Updated to standard structure handling

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2023.10.30 -- Updated to standard structure handling
+  * Adds IUPAC names, InChI and InChIKey as possible names for configurations
+  * Cleaned up output to be properly indented and laid out.
+
 2023.8.30 -- Support for spacegroup symmetry
 
 2023.7.27 -- Bugfix: printing bond order info

mopac_step/__init__.py

@@ -43,40 +43,6 @@
 # Handle versioneer
 from ._version import get_versions
 
-# Parameters used for handling the structure if it is changed.
-structure_handling_parameters = {
-    "structure handling": {
-        "default": "be put in a new configuration",
-        "kind": "enum",
-        "default_units": "",
-        "enumeration": (
-            "overwrite the current configuration",
-            "be put in a new configuration",
-        ),
-        "format_string": "s",
-        "description": "Optimized structure will",
-        "help_text": (
-            "Whether to overwrite the current configuration, or create a new "
-            "configuration or system and configuration for the new structure"
-        ),
-    },
-    "configuration name": {
-        "default": "optimized with <Hamiltonian>",
-        "kind": "string",
-        "default_units": "",
-        "enumeration": (
-            "optimized with <Hamiltonian>",
-            "keep current name",
-            "use SMILES string",
-            "use Canonical SMILES string",
-            "use configuration number",
-        ),
-        "format_string": "s",
-        "description": "Configuration name:",
-        "help_text": "The name for the new configuration",
-    },
-}
-
 __author__ = """Paul Saxe"""
 __email__ = "psaxe@molssi.org"
 versions = get_versions()

mopac_step/energy.py

@@ -34,6 +34,7 @@ def __init__(self, flowchart=None, title="Energy", extension=None):
         self._calculation = "energy"
         self._model = None
         self._metadata = mopac_step.metadata
+        self._use_mozyme = None
         self.parameters = mopac_step.EnergyParameters()
         self.description = "A single point energy calculation"
 
@@ -83,13 +84,17 @@ def description_text(self, P=None):
             )
 
         # MOZYME localized molecular orbitals.
-        if P["MOZYME"] == "always":
+        if ["MOZYME"] == "always" or (
+            self._use_mozyme is not None and self._use_mozyme
+        ):
             text += (
                 "\n\nThe SCF will be solved using localized molecular orbitals "
                 "(MOZYME), which is faster than the traditional method for larger "
                 "systems."
             )
             used_mozyme = True
+        elif self._use_mozyme is not None and not self._use_mozyme:
+            used_mozyme = False
         elif P["MOZYME"] == "for larger systems":
             text += (
                 "\n\nThe SCF will be solved using localized molecular orbitals "
@@ -171,9 +176,19 @@ def get_input(self):
             if isinstance(PP[key], units_class):
                 PP[key] = "{:~P}".format(PP[key])
 
+        if P["MOZYME"] == "always":
+            self._use_mozyme = True
+        elif (
+            P["MOZYME"] == "for larger systems"
+            and configuration.n_atoms >= P["nMOZYME"]
+        ):
+            self._use_mozyme = True
+        else:
+            self._use_mozyme = False
+
         # Save the description for later printing
         self.description = []
-        self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+        self.description.append(__(self.description_text(PP), **PP, indent=4 * " "))
 
         # Start gathering the keywords
         keywords = copy.deepcopy(P["extra keywords"])
@@ -748,16 +763,14 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
         else:
             data = data_sections[0]
 
-        if "GRADIENT_NORM" in data:
-            tmp = data["GRADIENT_NORM"]
-            table["Property"].append("Gradient Norm")
-            table["Value"].append(f"{tmp:.2f}")
-            table["Units"].append("kcal/mol/Å")
-
         if "POINT_GROUP" in data and data["POINT_GROUP"] != "":
-            text += "The molecule has {POINT_GROUP} symmetry."
+            table["Property"].append("Symmetry")
+            table["Value"].append(data["POINT_GROUP"])
+            table["Units"].append("")
         else:
-            text += "The symmetry of the molecule was not determined."
+            table["Property"].append("Symmetry")
+            table["Value"].append("?")
+            table["Units"].append("")
 
         if "HEAT_OF_FORMATION" in data:
             tmp = data["HEAT_OF_FORMATION"]
@@ -794,10 +807,16 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
                         text += (
                             " You followed up with an exact calculation. A large "
                             "difference in the energy could indicate a problem "
-                            "with the localcized molecular orbitals. Check the MOPAC "
+                            "with the localized molecular orbitals. Check the MOPAC "
                             "output carefully!"
                         )
 
+        if "GRADIENT_NORM" in data:
+            tmp = data["GRADIENT_NORM"]
+            table["Property"].append("Gradient Norm")
+            table["Value"].append(f"{tmp:.2f}")
+            table["Units"].append("kcal/mol/Å")
+
         if "SPIN_COMPONENT" in data:
             tmp = data["SPIN_COMPONENT"]
             table["Property"].append("Sz")
@@ -995,9 +1014,9 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
                     )
                 )
 
-        text = str(__(text, **data, indent=self.indent + 4 * " "))
+        text = str(__(text, **data, indent=8 * " "))
         text += "\n\n"
-        text += textwrap.indent("\n".join(text_lines), self.indent + 7 * " ")
+        text += textwrap.indent("\n".join(text_lines), 12 * " ")
 
         if "BOND_ORDERS" in data:
             text += self._bond_orders(
@@ -1019,7 +1038,7 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
         elif "CPU_TIME" in data:
             t0 = data_sections[0]["CPU_TIME"]
             text = f"This calculation took {t0:.2f} s."
-        printer.normal(str(__(text, **data, indent=self.indent + 4 * " ")))
+        printer.normal(str(__(text, **data, indent=4 * " ")))
 
         # Put any requested results into variables or tables
         self.store_results(
@@ -1073,41 +1092,34 @@ def _bond_orders(self, control, bond_order_matrix, configuration):
             table = {
                 "i": [name[i] for i in bond_i],
                 "j": [name[j] for j in bond_j],
-                "bond order": orders,
+                "bond order": [f"{o:6.3f}" for o in orders],
                 "bond multiplicity": bond_order_str,
             }
             tmp = tabulate(
                 table,
                 headers="keys",
-                tablefmt="pretty",
+                tablefmt="psql",
                 disable_numparse=True,
-                colalign=("center", "center", "right", "center"),
+                colalign=("center", "center", "center", "center"),
             )
             length = len(tmp.splitlines()[0])
             text_lines.append("\n")
             text_lines.append("Bond Orders".center(length))
-            text_lines.append(
-                tabulate(
-                    table,
-                    headers="keys",
-                    tablefmt="psql",
-                    colalign=("center", "center", "decimal", "center"),
-                )
-            )
+            text_lines.append(tmp)
             text += "\n\n"
-            text += textwrap.indent("\n".join(text_lines), self.indent + 7 * " ")
+            text += textwrap.indent("\n".join(text_lines), 12 * " ")
 
         if control == "yes, and apply to structure":
             ids = configuration.atoms.ids
             iatoms = [ids[i] for i in bond_i]
             jatoms = [ids[j] for j in bond_j]
-            configuration.bonds.delete()
+            configuration.bonds.new_bondset()
             configuration.bonds.append(i=iatoms, j=jatoms, bondorder=bond_order)
             text2 = (
                 "\nReplaced the bonds in the configuration with those from the "
                 "calculated bond orders.\n"
             )
 
-            text += str(__(text2, indent=self.indent + 4 * " "))
+            text += str(__(text2, indent=8 * " "))
 
         return text

mopac_step/energy_parameters.py

@@ -293,5 +293,10 @@ def __init__(self, defaults={}, data=None):
         parameters given in the class"""
 
         super().__init__(
-            defaults={**EnergyParameters.parameters, **defaults}, data=data
+            defaults={
+                **EnergyParameters.parameters,
+                **seamm.standard_parameters.structure_handling_parameters,
+                **defaults,
+            },
+            data=data,
         )

mopac_step/forceconstants.py

@@ -124,7 +124,7 @@ def get_input(self):
 
         # Save the description for later printing
         self.description = []
-        self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+        self.description.append(__(self.description_text(PP), **PP, indent=4 * " "))
 
         _, configuration = self.get_system_configuration(None)
 

mopac_step/forceconstants_parameters.py

@@ -90,8 +90,16 @@ def __init__(self, defaults={}, data=None):
         super().__init__(
             defaults={
                 **ForceconstantsParameters.parameters,
-                **mopac_step.structure_handling_parameters,
                 **defaults,
             },
             data=data,
         )
+
+        # Do any local editing of defaults
+        tmp = self["system name"]
+        tmp._data["enumeration"] = (*tmp.enumeration, "MOPAC standard orientation")
+        tmp.default = "keep current name"
+
+        tmp = self["configuration name"]
+        tmp._data["enumeration"] = ["MOPAC standard orientation", *tmp.enumeration]
+        tmp.default = "MOPAC standard optimization"

mopac_step/ir.py

@@ -113,7 +113,7 @@ def get_input(self):
 
         # Save the description for later printing
         self.description = []
-        self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+        self.description.append(__(self.description_text(PP), **PP, indent=4 * " "))
 
         # Remove the 1SCF keyword from the energy setup
         inputs = super().get_input()
@@ -221,7 +221,7 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
             colalign=("center", "decimal", "decimal", "decimal", "left"),
         )
         text_lines += "\n"
-        text = textwrap.indent(text_lines, self.indent + 7 * " ")
+        text = textwrap.indent(text_lines, 8 * " ")
         printer.normal(text)
 
         # And the vibrational modes to a csv file

mopac_step/ir_parameters.py

@@ -35,8 +35,16 @@ def __init__(self, defaults={}, data=None):
         super().__init__(
             defaults={
                 **IRParameters.parameters,
-                **mopac_step.structure_handling_parameters,
                 **defaults,
             },
             data=data,
         )
+
+        # Do any local editing of defaults
+        tmp = self["system name"]
+        tmp._data["enumeration"] = (*tmp.enumeration, "MOPAC standard orientation")
+        tmp.default = "keep current name"
+
+        tmp = self["configuration name"]
+        tmp._data["enumeration"] = ["MOPAC standard orientation", *tmp.enumeration]
+        tmp.default = "MOPAC standard optimization"

mopac_step/lewis_structure.py

@@ -446,7 +446,7 @@ def analyze(self, indent="", lines=[], n_calculations=None):
             if same:
                 iatoms = [ids[i] for i in bonds["i"]]
                 jatoms = [ids[j] for j in bonds["j"]]
-                configuration.bonds.delete()
+                configuration.new_bondset()
                 configuration.bonds.append(
                     i=iatoms, j=jatoms, bondorder=bonds["bondorder"]
                 )
@@ -462,7 +462,7 @@ def analyze(self, indent="", lines=[], n_calculations=None):
                             iatoms.append(ids[i])
                             jatoms.append(ids[j])
                             bondorders.append(1)
-                configuration.bonds.delete()
+                configuration.new_bondset()
                 configuration.bonds.append(
                     i=iatoms, j=jatoms, bondorder=bonds["bondorder"]
                 )
@@ -479,4 +479,4 @@ def analyze(self, indent="", lines=[], n_calculations=None):
             t_total = data["CPU_TIME"]
             text += f"\nThe Lewis structure took a total of {t_total:.2f} s.\n"
 
-        printer.normal(textwrap.indent(text, self.indent + 4 * " "))
+        printer.normal(textwrap.indent(text, 4 * " "))