Bugfix -- bondsets, and writing input and stopping.

HISTORY.rst

@@ -1,6 +1,9 @@
 =======
 History
 =======
+2023.12.18 -- Added readonly flag
+ * Added a flag to prepare the input but not run the calculation.
+
 2023.11.15 -- More updates for v2022.1.0
  * Added PM6-ORG Hamiltonian to options
  * Added other new data types for the AUX file.

mopac_step/energy.py

@@ -713,6 +713,9 @@ def get_input(self):
  else:
  logger.error(f"Don't recognize the MOZYME follow-up: '{follow_up}'")
 
+ # Set the attribute in the main MOPAC step for writing just the input
+ self.parent.input_only = P["input only"]
+
  return result
 
  def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
@@ -1113,7 +1116,7 @@ def _bond_orders(self, control, bond_order_matrix, configuration):
  ids = configuration.atoms.ids
  iatoms = [ids[i] for i in bond_i]
  jatoms = [ids[j] for j in bond_j]
- configuration.bonds.new_bondset()
+ configuration.new_bondset()
  configuration.bonds.append(i=iatoms, j=jatoms, bondorder=bond_order)
  text2 = (
  "\nReplaced the bonds in the configuration with those from the "

mopac_step/energy_parameters.py

@@ -12,6 +12,18 @@ class EnergyParameters(seamm.Parameters):
  """The control parameters for creating a structure from SMILES"""
 
  parameters = {
+ "input only": {
+ "default": "no",
+ "kind": "boolean",
+ "default_units": "",
+ "enumeration": (
+ "yes",
+ "no",
+ ),
+ "format_string": "s",
+ "description": "Write the input files and stop:",
+ "help_text": "Don't run MOPAC. Just write the input files.",
+ },
  "structure": {
  "default": "default",
  "kind": "enumeration",

mopac_step/mopac.py

@@ -54,11 +54,21 @@ def __init__(
  )
  self._data = {}
  self._lattice_opt = True
+ self._input_only = False
 
  super().__init__(
  flowchart=flowchart, title=title, extension=extension, logger=logger
  )
 
+ @property
+ def input_only(self):
+ """Whether to write the input only, not run MOPAC."""
+ return self._input_only
+
+ @input_only.setter
+ def input_only(self, value):
+ self._input_only = value
+
  def description_text(self, P=None):
  """Return a short description of this step.
 
@@ -83,6 +93,10 @@ def description_text(self, P=None):
 
  def run(self, printer=printer):
  """Run MOPAC"""
+ # Create the directory
+ directory = Path(self.directory)
+ directory.mkdir(parents=True, exist_ok=True)
+
  system, configuration = self.get_system_configuration(None)
  n_atoms = configuration.n_atoms
  if n_atoms == 0:
@@ -255,35 +269,44 @@ def run(self, printer=printer):
  text += "\n"
  node = node.next()
 
- files = {"mopac.dat": text}
- self.logger.debug("mopac.dat:\n" + files["mopac.dat"])
- os.makedirs(self.directory, exist_ok=True)
- for filename in files:
- with open(os.path.join(self.directory, filename), mode="w") as fd:
- fd.write(files[filename])
- local = seamm.ExecLocal()
- return_files = ["mopac.arc", "mopac.out", "mopac.aux"]
- result = local.run(
- cmd=[str(mopac_exe), "mopac.dat"],
- files=files,
- return_files=return_files,
- env=env,
- in_situ=True,
- directory=self.directory,
- )
+ # Check for successful run, don't rerun
+ success = directory / "success.dat"
+ if not success.exists():
+ files = {"mopac.dat": text}
+ self.logger.debug("mopac.dat:\n" + files["mopac.dat"])
+ for filename in files:
+ path = directory / filename
+ path.write_text(files[filename])
+
+ if not self.input_only:
+ local = self.flowchart.executor
+ print(f"{self.flowchart=} --> {local=}")
+ return_files = ["mopac.arc", "mopac.out", "mopac.aux"]
+ result = local.run(
+ cmd=[str(mopac_exe), "mopac.dat"],
+ files=files,
+ return_files=return_files,
+ env=env,
+ in_situ=True,
+ directory=self.directory,
+ )
 
- if not result:
- self.logger.error("There was an error running MOPAC")
- return None
+  if not result:
+  self.logger.error("There was an error running MOPAC")
+  return None
 
- self.logger.debug("\n" + pprint.pformat(result))
+  self.logger.debug("\n" + pprint.pformat(result))
 
- self.logger.debug(
- "\n\nOutput from MOPAC\n\n" + result["mopac.out"]["data"] + "\n\n"
- )
+ self.logger.debug(
+ "\n\nOutput from MOPAC\n\n" + result["mopac.out"]["data"] + "\n\n"
+ )
+
+ # Ran successfully, put out the success file
+ success.write_text("success")
 
- # Analyze the results
- self.analyze(n_calculations=n_calculations)
+ if not self.input_only:
+ # Analyze the results
+ self.analyze(n_calculations=n_calculations)
 
  # Close the reference handler, which should force it to close the
  # connection.

mopac_step/tk_energy.py

@@ -55,6 +55,11 @@ def create_dialog(self, title="Edit MOPAC Energy Step"):
  self.logger.debug("Creating the dialog")
  frame = super().create_dialog(title=title, widget="notebook", results_tab=True)
 
+ P = self.node.parameters
+
+ # Just write input
+ self["input only"] = P["input only"].widget(frame)
+
  # Frame to isolate widgets
  e_frame = self["energy frame"] = ttk.LabelFrame(
  frame,
@@ -66,9 +71,8 @@ def create_dialog(self, title="Edit MOPAC Energy Step"):
  )
 
  # Create all the widgets
- P = self.node.parameters
  for key in mopac_step.EnergyParameters.parameters:
- if key not in ("results", "extra keywords", "create tables"):
+ if key not in ("results", "extra keywords", "create tables", "input only"):
  self[key] = P[key].widget(e_frame)
 
  # Set the callbacks for changes
@@ -89,8 +93,12 @@ def reset_dialog(self, widget=None):
  for slave in frame.grid_slaves():
  slave.grid_forget()
 
- # Put in the energy frame
  row = 0
+ # Whether to just write input
+ self["input only"].grid(row=row, column=0, sticky=tk.W)
+ row += 1
+
+ # Put in the energy frame
  self["energy frame"].grid(row=row, column=0, sticky=tk.EW)
  row += 1
 

versioneer.py

@@ -339,9 +339,9 @@ def get_config_from_root(root):
  # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
  # the top of versioneer.py for instructions on writing your setup.cfg .
  setup_cfg = os.path.join(root, "setup.cfg")
- parser = configparser.SafeConfigParser()
+ parser = configparser.ConfigParser()
  with open(setup_cfg, "r") as f:
- parser.readfp(f)
+ parser.read_file(f)
  VCS = parser.get("versioneer", "VCS") # mandatory
 
  def get(parser, name):