Commits · 9e6762f916898db34a0db227bf36e3149951b7e0 · tsoc / openmm

"platforms/cuda2/include/CudaKernelFactory.h" did not exist on "62cf5c93850be4c41489589879a903aee34047f9"

06 Dec, 2019 1 commit
- Construct 1-3 and 1-4 exclusion pairs from bond instead of angle and dihedral · 9e6762f9
  Zheng Gong authored Dec 06, 2019
  
  9e6762f9
04 Dec, 2019 1 commit
- Merge pull request #1 from openmm/master · 83b8ea75
  Zheng GONG authored Dec 04, 2019
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Update from upstream
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  83b8ea75
03 Dec, 2019 2 commits
- Merge pull request #2490 from mcs95/ignore_external_bonds · 2ca749a1
  peastman authored Dec 03, 2019
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Signature modification to Modeller.addExtraParticles()
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  2ca749a1
- Add pydoc · 17dbc362
  Maria Chiara Storer authored Dec 03, 2019
  
  17dbc362
02 Dec, 2019 1 commit

Signature modification to Modeller.addExtraParticles() · 842a671a

Maria Chiara Storer authored Dec 02, 2019

Within Modeller.addExtraParticles(), add the ability to pass down
an option to modify compiled.matchResidueToTemplate() 's
ignoreExternalBonds parameter.

https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=11264&p=0&start=0&view=&sid=e384beeb08f3bfd767dcfb546006ad63

842a671a

21 Nov, 2019 1 commit
- Merge pull request #2476 from peastman/functions · 75c1fcb6
  peastman authored Nov 21, 2019
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Optimized processing of expressions with tabulated functions
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  75c1fcb6
19 Nov, 2019 2 commits
- Optimized processing of expressions with tabulated functions · 5eb439d8
  peastman authored Nov 19, 2019
  
  5eb439d8
- Merge pull request #2475 from mjw99/ThreeParticleAverageSite_Doxygen_fix · 97b972e9
  peastman authored Nov 18, 2019
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ThreeParticleAverageSite Doxygen fix #2473
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  97b972e9
18 Nov, 2019 2 commits
- ThreeParticleAverageSite Doxygen fix #2473 · a2940162
  Mark J. Williamson authored Nov 18, 2019
  
  a2940162
- Merge pull request #2472 from peastman/travis · 79a01ce9
  peastman authored Nov 18, 2019
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Update travis to test more recent Python versions
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  79a01ce9
15 Nov, 2019 2 commits
- Python 3.8 is only available on a new OS · d502caee
  peastman authored Nov 15, 2019
  
  d502caee
- Update travis to test more recent Python versions · 49758d01
  peastman authored Nov 15, 2019
  
  49758d01
13 Nov, 2019 1 commit
- Merge pull request #2469 from peastman/steps · 8dfdd485
  peastman authored Nov 13, 2019
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runForClockTime() updates currentStep correctly
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  8dfdd485
12 Nov, 2019 1 commit
- runForClockTime() updates currentStep correctly · e275bd08
  peastman authored Nov 12, 2019
  
  e275bd08
11 Nov, 2019 2 commits
- Merge pull request #2466 from ljmartin/simtemp-scale-velocities · 6024e7c0
  peastman authored Nov 11, 2019
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Get and scale velocities using numpy during simulated tempering
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  6024e7c0
- Get and scale velocities during simulated tempering using numpy, for speed · 9c4766f0
  ljmartin authored Nov 11, 2019
  
  9c4766f0
07 Nov, 2019 1 commit
- Merge pull request #2464 from peastman/element · 5aa19c2d
  peastman authored Nov 07, 2019
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Improved determination of elements from Gromacs top files
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  5aa19c2d
05 Nov, 2019 1 commit
- Improved determination of elements from Gromacs top files · 8316b626
  peastman authored Nov 05, 2019
  
  8316b626
01 Nov, 2019 4 commits
- Merge pull request #2461 from peastman/voxellimit · ba62a938
  peastman authored Nov 01, 2019
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Prevent memory from exploding when particles get too spread out
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  ba62a938
- Prevent memory from exploding when particles get too spread out · 9930e6f6
  peastman authored Nov 01, 2019
  
  9930e6f6
- Merge pull request #2460 from peastman/doxygen · 5312c2fe
  peastman authored Nov 01, 2019
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Fixed errors with Doxygen 1.8.16
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  5312c2fe
- Fixed errors with Doxygen 1.8.16 · eac71bff
  peastman authored Nov 01, 2019
  
  eac71bff
31 Oct, 2019 1 commit
- Merge pull request #2452 from peastman/template · e2449914
  peastman authored Oct 31, 2019
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Allow multiple matching templates if they assign identical parameters
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  e2449914
29 Oct, 2019 3 commits
- Merge pull request #2455 from FrazerClews/frazer/passByReference · 035d5188
  peastman authored Oct 29, 2019
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make std::string pass as references, not values
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  035d5188
- Minor cleanup based on comments · c6225e7a
  peastman authored Oct 29, 2019
  
  c6225e7a
- make std::string pass as references, not values · 109a83de
  Frazer Leslie Clews authored Oct 24, 2019
  
  109a83de
28 Oct, 2019 2 commits
- Merge pull request #2440 from JoaoRodrigues/bugfix_ion_concentration · 41d061dd
  peastman authored Oct 28, 2019
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Fixes _addIons behavior for membrane systems.
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  41d061dd
- Allow multiple matching templates if they assign identical parameters · d88ddb3b
  peastman authored Oct 28, 2019
  
  d88ddb3b
25 Oct, 2019 5 commits
- Merge pull request #2447 from peastman/energy · ad7a55b8
  peastman authored Oct 25, 2019
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Avoid unnecessary force evaluation when computing kinetic energy
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  ad7a55b8
- Merge pull request #2448 from JoaoRodrigues/restrain_existing_H · 466a826e
  peastman authored Oct 25, 2019
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Restraint existing atoms during addHydrogens
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  466a826e
- Added test for addHydrogens to check for atom positions · 46b334ce
  João Rodrigues authored Oct 25, 2019
  
  46b334ce
- Fix position of existing atoms on addHydrogens() · ed57e864
  João Rodrigues authored Oct 25, 2019
  
  ed57e864
- Avoid unnecessary force evaluation when computing kinetic energy · 88209091
  Peter Eastman authored Oct 25, 2019
  
  88209091
24 Oct, 2019 6 commits
- Merge pull request #2436 from peastman/baoab · c7441b96
  peastman authored Oct 24, 2019
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Create BAOABLangevinIntegrator
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  c7441b96
- Merge pull request #2445 from peastman/clplatform · 8ac16493
  peastman authored Oct 24, 2019
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Catch exception when cl::Platform::get() fails.
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  8ac16493
- Added comments to BAOAB kernels · 6333db3a
  peastman authored Oct 24, 2019
  
  6333db3a
- Catch exception when cl::Platform::get() fails. · 930d985e
  peastman authored Oct 24, 2019
  
  930d985e
- Merge pull request #2444 from FrazerClews/frazer/prefixOperator · 2fb47a51
  peastman authored Oct 24, 2019
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make non-primitave types pre increment instead of post increment
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  2fb47a51
- make non-primitave types pre increment instead of post increment · c6577ea6
  Frazer Leslie Clews authored Oct 24, 2019
  
  c6577ea6
23 Oct, 2019 1 commit
- Merge pull request #2441 from peastman/clplatform · 7a02c59b
  peastman authored Oct 23, 2019
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Do not register OpenCL platform if no implementations are available
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  7a02c59b