[Openmd-users] Update

[Dan Gezelter]

Brett,

  You found a bug.  The self interactions for shifted force and shifted pot require summing up the net charge on topologically connected molecules.  We'd never tested a system that has multiple electrostatic atoms (e.g. charges, dipoles, quadrupoles) on a single molecule where there were *only* non-charge atoms.  I think I've fixed the problem (you can get the new code with "svn update"), or you can send me the infringing md file and I'll test it for you and release version 1.1.1

 --Dan


On Jul 29, 2010, at 6:00 AM, Brett Donovan wrote:

> Hi Dan
> 
> I think I might be something stupid here, in the META data section, if
> I include:
> 
> electrostaticSummationMethod = "SHIFTED_FORCE";
> 
> in the META section I get the following error:
> 
> OpenMD FATAL ERROR:
>        Location: electrostatic
>        getCharge was called for an atom type that isn't a charge!
> 
> Any ideas what I am doing wrong?
> 
> 
> =====
> 
> On another note for your own internal interest, I have run so far up
> to 512 processors concurrently. The load balancing looks great! I have
> put a plot in here so you can see how things scale.
> 
> 
> Best wishes
> 
> Brett
> 
> 
> 
> 
> 
> 
> On Tue, Jul 27, 2010 at 3:31 PM, Brett Donovan <brettdonovan at gmail.com> wrote:
>> Ah, I think there might be some ambiguity as the manual suggests that
>> the default is "shifted_force". So assuming I do not expressly put
>> this in the META section and I was expecting to get shifted force. I
>> guess its an issue of what takes precedence here, either the
>> cutoffRadius=switchingRadius or the explicit switch in the META
>> section.
>> 
>> its not a problem now I know to put a n/v pair in the META section.
>> 
>> Best
>> 
>> B
>> 
>> On Tue, Jul 27, 2010 at 3:20 PM, Dan Gezelter <gezelter at nd.edu> wrote:
>>> Brett,
>>> 
>>> If you leave out the electrostaticSummationMethod and just have cutoffRadius set to the same value as switchingRadius, you get the shifted potential:  V(r) = V_{LJ}(r) - V_{rcut}
>>> 
>>>  --Dan
>>> 
>>> On Jul 27, 2010, at 10:17 AM, Brett Donovan wrote:
>>> 
>>>> Hi Dan
>>>> 
>>>> Do I need to have  electrostaticSummationMethod, set at a value to get
>>>> this Force shifted LJ potential? So if I leave it out and have the
>>>> cutoffRadius = switchingRadius, will I get Force shifted or potential
>>>> shifted?
>>>> 
>>>> Thanks
>>>> 
>>>> B
>>>> 
>>>> On Tue, Jul 27, 2010 at 2:57 PM, Dan Gezelter <gezelter at nd.edu> wrote:
>>>>>> 
>>>>>>  You had me worried, so I just checked by printing out inside the LJ code that calculates the potential.  With cutoffRadius and switchingRadius set to the same value, and electrostaticSummationMethod set to "SHIFTED_FORCE", you do indeed get the shifted LJ potential.
>>>>> 
>>>>> 
>>>>> Clarification:  You get the FORCE-shifted LJ potential.   V(r) = V_{LJ}(r) - V_{rcut} -  V'_{LJ}(rcut) * (r - rcut)
>>>>> 
>>>>>  --D
>>>>> 
>>>>> ***********************************************
>>>>>  J. Daniel Gezelter
>>>>>  Associate Professor of Chemistry
>>>>>  Director of Graduate Admissions
>>>>>  Department of Chemistry and Biochemistry
>>>>>  251 Nieuwland Science Hall
>>>>>  University of Notre Dame
>>>>>  Notre Dame, IN 46556-5670
>>>>> 
>>>>>  phone:  +1 (574) 631-7595
>>>>>  fax:    +1 (574) 631-6652
>>>>>  e-mail: gezelter at nd.edu
>>>>>  web:    http://www.nd.edu/~gezelter
>>>>> ************************************************
>>>>> 
>>>>> 
>>>>> 
>>> 
>>> ***********************************************
>>>  J. Daniel Gezelter
>>>  Associate Professor of Chemistry
>>>  Director of Graduate Admissions
>>>  Department of Chemistry and Biochemistry
>>>  251 Nieuwland Science Hall
>>>  University of Notre Dame
>>>  Notre Dame, IN 46556-5670
>>> 
>>>  phone:  +1 (574) 631-7595
>>>  fax:    +1 (574) 631-6652
>>>  e-mail: gezelter at nd.edu
>>>  web:    http://www.nd.edu/~gezelter
>>> ************************************************
>>> 
>>> 
>>> 
>> 
> <PlottedPerform.agr>

***********************************************
  J. Daniel Gezelter
  Associate Professor and
  Director of Graduate Admissions
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  fax:    +1 (574) 631-6652
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
************************************************