alphataubio

added two subsections: - Troubleshooting segmentation faults on GPUs - Troubleshooting memory allocation on GPUs and reformatted code blocks for readability on smaller screen devices. **Summary** **Related Issue(s)** **Author(s)** **Licensing**...

Improve Kokkos unit testing

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**Summary** add kokkos unit tests for angles, bonds, dihedral, improper, fixes, ... **Related Issue(s)** n/a **Author(s)** @alphataubio **Licensing** By submitting this pull request, I agree, that my contribution will be...

Add Kokkos version of spica pair and angle styles

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**Summary** Add pair_style lj/spica/coul/long/kk and angle_style spica/kk **Related Issue(s)** n/a **Author(s)** Mitch Murphy [email protected] **Licensing** By submitting this pull request, I agree, that my contribution will be included in LAMMPS...

BUG: ValueError in npyio.py loading oxdna topology and trajectory

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**Describe the bug** topology and trajectory created with recent version of oxDNA 3.6.1 does not load in MN **To Reproduce** [http://tacoxdna.sissa.it/XYZ_oxDNA] - generate test.oxdna using tacoxdna [https://lorenzo-rovigatti.github.io/oxDNA/relaxation.html] - First stage:...

TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'

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**Describe the bug** loading MD lammps cg spica trajectory gives error and does not load. **To Reproduce** Topology: 4ypg-e.psf Trajectory: 4ypg-20fs.lammpsdump "Load" **Expected behavior** load md lammps trajectory without error...

parallel optimization using OPENMP

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where are the 2-3 most computationally-intensive loops in the fortran code that could be parallelized using OPENMP ?

Add KOKKOS versions of fixes

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**Summary** Add KOKKOS versions: - [x] `fix cmap/kk` (to have all needed fixes in KOKKOS for performance on GPUs) - [x] `fix nve/limit/kk` (to relax overlapped systems with KOKKOS) -...

EXTRA-COMMAND: read_psf, read_sdf, write_pdb

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**Summary** - [x] `compute property/local` add pmolecule1, pmolecule2 to store molecule ID of two atoms in each pair - [x] `read_psf` - [x] `write_psf` - [x] `read_sdf` read data from...

[BUG] EXPECT_FP_LE_WITH_EPS false negative

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**Summary** test macro EXPECT_FP_LE_WITH_EPS in unittest/force-styles/test_main.h gives a false negative when comparing floating numbers that are close and very small (ie. are essentially both zero to floating point precision), yielding...

documentation style proposal

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**Summary** In the sphinx theme, there are currently blue admonition boxes for Notes, red for Error, and yellow for Warning. My documentation style proposal is: (1) use GREEN admonition boxes...