Merge pull request #65 from jan-janssen/atomistics_evcurve

Calculate Energy volume curve with atomistics package

environment.yml

@@ -2,6 +2,7 @@ channels:
   - conda-forge
 dependencies:
   - ase =3.23.0
+  - atomistics =0.1.32
   - langchain =0.2.5
   - numexpr =2.10.0
   - langchain-openai =0.1.8

langsim/tools/interface.py

@@ -1,10 +1,14 @@
 import os
 from ase.atoms import Atoms
 from ase.build import bulk
-from ase.constraints import UnitCellFilter
 from ase.eos import calculate_eos, plot
 from ase.optimize import LBFGS
-from ase.units import kJ
+from atomistics.calculators import evaluate_with_ase
+from atomistics.workflows import optimize_positions_and_volume
+from atomistics.workflows.evcurve.helper import (
+    analyse_structures_helper,
+    generate_structures_helper,
+)
 import pandas
 from langchain.agents import tool
 from mendeleev.fetch import fetch_table
@@ -48,10 +52,13 @@ def get_atom_dict_equilibrated_structure(
         AtomsDict: DataClass representing the equilibrated atomic structure
     """
     try:
-        atoms = Atoms(**atom_dict.dict())
-        atoms.calc = get_calculator(calculator_str=calculator_str)
-        ase_optimizer_obj = LBFGS(UnitCellFilter(atoms))
-        ase_optimizer_obj.run(fmax=0.000001)
+        task_dict = optimize_positions_and_volume(structure=Atoms(**atom_dict.dict()))
+        atoms = evaluate_with_ase(
+            task_dict=task_dict,
+            ase_calculator=get_calculator(calculator_str=calculator_str),
+            ase_optimizer=LBFGS,
+            ase_optimizer_kwargs={"fmax": 0.000001},
+        )["structure_with_optimized_positions_and_volume"]
         return AtomsDict(**{k: v.tolist() for k, v in atoms.todict().items()})
     except Exception as error:
         # handle the exception
@@ -98,11 +105,24 @@ def get_bulk_modulus(atom_dict: AtomsDict, calculator_str: str) -> str:
         str: Bulk Modulus in GPa
     """
     try:
-        atoms = Atoms(**atom_dict.dict())
-        atoms.calc = get_calculator(calculator_str=calculator_str)
-        eos = calculate_eos(atoms)
-        v, e, B = eos.fit()
-        return B / kJ * 1.0e24
+        structure_dict = generate_structures_helper(
+            structure=Atoms(**atom_dict.dict()),
+            vol_range=0.05,
+            num_points=11,
+            strain_lst=None,
+            axes=("x", "y", "z"),
+        )
+        result_dict = evaluate_with_ase(
+            task_dict={"calc_energy": structure_dict},
+            ase_calculator=get_calculator(calculator_str=calculator_str),
+        )
+        fit_dict = analyse_structures_helper(
+            output_dict=result_dict,
+            structure_dict=structure_dict,
+            fit_type="polynomial",
+            fit_order=5,
+        )
+        return fit_dict["bulkmodul_eq"]
     except Exception as error:
         # handle the exception
         return "An exception occurred: {}"
@@ -124,11 +144,24 @@ def get_equilibrium_volume(atom_dict: AtomsDict, calculator_str: str) -> str:
     Returns:
         str: Equilibrium volume in Angstrom^3
     """
-    atoms = Atoms(**atom_dict.dict())
-    atoms.calc = get_calculator(calculator_str=calculator_str)
-    eos = calculate_eos(atoms)
-    v, e, B = eos.fit()
-    return v
+    structure_dict = generate_structures_helper(
+        structure=Atoms(**atom_dict.dict()),
+        vol_range=0.05,
+        num_points=11,
+        strain_lst=None,
+        axes=("x", "y", "z"),
+    )
+    result_dict = evaluate_with_ase(
+        task_dict={"calc_energy": structure_dict},
+        ase_calculator=get_calculator(calculator_str=calculator_str),
+    )
+    fit_dict = analyse_structures_helper(
+        output_dict=result_dict,
+        structure_dict=structure_dict,
+        fit_type="polynomial",
+        fit_order=5,
+    )
+    return fit_dict["volume_eq"]
 
 
 @tool

setup.py

@@ -8,6 +8,7 @@
     packages=find_packages(),
     install_requires=[
         "ase==3.23.0",
+        "atomistics==0.1.32",
         "langchain==0.2.5",
         "numexpr==2.10.0",
         "langchain-openai==0.1.8",
@@ -23,4 +24,4 @@
             "langchain-experimental==0.0.61",
         ],
     }
-)
+)

tests/test_interface.py

@@ -27,11 +27,11 @@ def test_structure(self):
 
     def test_bulk_modulus(self):
         b0 = get_bulk_modulus.invoke({"atom_dict": self.structure, "calculator_str": self.calculator_str})
-        self.assertAlmostEqual(b0, 39.518515298270835)
+        self.assertAlmostEqual(b0, 39.73699875059587)
 
     def test_equilibrium_volume(self):
         v0 = get_equilibrium_volume.invoke({"atom_dict": self.structure, "calculator_str": self.calculator_str})
-        self.assertAlmostEqual(v0, 15.931553356465589)
+        self.assertAlmostEqual(v0, 15.931368308723524)
 
 
 class TestInterfaceMace(TestCase):
@@ -51,7 +51,7 @@ def test_structure(self):
 
     def test_bulk_modulus(self):
         b0 = get_bulk_modulus.invoke({"atom_dict": self.structure, "calculator_str": self.calculator_str})
-        self.assertTrue(np.isclose(b0, 63.866120321206715, atol=10**-2))
+        self.assertTrue(np.isclose(b0, 63.508867430434144, atol=10**-2))
 
     def test_equilibrium_volume(self):
         v0 = get_equilibrium_volume.invoke({"atom_dict": self.structure, "calculator_str": self.calculator_str})