Merge pull request #292 from libAtoms/dft_SCF_convergence_status

DFT calculator convergence test

complete_pytest.tin

@@ -66,7 +66,7 @@ echo "summary line $l"
 # ===== 152 passed, 17 skipped, 3 xpassed, 78 warnings in 4430.81s (1:13:50) =====
 lp=$( echo $l | sed -E -e 's/ in .*//' -e 's/\s*,\s*/\n/g' )
 
-declare -A expected_n=( ["passed"]="163" ["skipped"]="21" ["warnings"]=803 ["xfailed"]=2 ["xpassed"]=1 )
+declare -A expected_n=( ["passed"]="164" ["skipped"]="21" ["warnings"]=803 ["xfailed"]=2 ["xpassed"]=1 )
 IFS=$'\n'
 for out in $lp; do
     out_n=$(echo $out | sed -e 's/^=* //' -e 's/ .*//' -e 's/,//')

setup.py

@@ -2,7 +2,7 @@
 
 setuptools.setup(
     name="wfl",
-    version="0.2.1",
+    version="0.2.2",
     packages=setuptools.find_packages(exclude=["tests"]),
     install_requires=["click>=7.0", "numpy", "ase>=3.21", "pyyaml", "spglib", "docstring_parser",
                       "expyre-wfl @ https://github.com/libAtoms/ExPyRe/tarball/main",

tests/calculators/test_vasp.py

@@ -362,3 +362,40 @@ def test_vasp_multi_calc(tmp_path):
 
     assert np.abs(e_GGA - e_test) < 1.0e-4
     assert n_loop_test < n_loop_GGA - 2
+
+
+def test_vasp_unconverged(tmp_path):
+    ase.io.write(tmp_path / 'vasp_in.xyz', Atoms('Si', cell=(2, 2, 2), pbc=[True] * 3), format='extxyz')
+
+    configs_eval = generic.calculate(
+        inputs=ConfigSet(tmp_path / 'vasp_in.xyz'),
+        outputs=OutputSpec('vasp_out.regular.xyz', file_root=tmp_path),
+        calculator=Vasp(workdir=tmp_path, encut=200, kspacing=1.0, pp=os.environ['PYTEST_VASP_POTCAR_DIR'],
+                        keep_files=True),
+        output_prefix='TEST_')
+
+    run_dir = list(tmp_path.glob('run_VASP_*'))
+    nfiles = len(list(os.scandir(run_dir[0])))
+
+    assert nfiles == 18
+
+    ats = list(configs_eval)
+    print("initial run converged?", ats[0].info["TEST_converged"])
+    assert ats[0].info["TEST_converged"]
+
+
+    configs_eval = generic.calculate(
+        inputs=ConfigSet(tmp_path / 'vasp_in.xyz'),
+        outputs=OutputSpec('vasp_out.unconverged.xyz', file_root=tmp_path),
+        calculator=Vasp(workdir=tmp_path, encut=200, nelm=6, kspacing=1.0, pp=os.environ['PYTEST_VASP_POTCAR_DIR'],
+                        keep_files=True),
+        output_prefix='TEST_')
+
+    run_dir = list(tmp_path.glob('run_VASP_*'))
+    nfiles = len(list(os.scandir(run_dir[0])))
+
+    assert nfiles == 18
+
+    ats = list(configs_eval)
+    print("second run converged?", ats[0].info["TEST_converged"])
+    assert not ats[0].info["TEST_converged"]

tests/test_optimize.py

@@ -181,7 +181,7 @@ def test_relax_fixed_vol(cu_slab):
 
 def test_subselect_from_traj(cu_slab):
 
-    calc = EMT()
+    calc = (EMT, [], {})
 
     cu_slab_optimised = cu_slab.copy()
     cu_slab_optimised.set_positions(expected_relaxed_positions_constant_pressure)

tests/test_remote_run.py

@@ -144,7 +144,7 @@ def do_generic_calc(tmp_path, sys_name, monkeypatch, remoteinfo_env):
     monkeypatch.setenv('WFL_EXPYRE_NO_MARK_PROCESSED', '1')
 
     t0 = time.time()
-    results = generic.calculate(inputs=ci, outputs=co, calculator=calc, properties=["energy", "forces"],
+    results = generic.calculate(inputs=ci, outputs=co, calculator=(EMT, [], {}), properties=["energy", "forces"],
                           autopara_info={"remote_info": ri})
     dt = time.time() - t0
     print('remote parallel calc_time', dt)
@@ -161,7 +161,7 @@ def do_generic_calc(tmp_path, sys_name, monkeypatch, remoteinfo_env):
     co = OutputSpec(tmp_path / f'ats_o_{sys_name}.xyz')
 
     t0 = time.time()
-    results = generic.calculate(inputs=ci, outputs=co, calculator=calc, properties=["energy", "forces"],
+    results = generic.calculate(inputs=ci, outputs=co, calculator=(EMT, [], {}), properties=["energy", "forces"],
                           autopara_info={"remote_info": ri})
     dt_rerun = time.time() - t0
     print('remote parallel calc_time', dt_rerun)
@@ -293,18 +293,18 @@ def test_resubmit_killed_jobs(tmp_path, expyre_systems, monkeypatch, remoteinfo_
 def do_resubmit_killed_jobs(tmp_path, sys_name, monkeypatch, remoteinfo_env):
     # make sure that jobs that time out can be resubmitted automatically
     ri = {'sys_name': sys_name, 'job_name': 'pytest_'+sys_name,
-          'resources': {'max_time': '1m', 'num_nodes': 1},
+          'resources': {'max_time': '10s', 'num_nodes': 1},
           'num_inputs_per_queued_job': 1, 'check_interval': 10}
     remoteinfo_env(ri)
 
     print("RemoteInfo", ri)
 
     ats = [Atoms('C') for _ in range(3)]
-    n = 20
+    n = 40
     ats[1] = Atoms(f'C{n**3}', positions=np.asarray(np.meshgrid(range(n), range(n), range(n))).reshape((3, -1)).T,
                    cell=[n]*3, pbc=[True]*3)
 
-    calc = EMT()
+    calc = (EMT, [], {})
 
     # first just ignore failures
     ri['ignore_failed_jobs'] = True
@@ -324,12 +324,9 @@ def do_resubmit_killed_jobs(tmp_path, sys_name, monkeypatch, remoteinfo_env):
     ri['resubmit_killed_jobs'] = True
     monkeypatch.setenv('WFL_EXPYRE_INFO', json.dumps({"test_resubmit_killed_jobs": ri}))
     print("BOB ######### second run, should time out")
-    try:
+    with pytest.raises(ExPyReJobDiedError):
         results = generic.calculate(inputs=ConfigSet(ats), outputs=OutputSpec(), calculator=calc, properties=["energy", "forces"],
                               raise_calc_exceptions=True, autopara_info=AutoparaInfo(remote_label="test_resubmit_killed_jobs"))
-    except ExPyReJobDiedError:
-        # ignore timeout in initial call
-        pass
 
     # now resubmit with longer time
     ri['resources']['max_time'] = '5m'

wfl/calculators/generic.py

@@ -55,7 +55,13 @@ def _run_autopara_wrappable(atoms, calculator, properties=None, output_prefix='_
         calculator_default = None
 
     if output_prefix == '_auto_':
-        output_prefix = calculator.__class__.__name__ + '_'
+        if isinstance(calculator, tuple):
+            # constructor, get name directly
+            calc_class = calculator[0].__name__
+        else:
+            # calculator object, get name from class
+            calc_class = calculator.__class__.__name__
+        output_prefix = calc_class + '_'
 
     at_out = []
     for at in atoms_to_list(atoms):

wfl/calculators/utils.py

@@ -66,6 +66,11 @@ def save_results(atoms, properties, results_prefix=None):
         config_results['dipole'] = atoms.get_dipole_moment()
     if 'magmom' in properties:
         config_results['magmom'] = atoms.get_magnetic_moment()
+    try:
+        if results_prefix is not None:
+            config_results['converged'] = atoms.calc.converged
+    except AttributeError as exc:
+        pass
 
     # copy per-atom results
     if 'forces' in properties:
@@ -78,8 +83,6 @@ def save_results(atoms, properties, results_prefix=None):
         atoms_results['magmoms'] = atoms.get_magnetic_moments()
     if 'energies' in properties:
         atoms_results['energies'] = atoms.get_potential_energies()
-    if 'converged' in properties and results_prefix is not None:
-        config_results['converged'] = atoms.get_calculator().read_convergence()
 
     if "extra_results" in dir(atoms.calc):
         if results_prefix is None and (len(atoms.calc.extra_results.get("config", {})) > 0 or