Add date_start and date_end for openmx parser + tests

electronicparsers/openmx/parser.py

@@ -21,13 +21,14 @@
 import logging
 from typing import Optional
 import numpy as np
+from datetime import datetime
 import re
 import io
 from os import path
 
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg as units
-from runschema.run import Run, Program
+from runschema.run import Run, Program, TimeRun
 from runschema.calculation import (
     Calculation,
     ScfIteration,
@@ -164,6 +165,19 @@ def convert_eigenvalues(string):
 
 mainfile_parser = TextParser(
     quantities=[
+        Quantity(
+            'date_start',
+            r'\s+([A-Z]{1}[a-z]{2}\s[A-Z]{1}[a-z]{2}\s\d{1,2}\s\d{2}:\d{2}:\d{2}\s\d{4})',
+            repeats=False,
+            flatten=False,
+            dtype=str,
+        ),
+
+        Quantity(
+            'elapsed_time',
+            r'\s+Elapsed.Time.\s+([\d.]+)',
+            repeats=False,
+        ),
         Quantity(
             'program_version',
             r'This calculation was performed by OpenMX Ver. ([\d\.]+)\s*',
@@ -716,6 +730,16 @@ def parse(self, mainfile: str, archive: EntryArchive, logger):
         sec_run.program = Program(
             name='OpenMX', version=str(mainfile_parser.get('program_version'))
         )
+        date_start = mainfile_parser.get('date_start')
+        date_start_timestamp = datetime.strptime(
+                    date_start, '%a %b %d %H:%M:%S %Y').timestamp()
+        sec_run.time_run = TimeRun()
+        sec_run.time_run.date_start = date_start_timestamp
+
+        elapsed_time = mainfile_parser.get('elapsed_time')
+        if elapsed_time is not None:
+            date_end = date_start_timestamp + elapsed_time
+            sec_run.time_run.date_end = date_end
 
         sec_run.clean_end = mainfile_parser.get('have_timing') is not None
 

tests/test_openmxparser.py

@@ -19,6 +19,7 @@
 import pytest
 import logging
 import numpy as np
+from datetime import datetime
 
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg as units
@@ -99,6 +100,13 @@ def test_AlN(parser):
     run = archive.run[0]
     assert run.program.version == '3.9.2'
     assert run.clean_end
+
+    date_start_timestamp = datetime(2021, 4, 17, 18, 14, 52).timestamp()
+    assert run.time_run.date_start.magnitude == date_start_timestamp
+
+    date_end_timestamp = datetime(2021, 4, 17, 18, 19, 12, 811000).timestamp()
+    assert run.time_run.date_end.magnitude == date_end_timestamp
+
     scc = run.calculation
     assert len(scc) == 5
     assert scc[0].energy.total.value.magnitude == approx(Ha_to_J(-25.194346653540))
@@ -184,6 +192,13 @@ def test_C2N2(parser):
     run = archive.run[0]
     assert run.program.version == '3.9.2'
     assert run.clean_end
+
+    date_start_timestamp = datetime(2021, 5, 27, 9, 7, 27).timestamp()
+    assert run.time_run.date_start.magnitude == date_start_timestamp
+
+    date_end_timestamp = datetime(2021, 5, 27, 9, 13, 7, 525000).timestamp()
+    assert run.time_run.date_end.magnitude == date_end_timestamp
+
     scc = run.calculation
     assert len(scc) == 100
     assert scc[0].temperature.magnitude == approx(300.0)
@@ -253,6 +268,12 @@ def test_CrO2(parser):
 
     run = archive.run[0]
 
+    date_start_timestamp = datetime(2021, 7, 16, 11, 49, 7).timestamp()
+    assert run.time_run.date_start.magnitude == date_start_timestamp
+
+    date_end_timestamp = datetime(2021, 7, 16, 11, 50, 11, 133000).timestamp()
+    assert run.time_run.date_end.magnitude == date_end_timestamp
+
     method = run.method[0]
     assert method.electronic.n_spin_channels == 2
     assert method.electronic.method == 'DFT+U'