Re: [ESPResSo-users] Fwd: Brownian dynamics

[Peter Košovan]

Hi all,

I just want to add that in the last few days with my student Jakub we were also trying to compile espresso with SD and encountered similar problems. But we managed to compile it with cuda and arpack, so the origin of this problem is probably different.

Could perhaps David comment on that?

With best regards,

peter

On Fri, Apr 8, 2016 at 9:27 AM, Lei Liu <address@hidden> wrote:

---------- Forwarded message ----------
From: Lei Liu <address@hidden>
Date: Fri, Apr 8, 2016 at 4:23 PM
Subject: Re: [ESPResSo-users] Brownian dynamics
To: David Schwörer <address@hidden>

Dear all,

I am also interested in the (over-damped) Brownian dynamics.

Based on David's suggestion, I downloaded current developing version of Espresso,
and want to compile it with SD integrator.

Since I don't have experiences with cuda,
I commented the requirements of cuda and arpack for SD in  the file "/src/features.def",

as well as the error message output at the head of the file "/src/core/integrate_sd.hpp" ,
boot-trapped in the source code directory, and then tried to configure and make it.

It went through the compiling in the core directory,
but reported following errors in the file "integrate_sd_tcl.cpp":

error: 'sd_set_particles_apart' was not declared in this scope.

error: 'sd_test' was not declared in this scope
error: 'integrate_sd' was not declared in this scope.

I don't understand what caused the problem here,

because I do find the statement '#include "integrate_sd.hpp" ' at the head of file "integrate_sd_tcl.cpp".

If anyone known the reason or has some experiences about compiling SD integrator with cpu,

I would appreciate quite a lot.

Best regards

Lei
------------------------------

Korea Institute for Advanced Research

85 Hoegiro, Dongdaemun-gu
Seoul 02455
Republic of Korea

On Fri, Dec 18, 2015 at 7:27 AM, David Schwörer <address@hidden> wrote:

Hi,

Together with the Stokesian Dynamics integrator I implemented a BD
integrator as well.
It should work, if you compile with the SD enabled, you should be able
to use

part 0 pos 0 0 0
setmd time_step 0.1
setmd sd_visc 1
setmd sd_radius 1
integrate_sd 1
puts [part 0 print pos]

If you cannot meet the requirements for SD (CUDA etc.), I could try to
patch it, that BD can be compiled without SD.

Kind Regards,
David

On 12/17/2015 01:20 PM, Dudo wrote:
> Hi,
>
> please, is there a project or a feature of Espresso running Brownian
> dynamics?
> I figured out, that just setting mass to zero doesn't work :-)
> In the integrator (integrate.cpp) there is also velocity scaling which
> goes
> to infinity with the mass zero..
>
> Kind regards,
> Dusan
>
> --
> _____________________
> Faculté de biologie et de médecine
> Center for Integrative Genomics
> GENOPODE UNIL-SORGE
> Université de Lausanne
> CH1015 Lausanne, Suisse [+]
>
> RG: https://www.researchgate.net/profile/Dusan_Racko
> Scholar: https://goo.gl/oRVrGV
>
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic [‡]
> tel: +421 2 3229 4321

--

Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry

Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie

Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951290

Fax +420224919752