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new feature DFTB+ (#511)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: liaoruihao <liaoruihao@liaoruihaodeMacBook-Pro.local>
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‎README.md‎

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@@ -88,11 +88,12 @@ The `System` or `LabeledSystem` can be constructed from the following file forma
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| Amber | multi | True | True | LabeledSystem | 'amber/md' |
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| Amber/sqm | sqm.out | False | False | System | 'sqm/out' |
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| Gromacs | gro | True | False | System | 'gromacs/gro' |
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| ABACUS | STRU | False | False | System | 'abacus/stru' |
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| ABACUS | STRU | False | False | System | 'abacus/stru' |
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| ABACUS | STRU | False | True | LabeledSystem | 'abacus/scf' |
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| ABACUS | cif | True | True | LabeledSystem | 'abacus/md' |
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| ABACUS | STRU | True | True | LabeledSystem | 'abacus/relax' |
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| ase | structure | True | True | MultiSystems | 'ase/structure' |
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| DFTB+ | dftbplus | False | True | LabeledSystem | 'dftbplus' |
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The Class `dpdata.MultiSystems` can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems.

‎dpdata/dftbplus/__init__.py‎

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‎dpdata/dftbplus/output.py‎

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from typing import Tuple
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import numpy as np
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def read_dftb_plus(fn_1: str, fn_2: str) -> Tuple[str, np.ndarray, float, np.ndarray]:
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"""Read from DFTB+ input and output.
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Parameters
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----------
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fn_1 : str
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DFTB+ input file name
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fn_2 : str
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DFTB+ output file name
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Returns
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-------
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str
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atomic symbols
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np.ndarray
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atomic coordinates
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float
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total potential energy
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np.ndarray
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atomic forces
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"""
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coord = None
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symbols = None
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forces = None
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energy = None
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with open(fn_1) as f:
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flag = 0
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for line in f:
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if flag == 1:
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flag += 1
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elif flag == 2:
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components = line.split()
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flag += 1
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elif line.startswith("Geometry"):
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flag = 1
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coord = []
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symbols = []
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elif flag in (3, 4, 5, 6):
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s = line.split()
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components_num = int(s[1])
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symbols.append(components[components_num - 1])
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coord.append([float(s[2]), float(s[3]), float(s[4])])
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flag += 1
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if flag == 7:
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flag = 0
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with open(fn_2) as f:
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flag = 0
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for line in f:
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if line.startswith("Total Forces"):
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flag = 8
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forces = []
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elif flag in (8, 9, 10, 11):
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s = line.split()
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forces.append([float(s[1]), float(s[2]), float(s[3])])
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flag += 1
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if flag == 12:
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flag = 0
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elif line.startswith("Total energy:"):
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s = line.split()
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energy = float(s[2])
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flag = 0
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symbols = np.array(symbols)
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forces = np.array(forces)
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coord = np.array(coord)
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assert coord.shape == forces.shape
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return symbols, coord, energy, forces

‎dpdata/plugins/dftbplus.py‎

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import numpy as np
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from dpdata.dftbplus.output import read_dftb_plus
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from dpdata.format import Format
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from dpdata.unit import EnergyConversion, ForceConversion
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energy_convert = EnergyConversion("hartree", "eV").value()
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force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
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@Format.register("dftbplus")
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class DFTBplusFormat(Format):
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"""The DFTBplusFormat class handles files in the DFTB+ format.
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This class provides a method to read DFTB+ files from a labeled system and
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returns a dictionary containing various properties of the system.For more
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information, please refer to the official documentation at the following URL:
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https://dftbplus.org/documentation
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Attributes
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----------
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None
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Methods
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-------
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from_labeled_system(file_paths, **kwargs): Reads system information from files.
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"""
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def from_labeled_system(self, file_paths, **kwargs):
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"""Reads system information from the given DFTB+ file paths.
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Parameters
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----------
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file_paths : tuple
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A tuple containing the input and output file paths.
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- Input file (file_in): Contains information about symbols and coord.
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- Output file (file_out): Contains information about energy and force.
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**kwargs : dict
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other parameters
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"""
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file_in, file_out = file_paths
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symbols, coord, energy, forces = read_dftb_plus(file_in, file_out)
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last_occurrence = {v: i for i, v in enumerate(symbols)}
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atom_names = np.array(sorted(np.unique(symbols), key=last_occurrence.get))
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atom_types = np.array([np.where(atom_names == s)[0][0] for s in symbols])
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atom_numbs = np.array([np.sum(atom_types == i) for i in range(len(atom_names))])
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natoms = coord.shape[0]
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return {
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"atom_types": atom_types,
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"atom_names": list(atom_names),
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"atom_numbs": list(atom_numbs),
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"coords": coord.reshape((1, natoms, 3)),
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"energies": np.array([energy * energy_convert]),
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"forces": (forces * force_convert).reshape((1, natoms, 3)),
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"cells": np.zeros((1, 3, 3)),
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"orig": np.zeros(3),
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"nopbc": True,
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}

‎tests/dftbplus/detailed.out‎

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Fermi distribution function
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Calculation with static geometry
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********************************************************************************
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iSCC Total electronic Diff electronic SCC error
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88 -0.33554958E+01 -0.31884693E-07 0.11352275E-06
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********************************************************************************
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Total charge: -0.00000000
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Atomic gross charges (e)
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Atom Charge
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1 -0.48336965
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2 0.03575828
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3 0.22380553
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4 0.22380583
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Nr. of electrons (up): 8.00000000
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Atom populations (up)
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Atom Population
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1 5.48336965
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2 0.96424172
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3 0.77619447
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4 0.77619417
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l-shell populations (up)
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Atom Sh. l Population
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1 1 0 1.65733979
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1 2 1 3.82602986
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2 1 0 0.96424172
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2 2 1 0.00000000
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3 1 0 0.77619447
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3 2 1 0.00000000
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4 1 0 0.77619417
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4 2 1 0.00000000
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Orbital populations (up)
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Atom Sh. l m Population Label
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1 1 0 0 1.65733979 s
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1 2 1 -1 1.21678996 p_y
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1 2 1 0 1.46556336 p_z
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1 2 1 1 1.14367654 p_x
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2 1 0 0 0.96424172 s
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2 2 1 -1 0.00000000 p_y
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2 2 1 0 0.00000000 p_z
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2 2 1 1 0.00000000 p_x
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3 1 0 0 0.77619447 s
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3 2 1 -1 0.00000000 p_y
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3 2 1 0 0.00000000 p_z
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3 2 1 1 0.00000000 p_x
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4 1 0 0 0.77619417 s
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4 2 1 -1 0.00000000 p_y
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4 2 1 0 0.00000000 p_z
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4 2 1 1 0.00000000 p_x
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Fermi level: -0.2370222488 H -6.4497 eV
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Band energy: -3.2187242078 H -87.5859 eV
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TS: 0.0000000000 H 0.0000 eV
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Band free energy (E-TS): -3.2187242078 H -87.5859 eV
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Extrapolated E(0K): -3.2187242078 H -87.5859 eV
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Input / Output electrons (q): 8.0000000000 8.0000000000
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Energy H0: -3.3599884076 H -91.4299 eV
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Energy SCC: 0.0056352830 H 0.1533 eV
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Energy 3rd: -0.0011426808 H -0.0311 eV
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Total Electronic energy: -3.3554958054 H -91.3077 eV
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Repulsive energy: 0.0590974170 H 1.6081 eV
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Total energy: -3.2963983884 H -89.6996 eV
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Extrapolated to 0: -3.2963983884 H -89.6996 eV
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Total Mermin free energy: -3.2963983884 H -89.6996 eV
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Force related energy: -3.2963983884 H -89.6996 eV
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SCC converged
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Total Forces
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1 0.016567056203 0.002817951422 0.005634574270
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2 -0.018803818530 -0.000002880649 -0.000006015442
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3 0.001118562874 -0.005291070259 -0.000870711110
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4 0.001118199454 0.002475999486 -0.004757847718
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Maximal derivative component: 0.188038E-01 au
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Dipole moment: -0.06792979 -0.20495079 -0.40960550 au
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Dipole moment: -0.17266032 -0.52093298 -1.04111341 Debye
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‎tests/dftbplus/dftb_pin.hsd‎

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Geometry = GenFormat {
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4 C
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N H
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1 1 1.014150 0.112320 0.047370
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2 2 3.909390 0.037985 -0.101159
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3 2 0.702550 -0.851820 -0.060860
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4 2 0.702550 0.603740 -0.789160
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}
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Driver = {}
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Hamiltonian = DFTB {
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SCC = Yes
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MaxAngularMomentum = {
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N = "p"
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H = "p"
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}
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SlaterKosterFiles = {
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N-N = "/home/jz748/devel/git/Programs/Amber18/dat/slko/3ob-3-1/N-N.skf"
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H-H = "/home/jz748/devel/git/Programs/Amber18/dat/slko/3ob-3-1/H-H.skf"
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H-N = "/home/jz748/devel/git/Programs/Amber18/dat/slko/3ob-3-1/H-N.skf"
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N-H = "/home/jz748/devel/git/Programs/Amber18/dat/slko/3ob-3-1/N-H.skf"
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}
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ThirdOrderFull = Yes
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HubbardDerivs = {
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H = -0.1857
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N = -0.1535
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}
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HCorrection = Damping {
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Exponent = 4.0
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}
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PolynomialRepulsive = {}
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ShellResolvedSCC = No
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OldSKInterpolation = No
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RangeSeparated = None {}
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ReadInitialCharges = No
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InitialCharges = {}
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SCCTolerance = 1.0000000000000001E-005
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ConvergentSCCOnly = Yes
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SpinPolarisation = {}
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ElectricField = {}
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Solver = RelativelyRobust {}
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Charge = 0.0000000000000000
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MaxSCCIterations = 100
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OnSiteCorrection = {}
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Dispersion = {}
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Solvation = {}
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Electrostatics = GammaFunctional {}
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ThirdOrder = No
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Differentiation = FiniteDiff {
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Delta = 1.2207031250000000E-004
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}
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ForceEvaluation = "Traditional"
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Mixer = Broyden {
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MixingParameter = 0.20000000000000001
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InverseJacobiWeight = 1.0000000000000000E-002
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MinimalWeight = 1.0000000000000000
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MaximalWeight = 100000.00000000000
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WeightFactor = 1.0000000000000000E-002
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}
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Filling = Fermi {
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Temperature = 0.0000000000000000
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}
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}
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Options = {
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WriteDetailedOut = Yes
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WriteAutotestTag = No
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WriteDetailedXML = No
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WriteResultsTag = No
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RestartFrequency = 20
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RandomSeed = 0
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WriteHS = No
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WriteRealHS = No
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MinimiseMemoryUsage = No
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ShowFoldedCoords = No
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TimingVerbosity = 1
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WriteChargesAsText = No
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}
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Analysis = {
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CalculateForces = Yes
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ProjectStates = {}
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WriteEigenvectors = No
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WriteBandOut = Yes
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MullikenAnalysis = Yes
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WriteNetCharges = No
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AtomResolvedEnergies = No
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}
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ParserOptions = {
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ParserVersion = 11
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WriteHSDInput = Yes
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StopAfterParsing = No
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IgnoreUnprocessedNodes = No
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}
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Reks = None {}
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ExcitedState = {}

‎tests/test_dftbplus.py‎

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import unittest
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import numpy as np
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from comp_sys import CompLabeledSys, IsNoPBC
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from context import dpdata
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class TestDeepmdLoadAmmonia(unittest.TestCase, CompLabeledSys, IsNoPBC):
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def setUp(self):
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energy_convert = dpdata.unit.EnergyConversion("hartree", "eV").value()
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force_convert = dpdata.unit.ForceConversion(
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"hartree/bohr", "eV/angstrom"
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).value()
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self.system_1 = dpdata.LabeledSystem(
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("dftbplus/dftb_pin.hsd", "dftbplus/detailed.out"), fmt="dftbplus"
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)
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self.system_2 = dpdata.LabeledSystem(
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data={
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"atom_types": np.array([0, 1, 1, 1]),
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"atom_names": ["N", "H"],
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"atom_numbs": [1, 3],
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"coords": np.array(
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[
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[
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[1.014150, 0.112320, 0.047370],
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[3.909390, 0.037985, -0.101159],
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[0.702550, -0.851820, -0.060860],
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[0.702550, 0.603740, -0.789160],
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]
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]
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),
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"energies": np.array([-3.2963983884]) * energy_convert,
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"forces": np.array(
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[
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[
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[0.016567056203, 0.002817951422, 0.005634574270],
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[-0.018803818530, -0.000002880649, -0.000006015442],
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[0.001118562874, -0.005291070259, -0.000870711110],
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[0.001118199454, 0.002475999486, -0.004757847718],
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]
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]
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)
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* force_convert,
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"cells": np.zeros((1, 3, 3)),
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"orig": np.zeros(3),
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"nopbc": True,
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}
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)
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self.places = 6
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self.e_places = 6
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self.f_places = 6
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self.v_places = 6
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if __name__ == "__main__":
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unittest.main()

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