Re: [ESPResSo-devel] [bug #46210] "analyze pressure" affecting simulation

[Marcello Sega]

Hi,

We're using that in Vienna! We might put some effort to implement it properly in the future, so maybe for the time being we could leave it in as is...

M

On 16 Oct 2015 23:33, "Florian Weik" <address@hidden> wrote:

Hi,

what Axel said. This is broken and can't be fixed easily in the current structure as it expects only pair interactions at this points. This probably won't fix. I am in favor of doping the interaction,

as it could actually be implemented as simple pair interaction with rotation and torques, and since this is a cruel hack I'm not motivated to put any effort into fixing it since apparently the original author was not motivated to do a clean implementation. Is anybody else using that?

See also

https://github.com/espressomd/espresso/issues/439

Cheers,

Florian

On Fri, Oct 16, 2015 at 10:30 PM, Axel Arnold <address@hidden> wrote:

Hi all,

the culprit is the LJ-angle interaction, which changes particle forces directly, rather than returning them. That works for force calculation, but when you calculate the pressure, your pressure is lacking the LJ-angle interaction, and your forces are f****ed up. You can get the simulation working by using the recalc_forces option of integrate, but your pressure values are still be wrong.

So, just don’t use that interaction or fix the interaction to behave well (that is, like any other two-particle interaction).

Best,

Axel

Am 15.10.2015 um 22:09 schrieb Nicholas Jin <address@hidden>:

Hi Peter,

I have created a barebones tcl script that replicates the simulation I am trying to run. I have attached it below (demo.tcl).
As a warning, this script writes 1000 pdb files to whatever directory it's currently in.

Commenting out the set pressure [analyze pressure] causes qualitatively massive changes in the simulation.

Espresso 3.3.0 is compiled with the following features:

/* Generic features */

#define PARTIAL_PERIODIC

#define EXTERNAL_FORCES

#define CONSTRAINTS

#define EXCLUSIONS

#define COMFORCE

#define COMFIXED

#define MOLFORCES

#define NPT

#define DPD

/* Interaction features */

#define TABULATED

#define LENNARD_JONES

#define LENNARD_JONES_GENERIC

#define LJ_ANGLE

#define SMOOTH_STEP

#define BOND_ANGLE

Thanks for your help!
Nick

On Thu, Oct 15, 2015 at 4:22 AM, Peter Košovan <address@hidden> wrote:

Hi Nick,

I believe that analyze pressure is used by many people and if none has reported an exploding simulation upon the call, I suspect this issue is related to some specific feature of your simulations.

Providing a minimal example to enable others reproduce the bug would be very helpful. Otherwise, only a person fully familiar with your simulations can diagnose the problem.

Best,

peter

On Wed, Oct 14, 2015 at 10:15 PM, Nicholas Jin <address@hidden> wrote:

URL:
  <http://savannah.nongnu.org/bugs/?46210>

                 Summary: "analyze pressure" affecting simulation
                 Project: ESPResSo
            Submitted by: njin
            Submitted on: Wed 14 Oct 2015 08:15:00 PM GMT
                Category: Simulation core
                Severity: 3 - Normal
                  Status: None
             Assigned to: None
             Open/Closed: Open
         Discussion Lock: Any
                 Release: None
           Fixed Release: None

    _______________________________________________________

Details:

Hi all,

The tcl command "analyze pressure" is causing misbehavior in my simulations.
Absent this analysis command everything runs fine, but once the analysis runs
the simulation explodes.

This occurs in espresso-3.3.0. Let me know what other information you might
need to diagnose this issue.

Best,
Nick (address@hidden)




    _______________________________________________________

Reply to this item at:

  <http://savannah.nongnu.org/bugs/?46210>

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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/
Tel. +420221951290

Fax +420224919752

---

Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze:

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b) stanovuje, že smlouva musí mít písemnou formu,

c) vylučuje přijetí nabídky s dodatkem či odchylkou,

d) stanovuje, že smlouva je uzavřena teprve výslovným dosažením shody na všech náležitostech smlouvy.

<demo.tcl>

--------------------------------------------

Axel Arnold
Richard-Wagner-Ring 16
76437 Rastatt
Email: address@hidden
Telefon: +49 173 870 6659

--

Florian Weik

address@hidden
++49 157 85939252