Update main (#22)

MolarVerse · Jun 9, 2024 · b2eae82 · b2eae82
2 parents 8d13e04 + c0e4f93
commit b2eae82
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Showing 6 changed files with 50 additions and 94 deletions.
diff --git a/ThermoScreening/calculator/dftbplus.py b/ThermoScreening/calculator/dftbplus.py
@@ -92,11 +92,8 @@ def potential_energy(self):
             Potential energy of the optimized geometry.
         """
         self.atoms.calc = self
-        return (
-            self.atoms.get_potential_energy()
-            * PhysicalConstants["eV"]
-            / PhysicalConstants["H"]
-        )
+        return (self.atoms.get_potential_energy() * PhysicalConstants["eV"] /
+                PhysicalConstants["H"])
 
     def read(self):
         """
@@ -263,18 +260,16 @@ def write(self):
         """
 
         # use f-strings to write the modes_in.hsd file
-        string = (
-            "Geometry = GenFormat {\n"
-            f"    <<< {self.geometry}\n"
-            "}\n"
-            "\n"
-            "Hessian = {\n"
-            f"    <<< {self.hessian}\n"
-            "}\n"
-            "\n"
-            "Atoms = 1:-1\n"
-            "\n"
-        )
+        string = ("Geometry = GenFormat {\n"
+                  f"    <<< {self.geometry}\n"
+                  "}\n"
+                  "\n"
+                  "Hessian = {\n"
+                  f"    <<< {self.hessian}\n"
+                  "}\n"
+                  "\n"
+                  "Atoms = 1:-1\n"
+                  "\n")
 
         with open("modes_in.hsd", "w") as f:
             f.write(string)
@@ -329,13 +324,12 @@ def read(self):
 
 
 # --------------------------------------------------------------------------- #
-
 """
 DFTB+ parameters for the 3ob-3-1 Slater-Koster files.
 """
 
 dftb_3ob_parameters = dict(
-    # SCC 
+    # SCC
     Hamiltonian_SCC="Yes",
     Hamiltonian_MaxSCCIterations=250,
     Hamiltonian_SCCTolerance='1.0e-7',
@@ -374,4 +368,7 @@ def read(self):
     Analysis_="",
     Analysis_CalculateForces="Yes",
     Analysis_MullikenAnalysis="Yes",
-)
+
+    # Parser options
+    ParserOptions_ParserVersion=12,
+)
diff --git a/examples/.gitignore b/examples/.gitignore
diff --git a/examples/Notebooks/.gitignore b/examples/Notebooks/.gitignore
@@ -0,0 +1,8 @@
+# Ignore dftbplus output files
+*.out
+*.xyz
+*.gen
+*.hsd
+*.bin
+*.cosmo
+*.tag
diff --git a/examples/Notebooks/dftbplus/ThermoScreening.ipynb b/examples/Notebooks/dftbplus/ThermoScreening.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26,9 +26,10 @@
     "from ase.io import read, write\n",
     "\n",
     "import os\n",
+    "\n",
     "skf_dir = 'skf-files/3ob-3-1'\n",
     "\n",
-    "# set DFTB perfix and path \n",
+    "# set DFTB perfix and path\n",
     "os.environ['DFTB_PREFIX'] = os.path.join(os.environ['HOME'], skf_dir)\n",
     "os.environ['OMP_NUM_THREADS'] = '6'"
    ]
@@ -42,18 +43,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "dftb_parameters = dict(\n",
-    "    # SCC \n",
+    "    # SCC\n",
     "    Hamiltonian_SCC=\"Yes\",\n",
     "    Hamiltonian_MaxSCCIterations=250,\n",
     "    Hamiltonian_SCCTolerance='1.0e-6',\n",
     "    Hamiltonian_ReadInitialCharges=\"No\",\n",
-    "\n",
-    "    Hamiltonian_ShellResolvedScc = \"No\",\n",
+    "    Hamiltonian_ShellResolvedScc=\"No\",\n",
     "\n",
     "    # Fermi smearing\n",
     "    Hamiltonian_Filling=\"Fermi {\",\n",
@@ -81,20 +81,20 @@
     "    Hamiltonian_MaxAngularMomentum_=\"\",\n",
     "\n",
     "    # Solvation model\n",
-    "    Hamiltonian_Solvation_ = \"Cosmo\",\n",
-    "    Hamiltonian_Solvation_Radii = \"VanDerWaalsRadiiD3 {}\",\n",
-    "    Hamiltonian_Solvation_RadiiScaling = 1.55,\n",
-    "    Hamiltonian_Solvation_AngularGrid = 110,\n",
-    "    Hamiltonian_Solvation_Solver = \"DomainDecomposition{\",\n",
-    "    Hamiltonian_Solvation_Solver_MaxMoment = 10,\n",
-    "    Hamiltonian_Solvation_Solver_Accuracy = 1.0e-8,\n",
-    "    Hamiltonian_Solvation_Solver_Regularisation = 0.2,\n",
+    "    Hamiltonian_Solvation_=\"Cosmo\",\n",
+    "    Hamiltonian_Solvation_Radii=\"VanDerWaalsRadiiD3 {}\",\n",
+    "    Hamiltonian_Solvation_RadiiScaling=1.55,\n",
+    "    Hamiltonian_Solvation_AngularGrid=110,\n",
+    "    Hamiltonian_Solvation_Solver=\"DomainDecomposition{\",\n",
+    "    Hamiltonian_Solvation_Solver_MaxMoment=10,\n",
+    "    Hamiltonian_Solvation_Solver_Accuracy=1.0e-8,\n",
+    "    Hamiltonian_Solvation_Solver_Regularisation=0.2,\n",
     "    Hamiltonian_Solvation_Solvent=\"\"\"FromConstants{\n",
     "        Epsilon = 37.0,\n",
     "        MolecularMass [amu] = 73.1,\n",
     "        Density [kg/l] = 0.95\n",
     "      }\"\"\",\n",
-    "    Hamiltonian_Solvation_empty = \"FreeEnergyShift [kcal/mol] = 0.0\",\n",
+    "    Hamiltonian_Solvation_empty=\"FreeEnergyShift [kcal/mol] = 0.0\",\n",
     "\n",
     "    # Hubbard derivatives\n",
     "    Hamiltonian_ThirdOrderFull=\"Yes\",\n",
@@ -120,45 +120,11 @@
     "    Analysis_CalculateForces=\"Yes\",\n",
     "    Analysis_MullikenAnalysis=\"Yes\",\n",
     "\n",
-    "    # Parser options\n",
-    "    # ParserOptions_ParserVersion=\"14\"\n",
-    "    \n",
-    "  \n",
+    "    # ParserVersion\n",
+    "    ParserOptions_ParserVersion=12,\n",
     ")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "----\n",
-    "\n",
-    "TODO:\n",
-    "- install `wfl` - not in pypi >:( - https://github.com/libAtoms/workflow\n",
-    "- rdkit NOT in dependencies of `wfl`\n",
-    "- restart kernel after installation\n",
-    "\n",
-    "Commands to install `wfl` and `rdkit`:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# pip install git+https://github.com/libAtoms/workflow.git"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# pip install rdkit"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -168,12 +134,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "from wfl.generate import smiles\n",
-    "from ase.calculators.dftb import Dftb\n",
     "\n",
     "# quinone smile\n",
     "smile = 'C1=CC(=O)C=CC1=O'\n",
@@ -191,7 +156,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -246,26 +211,12 @@
     "# hartree to j/mol\n",
     "hartree = 2625500.2\n",
     "\n",
-    "redox1 = - (neg1 - zero) * hartree / F\n",
-    "redox2 = - (neg2 - neg1) * hartree / F\n",
+    "redox1 = -(neg1 - zero) * hartree / F\n",
+    "redox2 = -(neg2 - neg1) * hartree / F\n",
     "\n",
     "print(f'{smile} redox1: {redox1} V')\n",
     "print(f'{smile} redox2: {redox2} V')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -284,7 +235,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

diff --git a/pyproject.toml b/pyproject.toml
@@ -28,7 +28,7 @@ dependencies = [
     "beartype",
     "ase",
     "rdkit",
-    "wfl@git+https://github.com/libAtoms/workflow.git",
+    "wfl",
 ]
 
 [project.optional-dependencies]

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -3,6 +3,7 @@
 import shutil
 # (c) Jakob Gamper
 
+
 @pytest.fixture(scope="function")
 def tmpdir():
 
@@ -35,4 +36,4 @@ def test_with_data_dir(example_dir):
     yield tmpdir
 
     os.chdir("..")
-    shutil.rmtree(tmpdir)
+    shutil.rmtree(tmpdir)