RMG-database v2.1.6 release

Author: mliu49

.travis.yml

@@ -2,44 +2,37 @@ language: python
 sudo: false
 python:
   - "2.7"
-virtualenv:
-    system_site_packages: true
 env:
   global:
     - secure: "L2ja+ZnV83w4qG3E8FwTjm0D6IWNOnj5wuFOjYTwbzQP4OAgLAWBzCMtxzWy5sMxFLtRgkswBH1d5f5kg8Ab7GIyAMFgQwe8UFqMJ+N05QNszE1mJkAvJtv2XN7669XXQhTt5EXfHrCcGZaODVnI2CEA8GB5DxiHO2Lcqf/xvgE="
     - secure: fd2HDrPvxMLHOXar7HyUZh0v+C5WkCfzhRzlBn+aePayrQn5FFrT68ENyr1v4sIpKESxYUOAwqtpDPUhF3M596GgGeU5yQc4q+sZmfwbVrjOvKCYuA5037vHmkWP1+mxQtRJMz/DC6vAoyasZkN5WD2n6WYIGupu/FxIJzYyzMM=
     - secure: N/LNeY6kM4g2TOWiwuZhevrFOVSSDXj42hOWmbWVfwjLxVTMpFO29os3TiXxod8q6ezpDkXi5yVcGGtKLQZr6CgoiGW8zS+UKsUntKH4HI4dZdK+hKAKwaWU641aDNIq/XqSzNJ8v7ZmLLo3sk878aTHODPRPBfb7Q9wk2l3sDs=
     - secure: jSRuOGP7vghJet6oelSprSLGBd/eYuUaU3UM+QnZW0GhETWyXxjg/17hpl2R2NzVLhVz2m0KRaoT9JmG+EyJ9NW47JwTaKL+CNtxg2gPTM3/6iVNdVrXM1vOTvaJhtZ/C2SbLDg/+JPLLUMfT9/9oXkiz+enh7VzZuZDywgoTsw=
     - secure: Y4tbLIssPDkRQZp2lLUtou/YZr3APmhfD3o3tUcv1mqveeg6NBYZ8o6bLSULO3wdm88s1sug23VbP+Gt74XN4Ylbt4GjhKkOxvd+Vut7dR0o0cxsH372AWHYPicCOkuYAfeDK5cqxeXkGibHW1eBdduAAT82wcW5NcD9USyv9ig=
-addons:
-  apt:
-    packages:
-    - git
 
 before_install:
+  - cd ..
   # Set up anaconda
-  - wget http://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b -p $HOME/miniconda
+  - wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH=$HOME/miniconda/bin:$PATH
   # Update conda itself
   - conda update --yes conda
-  - cd ..
-  # this is the RMG-database project, so need to fetch RMG-Py
+  - conda info -a
+  # This is the RMG-database project, so need to fetch RMG-Py
   - git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git
-  # Add RMG-Py to PYTHONPATH
-  - export PYTHONPATH=$TRAVIS_BUILD_DIR/RMG-Py:$PYTHONPATH
   - cd RMG-Py
 
 install:
-  - conda env create -f environment_linux.yml
+  - conda env create -q -f environment_linux.yml
   - source activate rmg_env
+  - conda list
   - make
 
 script:
   - make test-database
   - make test-all
-  - cd $TRAVIS_BUILD_DIR
 
 after_success:
-  - bash ./deploy.sh
+  - cd $TRAVIS_BUILD_DIR
+  - bash ./deploy.sh

input/forbiddenStructures.py

@@ -35,37 +35,6 @@
 """,
 )
 
-#entry(
-#    label = "N_monorad_3singleBonds",
-#    group = 
-#"""
-#1 N u1 p0 {2,S} {3,S} {4,S}
-#2 R ux {1,S}
-#3 R ux {1,S}
-#4 R ux {1,S}
-#""",
-#    shortDesc = u"""""",
-#    longDesc = 
-#u"""
-#restricts H2NO, see RMG-Py issue #514
-#""",
-#)
-
-#entry(
-#    label = "N_birad_singlet_2singleBonds",
-#    group = 
-#"""
-#1 N u0 p1 {2,S} {3,S}
-#2 R ux {1,S}
-#3 R ux {1,S}
-#""",
-#    shortDesc = u"""""",
-#    longDesc = 
-#u"""
-#restricts NH3, see RMG-Py issue #514
-#""",
-#)
-
 entry(
     label = "N_birad_triplet_2singleBonds",
     group = 
@@ -90,7 +59,7 @@
     shortDesc = u"""""",
     longDesc = 
 u"""
-restricts [C], see RMG-Py issue #514
+
 """,
 )
 
@@ -336,113 +305,6 @@
 # """,
 # )
 
-entry(
-    label = "3H-Pyrazol",
-    group = 
-"""
-multiplicity [2,3,4,5]
-1 C ux {2,[S,D]} {5,[S,D]}
-2 C ux {1,[S,D]} {3,[S,D]}
-3 C ux {2,[S,D]} {4,[S,D]}
-4 N ux {3,[S,D]} {5,[S,D]}
-5 N ux {1,[S,D]} {4,[S,D]}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-EA sims (xa1450 & xa1451) crashed with error: Invalid k(E) values computed for path reaction "C(=[CH])[N]N=C(1479) <=> C1[CH]C=N[N]1(1659)"
-EA sims (xa1452 & xa1453) crashed with error: Invalid k(E) values computed for path reaction "C(=[CH])[N]N=C(1478) <=> C1C=C[N][N]1(1824)"
-See RMG-Py issue #253
-""",
-)
-
-entry(
-    label = "C=N[N]C#[C]",
-    group = 
-"""
-multiplicity [3]
-1 C u0 p0 c0 {2,D} {6,S} {7,S}
-2 N u0 p1 c0 {1,D} {3,S}
-3 N u1 p1 c0 {2,S} {4,S}
-4 C u0 p0 c0 {3,S} {5,T}
-5 C u1 p0 c0 {4,T}
-6 H u0 p0 c0 {1,S}
-7 H u0 p0 c0 {1,S}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-EA sims (xa1456-xa1459) crashed with error:
-Did not find reverse reaction in reaction family H_Abstraction for reaction <Molecule "N(=C=[CH])N=[CH]"> + <Molecule "C=N[N]C#[C]"> <=> <Molecule "C=N[N]C#C"> + <Molecule "N(=C=[C])N=[CH]">.
-See RMG-Py issue #806
-""",
-)
-
-entry(
-    label = "C1=CO[N][N]1",
-    group = 
-"""
-multiplicity [3]
-1 C u0 p0 c0 {2,D} {5,S} {6,S}
-2 C u0 p0 c0 {1,D} {3,S} {7,S}
-3 O u0 p2 c0 {2,S} {4,S}
-4 N u1 p1 c0 {3,S} {5,S}
-5 N u1 p1 c0 {1,S} {4,S}
-6 H u0 p0 c0 {1,S}
-7 H u0 p0 c0 {2,S}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-EA sims (xa1462-xa1465) crashed with error:
-Invalid k(E) values computed for path reaction "C(=[CH])N=[N+][O-](2989) <=> C1=CO[N][N]1(3358)".
-""",
-)
-
-entry(
-    label = "C1N[C](N1)[O]",
-    group = 
-"""
-multiplicity [3]
-1 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S}
-2 N u0 p1 c0 {1,S} {3,S} {8,S}
-3 C u1 p0 c0 {2,S} {4,S} {5,S}
-4 N u0 p1 c0 {1,S} {3,S} {9,S}
-5 O u1 p2 c0 {3,S}
-6 H u0 p0 c0 {1,S}
-7 H u0 p0 c0 {1,S}
-8 H u0 p0 c0 {2,S}
-9 H u0 p0 c0 {4,S}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-EA sim (xa1467) crashed with error:
-Mcoll = numpy.zeros((Nisom,Ngrains,NJ,Ngrains,NJ), numpy.float64)
-""",
-)
-
-entry(
-    label = "C(=[CH])[O-][N+]#N",
-    group = 
-"""
-multiplicity [2]
-1 C u0 p0 c0 {2,D} {4,S} {7,S}
-2 C u1 p0 c0 {1,D} {3,S}
-3 H u0 p0 c0 {2,S}
-4 O u0 p2 c-1 {1,S} {5,S}
-5 N u0 p0 c+1 {4,S} {6,T}
-6 N u0 p1 c0 {5,T}
-7 H u0 p0 c0 {1,S}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-EA sim (xa1479) crashed with error:
-Invalid k(E) values computed for path reaction "C(=[CH])[O-][N+]#N(6454) <=> c1cn[n+][o-]1(6594)".
-""",
-)
-
 entry(
     label = "cyclobutyne",
     group =
@@ -616,4 +478,40 @@
 Certain unsaturated versions of this strained tricyclic cause RMG
 to crash.
 """,
-)
+)
+
+entry(
+    label = "CO_birad",
+    group =
+"""
+multiplicity [3]
+1 C u2 p0 c0 {2,D}
+2 O u0 p2 c0 {1,D}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Forbidden after discussion with whgreen.
+This species should quickly transform into a closed shell [C-]#[O+].
+We don't need it as a resonance structure of carbon monoxide for reactivity since carbon monoxide has its designated
+reaction families (CO_Disprop, R_Add_COm).
+""",
+)
+
+entry(
+    label = "CS_birad",
+    group =
+"""
+multiplicity [3]
+1 C u2 p0 c0 {2,D}
+2 S u0 p2 c0 {1,D}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Forbidden after discussion with whgreen.
+This species should quickly transform into a closed shell [C-]#[S+] similar to the carbon monoxide case above.
+We don't need it as a resonance structure of carbon monsulfide for reactivity since carbon monsulfide has its designated
+reaction families (CO_Disprop [also deals with CS], R_Add_CSm).
+""",
+)