README 816 B

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  1. The files in this directory test various aspects of reactions. These are
  2. derived from the tests I used for validation against old mcell behavior, as
  3. well as against Boris' trimolecular code when I merged with macromolecules.
  4. I'll give a summary below of what each file is, with more detailed information
  5. in the header of each MDL file.
  6. Note that most files which use the trimolecular pathway have TIME_STEP_MAX set
  7. to 1.0. They all should, I think. The trimolecular code doesn't seem to
  8. safely use safe_diffusion_step, so in order to make fair comparisons for
  9. correctness, I turned off adaptive timesteps.
  10. * Test 01: All volume rxn types, traditional + trimol. code paths
  11. * Test 02: Same as test 1, but without ACCURATE_3D_REACTIONS
  12. * Test 06: All surface rxn types (vol surf, surf surf, vol vol surf, etc.)