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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file.

[2.70] - 10/13/2020

  • This release forcues on GPU performance improvements
  • Using Random123 to be able to generate the same random number on GPU and port Translation and Rotation of molecules to the GPU
  • Upgraded to C++14
  • Lots of bug fixes
  • Upgraded our CMake to 3.8 and use built-in CUDA support

[2.60] - 6/16/2020

  • Changed the way we calculate pair interactions. The new approach allows us to optimize GPU by reducing the amount of cudaMemcpy needed.
  • Added C++11 support to our code base and removed any using namespace std; statements.
  • GPU memory management class to watch the allocation and deallocation of GPU memories.
  • Bug fixes related to lambda functionalities on GPU

[2.51] - 4/30/2020

  • Fixed a bug with EwaldCached
  • Fixed a warning due to ignoring return value of fscanf

[2.50] - 1/20/2020

  • Addes support for force biased multiparticle move
  • Added support for free energy calculations using TI and FEP methods
  • Support for multiple simulation with different temperatures using MPI
  • Added support for Exponential-6 forcefield
  • Support for restarting simulation using checkpoint
  • Added support for new GPU architectures 7.0 and 7.5
  • Added an error message when GPU version was used but there was no GPU present (#126)
  • Read PDB file more efficiently when recalculating trajectory (#131)
  • Fixed detecting simulation box shape (orthogonal and non-orthogonal) (#134)
  • Fixed bugs in PDB reader and support for HETATM field in PDB file
  • Fixed bugs in PSF reader
  • Fixed Case sensitive keywords (#100)
  • Fixed the timing report on Windows (#89)
  • Added minimum volume in case the difference in box sizes were large (#94)
  • Fixed the issue where cutoff value is larger than half of minimum box length (#98)
  • Added an error message when charges detected and ewald was set to false (#99)
  • Fixed compiling issue on Visual Studio (#110)
  • Fixed the issue where GOMC did not read CHARMM parameter files missing Urey-Bradley terms (#147)
  • Reduced GOMC reposity size

[2.40] - 3/15/2019

  • Added support for Cyclic molecules.
  • Added Inter Molecular Exchange Monte Carlo move in GCMC and GEMC simulation.
  • Added Intra Molecular Exchange Monte Carlo move.
  • Added Crankshaft move.
  • Added separate cutoff for short range electrostatic, for each simulation box.
  • Added reporting the molecule density value for each species.
  • Added support to process the configuration file's keyword with case-insensitive.
  • Changed printing format to scientific mode.
  • Fixed the overlap detection with hard cutoff value.
  • Fixed a bug where, cutoff value was greater than half of the box length and no error was generated.
  • Fixed to the bug in the updating adjustable value in MoveSetting, when we have more than one component.
  • Fixed to the bug in GPU pressure calculation for NPT simulation.
  • Fixed a bug where we were selecting invalid box. This was caused by double precision error.

[2.31] - 5/21/2018

  • Compiling problem fixed on CYGWIN
  • Fix to the error checking of volume exchange if simulation volume became negative
  • Fix the equation to impose fix angle if the angle is less than 90. Generate error if constrained angle is not possible.
  • Fixed a bug where move timings were 0 in windows.
  • Fixed the issue where input files imported from NVT to NPT had zero volume, default value of 500 will be assigned in those cases.

[2.30] - 5/10/2018

  • Added Regrowth move
  • Cleaned up the code and removed any memory leaks and bugs.
  • Redesigned Ewald, EwaldCached, and NoEwald to be more efficient and allocate less memory.
  • Added an error when multiple atoms have zero coordinates.
  • Added an error when resorvoir is empty and should print an error message and exit.
  • Fixed some typo in output.
  • Fix a bug where seed number output and input was not the same size, so we changed int to uint while reading to avoid overflow. They both use uint now.
  • Increase memory allocation for NPT simulation in Ewald.
  • Fixed a bug in PickWeighted() function where it was return a value larger than the array.
  • Printing individual timing information for each move.
  • To avoid getting large energy we are recalculating the total system at equilbrium step.
  • Print CBMC information including first atom trial, secondary atom trials, angle trials, and dihedral trials.
  • Fix a bug where in windows the clock() function was returning a wrong value
  • Fix compiler warning for macOS in ConfigSetup file

[2.20] - 1/2/2018

  • Non orthogonal implementation
  • Removed CUB library from our source code and we will automatically download CUB library before compiling (newest version all the time!).
  • Removed compute_20 and compute_21 since they are depricated and CUDA 9 will generate fatal error.
  • Fixed a problem where the input reader will skip random_seed because there was a "info" print in an "else if" and would block anything after that.
  • Fixed a bug in MoveSettings where two for loops where not initialized.
  • Fixed a bug where in simulation of polar molecules, if any atom of the molecule has no VDW parameter (e.g. water), there is a chance that during insertion, atom of opposite charge will overlap and generate a very large energy value. Current mechanism of avoiding overlap is not working properly
  • Fixed a bug where STDOUT was printing out garbage because input reader was passing empty vector.
  • Fixed a problem where we were receiving seg fault at the end of the simulation (removed [] from destructor in Static.cpp).

[2.11] - 9/25/2017

  • Bug fixes

[2.1] - 9/4/2017

  • Adsorption
  • Fixed the bug where GPU and CPU total energy calculations where slighty different.
  • Removed some unused variables
  • Removed some warnings
  • Fixed pow function ambiguity in some compilers like clang
  • Fixed compiling bug for Clock.h when using clang (mac users)
  • Set a maximum of 9999999999 for output energies

[2.0] - 6/11/2017

  • NPT added
  • GPU implementation has been added to the project

[1.9] - 12/12/2016

  • Revision on output. We now only generate one output file.
  • Bug fixes
  • Printing some hardware information
  • Changes to example files which can be found at GOMC_Examples repository

[1.8] - 10/12/2016

  • Parallelizing CBMC branched algorithm using OpenMP
  • Bug Fixes

[1.7] - 04/21/2016

  • Fix the bug of free Ewald class, which returns memory segmentation fault if ewald is not activated. TO DO: IntraSwap does not work properly. The bug is going to be fixed.

##[1.6] - 04/01/2016

  • IntraSwap is added into the code.
  • Blockoutput, fluctoutput are modified to print out ewald energies.
  • Tests of this modification are not done yet.

[1.7] - 03/24/2016

  • I/O fixes

[1.6] - 03/24/2016

  • Code cleaning

[1.5] - 03/24/2016

  • Support for Ewald Summation

##[1.00] - 3/15/2016

  • Fix the bug of GEMC simulation. Now all NVT, GCMC, and GEMC are working.
  • Enable the Cache version of GEMC to save time; however, the scalability is limited.

##[1.00] - 01/25/2016

  • Fix the coherence issue on two boxes simulations, including NPT, GEMC, and two boxes GCMC simulations.

  • To fix the issue, Calp() and SetupRecip() have to be recalculated everytime before and after the volume transfer; RecipSinSum and RecipCosSum arrays have to be synchronized in two boxes simulations; GEMC_NVT is different from GEMC_NPT, the difference between GEMC_NVT and GEMC_NPT requires "if" statement.

? GEMC is returning good result from computation; however, it does not return correct results. A potential bug inside of the computation logic.

[1.1] - 01/20/2016

  • Supporting Martini forcefield

##[1.00] - 12/22/2015

  • Update CPUSide.cpp, move hist into the ifdef of GCMC. Target at the floating operation issue returned by NVT and GEMC simulations.

##[1.00] Ewald branch - 12/8/2015

  • Improve the initialization of Ewald's parameters, so that non-ewald simulation can also run on ewald code without crashing.
  • CMakeList.txt file is added.

##[1.00] - 12/4/2015

  • Added Examples of water and DME for NVT and GCMC
  • Added bin/linux, which contains all executable files for linux

[1.0] - 10/18/2015

  • Changes for input file system.
  • Added Cell list optimization to the GPU and the Serial code.

[0.972] - 5/11/2015

  • Fixes for PDB output for NVT in the GPU code.

[0.971] - 5/6/2015

  • Added missing CMAKE files for GOMC serial.
  • Updates to the test systems to be compatible with the new input formats.

[0.97] - 4/11/2015

  • Added support for grand canonical ensemble.
  • Fixed calculation of angular weights for branched molecules coupled-decoupled configuration bias algorithm.
  • Improved move adjustments for better targeting of desired acceptance rate.
  • Various minor bug fixes for fringe conditions.
  • Improvements to I/O handling, inclusion of new output types relating to grand canonical ensemble (fluctuations, energy/particle samples, and distribution of molecule counts).