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# fmt: off
"""Tests for the Castep.read method"""
from io import StringIO
import numpy as np
import pytest
from ase.constraints import FixAtoms, FixCartesian
from ase.io.castep.castep_reader import (
_read_forces,
_read_fractional_coordinates,
_read_header,
_read_hirshfeld_charges,
_read_hirshfeld_details,
_read_mulliken_charges,
_read_stress,
_read_unit_cell,
_set_energy_and_free_energy,
read_castep_castep,
)
from ase.units import GPa
HEADER = """\
************************************ Title ************************************
***************************** General Parameters ******************************
output verbosity : normal (1)
write checkpoint data to : castep.check
type of calculation : single point energy
stress calculation : off
density difference calculation : off
electron localisation func (ELF) calculation : off
Hirshfeld analysis : off
polarisation (Berry phase) analysis : off
molecular orbital projected DOS : off
deltaSCF calculation : off
unlimited duration calculation
timing information : on
memory usage estimate : on
write extra output files : on
write final potential to formatted file : off
write final density to formatted file : off
write BibTeX reference list : on
write OTFG pseudopotential files : on
write electrostatic potential file : on
write bands file : on
checkpoint writing : both castep_bin and check files
random number generator seed : 42
*********************** Exchange-Correlation Parameters ***********************
using functional : Local Density Approximation
DFT+D: Semi-empirical dispersion correction : off
************************* Pseudopotential Parameters **************************
pseudopotential representation : reciprocal space
<beta|phi> representation : reciprocal space
spin-orbit coupling : off
**************************** Basis Set Parameters *****************************
basis set accuracy : FINE
finite basis set correction : none
**************************** Electronic Parameters ****************************
number of electrons : 8.000
net charge of system : 0.000
treating system as non-spin-polarized
number of bands : 8
********************* Electronic Minimization Parameters **********************
Method: Treating system as metallic with density mixing treatment of electrons,
and number of SD steps : 1
and number of CG steps : 4
total energy / atom convergence tol. : 0.1000E-04 eV
eigen-energy convergence tolerance : 0.1000E-05 eV
max force / atom convergence tol. : ignored
periodic dipole correction : NONE
************************** Density Mixing Parameters **************************
density-mixing scheme : Broyden
max. length of mixing history : 20
*********************** Population Analysis Parameters ************************
Population analysis with cutoff : 3.000 A
Population analysis output : summary and pdos components
*******************************************************************************
""" # noqa: E501
# Some keyword in the .param file triggers a more detailed header.
HEADER_DETAILED = """\
************************************ Title ************************************
***************************** General Parameters ******************************
output verbosity : normal (1)
write checkpoint data to : castep.check
type of calculation : single point energy
stress calculation : off
density difference calculation : off
electron localisation func (ELF) calculation : off
Hirshfeld analysis : off
polarisation (Berry phase) analysis : off
molecular orbital projected DOS : off
deltaSCF calculation : off
unlimited duration calculation
timing information : on
memory usage estimate : on
write extra output files : on
write final potential to formatted file : off
write final density to formatted file : off
write BibTeX reference list : on
write OTFG pseudopotential files : on
write electrostatic potential file : on
write bands file : on
checkpoint writing : both castep_bin and check files
output length unit : A
output mass unit : amu
output time unit : ps
output charge unit : e
output spin unit : hbar/2
output energy unit : eV
output force unit : eV/A
output velocity unit : A/ps
output pressure unit : GPa
output inv_length unit : 1/A
output frequency unit : cm-1
output force constant unit : eV/A**2
output volume unit : A**3
output IR intensity unit : (D/A)**2/amu
output dipole unit : D
output efield unit : eV/A/e
output entropy unit : J/mol/K
output efield chi2 unit : pm/V
wavefunctions paging : none
random number generator seed : 90945350
data distribution : optimal for this architecture
optimization strategy : balance speed and memory
*********************** Exchange-Correlation Parameters ***********************
using functional : Local Density Approximation
relativistic treatment : Koelling-Harmon
DFT+D: Semi-empirical dispersion correction : off
************************* Pseudopotential Parameters **************************
pseudopotential representation : reciprocal space
<beta|phi> representation : reciprocal space
spin-orbit coupling : off
**************************** Basis Set Parameters *****************************
plane wave basis set cut-off : 180.0000 eV
size of standard grid : 1.7500
size of fine gmax : 12.0285 1/A
finite basis set correction : none
**************************** Electronic Parameters ****************************
number of electrons : 8.000
net charge of system : 0.000
treating system as non-spin-polarized
number of bands : 8
********************* Electronic Minimization Parameters **********************
Method: Treating system as metallic with density mixing treatment of electrons,
and number of SD steps : 1
and number of CG steps : 4
total energy / atom convergence tol. : 0.1000E-04 eV
eigen-energy convergence tolerance : 0.1000E-05 eV
max force / atom convergence tol. : ignored
convergence tolerance window : 3 cycles
max. number of SCF cycles : 30
number of fixed-spin iterations : 10
smearing scheme : Gaussian
smearing width : 0.2000 eV
Fermi energy convergence tolerance : 0.2721E-13 eV
periodic dipole correction : NONE
************************** Density Mixing Parameters **************************
density-mixing scheme : Broyden
max. length of mixing history : 20
charge density mixing amplitude : 0.8000
cut-off energy for mixing : 180.0 eV
*********************** Population Analysis Parameters ************************
Population analysis with cutoff : 3.000 A
Population analysis output : summary and pdos components
*******************************************************************************
""" # noqa: E501
# Some XC functionals cannot be mapped by ASE to keywords; e.g. from Castep 25
HEADER_PZ_LDA = """\
************************************ Title ************************************
***************************** General Parameters ******************************
output verbosity : normal (1)
write checkpoint data to : castep.check
type of calculation : single point energy
stress calculation : on
density difference calculation : off
electron localisation func (ELF) calculation : off
Hirshfeld analysis : off
polarisation (Berry phase) analysis : off
molecular orbital projected DOS : off
deltaSCF calculation : off
unlimited duration calculation
timing information : on
memory usage estimate : on
write extra output files : on
write final potential to formatted file : off
write final density to formatted file : off
write BibTeX reference list : on
write OTFG pseudopotential files : on
write electrostatic potential file : on
write bands file : on
checkpoint writing : both castep_bin and check files
random number generator seed : 112211524
*********************** Exchange-Correlation Parameters ***********************
using functional : Perdew-Zunger Local Density Approximation
DFT+D: Semi-empirical dispersion correction : off
************************* Pseudopotential Parameters **************************
pseudopotential representation : reciprocal space
<beta|phi> representation : reciprocal space
spin-orbit coupling : off
**************************** Basis Set Parameters *****************************
basis set accuracy : FINE
finite basis set correction : none
**************************** Electronic Parameters ****************************
number of electrons : 28.00
net charge of system : 0.000
treating system as non-spin-polarized
number of bands : 18
********************* Electronic Minimization Parameters **********************
Method: Treating system as metallic with density mixing treatment of electrons,
and number of SD steps : 1
and number of CG steps : 4
total energy / atom convergence tol. : 0.1000E-04 eV
eigen-energy convergence tolerance : 0.1429E-06 eV
max force / atom convergence tol. : ignored
periodic dipole correction : NONE
************************** Density Mixing Parameters **************************
density-mixing scheme : Pulay
max. length of mixing history : 20
*********************** Population Analysis Parameters ************************
Population analysis with cutoff : 3.000 A
Population analysis output : summary and pdos components
*******************************************************************************
""" # noqa: E501,W291,W293
def test_header():
"""Test if the header blocks can be parsed correctly."""
out = StringIO(HEADER)
parameters = _read_header(out)
parameters_ref = {
'task': 'SinglePoint',
'iprint': 1,
'calculate_stress': False,
'xc_functional': 'LDA',
'sedc_apply': False,
'basis_precision': 'FINE',
'finite_basis_corr': 0,
'elec_energy_tol': 1e-5,
'mixing_scheme': 'Broyden',
}
assert parameters == parameters_ref
def test_header_detailed():
"""Test if the header blocks can be parsed correctly."""
out = StringIO(HEADER_DETAILED)
parameters = _read_header(out)
parameters_ref = {
'task': 'SinglePoint',
'iprint': 1,
'calculate_stress': False,
'opt_strategy': 'Default',
'xc_functional': 'LDA',
'sedc_apply': False,
'cut_off_energy': 180.0,
'finite_basis_corr': 0,
'elec_energy_tol': 1e-5,
'elec_convergence_win': 3,
'mixing_scheme': 'Broyden',
}
assert parameters == parameters_ref
def test_header_castep25():
"""Test if header block with unknown XC functional is parsed correctly"""
out = StringIO(HEADER_PZ_LDA)
parameters = _read_header(out)
parameters_ref = {
"task": "SinglePoint",
"iprint": 1,
"calculate_stress": True,
"xc_functional": "Perdew-Zunger Local Density Approximation",
"sedc_apply": False,
"basis_precision": "FINE",
"finite_basis_corr": 0,
"elec_energy_tol": 1e-5,
"mixing_scheme": "Pulay",
}
assert parameters == parameters_ref
UNIT_CELL = """\
-------------------------------
Unit Cell
-------------------------------
Real Lattice(A) Reciprocal Lattice(1/A)
-0.0287130 2.6890780 2.6889378 -1.148709953 1.163162213 1.161190328
2.6890780 -0.0287130 2.6889378 1.163162214 -1.148709951 1.161190326
2.6938401 2.6938401 -0.0335277 1.159077172 1.159077170 -1.146760802
""" # noqa: E501
def test_unit_cell():
"""Test if the Unit Cell block can be parsed correctly."""
out = StringIO(UNIT_CELL)
out.readline()
out.readline()
cell = _read_unit_cell(out)
cell_ref = [
[-0.0287130, +2.6890780, +2.6889378],
[+2.6890780, -0.0287130, +2.6889378],
[+2.6938401, +2.6938401, -0.0335277],
]
np.testing.assert_allclose(cell, cell_ref)
FRACTIONAL_COORDINATES = """\
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Fractional coordinates of atoms x
x Number u v w x
x---------------------------------------------------------------x
x Si 1 -0.000000 -0.000000 0.000000 x
x Si 2 0.249983 0.249983 0.254121 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
"""
def test_fractional_coordinates():
"""Test if fractional coordinates can be parsed correctly."""
out = StringIO(FRACTIONAL_COORDINATES)
out.readline()
out.readline()
species, custom_species, positions_frac = \
_read_fractional_coordinates(out, 2)
positions_frac_ref = [
[-0.000000, -0.000000, -0.000000],
[+0.249983, +0.249983, +0.254121],
]
np.testing.assert_array_equal(species, ['Si', 'Si'])
assert custom_species is None
np.testing.assert_allclose(positions_frac, positions_frac_ref)
FORCES = """\
************************** Forces **************************
* *
* Cartesian components (eV/A) *
* -------------------------------------------------------- *
* x y z *
* *
* Si 1 -0.02211 -0.02210 -0.02210 *
* Si 2 0.02211 0.02210 0.02210 *
* *
************************************************************
"""
CONSTRAINED_FORCES = """\
******************************** Constrained Forces ********************************
* *
* Cartesian components (eV/A) *
* -------------------------------------------------------------------------------- *
* x y z *
* *
* Si 1 0.00000(cons'd) 0.00000(cons'd) 0.00000(cons'd) *
* Si 2 -0.00252 -0.00252 0.00000(cons'd) *
* *
************************************************************************************
""" # noqa: E501
def test_forces():
"""Test if the Forces block can be parsed correctly."""
out = StringIO(FORCES)
out.readline()
forces, constraints = _read_forces(out, n_atoms=2)
forces_ref = [
[-0.02211, -0.02210, -0.02210],
[+0.02211, +0.02210, +0.02210],
]
np.testing.assert_allclose(forces, forces_ref)
assert not constraints
def test_constrainted_forces():
"""Test if the Constrainted Forces block can be parsed correctly."""
out = StringIO(CONSTRAINED_FORCES)
out.readline()
forces, constraints = _read_forces(out, n_atoms=2)
forces_ref = [
[+0.00000, +0.00000, +0.00000],
[-0.00252, -0.00252, +0.00000],
]
constraints_ref = [
FixAtoms(0),
FixCartesian(1, mask=(0, 0, 1)),
]
np.testing.assert_allclose(forces, forces_ref)
assert all(constraints[0].index == constraints_ref[0].index)
assert all(constraints[1].index == constraints_ref[1].index)
assert all(constraints[1].mask == constraints_ref[1].mask)
STRESS = """\
***************** Stress Tensor *****************
* *
* Cartesian components (GPa) *
* --------------------------------------------- *
* x y z *
* *
* x -0.006786 -0.035244 0.023931 *
* y -0.035244 -0.006786 0.023931 *
* z 0.023931 0.023931 -0.011935 *
* *
* Pressure: 0.0085 *
* *
*************************************************
"""
def test_stress():
"""Test if the Stress Tensor block can be parsed correctly."""
out = StringIO(STRESS)
out.readline()
results = _read_stress(out)
stress_ref = [
-0.006786,
-0.006786,
-0.011935,
+0.023931,
+0.023931,
-0.035244,
]
stress_ref = np.array(stress_ref) * GPa
pressure_ref = 0.0085 * GPa
np.testing.assert_allclose(results['stress'], stress_ref)
np.testing.assert_allclose(results['pressure'], pressure_ref)
# bulk("AlP", "zincblende", a=5.43)
MULLIKEN_SPIN_UNPOLARIZED = """\
Atomic Populations (Mulliken)
-----------------------------
Species Ion s p d f Total Charge (e)
==========================================================================
Al 1 0.935 1.361 0.000 0.000 2.296 0.704
P 1 1.665 4.039 0.000 0.000 5.704 -0.704
==========================================================================
"""
# bulk("MnTe", "zincblende", a=6.34)
MULLIKEN_SPIN_POLARIZED = """\
Atomic Populations (Mulliken)
-----------------------------
Species Ion Spin s p d f Total Charge(e) Spin(hbar/2)
==============================================================================================
Mn 1 up: 1.436 3.596 4.918 0.000 9.950 -0.114 4.785
1 dn: 1.293 3.333 0.538 0.000 5.164
Te 1 up: 0.701 2.229 0.000 0.000 2.929 0.114 -0.027
1 dn: 0.763 2.194 0.000 0.000 2.956
==============================================================================================
""" # noqa: E501
def test_mulliken_spin_unpolarized():
"""Test if the Atomic Populations block can be parsed correctly."""
out = StringIO(MULLIKEN_SPIN_UNPOLARIZED)
out.readline() # read header
results = _read_mulliken_charges(out)
np.testing.assert_allclose(results['charges'], [+0.704, -0.704])
assert 'magmoms' not in results
def test_mulliken_spin_polarized():
"""Test if the Atomic Populations block can be parsed correctly."""
out = StringIO(MULLIKEN_SPIN_POLARIZED)
out.readline() # read header
results = _read_mulliken_charges(out)
np.testing.assert_allclose(results['charges'], [-0.114, +0.114])
np.testing.assert_allclose(results['magmoms'], [+4.785, -0.027])
HIRSHFELD_DETAILS = """\
Species 1, Atom 1 : Al
Fractional coordinates :
0.000000000 0.000000000 0.000000000
Cartesian coordinates (A) :
0.000000000 0.000000000 0.000000000
Free atom total nuclear charge (e) :
3.000000000
Free atom total electronic charge on real space grid (e) :
-3.000000000
SCF total electronic charge on real space grid (e) :
-8.000000000
cut-off radius for r-integrals :
10.000000000
Free atom volume (Bohr**3) :
67.048035000
Hirshfeld total electronic charge (e) :
-2.821040742
Hirshfeld net atomic charge (e) :
0.178959258
Hirshfeld atomic volume (Bohr**3) :
61.353953500
Hirshfeld / free atomic volume :
0.915074595
Species 2, Atom 1 : P
Fractional coordinates :
0.250000000 0.250000000 0.250000000
Cartesian coordinates (A) :
1.357500000 1.357500000 1.357500000
Free atom total nuclear charge (e) :
5.000000000
Free atom total electronic charge on real space grid (e) :
-5.000000000
SCF total electronic charge on real space grid (e) :
-8.000000000
cut-off radius for r-integrals :
10.000000000
Free atom volume (Bohr**3) :
70.150468179
Hirshfeld total electronic charge (e) :
-5.178959258
Hirshfeld net atomic charge (e) :
-0.178959258
Hirshfeld atomic volume (Bohr**3) :
66.452900385
Hirshfeld / free atomic volume :
0.947290904
"""
def test_hirshfeld_details():
"""Test if the Hirshfeld block of ispin > 1 can be parsed correctly."""
out = StringIO(HIRSHFELD_DETAILS)
results = _read_hirshfeld_details(out, 2)
np.testing.assert_allclose(
results['hirshfeld_volume_ratios'],
[0.915074595, 0.947290904],
)
HIRSHFELD_SPIN_UNPOLARIZED = """\
Hirshfeld Analysis
------------------
Species Ion Hirshfeld Charge (e)
======================================
Al 1 0.18
P 1 -0.18
======================================
"""
HIRSHFELD_SPIN_POLARIZED = """\
Hirshfeld Analysis
------------------
Species Ion Hirshfeld Charge (e) Spin (hbar/2)
===================================================
Mn 1 0.06 4.40
Te 1 -0.06 0.36
===================================================
"""
def test_hirshfeld_spin_unpolarized():
"""Test if the Hirshfeld Analysis block can be parsed correctly."""
out = StringIO(HIRSHFELD_SPIN_UNPOLARIZED)
out.readline() # read header
results = _read_hirshfeld_charges(out)
np.testing.assert_allclose(results['hirshfeld_charges'], [+0.18, -0.18])
assert 'hirshfeld_magmoms' not in results
def test_hirshfeld_spin_polarized():
"""Test if the Hirshfeld Analysis block can be parsed correctly."""
out = StringIO(HIRSHFELD_SPIN_POLARIZED)
out.readline() # read header
results = _read_hirshfeld_charges(out)
np.testing.assert_allclose(results['hirshfeld_charges'], [+0.06, -0.06])
np.testing.assert_allclose(results['hirshfeld_magmoms'], [+4.40, +0.36])
def test_energy_and_free_energy_metallic():
"""Test if `energy` and `free_energy` is set correctly.
This test is made based on the following output obtained for Si.
```
Final energy, E = -340.9490879813 eV
Final free energy (E-TS) = -340.9490902954 eV
(energies not corrected for finite basis set)
NB est. 0K energy (E-0.5TS) = -340.9490891384 eV
(SEDC) Total Energy Correction : -0.567289E+00 eV
Dispersion corrected final energy*, Ecor = -341.5163768370 eV
Dispersion corrected final free energy* (Ecor-TS) = -341.5163791511 eV
NB dispersion corrected est. 0K energy* (Ecor-0.5TS) = -341.5163779940 eV
For future reference: finite basis dEtot/dlog(Ecut) = -0.487382eV
Total energy corrected for finite basis set = -341.516014 eV
```
""" # noqa: E501
results = {
'energy_without_dispersion_correction': -340.9490879813,
'free_energy_without_dispersion_correction': -340.9490902954,
'energy_zero_without_dispersion_correction': -340.9490891384,
}
results.update(results)
_set_energy_and_free_energy(results)
assert results['energy'] == -340.9490891384
assert results['free_energy'] == -340.9490902954
results_dispersion_correction = {
'energy_with_dispersion_correction': -341.5163768370,
'free_energy_with_dispersion_correction': -341.5163791511,
'energy_zero_with_dispersion_correction': -341.5163779940,
}
results.update(results_dispersion_correction)
_set_energy_and_free_energy(results)
assert results['energy'] == -341.5163779940
assert results['free_energy'] == -341.5163791511
results.update({'energy_with_finite_basis_set_correction': -341.516014})
_set_energy_and_free_energy(results)
assert results['energy'] == -341.5163779940
assert results['free_energy'] == -341.5163791511
def test_energy_and_free_energy_non_metallic():
"""Test if `energy` and `free_energy` is set correctly.
This test is made based on the following output obtained for Si.
```
Final energy = -340.9491006696 eV
(energy not corrected for finite basis set)
(SEDC) Total Energy Correction : -0.567288E+00 eV
Dispersion corrected final energy* = -341.5163888035 eV
For future reference: finite basis dEtot/dlog(Ecut) = -0.487570eV
Total energy corrected for finite basis set = -341.516024 eV
```
"""
results = {'energy_without_dispersion_correction': -340.9491006696}
_set_energy_and_free_energy(results)
assert results['energy'] == -340.9491006696
assert results['free_energy'] == -340.9491006696
results.update({'energy_with_dispersion_correction': -341.5163888035})
_set_energy_and_free_energy(results)
assert results['energy'] == -341.5163888035
assert results['free_energy'] == -341.5163888035
results.update({'energy_with_finite_basis_set_correction': -341.516024})
_set_energy_and_free_energy(results)
assert results['energy'] == -341.516024
assert results['free_energy'] == -341.5163888035
@pytest.mark.filterwarnings('ignore::UserWarning')
def test_md_images(datadir):
"""Test if multiple images can be read for the MolecularDynamics task."""
images = read_castep_castep(f'{datadir}/castep/md.castep', index=':')
assert len(images) == 3 # 0th, 1st, 2nd steps
# `read_castep_castep_old` could parse multi-images but not forces / stress
# check if new `read_castep_castep` can do
atoms = images[-1]
forces_ref = [
[-0.09963, +0.10729, -0.00665],
[+0.09339, +0.01482, +0.01147],
[-0.02828, -0.11817, -0.03557],
[+0.14991, -0.01604, +0.02132],
[-0.03495, +0.04016, -0.03526],
[+0.07136, -0.07883, +0.04578],
[-0.26870, -0.12445, -0.14684],
[+0.11690, +0.17523, +0.14574],
]
np.testing.assert_array_almost_equal(atoms.get_forces(), forces_ref)
stress_ref = [
+0.390672, +0.388091, +0.385978, -0.276337, -0.061901, -0.144025,
]
np.testing.assert_array_almost_equal(atoms.get_stress() / GPa, stress_ref)
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