始结构，即面心立方晶体和液态结构。该子目录包含以下文件：（1）min.data -> 最低能量点数据库（2）odata.connect -> 运行OPTIM连接的输入文件（3）pathdata -> PATHSAMPLE输入文件（4）points.min -> 数据库中两个最低能量点的二进制坐标文件（5）min.A -> 指定一个端点（液态）的数据库条目文件（6）min.B -> 指定一个端点（晶体）的数据库条目文件。我们还提供了以下可读格式的最低能量点坐标：（7）points.min.1（8）points.min.2 文件1-6是PATHSAMPLE运行所必需的，一旦PATHSAMPLE运行并找到过渡态，将生成另外两个数据库文件：（9）ts.data（10）points.ts。生成的数据库以及编号为1-6、9和10的文件是后续分析步骤所必需的，除非另有说明。在./1.start/中，pathdata输入文件指导PATHSAMPLE在一个核心上运行，以在后续的连接尝试中为多个核心提供足够的最低能量点。在./2.continue/中，我们提供了一个pathdata输入文件（替换（3）），以在多个核心上继续分析。在./3.untrap/中，我们提供了一个新的pathdata文件和一个新的min.B文件，新的min.B文件现在包括了所有4个完美的晶体。此外，还有3个额外的文件：（1）metric -> 提供晶格角度和%FCC的示例文件（2）metric.ordered -> 按顺序排列的metric文件版本（3）getmetricordered.f90 -> 用于重新排列metric文件的代码。这些文件特定于我们分析中生成的数据库，任何根据步骤1和2创建的新数据库都需要重新创建这些文件。对于特定的采样关键词，请参考PATHSAMPLE和OPTIM用户手册。（参见http://www-wales.ch.cam.ac.uk/PATHSAMPLE/和http://www-wales.ch.cam.ac.uk/OPTIM/）。如有进一步疑问，请发送电子邮件至David J. Wales教授（[e-mail]）。BLJ60。BLJ60目录（./pathsample.BLJ60/）包含了对BLJ60进行研究的完整数据库，并包含以下文件：（1）min.data -> 最低能量点数据库（2）ts.data -> 过渡态数据库（3）points.min -> 数据库中最低能量点的二进制坐标文件（4）points.ts -> 数据库中过渡态的二进制坐标文件（5）min.A -> 指定一个端点（液态）的数据库条目文件（6）min.B -> 指定一个端点（晶体）的数据库条目文件（7）odata.connect -> 运行OPTIM连接的输入文件（8）perm.allow -> OPTIM和PATHSAMPLE的输入文件，显示哪些原子可以进行置换。二进制文件是用PGI版本7.1（64位）fortran编译器编译的OPTIM和PATHSAMPLE生成的。