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Re: [ESPResSo-users] help

From: Axel Arnold
Subject: Re: [ESPResSo-users] help
Date: Mon, 18 Jun 2012 19:22:46 +0200
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On Monday 18 June 2012, mehdi ezatabadi wrote:
> Dear Dr.Arnold
> In the past step of my project I used the espresso command to make the
> neighbor list of particles to see if they made special structures. The
> command was:
> set nbhood [analyze nbhood idParticle cutOffRadious]

This command won't help you. It uses the analysis data structures which are 
not up-to-date during the integration, and are not parallel.

> In condensed material simulations I figured it out that lots of
> complementary bases would interact which a single base that is different
> from the physics of base pair(A_T     C_G) interactions. Now I dont know
> how to include it in Integration by Espresso. Usually in the tcl program we
> define the interactions among the types of particles. But now I should look
> at the particles at every step and then decide which particles interact
> with each other.

Yes, and that requires a bit of coding, as I said. You might want to take a 
_good_ look e.g. at the technical slides from the Espresso workshop last year 

The steps are roughly, plus a lot of debugging
- make a new interaction, e.g. copy the Lennard-Jones code, and adjust all the 
places the LJ code appears (#ifdef LENNARD_JONES).

- make the global maximal cutoff twice the one of your A-T interaction, in 
order to get all T-particles surrounding one A-particle onto one processor. 
(recalc_maximal_cutoff_nonbonded in interaction_data.c)

- to loop over the neighbors of a particle, calculate its cell position in the 
domain decomposition (compare dd_position_to_cell in domain_decomposition.c), 
then loop over all surrounding cells and their particles (compare 
calc_link_cell in domain_decomposition.c, but of course restrict to the 
relevant cells).

- alternatively, you can directly loop over all A-particles and their T-
neighbors, might be faster. That you wold add as a separate calc_link_cell-
like loop to calc_forces in forces.c.

If you look for an easier route, good luck, I am not aware of one. And I wrote 
most of the short ranged force calculation.


JP Dr. Axel Arnold      Tel: +49 711 685 67609
ICP, Universit├Ąt Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany

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