From 56533a3c7b9b520a526de3fe9b6f776eb02fa1d5 Mon Sep 17 00:00:00 2001
From: Paul Saxe <paul@thesaxes.net>
Date: Tue, 14 May 2024 16:20:27 -0400
Subject: [PATCH 1/2] Added support for output of energy & gradients to JSON

---
 HISTORY.rst            |  3 +++
 mopac_step/energy.py   |  5 +++++
 mopac_step/metadata.py | 14 ++++++++++++++
 3 files changed, 22 insertions(+)

diff --git a/HISTORY.rst b/HISTORY.rst
index ecaf826..09164db 100644
--- a/HISTORY.rst
+++ b/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
diff --git a/mopac_step/energy.py b/mopac_step/energy.py
index 1a79aa2..e1e0e2e 100644
--- a/mopac_step/energy.py
+++ b/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,
diff --git a/mopac_step/metadata.py b/mopac_step/metadata.py
index 2d21d86..ee3fc67 100644
--- a/mopac_step/metadata.py
+++ b/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",

From a409eff09a7cdb2d73a369d3bdb1671bcc29ffb2 Mon Sep 17 00:00:00 2001
From: Paul Saxe <paul@thesaxes.net>
Date: Tue, 14 May 2024 16:28:59 -0400
Subject: [PATCH 2/2] Updating CI configuration

---
 .github/workflows/BranchCI.yaml   | 1 -
 .github/workflows/CI.yaml         | 6 +-----
 devtools/conda-envs/test_env.yaml | 1 +
 3 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/BranchCI.yaml b/.github/workflows/BranchCI.yaml
index 55fa6f9..48c4467 100644
--- a/.github/workflows/BranchCI.yaml
+++ b/.github/workflows/BranchCI.yaml
@@ -4,7 +4,6 @@ on:
   push:
     branches-ignore:
       - 'main'
-      - 'master'
 
 jobs:
   branch-ci:
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 3d425a5..32f7673 100644
--- a/.github/workflows/CI.yaml
+++ b/.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:
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 83f3b33..2d64d03 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -20,6 +20,7 @@ dependencies:
   - flake8
   - pytest
   - pytest-cov
+  - seamm-installer
 
   # Documentation
   - pydata-sphinx-theme