LAMMPSBaseParser: Fix the parsing of the performance data

The parser attempts to extract the measure of the steps per second from
the logfile through a regex to match the following syntax:

    Performance: 39.271 ns/day, 0.611 hours/ns, 45452.422 timesteps/s

However, this line can also appear in the form:

    Performance: 140354.357 tau/day, 324.894 timesteps/s, 162.447 Matom-step/s

The regex is updated to be indifferent as to the position of the measure
and simply look for the float preceding the `timesteps/s` marker. A test
is added with an example log file with the latter format.

aiida_lammps/common/raw_parsers.py

@@ -47,14 +47,13 @@ def parse_logfile(filename: str = None, file_contents: str = None) -> Union[dict
     end_found = False
     parsed_data = {}
     global_parsed_data = {}
-    perf_regex = re.compile(
-        r"Performance\:\s(.+)\sns\/day,\s(.+)\shours\/ns\,\s(.+)\stimesteps\/s\s*"
-    )
+
+    perf_regex = re.compile(r".*Performance\:.*\,\s+([0-9\.]*)\stimesteps\/s.*")
+    performance_match = perf_regex.search(file_contents or "")
+    if performance_match:
+        global_parsed_data["steps_per_second"] = float(performance_match.group(1))
 
     for index, line in enumerate(data):
-        if perf_regex.match(line):
-            _, _, step_sec = perf_regex.match(line).groups()
-            global_parsed_data["steps_per_second"] = float(step_sec)
         if "binsize" in line:
             global_parsed_data["binsize"] = ast.literal_eval(
                 line.split()[2].replace(",", "")

tests/input_files/parsers/log_alt.lammps

@@ -0,0 +1,60 @@
+LAMMPS (3 Nov 2022)
+  In general, for best performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads
+  For best performance with OpenMP 3.1 set OMP_PROC_BIND=true
+  For unit testing set OMP_PROC_BIND=false
+  using 1 OpenMP thread(s) per MPI task
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+Created orthogonal box = (0 0 0) to (83.97981 83.97981 83.97981)
+  6 by 4 by 5 MPI processor grid
+Created 500000 atoms
+  using lattice units in orthogonal box = (0 0 0) to (83.97981 83.97981 83.97981)
+  create_atoms CPU = 0.003 seconds
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 20 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 60 60 60
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/kk, perpetual
+      attributes: half, newton on, kokkos_device
+      pair build: half/bin/kk/device
+      stencil: half/bin/3d
+      bin: kk/device
+Setting up Verlet run ...
+  Unit style    : lj
+  Current step  : 0
+  Time step     : 0.005
+Per MPI rank memory allocation (min/avg/max) = 2.039 | 2.065 | 2.082 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -6.7733681      0             -4.6133724     -5.0196717    
+      1000   0.70380068    -5.6761498      0             -4.6204508      0.70370101   
+Loop time of 3.07792 on 120 procs for 1000 steps with 500000 atoms
+
+Performance: 140354.357 tau/day, 324.894 timesteps/s, 162.447 Matom-step/s
+99.4% CPU use with 120 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6398     | 1.7065     | 1.7679     |   2.2 | 55.44
+Neigh   | 0.33289    | 0.34561    | 0.39959    |   1.4 | 11.23
+Comm    | 0.8538     | 0.95433    | 1.0342     |   3.8 | 31.01
+Output  | 0.00017888 | 0.00025242 | 0.0003793  |   0.0 |  0.01
+Modify  | 0.053668   | 0.055804   | 0.058023   |   0.4 |  1.81
+Other   |            | 0.01547    |            |       |  0.50
+
+Nlocal:        4166.67 ave        4239 max        4109 min
+Histogram: 5 4 16 24 34 11 14 8 1 3
+Nghost:        5717.37 ave        5790 max        5627 min
+Histogram: 3 2 8 10 21 20 31 11 10 4
+Neighs:         156192 ave      160654 max      152682 min
+Histogram: 4 6 13 25 27 23 12 7 2 1
+
+Total # of neighbors = 18743047
+Ave neighs/atom = 37.486094
+Neighbor list builds = 50
+Dangerous builds not checked
+final_etotal: -4.62045083768868
+Total wall time: 0:00:03

tests/test_parsers.py

@@ -85,6 +85,41 @@ def test_lammps_base(db_test_app, data_regression):
     data_regression.check({"results": calcfunction.outputs.results.get_dict()})
 
 
+def test_lammps_base_timing_info(db_test_app, data_regression):
+    """Test that the timing performance is properly parsed."""
+    filename = os.path.join(
+        TEST_DIR,
+        "input_files",
+        "parsers",
+        "log_alt.lammps",
+    )
+    retrieved = FolderData()
+    retrieved.base.repository.put_object_from_file(filename, "log.lammps")
+    retrieved.base.repository.put_object_from_filelike(
+        io.StringIO(""), "_scheduler-stdout.txt"
+    )
+    retrieved.base.repository.put_object_from_filelike(
+        io.StringIO(""), "_scheduler-stderr.txt"
+    )
+    inputs = {"script": SinglefileData(io.StringIO(""))}
+    calc_node = db_test_app.generate_calcjob_node(
+        "lammps.base", retrieved, inputs=inputs
+    )
+    parser = ParserFactory("lammps.base")
+    with db_test_app.sandbox_folder() as temp_path:
+        (
+            results,
+            calcfunction,
+        ) = parser.parse_from_node(  # pylint: disable=unused-variable
+            calc_node,
+            retrieved_temporary_folder=temp_path.abspath,
+        )
+
+    assert calcfunction.is_finished_ok
+    assert "results" in calcfunction.outputs
+    data_regression.check({"results": calcfunction.outputs.results.get_dict()})
+
+
 @pytest.mark.parametrize(
     "plugin_name", ["lammps.force", "lammps.optimize", "lammps.md", "lammps.md.multi"]
 )

tests/test_parsers/test_lammps_base_timing_info.yml

@@ -0,0 +1,15 @@
+results:
+  compute_variables:
+    bin: kk/device
+    bins:
+    - 60
+    - 60
+    - 60
+    binsize: 1.4
+    ghost_atom_cutoff: 2.8
+    master_list_distance_cutoff: 2.8
+    max_neighbors_atom: 2000
+    steps_per_second: 324.894
+    total_wall_time: 0:00:03
+    total_wall_time_seconds: 3
+    units_style: lattice