Merge pull request #23 from molssi-seamm/dev

Fixed bug with ncores, and added structure to orbital plots.

HISTORY.rst

@@ -2,6 +2,10 @@
 History
 =======
 
+2023.8.22 -- Enhancement of orbital plots
+   * Added structure to the orbital plots
+   * Fixed a bug if the default nouber of cores was not 'available'
+
 2023.6.4 -- Enhancements
    * Added thermochemistry substep to compute the vibrational and other corrections for
      thermochemistry.

psi4_step/energy.py

@@ -6,6 +6,8 @@
 import logging
 from pathlib import Path
 
+from openbabel import openbabel
+
 import psi4_step
 import seamm
 import seamm.data
@@ -295,11 +297,6 @@ def analyze(self, indent="", data={}, out=[]):
         """Parse the output and generating the text output and store the
         data in variables for other stages to access
         """
-
-        # P = self.parameters.current_values_to_dict(
-        #     context=seamm.flowchart_variables._data
-        # )
-
         # Read in the results from json
         directory = Path(self.directory)
         json_file = directory / "properties.json"
@@ -324,6 +321,17 @@ def analyze(self, indent="", data={}, out=[]):
             printer.normal(__(text, **data, indent=self.indent + 4 * " "))
             raise RuntimeError(text)
 
+        # Write the structure locally for use in density and orbital plots
+        system, configuration = self.get_system_configuration()
+        obConversion = openbabel.OBConversion()
+        obConversion.SetOutFormat("sdf")
+        obMol = configuration.to_OBMol(properties="all")
+        title = f"SEAMM={system.name}/{configuration.name}"
+        obMol.SetTitle(title)
+        sdf = obConversion.WriteString(obMol)
+        path = directory / "structure.sdf"
+        path.write_text(sdf)
+
         printer.normal(__(text, **data, indent=self.indent + 4 * " "))
 
     def plot_input(self):

psi4_step/optimization.py

@@ -137,15 +137,10 @@ def get_input(self, calculation_type="optimize"):
 
         return "\n".join(lines)
 
-    def analyze(self, indent="", data={}, out=[]):
+    def analyze_sv(self, indent="", data={}, out=[]):
         """Parse the output and generating the text output and store the
         data in variables for other stages to access
         """
-
-        # P = self.parameters.current_values_to_dict(
-        #     context=seamm.flowchart_variables._data
-        # )
-
         # Read in the results from json
         directory = Path(self.directory)
         json_file = directory / "properties.json"

psi4_step/psi4.py

@@ -358,7 +358,7 @@ def run(self):
         if n_threads < 1:
             n_threads = 1
         if seamm_options["ncores"] != "available":
-            n_threads = min(n_threads, int(options["max_cores"]))
+            n_threads = min(n_threads, int(options["ncores"]))
         self.logger.info(f"Psi4 will use {n_threads} threads.")
 
         # How much memory to use
@@ -531,21 +531,6 @@ def analyze(self, indent="", **kwargs):
             indent: str
                 An extra indentation for the output
         """
-
-        # Get the first real node
-        node = self.subflowchart.get_node("1").next()
-
-        # Loop over the subnodes, asking them to do their analysis
-        while node is not None:
-            for value in node.description:
-                printer.important(value)
-
-            node.analyze()
-
-            printer.normal("")
-
-            node = node.next()
-
         # Update the structure
         directory = Path(self.directory)
         structure_file = directory / "final_structure.json"
@@ -571,6 +556,20 @@ def analyze(self, indent="", **kwargs):
                 )
                 printer.important("")
 
+        # Get the first real node
+        node = self.subflowchart.get_node("1").next()
+
+        # Loop over the subnodes, asking them to do their analysis
+        while node is not None:
+            for value in node.description:
+                printer.important(value)
+
+            node.analyze()
+
+            printer.normal("")
+
+            node = node.next()
+
     def _convert_structure(self, name=None, no_com=True, no_reorient=True):
         """Convert the structure to the input for Psi4."""