From fe0d9f5c34f1d40f5a99257de582283a37022a44 Mon Sep 17 00:00:00 2001
From: "Himanen, Lauri (himanel1)" <lauri.himanen@aalto.fi>
Date: Wed, 18 May 2016 21:39:50 +0300
Subject: [PATCH] Added more testing tools, updated stress tensor parsing.
---
.gitignore | 1 +
.../versions/cp2k262/commonmatcher.py | 87 +++++++++++--------
.../versions/cp2k262/inputparser.py | 14 +++
.../versions/cp2k262/singlepointparser.py | 42 +++++++--
test/unittests/cp2k_2.6.2/run_tests.py | 60 ++++++++++++-
5 files changed, 157 insertions(+), 47 deletions(-)
diff --git a/.gitignore b/.gitignore
index 85d5d27..d36cb68 100644
--- a/.gitignore
+++ b/.gitignore
@@ -64,6 +64,7 @@ test/**/*.restart.bak-3
test/**/*.wfn.bak-1
test/**/*.wfn.bak-2
test/**/*.wfn.bak-3
+test/**/*.png
parser/parser-cp2k/cp2kparser/versions/**/input_data/*.xml
parser/parser-cp2k/cp2kparser/versions/**/input_data/*.html
test/unittests/BASIS_SET
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
index 0920af7..6a2a4db 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
@@ -37,31 +37,8 @@ class CommonMatcher(object):
'x_cp2k_md_force_atom_float': CachingLevel.Cache,
}
- def adHoc_cp2k_section_cell(self):
- """Used to extract the cell information.
- """
- def wrapper(parser):
- # Read the lines containing the cell vectors
- a_line = parser.fIn.readline()
- b_line = parser.fIn.readline()
- c_line = parser.fIn.readline()
-
- # Define the regex that extracts the components and apply it to the lines
- regex_string = r" CELL\| Vector \w \[angstrom\]:\s+({0})\s+({0})\s+({0})".format(self.regex_f)
- regex_compiled = re.compile(regex_string)
- a_result = regex_compiled.match(a_line)
- b_result = regex_compiled.match(b_line)
- c_result = regex_compiled.match(c_line)
-
- # Convert the string results into a 3x3 numpy array
- cell = np.zeros((3, 3))
- cell[0, :] = [float(x) for x in a_result.groups()]
- cell[1, :] = [float(x) for x in b_result.groups()]
- cell[2, :] = [float(x) for x in c_result.groups()]
-
- # Push the results to the correct section
- parser.backend.addArrayValues("simulation_cell", cell, unit="angstrom")
- return wrapper
+ #===========================================================================
+ # SimpleMatcher trees
# SimpleMatcher for the header that is common to all run types
def header(self):
@@ -84,6 +61,7 @@ class CommonMatcher(object):
),
SM( r" CP2K\| Input file name\s+(?P<x_cp2k_input_filename>.+$)",
sections=['x_cp2k_section_filenames'],
+ otherMetaInfo=['section_XC_functionals', 'XC_functional_name', 'XC_functional_weight', 'XC_functional', 'configuration_periodic_dimensions', "stress_tensor_method"],
subMatchers=[
SM( r" GLOBAL\| Basis set file name\s+(?P<x_cp2k_basis_set_filename>.+$)"),
SM( r" GLOBAL\| Geminal file name\s+(?P<x_cp2k_geminal_filename>.+$)"),
@@ -115,6 +93,8 @@ class CommonMatcher(object):
]
)
+ #===========================================================================
+ # Section close triggers
def onClose_section_method(self, backend, gIndex, section):
"""When all the functional definitions have been gathered, matches them
with the nomad correspondents and combines into one single string which
@@ -122,19 +102,22 @@ class CommonMatcher(object):
"""
# Transform the CP2K self-interaction correction string to the NOMAD
# correspondent, and push directly to the superBackend to avoid caching
- sic_cp2k = section["self_interaction_correction_method"][0]
- sic_map = {
- "NO": "",
- "AD SIC": "SIC_AD",
- "Explicit Orbital SIC": "SIC_EXPLICIT_ORBITALS",
- "SPZ/MAURI SIC": "SIC_MAURI_SPZ",
- "US/MAURI SIC": "SIC_MAURI_US",
- }
- sic_nomad = sic_map.get(sic_cp2k)
- if sic_nomad is not None:
- backend.superBackend.addValue('self_interaction_correction_method', sic_nomad)
- else:
- logger.warning("Unknown self-interaction correction method used.")
+ try:
+ sic_cp2k = section["self_interaction_correction_method"][0]
+ sic_map = {
+ "NO": "",
+ "AD SIC": "SIC_AD",
+ "Explicit Orbital SIC": "SIC_EXPLICIT_ORBITALS",
+ "SPZ/MAURI SIC": "SIC_MAURI_SPZ",
+ "US/MAURI SIC": "SIC_MAURI_US",
+ }
+ sic_nomad = sic_map.get(sic_cp2k)
+ if sic_nomad is not None:
+ backend.superBackend.addValue('self_interaction_correction_method', sic_nomad)
+ else:
+ logger.warning("Unknown self-interaction correction method used.")
+ except:
+ pass
def onClose_x_cp2k_section_filenames(self, backend, gIndex, section):
"""
@@ -148,6 +131,34 @@ class CommonMatcher(object):
else:
logger.warning("The input file of the calculation could not be found.")
+ #===========================================================================
+ # Ad hoc parsing
+ def adHoc_cp2k_section_cell(self):
+ """Used to extract the cell information.
+ """
+ def wrapper(parser):
+ # Read the lines containing the cell vectors
+ a_line = parser.fIn.readline()
+ b_line = parser.fIn.readline()
+ c_line = parser.fIn.readline()
+
+ # Define the regex that extracts the components and apply it to the lines
+ regex_string = r" CELL\| Vector \w \[angstrom\]:\s+({0})\s+({0})\s+({0})".format(self.regex_f)
+ regex_compiled = re.compile(regex_string)
+ a_result = regex_compiled.match(a_line)
+ b_result = regex_compiled.match(b_line)
+ c_result = regex_compiled.match(c_line)
+
+ # Convert the string results into a 3x3 numpy array
+ cell = np.zeros((3, 3))
+ cell[0, :] = [float(x) for x in a_result.groups()]
+ cell[1, :] = [float(x) for x in b_result.groups()]
+ cell[2, :] = [float(x) for x in c_result.groups()]
+
+ # Push the results to the correct section
+ parser.backend.addArrayValues("simulation_cell", cell, unit="angstrom")
+ return wrapper
+
def getOnCloseTriggers(self):
"""
Returns:
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
index 6bab307..48dec90 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
@@ -125,6 +125,20 @@ class CP2KInputParser(BasicParser):
force_file_path = self.normalize_cp2k_path(force_file, "xyz")
self.file_service.set_file_id(force_file_path, "force_file_single_point")
+ #=======================================================================
+ # Stress tensor calculation method
+ stress_tensor_method = self.input_tree.get_keyword("FORCE_EVAL/STRESS_TENSOR")
+ if stress_tensor_method != "NONE":
+ mapping = {
+ "NUMERICAL": "Numerical",
+ "ANALYTICAL": "Analytical",
+ "DIAGONAL_ANALYTICAL": "Diagonal analytical",
+ "DIAGONAL_NUMERICAL": "Diagonal numerical",
+ }
+ stress_tensor_method = mapping.get(stress_tensor_method)
+ if stress_tensor_method is not None:
+ self.backend.addValue("stress_tensor_method", stress_tensor_method)
+
def normalize_cp2k_path(self, path, extension, name=""):
"""The paths in CP2K input can be given in many ways. This function
tries to normalize these forms into a valid path.
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
index dcdd0bf..0fde035 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
@@ -43,9 +43,11 @@ class CP2KSinglePointParser(MainHierarchicalParser):
]
),
SM( r" \*\*\* SCF run converged in\s+(\d+) steps \*\*\*",
+ otherMetaInfo=["single_configuration_calculation_converged"],
adHoc=self.adHoc_single_point_converged()
),
SM( r" \*\*\* SCF run NOT converged \*\*\*",
+ otherMetaInfo=["single_configuration_calculation_converged"],
adHoc=self.adHoc_single_point_not_converged()
),
SM( r" Electronic kinetic energy:\s+(?P<electronic_kinetic_energy__hartree>{})".format(self.cm.regex_f)),
@@ -55,12 +57,22 @@ class CP2KSinglePointParser(MainHierarchicalParser):
SM( r" ENERGY\| Total FORCE_EVAL \( \w+ \) energy \(a\.u\.\):\s+(?P<energy_total__hartree>{0})".format(self.cm.regex_f)),
SM( r" ATOMIC FORCES in \[a\.u\.\]"),
SM( r" # Atom Kind Element X Y Z",
- adHoc=self.adHoc_atom_forces()
- ),
- SM( r" NUMERICAL STRESS TENSOR [GPa]"),
- SM( r"\s+X\s+Y\s+Z",
- adHoc=self.adHoc_stress_tensor()
+ adHoc=self.adHoc_atom_forces(),
+ otherMetaInfo=["atom_forces"],
),
+ SM( r" (?:NUMERICAL )?STRESS TENSOR \[GPa\]",
+ sections=["section_stress_tensor"],
+ otherMetaInfo=["stress_tensor"],
+ subMatchers=[
+ SM( r"\s+X\s+Y\s+Z",
+ adHoc=self.adHoc_stress_tensor()
+ ),
+ SM( " 1/3 Trace\(stress tensor\):\s+(?P<x_cp2k_stress_tensor_one_third_of_trace__GPa>{})".format(self.cm.regex_f)),
+ SM( " Det\(stress tensor\)\s+:\s+(?P<x_cp2k_stress_tensor_determinant__GPa3>{})".format(self.cm.regex_f)),
+ SM( " EIGENVECTORS AND EIGENVALUES OF THE STRESS TENSOR",
+ adHoc=self.adHoc_stress_tensor_eigenpairs()),
+ ]
+ )
]
)
]
@@ -72,6 +84,7 @@ class CP2KSinglePointParser(MainHierarchicalParser):
self.root_matcher = SM("",
forwardMatch=True,
sections=['section_run', "section_single_configuration_calculation", "section_system", "section_method"],
+ otherMetaInfo=["atom_forces"],
subMatchers=[
self.cm.header(),
self.energy_force
@@ -238,10 +251,23 @@ class CP2KSinglePointParser(MainHierarchicalParser):
row2 = [float(x) for x in parser.fIn.readline().split()[-3:]]
row3 = [float(x) for x in parser.fIn.readline().split()[-3:]]
stress_array = np.array([row1, row2, row3])
- gid = parser.backend.openSection("section_stress_tensor")
- parser.backend.addArrayValues("stress_tensor_value", stress_array, unit="GPa")
- parser.backend.closeSection("section_stress_tensor", gid)
+ parser.backend.addArrayValues("stress_tensor", stress_array, unit="GPa")
+
+ return wrapper
+ def adHoc_stress_tensor_eigenpairs(self):
+ """Parses the stress tensor eigenpairs.
+ """
+ def wrapper(parser):
+ parser.fIn.readline()
+ eigenvalues = np.array([float(x) for x in parser.fIn.readline().split()][::-1])
+ parser.fIn.readline()
+ row1 = [float(x) for x in parser.fIn.readline().split()]
+ row2 = [float(x) for x in parser.fIn.readline().split()]
+ row3 = [float(x) for x in parser.fIn.readline().split()]
+ eigenvectors = np.fliplr(np.array([row1, row2, row3]))
+ parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvalues", eigenvalues, unit="GPa")
+ parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvectors", eigenvectors)
return wrapper
def adHoc_single_point_converged(self):
diff --git a/test/unittests/cp2k_2.6.2/run_tests.py b/test/unittests/cp2k_2.6.2/run_tests.py
index 81f8ec7..9d3c37c 100644
--- a/test/unittests/cp2k_2.6.2/run_tests.py
+++ b/test/unittests/cp2k_2.6.2/run_tests.py
@@ -170,6 +170,39 @@ class TestSelfInteractionCorrectionMethod(unittest.TestCase):
self.assertEqual(sic, "SIC_MAURI_US")
+#===============================================================================
+class TestStressTensorMethods(unittest.TestCase):
+ """Tests that the stress tensor can be properly parsed for different
+ calculation methods.
+ """
+ def test_none(self):
+ get_results("stress_tensor/none", "section_stress_tensor")
+
+ def test_analytical(self):
+ results = get_results("stress_tensor/analytical", ["stress_tensor_method", "stress_tensor"])
+ method = results["stress_tensor_method"]
+ results["stress_tensor"]
+ self.assertEqual(method, "Analytical")
+
+ def test_numerical(self):
+ results = get_results("stress_tensor/numerical", ["stress_tensor_method", "stress_tensor"])
+ method = results["stress_tensor_method"]
+ results["stress_tensor"]
+ self.assertEqual(method, "Numerical")
+
+ def test_diagonal_analytical(self):
+ results = get_results("stress_tensor/diagonal_analytical", ["stress_tensor_method", "stress_tensor"])
+ method = results["stress_tensor_method"]
+ results["stress_tensor"]
+ self.assertEqual(method, "Diagonal analytical")
+
+ def test_diagonal_numerical(self):
+ results = get_results("stress_tensor/diagonal_numerical", ["stress_tensor_method", "stress_tensor"])
+ method = results["stress_tensor_method"]
+ results["stress_tensor"]
+ self.assertEqual(method, "Diagonal numerical")
+
+
#===============================================================================
class TestConfigurationPeriodicDimensions(unittest.TestCase):
"""Tests that the self-interaction correction can be properly parsed.
@@ -336,7 +369,7 @@ class TestEnergyForce(unittest.TestCase):
self.assertEqual(result, 0)
def test_stress_tensor(self):
- result = self.results["stress_tensor_value"]
+ result = self.results["stress_tensor"]
expected_result = convert_unit(
np.array([
[7.77641684, -0.00000106, -0.00000106],
@@ -347,6 +380,30 @@ class TestEnergyForce(unittest.TestCase):
)
self.assertTrue(np.array_equal(result, expected_result))
+ def test_stress_tensor_eigenvalues(self):
+ result = self.results["x_cp2k_stress_tensor_eigenvalues"]
+ expected_result = convert_unit(np.array([7.77641809, 7.77641797, 7.77641485]), "GPa")
+ self.assertTrue(np.array_equal(result, expected_result))
+
+ def test_stress_tensor_eigenvectors(self):
+ result = self.results["x_cp2k_stress_tensor_eigenvectors"]
+ expected_result = np.array([
+ [0.00094549, -0.79967815, 0.60042815],
+ [-0.70749682, 0.42379757, 0.56554741],
+ [0.70671590, 0.42533573, 0.56536905],
+ ])
+ self.assertTrue(np.array_equal(result, expected_result))
+
+ def test_stress_tensor_determinant(self):
+ result = self.results["x_cp2k_stress_tensor_determinant"]
+ expected_result = convert_unit(4.70260626E+02, "GPa^3")
+ self.assertTrue(np.array_equal(result, expected_result))
+
+ def test_stress_tensor_one_third_of_trace(self):
+ result = self.results["x_cp2k_stress_tensor_one_third_of_trace"]
+ expected_result = convert_unit(7.77641697E+00, "GPa")
+ self.assertTrue(np.array_equal(result, expected_result))
+
#===============================================================================
if __name__ == '__main__':
pass
@@ -357,6 +414,7 @@ if __name__ == '__main__':
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
--
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