Enhancement: improved output and aded to results

* Added energy, etc. to results
* Added more detail to printed output
* Fixed bugs with the GUI and with labeling substeps.

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.10.15 -- Enhancement: improved output and aded to results
+    * Added energy, etc. to results
+    * Added more detail to printed output
+    * Fixed bugs with the GUI and with labeling substeps.
 
 2024.10.13 -- Added geomeTRIC minimizer
     * Added transition states as a target

structure_step/structure.py

@@ -451,11 +451,13 @@ def description_text(self, P=None, short=False, natoms=None):
         if P is None:
             P = self.parameters.values_to_dict()
 
+        result = self.header + "\n"
         if P["approach"] == "Optimization":
+            text = ""
             if P["optimizer"].lower().endswith("/geometric"):
-                text = self.describe_geomeTRIC_optimizer(P=P)
+                result += self.describe_geomeTRIC_optimizer(P=P)
             else:
-                text = "The structure will be optimized using the "
+                text += "The structure will be optimized using the "
                 text += "{optimizer} optimizer, converging to {convergence} "
 
             max_steps = P["max steps"]
@@ -472,6 +474,8 @@ def description_text(self, P=None, short=False, natoms=None):
                 text += " The workflow will continue if the structure "
                 text += "does not converge."
 
+        result += "\n" + str(__(text, **P, indent=7 * " "))
+
         # Make sure the subflowchart has the data from the parent flowchart
         self.subflowchart.root_directory = self.flowchart.root_directory
         self.subflowchart.executor = self.flowchart.executor
@@ -480,12 +484,14 @@ def description_text(self, P=None, short=False, natoms=None):
         if not short:
             # Get the first real node
             node = self.subflowchart.get_node("1").next()
-            text += "\n\nThe energy and forces will be calculated as follows:\n"
+            result += "\n\n    The energy and forces will be calculated as follows:\n"
 
             # Now walk through the steps in the subflowchart...
             while node is not None:
                 try:
-                    text += __(node.description_text(), indent=3 * " ").__str__()
+                    result += str(
+                        __(node.description_text(), indent=7 * " ", wrap=False)
+                    )
                 except Exception as e:
                     print(f"Error describing structure flowchart: {e} in {node}")
                     self.logger.critical(
@@ -502,10 +508,10 @@ def description_text(self, P=None, short=False, natoms=None):
                         f"{sys.exc_info()[0]} in {str(node)}"
                     )
                     raise
-                text += "\n"
+                result += "\n"
                 node = node.next()
 
-        return self.header + "\n" + __(text, **P, indent=4 * " ").__str__()
+        return result
 
     def plot(self, E_units="", F_units=""):
         """Generate a plot of the convergence of the geometry optimization."""
@@ -656,6 +662,15 @@ def run(self):
         else:
             raise ValueError(f"Unknown approach '{P['approach']}' in Structure")
 
+        # Print the results
+        self.analyze()
+
+        # Store results to db, variables, tables, and json as requested
+        self.store_results(
+            configuration=self._working_configuration,
+            data=self._results,
+        )
+
         return next_node
 
     def run_ase_optimizer(self, P, PP):
@@ -806,6 +821,7 @@ def set_id(self, node_id=()):
 
     def set_subids(self, node_id=()):
         """Set the ids of the nodes in the subflowchart"""
+        self.subflowchart.reset_visited()
         node = self.subflowchart.get_node("1").next()
         n = 1
         while node is not None:

structure_step/structure_parameters.py

@@ -91,8 +91,8 @@ class StructureParameters(seamm.Parameters):
                 "transition state",
             ),
             "format_string": "",
-            "description": "Approach:",
-            "help_text": "The approach or method for determining the structure.",
+            "description": "Target:",
+            "help_text": "The type of structure that is the target.",
         },
         "optimizer": {
             "default": "geomeTRIC/geomeTRIC",

structure_step/tk_structure.py

@@ -163,8 +163,8 @@ def create_dialog(self):
 
         # and binding to change as needed
         for key in (
-            "approach",
             "target",
+            "approach",
             "optimizer",
             "convergence formula",
             "convergence",
@@ -259,11 +259,14 @@ def reset_structure_frame(self, widget=None):
             optimizer = self["optimizer"].get()
             convergence = self["convergence"].get()
 
-            optimizers = [
-                k
-                for k, v in self.metadata["optimizers"].items()
-                if target in v["targets"]
-            ]
+            if self.is_expr(target):
+                optimizers = [k for k, v in self.metadata["optimizers"].items()]
+            else:
+                optimizers = [
+                    k
+                    for k, v in self.metadata["optimizers"].items()
+                    if target in v["targets"]
+                ]
             self["optimizer"].config(values=optimizers)
             if optimizer not in optimizers:
                 optimizer = optimizers[0]