Commits · 617f142182d80d9a4e3bbb839edb1fb5b9bb250f · tsoc / openmm

12 Apr, 2019 1 commit
- Update version number to 7.4.0 to match nightly conda dev builds · 617f1421
  Chodera authored Apr 12, 2019
  
  617f1421
09 Apr, 2019 1 commit

Created HippoNonbondedForce (#2296) · 1eec1e15

peastman authored Apr 09, 2019

* Created API for HIPPO force field

* Beginning of reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Completed reference of HIPPO with no cutoff

* Beginning cutoffs/PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Completed reference implementation of HIPPO

* Cleanup and optimization to HIPPO reference

* Further cleanup to HIPPO

* Combined direct space interactions into a single loop

* Compute direct space interactions in quasi-internal frame

* Beginning of CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Finished CUDA implementation of HIPPO

* More features and test cases for HippoNonbondedForce

* Serialization and Python API for HippoNonbondedForce

* Fixed sign error in computing forces

1eec1e15

04 Apr, 2019 2 commits
- Merge pull request #2294 from jchodera/fix-sphinx · 0b22cac1
  peastman authored Apr 04, 2019
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Fix unicode error in sphinx compilation
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  0b22cac1
- Fix unicode error in sphinx compilation · 3a8941b5
  John Chodera authored Apr 03, 2019
  
  3a8941b5
22 Mar, 2019 3 commits
- Merge pull request #2273 from tristanic/customgbforces · a4dec7b9
  peastman authored Mar 22, 2019
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Customgbforces
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  a4dec7b9
- Merge pull request #2290 from peastman/atan2 · e1056ad1
  peastman authored Mar 22, 2019
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Support atan2() in custom expressions
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  e1056ad1
- Removed spurious "import numpy" line · d2ea8772
  tic20 authored Mar 22, 2019
  
  d2ea8772
21 Mar, 2019 4 commits
- Document that atan2 can be used in custom expressions · b24c1d1a
  peastman authored Mar 21, 2019
  
  b24c1d1a
- Fixed compilation error · c557c0b0
  Peter Eastman authored Mar 21, 2019
  
  c557c0b0
- Support atan2() in custom expressions · 00e2c6a3
  peastman authored Mar 21, 2019
  
  00e2c6a3
- Merge pull request #2289 from peastman/asmjit · 6e3c2142
  peastman authored Mar 21, 2019
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Upgraded to latest version of asmjit
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  6e3c2142
20 Mar, 2019 3 commits
- Upgraded to latest version of asmjit · 0e0558b9
  peastman authored Mar 20, 2019
  
  0e0558b9
- Merge pull request #2287 from peastman/groups · b6e79d4a
  peastman authored Mar 20, 2019
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Improved performance of interaction groups on CPU
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  b6e79d4a
- Improved performance of interaction groups on CPU · b26b74c0
  Peter Eastman authored Mar 19, 2019
  
  b26b74c0
05 Mar, 2019 10 commits
- Merge pull request #2274 from JoaoRodrigues/ion_fix · 7ada5dd0
  peastman authored Mar 05, 2019
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Improved ion addition to both addSolvent() and addMembrane()
```
  7ada5dd0
- Removed duplicated code. Fixed comment on rounding integers. · 6b6f92a0
  João Rodrigues authored Mar 05, 2019
  
  6b6f92a0
- Merge pull request #2279 from peastman/ccma · 0ee983bc
  peastman authored Mar 05, 2019
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Optimized building constraint matrix
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  0ee983bc
- Merge pull request #2278 from peastman/win · cc5ecb7c
  peastman authored Mar 05, 2019
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Fixed compilation error on Windows
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  cc5ecb7c
- Optimized building constraint matrix · f24a84f8
  peastman authored Mar 05, 2019
  
  f24a84f8
- Fixed compilation error on Windows · 93e232df
  peastman authored Mar 05, 2019
  
  93e232df
- Make Numpy optional in CustomGBForces · 3111d8cf
  tic20 authored Mar 05, 2019
  
  3111d8cf
- Fix squaring of units. Ensure addSolvent passes the right data structure to addIons · 8c8dbed1
  João Rodrigues authored Mar 04, 2019
  
  8c8dbed1
- Ensure coords are always in the proper units and not converted to floats · b9936fb9
  João Rodrigues authored Mar 04, 2019
  
  b9936fb9
- Ensure we only get keys of the dictionary · b0b7548a
  João Rodrigues authored Mar 04, 2019
  
  b0b7548a
02 Mar, 2019 1 commit
- Merge pull request #2269 from tristanic/master · 8ce5a685
  peastman authored Mar 01, 2019
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Avoid repeated matching of duplicate impropers
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  8ce5a685
01 Mar, 2019 1 commit
- Implemented private _addIons method that improves placement of ions in... · ec1c8ebe
  João Rodrigues authored Mar 01, 2019
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Implemented private _addIons method that improves placement of ions in solvated box, specially for membrane systems
```
  ec1c8ebe
27 Feb, 2019 3 commits
- Fixed bug in _mbondi_radii() · 0de32856
  tic20 authored Feb 27, 2019
  
  0de32856
- Numpyfication of custom GB forces · 74f6ea57
  tic20 authored Feb 27, 2019
  
  74f6ea57
- Fixed typo in proper dihedral signature · 913410fc
  tic20 authored Feb 27, 2019
  
  913410fc
26 Feb, 2019 5 commits
- Removed incorrect improper signature code · 10320b39
  tic20 authored Feb 26, 2019
  
  10320b39
- Corrected behaviour of improper caching. · cebb9934
  tic20 authored Feb 26, 2019
  
  cebb9934
- Also cache proper torsion search. · f9540d88
  tic20 authored Feb 26, 2019
```
Has a much smaller effect compared to caching the improper search, but non-negligible and easy to do.
```
  f9540d88
- Merge branch 'master' of github.com:tristanic/openmm · c3e361d2
  tic20 authored Feb 26, 2019
  
  c3e361d2
- Optimisation: improper matching in PeriodicTorsionGenerator.createForce · 307b34cb
  tic20 authored Feb 26, 2019
  
  307b34cb
22 Feb, 2019 2 commits
- Merge pull request #2266 from peastman/vector · dd4eed16
  peastman authored Feb 22, 2019
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Fixed bug in vector operations in CustomIntegrator on CUDA
```
  dd4eed16
- Fixed bug in vector operations in CustomIntegrator on CUDA · ddcd2f66
  Peter Eastman authored Feb 22, 2019
  
  ddcd2f66
21 Feb, 2019 1 commit
- Merge pull request #1 from pandegroup/master · e182a5be
  Tristan Croll authored Feb 21, 2019
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Sync with official repository
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  e182a5be
20 Feb, 2019 2 commits
- Merge pull request #2263 from tristanic/master · f36f2dba
  peastman authored Feb 20, 2019
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simple optimization to ForceField class
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  f36f2dba
- Leave XML data structure unchanged during parsing. · 0515bdf6
  tic20 authored Feb 20, 2019
  
  0515bdf6
19 Feb, 2019 1 commit
- Merge pull request #2264 from tristanic/files · 1586d560
  peastman authored Feb 19, 2019
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Ensuring opened files are properly closed
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  1586d560