BugFix: Geometry Optimizer changed to Rational (#23)

Geometry optimizer was changed to Rational due to convergence issues.
MolarVerse · Aug 1, 2024 · b21764a · b21764a
2 parents b2eae82 + 5477c80
commit b21764a
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Showing 5 changed files with 31 additions and 22 deletions.
diff --git a/ThermoScreening/calculator/dftbplus.py b/ThermoScreening/calculator/dftbplus.py
@@ -11,7 +11,7 @@
 
 class Geoopt(Dftb):
     """
-    Custom DFTB+ calculator to optimize the system with LBFGS solver.
+    Custom DFTB+ calculator to optimize the system with the 'GeometryOptimisation' driver (Rational).
     It is a subclass of ase.calculators.dftb.Dftb. It uses the
     'LBFGS' driver.
 
@@ -72,7 +72,8 @@ def __init__(
             label=label,
             slako_dir=BASE_PATH + "../external/slakos/3ob-3-1/",
             Hamiltonian_Charge=charge,
-            Driver_="LBFGS",
+            Driver_="GeometryOptimisation",
+            Driver_Optimiser="Rational {}",
             Driver_MaxForceComponent=max_force,
             Driver_OutputPrefix="geo_opt",
             **kwargs,

diff --git a/examples/Notebooks/dftbplus/ThermoScreening.ipynb b/examples/Notebooks/dftbplus/ThermoScreening.ipynb
@@ -48,6 +48,10 @@
    "outputs": [],
    "source": [
     "dftb_parameters = dict(\n",
+    "\n",
+    "    # Driver\n",
+    "    # Driver_MaxSteps=1000,\n",
+    "  \n",
     "    # SCC\n",
     "    Hamiltonian_SCC=\"Yes\",\n",
     "    Hamiltonian_MaxSCCIterations=250,\n",
@@ -117,7 +121,7 @@
     "\n",
     "    # Analysis\n",
     "    Analysis_=\"\",\n",
-    "    Analysis_CalculateForces=\"Yes\",\n",
+    "    Analysis_PrintForces=\"Yes\",\n",
     "    Analysis_MullikenAnalysis=\"Yes\",\n",
     "\n",
     "    # ParserVersion\n",
@@ -235,7 +239,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

diff --git a/pyproject.toml b/pyproject.toml
@@ -21,7 +21,7 @@ classifiers = [
 ]
 
 dependencies = [
-    "numpy",
+    "numpy < 2.0",
     "argparse",
     "scipy",
     "pymatgen",

diff --git a/tests/calculator/test_dftbplus.py b/tests/calculator/test_dftbplus.py
@@ -15,8 +15,10 @@ class TestDftbplus:
 
     # Test the DFTB+ calculator
     def test_dftb(self):
-        assert os.system("which dftb+ > /dev/null") == 0, "DFTB+ is not installed."
-        assert os.system("which modes > /dev/null") == 0, "Modes is not installed."
+        assert os.system(
+            "which dftb+ > /dev/null") == 0, "DFTB+ is not installed."
+        assert os.system(
+            "which modes > /dev/null") == 0, "Modes is not installed."
 
     # Test the Geoopt class
     @pytest.mark.parametrize("example_dir", ["calculator"])
@@ -57,9 +59,12 @@ def test_hessian(self, test_with_data_dir):
 
         # create an instance of the Hessian class
         optimizer = Geoopt(atoms, charge=0, **dftb_3ob_parameters)
-        hessian = Hessian(
-            optimizer.read(), charge=0, **dftb_3ob_parameters, delta=0.0005
-        )
+        atoms = optimizer.read()
+        print(atoms.get_positions())
+        hessian = Hessian(optimizer.read(),
+                          charge=0,
+                          **dftb_3ob_parameters,
+                          delta=0.0005)
 
         assert hessian.atoms == optimizer.read()
         assert hessian.label == "second_derivative"
@@ -79,9 +84,10 @@ def test_modes(self, test_with_data_dir):
 
         # create an instance of the Modes class
         optimizer = Geoopt(atoms, charge=0, **dftb_3ob_parameters)
-        hessian = Hessian(
-            optimizer.read(), charge=0, **dftb_3ob_parameters, delta=0.0005
-        )
+        hessian = Hessian(optimizer.read(),
+                          charge=0,
+                          **dftb_3ob_parameters,
+                          delta=0.0005)
 
         assert os.path.exists("hessian.out")
         assert os.path.exists("geo_opt.gen")
@@ -99,16 +105,14 @@ def test_modes(self, test_with_data_dir):
 
         assert np.allclose(
             wave_numbers[6:],
-            [
-                1.46185721e03,
-                3.60476561e03,
-                3.87736051e03,
-            ],
+            [1462.29964226, 3604.10862879, 3876.6277397],
             atol=1e-5,
         )
 
     @pytest.mark.parametrize("example_dir", ["calculator"])
     def test_dftbplus_thermo(self, test_with_data_dir):
         atoms = ase_io.read("water.xyz")
         thermo = dftbplus_thermo(atoms, **dftb_3ob_parameters, delta=0.0005)
-        assert np.allclose(thermo.total_EeGtot(),-4.063049633277606 , atol=1e-5) # old value -4.064982703661
+        assert np.allclose(thermo.total_EeGtot(),
+                           -4.0595598803365744,
+                           atol=1e-5)
diff --git a/tests/data/calculator/water.xyz b/tests/data/calculator/water.xyz
@@ -1,5 +1,5 @@
 3
 Properties=species:S:1:pos:R:3 pbc="F F F"
-O       -0.00566600       0.40130200      -0.00000000
-H        0.79261600      -0.19855100       0.00000000
-H       -0.78695000      -0.20275100      -0.00000000
+O       -0.00566600       0.40130200      -1.00000000
+H        0.79261600      -0.19855100      -1.00000000
+H       -0.78695000      -0.20275100      -1.00000000