[OpenFOAM] Visualising molecular dynamics results

santos · July 23, 2008, 17:16

Dear all,

Is anybody able to visualise either the mesh and/or the results of the new molecular dynamics solvers (gnemdFoam and mdEquilibrationFoam) in Paraview?

In case you can visualise them, could you please provide some guidelines?

Jose Santos

david_h · July 25, 2008, 11:25

Jose Santos,

I had similar problems using paraview. My guess is that the length scales of the molecular dynamics solvers are smaller than some threshold which effectively disables "auto-scale" in paraview. It essentially paraview assumes that all the coordinates are zero.

If you play around with the various scale parameters in the display and properties panels you should be able to view the objects.

Dave

santos · July 25, 2008, 12:47

David,

Thank you for your reply. In fact, after playing around with scale parameter, I could finally see the mesh and the molecules. It was necessary a scale value of 100 million!

Regards,
Jose Santos

July 23, 2008, 17:16	Visualising molecular dynamics results	#1
santos Senior Member Jose Luis Santos Join Date: Mar 2009 Location: Portugal Posts: 215 Rep Power: 18	Dear all, Is anybody able to visualise either the mesh and/or the results of the new molecular dynamics solvers (gnemdFoam and mdEquilibrationFoam) in Paraview? In case you can visualise them, could you please provide some guidelines? Jose Santos

July 25, 2008, 11:25	Jose Santos, I had similar	#2
david_h Member E. David Huckaby Join Date: Mar 2009 Posts: 57 Rep Power: 17	Jose Santos, I had similar problems using paraview. My guess is that the length scales of the molecular dynamics solvers are smaller than some threshold which effectively disables "auto-scale" in paraview. It essentially paraview assumes that all the coordinates are zero. If you play around with the various scale parameters in the display and properties panels you should be able to view the objects. Dave

July 25, 2008, 12:47	David, Thank you for your r	#3
santos Senior Member Jose Luis Santos Join Date: Mar 2009 Location: Portugal Posts: 215 Rep Power: 18	David, Thank you for your reply. In fact, after playing around with scale parameter, I could finally see the mesh and the molecules. It was necessary a scale value of 100 million! Regards, Jose Santos

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