Merge pull request #3 from molssi-seamm/dev

Fixed issue of orbital numbers off by one, and truncated output to Job.out

HISTORY.rst

@@ -2,6 +2,11 @@
 History
 =======
 
+2023.10.22 Bug fixes: orbital plots and output
+    * The plots of the HOMO and LUMO were shifted by one orbital due to some code
+      counting from 1 and other, from 0. Sigh.
+    * The output to Job.out was inadvertently truncated.
+
 2023.10.7 Added structure file for plots of density and orbitals.
     * Always write the current structure as 'structure.sdf' in the directory where the
       cube files for orbitals and densities are written. The Dashboard picks up this

gaussian_step/energy.py

@@ -295,6 +295,7 @@ def analyze(self, indent="", data={}, table=None):
         metadata = gaussian_step.metadata["results"]
         if "Total Energy" not in data:
             text += "Gaussian did not produce the energy. Something is wrong!"
+            printer.normal(__(text, indent=self.indent + 4 * " "))
 
         for key in (
             "Total Energy",
@@ -518,17 +519,17 @@ def analyze(self, indent="", data={}, table=None):
                 text += "\n\n"
                 text += textwrap.indent("\n".join(text_lines), self.indent + 7 * " ")
 
+        printer.normal(text)
+
         # Write the structure locally for use in density and orbital plots
         obConversion = openbabel.OBConversion()
         obConversion.SetOutFormat("sdf")
         obMol = configuration.to_OBMol(properties="all")
         title = f"SEAMM={system.name}/{configuration.name}"
         obMol.SetTitle(title)
-        text = obConversion.WriteString(obMol)
+        sdf = obConversion.WriteString(obMol)
         path = directory / "structure.sdf"
-        path.write_text(text)
-
-        printer.normal(text)
+        path.write_text(sdf)
 
         text = self.make_plots(data)
         if text != "":

gaussian_step/substep.py

@@ -264,7 +264,7 @@ def make_plots(self, data):
                 tmp = orbitals
                 orbitals = []
                 for x in tmp:
-                    if x > 0 and x <= n_orbitals:
+                    if x >= 0 and x < n_orbitals:
                         orbitals.append(x)
 
                 if spin_polarized:
@@ -282,7 +282,7 @@ def make_plots(self, data):
                         filename = f"{l2}LUMO.cube"
                     else:
                         filename = f"{l2}LUMO+{mo - homo - 1}.cube"
-                    args = f"1 {l1}MO={mo} gaussian.fchk {filename} {npts} h"
+                    args = f"1 {l1}MO={mo + 1} gaussian.fchk {filename} {npts} h"
 
                     # And run CUBEGEN
                     try: