Commits · 31abb2f7a34e8ef5c17bc52207fb0d226bf5d703 · tsoc / openmm

02 Nov, 2023 1 commit
- Fixed some incorrect comments (#4294) · 31abb2f7
  Peter Eastman authored Nov 02, 2023
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* Fixed some incorrect comments

* Fixed some incorrect comments

* Fixed typo
```
  31abb2f7
12 Jun, 2023 1 commit
- Attempt at fixing errors with barostat (#4106) · add2bbee
  Peter Eastman authored Jun 12, 2023
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* Attempt at fixing errors with barostat

* Missing ContextSelector
```
  add2bbee
05 May, 2023 1 commit
- Fixed an incorrectly sized array (#4061) · ed049af1
  Peter Eastman authored May 04, 2023
  
  ed049af1
31 Jan, 2023 1 commit
- Use CompiledExpression for CustomCVForce energy expression (#3898) · 17b61225
  Peter Eastman authored Jan 31, 2023
  
  17b61225
30 Jun, 2022 1 commit

Peter Eastman authored Jun 30, 2022

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

1dac981a

27 Jan, 2022 1 commit

CustomNonbondedForce supports computed values (#3412) · 33c694d4

Peter Eastman authored Jan 27, 2022

* Reference implementation of computed values for CustomNonbondedForce

* CPU implementation of computed values for CustomNonbondedForce

* Common implementation of computed values for CustomNonbondedForce

* Serialization of computed values

* ForceField supports computed values

33c694d4

30 Sep, 2021 1 commit
- Barostat does not translate into a single periodic box (#3260) · aa8264d0
  Peter Eastman authored Sep 29, 2021
  
  aa8264d0
28 Feb, 2021 1 commit

Point based geometric functions for custom forces (#3037) · a85c2428

Peter Eastman authored Feb 28, 2021

* Began implementing geometric functions on points

* Started common implementation of point functions

* Completed implementation of point functions for CustomCompoundBondForce

* Implemented point functions for CustomCentroidBondForce

* Implemented point functions for CustomManyParticleForce

* Use point functions to simplify implementation of custom forces

* Removed unnecessary code

* Fixed typo

a85c2428

23 Dec, 2020 1 commit
- Fixed potential out of range index (#2960) · 84132b19
  peastman authored Dec 23, 2020
  
  84132b19
25 Nov, 2020 1 commit
- Fixed error using periodic exceptions with PME (#2935) · b49b82ef
  peastman authored Nov 24, 2020
  
  b49b82ef
27 May, 2020 1 commit
- Added Integrator.setIntegrationForceGroups() · 4a30156a
  peastman authored May 27, 2020
  
  4a30156a
05 May, 2020 1 commit

Minor fixes to Nose Hoover code (#2670) · 389f79e6

peastman authored May 05, 2020

* Fixed OpenCL compiler errors

* Fixed incorrect references to BAOAB

* Fixed a method that was incorrectly made public

389f79e6

04 May, 2020 1 commit

Nosé Hoover Middle scheme (#2600) · 5f374e1d

Andy Simmonett authored May 04, 2020

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default

5f374e1d

14 Apr, 2020 1 commit
- Fixed an edge condition that could cause errors in CMAPTorsionForce · 09d17766
  peastman authored Apr 14, 2020
  
  09d17766
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

21 Feb, 2020 1 commit
- NonbondedForce can optionally apply periodic boundary conditions to exceptions · ae07d525
  peastman authored Feb 21, 2020
  
  ae07d525
14 Feb, 2020 1 commit
- Renamed BAOABLangevinIntegrator to LangevinMiddleIntegrator · 65ee8fd7
  Peter Eastman authored Feb 14, 2020
  
  65ee8fd7
04 Feb, 2020 1 commit
- Converted from BAOAB to leapfrog · ba9f6b0a
  Peter Eastman authored Feb 03, 2020
  
  ba9f6b0a
11 Dec, 2019 1 commit
- Clean up reference code, fix silly CUDA bug I just introduced · 2c78200c
  Andy Simmonett authored Dec 11, 2019
  
  2c78200c
12 Nov, 2019 1 commit
- Add CUDA and OpenCL hardwall constraints and Drude integration with serialization · 7f1dd6a3
  Andy Simmonett authored Nov 12, 2019
  
  7f1dd6a3
07 Nov, 2019 1 commit
- Fix reference pair integrator, implement hardwall constraint with test · 512328b2
  Andy Simmonett authored Nov 07, 2019
  
  512328b2
25 Oct, 2019 1 commit
- Avoid unnecessary force evaluation when computing kinetic energy · 88209091
  Peter Eastman authored Oct 25, 2019
  
  88209091
24 Oct, 2019 7 commits
- Minor cleanup, make chain propagation private · 3251d4e4
  Andy Simmonett authored May 30, 2019
  
  3251d4e4
- Nose-Hoover chain no longer derives from Force · 182f7f15
  Andy Simmonett authored May 22, 2019
  
  182f7f15
- Add Cuda velocity verlet implementation, correct virtual site computation · 6ed75b19
  Andy Simmonett authored May 13, 2019
  
  6ed75b19
- Fix bug in NHC propagation, tests all pass · 63a9e6c2
  Andy Simmonett authored May 11, 2019
  
  63a9e6c2
- Harmonic oscillator works for Nose-Hoover thermostat · 55ff3ecd
  Andy Simmonett authored May 10, 2019
  
  55ff3ecd
- Clean up implementation of NHC, add propagator test · d12f9f89
  Andy Simmonett authored May 10, 2019
  
  d12f9f89
- Initial velocity verlet, with some nose hoover implementation · c692624f
  Andy Simmonett authored May 08, 2019
  
  c692624f
18 Oct, 2019 1 commit
- Bug fixes to BAOABLangevinIntegrator · bc71de2c
  Peter Eastman authored Oct 18, 2019
  
  bc71de2c
07 Oct, 2019 1 commit
- Reference implementation of BAOABLangevinIntegrator · 6aad09c3
  peastman authored Oct 07, 2019
  
  6aad09c3
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

05 Mar, 2019 1 commit
- Optimized building constraint matrix · f24a84f8
  peastman authored Mar 05, 2019
  
  f24a84f8
22 Jan, 2019 2 commits
- Use regular doubles instead of long double. · 885b63c3
  Yutong Zhao authored Jan 22, 2019
  
  885b63c3
- Properly define GBSAOBC alpha beta gamma constants to be doubles. · e8126dd7
  Yutong Zhao authored Jan 22, 2019
  
  e8126dd7
23 Jul, 2018 2 commits
- Optimization to custom forces on CPU · 89f52648
  peastman authored Jul 23, 2018
  
  89f52648
- Optimized CustomCVForce.updateParametersInContext() · fc79cc94
  peastman authored Jul 23, 2018
  
  fc79cc94
17 Jul, 2018 1 commit
- Added CustomCVForce.updateParametersInContext() · 9e0f5f3d
  peastman authored Jul 17, 2018
  
  9e0f5f3d
03 Jul, 2018 1 commit
- Code cleanup to reference and CPU platforms · 9f37b18b
  peastman authored Jul 03, 2018
  
  9f37b18b
27 Apr, 2018 1 commit
- Reference implementation of vector functions for CustomIntegrator · ad285083
  peastman authored Apr 27, 2018
  
  ad285083