__init__.py adding lenard-jones potential

CMakeLists.txt

@@ -76,7 +76,7 @@ if("${BUILD_TESTING}")
         py_${PROJECT_NAME}
         "${${PROJECT_NAME}_PYTHON_TEST_DIR}/unit_tests/test_${PROJECT_NAME}.py"
         DEPENDS nwchemex
-        SUBMODULES simde chemist pluginplay parallelzone friendzone chemcache nwchemex
+        SUBMODULES simde chemist pluginplay parallelzone friendzone chemcache nwchemex tensorwrapper integrals scf nux
     )
 
 endif()

src/python/structurefinder/__init__.py

@@ -13,10 +13,12 @@
 # limitations under the License.
 
 from .pyberny import load_pyberny_modules
+from .lj_potential.lennard_jones_potential_module import load_lennard_jones_potential
 
 
 def load_modules(mm):
     """
     Loads the collection of all modules provided by StructureFinder.
     """
     load_pyberny_modules(mm)
+    load_lennard_jones_potential(mm)

src/python/structurefinder/lj_potential/lennard_jones_potential_module.py

@@ -0,0 +1,72 @@
+# 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.
+"""
+@author: Felix Rojas
+"""
+
+import numpy as np
+import pluginplay as pp
+from simde import TotalEnergy
+import tensorwrapper as tw
+
+
+class LennardJonesPotential(pp.ModuleBase):
+    # Module Construct --------------------------------------------------------
+    def __init__(self):
+        """
+        This module Evaluates the Lennard-Jones 1D potential function (E)
+        """
+        pp.ModuleBase.__init__(self)
+        self.description("Lennard-Jones 1D potential function")
+        self.satisfies_property_type(TotalEnergy())
+
+    #--------------------------------------------------------------------------
+
+    # Module run_ member function ---------------------------------------------
+    def run_(self, inputs, submods):
+        """
+        Parameters
+        ----------
+        inputs : Diatomic distance, 
+        TYPE ---> Float
+
+        Returns
+        -------
+        E: Lennard-Jonnes 1D potential Energy, 
+        TYPE ---> Float 
+        """
+        pt = TotalEnergy()
+        chem_sys, = pt.unwrap_inputs(inputs)
+        mol = chem_sys.molecule
+        coor_0 = np.array([mol.at(0).x, mol.at(0).y, mol.at(0).z])
+        coor_1 = np.array([mol.at(1).x, mol.at(1).y, mol.at(1).z])
+        #----------------------------------------------------------------------
+        assert (mol.size() == 2)  #<--- To check molcule size contains 2-atoms
+        #----------------------------------------------------------------------
+        r = np.linalg.norm(coor_0 - coor_1)
+        #-------------- LENNARD-JONES FUNCTION --------------------------------
+        E = 4 * ((1 / r**12) - (1 / r**6))
+        #------------- ANALYTIC FORCE -----------------------------------------
+        DE_x = -24 * ((2 / r**13) - (1 / r**7))
+        FC = -DE_x
+        #----------------------------------------------------------------------
+        E = tw.Tensor(np.array(E))
+        rv = self.results()
+        return pt.wrap_results(rv, E)
+
+    #--------------------------------------------------------------------------
+
+
+def load_lennard_jones_potential(mm):
+    mm.add_module("Lennard-Jones", LennardJonesPotential())

src/python/structurefinder/pyberny/__init__.py

@@ -16,6 +16,7 @@
 from simde import EnergyNuclearGradientStdVectorD, TotalEnergy, MoleculeFromString
 from berny import Berny, geomlib
 import chemist
+import numpy as np
 
 
 class GeomoptViaPyberny(pp.ModuleBase):
@@ -70,7 +71,7 @@ def run_(self, inputs, submods):
                 EnergyNuclearGradientStdVectorD(), geom,
                 geom_points.as_point_set())
             print('Interim gradient: \n' + str(gradients) + '\n')
-            optimizer.send((energy, gradients))
+            optimizer.send((np.array(energy).item(), gradients))
 
         opt_geom = geom.molecule.nuclei
         print(

tests/python/unit_tests/test_lennard_jones_potential/__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.

tests/python/unit_tests/test_lennard_jones_potential/test_lennard_jones_potential.py

@@ -0,0 +1,35 @@
+# Copyright 2024 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.
+import numpy as np
+import structurefinder
+import nwchemex
+import pluginplay as pp
+import chemist
+import unittest
+from simde import TotalEnergy
+
+
+class TestLennardJonesPotential(unittest.TestCase):
+
+    def test_lennard_jones_potential(self):
+        result = self.mm.run_as(TotalEnergy(), "Lennard-Jones",
+                                chemist.ChemicalSystem(self.mol))
+        self.assertEqual(np.array(result).item(), -1.0)
+
+    def setUp(self):
+        self.mm = pp.ModuleManager()
+        structurefinder.load_modules(self.mm)
+        self.mol = chemist.Molecule()
+        self.mol.push_back(chemist.Atom("H", 1, 1.0079, 0.0, 0.0, 0.0))
+        self.mol.push_back(chemist.Atom("H", 1, 1.0079, 0.0, 0.0, 2**(1 / 6)))

tests/python/unit_tests/test_optimizers/test_pybernyop.py

@@ -14,6 +14,7 @@
 
 import structurefinder
 import nwchemex
+import numpy as np
 import pluginplay as pp
 import chemist
 import unittest
@@ -35,7 +36,8 @@ def test_optimize_pyberny(self):
         egy = mm.run_as(TotalEnergy(), "PyBerny",
                         chemist.ChemicalSystem(self.mol))
         print("Energy = " + str(egy))
-        self.assertAlmostEqual(egy, -1.117505879316, 10)
+        print(np.array(egy).item())
+        self.assertAlmostEqual(np.array(egy).item(), -1.117505879316, 10)
 
     def setUp(self):
         self.mol = chemist.Molecule()