Merge pull request #241 from SCM-NV/template

ENH: Add the new `pressure` generic property to `cp2k_mm`

src/qmflows/cp2k_utils.py

@@ -419,6 +419,8 @@ def _raise_df_exc_seq(columns: Sequence[str], prm_map: MappingSequence, ex: Exce
         pass
     elif msg.startswith('Shape of passed values is '):
         pass
+    elif msg.startswith('setting an array element with a sequence'):
+        pass
     else:
         raise ex  # an Exception was raised due to some other unforseen reason
 

src/qmflows/data/dictionaries/propertiesCP2KMM.yaml

@@ -56,3 +56,10 @@ lattice:
         column_start: 2
         column_stop: 11
         row_start: 1
+pressure:
+    file_ext: out
+    function: extract_line_values
+    kwargs:
+        pattern: MD| Pressure
+        pos: 3
+    parser: generic_parsers

src/qmflows/parsers/__init__.py

@@ -1,9 +1,10 @@
 """Parsers API."""
 
-from .generic_parsers import (awk_file, extract_line_value)
+from .generic_parsers import (awk_file, extract_line_value, extract_line_values)
 from .xyzParser import (parse_string_xyz, readXYZ,
                         manyXYZ, string_to_plams_Molecule)
 
 __all__ = [
-    'awk_file', 'extract_line_value', 'parse_string_xyz', 'readXYZ', 'manyXYZ',
-    "string_to_plams_Molecule"]
+    'awk_file', 'extract_line_value', 'extract_line_values', 'parse_string_xyz',
+    'readXYZ', 'manyXYZ', 'string_to_plams_Molecule',
+]

src/qmflows/parsers/generic_parsers.py

@@ -1,10 +1,11 @@
 """Use the AWK command line to read output files."""
 
-__all__ = ['awk_file', 'extract_line_value']
+__all__ = ['awk_file', 'extract_line_value', 'extract_line_values']
 
 import subprocess
-from typing import Union, List, Optional
+from typing import Union, List, Optional, Any
 
+import numpy as np
 from pyparsing import OneOrMore, SkipTo, Suppress
 
 from .parser import parse_file
@@ -72,3 +73,24 @@ def extract_line_value(file_name: PathLike,
     last_line = properties[-1].split()
 
     return float(last_line[pos])
+
+
+def extract_line_values(
+    file_name: PathLike,
+    pattern: Optional[str] = None,
+    pos: int = 0,
+    start: Optional[int] = None,
+    stop: Optional[int] = None,
+    step: Optional[int] = None,
+    dtype: Any = np.float64,
+) -> np.ndarray:
+    """Get multiply field records from a file.
+
+    Search for lines containing `pattern` and return all line
+    containing that value in the range defined by `start`, `stop` and `step`.
+    :returns: value at position `pos` in all found lines, containing pattern.
+    """
+    parse_Line = OneOrMore(Suppress(SkipTo(pattern)) + SkipTo('\n'))
+    properties = parse_file(parse_Line, file_name)
+    iterator = (i.split()[pos] for i in properties[start:stop:step])
+    return np.fromiter(iterator, dtype=dtype)

src/qmflows/parsers/orca_parser.py

@@ -156,9 +156,9 @@ def read_column_orbitals(lines: Sequence[str]) -> Tuple[np.ndarray, np.ndarray]:
     0H   1px        0.002631  0.023125  0.025515 -0.010664  0.005733  0.008004
     0H   1py       -0.001684 -0.022031 -0.006086 -0.022644 -0.013760  0.008735
     """
-    energies = np.array(lines[1].split(), dtype=np.float)
+    energies = np.array(lines[1].split(), dtype=np.float64)
 
     coefficients = np.array(
-        [z.split()[2:] for z in lines[4:]], dtype=np.float)
+        [z.split()[2:] for z in lines[4:]], dtype=np.float64)
 
     return energies, coefficients

test/test_cp2k_mm_mock.py

@@ -63,7 +63,7 @@ def mock_runner(mocker_instance: MockFixture,
     return run_mocked
 
 
-def test_cp2k_singlepoint_mock(mocker) -> None:
+def test_cp2k_singlepoint_mock(mocker: MockFixture) -> None:
     """Mock a call to CP2K."""
     s = SETTINGS.copy()
     s.specific.cp2k += geometry.specific.cp2k_mm
@@ -79,7 +79,7 @@ def test_cp2k_singlepoint_mock(mocker) -> None:
     assertion.isclose(result.energy, ref, rel_tol=10**-4)
 
 
-def test_c2pk_opt_mock(mocker) -> None:
+def test_c2pk_opt_mock(mocker: MockFixture) -> None:
     """Mock a call to CP2K."""
     s = SETTINGS.copy()
     s.specific.cp2k += singlepoint.specific.cp2k_mm
@@ -105,7 +105,7 @@ def test_c2pk_opt_mock(mocker) -> None:
     assertion.le(r_mean, 0.1)
 
 
-def test_c2pk_freq_mock(mocker) -> None:
+def test_c2pk_freq_mock(mocker: MockFixture) -> None:
     """Mock a call to CP2K."""
     s = SETTINGS.copy()
     s.specific.cp2k += freq.specific.cp2k_mm
@@ -127,7 +127,7 @@ def test_c2pk_freq_mock(mocker) -> None:
     assertion.isclose(H, H_ref, rel_tol=0.1)
 
 
-def test_c2pk_md_mock(mocker) -> None:
+def test_c2pk_md_mock(mocker: MockFixture) -> None:
     """Mock a call to CP2K."""
     s = SETTINGS.copy()
     s.specific.cp2k += md.specific.cp2k_mm
@@ -141,7 +141,7 @@ def test_c2pk_md_mock(mocker) -> None:
     assertion.isfile(result.results['cp2k-1_1000.restart'])
 
 
-def test_c2pk_cell_opt_mock(mocker) -> None:
+def test_c2pk_cell_opt_mock(mocker: MockFixture) -> None:
     """Mock a call to CP2K."""
     mol = Molecule(PATH / 'cspbbr3_3d.xyz')
 
@@ -183,3 +183,14 @@ def test_c2pk_cell_opt_mock(mocker) -> None:
     np.testing.assert_allclose(result.coordinates, ref_coordinates)
     np.testing.assert_allclose(result.forces, ref_forces)
     np.testing.assert_allclose(result.lattice, ref_lattice)
+
+
+def test_c2pk_npt_mock(mocker: MockFixture) -> None:
+    """Mock a call to CP2K."""
+    s = Settings()
+    job = cp2k_mm(s, None)
+    run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_npt")
+    result = run_mocked(job)
+
+    ref_pressure = np.load(PATH / 'pressure.npy')
+    np.testing.assert_allclose(result.pressure, ref_pressure)