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License: GNU General Public License v2.0
README for the Analysis of molecular systems through molecular dynamics Malcolm Ramsay 2015 OVERVIEW -------- This is a series of Makefiles that run the simulation and analysis of molecular systems. Simulations are performed using LAMMPS, available at http://lammps.sandia.gov with the packages molecule and rigid used required on install. For LAMMPS to work correctly at least the 09 Dec 2014 version is required. GNU Make is used to check the currency of the various components and whether they are required to be computed. GNU Make 3.81 is the version that has been used in development. Compatability issues with older versions are not expected. Directory Structure ------------------- It is expected that this file is in the directory $HOME/make or at least with a symbolic link in that directory. The directory in which the simulations are run is given in the settings file. This directory structure allows the separation of this folder from the resutls, often on a drive with more storage space. Prerequisites ------------- This is a list of the programs used by this package and the versions used in development. Older versions may work, however there are known compatability issues with older versions of some of the programs listed. GNU Make 3.81 Python 2.7.8 LAMMPS 09 Dec 2014 with packages molecule and rigid gcc 4.6.3 or Apple LLVM 6.1.0 gnuplot 5.0 Tex Live 2014 anlysis 1.0 https://github.com/malramsay64/analysis.git MAKEFILES --------- COMMANDS make - compiles the code for the analysis of the lammpstrj files. make clean - cleans the binary files from the compilation of the anlysis code. make files - generates the input files for all the molecules in settings make clean-files - removes all the files generated by make files and everything at a later step in the process make lammps - runs the lammps simulation using the parameters defined in the settings file make clean-lammps - removes all the results from the lammps simulations and all files in later steps make contact - performs the analysis of the output from the simulations generating a series of output files that are used for plotting make clean-contact- removes all the files generated by the analysis and all of the following stages make plot - generates plots from the output of the contact analysis. The plotting is done using gnuplot with all files output to the directory myplot. make clean-plot - removes all the files from the plotting and following steps. make collate - collates the data from each molecule naming each according to the molecule and the temperature which contained it. make clean-collate- removes all the collated files make contact-all - performs the analysis for all folders in the PREFIX directory which contain a lammps output file. This allows collated data to be generated without listing all the current temperatures. make clean-contact-all - removes all the analysis data from every folder in the PREFIX directory that contains a lammps output file. make touch-lammps - updates the modified time such that it appears that lammps just finished ruinning the analysis. make present - creates a pdf with all the plots and data specified in the settings file. make clean-present- removes the pdf and working files. DEFINING MOLECULES ------------------ All the simulation and molecule variables are set in the settings file. The molecule variables will accept a list of values and generate all possible combinations of the resulting values. SNOWMEN - Radius - Distance TRIMERS - Radius - Distance - Theta CRYSTAL PHASES The different crystal phases are defined by their wallpaper group, with all possible combinations of the molecules and crystal phases are tested, however only those crystals defined by svg files in the crystals directory are created. The boundary is a value that corresponds to the direction in which the additional molecules and corresponding crystal/liquid boundary is oriented. RUNNING MD ---------- LAMMPS COOLING HEATING Defining Crystals ANALYSIS -------- PROGRAM PLOTS
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