Code

RMG-Cat!!!#1537

Code

Merged

mliu49 merged 97 commits intomasterReactionMechanismGenerator/RMG-Py:masterfrom catmergeReactionMechanismGenerator/RMG-Py:catmergeCopy head branch name to clipboardApr 25, 2019

+8,689-226

Commits

Commits on Apr 25, 2019

• Add atomtypes X, Xv, and Xo for surface sites.

  Show description for b617d1d
  

  rwest

  authored and

  mliu49

  committed
  b617d1d

• Added Species.isSurfaceSpecies() method

  Show description for 53a3fcd
  

  rwest

  authored and

  mliu49

  committed
  53a3fcd

• Make containsSurfaceSite() and add isSurfaceSite()

  Show description for 95eacc6
  

  rwest

  authored and

  mliu49

  committed
  95eacc6

• Some unit tests for Group.containsSurfaceSite and .isSurfaceSite

  

  rwest

  authored and

  mliu49

  committed
  7045542

• Made a SurfaceRateCoefficient Quantity

  Show description for 2801e68
  

  rwest

  authored and

  mliu49

  committed
  2801e68

• Made a 'surface' module in rmgpy.kinetics

  Show description for 6e29878
  

  rwest

  authored and

  mliu49

  committed
  6e29878

• Copy liquid solver to surface solver.

  Show description for c9a7ec9
  

  rwest

  authored and

  mliu49

  committed
  c9a7ec9

• Convert LiquidReactor into SurfaceReactor.

  Show description for 139787d
  

  rwest

  authored and

  mliu49

  committed
  139787d

• Surface solver updated.

  

  rwest

  authored and

  mliu49

  committed
  1f1ed53

• Some more imports in solver/__init__

  

  rwest

  authored and

  mliu49

  committed
  0584ec4

• Copied simpleTest to surfaceTest for unit testing the SurfaceReactor

  

  rwest

  authored and

  mliu49

  committed
  f7dc247

• Changed whitespace and linebreaks in surfaceTest.py

  Show description for 19b192e
  

  rwest

  authored and

  mliu49

  committed
  19b192e

• Turned surfaceTest into a real surfaceTest

  Show description for 05a6a22
  

  rwest

  authored and

  mliu49

  committed
  05a6a22

• Add a CH3 adsorption test to rmgpy/solver/surfaceTest.py

  Show description for b4cdd58
  

  rwest

  authored and

  mliu49

  committed
  b4cdd58

• Made an input file for testing surface jobs.

  Show description for 6e44aad
  

  rwest

  authored and

  mliu49

  committed
  6e44aad

• Don't adsorb molecules that are already adsorbed.

  Show description for 159e8ac
  

  rwest

  authored and

  mliu49

  committed
  159e8ac

• Draw surface bonds vertically upwards

  Show description for 13a692e
  

  rwest

  authored and

  mliu49

  committed
  13a692e

• Draw monoatomic adsorbates vertically above surface site.

  

  rwest

  authored and

  mliu49

  committed
  4109c01

• Colour the surface site X atoms when drawing.

  Show description for cd83615
  

  rwest

  authored and

  mliu49

  committed
  cd83615

• Approximate Cp0 and CpInf for adsorbed species.

  Show description for b74f17e
  

  rwest

  authored and

  mliu49

  committed
  b74f17e

• Ensure desorption has a gas phase species.

  Show description for 457d41a
  

  rwest

  authored and

  mliu49

  committed
  457d41a

• Tweak alignment of images in HTML output.

  Show description for a56172e
  

  rwest

  authored and

  mliu49

  committed
  a56172e

• Preserve 'X' in chemkin species names for surface species.

  Show description for 84609b6
  

  rwest

  authored and

  mliu49

  committed
  84609b6

• Try parsing STICK lines when reading chemkin files

  

  rwest

  authored and

  mliu49

  committed
  fe1ceb0

• Input file for catalytic combustion of methane.

  Show description for 48a3496
  

  cfgoldsmith

  authored and

  mliu49

  committed
  48a3496

• Prevent gas reaction template matching adsorbate and vice versa.

  Show description for 61e93c3
  

  rwest

  authored and

  mliu49

  committed
  61e93c3

• Allow it to draw vdW-adsorbed molecules

  Show description for 3d9ab8a
  

  rwest

  authored and

  mliu49

  committed
  3d9ab8a

• Don't estimate transport properties for surface species.

  Show description for 0455a54
  

  rwest

  authored and

  mliu49

  committed
  0455a54

• Don't crash drawing physisorbed H2

  

  rwest

  authored and

  mliu49

  committed
  467e99f

• Facilitate using 'eV/molecule' for energy units

  Show description for 5fa87e7
  

  rwest

  authored and

  mliu49

  committed
  5fa87e7

• adsorption.py testing database file copied from RMG-database repo.

  Show description for 3177452
  

  mazeau

  authored and

  mliu49

  committed
  3177452

• trying to make separate chemkin files for surface and gas reactions

  

  mazeau

  authored and

  mliu49

  committed
  ee2e32e

• Chemkin writing checks Arrhenius units (but ignores SurfaceArrhenius)

  Show description for 4fe26e9
  

  rwest

  authored and

  mliu49

  committed
  4fe26e9

• Chemkin file writing for surface models.

  

  rwest

  authored and

  mliu49

  committed
  bb58519

• If cantera conversion fails, try again without Transport data file.

  Show description for a8b1d23
  

  rwest

  authored and

  mliu49

  committed
  a8b1d23

• Generates Cantera files for surface (heterogeneous) systems.

  Show description for cabb58a
  

  rwest

  authored and

  mliu49

  committed
  cabb58a

• Prevent resonance structure generation from making charged adsorbates.

  Show description for b1934cf
  

  rwest

  authored and

  mliu49

  committed
  b1934cf

• Don't check collision limit violations for surface reactions.

  Show description for 77893ba
  

  rwest

  authored and

  mliu49

  committed
  77893ba

• In databaseTest don't check surface reactions for reasonable rates.

  Show description for df927a7
  

  rwest

  authored and

  mliu49

  committed
  df927a7

• Reaction families and database can take SurfaceArrhenius, StickingCoefficient

  Show description for 8de0c41
  

  rwest

  authored and

  mliu49

  committed
  8de0c41

• Adding special termolecular treatment for bidentate surface reactions.

  Show description for 95d48ca
  

  rwest

  authored and

  mliu49

  committed
  95d48ca

• Surface testing input file updates

  

  rwest

  authored and

  mliu49

  committed
  51e2b07

• SurfaceReactor can now be loaded in rmgpy/tools/loader

  

  rwest

  authored and

  mliu49

  committed
  dfff29b

• Add m^4/(mol^2*s) units for SurfaceRateCoefficient

  Show description for 0aefb52
  

  rwest

  authored and

  mliu49

  committed
  0aefb52

• Add StickingCoefficientBEP and SurfaceArrheniusBEP kinetics.

  Show description for 677395b
  

  rwest

  authored and

  mliu49

  committed
  677395b

• ConsistencyChecker skips atom X (surface site)

  

  rwest

  authored and

  mliu49

  committed
  5d95c63

• Molecule.updateCharge gives surface sites zero charge

  

  rwest

  authored and

  mliu49

  committed
  45632f5

• Surface sites aren't given lone pairs.

  

  rwest

  authored and

  mliu49

  committed
  29a4a9a

• Reaction has isSurfaceReaction and getSurfaceRateCoefficient

  

  rwest

  authored and

  mliu49

  committed
  952b392

• rmgpy.kinetics module imports surface rate types

  Show description for 96933bf
  

  rwest

  authored and

  mliu49

  committed
  96933bf

• Can read input files describing surface reactors.

  

  rwest

  authored and

  mliu49

  committed
  d8e45c0

• adding terminationRateRatio to surface reactor

  

  mazeau

  authored and

  mliu49

  committed
  44f0654

• Estimate thermo for adsorbates.

  Show description for 87f4b0b
  

  rwest

  authored and

  mliu49

  committed
  87f4b0b

• Correct binding energies using Linear Scaling Relationships

  

  rwest

  authored and

  mliu49

  committed
  a7a3ccb

• Can read binding energies (for linear scaling relationships) from input file

  Show description for 636c914
  

  rwest

  authored and

  mliu49

  committed
  636c914

• Simple unit test for Molecules containing surface sites

  

  rwest

  authored and

  mliu49

  committed
  cd0cd03

• EVERYTHING ELSE from cat branch

  

  rwest

  authored and

  mliu49

  committed
  af19fb0

• Try checking Cython code in test coverage reports.

  Show description for 8fa5324
  

  rwest

  authored and

  mliu49

  committed
  8fa5324

• databaseTest checks units for surface reaction libraries

  Show description for 15714f8
  

  rwest

  authored and

  mliu49

  committed
  15714f8

• More helpful debugging message in databaseTest.

  Show description for 1ede04e
  

  rwest

  authored and

  mliu49

  committed
  1ede04e

• Example input files reflect new reaction library organization.

  Show description for 1fb6145
  

  rwest

  authored and

  mliu49

  committed
  1fb6145

• Moved example input files into examples/rmg/catalysis

  

  rwest

  authored and

  mliu49

  committed
  72cf85d

• change database tests to list all errors in a test before failing

  

  mjohnson541

  authored and

  mliu49

  committed
  0eb061b

• Updated default binding energies for Pt(111).

  Show description for 2e4bc8c
  

  rwest

  authored and

  mliu49

  committed
  2e4bc8c

• Updating example input files.

  

  rwest

  authored and

  mliu49

  committed
  c306f2c

• change generateReactions processing to use a list of groups/logic nodes instead of entries

  

  mjohnson541

  authored and

  mliu49

  committed
  d688028

• Copied the liquid file to surface.rst

  Show description for a132677
  

  mazeau

  authored and

  mliu49

  committed
  a132677

• Added surfaces.rst to index

  

  mazeau

  authored and

  mliu49

  committed
  9375e4c

• Outlined what we need in documentation

  

  rwest

  authored and

  mliu49

  committed
  b555698

• Added examples to surfaces documentation

  

  rwest

  authored and

  mliu49

  committed
  576fa11

• Added a description of the RMG-Cat specific surface reactors and adsorbate representation to the documentation.

  

  kblondal

  authored and

  mliu49

  committed
  97c872b

• Added descriptions of surface thermo libraries, kinetics libraries and reaction families to RMG-Cat documentation.

  

  kblondal

  authored and

  mliu49

  committed
  0082201

• Added more to the RMG-Cat documentation.

  Show description for d7f2a5e
  

  kblondal

  authored and

  mliu49

  committed
  d7f2a5e

• Added more to the RMG-Cat documentation.

  Show description for 519c872
  

  kblondal

  authored and

  mliu49

  committed
  519c872

• Fix a change that ended up here when rebasing.

  

  rwest

  authored and

  mliu49

  committed
  db8d04a

• Edits so far to catalysis documentation.

  

  rwest

  authored and

  mliu49

  committed
  9a2d5a5

• More edits to catalysis documentation

  

  rwest

  authored and

  mliu49

  committed
  5b0b022

• More edits to surface documentation

  

  rwest

  authored and

  mliu49

  committed
  d4bc4e0

• Added source/_build to documentation/.gitignore

  Show description for ac6fd24
  

  rwest

  authored and

  mliu49

  committed
  ac6fd24

• N scaling is a go... like 90 percent sure

  Show description for 13130f4
  

  mazeau

  authored and

  mliu49

  committed
  13130f4

• Add unit tests for generating reactions in termolecular reaction families

  Show description for ccd58c4
  mliu49

  committed
  ccd58c4

• Added F and I default lone pairs to molecule group.py

  

  alongd

  authored and

  mliu49

  committed
  6dd2e42

• New catalystProperties input file block.

  Show description for 7aafbd9
  

  rwest

  authored and

  mliu49

  committed
  7aafbd9

• Added catalystProperties input file block description to RMG-Cat documentation

  

  kblondal

  authored and

  mliu49

  committed
  3186bc3

• remove core reaction dump from surfaceTest.py

  

  mjohnson541

  authored and

  mliu49

  committed
  9ce21c5

• allow ranged reactors to process surface reactor initial conditions

  

  mjohnson541

  authored and

  mliu49

  committed
  3fe5a8d

• enable filter for surfaceReactor, note this uses gas phase thresholds for now

  

  mjohnson541

  authored and

  mliu49

  committed
  af8e454

• prevent use of filterReactions=True until better values available

  

  mjohnson541

  authored and

  mliu49

  committed
  f62e7c6

• Add to documentation of new catalystProperties block.

  Show description for bf8d763
  

  rwest

  authored and

  mliu49

  committed
  bf8d763

• Tests: Added Atom and Molecule tests

  Show description for a9a9bcb
  

  alongd

  authored and

  mliu49

  committed
  a9a9bcb

• Reduce code duplication.

  Show description for b828b98
  

  rwest

  authored and

  mliu49

  committed
  b828b98

• remove plotting from surfaceTest.py

  

  mjohnson541

  authored and

  mliu49

  committed
  8bd9e13

• Alert users when using default binding energies.

  

  rwest

  authored and

  mliu49

  committed
  e168f43

• Fixed typo for deltaAtomicAdsorptionEnergy

  

  kblondal

  authored and

  mliu49

  committed
  f26dc29

• Automatically update file headers

  mliu49

  committed
  adf1f5a

• add comments to input files.

  

  dranasinghe

  authored and

  mliu49

  committed
  8f4296d

• ensure struct is defined in __matchReactantToTemplate

  

  mjohnson541

  authored and

  mliu49

  committed
  51a8656