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Speed and functionality improvements for 'hbond' command #485

Merged
merged 57 commits into from
Apr 19, 2017
Merged

Speed and functionality improvements for 'hbond' command #485

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dea5d06
DRR - Cpptraj: Add hbond timing info
drroe Apr 11, 2017
4d65a83
DRR - Cpptraj: Test new hydrogen bond action that arranges things by …
drroe Apr 11, 2017
df323da
DRR - Cpptraj: Add test hbond2 action
drroe Apr 12, 2017
35705f9
DRR - Cpptraj: Finish initial solute-solute hbond calculation. Seems …
drroe Apr 12, 2017
4526299
DRR - Cpptraj: Ensure donor-only sites will be calculated.
drroe Apr 12, 2017
78f12eb
DRR - Cpptraj: Add print code. MPI code added too but not yet working.
drroe Apr 12, 2017
023e553
DRR - Cpptraj: Ensure UU hydrogen bonds in map are truely unique by u…
drroe Apr 12, 2017
3005b65
DRR - Cpptraj: Try to improve insertion speed into hbond map
drroe Apr 12, 2017
2a613e9
DRR - Cpptraj: Add solvent Hbond calc. Speedup in initial testing is …
drroe Apr 13, 2017
f91a993
DRR - Cpptraj: HBmapType to UUmapType
drroe Apr 13, 2017
f12ebf2
DRR - Cpptraj: Ensure solvent is ignored when solute donor or accepto…
drroe Apr 13, 2017
902943e
DRR - Cpptraj: Recognize ions
drroe Apr 13, 2017
2248a30
DRR - Cpptraj: Add solute/solvent hydrogen and ion count
drroe Apr 13, 2017
86e1b0f
DRR - Cpptraj: Add bridging calc
drroe Apr 13, 2017
3932a7a
DRR - Cpptraj: Properly init some variables. Fix spacing.
drroe Apr 13, 2017
cde9c40
DRR - Cpptraj: Remove unused class variable.
drroe Apr 13, 2017
34c36b2
DRR - Cpptraj: Add nointramol functionality. Slows down the code a li…
drroe Apr 13, 2017
256bb2f
DRR - Cpptraj: Start fixing the MPI consolidation
drroe Apr 13, 2017
75cf546
DRR - Cpptraj: Add sort option for data file write. This allows compa…
drroe Apr 13, 2017
b5250ce
DRR - Cpptraj: Hide some debug info
drroe Apr 13, 2017
88d886c
DRR - Cpptraj: Send solvent hbond data with solute hbonds. Properly f…
drroe Apr 13, 2017
3028de8
DRR - Cpptraj: Remove obsolete code. Ensure UU/UV time series data pr…
drroe Apr 13, 2017
34bbe56
DRR - Cpptraj: OpenMP-parallelize solute hbonds. OK speedup for now (…
drroe Apr 13, 2017
9e90a6f
DRR - Cpptraj: Properly handle nointramol variable in openmp
drroe Apr 13, 2017
a59ea34
DRR - Cpptraj: Create AddUV function
drroe Apr 13, 2017
484dae0
DRR - Cpptraj: Openmp parallelize the UV calc
drroe Apr 13, 2017
0dd6010
DRR - Cpptraj: Simplify code a bit by using the numHB variable as myt…
drroe Apr 13, 2017
96b7fb8
DRR - Cpptraj: Remove old code
drroe Apr 13, 2017
83ef1cb
DRR - Cpptraj: Add specified solute mask tests.
drroe Apr 14, 2017
645cc24
DRR - Cpptraj: Add no angle cut test
drroe Apr 14, 2017
f31b325
DRR - Cpptraj: Still calc angle even when cutoff is -1 so the average…
drroe Apr 14, 2017
32a345c
DRR - Cpptraj: Add bridge class - not yet used. Will eventually be ne…
drroe Apr 16, 2017
6763a66
DRR - Cpptraj: When 'nointramol', ignore solvent-solute bridges that …
drroe Apr 16, 2017
0e017fd
DRR - Cpptraj: Add missing test file.
drroe Apr 17, 2017
45afa0b
DRR - Cpptraj: Make use of new bridge class
drroe Apr 17, 2017
ffa6609
DRR - Cpptraj: Fix MPI compilation
drroe Apr 17, 2017
271d5c8
DRR - Cpptraj: For backwards compatibility store solute donor H/accep…
drroe Apr 17, 2017
094c2e2
DRR - Cpptraj: MPI data set creation use UU_Set_Idx
drroe Apr 17, 2017
ce65438
DRR - Cpptraj: Data set ordering for hbond UU series data can now be …
drroe Apr 17, 2017
678906c
DRR - Cpptraj: Add save files for new test
drroe Apr 17, 2017
d4def22
DRR - Cpptraj: Use typedef
drroe Apr 17, 2017
f937d64
DRR - Cpptraj: Consolidate UU series set creation.
drroe Apr 18, 2017
7861999
DRR - Cpptraj: Fix variable naming to better reflect what is actually…
drroe Apr 18, 2017
968c1ff
DRR - Cpptraj: Start adding bridgebyatom option
drroe Apr 18, 2017
10c440a
DRR - Cpptraj: Fix up output formatting.
drroe Apr 18, 2017
5ed6b99
DRR - Cpptraj: Finish bridgebyatom option.
drroe Apr 18, 2017
401baaf
DRR - Cpptraj: Add but do not yet enable the bridge nointramol test
drroe Apr 18, 2017
765761f
DRR - Cpptraj: Version bump. New hbond functionality is different fro…
drroe Apr 18, 2017
3d8b2f6
DRR - Cpptraj: Remove old hbond code.
drroe Apr 18, 2017
901bb1d
DRR - Cpptraj: Enable tests for new hbond code.
drroe Apr 18, 2017
49ac0a0
DRR - Cpptraj: Fix memory estimation.
drroe Apr 18, 2017
e65e8ae
DRR - Cpptraj: Fix up code docs.
drroe Apr 18, 2017
ac011ed
DRR - Cpptraj: Split nointramol functionality into two loops again; r…
drroe Apr 18, 2017
98f5100
DRR - Cpptraj: Hide timing info behind ifdef
drroe Apr 18, 2017
dc211af
DRR - Cpptraj: Improve stability of bridge sort by comparing residues…
drroe Apr 18, 2017
9f3758d
Merge branch 'master' into hbond_improve_speed
drroe Apr 18, 2017
81236bd
DRR - Cpptraj: Properly initialize class variable in constructors.
drroe Apr 18, 2017
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1,112 changes: 0 additions & 1,112 deletions src/Action_Hbond.cpp
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121 changes: 0 additions & 121 deletions src/Action_Hbond.h
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