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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