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[ESPResSo] Espresso modifications

From: Michael Winokur
Subject: [ESPResSo] Espresso modifications
Date: Thu, 11 Feb 2010 16:55:57 -0600

Dear Axel and Espresso maintainers,

Sorry for the long delay in communications but I encountered many unforeseen problems in suitably modifying the code.  Basically the original paper I was using for the equations of motion was broken (which I failed to initially recognize) and there were limitations in the original espresso GB source (I'm not convinced it was 100% correct).  It wasn't until I looked at another paper and the source code from IMD  (The ITAP Molecular Dynamics Program) that things started to work properly.  [In the later I believe there is a small but significant sign error in their dU/dc (i.e., c is the torsion angle between GB particles) term.]   I'm not a theorist and so I am not comfortable with tackling these kind of partial derivative.
Here is what I have added:

1.  Gay-Berne particle pair interaction  gb.c
     Espresso typically allows for an r cutoff which I've added to my version of gb.c but the IMD source doesn't include this option.  
2.  Gay-Berne subtracted interaction subt_gb.c
3.  connected GB particles gb_dihed.c
4.  Anisotropic Rotational inertia parameters.
5. A submapping scheme so that vmd program can display a subparticle structure.

other subroutines modified in the process
energy.h, energy.c, forces.h, forces.c, communication.h, communication.c, thermostat.c, thermostat.h (I'm not 100% certain that I really reproduce the results dictated by the equipartition theorem.) particle_data.c, particle_data.h, interaction_data.c, interaction_data.h, imd.c, imd.h, rotation.c and myconfig.h

At the moment the GB interaction is between identical particles.  It should be relatively easy to introduce a scaling factor that allows for different shape objects (e.g. the interaction between a GB and united atom pair ) but I need to study the MD of ortho-terphenyl first before I start venturing into this area.

It is really is nice to see F=ma and T=I alpha...and at zero temperature the runs downhill.

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