Commits · af953fadc551d586fa1758b7929e3f4ac3897831 · tsoc / openmm

"vscode:/vscode.git/clone" did not exist on "c698141a569e16b418a6575af7a4f766965d275d"

10 Jun, 2019 2 commits
- Try to fix all builds in docker containers. · af953fad
  Jason Swails authored Jun 10, 2019
  
  af953fad
- Merge branch 'master' of github.com:/pandegroup/openmm into feature/cuda-docker · 2e8eef42
  Jason Swails authored Jun 10, 2019
  
  2e8eef42
04 Jun, 2019 1 commit
- Merge pull request #2312 from peastman/sqrt · df52ff73
  peastman authored Jun 04, 2019
```
Algebraic optimizations
```
  df52ff73
03 Jun, 2019 2 commits

Merge pull request #2314 from dprada/dna_amber_names · 5a244b5c
peastman authored Jun 03, 2019
```
Adding alternative names of terminal nucleic acids (5' and 3') and atoms H2', H2'', H5' and H5''.
```
5a244b5c

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3).... · a9a7f2cc

Diego Prada authored Jun 03, 2019

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3). Adding alternative names of atoms H2', H2'', H5' and H5'' for nucleic acids.

a9a7f2cc

01 Jun, 2019 1 commit
- Algebraic optimizations · 0bf7b063
  peastman authored Jun 01, 2019
  
  0bf7b063
08 May, 2019 2 commits
- Merge pull request #2307 from peastman/pdbxlabel · e0b3c2bd
  peastman authored May 08, 2019
```
PDBxFile is more robust
```
  e0b3c2bd
- PDBxFile is more robust · 21cb4f94
  peastman authored May 08, 2019
  
  21cb4f94
30 Apr, 2019 1 commit
- Merge pull request #2305 from peastman/setpos · 25e12f36
  peastman authored Apr 30, 2019
```
Optimized setPositions() from Python
```
  25e12f36
29 Apr, 2019 1 commit
- Optimized setPositions() from Python · a7bc22fb
  Peter Eastman authored Apr 29, 2019
  
  a7bc22fb
16 Apr, 2019 3 commits
- Merge pull request #2301 from peastman/hippo2 · 9b523076
  peastman authored Apr 16, 2019
```
Improvements to HippoNonbondedForce
```
  9b523076
- Fixed error on older Pythons · c60568b2
  Peter Eastman authored Apr 16, 2019
  
  c60568b2
- ForceField supports HippoNonbondedForce · 78d42678
  Peter Eastman authored Apr 16, 2019
  
  78d42678
12 Apr, 2019 4 commits
- Merge pull request #2299 from jchodera/update-version-number · 43f619bc
  peastman authored Apr 12, 2019
```
Update version number to 7.4.0 to match nightly conda dev builds
```
  43f619bc
- Update version number to 7.4.0 to match nightly conda dev builds · 617f1421
  Chodera authored Apr 12, 2019
  
  617f1421
- Added a separate scale factor for charge transfer · 682da7b2
  Peter Eastman authored Apr 12, 2019
  
  682da7b2
- Minor optimizations to HIPPO · b53c0f10
  Peter Eastman authored Apr 12, 2019
  
  b53c0f10
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
```
Fix unicode error in sphinx compilation
```
  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
```
Customgbforces
```
  a4dec7b9
- Merge pull request #2290 from peastman/atan2 · e1056ad1
  peastman authored Mar 22, 2019
```
Support atan2() in custom expressions
```
  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
```
Upgraded to latest version of asmjit
```
  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
```
Improved performance of interaction groups on CPU
```
  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
```
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
```
Optimized building constraint matrix
```
  0ee983bc
- Merge pull request #2278 from peastman/win · cc5ecb7c
  peastman authored Mar 05, 2019
```
Fixed compilation error on Windows
```
  cc5ecb7c
- Optimized building constraint matrix · f24a84f8
  peastman authored Mar 05, 2019
  
  f24a84f8
- Fixed compilation error on Windows · 93e232df
  peastman authored Mar 05, 2019
  
  93e232df
- Docker containers do not have 'module' command. · 4ec26e2f
  Jason Swails authored Mar 05, 2019
  
  4ec26e2f
- Make Numpy optional in CustomGBForces · 3111d8cf
  tic20 authored Mar 05, 2019
  
  3111d8cf
- Enable docker for GPU builds · a150d570
  Jason Swails authored Mar 05, 2019
```
I finally got nvidia-docker2 installed and actually working on my Gentoo
machine (I had to disable their restriction of using GPU devices to
users in the 'video' group, since the nvidia container runtime hook
didn't run as a user with those privileges, and I can't figure out what
user it was running as).

The other GPU-enabled node I added to the Jenkins array runs Ubuntu, and
that one already has nvidia-docker2 installed and running correctly on
it.
```
  a150d570
- Fix squaring of units. Ensure addSolvent passes the right data structure to addIons · 8c8dbed1
  João Rodrigues authored Mar 04, 2019
  
  8c8dbed1