medgbb / dynsf Goto Github PK

=======
 Dynsf
=======

Dynsf is a simple tool for calculaton partial dynamical structure factors
from molecular dynamics (MD) simulations.

The main input consists of a trajectory output from a MD simulation;
i.e. a file containing snapshots of the particle coordinates, and
optionally velocities, for consecutively and equally spaced points
in (simulation) time.

Dynsf can by itself read and parse standard lammpsdump-style trajectories.
If libgmx (gromacs lib) is available, dynsf can use it to read
gromacs xtc-files.
If VMD is available, dynsf can use VMD's molfileplugin to read other
formats (with some limitations) as well.

Dynsf is controlled via command line options, provided at command
invokation. The main difficulties in using dynsf lies in deciding which
particular values to use.

Output can be written in standard matlab/octave-stype .m-files, and/or as
python pickle-files.

The most time critical part of the processing consists of the calculation
of the fourier transformed densities, rho(k). This part is implemented in
C, and is greatly improved by parallelizing it using OpenMP or OpenACC.
The time correlation calculation is performed explicitly in python (using
numpy arrays), and is parallelized with python threads (which works rather
well thanks to numpy releasing the python GIL).



==============
 Installation
==============


 Requirements
 ------------

Python 2.6/2.7, numpy, and a C99-complient C-compiler.


 Quickstart
 ----------

1. Decide a installation prefix (e.g. $HOME/opt/ or such)
2. Install, "python ./setup.py install --prefix=$HOME/opt"
3. Set PYTHONPATH to include newly installed site-packages directory
   (e.g. $HOME/opt/lib64/python2.7/site-packages)
4. Set PATH to include newly installed bin directory
   (e.g. $HOME/opt/bin)


 Tune


================================
 Various implementation details
================================


 General overview
 ----------------

Trajectories are read frame (single MD timestep) by frame by a
trajectory_reader, which is an iterable object. Each frame produced by the
trajectory_reader is represented as a dict object containing particle
positions etc.

The trajectory_iterator is then wrapped in a "window generator", producing
a sliding window of frames through the trajectory. The size of the window
is decided by the requested number of time frames to consider for time
correlation. The argument --nt determines the width (time length) of the
window, and the argument --stride determines how many frames to move the
window between two consecutive windows.

Each frame in a window will be processed to have its particle positions
(and velocities) split info particle types/species, and for each particle
type the corresponding fourier transform of its density (and current) will
be calculated.
Information about which particle belongs to which type/species comes either
from the trajectory file (if available), or from a separate index file
(gromacs ndx-style).

For each window, time correlations ranging from delta_t=0 (the "static"
correlation) to delta_t=<window width> is calculated.
The time correlations are averaged over all windows considered.

Each of the averaged time correlations are then further averaged in the
reciprocal domain by mapping it into --k-bins values ranging from 0
to --k-max (for an isotropic media, only the absolute of the k-vector is
of interest).

For each output format choosen, output is written.


 Calls to external libraries
 ---------------------------

All call to external libraries are used using ctypes.
The main reason for choosing ctypes over e.g. swig/weave/f2py/... is
portability. Ctypes is included with python, and uses libffi so there is
no need for a compiler. A drawback is that lots of API stuff needs to be
explicitly set up in python code.
If there is a change in the API to the external libraries used, some part
of the dynsf code need to be modified.