Merge pull request #124 from molssi-seamm/dev

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):