8000 Fix unwrapping and diffusion imaging for NPT trajectories by drroe · Pull Request #1027 · Amber-MD/cpptraj · GitHub
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Fix unwrapping and diffusion imaging for NPT trajectories #1027

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Merged
merged 16 commits into from
May 10, 2023
Merged

Fix unwrapping and diffusion imaging for NPT trajectories #1027

merged 16 commits into from
May 10, 2023

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drroe
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@drroe drroe commented May 10, 2023

Version 6.19.0.

Previously, unwrapping and imaging for the diffusion calculation were done in a manner that became very inaccurate for long time scales. Now unwrapping and the imaging for the diffusion calculation are done entirely in fractional space, which largely eliminates this problem.

Also correctly read time information from DCD trajectories, and adds 3 new keywords for controlling time info written to DCD trajectories:

	dt      : Set trajectory time step in ps.
	nstep   : # steps between frames.
	step0   : Initial step.

Daniel R. Roe added 16 commits May 9, 2023 15:34
Do unwrapping entirely in fractional space to avoid problems unwrapping
8125772 
NPT trajectories
Add dt keyword for dcd trajout to set time step. Ensure time step is
592b96b 
written in AKMA units.
Use the image list so bymol and byres are honored
cd4bd8f
Cannot use push_back in an OpenMP loop
3e34938
Fix imaging in diffusion calc for NPT simulations
8d48c84
If using a reference structure, ensure frac coords get calcd for it
042a2ee
Explicitly make tests byatom
1d8073b
Update help
44edd18
Remove the old unwrap routines
193ebb6
Remove old Unwrap templates
e79f2e3
Fix up unwrap manual entry; note that default is actually unwrap by atom
de79feb
Add dt option to dcd trajout
4fd05d5
6.19.0. Minor version bump for fixed unwrapping and fixed diffusion i…
95a32f7 
…maging for

NPT
Properly read time from charmm dcd. Add t0 and nstep options to charmm
90b271e 
trajout
Add options to manual. Change t0 to step0
f3b3f50
Get rid of old unused function definitions
eb3ab08
@drroe drroe added enhancement bugfix New keywords New keywords for existing commands. labels May 10, 2023
@drroe drroe self-assigned this May 10, 2023
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drroe commented May 10, 2023

Jenkins failure is the spurious pytraj one. Ignoring it.

@drroe drroe merged commit 1a35547 into Amber-MD:master May 10, 2023
@drroe drroe deleted the check.unwrap.frac branch May 10, 2023 18:26
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