Commits · 1eec1e155e41a7657296cd46e9eb81292a8147b8 · tsoc / openmm

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

16 Mar, 2018 1 commit
- Bug fix · f6c70d6e
  Peter Eastman authored Mar 16, 2018
  
  f6c70d6e
15 Mar, 2018 1 commit
- Bug fixes · 2df35b4e
  peastman authored Mar 14, 2018
  
  2df35b4e
12 Mar, 2018 1 commit
- CustomNonbondedForce with interaction groups uses neighbor list in CUDA · 7639d0bd
  Peter Eastman authored Mar 12, 2018
  
  7639d0bd
12 Feb, 2018 1 commit
- Began converting CudaArrays. · b8c86406
  Peter Eastman authored Feb 12, 2018
  
  b8c86406
02 Dec, 2016 1 commit
- Fixed error building neighbor list with triclinic boxes · 5e535679
  Peter Eastman authored Dec 02, 2016
  
  5e535679
30 Nov, 2016 1 commit
- Disable fine-grained pair list · b7d91a8e
  Peter Eastman authored Nov 30, 2016
  
  b7d91a8e
13 Oct, 2016 1 commit
- Further improvements to pair list · 7c911459
  Peter Eastman authored Oct 13, 2016
  
  7c911459
14 Sep, 2016 1 commit
- Beginning of implementing fine grained pair list · 5fa4345f
  Peter Eastman authored Sep 14, 2016
  
  5fa4345f
27 Jul, 2016 1 commit
- Began CUDA implementation of parameter derivatives · eae8def5
  Peter Eastman authored Jul 27, 2016
  
  eae8def5
25 May, 2016 1 commit
- Improved method for resizing neighbor list · 6cc2edd1
  Peter Eastman authored May 25, 2016
  
  6cc2edd1
21 Sep, 2015 1 commit
- Changes to generating nonbonded kernels · a47300e6
  Peter Eastman authored Sep 21, 2015
  
  a47300e6
27 Aug, 2015 1 commit
- Python 2/3 compatibility in single code base, plus python 3 testing on travis. · b7088b74
  peastman authored Aug 10, 2015
  
  b7088b74
10 Aug, 2015 1 commit
- Ensure neighbor list is large enough on first step · cb599d67
  Peter Eastman authored Aug 10, 2015
  
  cb599d67
03 Aug, 2015 1 commit
- Fixed segfault in AmoebaMultipoleForce · d33b232e
  peastman authored Aug 03, 2015
  
  d33b232e
07 Jul, 2015 1 commit
- CUDA allows different force groups to have different cutoffs · 85532a52
  Peter Eastman authored Jul 07, 2015
  
  85532a52
10 Mar, 2015 1 commit
- More bug fixes to multi-GPU · f7ef2dd0
  peastman authored Mar 10, 2015
  
  f7ef2dd0
06 Mar, 2015 2 commits
- For multi-GPU, exceeding the size of the neighbor list causes the forces to be marked as invalid · bd666c27
  peastman authored Mar 06, 2015
  
  bd666c27
- Load balancing between GPUs forces the neighbor list to be rebuilt · 62f7c44c
  peastman authored Mar 06, 2015
  
  62f7c44c
05 Jan, 2015 1 commit
- Beginning of CUDA support for triclinic boxes · 61458a5f
  Peter Eastman authored Jan 05, 2015
  
  61458a5f
04 Nov, 2014 1 commit
- Improvements to multi-GPU performance · f32c804b
  peastman authored Nov 04, 2014
  
  f32c804b
08 Jul, 2013 1 commit
- Only enable shuffle optimization on CUDA 5.5 or later · b8b00973
  peastman authored Jul 08, 2013
  
  b8b00973
04 Jun, 2013 1 commit

Converted the array containing atom block indices for the neighbor list from... · 2ff0b0ae

peastman authored Jun 04, 2013

Converted the array containing atom block indices for the neighbor list from ushort2 to int.  This removes the hard limit of 2 million atoms.

2ff0b0ae

24 May, 2013 5 commits
- Enabled shuffle for double precision · 8a8873c6
  peastman authored May 24, 2013
  
  8a8873c6
- Fixed bug on pre-Kepler GPUs. Also simplified code a little bit. · 33df8402
  peastman authored May 24, 2013
  
  33df8402
- minor bug fixes · 562283df
  Yutong Zhao authored May 23, 2013
  
  562283df
- bugfix to ifdef conditions in nonbonded.cu · f4591cad
  Yutong Zhao authored May 23, 2013
  
  f4591cad
- nonbonded.cu will now use shuffles on sm_30 or higher · ec39f6ff
  Yutong Zhao authored May 23, 2013
  
  ec39f6ff
22 May, 2013 1 commit
- first working version with shuffle - but breaks lots of existing tests · 44665537
  Yutong Zhao authored May 21, 2013
  
  44665537
03 May, 2013 1 commit
- Very minor optimizations and cleanup to building neighborlist · 78f8d078
  Peter Eastman authored May 03, 2013
  
  78f8d078
23 Apr, 2013 1 commit
- Fixed some incorrect argument indices · 4e9167d0
  Peter Eastman authored Apr 23, 2013
  
  4e9167d0
19 Apr, 2013 1 commit

Fixes a hard to catch bug when a boundingBoxSize increases in size in between... · 282c6f2c

Yutong Zhao authored Apr 19, 2013

Fixes a hard to catch bug when a boundingBoxSize increases in size in between a timestep, but does not trigger a rebuild of the neighbourlist. Affects the usage of singlePeriodicCopy in nonbonded force.

282c6f2c

22 Mar, 2013 1 commit
- Merged 5.1Optimizations branch back to trunk · 93c467b2
  Peter Eastman authored Mar 22, 2013
  
  93c467b2
04 Dec, 2012 1 commit
- Fixed error in updateNeighborListSize() when createInteractionKernel() has not... · e3d94aa2
  Lee-Ping Wang authored Dec 04, 2012
```
Fixed error in updateNeighborListSize() when createInteractionKernel() has not been called (e.g. with AmoebaVdwForce)
```
  e3d94aa2
26 Oct, 2012 1 commit
- Bug fixes · 61bb8786
  Peter Eastman authored Oct 26, 2012
  
  61bb8786
19 Oct, 2012 1 commit
- The test for identical exceptions between nonbonded forces is order insensitive · ff7f1035
  Peter Eastman authored Oct 19, 2012
  
  ff7f1035
18 Oct, 2012 2 commits

CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are... · 93497df6
Lee-Ping Wang authored Oct 18, 2012
```
CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are now fully reverted to 3478.
```
93497df6

LPW attempted bugfixes: (1) Changed unit multipliers in... · 68593ba6

Lee-Ping Wang authored Oct 18, 2012

LPW attempted bugfixes: (1) Changed unit multipliers in AmoebaVdwForce::getParticleParameters (2) Sorted vectors in exclusionLists so it agrees with atomExclusions

68593ba6

10 Oct, 2012 1 commit

OpenCLArray is no longer templatized and doesn't provide a host buffer. This... · 1107aa83

Peter Eastman authored Oct 10, 2012

OpenCLArray is no longer templatized and doesn't provide a host buffer.  This is in preparation for adding mixed/double precision support.

1107aa83

05 Oct, 2012 1 commit
- Fixed performance bug in mixed precision · 5980100d
  Peter Eastman authored Oct 05, 2012
  
  5980100d