Erastova-group/ClayCode

Issues

• handle UCs with substitutions affecting charges across PBC

  #57 opened a year ago by punkpony
  0

• progress bar writes to new line

  #56 opened a year ago by punkpony
  0

• keyword for naming the output folder

  #55 opened a year ago by punkpony
  0

• new built handling of old files

  #54 opened a year ago by punkpony
  0

• if crashes temp files deleted - better keep

  #52 opened a year ago by punkpony
  1

• `Inserting -1 Na atoms`

  #53 opened a year ago by punkpony
  0

• check new UC cells

  #51 opened a year ago by punkpony
  0

• Check input files etc for correct specification indications of UC_INDEX_RATIOS

  #45 opened a year ago by hp115
  0

• allow entry of charge value as '+4'

  #50 opened a year ago by punkpony
  0

• split IL ions to be added above and below

  #48 opened a year ago by punkpony
  0

• make builder/tests a developer test only

  #49 opened a year ago by punkpony
  0

• `BOX_HEIGH: 0` handling

  #47 opened a year ago by punkpony
  0

• claycode documentations + tutorials online

  #46 opened a year ago by punkpony
  0

• Make sure FF files are in final output topology files

  #27 opened a year ago by punkpony
  0

• repeat solvation loop small display issue

  #36 opened a year ago by punkpony
  0

• interlayer solvation issues - leads to a crash of EM

  #26 opened a year ago by punkpony
  4

• .log file for ClayCode run

  #34 opened a year ago by punkpony
  1

• Decide what FFs to share

  #44 opened a year ago by punkpony
  1

• asking for csv when provided UC_INDEX_LIST and _RATIOS

  #43 opened a year ago by punkpony
  1

• IL_SOLV: False should ignore any other IL entries

  #38 opened a year ago by punkpony
  0

• check .csv to match clay compositions

  #23 opened a year ago by punkpony
  1

• clean up the test yaml & csv into a separate dir

  #29 opened a year ago by punkpony
  0

• Clean up the ClayCode - remove things that do not belong

  #32 opened 2 years ago by punkpony
  1

• tutorial/ user guide work

  #24 opened 2 years ago by punkpony
  1

• Add simulation input generator

  #9 opened 2 years ago by hp115
  1

• Force fields for release

  #33 opened 2 years ago by punkpony
  0

• `GROMACS raised error code 1!` <- unclear

  #37 opened 2 years ago by punkpony
  0

• output to the screen during run

  #35 opened 2 years ago by punkpony
  0

• Share data between analysis and setup code

  #2 opened 2 years ago by hp115
  1

• file path to .csv is relative to where code is run from, not the location of .yaml

  #31 opened 2 years ago by punkpony
  0

• calling gmx from ClayCode fails silently for Linux

  #28 opened 2 years ago by punkpony
  1

• Make Tutorial + Examples folder

  #16 opened 2 years ago by punkpony
  1

• add unit testing w pytest

  #25 opened 2 years ago by punkpony
  0

• branches keep tidy

  #30 opened 2 years ago by punkpony
  0

• Fix ClayCode builder run

  #15 opened 2 years ago by hp115
  1

• Add warnings

  #17 opened 2 years ago by punkpony
  0

• write screen output into a .log

  #20 opened 2 years ago by punkpony
  0

• Change IL ion specifications

  #21 opened 2 years ago by hp115
  0

• check reason for crash when assembling MMT UCs

  #22 opened 2 years ago by punkpony
  1

• Add analysis to ClayCode

  #1 opened 2 years ago by hp115
  2

• Allow for charges to be a little bit off from the target - add warning

  #19 opened 2 years ago by punkpony
  0

• Add UCs for MMT

  #3 opened 2 years ago by punkpony
  2

• check UC matching by the size (e.g 5% diff acceptable)

  #18 opened 2 years ago by punkpony
  0

• Fix ClayCode installation procedure

  #14 opened 2 years ago by hp115
  0

• Model setup no longer from config/buildprms.py

  #5 opened 2 years ago by hp115
  1

• Add clay setup as builder

  #4 opened 2 years ago by hp115
  0

• target stoics vs result stoichiometry check

  #7 opened 2 years ago by punkpony
  1

• Add docstrings

  #8 opened 2 years ago by hp115
  0

• user input file - move out from config/buildprm.py

  #6 opened 2 years ago by punkpony
  0