Fcuantico patch 1

.gitignore

@@ -14,5 +14,9 @@
 
 __pycache__/
 build/
-venv/
+.venv/
 install/
+toolchain.cmake
+.vscode/
+StructureFinder.code-workspace
+

src/python/structurefinder/__init__.py

@@ -14,6 +14,7 @@
 
 from .pyberny import load_pyberny_modules
 from .lj_potential.lennard_jones_potential_module import load_lennard_jones_potential
+from .fire.backward_euler.backward_euler import load_backwardeulerfire_modules
 
 
 def load_modules(mm):
@@ -22,3 +23,4 @@ def load_modules(mm):
     """
     load_pyberny_modules(mm)
     load_lennard_jones_potential(mm)
+    load_backwardeulerfire_modules(mm)

src/python/structurefinder/fire/__init__.py

@@ -0,0 +1,13 @@
+# Copyright 2025 NWChemEx Community
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

src/python/structurefinder/fire/backward_euler/__init__.py

@@ -0,0 +1,89 @@
+# Copyright 2023 NWChemEx-Project
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import pluginplay as pp
+from simde import EnergyNuclearGradientStdVectorD, TotalEnergy, MoleculeFromString
+from berny import Berny, geomlib
+import chemist
+import numpy as np
+import tensorwrapper as tw
+
+
+class GeomoptViaPyberny(pp.ModuleBase):
+
+    def __init__(self):
+        pp.ModuleBase.__init__(self)
+        self.satisfies_property_type(TotalEnergy())
+        self.description("Performs PyBerny optimization")
+        self.add_submodule(TotalEnergy(), "Energy")
+        self.add_submodule(EnergyNuclearGradientStdVectorD(), "Gradient")
+        self.add_submodule(MoleculeFromString(), "StringConv")
+
+    def run_(self, inputs, submods):
+        pt = TotalEnergy()
+        mol, = pt.unwrap_inputs(inputs)
+        molecule = mol.molecule
+
+        # Convert Chemist Chemical System to XYZ
+        xyz = ""
+        xyz += (str(molecule.size()) + "\n\n")
+        for i in range(molecule.size()):
+            xyz += (molecule.at(i).name + " " + str(molecule.at(i).x) + " " +
+                    str(molecule.at(i).y) + " " + str(molecule.at(i).z) + "\n")
+
+        # Loads the geometry string into the Berny optimizer
+        # object.
+        optimizer = Berny(geomlib.loads(xyz, fmt='xyz'))
+
+        for geom in optimizer:
+
+            # Converts the "Berny" geometry object to Chemical System
+            geom2xyz = geom.dumps('xyz')
+            print('Berny Geom to XYZ value: \n' + geom2xyz + '\n')
+            lines = geom2xyz.split('\n')
+            print('Lines of geom2xyz: \n' + str(lines) + '\n')
+            mol_string = '\n'.join(lines[2:])
+            print('Lines to string: \n' + mol_string + '\n')
+            xyz2chem_mol = submods["StringConv"].run_as(
+                MoleculeFromString(), mol_string)
+            print('String conversion from xyz to chem sys: \n' +
+                  str(xyz2chem_mol.nuclei) + '\n')
+            geom = chemist.ChemicalSystem(xyz2chem_mol)
+            print('Chemical system of xyz2chem_mol: \n' +
+                  str(geom.molecule.nuclei) + '\n')
+            geom_nuclei = geom.molecule.nuclei.as_nuclei()
+            geom_points = geom_nuclei.charges.point_set
+
+            # Main optimizer operation
+            energy = submods["Energy"].run_as(TotalEnergy(), geom)
+            print('Interim energy: \n' + str(energy) + '\n')
+            gradients = submods["Gradient"].run_as(
+                EnergyNuclearGradientStdVectorD(), geom,
+                geom_points.as_point_set())
+            print('Interim gradient: \n' + str(gradients) + '\n')
+            optimizer.send((energy, gradients))
+
+        opt_geom = geom.molecule.nuclei
+        print(
+            'Resulting relaxed geometry (assigned to variable opt_geom): \n' +
+            str(opt_geom))
+        # Optimized energy is of type "float"
+        e = tw.Tensor(energy)
+        print(e)
+        rv = self.results()
+        return pt.wrap_results(rv, e)
+
+
+def load_pyberny_modules(mm):
+    mm.add_module("PyBerny", GeomoptViaPyberny())