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Commits on Jan 30, 2016
  1. Update sourceforge web pages

    connie committed Jan 30, 2016
Commits on Sep 29, 2015
  1. Add more forbidden groups to Diels_alder for preventing 1 double bond…

    … in aromatic from being part of diene
    
    This prevents molecules like styrene from breaking aromaticity
    connie committed Sep 29, 2015
Commits on Sep 28, 2015
  1. Add benzene to forbidden groups as both diene and dienophile in Diels…

    …_alder_addition family
    connie committed Sep 28, 2015
Commits on Sep 23, 2015
Commits on Sep 20, 2015
Commits on May 20, 2015
  1. Caleb's sulfur libraries

    connie committed Apr 22, 2015
  2. Some fixes to thermo groups.

    -Remove duplicate Ss-CsCd group.
    -Point Cs-COsOsSs to its child in library
    connie committed May 19, 2015
Commits on May 13, 2015
Commits on Apr 22, 2015
Commits on Mar 18, 2015
Commits on Feb 27, 2015
Commits on Nov 13, 2014
  1. Bugfixes to H_Abstraction.

    Removed O_rad/Cd\H_Cd\H\Cs|Cs group since it was identical
    to O_rad/Cd\H_Cd\H\Cs.  It was not in the tree anyway.
    
    Also changed GAV rate rule 4044's alpha value to 0 which seemed like
    a typo.
    connie committed Nov 13, 2014
  2. Fixes to some groups in R_Addition_Multiple_Bond.

    Fixes the bugs from 45228e8
    
    The ligands were correctly named to Ct, but their connectivity makes
    these groups invalid, so the bonds were changed from double to triple.
    connie committed Nov 13, 2014
Commits on Nov 12, 2014
Commits on Nov 6, 2014
Commits on Oct 2, 2014
  1. Include species names when reading thermo data estimator species lists.

    Main reason is to improve utility of error messages (eg. when
    you have the same chemgraph in the file more than once). 
    Hopefully there are no unintended negative consequences.
    rwest committed Oct 2, 2014
Commits on Sep 16, 2014
  1. Few additional rate rules for intra H migrations. Mainly related to t…

    …he currently discovered pathways to benzene from butadiene + allyl.
    agvandeputte committed with shamelmerchant Sep 16, 2014
Commits on Aug 18, 2014
  1. Correcting Alkene+OH addition arte coefficient

    The previous estimate was x10 too fast, not sure what went wrong.
    Probably when I flipped it using the thermochemistry it resulted
    in an error. Replacing the rate by Zador et al. propene + OH
    rate coefficient.
    shamelmerchant committed Aug 18, 2014
Commits on Jul 14, 2014
  1. New criterium for intra_R_Add_Endocyclic and intra_R_Add_exocyclic

    Consider only addition reactions when the rad and double bond are not part
    of two different rings that have 2 or more atoms in common.x
    agvandeputte committed with shamelmerchant Jul 13, 2014
Commits on Jul 7, 2014
  1. Adding the option to set max C atoms for a Pdep Network

    This option provides more flexibility to determine if we need
    to treat a reaction as pressure dependent. Ideally we should not
    recommend using this option since whether to treat a reaction as
    Pdep or not depends on the total number of atoms in a reaction (i.e net degree
    of freedome determines whether a molecule can undergo internal relaxation).
    
    However for some practical consideration when your fuel is unsaturated
    and leads to a lot of aromatic species (mostly heavy atoms due to decrease
    in saturation) we might want to specify the Carbon number or total number of
    Heavy atoms (not yet implemented).
    shamelmerchant committed Jul 7, 2014
  2. Made small changes to the thermolibraries.

    a) Modified the Cd-(Cd)(Cd) thermo group which appears to be 7 kcal/mol too low
    b) Added a HBI for indenyl
    c) Added ring correction for cycloheptatetraene
    agvandeputte committed with shamelmerchant Jul 7, 2014
  3. Fixing missing thermo comments

    Because we made a copy of the chemgraph to get the thermo and
    were calling the comments from this new graph, there were cases - when the
    molecule was not aromatic it would return an empty string.
    
    We now only call the comments from the thermo_graph if the species is aromatic and not present in a thermo library.
    
    Sigh another Sunday (10:00 pm) bug fix!
    shamelmerchant committed Jul 7, 2014