Merge remote-tracking branch 'upstream/main' into stuff

Author: janosh

.github/workflows/test.yml

@@ -8,7 +8,13 @@ on:
 
 jobs:
   test:
+    if: github.repository_owner == 'hackingmaterials' # don't run on forks
     runs-on: ubuntu-latest
+    services:
+      mongodb:
+        image: mongo
+        ports:
+          - 27017:27017
 
     steps:
       - name: Checkout repo
@@ -19,23 +25,23 @@ jobs:
         with:
           python-version: 3.7
 
-      - name: Install C++ dependencies
+      - name: Install OpenBabel
         run: |
-          sudo apt-get install openbabel
+          # underlying C++ lib needed for Python openbabel wrapper installed by `pip install .`
+          sudo apt-get install libopenbabel-dev
+          # https://github.com/openbabel/openbabel/issues/2408#issuecomment-1014466193
+          sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
 
       - name: Cache pip
         uses: actions/cache@v2
-        id: pip-cache
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements-ci.txt', 'setup.py') }}
           restore-keys: |
             ${{ runner.os }}-pip-
 
       - name: Install dependencies
-        if: steps.pip-cache.outputs.cache-hit != 'true'
         run: |
-          pip install -r requirements.txt
           pip install -r requirements-ci.txt
           pip install .[complete]
 

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

atomate/vasp/analysis/linear_response.py

@@ -15,6 +15,7 @@ def procure_response_dict(
     response_dict,
     perturb_dict,
     rkey,
+    # keys,
     ldaul_vals,
     analyzer_gs,
     calcs_skipped,
@@ -27,10 +28,13 @@ def procure_response_dict(
     # perform magnetic ordering analysis
     analyzer_output = CollinearMagneticStructureAnalyzer(struct_final, threshold=0.61)
     magnet_order = analyzer_output.ordering.value
+    # if rkey == keys[0]:  # store ground state ordering
+    #     magnet_order_gs = magnet_order
 
     # check if ordering matches ground state configuration
     if analyzer_gs:
         if not analyzer_gs.matches_ordering(struct_final):
+            # use_calc = False
             calcs_skipped.append(
                 {
                     "ICHARG": incar_dict.get("ICHARG", 0),
@@ -168,6 +172,9 @@ def obtain_response_matrices(
 
                         v = response_dict[keys[ll]][f"site{j}"][v_key][idx]
                         n = response_dict[keys[ll]][f"site{i}"][n_key][idx]
+                        # order = response_dict[keys[ll]]["magnetic order"][l]
+
+                        # if order == magnet_order_gs:
 
                         isolated_response = v != 0.0
 

atomate/vasp/firetasks/parse_outputs.py

@@ -1034,9 +1034,10 @@ def run_task(self, fw_spec):
                     response_dict,
                     perturb_dict,
                     rkey,
-                    keys,
+                    # keys,
                     ldaul_vals,
                     analyzer_gs,
+                    calcs_skipped,
                 )
 
         for j in range(num_perturb_sites):

atomate/vasp/test_files/atomate/.circleci/config.yml

@@ -7,7 +7,7 @@
 from pymatgen.core import Structure
 
 from atomate.utils.testing import AtomateTest
-from atomate.vasp.powerups import use_fake_vasp, use_potcar_spec
+from atomate.vasp.powerups import add_modify_incar, use_fake_vasp, use_potcar_spec
 from atomate.vasp.workflows.base.electrode import get_ion_insertion_wf
 
 __author__ = "Jimmy Shen"
@@ -18,11 +18,6 @@
 ref_dir = module_dir / "../../test_files"
 wf_dir = ref_dir / "insertion_wf"
 
-VASP_CMD = None  # for fake VASP
-DEBUG_MODE = (
-    False  # If true, retains the database and output dirs at the end of the test
-)
-
 
 class TestInsertionWorkflow(AtomateTest):
     def setUp(self):
@@ -32,57 +27,14 @@ def setUp(self):
         calc_dirs = {n_: input_output_dirs / n_ for n_ in names}
         base_struct = Structure.from_file(wf_dir / "YPO4-static/inputs/POSCAR")
         sm = StructureMatcher(ltol=0.6, stol=0.6, angle_tol=9)
-        # Run the workflow with fake vasp
-        wf = get_ion_insertion_wf(
-            structure=base_struct,
-            structure_matcher=sm,
-            working_ion="Mg",
-            volumetric_data_type="AECCAR",
-            db_file=db_dir / "db.json",
-            vasp_powerups=[
-                {
-                    "powerup_name": "add_modify_incar",
-                    "kwargs": {"modify_incar_params": {"incar_update": {"KPAR": 8}}},
-                },
-                {
-                    "powerup_name": "use_fake_vasp",
-                    "kwargs": {
-                        "ref_dirs": calc_dirs,
-                        "check_incar": False,
-                        "check_kpoints": False,
-                        "check_poscar": False,
-                        "check_potcar": False,
-                    },
-                },
-                {"powerup_name": "use_potcar_spec", "kwargs": {}},
-            ],
-            optimizefw_kwargs={"ediffg": -0.05},
-        )
 
-        wf_stop_early = get_ion_insertion_wf(
+        # Run the workflow with fake VASP
+        wf = get_ion_insertion_wf(
             structure=base_struct,
             structure_matcher=sm,
             working_ion="Mg",
             volumetric_data_type="AECCAR",
             db_file=db_dir / "db.json",
-            max_inserted_atoms=1,
-            vasp_powerups=[
-                {
-                    "powerup_name": "add_modify_incar",
-                    "kwargs": {"modify_incar_params": {"incar_update": {"KPAR": 8}}},
-                },
-                {
-                    "powerup_name": "use_fake_vasp",
-                    "kwargs": {
-                        "ref_dirs": calc_dirs,
-                        "check_incar": False,
-                        "check_kpoints": False,
-                        "check_poscar": False,
-                        "check_potcar": False,
-                    },
-                },
-                {"powerup_name": "use_potcar_spec", "kwargs": {}},
-            ],
             optimizefw_kwargs={"ediffg": -0.05},
         )
 
@@ -94,9 +46,20 @@ def setUp(self):
             check_poscar=False,
             check_potcar=False,
         )
+        wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"KPAR": 8}})
         wf = use_potcar_spec(wf)
         self.wf = wf
 
+        wf_stop_early = get_ion_insertion_wf(
+            structure=base_struct,
+            structure_matcher=sm,
+            working_ion="Mg",
+            volumetric_data_type="AECCAR",
+            db_file=db_dir / "db.json",
+            max_inserted_atoms=1,
+            optimizefw_kwargs={"ediffg": -0.05},
+        )
+
         wf_stop_early = use_fake_vasp(
             wf_stop_early,
             calc_dirs,
@@ -105,6 +68,7 @@ def setUp(self):
             check_poscar=False,
             check_potcar=False,
         )
+        wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"KPAR": 8}})
         wf_stop_early = use_potcar_spec(wf_stop_early)
         self.wf_stop_early = wf_stop_early
 
@@ -119,8 +83,10 @@ def test_has_inserted(self):
                 }
             ),
         )
-        formula = self.get_task_collection(coll_name="tasks").distinct("formula_pretty")
-        self.assertEqual(set(formula), {"Y2Mg(PO4)2", "YPO4"})
+        formulas = self.get_task_collection(coll_name="tasks").distinct(
+            "formula_pretty"
+        )
+        self.assertEqual(set(formulas), {"YPO4"})
 
         self.lp.add_wf(self.wf)
         rapidfire(
@@ -133,7 +99,7 @@ def test_has_inserted(self):
             ),
         )
         # Check that all of the inserted pretty formulas are present
-        formula = self.get_task_collection(coll_name="tasks").distinct("formula_pretty")
-        self.assertEqual(
-            set(formula), {"Y2Mg(PO4)2", "Y2Mg3(PO4)2", "YMg2PO4", "YMgPO4", "YPO4"}
+        formulas = self.get_task_collection(coll_name="tasks").distinct(
+            "formula_pretty"
         )
+        self.assertEqual(set(formulas), {"YPO4"})

atomate/vasp/test_files/atomate/.circleci/images/py3/Dockerfile

@@ -6,7 +6,7 @@
 Advanced Storage Stratagies
 ==================
 
-Storing data greater than 16 Mb 
+Storing data greater than 16 Mb
 ============
 
 Introduction
@@ -56,7 +56,7 @@ Note, this AWS profile needs to be available anywhere the ``VaspCalcDb.insert_ta
 Usage
 -----------
 
-Example: store the charge density 
+Example: store the charge density
 
 To parse a completed calculation directory.  We need to instantiate the ``drone`` with the ``parse_aeccar`` or ``parse_chgcar`` flag.
 
@@ -72,7 +72,7 @@ Some workflows like the ``StaticWF`` will pass the parsing flags like ``parse_ch
 To access the data using the task_id we can call
 
 .. code-block:: python
-    
+
     chgcar = mmdb.get_chgcar(task_id)
 
 Similar functionalities exist for the band structure and DOS.

atomate/vasp/workflows/tests/test_insertion_workflow.py

@@ -28,6 +28,14 @@ atomate.qchem.workflows.base.fragmentation module
    :undoc-members:
    :show-inheritance:
 
+atomate.qchem.workflows.base.reaction\_path module
+--------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.base.reaction_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.qchem.workflows.base.torsion\_potential module
 ------------------------------------------------------
 

docs/_sources/advanced_stores.rst.txt

@@ -36,6 +36,14 @@ atomate.qchem.workflows.tests.test\_parse\_pass\_write module
    :undoc-members:
    :show-inheritance:
 
+atomate.qchem.workflows.tests.test\_reaction\_path module
+---------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.tests.test_reaction_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.qchem.workflows.tests.test\_torsion\_potential module
 -------------------------------------------------------------