Merge pull request #123 from molssi-seamm/dev

Updates for v2022.1.0 including PM6-ORG

Author: seamm

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2023.11.15 -- More updates for v2022.1.0
+  * Added PM6-ORG Hamiltonian to options
+  * Added other new data types for the AUX file.
+    
 2023.11.14 -- Updated for MOPAC v2022.1.0
   * MOPAC v2022.1.0 added GRADIENT_NORM_UPDATED to the AUX file. This updates adds it to
     the results recognized by the plug-in

mopac_step/metadata.py

@@ -38,6 +38,13 @@
                         "optimization": True,
                         "code": "mopac",
                     },
+                    "PM6-ORG": {
+                        "elements": "1-60,62-83",
+                        "periodic": True,
+                        "reactions": True,
+                        "optimization": True,
+                        "code": "mopac",
+                    },
                     "PM6-D3": {
                         "description": (
                             "The PM6 Hamiltonian with Grimme's corrections for "
@@ -1505,13 +1512,25 @@
         "type": "float",
         "units": "kcal/mol/Å",
     },
-    "GRADIENT_UPDATED": {
+    "GRADIENTS_UPDATED": {
         "calculation": ["optimization"],
         "description": "forces in trajectory",
         "dimensionality": ["nsteps", [3, "n_atoms"]],
         "type": "float",
         "units": "kcal/mol/Å",
     },
+    "VOIGT_STRESS": {
+        "description": "Voigt stress",
+        "dimensionality": [6],
+        "type": "float",
+        "units": "GPa",
+    },
+    "VOIGT_STRESS_UPDATED": {
+        "description": "Voigt stress in trajectory",
+        "dimensionality": [6],
+        "type": "float",
+        "units": "GPa",
+    },
     "HEAT_CAPACITY_TOT": {
         "calculation": ["thermodynamics", "vibrations"],
         "description": "heat capacity",

mopac_step/optimization.py

@@ -83,7 +83,7 @@ def description_text(self, P=None):
         text += "\n\n"
 
         if self.is_expr(P["hamiltonian"]):
-            kwargs = {}
+            kwargs = {"Hamiltonian": "{{" + P["hamiltonian"] + "}}"}
         else:
             kwargs = {"Hamiltonian": P["hamiltonian"]}
         text += seamm.standard_parameters.structure_handling_description(P, **kwargs)