[Openmd-users] Update

[Dan Gezelter]

Brett,

  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.

I suppose we need a better keyword than "electrostaticSummationMethod" to clear this up in the future.  Any suggestions?

In a development branch, we've been converting over the LJ and EAM modules to C++ this past week. Once the rest of the force modules move to C++  we can implement an explicit non-bonded registry.  We've got a few more modules to migrate (Gay-Berne, electrostatics, Sutton-Chen, Sticky, Morse, Buckingham), but a lot of the heavy lifting was done with the first two. 

Best regards,

 --Dan

On Jul 27, 2010, at 8:45 AM, Brett Donovan wrote:

> Hi Dan
> 
> Just a quick follow up on this, I note in the documentation near
> "electrostaticSummationMethod" that the default is LJ forced shifted.
> Will this guarantee that if I set the cutoffRadius = switchingRadius
> that indeed the potential form will be sfLJ? or will it be just the
> cut potential form? Sorry to be so pedantic.
> 
> On the other note about the interaction Matrix, any ideas when you
> think this will be implemented?
> 
> Best wishes,
> 
> Brett
> 
> On Fri, Jul 16, 2010 at 3:27 PM, Dan Gezelter <gezelter at nd.edu> wrote:
>> Brett,
>> 
>>  The LJ potential truncation depends on how you specified things in the md file.
>> 
>> In general, OpenMD will use a cubic switching function, s(r), with these parameters setting the upper and lower bounds for the switching function:
>> 
>> cutoffRadius = 9.0;
>> switchingRadius = 7.65;
>> 
>> V(r) = V_{LJ}(r) * s(r)   (r < rcut)
>> V(r) = 0                  (r > rcut)
>> 
>> If you set both to the same value, e.g.
>> 
>> cutoffRadius = 15.0;
>> switchingRadius = 15.0;
>> 
>> then the LJ behavior will default to shifted potential,  V(r) = V_{LJ}(r) - V_{LJ}(rcut).
>> 
>> You can explicitly override the default cutoff behavior using electrostaticSummationMethod.  In this version of OpenMD, we're tethering the LJ shifting behavior to the electrostatic behavior:
>> 
>> electrostaticSummationMethod = "SHIFTED_FORCE";      // guarantees shifted frc
>> electrostaticSummationMethod = "SHIFTED_POTENTIAL";  // guarantees shifted pot
>> 
>> I.e.
>> 
>>  shifted Force:  V(r) = V_{LJ}(r) - V_{rcut} -  V'_{LJ}(rcut) * (r - rcut)
>>  shifted Pot:    V(r) = V_{LJ}(r) - V_{LJ}(rcut)
>> 
>> As for the interaction matrix, we're in the process of adding "explicit non-bonded interactions" to the next version, and this would allow you to specify sigma and epsilon values (or even other functional forms) that could override the default mixing rules.  The necessary infrastructure isn't completely in place yet, but this is certainly on our radar.
>> 
>>  --Dan
>> 
>> On Jul 16, 2010, at 6:12 AM, Brett Donovan wrote:
>> 
>>> Dear Dan
>>> 
>>> I've been busy running on our cluster here, all seems to be working
>>> well on up to a few hundred processors. I have a few questions etc
>>> regarding the potentials and LJ interaction matrix.
>>> 
>>> Potential - what is the exact form of the potential employed? I think
>>> you said these are cut and shifted potentials, if there somewhere this
>>> is documented?
>>> 
>>> Interaction Matrix - there might be need to employ a slight deviation
>>> away from the LB mixing rules. Is there a smart and easy way to employ
>>> this? i.e. SSD and AMIDE has a scaling factor rather than just
>>> \epsilon = \sqrt(\epsilon_A\epsilon_B), we could have \epsilon =
>>> \alpha \sqrt(\epsilon_A\epsilon_B)
>>> 
>>> Best wishes
>>> 
>>> Brett
>> 
>> ***********************************************
>>  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
************************************************