RMG-database v2.1.3 release

Author: mliu49

.travis.yml

@@ -7,6 +7,10 @@ virtualenv:
 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:
@@ -34,7 +38,7 @@ install:
 
 script:
   - make test-database
-  - make test
+  - make test-all
   - cd $TRAVIS_BUILD_DIR
 
 after_success:

Makefile

@@ -38,3 +38,39 @@
 """
 )
 
+
+forbidden(
+    label = "N2O2a",
+    group =
+"""
+multiplicity [3]
+1 *3 O u0 p2 c0 {2,S} {3,S}
+2 *2 N u0 p1 c0 {1,S} {4,D}
+3 *4 O u1 p2 c0 {1,S}
+4 *1 N u1 p1 c0 {2,D}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+N2O2 reacts in this family to form a singlet O2 (O=O)
+See RMG-Py issue #1020
+""",
+)
+
+forbidden(
+    label = "N2O2b",
+    group =
+"""
+multiplicity [3]
+1 *2 O u0 p2 c0 {2,S} {3,S}
+2 *3 N u0 p1 c0 {1,S} {4,D}
+3 *1 O u1 p2 c0 {1,S}
+4 *4 N u1 p1 c0 {2,D}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Same as above, inverse atom labeling
+""",
+)
+

input/kinetics/families/1,4_Linear_birad_scission/groups.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python
 # encoding: utf-8
 
-name = "Oa_R_Recombination/groups"
+name = "Birad_R_Recombination/groups"
 shortDesc = u""
 longDesc = u"""
-This reaction family is reserved for O_atom (triplet only). The forbidden groups
-at the bottom prevent it from reacting with other forms of O.
+This reaction family is reserved for recombination of O_atom, S_atom, N_R_birad (triplets only).
+The forbidden groups at the bottom prevent it from reacting with other forms of O, S, NH.
 """
 
-template(reactants=["Y_rad", "Oa"], products=["YO."], ownReverse=False)
+template(reactants=["Y_rad", "Birad"], products=["YOS."], ownReverse=False)
 
-reverse = "RO_Bond_Dissociation"
+reverse = "ROS_Bond_Dissociation"
 
 recipe(actions=[
     ['FORM_BOND', '*1', 1, '*2'],
@@ -30,10 +30,95 @@
 
 entry(
     index = 2,
+    label = "Birad",
+    group = 
+"""
+1 *2 R!H u2
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 50,
     label = "Oa",
     group = 
 """
-1 *2 O u2
+1 *2 O u2 p2
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 51,
+    label = "Sa",
+    group = 
+"""
+1 *2 S u2 p2
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 52,
+    label = "N_R_birad",
+    group = 
+"""
+1 *2 N u2 p1
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 53,
+    label = "N_birad/H",
+    group = 
+"""
+1 *2 N u2 p1 {2,S}
+2    H u0 p0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 54,
+    label = "N_birad/C",
+    group = 
+"""
+1 *2 N u2 p1 {2,S}
+2    C ux    {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 55,
+    label = "N_birad/O",
+    group = 
+"""
+1 *2 N u2 p1 {2,S}
+2    O ux    {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 56,
+    label = "N_birad/N",
+    group = 
+"""
+1 *2 N u2 p1 {2,S}
+2    N ux    {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 57,
+    label = "N_birad/S",
+    group = 
+"""
+1 *2 N u2 p1 {2,S}
+2    S ux    {1,S}
 """,
     kinetics = None,
 )
@@ -673,48 +758,82 @@
                 L5: C_rad/Cs
                 L5: C_rad/TDMustO
             L4: C_rad/ThreeDe
-L1: Oa
+L1: Birad
+    L2: Oa
+    L2: Sa
+    L2: N_R_birad
+        L3: N_birad/H
+        L3: N_birad/C
+        L3: N_birad/O
+        L3: N_birad/N
+        L3: N_birad/S
 """
 )
 
 forbidden(
-    label = "O2_1centeredBirad",
+    label = "O2_p1",
     group = 
 """
-1 *1 O u2 p1 {2,S}
-2    R u0 {1,S}
+1 *2 O u2 p1
 """,
     shortDesc = u"""""",
     longDesc = 
 u"""
-
+This family is intended to handle
+[O] u2 p2,    or
+[S] u2 p2,    or
+[NH] u2 p1,
+instances with a different number of lone pairs are forbidden
 """,
 )
-
+ 
 forbidden(
-    label = "O2_birad",
+    label = "S2_p1",
     group = 
 """
-1 *1 O u1 p2 {2,S}
-2    O u1 p2 {1,S}
+1 *2 S u2 p1
 """,
     shortDesc = u"""""",
     longDesc = 
 u"""
-
+This family is intended to handle
+[O] u2 p2,    or
+[S] u2 p2,    or
+[NH] u2 p1,
+instances with a different number of lone pairs are forbidden
 """,
 )
-
+ 
 forbidden(
-    label = "O_atom_singlet",
+    label = "S2_p0",
     group = 
 """
-1 *1 O u0 p3
+1 *2 S u2 p0
 """,
     shortDesc = u"""""",
     longDesc = 
 u"""
+This family is intended to handle
+[O] u2 p2,    or
+[S] u2 p2,    or
+[NH] u2 p1,
+instances with a different number of lone pairs are forbidden
+""",
+)
 
+forbidden(
+    label = "OS_chain",
+    group = 
+"""
+1 *1 [O,S] u1 p2 {2,S}
+2    [O,S] u0 p2 {1,S} {3,S}
+3    [O,S] u0 p2 {2,S} {4,S}
+4    [O,S] u1 p2 {3,S}
+""",
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+Group added to forbid this family from forming S-O chains
 """,
 )
 

…s/Oa_R_Recombination/NIST/dictionary.txt …irad_R_Recombination/NIST/dictionary.txtinput/kinetics/families/Oa_R_Recombination/NIST/dictionary.txt renamed to input/kinetics/families/Birad_R_Recombination/NIST/dictionary.txt input/kinetics/families/Oa_R_Recombination/NIST/dictionary.txt renamed to input/kinetics/families/Birad_R_Recombination/NIST/dictionary.txt

@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Birad_R_Recombination/rules"
+shortDesc = u""
+longDesc = u"""
+
+"""
+entry(
+    index = 1000,
+    label = "Y_rad;Oa",
+    kinetics = ArrheniusEP(
+        A = (1e+13, 'cm^3/(mol*s)'),
+        n = 0,
+        alpha = 0,
+        E0 = (0, 'kcal/mol'),
+        Tmin = (300, 'K'),
+        Tmax = (1500, 'K'),
+    ),
+    rank = 2,
+)
+
+entry(
+    index = 2000,
+    label = "Y_rad;Sa",
+    kinetics = ArrheniusEP(
+        A = (1e+13, 'cm^3/(mol*s)'),
+        n = 0,
+        alpha = 0,
+        E0 = (0, 'kcal/mol'),
+        Tmin = (300, 'K'),
+        Tmax = (1500, 'K'),
+    ),
+    rank = 2,
+)
+
+entry(
+    index = 2000,
+    label = "Y_rad;N_R_birad",
+    kinetics = ArrheniusEP(
+        A = (1e+13, 'cm^3/(mol*s)'),
+        n = 0,
+        alpha = 0,
+        E0 = (0, 'kcal/mol'),
+        Tmin = (300, 'K'),
+        Tmax = (1500, 'K'),
+    ),
+    rank = 2,
+)
+

…ies/Oa_R_Recombination/NIST/reactions.py …/Birad_R_Recombination/NIST/reactions.pyinput/kinetics/families/Oa_R_Recombination/NIST/reactions.py renamed to input/kinetics/families/Birad_R_Recombination/NIST/reactions.py input/kinetics/families/Oa_R_Recombination/NIST/reactions.py renamed to input/kinetics/families/Birad_R_Recombination/NIST/reactions.py

@@ -0,0 +1,57 @@
+O
+multiplicity 3
+1 *2 O u2 p2 c0
+
+S
+multiplicity 3
+1 *2 S u2 p2 c0
+
+NH
+multiplicity 3
+1 *2 N u2 p1 c0 {2,S}
+2    H u0 p0 c0 {1,S}
+
+HSO
+multiplicity 2
+1    S u0 p2 c0 {2,S} {3,S}
+2 *1 O u1 p2 c0 {1,S}
+3    H u0 p0 c0 {1,S}
+
+HSOO
+multiplicity 2
+1    S u0 p2 c0 {2,S} {4,S}
+2 *1 O u0 p2 c0 {1,S} {3,S}
+3 *2 O u1 p2 c0 {2,S}
+4    H u0 p0 c0 {1,S}
+
+NO
+multiplicity 2
+1 *1 N u1 p1 c0 {2,D}
+2    O u0 p2 c0 {1,D}
+
+NO2_p
+multiplicity 2
+1 *1 N u0 p1 c0 {2,D} {3,S}
+2    O u0 p2 c0 {1,D}
+3 *2 O u1 p2 c0 {1,S}
+
+NO2_r
+multiplicity 2
+1    O u0 p2 c0 {2,D}
+2 *1 N u1 p0 c+1 {1,D} {3,S}
+3    O u0 p3 c-1 {2,S}
+
+HNNO2
+multiplicity 2
+1 *2 N u1 p1 c0 {2,S} {3,S}
+2    H u0 p0 c0 {1,S}
+3 *1 N u0 p0 c+1 {1,S} {4,S} {5,D}
+4    O u0 p3 c-1 {3,S}
+5    O u0 p2 c0 {3,D}
+
+SNO
+multiplicity 2
+1 *2 S u1 p2 c0 {2,S}
+2 *1 N u0 p1 c0 {1,S} {3,D}
+3    O u0 p2 c0 {2,D}
+