Particulars

A set of Molecular-Dynamics programs, primarily to simulate glassy systems

Copyright (C) 2015-2018 Vishnu V. Krishnan : vishnugb@gmail.com

Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved.  This file is offered as-is,
without any warranty.

I use CMake to build and compile the program, so you may want to take a look at CMakeLists.txt to modify any options.

The program requires a data directory structure as follows:

mkdir data
mkdir data/Position
mkdir data/RadDistFunc

To begin, make a build directory, and run cmake from there, and then make to build, as follows: Replace Release with Debug to enable all error checks and debug symbols.

mkdir Build && cd Build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
./prog

ADDITIONAL INFORMATION

• All module file names indicate their function.
• Procedures names begin with the name of the module thay belong to.
• Use one 'main_' file. It calls procedures from the modules.
• Unless specified, all procedures work in 3 dimensions.
• In the parameters file, you may switch from density control to box side length control

COMPILE TIME OPTIONS:

Add module files before the main Program in order of increasing dependencies (i.e. module with no deps first ...)

Use the following compiler option to change to double precision: intel : -real-size 64 gnu : -fdefault-real-8 But prefer -freal-4-real-8, because its implementation is supposedly less buggy

Use the following compiler option to change to prevent integer overflow: intel : -integer-size 64 gnu : -fdefault-integer-8 or -finteger-4-integer-8

Use the following compiler option if you want the 'percentage complete' indication. Else, comment out relevant code: intel : -assume bscc gnu : -fbackslash

Add the following OpenMP compiler options only if the supported OMP is .GE. 3.1 . This due to array REDUCTION support intel : -qopenmp gnu : -fopenmp

Use the following in ifort, to enable allocation upon assignment (no need to allocate/deallocate). Not necessary in gfortran intel: -assume realloc_lhs

To use the apptopriate memory model use the following flags: -mcmodel=<x> where : small(default), medium, large

To optimize for speed, use the following: intel : -O3 -xHost very agressive: -fast gnu : -O3 -march=native

Set OpenMP environment variables in .bashrc as follows: export OMP_PLACES=<place> where : threads, cores, sockets export OMP_NUM_THREADS=<number> where is less than or equal to number of cores

Use the following compiler option to use the pre-processor: intel : -fpp gnu : -cpp NOT NECESSARY if the relevant file has the '.F90' extension

Use the following during initial compilations, to see all generated warnings: intel : -check -warn -diag-enable=all gnu : -fcheck=all -Wall -Wextra -pedantic

One no longer needs to add IMPLICIT NONE every where; just use: intel : -implicitnone gnu : -fimplicit-none

CURRENTLY USED OPTIONS:

ifort -I./lapack95_modules_ifort -O3 -xHost -real-size 64 -qopenmp -assume bscc -assume realloc_lhs parameters.f90 random_init.F90 lattice.f90 thermostat.f90 force.f90 plot.f90 integration.f90 diagnostics.f90 main.f90 -lblas -llapack ./lapack95_modules_ifort/lapack95.a

gfortran -I./lapack95_modules_gfort -O3 -march=native -fdefault-real-8 -fopenmp -fbackslash parameters.f90 random_init.F90 lattice.f90 thermostat.f90 force.f90 plot.f90 integration.f90 diagnostics.f90 main.f90 -lblas -llapack ./lapack95_modules_gfort/lapack95.a

MISCELLANEOUS:

Use the following to prevent hang up signals (due to logouts, terminal closures etc.) from killing the program: nohup <compile command> &

You may make videos using: ffmpeg -framerate 7 -pattern_type glob -i '*.png' -c:v libx264 -r 30 -pix_fmt yuv420p out.mp4 ffmpeg -framerate 7 -pattern_type glob -i '*.png' -c:v libvpx-vp9 -b:v 1M -threads 8 -speed 1 -tile-columns 6 -frame-parallel 1 -f webm out.webm

Create and update archived backups with the following: c:create, x:extract, u:update, v:verbose, p:permissions, f:file_name tar -cvpf code.tar *.f90 *.sh *.txt tar -xvpf code.tar

TO DO:

• convert velocity arrays in MODULE thermostat to INTENT(OUT)
• examine using 2D arrays instead of separate arrays for each dimension
• convert from 3 - 1D arrays to assumed shape arrays with the CONTIGUOUS attribute
• look for possiblities of DO CONCURRENT
• use 'set term tikz latex' in plot for LaTeX