Merge pull request #58 from molssi-seamm/dev

Bugfix and improvements

HISTORY.rst

@@ -1,6 +1,13 @@
 =======
 History
 =======
+2024.7.25 -- Bugfix and improvements
+ * Bugfix: Fixed issue with the initial seamm.ini file, created if it is missing from
+ the installation.
+ * Added the ability to set the number of points in the trajectories rather than the
+ sampling rate.
+ * Added diagnositic information and timings to available results.
+
 2024.7.21.1 -- Minor internal change for GUI
  * Switched to new functionality in the SEAMM widgets to simplify the layout of the
  trajectories panel.

lammps_step/energy.py

@@ -50,6 +50,11 @@ def header(self):
  """A printable header for this section of output"""
  return "Step {}: {}".format(".".join(str(e) for e in self._id), self.title)
 
+ @property
+ def results(self):
+ """The storage for the results in the main LAMMPS step."""
+ return self.flowchart.parent._results
+
  @property
  def version(self):
  """The semantic version of this module."""
@@ -180,6 +185,20 @@ def analyze(self, indent="", data={}, table=None, output=[], **kwargs):
  energy = float(tmp[i])
  data["energy"] = energy
  data["energy,units"] = "kcal/mol"
+ if line.startswith("Loop time of"):
+ try:
+ tmp = line.split()
+ _time = round(float(tmp[3]), 2)
+ _procs = int(tmp[5])
+ _steps = int(tmp[8])
+ _natoms = int(tmp[11])
+ _type = self._calculation
+ self.results[f"t_{_type}"] = _time
+ self.results[f"np_{_type}"] = _procs
+ self.results[f"steps_{_type}"] = _steps
+ self.results[f"natoms_{_type}"] = _natoms
+ except Exception as _e:
+ print(f"LAMMPS loop time: {_e}")
 
  # See if forces have been dumped
  wdir = Path(self.directory)
@@ -226,6 +245,6 @@ def analyze(self, indent="", data={}, table=None, output=[], **kwargs):
  # Put any requested results into variables or tables
  self.store_results(
  configuration=configuration,
- data=data,
+ data=data | self.results,
  create_tables=self.parameters["create tables"].get(),
  )

lammps_step/lammps.py

@@ -33,7 +33,7 @@
 from seamm_ff_util import tabulate_angle
 import seamm_util
 import seamm_util.printing as printing
-from seamm_util import CompactJSONEncoder
+from seamm_util import CompactJSONEncoder, Configuration
 from seamm_util.printing import FormattedText as __
 
 # from pymbar import timeseries
@@ -171,6 +171,8 @@ def __init__(
  self._trajectory = []
  self._data = {}
 
+ self._results = {} # Sotrage for computational and timing results
+
  super().__init__(
  flowchart=flowchart, title="LAMMPS", extension=extension, logger=logger
  )
@@ -185,6 +187,11 @@ def git_revision(self):
  """The git version of this module."""
  return lammps_step.__git_revision__
 
+ @property
+ def results(self):
+ """The storage for results."""
+ return self._results
+
  @staticmethod
  def box_to_cell(lx, ly, lz, xy, xz, yz):
  """Convert the LAMMPS box definition to cell parameters."""
@@ -261,53 +268,56 @@ def create_parser(self):
  action="store_true",
  help="whether to write out html files for graphs, etc.",
  )
- parser.add_argument(
- parser_name,
- "--modules",
- nargs="*",
- default=None,
- help="the environment modules to load for LAMMPS",
- )
- parser.add_argument(
- parser_name,
- "--gpu-modules",
- nargs="*",
- default=None,
- help="the environment modules to load for the GPU version of LAMMPS",
- )
- parser.add_argument(
- parser_name,
- "--lammps-path",
- default=None,
- help="the path to the LAMMPS executables",
- )
- parser.add_argument(
- parser_name,
- "--lammps-serial",
- default="lmp_serial",
- help="the serial version of LAMMPS",
- )
- parser.add_argument(
- parser_name,
- "--lammps-mpi",
- default="lmp_mpi",
- help="the mpi version of LAMMPS",
- )
- parser.add_argument(
- parser_name,
- "--cmd-args",
- default="",
- help="the command-line arguments for LAMMPS, e.g. '-k on'",
- )
- parser.add_argument(
- parser_name,
- "--gpu-cmd-args",
- default="",
- help="the command-line arguments for GPU version of LAMMPS, e.g. '-k on'",
- )
- parser.add_argument(
- parser_name, "--mpiexec", default="mpiexec", help="the mpi executable"
- )
+ if False:
+ parser.add_argument(
+ parser_name,
+ "--modules",
+ nargs="*",
+ default=None,
+ help="the environment modules to load for LAMMPS",
+ )
+ parser.add_argument(
+ parser_name,
+ "--gpu-modules",
+ nargs="*",
+ default=None,
+ help="the environment modules to load for the GPU version of LAMMPS",
+ )
+ parser.add_argument(
+ parser_name,
+ "--lammps-path",
+ default=None,
+ help="the path to the LAMMPS executables",
+ )
+ parser.add_argument(
+ parser_name,
+ "--lammps-serial",
+ default="lmp_serial",
+ help="the serial version of LAMMPS",
+ )
+ parser.add_argument(
+ parser_name,
+ "--lammps-mpi",
+ default="lmp_mpi",
+ help="the mpi version of LAMMPS",
+ )
+ parser.add_argument(
+ parser_name,
+ "--cmd-args",
+ default="",
+ help="the command-line arguments for LAMMPS, e.g. '-k on'",
+ )
+ parser.add_argument(
+ parser_name,
+ "--gpu-cmd-args",
+ default="",
+ help=(
+ "the command-line arguments for GPU version of LAMMPS, e.g. '-k on'"
+ ),
+ )
+ parser.add_argument(
+ parser_name, "--mpiexec", default="mpiexec", help="the mpi executable"
+ )
 
  return result
 
@@ -382,6 +392,9 @@ def run(self):
  self.logger.error("LAMMPS run(): there is no structure!")
  raise RuntimeError("LAMMPS run(): there is no structure!")
 
+ # Initialize storage
+ self._results = {}
+
  next_node = super().run(printer)
 
  # Get the options
@@ -661,44 +674,51 @@ def _execute_single_sim(self, files, np=1, return_files=None):
  ini_dir = Path(self.global_options["root"]).expanduser()
  path = ini_dir / "lammps.ini"
 
- if path.exists():
- full_config.read(ini_dir / "lammps.ini")
- full_config.set("local", "_origin_", f"{ini_dir / 'lammps.ini'}")
-
- # If the section we need doesn't exists, get the default
- if not path.exists() or executor_type not in full_config:
+ # If the config file doesn't exists, get the default
+ if not path.exists():
  resources = importlib.resources.files("lammps_step") / "data"
  ini_text = (resources / "lammps.ini").read_text()
- full_config.read_string(ini_text)
- full_config.set("local", "_origin_", "lammps default ini file")
+ txt_config = Configuration(path)
+ txt_config.from_string(ini_text)
+
+ # Work out the conda info needed
+ txt_config.set_value("local", "conda", os.environ["CONDA_EXE"])
+ txt_config.set_value("local", "conda-environment", "seamm-lammps")
+ txt_config.save()
+ printer.normal(f"Wrote the LAMMPS configuration file to {path}")
+ printer.normal("")
+
+ full_config.read(ini_dir / "lammps.ini")
 
- # Getting desperate! Look for an executable in the path
  if executor_type not in full_config:
  path = shutil.which("lmp")
- if path is None:
+ mpi_path = shutil.which("mpirun")
+ if path is None or mpi_path is None:
  raise RuntimeError(
  f"No section for '{executor_type}' in LAMMPS ini file "
  f"({ini_dir / 'lammps.ini'}), nor in the defaults, nor "
  "in the path!"
  )
  else:
- full_config.add_section(executor_type)
- full_config.set(executor_type, "installation", "local")
+ txt_config = Configuration(path)
+ txt_config.add_section(executor_type)
+ txt_config.set_value(executor_type, "installation", "local")
+ txt_config.set_value(
+ executor_type,
+ "code",
+ f"{mpi_path} -np {{NTASKS}} {path}",
+ )
+ txt_config.set_value(
+ executor_type,
+ "python",
+ f"mpirun -np {{NTASKS}} {shutil.which('python')}",
+ )
+ txt_config.save()
+ printer.normal(f"Wrote the LAMMPS configuration file to {path}")
+ printer.normal("")
+ full_config.read(ini_dir / "lammps.ini")
  full_config.set(executor_type, "code", str(path))
 
- # And we may need python!
- full_config.set("local", "items", f"{full_config.items('local')}")
- if not full_config.has_option(executor_type, "python"):
- full_config.set(executor_type, "python", "mpirun -np {NTASKS} python")
- full_config.set(executor_type, "_python source_", "default value")
-
- # If the ini file does not exist, write it out!
- if not path.exists():
- with path.open("w") as fd:
- full_config.write(fd)
- printer.normal(f"Wrote the LAMMPS configuration file to {path}")
- printer.normal("")
-
  config = dict(full_config.items(executor_type))
  # Use the matching version of the seamm-mopac image by default.
  config["version"] = self.version
@@ -1675,6 +1695,13 @@ def analyze(self, indent="", nodes=None, **kwargs):
  sections[section] = []
  elif section is not None:
  sections[section].append(line)
+ if line.startswith("Total wall time:"):
+ try:
+ h, m, s = line.split()[3].split(":")
+ _time = 3600 * float(h) + 60 * float(m) + float(s)
+ self.results["t_lammps_wall"] = _time
+ except Exception as _e:
+ print(f"Wall time exception {_e}")
 
  for node in nodes:
  for value in node.description:

lammps_step/metadata.py

@@ -486,4 +486,102 @@
  "type": "float",
  "units": "",
  },
+ # Timings
+ "t_lammps_wall": {
+ "calculation": [
+ "energy",
+ "minimization",
+ "nve",
+ "nvt",
+ "npt",
+ ],
+ "description": "The wall clock time for LAMMPS",
+ "dimensionality": "scalar",
+ "type": "float",
+ "units": "s",
+ },
+ "t_nve": {
+ "calculation": ["nve"],
+ "description": "The time for the NVE step",
+ "dimensionality": "scalar",
+ "type": "float",
+ "units": "s",
+ },
+ "np_nve": {
+ "calculation": ["nve"],
+ "description": "The number of processors for the NVE step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "nsteps_nve": {
+ "calculation": ["nve"],
+ "description": "The number of steps in the NVE step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "natoms_nve": {
+ "calculation": ["nve"],
+ "description": "The number of atoms in the NVE step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "t_nvt": {
+ "calculation": ["nvt"],
+ "description": "The time for the NVT step",
+ "dimensionality": "scalar",
+ "type": "float",
+ "units": "s",
+ },
+ "np_nvt": {
+ "calculation": ["nvt"],
+ "description": "The number of processors for the NVT step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "nsteps_nvt": {
+ "calculation": ["nvt"],
+ "description": "The number of steps in the NVT step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "natoms_nvt": {
+ "calculation": ["nvt"],
+ "description": "The number of atoms in the NVT step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "t_npt": {
+ "calculation": ["npt"],
+ "description": "The time for the NPT step",
+ "dimensionality": "scalar",
+ "type": "float",
+ "units": "s",
+ },
+ "np_npt": {
+ "calculation": ["npt"],
+ "description": "The number of processors for the NPT step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "nsteps_npt": {
+ "calculation": ["npt"],
+ "description": "The number of steps in the NPT step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
+ "natoms_npt": {
+ "calculation": ["npt"],
+ "description": "The number of atoms in the NPT step",
+ "dimensionality": "scalar",
+ "type": "integer",
+ "units": "s",
+ },
 }