Merge pull request #343 from juliayang/development-liquids

Development liquids
mir-group · Jan 25, 2023 · 9c9786a · 9c9786a
2 parents 91614f2 + 50a19f2
commit 9c9786a
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Showing 2 changed files with 34 additions and 30 deletions.
diff --git a/.github/workflows/flare.yml b/.github/workflows/flare.yml
@@ -36,35 +36,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install Sphinx and Breathe
-      run: |
-        sudo apt-get update
-        sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx
-
-    - name: Run Doxygen
-      uses: mattnotmitt/doxygen-action@v1.1.0
-      with:
-        # Path to Doxyfile
-        doxyfile-path: "./Doxyfile" # default is ./Doxyfile
-        # Working directory
-        working-directory: "./docs" # default is .
-
-    - name: Run Sphinx
-      run: |
-        cd docs
-        pwd
-        ls
-        make html
-
-    - name: Publish the docs
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        # Default Doxyfile build documentation to html directory.
-        # Change the directory if changes in Doxyfile
-        publish_dir: ./docs/build/html
-      if: github.event_name == 'pull_request' && matrix.lapack == 'on' && matrix.omp == 'on'
-
     - name: Build
       run: |
         sudo apt install liblapacke liblapacke-dev
@@ -141,6 +112,33 @@ jobs:
         cd tests
         pytest test_lammps.py
 
+    - name: Install Sphinx and Breathe
+      run: |
+        sudo apt-get update
+        sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx
+    - name: Run Doxygen
+      uses: mattnotmitt/doxygen-action@v1.1.0
+      with:
+        # Path to Doxyfile
+        doxyfile-path: "./Doxyfile" # default is ./Doxyfile
+        # Working directory
+        working-directory: "./docs" # default is .
+
+    - name: Run Sphinx
+      run: |
+        cd docs
+        pwd
+        ls
+        make html
+    - name: Publish the docs
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        # Default Doxyfile build documentation to html directory.
+        # Change the directory if changes in Doxyfile
+        publish_dir: ./docs/build/html
+      if: github.event_name == 'pull_request' && matrix.lapack == 'on' && matrix.omp == 'on'
+
 #     - name: Run tutorial
 #       run: |
 #         cd tests

diff --git a/flare/bffs/sgp/sparse_gp.py b/flare/bffs/sgp/sparse_gp.py
@@ -288,12 +288,18 @@ def from_dict(in_dict):
             rel_efs_noise = train_struc.info.get("rel_efs_noise", [1, 1, 1])
             rel_e_noise, rel_f_noise, rel_s_noise = rel_efs_noise
 
+            # check for stress training since ASE atoms assert stress arrays of length 6
+            if not in_dict["stress_training"]:
+                struc_stress = np.array(None)
+            else:
+                struc_stress = train_struc.stress
+
             gp.update_db(
                 train_struc,
                 train_struc.forces,
                 custom_range=custom_range,
                 energy=energy,
-                stress=train_struc.stress,
+                stress=struc_stress,
                 mode="specific",
                 sgp=None,
                 update_qr=False,