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

[Marcello Sega]

Hi,

As far as I know, the virial can be calculated without problems for
multibody interactions (angle, torsional & Ewald are commonly used).
The problem comes usually with finding a definition for a local
stress, but that's not our case.

Leaving out for the time being the lj-angle contributions from the
pressure calculation seems to me reasonable, at some point I will
check which interactions are calculating properly their pressure
contribution.

Regarding affinity, there might be a clash with the affinity from
SHANCHEN: I see in

tcl/interaction_data_tcl.cpp

#ifdef AFFINITY

    REGISTER_NONBONDED("affinity", tclcommand_inter_parse_affinity);

#endif

*and*

#ifdef SHANCHEN

    REGISTER_NONBONDED("affinity",tclcommand_inter_parse_affinity);

#endif

I will soon change the shanchen affinity's name to something else,
just to avoid problems.

M.

On 17 Oct 2015 16:12, "Florian Weik" <address@hidden> wrote:
>
> Hi,
> Ok, I think a clean way to handle that is via the rotational degrees of 
> freedom. Non-pair forces like this can never be handled in the same way the 
> pair forces are handled (who are the extra forces for?).
> If I remember correctly the pressure calculation via the virials works only 
> for pair forces, so the multi-body interactions have to be excluded from the 
> virial calculation.
>
> For now I've moved the lj-angle out of the (inner) pair force loop and made 
> the particles const for the pair forces for good measure. The pressure 
> command should now have no side effects,
> albeit still not returning the correct pressure (see pull request). The fact 
> that the pressure calculation is only correct for some interactions is 
> reflected in the documentation.
> Of course this dug up other stuff. The affinity interaction from object in 
> fluid was also manipulating particles (bond creation). I am in general not in 
> favor of the force calculation changing the state.
> Changing forces is one thing, but integrate 0 actually can do all sorts of 
> things, like creating and removing bonds. I think it would be much cleaner to 
> do a second run through the particle pairs to
> do that if it is needed or just flag particles for modification. What do you 
> think?
>
> Cheers,
> Florian
>
> On Sat, Oct 17, 2015 at 9:35 AM, Marcello Sega <address@hidden> wrote:
>>
>> 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>
>>>>>>
>>>>>> _______________________________________________
>>>>>>   Message sent via/by Savannah
>>>>>>   http://savannah.nongnu.org/
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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:
>>>>> 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.
>>>>
>>>>
>>>> <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
>>>
>
>
>
> --
> Florian Weik
>
> address@hidden
> ++49 157 85939252
>