Commits · 8e8923a79d40e52f0e3311deeaa7eaf13d951a9f · tsoc / openmm

22 May, 2021 1 commit

Converted AMOEBA to common platform (#3120) · 8e8923a7

Peter Eastman authored May 22, 2021

* Began converting AMOEBA to common platform

* Beginning of OpenCL platform for AMOEBA

* Converted AmoebaVdwForce to common platform

* Cleaned up reference AMOEBA tests

* Began converting AmoebaMultipoleForce to common platform

* Continue converting AmoebaMultipoleForce to common platform

* Bug fixes

* Bug fix

* Continue converting AmoebaMultipoleForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Converted arrays from real3 to real

* Bug fix to OpenCL AmoebaGeneralizedKirkwoodForce

* Fixes for AMD GPUs

* Began converting HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Working on unifying PME kernels

* Fixed error on devices without 64 bit atomics

* Unified PME kernels

* Converted HippoNonbondedForce to common platform

* Creating OpenCL implementation of HippoNonbondedForce

* Continuing OpenCL implementation of HippoNonbondedForce

* Mostly finished OpenCL implementation of HippoNonbondedForce

* Eliminated three component vector types in host code

* Fix errors on CPU OpenCL

* Skip double precision tests for AMOEBA on OpenCL

* Bug fixes

* Bug fixes

* Fixed compilation error

8e8923a7

04 Mar, 2021 1 commit

Replaced several AMOEBA bonded forces with custom forces (#3046) · 1e42b8be

Peter Eastman authored Mar 04, 2021

* Replaced several AMOEBA bonded forces with custom forces

* Deleted obsolete AMOEBA forces

* Replaced AmoebaPiTorsionForce with custom force

1e42b8be

18 Aug, 2020 1 commit

Updated to latest values for physical constants (#2802) · b4543a46

peastman authored Aug 18, 2020

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

b4543a46

01 Jul, 2020 1 commit
- CUDA implementation of new features in AmoebaVdwForce · d925ed4b
  Peter Eastman authored Jul 01, 2020
  
  d925ed4b
30 Jun, 2020 1 commit
- Continuing to new features in AmoebaVdwForce · 5e392f97
  Peter Eastman authored Jun 30, 2020
  
  5e392f97
29 Oct, 2019 1 commit
- make std::string pass as references, not values · 109a83de
  Frazer Leslie Clews authored Oct 24, 2019
  
  109a83de
12 Sep, 2019 1 commit
- Fixed compilation error introduced by #2378 · 0885a51a
  Peter Eastman authored Sep 11, 2019
  
  0885a51a
11 Sep, 2019 1 commit
- bug fix TestVdw · 31786496
  Chengwen Liu authored Sep 10, 2019
  
  31786496
22 Aug, 2019 1 commit
- Added W-H combining rule · 7a791b94
  Chengwen Liu authored Aug 22, 2019
  
  7a791b94
21 Aug, 2019 1 commit
- Added Amoeba vdW softcore tests to both the reference and Cuda platforms · 9c95f25c
  Michael Schnieders authored Aug 21, 2019
  
  9c95f25c
19 Aug, 2019 1 commit
- AMOEBA vdW softcore is propogated through the Reference platform; pending some... · 36ad9ee7
  Michael Schnieders authored Aug 19, 2019
```
AMOEBA vdW softcore is propogated through the Reference platform; pending some feedback adding it to the CUDA code can begin
```
  36ad9ee7
12 Apr, 2019 2 commits
- 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

24 Mar, 2017 1 commit
- Use C++11 style loops · 083bc501
  peastman authored Mar 24, 2017
  
  083bc501
01 Mar, 2017 1 commit
- Fixed bugs in multipoles with ZOnly axis type · 14ea45bc
  Peter Eastman authored Feb 28, 2017
  
  14ea45bc
20 Jan, 2017 1 commit
- CUDA Extrapolated polaraization test now obeys precision argument, and handles... · 0699dea8
  Andy Simmonett authored Jan 20, 2017
```
CUDA Extrapolated polaraization test now obeys precision argument, and handles finite difference checks appropriately.
```
  0699dea8
19 Jan, 2017 1 commit

Trivial changes to AMOEBA plugin. · 1a2cf81e

Andy Simmonett authored Jan 19, 2017

o Variable renaming in multipole electrostatics code, to avoid confusion.
o CUDA test case only runs finite difference test for the double precision test.

1a2cf81e

22 Nov, 2016 1 commit
- Fixed bug with ZBisect axis type in AmoebaMultipoleForce · 308534a7
  Peter Eastman authored Nov 22, 2016
  
  308534a7
05 Jul, 2016 1 commit
- Removed the monopole contribution from the total dipole function, modified the tests accordingly. · 92d86ead
  Saurabh Belsare authored Jul 05, 2016
  
  92d86ead
01 Jul, 2016 1 commit
- Added tests for getLabFramePermanentDipoles and getTotalDipoles · 882de410
  Saurabh Belsare authored Jun 30, 2016
  
  882de410
16 Jun, 2016 1 commit
- Fixed compilation error on Windows · 4cf59381
  peastman authored Jun 16, 2016
  
  4cf59381
21 Apr, 2016 1 commit
- Unified names of platform properties · f12cb008
  Peter Eastman authored Apr 21, 2016
  
  f12cb008
20 Apr, 2016 1 commit
- CUDA implementation of periodic boundary conditions for AMOEBA bonded forces · 713cc0f9
  Peter Eastman authored Apr 20, 2016
  
  713cc0f9
14 Jan, 2016 1 commit
- CUDA implementation of GK with extrapolated polarization · e47f3ae1
  Peter Eastman authored Jan 13, 2016
  
  e47f3ae1
13 Jan, 2016 1 commit
- Finished CUDA implementation of PME with extrapolated polarization · 3bb595ce
  Peter Eastman authored Jan 13, 2016
  
  3bb595ce
07 Jan, 2016 1 commit
- Continuing CUDA implementation of extrapolated polarization · c2ea6c28
  Peter Eastman authored Jan 07, 2016
  
  c2ea6c28
03 Sep, 2015 1 commit
- Added AmoebaMultipoleForce::getPMEParametersInContext() · b20fe9a6
  peastman authored Sep 03, 2015
  
  b20fe9a6
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
20 Aug, 2015 1 commit
- CUDA implementation of spherical harmonics w/o PME · 474f600e
  peastman authored Aug 20, 2015
  
  474f600e
12 Aug, 2015 1 commit
- Show fewer warnings on Visual Studio · 7509c2bf
  Peter Eastman authored Aug 12, 2015
  
  7509c2bf
23 Feb, 2015 2 commits
- Cleaned up formatting in AMOEBA code · d95b90b9
  peastman authored Feb 23, 2015
  
  d95b90b9
- Deleted more debugging code · a568bb12
  peastman authored Feb 23, 2015
  
  a568bb12
08 Feb, 2015 2 commits
- Remove default and kludgey way to half-support backwards compatibility. · 8a01b345
  Jason Swails authored Feb 07, 2015
```
Update the Python application layer to use both force constants when building
the AmoebaStretchBendForce.
```
  8a01b345
- Update the CUDA Amoeba stretch-bend test with the same computeStretchBend as the · 104e827e
  Jason Swails authored Feb 07, 2015
```
one in the Reference platform (pulled over via meld to limit possible mistakes).
```
  104e827e
05 Feb, 2015 1 commit
- Finished CUDA implementation of triclinic boxes for AmoebaMultipoleForce · 5b846af6
  Peter Eastman authored Feb 05, 2015
  
  5b846af6
08 Jan, 2015 1 commit
- AmoebaVdwForce works with triclinic boxes · 46f7b76b
  Peter Eastman authored Jan 08, 2015
  
  46f7b76b
12 Aug, 2014 1 commit
- Fixed an overly strict test case · 8ffe6559
  peastman authored Aug 12, 2014
  
  8ffe6559
05 Dec, 2013 1 commit
- More fixes for problems on OS X 10.9 · 2cd817b4
  peastman authored Dec 04, 2013
  
  2cd817b4
07 Nov, 2013 1 commit
- Fixed compilation errors on OS X 10.9 · 9a26412b
  peastman authored Nov 07, 2013
  
  9a26412b