Merge pull request #131 from molssi-seamm/dev

Added support for output of energy & gradients to JSON

.github/workflows/BranchCI.yaml

@@ -4,7 +4,6 @@ on:
   push:
     branches-ignore:
       - 'main'
-      - 'master'
 
 jobs:
   branch-ci:

.github/workflows/CI.yaml

@@ -7,11 +7,7 @@ on:
   pull_request:
     branches:
       - "main"
-  schedule:
-    # Run on master by default Sunday morning at 3:30:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "30 3 * * 0"
+  workflow_dispatch:
 
 jobs:
   ci:

HISTORY.rst

@@ -1,6 +1,9 @@
 =======
 History
 =======
+2024.5.14 -- Added output of energy & gradients to JSON
+   * To support the Energy Scan step.
+
 2024.3.17 -- Updated installation
   * Updated the installation to reflect the new way to install SEAMM plug-ins to support
     both Conda and Docker

devtools/conda-envs/test_env.yaml

@@ -20,6 +20,7 @@ dependencies:
   - flake8
   - pytest
   - pytest-cov
+  - seamm-installer
 
   # Documentation
   - pydata-sphinx-theme

mopac_step/energy.py

@@ -1044,6 +1044,11 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
         printer.normal(str(__(text, **data, indent=4 * " ")))
 
         # Put any requested results into variables or tables
+        if "HEAT_OF_FORMATION" in data:
+            data["energy"] = data["HEAT_OF_FORMATION"]
+        if "GRADIENTS" in data:
+            tmp = np.array(data["GRADIENTS"])
+            data["gradients"] = tmp.reshape(-1, 3).tolist()
         self.store_results(
             configuration=configuration,
             data=data,

mopac_step/metadata.py

@@ -1245,6 +1245,20 @@
     An optional unit string for the value as returned by the code.
 """
 metadata["results"] = {
+    "energy": {
+        "calculation": ["energy", "optimization", "thermodynamics", "vibrations"],
+        "description": "enthalpy of formation",
+        "dimensionality": "scalar",
+        "type": "float",
+        "units": "kcal/mol",
+    },
+    "gradients": {
+        "calculation": ["energy", "optimization", "thermodynamics", "vibrations"],
+        "description": "gradients on the atoms",
+        "dimensionality": [3, "n_atoms"],
+        "type": "float",
+        "units": "kcal/mol/Å",
+    },
     "ERROR_MESSAGE": {
         "description": "An error message",
         "dimensionality": "scalar",