Commits · 83e921314a32606bef96311f5e1f91db74021e3c · tsoc / openmm

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24 Sep, 2020 1 commit
- Minor optimizations to CUDA kernels (#2861) · 938afab0
  peastman authored Sep 24, 2020
  
  938afab0
28 Aug, 2020 1 commit
- Fixed uninitialized memory (#2819) · cea03eea
  peastman authored Aug 27, 2020
  
  cea03eea
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

23 Mar, 2020 1 commit

Remove unused variables (#2605) · a752d258

Alex Henrie authored Mar 23, 2020

* Remove unused variable from CpuCustomGBForce::calculateIxn

* Remove unused variable from CpuCalcCustomManyParticleForceKernel::initialize

* Remove unused variable from CudaCalcCustomCVForceKernel::initialize

* Remove unused variable from ReferenceCalcCustomManyParticleForceKernel::initialize

* Remove unused variables from ReferenceObc::computeBornEnergyForces

* Remove unused variable from AmoebaTorsionTorsionForceProxy::serialize

a752d258

28 Feb, 2020 1 commit
- Remove CUDA kernels · 5adf0871
  Andy Simmonett authored Feb 27, 2020
  
  5adf0871
21 Feb, 2020 1 commit
- NonbondedForce can optionally apply periodic boundary conditions to exceptions · ae07d525
  peastman authored Feb 21, 2020
  
  ae07d525
08 Jan, 2020 1 commit

Common compute framework to unify CUDA and OpenCL code (#2488) · edbc8407

peastman authored Jan 08, 2020

* Began creating common compute framework to unify code between CUDA and OpenCL

* Began OpenCL implementation of common compute framework

* Common implementation of CMMotionRemover

* CUDA implementation of common compute interface

* Converted HarmonicBondForce to common compute API

* Converted standard bonded forces to common compute API

* Converted ExpressionUtilities to common compute API

* Created ComputeParameterSet

* Converted custom bonded forces to common compute API

* Converted CustomCentroidBondForce to common compute API

* Converted CustomManyParticleForce to common compute API

* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext

* Converted GayBerneForce to common compute API

* Removed obsolete kernels

* Converted verlet integrators to common compute API

* Converted Langevin and Brownian integrators to common compute API

* Converted CustomIntegrator to common compute API

* Converted CustomNonbondedForce to common compute API

* Removed uses of a deprecated API

* Fixed failing test cases

* Converted GBSAOBCForce to common compute API

* Began converting CustomGBForce to common compute API

* Finished converting CustomGBForce to common compute API

* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities

* Converted RMSDForce and AndersenThermostat to common compute API

* Converted CustomHbondForce to common compute API

* Merged scripts for encoding kernel sources

* Converted Drude plugin to common compute API

* Fixed errors in CMake scripts

* Attempt at fixing errors on Windows

* Added discussion of common compute API to developer guide

* Added Windows export macro for common classes

* Fixed error in CMMotionRemover

* Ubdated travis to newer Ubuntu version

* Fixed errors on CPU OpenCL

* Fixed Windows linking errors

* Added missing pragma for 32 bit atomics

* Replaced long long with mm_long

* More fixes to Windows linking

* Bug fix

edbc8407

11 Dec, 2019 2 commits
- Clean up reference code, fix silly CUDA bug I just introduced · 2c78200c
  Andy Simmonett authored Dec 11, 2019
  
  2c78200c
- Fix OpenCL and CUDA kernels after review · 88224d12
  Andy Simmonett authored Dec 11, 2019
  
  88224d12
04 Dec, 2019 1 commit
- Fix array resize problems in Cuda and OpenCL kernels · 0e396127
  Andy Simmonett authored Dec 04, 2019
  
  0e396127
15 Nov, 2019 1 commit
- Apply more cleanup after last review round. · 79ed6274
  Andy Simmonett authored Nov 15, 2019
  
  79ed6274
12 Nov, 2019 1 commit
- Add CUDA and OpenCL hardwall constraints and Drude integration with serialization · 7f1dd6a3
  Andy Simmonett authored Nov 12, 2019
  
  7f1dd6a3
25 Oct, 2019 1 commit
- Avoid unnecessary force evaluation when computing kinetic energy · 88209091
  Peter Eastman authored Oct 25, 2019
  
  88209091
24 Oct, 2019 9 commits
- Correct CUDA NHC implementation · cca3e11a
  Andy Simmonett authored Aug 27, 2019
  
  cca3e11a
- Start implementing changes from review - CUDA broken · 50efef13
  Andy Simmonett authored Aug 14, 2019
  
  50efef13
- Add Drude Nose-Hoover capability, with tests · f5df1076
  Andy Simmonett authored May 29, 2019
  
  f5df1076
- Nose-Hoover chain no longer derives from Force · 182f7f15
  Andy Simmonett authored May 22, 2019
  
  182f7f15
- Fix mixed precision bead propagation · 388704e7
  Andy Simmonett authored May 17, 2019
  
  388704e7
- Nose-Hoover working on CUDA · 6307eb0d
  Andy Simmonett authored May 16, 2019
  
  6307eb0d
- Nose-Hoover chain propagation works on CUDA · 799d4b1f
  Andy Simmonett authored May 14, 2019
  
  799d4b1f
- Add Nose-Hoover chain serialization on CUDA · 6278ef5f
  Andy Simmonett authored May 14, 2019
  
  6278ef5f
- Add Cuda velocity verlet implementation, correct virtual site computation · 6ed75b19
  Andy Simmonett authored May 13, 2019
  
  6ed75b19
18 Oct, 2019 1 commit
- Bug fixes to BAOABLangevinIntegrator · bc71de2c
  Peter Eastman authored Oct 18, 2019
  
  bc71de2c
08 Oct, 2019 1 commit
- CUDA implementation of BAOABLangevinIntegrator · a4bf00ee
  Peter Eastman authored Oct 08, 2019
  
  a4bf00ee
01 Oct, 2019 1 commit
- Make sure correct CUDA context is current · 2f6a3569
  Peter Eastman authored Oct 01, 2019
  
  2f6a3569
10 Sep, 2019 1 commit
- Added max step size option to variable step size integrators · 0620a02f
  peastman authored Sep 10, 2019
  
  0620a02f
14 Jun, 2019 1 commit
- CustomCVForce applies ForceInfos from inner context to the outer one · ab92c8ed
  Peter Eastman authored Jun 14, 2019
  
  ab92c8ed
11 Jun, 2019 1 commit
- Fixed race condition · dbbf7c3e
  Peter Eastman authored Jun 11, 2019
  
  dbbf7c3e
07 Jun, 2019 1 commit
- Revised how exclusions are computed with PME · da28ce0e
  Peter Eastman authored Jun 07, 2019
  
  da28ce0e
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

11 Feb, 2019 1 commit
- Bug fix · 588e5540
  Peter Eastman authored Feb 11, 2019
  
  588e5540
09 Feb, 2019 1 commit
- Fixed inconsistency in computing Ewald self energy · e9a2857a
  Peter Eastman authored Feb 08, 2019
  
  e9a2857a
23 Jan, 2019 1 commit
- Fixed error using tabulated functions with a CustomGBForce · 596be80f
  Peter Eastman authored Jan 23, 2019
  
  596be80f
11 Nov, 2018 1 commit
- Fixed potential uninitialized memory error setting up PME stream · 0e821614
  Peter Eastman authored Nov 11, 2018
  
  0e821614
30 Oct, 2018 1 commit
- Use separate events for different stream synchronizations · f03d9ae2
  Peter Eastman authored Oct 30, 2018
  
  f03d9ae2
26 Oct, 2018 1 commit
- Possible(?) fix for PME energy error · de4c93f8
  Peter Eastman authored Oct 26, 2018
  
  de4c93f8
10 Oct, 2018 1 commit
- Fixed error in parameter offsets for nonbonded exceptions · d1c6b858
  Peter Eastman authored Oct 10, 2018
  
  d1c6b858
04 Oct, 2018 1 commit
- Fix uninitialized variable when Coulomb terms are missing · 1f2697a1
  Andy Simmonett authored Oct 04, 2018
  
  1f2697a1
23 Sep, 2018 1 commit
- Fixed bugs in particle parameter offsets · b4c0bf3e
  peastman authored Sep 23, 2018
  
  b4c0bf3e
21 Sep, 2018 1 commit
- Fix OpenCL LJPME energy bug · c1025b3f
  Andy Simmonett authored Sep 21, 2018
  
  c1025b3f