add unit test workflow for sparc official files

.github/workflows/installation_test.yml

@@ -30,7 +30,7 @@ jobs:
     - name: Install dependencies
       run: |
         # mamba install -c conda-forge ase>=3.22 pymatgen flake8 pytest
-        mamba install -c alchem0x2a sparc
+        mamba install -c conda-forge sparc-x
         # pip install pyfakefs
     - name: Install package
       run: |
@@ -45,6 +45,7 @@ jobs:
       run: |
         # python -m pytest -svv tests/ --cov=sparc --cov-report=json --cov-report=html
         export SPARC_TESTS_DIR="./SPARC-master/tests"
+        export ASE_SPARC_COMMAND="mpirun -n 1 sparc"
         coverage run -a -m pytest -svv tests/
         coverage json --omit="tests/*.py"
         coverage html --omit="tests/*.py"

sparc/calculator.py

@@ -486,11 +486,15 @@ def _convert_special_params(self, atoms=None):
                 converted_sparc_params["EXCHANGE_CORRELATION"] = "PBE0"
             elif xc.lower() == "hf":
                 converted_sparc_params["EXCHANGE_CORRELATION"] = "HF"
-            # backward compatibility for HSE03. Note HSE06 is not supported yet 
+            # backward compatibility for HSE03. Note HSE06 is not supported yet
             elif (xc.lower() == "hse") or (xc.lower() == "hse03"):
                 converted_sparc_params["EXCHANGE_CORRELATION"] = "HSE"
             # backward compatibility for VASP-style XCs
-            elif (xc.lower() == "vdwdf1") or (xc.lower() == "vdw-df") or (xc.lower() == "vdw-df1"):
+            elif (
+                (xc.lower() == "vdwdf1")
+                or (xc.lower() == "vdw-df")
+                or (xc.lower() == "vdw-df1")
+            ):
                 converted_sparc_params["EXCHANGE_CORRELATION"] = "vdWDF1"
             elif (xc.lower() == "vdwdf2") or (xc.lower() == "vdw-df2"):
                 converted_sparc_params["EXCHANGE_CORRELATION"] = "vdWDF2"
@@ -499,7 +503,6 @@ def _convert_special_params(self, atoms=None):
             else:
                 # TODO: alternative exception
                 raise ValueError(f"xc keyword value {xc} is invalid!")
-
 
         # h --> gpts
         if "h" in params:

sparc/io.py

@@ -671,7 +671,9 @@ def write_sparc(filename, images, **kwargs):
     return
 
 
-@deprecated("Reading individual .ion is not recommended. Please use read_sparc instead.")
+@deprecated(
+    "Reading individual .ion is not recommended. Please use read_sparc instead."
+)
 def read_ion(filename, **kwargs):
     """Parse an .ion file inside the SPARC bundle using a wrapper around SparcBundle
     The reader works only when other files (.inpt) exist.
@@ -683,7 +685,10 @@ def read_ion(filename, **kwargs):
     atoms = sb._read_ion_and_inpt()
     return atoms
 
-@deprecated("Writing individual .ion file is not recommended. Please use write_sparc instead.")
+
+@deprecated(
+    "Writing individual .ion file is not recommended. Please use write_sparc instead."
+)
 def write_ion(filename, atoms, **kwargs):
     """Write .ion and .inpt files using the SparcBundle wrapper.
 

tests/test_calculator.py

@@ -39,6 +39,7 @@ def test_h_parameter():
 def test_xc_parameter():
     from sparc.calculator import SPARC
     from ase.build import bulk
+
     atoms = bulk("Al", cubic=True)
     with tempfile.TemporaryDirectory() as tmpdir:
         calc = SPARC(directory=tmpdir)
@@ -118,8 +119,6 @@ def test_xc_parameter():
         filecontent = open(Path(tmpdir) / "SPARC.inpt", "r").read()
         assert "EXCHANGE_CORRELATION: SCAN" in filecontent
 
-
-
 
 def test_conflict_param():
     from sparc.calculator import SPARC

tests/test_read_all_examples.py

@@ -12,10 +12,24 @@
 import tempfile
 import shutil
 
-skipped_names = ["Si2_domain_paral", "Si2_kpt_paral",
-                 "SiH4", "SiH4_quick",
-                 "H2O_sheet_quick", "H2O_sheet",
-                 "CdS_bandstruct"]
+skipped_names = [
+    "Si2_domain_paral",
+    "Si2_kpt_paral",
+    "SiH4",
+    "SiH4_quick",
+    "H2O_sheet_quick",
+    "H2O_sheet",
+    "CdS_bandstruct",
+]
+
+selected_quick_tests = [
+    "AlSi_orthogonal_quick_scf/standard",
+    "AlSi_primitive_quick_relax/standard",
+    "Cu_FCC/standard",
+    "BaTiO3_quick/standard",
+    "H2O_wire_quick/standard",
+]
+
 
 def test_read_all_tests():
     """Search all .inpt files within the tests dir."""
@@ -39,7 +53,7 @@ def test_read_all_tests():
             tmpdir = Path(tmpdir)
             for ext in [".ion", ".inpt"]:
                 shutil.copy(workdir / f"{parent_name}{ext}", tmpdir)
-            for ext in [".refout", "refstatic", "refgeopt", "refaimd"]:
+            for ext in [".refout", ".refstatic", ".refgeopt", ".refaimd"]:
                 origin_file = workdir / f"{parent_name}{ext}"
                 new_ext = ext.replace("ref", "")
                 new_file = tmpdir / f"{parent_name}{new_ext}"
@@ -55,6 +69,7 @@ def test_read_all_tests():
     if failed_counts > 0:
         raise RuntimeError("More than 1 test in output read test failed")
 
+
 def test_write_all_inputs():
     """Search all .inpt files within the tests dir."""
 
@@ -83,7 +98,11 @@ def test_write_all_inputs():
                 origin_inpt_dict["inpt"]["params"].pop(key, None)
             # Re-write the ion and inpt files
             try:
-                write_ion(tmpdir / "test.ion", origin_atoms, **origin_inpt_dict["inpt"]["params"])
+                write_ion(
+                    tmpdir / "test.ion",
+                    origin_atoms,
+                    **origin_inpt_dict["inpt"]["params"],
+                )
                 new_atoms = read_ion(tmpdir / "test.ion")
                 new_inpt_dict = _read_inpt(tmpdir / "test.inpt")
                 assert np.all(origin_atoms.pbc == new_atoms.pbc)
@@ -99,10 +118,83 @@ def test_write_all_inputs():
                     # Vector types can be list compared
                     elif isinstance(origin_val, (list, np.ndarray)):
                         assert np.all(origin_val == new_val)
-                    
+
             except Exception as e:
                 print("Failed: ", parent_name, workdir)
                 print("\t: Error is ", e)
                 failed_counts += 1
     if failed_counts > 0:
         raise RuntimeError("More than 1 test in inpt write test failed")
+
+
+def test_quick_examples():
+    """Perform quick tests on selected ref examples"""
+    from sparc.calculator import SPARC
+    from ase.build import molecule
+    from pathlib import Path
+    from sparc.io import read_sparc, read_ion, write_ion
+    from sparc.sparc_parsers.inpt import _read_inpt
+
+    dummy_calc = SPARC()
+    try:
+        cmd = dummy_calc._make_command()
+    except EnvironmentError:
+        print("Skip test since no sparc command found")
+        pytest.skip()
+
+    # Skipped tests are to avoid unwanted keywords
+    tests_dir = os.environ.get("SPARC_TESTS_DIR", "")
+    failed_counts = 0
+    print(f"Current test dir is {tests_dir}")
+    if len(tests_dir) == 0:
+        pytest.skip(allow_module_level=True)
+
+    tests_dir = Path(tests_dir)
+    for test_name in selected_quick_tests:
+        bundle = tests_dir / test_name
+        parent_name = test_name.split("/")[0]
+
+        atoms = read_sparc(bundle, index=0)
+        inpt_file = bundle / f"{parent_name}.inpt"
+        params = _read_inpt(inpt_file)["inpt"]["params"]
+        for key in ["CELL", "LATVEC_SCALE", "LATVEC", "BC"]:
+            params.pop(key, None)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            tmpdir = Path(tmpdir)
+            os.makedirs(tmpdir, exist_ok=True)
+            for ext in [".ion", ".inpt"]:
+                shutil.copy(bundle / f"{parent_name}{ext}", tmpdir)
+            for ext in [".refout", ".refstatic", ".refgeopt", ".refaimd"]:
+                origin_file = bundle / f"{parent_name}{ext}"
+                new_ext = ext.replace("ref", "")
+                new_file = tmpdir / f"{parent_name}{new_ext}"
+                if origin_file.is_file():
+                    shutil.copy(origin_file, new_file)
+            old_atoms = read_sparc(tmpdir, index=-1, include_all_files=True)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            tmpdir = Path(tmpdir)
+            calc = SPARC(directory=tmpdir, label=parent_name, **params)
+            calc.calculate(atoms=atoms)
+            new_atoms = read_sparc(tmpdir, index=-1, include_all_files=True)
+
+        print("old atoms", old_atoms)
+        print("new atoms", new_atoms)
+        assert len(old_atoms) == len(new_atoms)
+        assert np.all(old_atoms.pbc) == np.all(new_atoms.pbc)
+        if "energy" in old_atoms.calc.results:
+            assert np.isclose(
+                old_atoms.get_potential_energy(),
+                new_atoms.get_potential_energy(),
+                rtol=1.0e-6,
+                atol=1.0e-3,
+            )
+        if "forces" in old_atoms.calc.results:
+            assert np.isclose(
+                old_atoms.get_forces(), new_atoms.get_forces(), rtol=1.0e-3, atol=1.0e-2
+            ).all()
+        if "stress" in old_atoms.calc.results:
+            assert np.isclose(
+                old_atoms.get_stress(), new_atoms.get_stress(), rtol=1.0e-3, atol=1.0e-2
+            ).all()