[Openmd-users] Custom rigidBody and defining force field

[Martin Vala]

Hi Dan and all,

Maybe more accurate question. What frame are 4 quaternions set in dump file? Is it in space or rigid body frame?

Thanks a lot

Ciao

MartinOn Dec 4, 2014 1:00 AM, Martin Vala <mvala at saske.sk> wrote:
>
> Hi Dan,
>
> I was looking to the book you recommend me and i have to say that it very good source of information. Thank you for that. But one thing, i am still missing somehow. Let's assume, i would like to visualize direction of the rigid body in space frame for example, like an arrow from center of rigid body. My goal is to draw arrows of directions of rigid bodied in my system in some 3D program. Is there tool to do it? If no, can you give me hint how can i calculate it?
>
> Thanks
>
> Ciao
>
> Martin
>
> On 27.11.2014 20:05, Dan Gezelter wrote:
>>
>> Martin,
>>
>>
>>
>>   You do need to define the atom type in a force field file, and the force field can be quite a bit simpler than Amber for testing.  The other issue I saw was that the quaternions in this line:
>>
>>
>>
>>     0    pvqj 0.0 0.0 0.0 0.0 0.0 0.0  0.0 0.0 0.0  -1.8e-05 1.6e-06 1.9e-05
>>
>>
>>
>> only had 3 entries.  There should be 3 positions, 3 velocities, 4 quaternions, and 3 angular momentum variables.  The convention we use for quaternions is defined on page 88 of Allen & Tildesley's "Computer Simulation of Liquids" book.   To orient the principal body axis along the z-spatial coordinate, we could choose the following Euler angles:
>>
>>
>>
>> \theta = 0
>>
>> \phi = 0
>>
>> \psi = 0
>>
>>
>>
>> These correspond to a set of quaternions q = (1, 0, 0, 0).
>>
>>
>>
>> Anyway, I tested the three attached files, and you should be able to experiment further with these.  A couple of changes I made:  1) The _ (underscore) character has special meaning in the selection syntax, so I modified your atom types and rigid body definition.  2) The angular momentum was quite small, so I boosted it a bit so that you can observe the rotation in this simulation.
>>
>>
>>
>> Try this with the attached files:
>>
>>
>>
>>   openmd Ico.md
>>
>>   Dump2XYZ -i Ico.dump
>>
>>   jmol Ico.xyz          then go to "Tools" -> "Animate" -> "Once"
>>
>>
>>
>> Best regards,
>>
>>
>>
>>  --Dan Gezelter
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> On Nov 26, 2014, at 11:01 PM, Martin Vala <mvala at saske.sk> wrote:
>>>
>>>
>>>
>>> Hi all,
>>>
>>>
>>>
>>> i just notice that i didn't define rigid body in my previous configuration. I am attaching my updated config files. I am sorry for wrong configuration files. 
>>>
>>>
>>>
>>> Ciao
>>>
>>>
>>>
>>> Martin
>>>
>>>
>>>
>>> On 27.11.2014 11:37, Martin Vala wrote:
>>>
>>>> Hi All,
>>>>
>>>>
>>>>
>>>> sorry i misstyped my rigid body. It is icosahedron
>>>>
>>>>
>>>>
>>>> Ciao
>>>>
>>>>
>>>>
>>>> Martin
>>>>
>>>>
>>>>
>>>> On 27.11.2014 11:12, Martin Vala wrote:
>>>>
>>>>> Dear OpenMD users, 
>>>>>
>>>>>
>>>>>
>>>>> I would like to define my own rigid body with my own atoms (my custom atom is "My"). My rigid body is defined as icohexadral (in RB_My.md file - attached). I am also attaching RigidBody_01.md file. 
>>>>>
>>>>>
>>>>>
>>>>> Problem: 
>>>>>
>>>>>
>>>>>
>>>>> OpenMD FATAL ERROR: 
>>>>>
>>>>>         Can not find Matching Atom Type for[My_RB] 
>>>>>
>>>>>
>>>>>
>>>>> I am guessing that "My_RB" atom type is not defined in $FORCE_PARAM_PATH/Amber.frc (in my RB_My.md, i have forceField = "Amber";). So i will have to define my own MyForceField.frc file (or i will update Amber.frc file),where i will define "My" atom and whole force field defined in my this rigid body (probably define atom atom "My" and its interactions with others, e.g. interaction between atom "My" and "My", "My" and others, and so). Is it right? 
>>>>>
>>>>>
>>>>>
>>>>> If yes, then as first task, i would need to configure this rigid body to be fixed in its initial positions. Can you help me to set it up? 
>>>>>
>>>>>
>>>>>
>>>>> Thank you very much 
>>>>>
>>>>>
>>>>>
>>>>> Ciao 
>>>>>
>>>>>
>>>>>
>>>>> Martin 
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>>
>>>>> Openmd-users mailing list
>>>>>
>>>>>
>>>>>
>>>>> Openmd-users at openmd.org
>>>>>
>>>>> http://openmd.org/mailman/listinfo.cgi/openmd-users
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>> <RB_My.md><RigidBody_01.md>_______________________________________________
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