Re: [ESPResSo-users] Fwd: Brownian dynamics

[Lei Liu]

Hello David,

Yes, I have ready succeeded to run the simple script on my pc.

I would like to do a little bit more tests on this integrator, as well as its thermostat. 

Thanks a LOT for your help.

With my best wishes

Lei

On Fri, Apr 8, 2016 at 10:38 PM, David Schwörer <address@hidden> wrote:

Hi all,

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:
./bootstrap.sh
./configure --with-python-interface=no && make
./Espresso bd_simple.tcl

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.

Kind Regards,
David

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
> Lei
>
> 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,
>
>     peter
>
>     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

>         <mailto: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

>         <mailto: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 [+]
>             >
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>             >
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>
>
>
>
>
>
>
>
>     --
>     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/

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