Fcuantico patch 1 #7

fcuantico · 2025-06-18T17:19:16Z

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fcuantico · 2025-06-18T17:21:59Z

I think this how is done but not sure hopefully it will work:
So I want to propose and update to :

# Copyright 2024 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.

from simde import TotalEnergy, EnergyNuclearGradientStdVectorD


def _compare_mol_and_point(mol, points):
    """This function is essentially a work around for the comparisons not being
    exposed to Python.
    """
    if mol.size() != points.size():
        return False

    for i in range(mol.size()):
        atom_i = mol.at(i)
        point_i = points.at(i)

        for j in range(3):
            if round(atom_i.coord(j),16) != round(point_i.coord(j),16):  
                return False

    return True


def unwrap_inputs(pt, inputs):
    """ Code factorization for unwrapping a module's inputs.
    
    Many of our friends expose interfaces which are analogous to high-level
    property types like TotalEnergy, AOEnergy, and EnergyNuclearGradient.
    Furthermore, most of our friends expose all of these calculations through
    a single interface. The result is that many of our modules start by having
    dispatch logic akin to "if we're doing an energy calculation, unwrap this
    way." Or "if we're doing a gradient, unwrap this other way." This function
    factors that logic out into a single function.
    """

    mol = None
    if pt.type() == TotalEnergy().type():
        mol, = pt.unwrap_inputs(inputs)
    elif pt.type() == EnergyNuclearGradientStdVectorD().type():
        mol, point = pt.unwrap_inputs(inputs)

        if not _compare_mol_and_point(mol.molecule, point):
            raise RuntimeError(
                'Derivative must be computed at molecular geometry')
    else:
        raise RuntimeError('Property type: ' + str(pt.type()) +
                           ' is not registered')

    return mol

where the round( ,16) has been used to because I am getting the error:

press enter to continue [4.423185485e-315 4.42424859e-315 4.41864936e-315 ][0.0 0.0 1.0 ]

1: ======================================================================
1: ERROR: test_optimize_BEfire (test_optimizers.test_backward_euler_fire.Test_TotalEnergyNuclearOptimization.test_optimize_BEfire)
1: ----------------------------------------------------------------------
1: Traceback (most recent call last):
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/tests/python/unit_tests/test_optimizers/test_backward_euler_fire.py", line 48, in test_optimize_BEfire
1:     egy, pts = mm.run_as(TotalEnergyNuclearOptimization(), "BackwardEulerFire",
1:                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/src/python/structurefinder/fire/backward_euler/backward_euler.py", line 120, in run_
1:     backwardeuler_FIRE(molecule,numb_coord, R_xyz)
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/src/python/structurefinder/fire/backward_euler/backward_euler.py", line 101, in backwardeuler_FIRE
1:     G_0 =  grad_func(mol_coord,mol)           #<-- Initial Gradient
1:            ^^^^^^^^^^^^^^^^^^^^^^^^
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/src/python/structurefinder/fire/backward_euler/backward_euler.py", line 69, in grad_func
1:     return submods["Gradient"].run_as(EnergyNuclearGradientStdVectorD(), chemist.ChemicalSystem(current_molecule), current_points)
1:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/build/_deps/friendzone-src/src/python/friendzone/nwx2qcengine/__init__.py", line 95, in run_
1:     return _run_impl('gradient', inputs, self.results(),
1:            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/build/_deps/friendzone-src/src/python/friendzone/nwx2qcengine/__init__.py", line 36, in _run_impl
1:     mol = unwrap_inputs(pts[driver], inputs)
1:           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1:   File "/home/leothan/Documents/universities/ISU/PhD/Research/NWChemX/StructureFinder/build/_deps/friendzone-src/src/python/friendzone/utils/unwrap_inputs.py", line 55, in unwrap_inputs
1:     raise RuntimeError(
1: RuntimeError: Derivative must be computed at molecular geometry
1: 
1: ----------------------------------------------------------------------

and by using round( , 16) is fixed

jwaldrop107

I know this is still a work in progress, but there are some cleanliness things to deal with.

Testing/Temporary/CTestCostData.txt

Testing/Temporary/LastTest.log

tests/python/unit_tests/test_optimizers/test_pybernyop.py

jwaldrop107 · 2025-06-18T17:42:25Z

Regarding the suggested change to friendzone/utils/unwrap_inputs.py, you'll need to open a PR in that repository with the recommended changes.

fcuantico · 2025-06-18T18:05:42Z

I think I now did the change in the FriendZone repository

…er into fcuantico-patch-1

jwaldrop107

I know this is still a work in progress, but the following are some notes on needed changes that I wanted to highlight.

jwaldrop107 · 2025-07-02T23:47:54Z

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

+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())


Suggested change

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())

The contents in this file are just copy/paste from elsewhere. Everything but the license header can be deleted.

jwaldrop107 · 2025-07-02T23:48:54Z

src/python/structurefinder/fire/backward_euler/be2_DC_NVT.py

@@ -0,0 +1,129 @@
+#!/usr/bin/env python3


I think this whole file can be removed.

jwaldrop107 · 2025-07-02T23:49:19Z

src/python/structurefinder/fire/backward_euler/be2_DC_VarT.py

@@ -0,0 +1,137 @@
+#!/usr/bin/env python3


Similar to the other one, I think this whole file can be removed.

jwaldrop107 · 2025-07-02T23:51:57Z