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3.0 1.0 2.0 6.5 MB

GNU Octave interface to seplib

License: Other

Shell 0.05% MATLAB 4.84% Makefile 0.77% C 72.26% C++ 2.03% Cuda 20.05%

molsim's Introduction

molsim - Molecular dynamics with GNU Octave

molsim supports simulations of

simple Lennard-Jones systems,
molecular systems with bond, angle, and torsion potentials,
confined flow systems, eg., Couette and Poiseuille flows,
charged systems using shifted force and Wolf methods,
dissipative particle dynamics systems,
different ensembles,
and more . .

Installation

At the Octave prompt simply use the command

 
  >> pkg install "https://github.com/jesperschmidthansen/molsim/archive/refs/tags/v<version>.tar.gz"

where <version> is the version number.

An example

An example of an NVE water simulation script

   
    nloops = 1000; temp0 = 298.15/78.2;
    cutoff= 2.5; sigma=1.0; epsilon=1.0; aw=1.0; cutoff_sf = 2.9;
    lbond = 0.316; kspring = 68421; 
    angle = 1.97; kangle = 490;
   
    molsim('set', 'cutoff', cutoff_sf);
    molsim('set', 'timestep', 0.0005);
    molsim('set', 'exclusion', 'molecule'); 
  
    molsim('set', 'omp', 4);
  
    molsim('load', 'xyz', 'sys_water.xyz');  molsim('load', 'top', 'sys_water.top');
  
    for n=1:nloops 
      molsim('reset')
      
      molsim('calcforce', 'lj', 'OO', cutoff, sigma, epsilon, aw);
      molsim('calcforce', 'coulomb', 'sf', cutoff_sf);
      molsim('calcforce', 'bond', 0, lbond, kspring);
      molsim('calcforce', 'angle', 0, angle, kangle);
      
      molsim('integrate', 'leapfrog');
    endfor
    
    molsim('clear');

IMPORTANT NOTE: The 'sys_water.xyz' configuration file and 'sys_water.top' topology file must be in same directory from where you execute the script. They can be found under the project's resource/ folder

For further explanation check out the package tutorial under the project's doc/ folder

Contribution

I encourage anyone who uses or plans to use molsim to submit problematic issues - this includes issues regarding the documentation. I also welcome contributions to the code for the project, whether it is core features (seplib), post simulation data analysis programs, or extending the molsim wrapper.

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molsim's Issues

molsim('hello') fails

I gave the command
pkg install "https://github.com/jesperschmidthansen/molsim/archive/refs/tags/v1.0.0.tar.gz"
in Octave 9.0.1. There were some warnings and possibly an error:

source/sepintgr.c: In function 'sep_langevinGJF':
source/sepintgr.c:97:24: warning: comparison of integer expressions of different signedness: 'unsig
ned int' and 'long int' [-Wsign-compare]
   97 |   for ( unsigned n=0; n<sys->npart; n++ ){
      |                        ^
C:\PROGRA~1\GNUOCT~1\OCTAVE~1.1\mingw64\bin\ar.exe: creating libsep.a
molsim.c: In function 'action_get':
molsim.c:747:39: warning: passing argument 2 of 'mxCreateNumericArray' from incompatible pointer ty
pe [-Wincompatible-pointer-types]
  747 |     plhs[0] = mxCreateNumericArray(1, &nuau, mxINT32_CLASS, mxREAL);
      |                                       ^~~~~
      |                                       |
      |                                       const long int *
In file included from C:\PROGRA~1\GNUOCT~1\OCTAVE~1.1\mingw64\include\octave-9.0.1\octave/mex.h:68,

                 from molsim.h:4,
                 from molsim.c:2:
C:\PROGRA~1\GNUOCT~1\OCTAVE~1.1\mingw64\include\octave-9.0.1\octave/mexproto.h:184:67: note: expect
ed 'const mwSize *' {aka 'const long long int *'} but argument is of type 'const long int *'
  184 |                                                     const mwSize *dims,
      |                                                     ~~~~~~~~~~~~~~^~~~

molsim installed - hopefully without errors
...

When I do molsim('hello') I get this error message:
error: 'molsim' undefined near line 1, column 1
So I guess that last bit wasn't just a warning? Any idea what I might be doing wrong?
Thanks.

such introduction -> such introductions

is on the form -> is of the form

every 100 time step -> every 100 time steps
every ten time step -> every ten time steps

an-isotropic scaling -> anisotropic scaling

barostate -> barostat

particular useful -> particularly useful

short ranged -> short-range
long ranged -> long-range

are model -> are modelled

diheadral -> dihedral

simulation of model liquid toluene -> simulation of liquid toluene

in same molecule -> in the same molecule [in 2 places]

bond length, but same force -> bond lengths, but the same force

form torsion angle -> form a torsion angle

sheared memory -> shared memory

as function of number -> as a function of the number

I hope this is useful.

Memory management

Currently the command "clear all" correctly (I think) clears the memory. This should be automated in a safe manner some how.