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From: | Florian Weik |
Subject: | Re: [ESPResSo-devel] [bug #46210] "analyze pressure" affecting simulation |
Date: | Fri, 16 Oct 2015 23:32:50 +0200 |
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,AxelAm 15.10.2015 um 22:09 schrieb Nicholas Jin <address@hidden>:<demo.tcl>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!
NickOn Thu, Oct 15, 2015 at 4:22 AM, Peter Košovan <address@hidden> wrote:peterBest,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.Hi Nick,
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.--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)
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www.natur.cuni.cz/chemistry/fyzchem/Přírodovědecká fakulta Univerzity Karlovy v PrazeKatedra fyzikální a makromolekulární chemieFaculty of Science, Charles University in Prague, Czech RepublicDr. Peter Košovan
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Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze:a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení důvodu,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.--------------------------------------------
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