|Subject:||Re: [ESPResSo-users] Fwd: Brownian dynamics|
|Date:||Fri, 8 Apr 2016 23:23:57 +0900|
I changed the ifdefs, now it should be able compile with #define BD, but
without SD/CUDA/ARPACK. See: https://github.com/espressomd/espresso/pull/579
I haven't used the build system, but with:
./configure --with-python-interface=no && make
I was able to run the bd integrator.
If the python feature is needed, I could have a look at it ...
I am not sure about cmake - it failed at TCLTK - which I have not installed.
On 08/04/16 08:45, Lei Liu wrote:
> Hi Peter,
> thanks for your info.
> If it turns out that it not easy to compile it with CPU, that could be
> my solution.
> Best regards
> On Fri, Apr 8, 2016 at 4:38 PM, Peter Košovan
> <address@hidden <mailto:address@hidden>> wrote:
> 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,
> On Fri, Apr 8, 2016 at 9:27 AM, Lei Liu <address@hidden
> <mailto:address@hidden>> wrote:
> ---------- Forwarded message ----------
> From: *Lei Liu* <address@hidden <mailto: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
> 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
> <http://www.natur.cuni.cz/chemistry/fyzchem/>> <mailto:address@hidden>> wrote:
> 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,
> 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
> Tel. +420221951290
> Fax +420224919752
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