Merge pull request #121 from molssi-seamm/dev

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__ = "[email protected]"
 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 * " "))