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When the structure has a three-membered ring (e.g., an epoxide group), TopoTools will create an incorrect type of dihedral in which the first and last atom are the same.
How to reproduce this error…
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This would be very useful to help ensure things are looking right, but at the moment my Paraview simulations only show lines between pores.
I recall that @jhinebau once sent me a complex recipe f…
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I utilized topotools package to generate the topology from a coordinate set representing some polymer chains (PMMA) to equilibrate in the molten/amorphous phase. In these molecules there are sp2 Carbo…
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Dear Sir,
Tutorial-2, Step 2e: Hexane / Cyclohexane 1:1 mixture, simulation box is filled with equal of hexane and cyclohexane molecules.
How can i modify mixedhexanetodata.tcl so that i can …
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Hi Dear Prof Gostick,
Thank you for the OpenPNM sharing, and I have learnt a lot and benefited a lot. In the processing of understanding the code, I found that the find_cluster2(~invadedPs) in IP c…
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Hello,
When i try to run this input file on lammps i get this error "Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted."
…
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Willing to use gro2lam with the 43A1-S3 version 02 bonding & nonbonding parameters, the next error message is obtained:
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** Gathering dihedrals data
[ atomtypes ]
[ atomtypes ] found!
[ nonb…
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I want to switch a lammps data file to hoomd data file, so i want to ask if there is any available script to do this. If not, how about I write some code to do this job?
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Hi Peter.
Thank you for sharing the code.
I tried to redo some of the simulations published in your recent article Force-Field Prediction of Materials Properties in Metal-OrganicFrameworks
I s…
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## Summary
When restarting a data file with fix rigit/nvt/small I am getting error message:
>ERROR on proc 255: Rigid body atoms 656062 97848 missing on proc 255 at step 0 (../fix_rigid_small.cpp:33…