Merge branch 'main' into joback_sign_fix

.conda/meta.yaml

@@ -7,6 +7,7 @@ source:
   path: ../
 
 build:
+  noarch: generic
   number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
 
 requirements:

.github/workflows/CI.yml

@@ -64,7 +64,7 @@ jobs:
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: RMG-Py/environment.yml
           miniforge-variant: Mambaforge
@@ -149,23 +149,24 @@ jobs:
         run: mkdir stable_regression_results
 
       # Retrieve Stable Results for reference
-      # Will need to use this -> https://github.com/dawidd6/action-download-artifact
+      - name : Find ID of Reference Results
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          run_id=$(gh run list -R ReactionMechanismGenerator/RMG-Py --workflow="Continuous Integration" --branch main --limit 1 --json databaseId --jq '.[0].databaseId')
+          echo "CI_RUN_ID=$run_id" >> $GITHUB_ENV
+
       - name: Retrieve Stable Regression Results
         if: ${{ env.REFERENCE_JOB == 'false' }}
-        uses: dsnopek/action-download-artifact@91dda23aa09c68860977dd0ed11d93c0ed3795e7 # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2459#issuecomment-1582850815
+        uses: actions/download-artifact@v4
         with:
         # this will search for the last successful execution of CI on main and download
         # the stable regression results
-          workflow: CI.yml
-          workflow_conclusion: success
-          repo: ReactionMechanismGenerator/RMG-Py
-          branch: main
+          run-id: ${{ env.CI_RUN_ID }}
+          repository: ReactionMechanismGenerator/RMG-Py
+          github-token:  ${{ secrets.GH_PAT }}
           name: stable_regression_results
-          path: RMG-Py/stable_regression_results
-          search_artifacts: true  # retrieves the last run result, either scheduled daily or on push to main
-          ensure_latest: true     # ensures that the latest run is retrieved
-          # should result in a set of folders inside stable_regression_results
-          # each of which has the stable result for that example/test
+          path: stable_regression_results
 
       # Regression Testing - Actual Comparisons
       - name: Regression Tests - Compare to Baseline

.github/workflows/conda_build.yml

@@ -1,49 +1,36 @@
 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 $CONDA_TOKEN --user rmg .conda
+          # set a default value to the conda_token if needed (like from forks)
+          : "${CONDA_TOKEN:=${{ secrets.ANACONDA_TOKEN }}}"
+          : "${CONDA_TOKEN:=default_value}"
+          echo "CONDA_TOKEN=$CONDA_TOKEN" >> $GITHUB_ENV
+          conda config --add channels conda-forge
+          conda-build --token $CONDA_TOKEN --user rmg .conda

input/kinetics/families/Surface_Abstraction_Beta_vdW/groups.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Beta_vdW/groups"
+shortDesc = u""
+longDesc = u"""
+Surface abstraction of one atom to another adsorbate. The bond fission occurs not at the binding atom, but in the beta position of the adsorbate, that is the bond between Atom *2 and *3 is broken. Atom *1 binds to the surface (*5). A vdW species is formed. The bond order between *4 and the surface decreases. An example for this reaction is: COOH* + O* = OH* + CO2*. The bond between *2 and *3 must be single.
+
+
+ *1-*2--*3  *4            *1=*2   *3-*4
+  |         ||      ---->   :      |
+~*5~ +    ~*6~~           ~*5~ +  ~*6~~
+
+The rate, which should be in mol/m2/s, will be given by k * (mol/m2) * (mol/m2)
+so k should be in (m2/mol/s). 
+"""
+
+template(reactants=["Abstracting", "Donating"], products=["Adsorbate2","Adsorbate3"], ownReverse=False)
+
+reverse = "Surface_Abstraction_reverse_Beta_vdW"
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['FORM_BOND', '*3', 1, '*4'],
+    ['BREAK_BOND', '*1', 1, '*5'],
+    ['FORM_BOND', '*1', 0, '*5'],
+    ['CHANGE_BOND', '*1', 1, '*2'],
+    ['BREAK_BOND', '*2', 1, '*3'],
+    ['CHANGE_BOND', '*4',-1,'*6']
+])
+
+entry(
+    index = 1,
+    label = "Donating",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 R!H u0 px cx {1,S} {3,S}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="Abstracting",
+    group =
+"""
+1 *6 Xo  u0 {2,D}
+2 *4 R!H u0 px cx {1,D}	
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 3,
+    label = "R-C-H",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 C u0 px cx {1,S} {3,S}
+3 *3 H   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 4,
+    label = "R-O-H",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 O   u0 p2 cx {1,S} {3,S}
+3 *3 H   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 5,
+    label = "O",
+    group =
+"""
+1 *4 O   u0 p2 c0 {2,D}
+2 *6 Xo  u0 {1,D}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 6,
+    label = "R-CH3",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 C   u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
+3 *3 H   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+5    H   u0 {2,S}
+6    H   u0 {2,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: Abstracting
+    L2: O
+L1: Donating
+    L2: R-C-H
+	L3: R-CH3
+    L2: R-O-H
+"""
+)
+
+forbidden(
+    label = "Donating_Bidentate",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 R   u0 px cx {1,S} {3,S}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+5    Xo  u0 
+"""
+)
+
+forbidden(
+    label="Abstracting_Bidentate",
+    group =
+"""
+1 *6 Xo  u0 {2,D}
+2 *4 R!H u0 px cx {1,D}	
+3    Xo  u0 
+"""
+)
+

input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py

@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Beta_vdW/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+
+entry(
+    index = 1,
+    label = "Abstracting;Donating",
+    kinetics = SurfaceArrheniusBEP(
+        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"""
+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
+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)
+    """
+)
+
+entry(
+    index = 2,
+    label = "O;R-C-H",
+    kinetics = SurfaceArrheniusBEP(
+        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"""
+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
+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)
+"""
+)
+
+entry(
+    index = 3,
+    label = "O;R-O-H",
+    kinetics = SurfaceArrheniusBEP(
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha =0.65,
+        E0 = (15.4, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+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
+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)
+"""
+)
+
+entry(
+    index = 4,
+    label = "Abstracting;R-CH3",
+    kinetics = SurfaceArrheniusBEP(
+        A = (1.393e17, '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"""
+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
+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)
+Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
+"""
+)
+
+entry(
+    index = 5,
+    label = "O;R-CH3",
+    kinetics = SurfaceArrheniusBEP(
+        A = (1.393e17, '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"""
+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
+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)
+Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
+"""
+)