Error loading VTK output and lack of H on methane

[sundberg]

Hi!
I'm playing around with RASPA, trying to make a movie/snapshot of methane adsorption in a metal-organic framework.
1. The output in Movies work, where I can visualize both the framework and the methane molecules using iRASPA. However. there are no hydrogen atoms on the methane molecules?
2. The output in the VTK folder is not readable in iRASPA, getting error 'Import failed, Cannot read VTK header (line: 910 file: iraspagui/mainwindow.cpp)'. Furthermore, the AdsorbateAtoms.vtk file is almost emtpy, no coordinates. Do I need to add a specific swith to the raspa input file to generate this?

I'm using raspa version 2.0.41, with iRASPA 2.2.5 running on Fedora. Thanks!

Code Select Expand

SimulationType                MonteCarlo
NumberOfCycles                10000
NumberOfInitializationCycles  10000
PrintEvery                    100
RestartFile                   no

Forcefield                    ExampleMOFsForceField
UseChargesFromCIFFile         yes

Framework 0
FrameworkName HKUST-1
UnitCells 3 3 3
HeliumVoidFraction 0.16
ExternalTemperature 300.0
ExternalPressure 10000 25000 50000 75000 100000 500000 1000000 5000000 75000000 100000000 125000000 150000000 175000000 200000000 225000000 250000000
Movies yes
WriteMoviesEvery 100

Component 0 MoleculeName             methane
            MoleculeDefinition       ExampleDefinitions
            TranslationProbability   0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0

[David Dubbeldam]

1) Methane is often modeled as a united-atom (a single bead).
2) The VTK output that can be read by iRASPA is a VTK density-file (see 'ComputeDensityProfile3DVTKGrid').

[JY]

Dear Dr. Dubbeldam,

I tried importing the Density.vtk file from https://github.com/iRASPA/RASPA2/tree/master/examples/Visualization/UnitCell/Density/ERI/VTK to iRASPA, on a Windows machine, and I am getting similar error 'Import failed, Cannot read VTK header (line: 910 file: iraspagui/mainwindow.cpp)'. The contour plot however loads fine on VisIT. Have I missed anything here such as file renaming, etc.?

Thank you.

Best wishes,
JY

[David Dubbeldam]

These are old files, 'RASPA2/examples/Visualization' will be removed soon. These files you do not need to generate, you can directly use volume-rendering in iRASPA to visualize the framework.
Only for density volume-renderings do you need to regenerate the 3D VTK-densities using the latest version of RASPA.