Merge branch 'main' into mono_to_bidentate

ReactionMechanismGenerator · Apr 3, 2024 · af7f188 · af7f188
2 parents 27184d7 + 1ca7a52
commit af7f188
Show file tree

Hide file tree

Showing 15 changed files with 2,053 additions and 726 deletions.
diff --git a/.conda/bld.bat b/.conda/bld.bat
diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -7,6 +7,7 @@ source:
   path: ../
 
 build:
+  noarch: generic
   number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
 
 requirements:

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
@@ -1,49 +1,34 @@
 name: Conda Build
 
 on:
+  pull_request:
   push:
     branches:
       - stable
 jobs:
-  build-linux:
+  build:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-      - name: Conda info
+      - uses: actions/checkout@v4
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          conda-solver: libmamba
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Build Tools
+        run: conda install python anaconda-client conda-build
+      - name: Configure Auto-Upload
+        if: github.ref == 'refs/heads/stable'
         run: |
-          conda info
-          conda list
-      - name: Build Binary
-        env: 
-          CONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        run: |
-          conda install -y conda-build 
-          conda install -y anaconda-client 
-          conda config --add channels rmg
           conda config --set anaconda_upload yes
-          conda build --token $CONDA_TOKEN --user rmg .conda
-  build-osx:
-    runs-on: macos-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-      - name: Conda info
-        run: |
-          conda info
-          conda list
       - name: Build Binary
         env: 
           CONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-          conda install -y conda-build 
-          conda install -y anaconda-client 
-          conda config --add channels rmg
-          conda config --set anaconda_upload yes
-          conda build --token $CONDA_TOKEN --user rmg .conda
+          conda config --add channels conda-forge
+          conda-build --token $CONDA_TOKEN --user rmg .conda
diff --git a/input/kinetics/families/Surface_Abstraction_Single_vdW/groups.py b/input/kinetics/families/Surface_Abstraction_Single_vdW/groups.py
@@ -35,7 +35,7 @@
 """
 multiplicity [1]
 1 *1 Xv u0 p0 c0
-2 *2 R  u0 px cx {3,S}
+2 *2 R!H  u0 px cx {3,S}
 3 *3 R  u0 px cx {2,S}
 """,
     # Note: shuold we restrict it so atoms *2 and *3 have no charge?
@@ -48,21 +48,8 @@
     label = "Abstracting",
     group =
 """
-1 *5 X u0 p0 c0 {2,S}
-2 *4 R ux px cx {1,S}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 3,
-    label = "H-H",
-    group =
-"""
-multiplicity [1]
-1 *1 Xv u0 p0 c0
-2 *2 H  u0 p0 c0 {3,S}
-3 *3 H  u0 p0 c0 {2,S}
+1 *5 X   u0 p0 c0 {2,S}
+2 *4 R!H ux px cx {1,S}
 """,
     kinetics = None,
 )
@@ -588,7 +575,6 @@
 tree(
 """
 L1: Donating
-    L2: H-H
     L2: O-R
         L3: O-H
             L4: H2O

diff --git a/input/kinetics/families/Surface_Abstraction_Single_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_Single_vdW/rules.py
@@ -12,14 +12,18 @@
     index = 1,
     label = "Donating;Abstracting",
     kinetics = SurfaceArrheniusBEP(
-        A = (1.0e13, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.5,
-        E0 = (0, 'kcal/mol'),
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha =0.94,
+        E0 = (129.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
-    longDesc = u"""Made up"""
+    longDesc = u""" 
+These numbers for the general BEP are from the abstraction reaction of C-H to O.
+BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
+From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
+"""
 )
diff --git a/input/kinetics/families/Surface_Abstraction_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_vdW/rules.py
@@ -12,14 +12,18 @@
     index = 1,
     label = "AdsorbateVdW;Adsorbate1",
     kinetics = SurfaceArrheniusBEP(
-        A = (1.0e13, 'm^2/(mol*s)'),
-        n = 0,
-        alpha = 0.5,
-        E0 = (0, 'kcal/mol'),
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha =0.94,
+        E0 = (129.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
     ),
     rank = 0,
     shortDesc = u"""Default""",
-    longDesc = u"""Made up"""
+    longDesc = u""" 
+These numbers for the general BEP are from the abstraction reaction of C-H to O.
+BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
+From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
+"""
 )
diff --git a/input/kinetics/families/recommended.py b/input/kinetics/families/recommended.py
@@ -109,10 +109,7 @@
     'Surface_Adsorption_Dissociative',
     'Surface_Dissociation',
     'Surface_Abstraction',
-    'Surface_EleyRideal_Addition_Multiple_Bond',
-    'Surface_Migration',
     'Surface_Dissociation_Double_vdW',
-    'Surface_Addition_Single_vdW',
     'Surface_Dissociation_vdW',
     'Surface_Abstraction_vdW',
     'Surface_Dissociation_Beta',
@@ -121,13 +118,13 @@
     'Surface_Monodentate_to_Bidentate',
     'Surface_Dissociation_to_Bidentate', 
     'Surface_vdW_to_Bidentate',
-    'Surface_Abstraction_Single_vdW',
     'Surface_Adsorption_Dissociative_Double',
     'Surface_Abstraction_Beta',
     'Surface_Abstraction_Beta_double_vdW',
     'Surface_Dissociation_Double',
     'Surface_Dissociation_Beta_vdW',
     'Surface_Abstraction_Beta_vdW',
+    'Surface_Abstraction_Single_vdW',
 }
 
 # reaction families for halogen chemistry only
@@ -147,4 +144,8 @@
 # Surface chemistry families that are under development and not yet working well.
 surface_development = {
     #'Surface_Adsorption_Double',
+    'Surface_EleyRideal_Addition_Multiple_Bond',
+    'Surface_Migration',
+    'Surface_DoubleBond_to_Bidentate',
+    'Surface_Addition_Single_vdW',
 }
diff --git a/input/solvation/groups/group.py b/input/solvation/groups/group.py
@@ -4,8 +4,9 @@
 name = "group"
 shortDesc = u""
 longDesc = u""" 
-All groups are fitted by Yunsie Chung and Pierre Walker using experimental solute parameter data (manuscript in preparation)
-unless written otherwise.
+All groups are fitted using experimental solute parameter data unless written otherwise.
+See Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., 
+& Green, W. H. (2022). J. Chem. Inf. Model, 62(3), 433-446.
 """
 
 entry(

diff --git a/input/solvation/groups/halogen.py b/input/solvation/groups/halogen.py
@@ -4,8 +4,9 @@
 name = "halogen"
 shortDesc = u""
 longDesc = u""" 
-All groups are fitted by Yunsie Chung and Pierre Walker using experimental solute parameter data (manuscript in preparation)
-unless written otherwise.
+All groups are fitted using experimental solute parameter data unless written otherwise.
+See Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., 
+& Green, W. H. (2022). J. Chem. Inf. Model, 62(3), 433-446.
 """
 
 entry(

diff --git a/input/solvation/groups/longDistanceInteraction_cyclic.py b/input/solvation/groups/longDistanceInteraction_cyclic.py
@@ -4,8 +4,9 @@
 name = "longDistanceInteraction_cyclic"
 shortDesc = u""
 longDesc = u""" 
-All groups are fitted by Yunsie Chung and Pierre Walker using experimental solute parameter data (manuscript in preparation)
-unless written otherwise.
+All groups are fitted using experimental solute parameter data unless written otherwise.
+See Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., 
+& Green, W. H. (2022). J. Chem. Inf. Model, 62(3), 433-446.
 """
 
 entry(

diff --git a/input/solvation/groups/longDistanceInteraction_noncyclic.py b/input/solvation/groups/longDistanceInteraction_noncyclic.py
@@ -4,8 +4,9 @@
 name = "longDistanceInteraction_noncyclic"
 shortDesc = u""
 longDesc = u""" 
-All groups are fitted by Yunsie Chung and Pierre Walker using experimental solute parameter data (manuscript in preparation)
-unless written otherwise.
+All groups are fitted using experimental solute parameter data unless written otherwise.
+See Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., 
+& Green, W. H. (2022). J. Chem. Inf. Model, 62(3), 433-446.
 """
 
 entry(

diff --git a/input/solvation/groups/polycyclic.py b/input/solvation/groups/polycyclic.py
@@ -4,8 +4,9 @@
 name = "polycyclic"
 shortDesc = u""
 longDesc = u""" 
-All groups are fitted by Yunsie Chung and Pierre Walker using experimental solute parameter data (manuscript in preparation)
-unless written otherwise.
+All groups are fitted using experimental solute parameter data unless written otherwise.
+See Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., 
+& Green, W. H. (2022). J. Chem. Inf. Model, 62(3), 433-446.
 """
 
 entry(

diff --git a/input/solvation/groups/ring.py b/input/solvation/groups/ring.py
@@ -4,8 +4,9 @@
 name = "ring"
 shortDesc = u""
 longDesc = u""" 
-All groups are fitted by Yunsie Chung and Pierre Walker using experimental solute parameter data (manuscript in preparation)
-unless written otherwise.
+All groups are fitted using experimental solute parameter data unless written otherwise.
+See Chung, Y., Vermeire, F. H., Wu, H., Walker, P. J., Abraham, M. H., 
+& Green, W. H. (2022). J. Chem. Inf. Model, 62(3), 433-446.
 """
 
 entry(