|Subject:||Re: [ESPResSo-users] Fwd: Brownian dynamics|
|Date:||Fri, 8 Apr 2016 09:38:32 +0200|
---------- 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>It went through the compiling in the core directory,as well as the error message output at the head of the file "/src/core/integrate_sd.hpp" ,Since I don't have experiences with cuda,Based on David's suggestion, I downloaded current developing version of Espresso,Dear all,I am also interested in the (over-damped) Brownian dynamics.
and want to compile it with SD integrator.
I commented the requirements of cuda and arpack for SD in the file "/src/features.def",
boot-trapped in the source code directory, and then tried to configure and make it.
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 regardsLei
------------------------------Korea Institute for Advanced Research85 Hoegiro, Dongdaemun-gu
Republic of KoreaOn 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
part 0 pos 0 0 0
setmd time_step 0.1
setmd sd_visc 1
setmd sd_radius 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.
On 12/17/2015 01:20 PM, Dudo wrote:
> please, is there a project or a feature of Espresso running Brownian
> I figured out, that just setting mass to zero doesn't work :-)
> In the integrator (integrate.cpp) there is also velocity scaling which
> to infinity with the mass zero..
> Kind regards,
> 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
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