WHAM (SMOG 2 version) history

The SMOG 2 distribution provides an implementation of the WHAM algorithms (WHAM.jar) that are generally suited for use with data generated from SMOG models.

Updates

• 1.07
  • increased thread limit to 48
  • fixed bug that was causing cyclical cycles in convergence when using parallelization. Note that if WHAM was able to find convergence it gave correct results. The bug just increased time to convergence.
  • fixed bug that sometimes gave the entropy column of the free energy output relative to a different minimum. Now F=E-TS is always true for the output.
• 1.05
  • umbrellaType harmonicWalls added
  • multiple umbrella reweighting supported
  • faster umbrella implementation (using sparse arrays and indices everywhere)
  • general cleaning of code
• 1.04
  • only extra precision is allowed
  • up to 8 threads supported ( numThreads option)
  • changed how umbrellas are called (numUmbrella and umbrellaType option)
• 1.03
  • converted to SparseArrays everywhere to conserve memory
  • DOS only contains the non-zero bins now
  • sorted the lists in SparseArray* and made accessing them through binarySearches
  • added ability to compute Q2(Q1,T) and Q3(Q1,Q2*,T) with or without umbrella
  • changed the usage text
  • various error checking and usability enhancements
• 1.02
  • fixed bug where 2D high precision free energy plots did not shift to zero (bug also affected 1D in principle, but would rarely show up)
• 1.0
  • initial release

Page created and maintained by Jeff Noel and Paul Whitford