Fix solvating with truncated octahedral cells#1174

Merged

drroe merged 21 commits intoAmber-MD:masterfrom

drroe:fix.solvateoct

Mar 27, 2026

Commits on Mar 23, 2026

Truncated octahedron diagonal cut scaling fix suggested by Nikolai Skrynnikov and Stephan Schott.
Daniel R. Roe
committed

Commits on Mar 24, 2026

Fix minimage action setup when no data set name specified
Daniel R. Roe
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Try to implement toface keyword to check closest approach to unit cell face
Daniel R. Roe
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Add a toface test
Daniel R. Roe
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Add another toface test
Daniel R. Roe
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Store face a string. Ensure negative frac coords are wrapped back into 0.0 to 1.0 range.
Daniel R. Roe
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Fix up solvateoct diagonal check to be more like the original fixed code
Daniel R. Roe
committed

Commits on Mar 25, 2026

Original test save calculated when LEAPPI active, update for regular PI
Daniel R. Roe
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Add debug print of intermediate structures
Daniel R. Roe
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Try to handle the trunc oct box better in nsolvent
Daniel R. Roe
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Hide some debug info. Ensure all box lengths are properly enforced to be equal for truncoct
Daniel R. Roe
committed

Commits on Mar 26, 2026

Do clipping just like the original solvate command - results in nicer looking trunc oct cells
Daniel R. Roe
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Add the centering step
Daniel R. Roe
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Hide some debug info. Clean up output
Daniel R. Roe
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Remove unused code
Daniel R. Roe
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Add ifdef, update depends
Daniel R. Roe
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nsolvent now works with truncoct
Daniel R. Roe
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Remove old include
Daniel R. Roe
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Improve build manual entry
Daniel R. Roe
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V7.5.0. Minor version bump for fixed truncated octahedral cell calculation (thanks to N. Skrynnikov for the fix). Also enables truncated octahedron for 'nsolvent' keyword.
Daniel R. Roe
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Update manual PDF
Daniel R. Roe
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