__init__.py adding lenard-jones potential

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_Lenard_Jones_potential
 
 
 def load_modules(mm):
     """
     Loads the collection of all modules provided by StructureFinder.
     """
     load_pyberny_modules(mm)
+    load_Lenard_Jones_potential(mm)

src/python/structurefinder/lj_potential/lennard_jones_potential_module.py

@@ -0,0 +1,70 @@
+# 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
+
+
+class LJ_potential(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
+        #----------------------------------------------------------------------
+        rv = self.results()
+        return pt.wrap_results(rv, E)
+
+    #--------------------------------------------------------------------------
+
+
+def load_Lenard_Jones_potential(mm):
+    mm.add_module("Lenard-Jones", LJ_potential())

src/python/structurefinder/lj_potential/lj_potential.py

@@ -0,0 +1,69 @@
+# 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.
+import numpy as np
+import plugandplay as pp
+from simde import TotalEnergy
+
+
+class LJ_potential(pp.ModuleBase):
+    # Module Construct --------------------------------------------------------
+    def __init__(self):
+        """
+        This module Evaluates the Lennard-Jones 1D potential function (E), and 
+        calculates minus the gradient (Force) in Cartesian coordinates, 
+        according to the relation
+        
+                                 FC = - dE/dx       
+        """
+        pp.ModuleBase.__init__(self)
+        self.description("Lennard-Jones 1D potential function")
+        self.satisfies_property_type(TotalEnergy())
+
+    #--------------------------------------------------------------------------
+
+    # Module run_ member function ---------------------------------------------
+    def run_(self, inputs):
+        """
+        Parameters
+        ----------
+        inputs : x-coordinate, 
+        TYPE ---> Float
+    
+        Returns
+        -------
+        E: Lennard-Jonnes 1D potential Energy, 
+        TYPE ---> Float 
+        
+        FC: Force in cartesian coordinates evaluated at the given input, 
+        acording to the relation
+                                 FC = - dE/dx  
+        
+        TYPE ---> Float
+        """
+        pt = TotalEnergy()
+        x0 = pt.unwrap_inputs(inputs)
+        #-------------- LENNARD-JONES FUNCTION --------------------------------
+        E = lambda x: 4 * ((1 / x**12) - (1 / x**6))
+        #------------- ANALYTIC FORCE -----------------------------------------
+        DE_x = -24 * ((2 / x0**13) - (1 / x0**7))
+        FC = -DE_x
+        #----------------------------------------------------------------------
+        rv = self.results()
+        return pt.wrap_results(rv, E(x0), FC)
+
+    #--------------------------------------------------------------------------
+
+
+def load_Lenard_Jones_potential(mm):
+    mm.add_module("Lenard-Jones", LJ_potential())

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_LJ_potential.py

@@ -0,0 +1,34 @@
+# 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 structurefinder
+import nwchemex
+import pluginplay as pp
+import chemist
+import unittest
+from simde import TotalEnergy
+
+
+class Test_Lennard_jones_potential(unittest.TestCase):
+
+    def test_lennard_jones_potential(self):
+        result = self.mm.run_as(TotalEnergy(), "Lenard-Jones",
+                                chemist.ChemicalSystem(self.mol))
+        self.assertEqual(result, -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)))