Merge pull request #35 from molssi-seamm/dev

Standard structure handling and cleaned up output

HISTORY.rst

@@ -1,6 +1,12 @@
 =======
 History
 =======
+2023.11.10 -- Standard structure handling and cleaned up output
+ * Switched to standard structure handling and naming, giving consistent options
+ across SEAMM.
+ * Corrected issues with the model name in the properties.
+ * Generally cleaned up the output, mainly indentation.
+
 2023.11.8 -- Bugfix: Fermi level being an array caused problems
  * The Fermi level in DFTB+ is a vector with 1 or 2 elements, depending whether the
  calculation is spin-polarized. DFTB+ can handle different Fermi levels, but it is

dftbplus_step/base.py

@@ -99,6 +99,15 @@ def is_runable(self):
  """Indicate whether this not runs or just adds input."""
  return True
 
+ @property
+ def model(self):
+ """The model (chemistry) used to obtain results."""
+ return self.parent.model
+
+ @model.setter
+ def model(self, value):
+ self.parent.model = value
+
  def band_structure(
  self, input_path, sym_points, sym_names, Efermi=[0.0, 0.0], DOS=None
  ):

dftbplus_step/choose_parameters.py

@@ -12,12 +12,14 @@
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
 
+from .base import DftbBase
+
 logger = logging.getLogger(__name__)
 job = printing.getPrinter()
 printer = printing.getPrinter("DFTB+")
 
 
-class ChooseParameters(seamm.Node):
+class ChooseParameters(DftbBase):
  def __init__(
  self, flowchart=None, title="Choose Parameters", extension=None, logger=logger
  ):
@@ -88,7 +90,7 @@ def get_input(self):
  PP[key] = "{:~P}".format(PP[key])
 
  self.description = []
- self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+ self.description.append(__(self.description_text(PP), **PP, indent=4 * " "))
 
  # The parameter data
  parameter_set = P["dataset"]
@@ -113,7 +115,7 @@ def get_input(self):
  potentials = metadata[model]["potentials"]
  pairs = dataset["potential pairs"]
 
- self.parent._hamiltonian = parameter_set
+ self.model = parameter_set.replace(" - ", "/")
 
  if P["subset"] == "none" or P["subset"] == "":
  subset = None
@@ -122,7 +124,7 @@ def get_input(self):
  if " - " not in subset:
  # From a variable
  subset = f"{model} - {subset}"
- self.parent._hamiltonian += " + " + subset.split(" - ")[1]
+ self.model += "+" + subset.split(" - ")[1]
  subset = datasets[subset]
  subpairs = subset["potential pairs"]
 
@@ -216,7 +218,7 @@ def get_input(self):
  )
  elif model == "xTB":
  # Broadcast to the parent so that other substeps can use
- self.parent._hamiltonian = P["dataset"]
+ self.model = P["dataset"].replace(" - ", "/")
  self.parent._dataset = dataset
  self.parent._subset = None
 

dftbplus_step/dftbplus.py

@@ -248,7 +248,6 @@ def __init__(
  # Data to pass between substeps
  self._dataset = None # SLAKO dataset used
  self._subset = None # SLAKO modifier dataset applied to dataset
- self._hamiltonian = None # String name of the Hamiltonian
  self._reference_energies = None # Reference energies per element.
  self._reference_energy = None # for calculating energy of formation
  self._steps = None # The nodes for the steps run so far.
@@ -363,7 +362,7 @@ def description_text(self, P=None):
  text = self.header + "\n\n"
  while node is not None:
  try:
- text += __(node.description_text(), indent=3 * " ").__str__()
+ text += __(node.description_text(), indent=4 * " ").__str__()
  except Exception as e:
  print(
  "Error describing dftbplus flowchart: {} in {}".format(

dftbplus_step/energy.py

@@ -195,14 +195,14 @@ def get_input(self):
 
  # Set up the description.
  self.description = []
- self.description.append(__(self.description_text(PP), **PP, indent=self.indent))
+ self.description.append(__(self.description_text(PP), **PP, indent=4 * " "))
 
  # Determine the input and as we do so, replace any default values
  # in PP so that we print what is actually done
 
  dataset = self.parent._dataset
- parameter_set = self.parent._hamiltonian
- model, parameter_set_name = parameter_set.split(" - ", 1)
+ parameter_set = self.model
+ model, parameter_set_name = parameter_set.split("/", 1)
 
  if model == "DFTB":
  if "defaults" in dataset:
@@ -407,9 +407,9 @@ def get_input(self):
  # First check if we have shell resolved constants or not
  spin_constants = hamiltonian["SpinConstants"] = {}
  symbols = sorted([*set(atoms.symbols)])
- dataset_name = self.parent._hamiltonian
+ dataset_name = self.model
  # e.g. "DFTB - mio"
- key = dataset_name.split(" - ")[1]
+ key = dataset_name.split("/")[1]
  if key in spin_constant_data:
  constants = spin_constant_data[key]
  else:
@@ -496,7 +496,7 @@ def get_input(self):
  __(
  f"The mesh for the Brillouin zone integration is {na} x {nb} x {nc}"
  f" with offsets of {oa}, {ob}, and {oc}",
- indent=self.indent + 4 * " ",
+ indent=4 * " ",
  )
  )
 
@@ -711,11 +711,11 @@ def analyze(self, indent="", data={}, out=[]):
  except Exception as e:
  text += f"There was an error making the plots: {str(e)}"
  else:
- text += f"Orbital plots not supported for {self.parent._hamiltonian}"
+ text += f"Orbital plots not supported for {self.model}"
 
- 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 * " ")
 
  printer.normal(text)
 

dftbplus_step/optimization.py

@@ -61,6 +61,12 @@ def description_text(self, P=None):
  f" A maximum of {P['MaxSteps']} steps will be used."
  )
 
+ if self.model is None:
+ kwargs = {}
+ else:
+ kwargs = {"Hamiltonian": self.model}
+ text += seamm.standard_parameters.structure_handling_description(P, **kwargs)
+
  return (
  self.header
  + "\n"
@@ -85,7 +91,7 @@ def get_input(self):
  PP[key] = "{:~P}".format(PP[key])
 
  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)
 
@@ -136,26 +142,39 @@ def analyze(self, indent="", data={}, out=[]):
  context=seamm.flowchart_variables._data
  )
 
+ # Read the detailed output file to get the number of iterations
+ directory = Path(self.directory)
+ path = directory / "detailed.out"
+ lines = iter(path.read_text().splitlines())
+ data["nsteps"] = "unknown number of"
+ data["ediff"] = "unknown"
+ data["scc error"] = None
+ for line in lines:
+ if "Geometry optimization step:" in line:
+ data["nsteps"] = line.split()[3]
+ if "Diff electronic" in line:
+ tmp = next(lines).split()
+ data["ediff"] = float(tmp[2])
+
+ # Print the key results
+
+ text += (
+ "The geometry optimization converged in {nsteps} steps. "
+ "The last change in energy was {ediff:.6} Eh"
+ )
+ if P["SCC"] == "Yes" and data["scc error"] is not None:
+ text += " and the error in the charges of {scc error:.6}."
+ else:
+ text += "."
+
  # Update the structure
  if "final structure" in data:
  sdata = data["final structure"]
 
- system, starting_configuration = self.get_system_configuration(None)
- periodicity = starting_configuration.periodicity
- if (
- "structure handling" in P
- and P["structure handling"] == "Create a new configuration"
- ):
- configuration = system.create_configuration(
- periodicity=periodicity,
- atomset=starting_configuration.atomset,
- bondset=starting_configuration.bondset,
- cell_id=starting_configuration.cell_id,
- )
- else:
- configuration = starting_configuration
+ _, starting_configuration = self.get_system_configuration()
+ system, configuration = self.get_system_configuration(P)
 
- if periodicity == 3:
+ if starting_configuration.periodicity == 3:
  (
  lattice_in,
  fractionals_in,
@@ -190,45 +209,15 @@ def analyze(self, indent="", data={}, out=[]):
  )
 
  # And the name of the configuration.
- if "configuration name" in P:
- if P["configuration name"] == "optimized with <Hamiltonian>":
- hamiltonian = self.parent._hamiltonian
- configuration.name = f"optimized with {hamiltonian}"
- elif P["configuration name"] == "keep current name":
- pass
- elif P["configuration name"] == "use SMILES string":
- configuration.name = configuration.smiles
- elif P["configuration name"] == "use Canonical SMILES string":
- configuration.name = configuration.canonical_smiles
- elif P["configuration name"] == "use configuration number":
- configuration.name = str(configuration.n_configurations)
-
- # Read the detailed output file to get the number of iterations
- directory = Path(self.directory)
- path = directory / "detailed.out"
- lines = iter(path.read_text().splitlines())
- data["nsteps"] = "unknown number of"
- data["ediff"] = "unknown"
- data["scc error"] = None
- for line in lines:
- if "Geometry optimization step:" in line:
- data["nsteps"] = line.split()[3]
- if "Diff electronic" in line:
- tmp = next(lines).split()
- data["ediff"] = float(tmp[2])
-
- # Print the key results
-
- text += (
- "The geometry optimization converged in {nsteps} steps. "
- "The last change in energy was {ediff:.6} Eh"
- )
- if P["SCC"] == "Yes" and data["scc error"] is not None:
- text += " and the error in the charges of {scc error:.6}."
- else:
- text += "."
-
- printer.normal(__(text, **data, indent=self.indent + 4 * " "))
+ text += seamm.standard_parameters.set_names(
+ system,
+ configuration,
+ P,
+ _first=True,
+ Hamiltonian=self.model,
+ )
+
+ printer.normal(__(text, **data, indent=8 * " "))
 
  printer.normal("\n")
 

dftbplus_step/optimization_parameters.py

@@ -1,9 +1,10 @@
 # -*- coding: utf-8 -*-
 """Global control parameters for DFTB+
 """
+import logging
 
 import dftbplus_step
-import logging
+import seamm
 
 logger = logging.getLogger(__name__)
 
@@ -159,47 +160,33 @@ class OptimizationParameters(dftbplus_step.EnergyParameters):
  "description": "Alpha update on reset:",
  "help_text": "The factor for the update the alpha parameter on reset.",
  },
- # Put in the configuration handling options needed
- "structure handling": {
- "default": "Create a new configuration",
- "kind": "enum",
- "default_units": "",
- "enumeration": (
- "Overwrite the current configuration",
- "Create a new configuration",
- ),
- "format_string": "s",
- "description": "Configuration handling:",
- "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",
- },
  }
 
  def __init__(self, defaults={}, data=None):
  """Initialize the instance, by default from the default
  parameters given in the class"""
 
  super().__init__(
- defaults={**OptimizationParameters.parameters, **defaults}, data=data
+ defaults={
+ **OptimizationParameters.parameters,
+ **seamm.standard_parameters.structure_handling_parameters,
+ **defaults,
+ },
+ data=data,
  )
 
+ # Do any local editing of defaults
+ tmp = self["structure handling"]
+ tmp.description = "Structure handling:"
+
+ tmp = self["system name"]
+ tmp._data["enumeration"] = (*tmp.enumeration, "optimized with {Hamiltonian}")
+ tmp.default = "keep current name"
+
+ tmp = self["configuration name"]
+ tmp._data["enumeration"] = ["optimized with {Hamiltonian}", *tmp.enumeration]
+ tmp.default = "optimized with {Hamiltonian}"
+
  def update(self, data):
  """Update values from a dict
 
@@ -220,4 +207,8 @@ def update(self, data):
  if key in data:
  del data[key]
 
+ for key in ("system name", "configuration name"):
+ if key in data and data[key] == "optimized with <Hamiltonian>":
+ data[key] = "optimized with {Hamiltonian}"
+
  super().update(data)