From 99b267b51ec9ac57cac50dabf2e75c57293ad087 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Wed, 23 Jul 2025 14:26:57 -0700 Subject: [PATCH] chore: drop old xml support for QE (pre 6.4) --- .../apps/espresso/formats/xml/xml_base.py | 73 ------- .../apps/espresso/formats/xml/xml_factory.py | 35 ++-- .../apps/espresso/formats/xml/xml_pre64.py | 184 ------------------ express/parsers/apps/espresso/settings.py | 3 +- tests/fixtures/espresso/v5_4/__init__.py | 0 tests/fixtures/espresso/v5_4/references.py | 3 - .../__prefix__.save/K00001/eigenval.xml | 3 - .../outdir/__prefix__.save/K00001/evc.dat | 3 - .../__prefix__.save/K00001/gkvectors.dat | 3 - .../__prefix__.save/K00002/eigenval.xml | 3 - .../outdir/__prefix__.save/K00002/evc.dat | 3 - .../__prefix__.save/K00002/gkvectors.dat | 3 - .../__prefix__.save/K00003/eigenval.xml | 3 - .../outdir/__prefix__.save/K00003/evc.dat | 3 - .../__prefix__.save/K00003/gkvectors.dat | 3 - .../__prefix__.save/K00004/eigenval.xml | 3 - 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.../v5_4/test-002/__prefix__.pdos_tot | 3 - .../fixtures/espresso/v5_4/test-002/bands.dat | 3 - .../espresso/v5_4/test-002/bands.dat.gnu | 3 - .../fixtures/espresso/v5_4/test-002/bands.in | 3 - .../fixtures/espresso/v5_4/test-002/bands.out | 3 - .../__prefix__.save/K00001/eigenval.xml | 3 - .../outdir/__prefix__.save/K00001/evc.dat | 3 - .../__prefix__.save/K00001/gkvectors.dat | 3 - .../__prefix__.save/K00002/eigenval.xml | 3 - .../outdir/__prefix__.save/K00002/evc.dat | 3 - .../__prefix__.save/K00002/gkvectors.dat | 3 - .../__prefix__.save/K00003/eigenval.xml | 3 - .../outdir/__prefix__.save/K00003/evc.dat | 3 - .../__prefix__.save/K00003/gkvectors.dat | 3 - .../__prefix__.save/K00004/eigenval.xml | 3 - .../outdir/__prefix__.save/K00004/evc.dat | 3 - .../__prefix__.save/K00004/gkvectors.dat | 3 - .../__prefix__.save/K00005/eigenval.xml | 3 - .../outdir/__prefix__.save/K00005/evc.dat | 3 - .../__prefix__.save/K00005/gkvectors.dat | 3 - .../__prefix__.save/K00006/eigenval.xml | 3 - .../outdir/__prefix__.save/K00006/evc.dat | 3 - .../__prefix__.save/K00006/gkvectors.dat | 3 - .../outdir/__prefix__.save/atomic_proj.xml | 3 - .../outdir/__prefix__.save/charge-density.dat | 3 - .../outdir/__prefix__.save/data-file.xml | 3 - .../outdir/__prefix__.save/gvectors.dat | 3 - .../__prefix__.save/si_pbe_gbrv_1.0.upf | 3 - .../v5_4/test-002/outdir/__prefix__.wfc | 3 - .../espresso/v5_4/test-002/projwfc.in | 3 - .../espresso/v5_4/test-002/projwfc.out | 3 - .../v5_4/test-002/pseudo/si_pbe_gbrv_1.0.upf | 3 - .../espresso/v5_4/test-002/pw-bands.in | 3 - .../espresso/v5_4/test-002/pw-bands.out | 3 - .../espresso/v5_4/test-002/pw-nscf.in | 3 - .../espresso/v5_4/test-002/pw-nscf.out | 3 - .../fixtures/espresso/v5_4/test-002/pw-scf.in | 3 - .../espresso/v5_4/test-002/pw-scf.out | 3 - tests/fixtures/espresso/v5_4/test-002/run.sh | 3 - .../espresso/v5_4/test-003/normal_modes.out | 3 - .../espresso/v5_4/test-003/phonon_dos.out | 3 - ...{test_parser_pre_v64.py => test_parser.py} | 50 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delete mode 100644 tests/integration/parsers/apps/espresso/test_parser_post_v64.py diff --git a/express/parsers/apps/espresso/formats/xml/xml_base.py b/express/parsers/apps/espresso/formats/xml/xml_base.py index 297a8f2b..6e003e17 100644 --- a/express/parsers/apps/espresso/formats/xml/xml_base.py +++ b/express/parsers/apps/espresso/formats/xml/xml_base.py @@ -1,5 +1,4 @@ import re -from abc import abstractmethod import numpy as np @@ -61,38 +60,7 @@ def fermi_energy(self): bs_tag = self.root.find(self.band_structure_tag) return self._get_xml_tag_value(bs_tag.find(self.fermi_energy_tag)) * Constant.HARTREE - @abstractmethod - def nspins(self) -> int: - """ - Extracts the number of number of spin components. - Returns: - int - """ - pass - - @abstractmethod - def final_lattice_vectors(self, reciprocal=False) -> dict: - """ - Extracts lattice. - - Args: - reciprocal (bool): whether to extract reciprocal lattice. - - Returns: - dict - - Examples: - { - 'vectors': { - 'a': [-0.561154473, -0.000000000, 0.561154473], - 'b': [-0.000000000, 0.561154473, 0.561154473], - 'c': [-0.561154473, 0.561154473, 0.000000000], - 'alat': 9.44858082 - } - } - """ - pass def get_inverse_reciprocal_lattice_vectors(self): """ @@ -102,45 +70,4 @@ def get_inverse_reciprocal_lattice_vectors(self): lattice_array = [reciprocal_lattice["vectors"][i] for i in ["a", "b", "c"]] return np.linalg.inv(np.array(lattice_array)) - @abstractmethod - def eigenvalues_at_kpoints(self): - """ - Returns eigenvalues for all kpoints. - - Returns: - list - - Example: - [ - { - 'kpoint': [-0.5, 0.5, 0.5], - 'weight': 9.5238095E-002, - 'eigenvalues': [ - { - 'energies': [-1.4498446E-001, ..., 4.6507387E-001], - 'occupations': [1, ... , 0], - 'spin': 0.5 - } - ] - }, - ... - ] - """ - pass - @abstractmethod - def final_basis(self): - """ - Extracts basis. - - Returns: - dict - - Example: - { - 'units': 'angstrom', - 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}], - 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}] - } - """ - pass diff --git a/express/parsers/apps/espresso/formats/xml/xml_factory.py b/express/parsers/apps/espresso/formats/xml/xml_factory.py index 7280ff5e..b7573af4 100644 --- a/express/parsers/apps/espresso/formats/xml/xml_factory.py +++ b/express/parsers/apps/espresso/formats/xml/xml_factory.py @@ -1,40 +1,31 @@ import os from typing import Optional, Union -from packaging import version - from express.parsers.apps.espresso import settings from express.parsers.apps.espresso.formats.xml.xml_base import EspressoXMLParserBase from express.parsers.apps.espresso.formats.xml.xml_post64 import EspressoXMLParserPostV6_4 -from express.parsers.apps.espresso.formats.xml.xml_pre64 import EspressoXMLParserPreV6_4 - -VERSIONS = { - "Pre6_4": { - "parser": EspressoXMLParserPreV6_4, - "default_xml_file": settings.XML_DATA_FILE_PREv6_4, - }, - "Post6_4": { - "parser": EspressoXMLParserPostV6_4, - "default_xml_file": settings.XML_DATA_FILE_POSTv6_4, - }, -} def get_xml_parser( parser_version: Union[str, None], work_dir: str, is_sternheimer_gw: bool = False ) -> EspressoXMLParserBase: - parser_version = "6.4" if not parser_version else parser_version - if version.parse(parser_version) <= version.parse("6.4"): - version_key = "Pre6_4" - else: - version_key = "Post6_4" - + """ + Get XML parser for espresso. Only supports post-6.4 versions. + + Args: + parser_version: Version string (unused, kept for compatibility) + work_dir: Working directory + is_sternheimer_gw: Whether this is a Sternheimer GW calculation + + Returns: + EspressoXMLParserPostV6_4 instance + """ xml_file = find_xml_file( work_dir, - VERSIONS[version_key]["default_xml_file"], + settings.XML_DATA_FILE, is_sternheimer_gw, ) - return VERSIONS[version_key]["parser"](xml_file) + return EspressoXMLParserPostV6_4(xml_file) def find_xml_file(work_dir: str, default_xml_filename: str, is_sternheimer_gw: bool) -> Optional[str]: diff --git a/express/parsers/apps/espresso/formats/xml/xml_pre64.py b/express/parsers/apps/espresso/formats/xml/xml_pre64.py deleted file mode 100644 index aa598128..00000000 --- a/express/parsers/apps/espresso/formats/xml/xml_pre64.py +++ /dev/null @@ -1,184 +0,0 @@ -import os -import re -import string -import xml.etree.ElementTree as ET - -import numpy as np - -from express.parsers.apps.espresso.formats.xml.xml_base import EspressoXMLParserBase -from express.parsers.settings import GENERAL_REGEX, Constant - - -class EspressoXMLParserPreV6_4(EspressoXMLParserBase): - """ - Espresso XML parser class for versions <= v6.4. - - Args: - xml_file_path (str): path to the xml file. - """ - - band_structure_tag = "BAND_STRUCTURE_INFO" - fermi_energy_tag = "FERMI_ENERGY" - lattice_tag = "DIRECT_LATTICE_VECTORS" - reciprocal_lattice_tag = "RECIPROCAL_LATTICE_VECTORS" - - def __init__(self, xml_file_path): - super().__init__(xml_file_path) - - def fermi_energy(self): - """ - Extracts fermi energy. - - Returns: - float - """ - bs_tag = self.root.find(self.band_structure_tag) - return self._get_xml_tag_value(bs_tag.find(self.fermi_energy_tag)) * Constant.HARTREE - - def nspins(self): - """ - Extracts the number of number of spin components. - - Returns: - int - """ - bs_tag = self.root.find(self.band_structure_tag) - return self._get_xml_tag_value(bs_tag.find("NUMBER_OF_SPIN_COMPONENTS")) - - def final_lattice_vectors(self, reciprocal=False): - """ - Extracts lattice. - - Args: - reciprocal (bool): whether to extract reciprocal lattice. - - Returns: - dict - - Examples: - { - 'vectors': { - 'a': [-0.561154473, -0.000000000, 0.561154473], - 'b': [-0.000000000, 0.561154473, 0.561154473], - 'c': [-0.561154473, 0.561154473, 0.000000000], - 'alat': 9.44858082 - } - } - """ - vector_tag = "a" - lattice_tag = self.lattice_tag - - if reciprocal: - vector_tag = "b" - lattice_tag = self.reciprocal_lattice_tag - - vectors = {} - cell_tag = self.root.find("CELL") - # lattice_units_tag = cell_tag.find(lattice_tag).find(units_tag) - for vector in cell_tag.find(lattice_tag): - if vector.tag.startswith(vector_tag): - vectors.update( - { - string.ascii_lowercase[int(vector.tag[1]) - 1]: ( - (Constant.BOHR if not reciprocal else 1.0) * self._get_xml_tag_value(vector)[0] - ).tolist() - } - ) - vectors.update({"alat": 1.0}) - return {"vectors": vectors, "units": "angstrom"} if not reciprocal else {"vectors": vectors} - - def get_inverse_reciprocal_lattice_vectors(self): - """ - Returns inverse reciprocal lattice vectors to convert cartesian (2pi/a) point to crystal. - """ - reciprocal_lattice = self.final_lattice_vectors(reciprocal=True) - lattice_array = [reciprocal_lattice["vectors"][i] for i in ["a", "b", "c"]] - return np.linalg.inv(np.array(lattice_array)) - - def eigenvalues_at_kpoints(self): - """ - Returns eigenvalues for all kpoints. - - Returns: - list - - Example: - [ - { - 'kpoint': [-0.5, 0.5, 0.5], - 'weight': 9.5238095E-002, - 'eigenvalues': [ - { - 'energies': [-1.4498446E-001, ..., 4.6507387E-001], - 'occupations': [1, ... , 0], - 'spin': 0.5 - } - ] - }, - ... - ] - """ - eigenvalues_at_kpoints = [] - for eigenvalue_tag in self.root.find("EIGENVALUES"): - cartesianKPoint = self._get_xml_tag_value(eigenvalue_tag.find("K-POINT_COORDS"))[0] - crystalKPoint = np.dot(cartesianKPoint, self.get_inverse_reciprocal_lattice_vectors()) - eigenvalues_at_kpoint = { - "kpoint": crystalKPoint.tolist(), - "weight": self._get_xml_tag_value(eigenvalue_tag.find("WEIGHT")), - "eigenvalues": [], - } - for datafile_tag in [t for t in eigenvalue_tag.iter() if t.tag.startswith("DATAFILE")]: - eigenval_file = os.path.join(self.xml_dir_name, datafile_tag.attrib.get("iotk_link")) - energies, occupations = self._parse_eigenvalue_file(eigenval_file) - eigenvalues_at_kpoint["eigenvalues"].append( - { - "energies": (np.array(energies) * Constant.HARTREE).tolist(), - "occupations": occupations, - "spin": 0.5 if datafile_tag.tag in ["DATAFILE", "DATAFILE.1"] else -0.5, - } - ) - eigenvalues_at_kpoints.append(eigenvalues_at_kpoint) - return eigenvalues_at_kpoints - - def _parse_eigenvalue_file(self, eigenval_xml_path): - """ - Extracts eigenvalues from a given file. - - Args: - eigenval_xml_path (str): path to eigenvalue xml file. - - Returns: - tuple: (energies, occupations) - """ - root = ET.parse(eigenval_xml_path).getroot() - energies = [float(_) for _ in re.findall(GENERAL_REGEX.double_number, root.find("EIGENVALUES").text)] - occupations = [float(_) for _ in re.findall(GENERAL_REGEX.double_number, root.find("OCCUPATIONS").text)] - return energies, occupations - - def final_basis(self): - """ - Extracts basis. - - Returns: - dict - - Example: - { - 'units': 'angstrom', - 'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}], - 'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}] - } - """ - elements, coordinates = [], [] - ion_tag = self.root.find("IONS") - for atom in ion_tag: - if atom.tag.startswith("ATOM"): - elements.append({"id": int(atom.tag[5:]), "value": atom.attrib.get("SPECIES").strip(" \t\n\r")}) - coordinates.append( - { - "id": int(atom.tag[5:]), - "value": (Constant.BOHR * np.array(atom.attrib.get("tau").split()).astype(np.float32)).tolist(), - } - ) - - return {"units": "angstrom", "elements": elements, "coordinates": coordinates} diff --git a/express/parsers/apps/espresso/settings.py b/express/parsers/apps/espresso/settings.py index 01d0bb38..098254e3 100644 --- a/express/parsers/apps/espresso/settings.py +++ b/express/parsers/apps/espresso/settings.py @@ -2,8 +2,7 @@ PDOS_TOT_FILE = "pdos_tot" NEB_PATH_FILE_SUFFIX = ".path" -XML_DATA_FILE_PREv6_4 = "data-file.xml" -XML_DATA_FILE_POSTv6_4 = "__prefix__.xml" +XML_DATA_FILE = "__prefix__.xml" PHONON_DOS_FILE = "phonon_dos.out" PHONON_MODES_FILE = "normal_modes.out" AVERAGE_FILE = "avg.dat" diff --git a/tests/fixtures/espresso/v5_4/__init__.py b/tests/fixtures/espresso/v5_4/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/fixtures/espresso/v5_4/references.py b/tests/fixtures/espresso/v5_4/references.py deleted file mode 100644 index 2fc9f2ea..00000000 --- a/tests/fixtures/espresso/v5_4/references.py +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid 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426883f4..00000000 --- a/tests/fixtures/espresso/v5_4/test-002/pw-nscf.in +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:09fcc38f2e43d7a39a4b0aa142a4d0518040a355227b1e1cc736a5df6783350c -size 1101 diff --git a/tests/fixtures/espresso/v5_4/test-002/pw-nscf.out b/tests/fixtures/espresso/v5_4/test-002/pw-nscf.out deleted file mode 100644 index 7d4d06b5..00000000 --- a/tests/fixtures/espresso/v5_4/test-002/pw-nscf.out +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:bc146b53aedea64f932b55100104734f26c3017d55f6ecd991b24386671f2e48 -size 7998 diff --git a/tests/fixtures/espresso/v5_4/test-002/pw-scf.in b/tests/fixtures/espresso/v5_4/test-002/pw-scf.in deleted file mode 100644 index 3a67d80b..00000000 --- a/tests/fixtures/espresso/v5_4/test-002/pw-scf.in +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:dd41b189ea317b1678279d76550bc5ad119e529968d5b09a5840f00a57c37fdb -size 1134 diff --git a/tests/fixtures/espresso/v5_4/test-002/pw-scf.out b/tests/fixtures/espresso/v5_4/test-002/pw-scf.out deleted file mode 100644 index 311b0ec7..00000000 --- a/tests/fixtures/espresso/v5_4/test-002/pw-scf.out +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f583a95f73a869653a79bfe782226f56c6bf4f3ef6c0c43528cf81fc157b7387 -size 11553 diff --git a/tests/fixtures/espresso/v5_4/test-002/run.sh b/tests/fixtures/espresso/v5_4/test-002/run.sh deleted file mode 100755 index 1f4f4ed7..00000000 --- a/tests/fixtures/espresso/v5_4/test-002/run.sh +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:dc4d051a91b358abd9860204e19e3d29d841992a0df5c62ebc78e976837d9809 -size 403 diff --git a/tests/fixtures/espresso/v5_4/test-003/normal_modes.out b/tests/fixtures/espresso/v5_4/test-003/normal_modes.out deleted file mode 100644 index 8d8c9d0b..00000000 --- a/tests/fixtures/espresso/v5_4/test-003/normal_modes.out +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f2764d538dd14d07365f64d2ec3b41c7ce6d1a4d1aef6596945e9a8d46b81328 -size 63181 diff --git a/tests/fixtures/espresso/v5_4/test-003/phonon_dos.out b/tests/fixtures/espresso/v5_4/test-003/phonon_dos.out deleted file mode 100644 index f6d582bb..00000000 --- a/tests/fixtures/espresso/v5_4/test-003/phonon_dos.out +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d9bd12b401946effb2537ddcd133a37127966944fb4e990923bb34c535e910a3 -size 26250 diff --git a/tests/integration/parsers/apps/espresso/test_parser_pre_v64.py b/tests/integration/parsers/apps/espresso/test_parser.py similarity index 70% rename from tests/integration/parsers/apps/espresso/test_parser_pre_v64.py rename to tests/integration/parsers/apps/espresso/test_parser.py index 0be4490e..b5757774 100644 --- a/tests/integration/parsers/apps/espresso/test_parser_pre_v64.py +++ b/tests/integration/parsers/apps/espresso/test_parser.py @@ -1,21 +1,39 @@ # ruff: noqa: F403,F405 from express.parsers.apps.espresso.parser import EspressoParser -from tests.fixtures.espresso.v5_4.references import * +from tests.fixtures.espresso.v6_5.references import * from tests.integration import IntegrationTestBase -class TestEspressoParserPreV64(IntegrationTestBase): +class TestEspressoParser(IntegrationTestBase): + """Test espresso parser for post-6.4 versions, specifically XML parser.""" + def setUp(self): - super(TestEspressoParserPreV64, self).setUp() - self.parser = EspressoParser(work_dir=self.workDir, stdout_file=self.stdoutFile) + super(TestEspressoParser, self).setUp() + self.parser = EspressoParser(work_dir=self.workDir, stdout_file=self.stdoutFile, version="6.5.0") def tearDown(self): - super(TestEspressoParserPreV64, self).tearDown() + super(TestEspressoParser, self).tearDown() def test_espresso_total_energy(self): self.assertAlmostEqual(self.parser.total_energy(), TOTAL_ENERGY, places=2) - def test_espresso_ibz_k_points(self): + def test_espresso_fermi_energy(self): + self.assertAlmostEqual(self.parser.fermi_energy(), FERMI_ENERGY, places=2) + + def test_espresso_nspins(self): + self.assertEqual(self.parser.nspins(), NSPIN) + + def test_espresso_final_lattice_vectors(self): + self.assertDeepAlmostEqual(self.parser.final_lattice_vectors(), LATTICE, places=2) + + def test_espresso_eigenvalues_at_kpoints(self): + self.assertDeepAlmostEqual(self.parser.eigenvalues_at_kpoints()[0], EIGENVALUES_AT_KPOINTS_ZERO, places=2) + + def test_espresso_eigenvalues_at_kpoints_lsda(self): + self.assertDeepAlmostEqual(self.parser.eigenvalues_at_kpoints()[0], EIGENVALUES_AT_KPOINTS_ZERO_LSDA, places=2) + + def test_espresso_ibz_k_point(self): + print(self.parser.ibz_k_points()) self.assertDeepAlmostEqual(self.parser.ibz_k_points(), IBZ_KPOINTS, places=2) def test_espresso_dos(self): @@ -43,20 +61,12 @@ def test_espresso_total_energy_contributions(self): self.assertDeepAlmostEqual(self.parser.total_energy_contributions(), TOTAL_ENERGY_CONTRIBUTION, places=2) def test_espresso_phonon_dos(self): - self.assertDeepAlmostEqual(self.parser.phonon_dos(), PHONON_DOS, places=2) + pass + # self.assertDeepAlmostEqual(self.parser.phonon_dos(), PHONON_DOS, places=2) def test_espresso_phonon_dispersion(self): - self.assertDeepAlmostEqual(self.parser.phonon_dispersions(), PHONON_DISPERSIONS, places=2) - - # XML version dependent tests - def test_espresso_fermi_energy(self): - self.assertAlmostEqual(self.parser.fermi_energy(), FERMI_ENERGY, places=2) - - def test_espresso_nspins(self): - self.assertEqual(self.parser.nspins(), NSPIN) - - def test_espresso_final_lattice_vectors(self): - self.assertDeepAlmostEqual(self.parser.final_lattice_vectors(), LATTICE, places=2) + pass + # self.assertDeepAlmostEqual(self.parser.phonon_dispersions(), PHONON_DISPERSIONS, places=2) - def test_espresso_eigenvalues_at_kpoints(self): - self.assertDeepAlmostEqual(self.parser.eigenvalues_at_kpoints()[0], EIGENVALUES_AT_KPOINTS_ZERO, places=2) + def test_espresso_final_basis(self): + self.assertDeepAlmostEqual(self.parser.final_basis(), FINAL_BASIS, places=2) diff --git a/tests/integration/parsers/apps/espresso/test_parser_post_v64.py b/tests/integration/parsers/apps/espresso/test_parser_post_v64.py deleted file mode 100644 index 23effe90..00000000 --- a/tests/integration/parsers/apps/espresso/test_parser_post_v64.py +++ /dev/null @@ -1,72 +0,0 @@ -# ruff: noqa: F403,F405 -from express.parsers.apps.espresso.parser import EspressoParser -from tests.fixtures.espresso.v6_5.references import * -from tests.integration import IntegrationTestBase - - -class TestEspressoParserPostV64(IntegrationTestBase): - """Test espresso parser for versions > v6.4, specifically XML parser.""" - - def setUp(self): - super(TestEspressoParserPostV64, self).setUp() - self.parser = EspressoParser(work_dir=self.workDir, stdout_file=self.stdoutFile, version="6.5.0") - - def tearDown(self): - super(TestEspressoParserPostV64, self).tearDown() - - def test_espresso_total_energy_post_v64(self): - self.assertAlmostEqual(self.parser.total_energy(), TOTAL_ENERGY, places=2) - - def test_espresso_fermi_energy_post_v64(self): - self.assertAlmostEqual(self.parser.fermi_energy(), FERMI_ENERGY, places=2) - - def test_espresso_nspins_post_v64(self): - self.assertEqual(self.parser.nspins(), NSPIN) - - def test_espresso_final_lattice_vectors_post_v64(self): - self.assertDeepAlmostEqual(self.parser.final_lattice_vectors(), LATTICE, places=2) - - def test_espresso_eigenvalues_at_kpoints_post_v64(self): - self.assertDeepAlmostEqual(self.parser.eigenvalues_at_kpoints()[0], EIGENVALUES_AT_KPOINTS_ZERO, places=2) - - def test_espresso_eigenvalues_at_kpoints_lsda_post_v64(self): - self.assertDeepAlmostEqual(self.parser.eigenvalues_at_kpoints()[0], EIGENVALUES_AT_KPOINTS_ZERO_LSDA, places=2) - - def test_espresso_ibz_k_point_post_v64(self): - print(self.parser.ibz_k_points()) - self.assertDeepAlmostEqual(self.parser.ibz_k_points(), IBZ_KPOINTS, places=2) - - def test_espresso_dos_post_v64(self): - self.assertDeepAlmostEqual(self.parser.dos(), DOS, places=2) - - def test_espresso_convergence_electronic_post_v64(self): - self.assertDeepAlmostEqual(self.parser.convergence_electronic(), CONVERGENCE_ELECTRONIC, places=2) - - def test_espresso_convergence_ionic_post_v64(self): - self.assertDeepAlmostEqual(self.parser.convergence_ionic(), CONVERGENCE_IONIC, places=2) - - def test_espresso_stress_tensor_post_v64(self): - self.assertDeepAlmostEqual(self.parser.stress_tensor(), STRESS_TENSOR, places=2) - - def test_espresso_pressure_post_v64(self): - self.assertAlmostEqual(self.parser.pressure(), PRESSURE, places=2) - - def test_espresso_total_force_post_v64(self): - self.assertAlmostEqual(self.parser.total_force(), TOTAL_FORCE, places=2) - - def test_espresso_atomic_forces_post_v64(self): - self.assertDeepAlmostEqual(self.parser.atomic_forces(), ATOMIC_FORCES, places=2) - - def test_espresso_total_energy_contributions_post_v64(self): - self.assertDeepAlmostEqual(self.parser.total_energy_contributions(), TOTAL_ENERGY_CONTRIBUTION, places=2) - - def test_espresso_phonon_dos_post_v64(self): - pass - # self.assertDeepAlmostEqual(self.parser.phonon_dos(), PHONON_DOS, places=2) - - def test_espresso_phonon_dispersion_post_v64(self): - pass - # self.assertDeepAlmostEqual(self.parser.phonon_dispersions(), PHONON_DISPERSIONS, places=2) - - def test_espresso_final_basis_post_v64(self): - self.assertDeepAlmostEqual(self.parser.final_basis(), FINAL_BASIS, places=2) diff --git a/tests/manifest.yaml b/tests/manifest.yaml index 31f49dc5..a10820f3 100644 --- a/tests/manifest.yaml +++ b/tests/manifest.yaml @@ -6,141 +6,101 @@ test_nwchem_total_energy_contributions: workDir: fixtures/nwchem/test-001 stdoutFile: fixtures/nwchem/test-001/nwchem-total-energy.log + + test_espresso_total_energy: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out + workDir: fixtures/espresso/v6_5/test-004 + stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out test_espresso_fermi_energy: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out + workDir: fixtures/espresso/v6_5/test-004 + stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out test_espresso_nspins: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out + workDir: fixtures/espresso/v6_5/test-004 + stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out test_espresso_final_lattice_vectors: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out + workDir: fixtures/espresso/v6_5/test-004 + stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out test_espresso_eigenvalues_at_kpoints: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out + workDir: fixtures/espresso/v6_5/test-004 + stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_ibz_k_points: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out +test_espresso_eigenvalues_at_kpoints_lsda: + workDir: fixtures/espresso/v6_5/test-005 + stdoutFile: fixtures/espresso/v6_5/test-005/pw_scf.out + +test_espresso_ibz_k_point: + workDir: fixtures/espresso/v6_5/test-004 + stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out test_espresso_dos: - workDir: fixtures/espresso/v5_4/test-002 - stdoutFile: fixtures/espresso/v5_4/test-002/projwfc.out + workDir: fixtures/espresso/v6_5/test-006 + stdoutFile: fixtures/espresso/v6_5/test-006/projwfc.out test_espresso_convergence_electronic: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_convergence_ionic: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_stress_tensor: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_pressure: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_total_force: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_atomic_forces: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_total_energy_contributions: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out - -test_espresso_phonon_dos: - workDir: fixtures/espresso/v5_4/test-003 - stdoutFile: fixtures/espresso/v5_4/test-003/phonon_dos.out - -test_espresso_phonon_dispersion: - workDir: fixtures/espresso/v5_4/test-003 - stdoutFile: fixtures/espresso/v5_4/test-003/normal_modes.out - -test_espresso_total_energy_post_v64: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_fermi_energy_post_v64: +test_espresso_convergence_ionic: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_nspins_post_v64: +test_espresso_stress_tensor: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_final_lattice_vectors_post_v64: +test_espresso_pressure: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_eigenvalues_at_kpoints_post_v64: +test_espresso_total_force: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_eigenvalues_at_kpoints_lsda_post_v64: - workDir: fixtures/espresso/v6_5/test-005 - stdoutFile: fixtures/espresso/v6_5/test-005/pw_scf.out - -test_espresso_ibz_k_point_post_v64: +test_espresso_atomic_forces: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_dos_post_v64: - workDir: fixtures/espresso/v6_5/test-006 - stdoutFile: fixtures/espresso/v6_5/test-006/projwfc.out - -test_espresso_convergence_electronic_post_v64: +test_espresso_total_energy_contributions: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_convergence_ionic_post_v64: +test_espresso_final_basis: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_stress_tensor_post_v64: +test_espresso_phonon_dos: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_pressure_post_v64: +test_espresso_phonon_dispersion: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_total_force_post_v64: - workDir: fixtures/espresso/v6_5/test-004 - stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out +test_structure_espresso_basis: + structurePath: fixtures/espresso/v6_5/test-006/pw_scf.in + structureFormat: espresso-in -test_espresso_atomic_forces_post_v64: - workDir: fixtures/espresso/v6_5/test-004 - stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out +test_structure_espresso_lattice_bravais: + structurePath: fixtures/espresso/v6_5/test-006/pw_scf.in + structureFormat: espresso-in -test_espresso_total_energy_contributions_post_v64: +test_material_espresso_initial_structure: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_final_basis_post_v64: +test_material_espresso_final_structure: workDir: fixtures/espresso/v6_5/test-004 stdoutFile: fixtures/espresso/v6_5/test-004/pw_scf.out -test_espresso_phonon_dos_post_v64: - workDir: fixtures/espresso/v5_4/test-003 - stdoutFile: fixtures/espresso/v5_4/test-003/phonon_dos.out +test_material_from_structure: + structurePath: fixtures/espresso/v6_5/test-006/pw_scf.in + structureFormat: espresso-in + -test_espresso_phonon_dispersion_post_v64: - workDir: fixtures/espresso/v5_4/test-003 - stdoutFile: fixtures/espresso/v5_4/test-003/normal_modes.out test_vasp_total_energy: workDir: fixtures/vasp/test-001 @@ -198,13 +158,7 @@ test_vasp_magnetic_moments: workDir: fixtures/vasp/test-004 stdoutFile: fixtures/vasp/test-004/vasp.out -test_structure_espresso_basis: - structurePath: fixtures/espresso/v5_4/test-001/pw-scf.in - structureFormat: espresso-in -test_structure_espresso_lattice_bravais: - structurePath: fixtures/espresso/v5_4/test-001/pw-scf.in - structureFormat: espresso-in test_structure_vasp_basis: structurePath: fixtures/vasp/test-001/POSCAR @@ -231,21 +185,13 @@ test_material_vasp_final_structure: workDir: fixtures/vasp/test-001 stdoutFile: fixtures/vasp/test-001/vasp.out -test_material_espresso_initial_structure: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out -test_material_espresso_final_structure: - workDir: fixtures/espresso/v5_4/test-001 - stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out test_material_is_non_periodic: workDir: fixtures/vasp/test-001 stdoutFile: fixtures/vasp/test-001/vasp.out -test_material_from_structure: - structurePath: fixtures/espresso/v5_4/test-001/pw-scf.in - structureFormat: espresso-in + test_material_vasp_structure_order_of_elements: structurePath: fixtures/structural/test-003/POSCAR