dxtb/examples/batch-2.py at 53122ee43755d568f1a728abb6468924857ef1ce · grimme-lab/dxtb · GitHub

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#!/usr/bin/env python3
# This file is part of dxtb.
#
# SPDX-Identifier: Apache-2.0
# Copyright (C) 2024 Grimme Group
#
# 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.
"""
Obtaining the interaction energy of a dimer from a batched calculation.
"""

import tad_mctc as mctc
import torch

import dxtb

torch.set_printoptions(precision=10)


# S22 system 4: formamide dimer
numbers = mctc.batch.pack(
    (
        mctc.convert.symbol_to_number("C C N N H H H H H H O O".split()),
        mctc.convert.symbol_to_number("C O N H H H".split()),
    )
)

# coordinates in Bohr
positions = mctc.batch.pack(
    (
        torch.tensor(
            [
                [-3.81469488143921, +0.09993441402912, 0.00000000000000],
                [+3.81469488143921, -0.09993441402912, 0.00000000000000],
                [-2.66030049324036, -2.15898251533508, 0.00000000000000],
                [+2.66030049324036, +2.15898251533508, 0.00000000000000],
                [-0.73178529739380, -2.28237795829773, 0.00000000000000],
                [-5.89039325714111, -0.02589114569128, 0.00000000000000],
                [-3.71254944801331, -3.73605775833130, 0.00000000000000],
                [+3.71254944801331, +3.73605775833130, 0.00000000000000],
                [+0.73178529739380, +2.28237795829773, 0.00000000000000],
                [+5.89039325714111, +0.02589114569128, 0.00000000000000],
                [-2.74426102638245, +2.16115570068359, 0.00000000000000],
                [+2.74426102638245, -2.16115570068359, 0.00000000000000],
            ],
            dtype=torch.double,
        ),
        torch.tensor(
            [
                [-0.55569743203406, +1.09030425468557, 0.00000000000000],
                [+0.51473634678469, +3.15152550263611, 0.00000000000000],
                [+0.59869690244446, -1.16861263789477, 0.00000000000000],
                [-0.45355203669134, -2.74568780438064, 0.00000000000000],
                [+2.52721209544999, -1.29200800956867, 0.00000000000000],
                [-2.63139587595376, +0.96447869452240, 0.00000000000000],
            ],
            dtype=torch.double,
        ),
    )
)

# total charge of both system
charge = torch.tensor([0.0, 0.0], dtype=torch.double)


# instantiate calculator and calculate GFN1 energy in Hartree
calc = dxtb.calculators.GFN1Calculator(numbers, dtype=torch.double)
energy = calc.get_energy(positions, charge)

print("Testing dimer interaction energy:")
print(f"Calculated: {energy}")
print(
    "Expected:   tensor([-23.2835232516, -11.6302093800], dtype=torch.float64)"
)
# tensor([-23.2835232516, -11.6302093800], dtype=torch.float64)

e = energy[0] - 2 * energy[1]
# tensor(-0.0231044917, dtype=torch.float64)

print("\nInteraction energy in kcal/mol:")
print(f"Calculated: {e * mctc.units.AU2KCALMOL}")
print("Expected:   -14.4982874136")
# tensor(-14.4982874136, dtype=torch.float64)