diff --git a/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17.out.md5 b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17.out.md5
new file mode 100644
index 0000000000000000000000000000000000000000..ad0ef41e824577999c11d33d4baec2df970975ed
--- /dev/null
+++ b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17.out.md5
@@ -0,0 +1 @@
+fbcbdd6fc11f4e74751257626ce6d03f
diff --git a/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17_atomic_displacements_data_0.txt.md5 b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17_atomic_displacements_data_0.txt.md5
new file mode 100644
index 0000000000000000000000000000000000000000..790eae8b899411b9c1f8af49aadb9ab5993d438d
--- /dev/null
+++ b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17_atomic_displacements_data_0.txt.md5
@@ -0,0 +1 @@
+5963d231bfed4a4fdc3d9a27f6903026
diff --git a/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17_data.txt.md5 b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17_data.txt.md5
new file mode 100644
index 0000000000000000000000000000000000000000..9c0d4e946b8c531c6dfe16f732e87d75e79bdc40
--- /dev/null
+++ b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL17_data.txt.md5
@@ -0,0 +1 @@
+dcedfbda8976f92bc8775e1e1aa15362
diff --git a/docs/source/release/v4.3.0/indirect_geometry.rst b/docs/source/release/v4.3.0/indirect_geometry.rst
index da4c2242c5a0d8e6716d7bfa96c89aa3125fe02e..1e7455c3e72a4378db5959788c5dec1d3f50cd0d 100644
--- a/docs/source/release/v4.3.0/indirect_geometry.rst
+++ b/docs/source/release/v4.3.0/indirect_geometry.rst
@@ -9,4 +9,10 @@ Indirect Geometry Changes
putting new features at the top of the section, followed by
improvements, followed by bug fixes.
-:ref:`Release 4.3.0 <v4.3.0>`
\ No newline at end of file
+
+BugFixes
+########
+
+- The Abins file parser no longer fails to read data from non-periodic vibration calculations performed with CRYSTAL17.
+
+:ref:`Release 4.3.0 <v4.3.0>`
diff --git a/scripts/AbinsModules/GeneralAbInitioParser.py b/scripts/AbinsModules/GeneralAbInitioParser.py
index 871dfe53b38310b7fce45ebc78d983ad5d15669b..0cc3d00d42285346a2df1f760c293d34b0accf60 100644
--- a/scripts/AbinsModules/GeneralAbInitioParser.py
+++ b/scripts/AbinsModules/GeneralAbInitioParser.py
@@ -7,6 +7,7 @@
from __future__ import (absolute_import, division, print_function)
import six
+import re
import AbinsModules
@@ -17,18 +18,40 @@ class GeneralAbInitioParser(object):
def __init__(self):
pass
- def find_first(self, file_obj=None, msg=None):
+ def find_first(self, file_obj=None, msg=None, regex=None):
"""
Finds the first line with msg. Moves file current position to the next line.
:param file_obj: file object from which we read
- :param msg: keyword to find
+ :type file_obj: BinaryIO
+ :param msg: keyword to find (exact match)
+ :type msg: str
+ :param regex: regular expression to find (use *instead of* msg option).
+ This string will be compiled to a Python re.Pattern .
+ :type regex: str
"""
if not six.PY2:
- msg = bytes(msg, "utf8")
- while not self.file_end(file_obj=file_obj):
- line = file_obj.readline()
- if line.strip() and msg in line:
- return line
+ if msg is not None:
+ msg = bytes(msg, "utf8")
+ if regex is not None:
+ regex = bytes(regex, "utf8")
+
+ if msg and regex:
+ raise ValueError("msg or regex should be provided, not both")
+ elif msg:
+ while not self.file_end(file_obj=file_obj):
+ line = file_obj.readline()
+ if line.strip() and msg in line:
+ return line
+ raise ValueError("'{}' not found".format(msg))
+ elif regex:
+ test = re.compile(regex)
+ while not self.file_end(file_obj=file_obj):
+ line = file_obj.readline()
+ if test.match(line):
+ return(line)
+ raise ValueError("'{}' not found".format(regex))
+ else:
+ raise ValueError("No msg or regex provided: nothing to match")
def find_last(self, file_obj=None, msg=None):
"""
diff --git a/scripts/AbinsModules/GeneralLoadAbInitioTester.py b/scripts/AbinsModules/GeneralLoadAbInitioTester.py
index 5d6d26f129af3421196653572380bb3a77414039..08688c7f809dff764e6c5adb0124e17c5e4d6fc2 100644
--- a/scripts/AbinsModules/GeneralLoadAbInitioTester.py
+++ b/scripts/AbinsModules/GeneralLoadAbInitioTester.py
@@ -14,11 +14,16 @@ class GeneralLoadAbInitioTester(object):
_loaders_extensions = {"LoadCASTEP": "phonon", "LoadCRYSTAL": "out", "LoadDMOL3": "outmol", "LoadGAUSSIAN": "log"}
- # noinspection PyMethodMayBeStatic
- def _prepare_data(self, filename=None):
- """Reads reference values from ASCII file."""
+ @staticmethod
+ def _prepare_data(seedname):
+ """Reads reference values from ASCII files
- with open(AbinsModules.AbinsTestHelpers.find_file(filename + "_data.txt")) as data_file:
+ :param seedname: Reference data will read from the file {seedname}_data.txt, except for the atomic displacements
+ which are read from files {seedname}_atomic_displacements_data_{I}.txt, where {I} are k-point indices.
+ :type seedname: str
+ """
+
+ with open(AbinsModules.AbinsTestHelpers.find_file(seedname + "_data.txt")) as data_file:
correct_data = json.loads(data_file.read().replace("\n", " "))
num_k = len(correct_data["datasets"]["k_points_data"]["weights"])
@@ -26,9 +31,9 @@ class GeneralLoadAbInitioTester(object):
array = {}
for k in range(num_k):
- temp = np.loadtxt(
- AbinsModules.AbinsTestHelpers.find_file(
- filename + "_atomic_displacements_data_%s.txt" % k)).view(complex).reshape(-1)
+ temp = np.loadtxt(AbinsModules.AbinsTestHelpers.find_file(
+ "{seedname}_atomic_displacements_data_{k}.txt".format(seedname=seedname, k=k))
+ ).view(complex).reshape(-1)
total_size = temp.size
num_freq = int(total_size / (atoms * 3))
array[str(k)] = temp.reshape(atoms, num_freq, 3)
@@ -123,13 +128,16 @@ class GeneralLoadAbInitioTester(object):
data = self._read_ab_initio(loader=loader, filename=name, extension=extension)
# get correct data
- correct_data = self._prepare_data(filename=name)
+ correct_data = self._prepare_data(name)
# check read data
self._check_reader_data(correct_data=correct_data, data=data, filename=name, extension=extension)
# check loaded data
- self._check_loader_data(correct_data=correct_data, input_ab_initio_filename=name, extension=extension, loader=loader)
+ self._check_loader_data(correct_data=correct_data,
+ input_ab_initio_filename=name,
+ extension=extension,
+ loader=loader)
def _read_ab_initio(self, loader=None, filename=None, extension=None):
"""
@@ -146,15 +154,15 @@ class GeneralLoadAbInitioTester(object):
read_filename = AbinsModules.AbinsTestHelpers.find_file(filename=filename + "." + extension.upper())
ab_initio_reader = loader(input_ab_initio_filename=read_filename)
- data = self._get_reader_data(ab_initio_reader=ab_initio_reader)
+ data = self._get_reader_data(ab_initio_reader)
# test validData method
self.assertEqual(True, ab_initio_reader._clerk._valid_hash())
return data
- # noinspection PyMethodMayBeStatic
- def _get_reader_data(self, ab_initio_reader=None):
+ @staticmethod
+ def _get_reader_data(ab_initio_reader):
"""
:param ab_initio_reader: object of type GeneralAbInitioProgram
:returns: read data
@@ -165,3 +173,46 @@ class GeneralLoadAbInitioTester(object):
}
data["datasets"].update({"unit_cell": ab_initio_reader._clerk._data["unit_cell"]})
return data
+
+ @classmethod
+ def save_ab_initio_test_data(cls, ab_initio_reader, seedname):
+ """
+ Write ab initio calculation data to JSON file for use in test cases
+
+ :param ab_initio_reader: Reader after import of external calculation
+ :type ab_initio_reader: AbinsModules.GeneralAbInitioProgram
+ :param filename: Seed for text files for JSON output. Data will be written to the file {seedname}_data.txt,
+ except for the atomic displacements which are written to files {seedname}_atomic_displacements_data_{I}.txt,
+ where {I} are k-point indices.
+ :type filename: str
+
+ """
+
+ data = cls._get_reader_data(ab_initio_reader)
+ # Unpack advanced parameters into a dictionary for ease of comparison later.
+ # It might be wise to remove this and store escaped strings for consistency,
+ # but for now we don't want to disturb the old test data so follow its format.
+ data["attributes"]["advanced_parameters"] = json.loads(data["attributes"]["advanced_parameters"])
+
+ displacements = data["datasets"]["k_points_data"].pop("atomic_displacements")
+ for i, eigenvector in displacements.items():
+ with open('{seedname}_atomic_displacements_data_{i}.txt'.format(seedname=seedname, i=i), 'wt') as f:
+ eigenvector.flatten().view(float).tofile(f, sep=' ')
+
+ with open('{seedname}_data.txt'.format(seedname=seedname), 'wt') as f:
+ json.dump(cls._arrays_to_lists(data), f, indent=4, sort_keys=True)
+
+ @classmethod
+ def _arrays_to_lists(cls, mydict):
+ """Recursively convert numpy arrays in a nested dict to lists (i.e. valid JSON)
+
+ Returns a processed *copy* of the input dictionary: in-place values will not be altered."""
+ clean_dict = {}
+ for key, value in mydict.items():
+ if isinstance(value, np.ndarray):
+ clean_dict[key] = value.tolist()
+ elif isinstance(value, dict):
+ clean_dict[key] = cls._arrays_to_lists(value)
+ else:
+ clean_dict[key] = value
+ return clean_dict
diff --git a/scripts/AbinsModules/LoadCRYSTAL.py b/scripts/AbinsModules/LoadCRYSTAL.py
index 2c05bd5ded8ff6a5a03a484ecf14bf418f92ddc7..f82e8668975d8c5afc5947dbba6475b628fd0a5d 100644
--- a/scripts/AbinsModules/LoadCRYSTAL.py
+++ b/scripts/AbinsModules/LoadCRYSTAL.py
@@ -153,7 +153,7 @@ class LoadCRYSTAL(AbinsModules.GeneralAbInitioProgram):
"""
coord_lines = []
self._parser.find_first(file_obj=file_obj,
- msg="ATOM X(ANGSTROM) Y(ANGSTROM) Z(ANGSTROM)")
+ regex=r".*\s+ATOM\s+X\(ANGSTROM\)\s+Y\(ANGSTROM\)\s+Z\(ANGSTROM\)\s*$")
file_obj.readline() # Line: *******************************************************************************
diff --git a/scripts/test/AbinsLoadCRYSTALTest.py b/scripts/test/AbinsLoadCRYSTALTest.py
index 8d794d91e8fb538c024ee43a75f41c313756bb4f..4a4968e658ab4733012b6595124f34fc2e348cb6 100644
--- a/scripts/test/AbinsLoadCRYSTALTest.py
+++ b/scripts/test/AbinsLoadCRYSTALTest.py
@@ -17,7 +17,7 @@ class AbinsLoadCRYSTALTest(unittest.TestCase, AbinsModules.GeneralLoadAbInitioTe
# *************************** USE CASES ********************************************
# ===================================================================================
- # | Use cases: Gamma point calculation for CRYSTAL |
+ # | Use cases: Gamma point calculation for CRYSTAL |
# ===================================================================================
_gamma_crystal = "crystalB3LYP_LoadCRYSTAL"
_set_crystal = "crystal_set_key_LoadCRYSTAL"
@@ -28,7 +28,12 @@ class AbinsLoadCRYSTALTest(unittest.TestCase, AbinsModules.GeneralLoadAbInitioTe
_molecule = "toluene_molecule_LoadCRYSTAL"
# ===================================================================================
- # | Use cases: Phonon dispersion calculation for CRYSTAL |
+ # | Use case: Molecular calculation with CRYSTAL17 |
+ # ===================================================================================
+ _molecule17 = "toluene_molecule_LoadCRYSTAL17"
+
+ # ===================================================================================
+ # | Use cases: Phonon dispersion calculation for CRYSTAL |
# ===================================================================================
_phonon_dispersion_v1 = "mgo-GX_LoadCRYSTAL"
_phonon_dispersion_v2 = "MgO-222-DISP_LoadCRYSTAL"
@@ -40,6 +45,9 @@ class AbinsLoadCRYSTALTest(unittest.TestCase, AbinsModules.GeneralLoadAbInitioTe
def test_molecule(self):
self.check(name=self._molecule, loader=AbinsModules.LoadCRYSTAL)
+ def test_molecule17(self):
+ self.check(name=self._molecule17, loader=AbinsModules.LoadCRYSTAL)
+
def test_phonon_dispersion_crystal(self):
self.check(name=self._phonon_dispersion_v1, loader=AbinsModules.LoadCRYSTAL)
self.check(name=self._phonon_dispersion_v2, loader=AbinsModules.LoadCRYSTAL)