From dfbca121dfce321c93d3ebb166ee91f33358ddb9 Mon Sep 17 00:00:00 2001
From: Eric Hartmann <hartmaec@rh05659.villa-bosch.de>
Date: Thu, 21 Mar 2024 18:12:23 +0100
Subject: [PATCH] feat: make arrhenius equation variables accessible

---
 src/homolysis/kimmdy-yaml-schema.json | 25 ++++++++++++++++++++++++-
 src/homolysis/reaction.py             |  4 +++-
 tests/test_default_reactions.py       | 12 ++++++------
 3 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/src/homolysis/kimmdy-yaml-schema.json b/src/homolysis/kimmdy-yaml-schema.json
index e317996..9ee6230 100644
--- a/src/homolysis/kimmdy-yaml-schema.json
+++ b/src/homolysis/kimmdy-yaml-schema.json
@@ -24,13 +24,36 @@
       "enum": ["rfkmc", "frm", "extrande", "extrande_mod"],
       "default": "rfkmc"
     },
+
     "check_bound": {
       "type": "boolean",
       "pytype": "bool",
       "description": "Check the topology for bonds between plumed atom pairs",
       "default": false
+    },
+    "arrhenius_equation": {
+      "title": "arrhenius_equation",
+      "type": "object",
+      "description": "For setting values in the arrhenius equation",
+      "properties": {
+        "frequency_factor": {
+          "type": "float",
+          "description": "Frequency factor",
+          "pytype": "float",
+          "minimum": 0,
+          "default": 0.288
+        },
+        "temperature": {
+          "type": "float",
+          "description": "Temperature",
+          "pytype": "float",
+          "minimum": 0,
+          "default": 300
+        }       
+      },
+      "required": [ "frequency_factor", "temperature" ],
+      "additionalProperties": false
     }
-
   },
   "required": [ "edis", "itp" ]
 }
diff --git a/src/homolysis/reaction.py b/src/homolysis/reaction.py
index 299f13c..9a3b2e7 100644
--- a/src/homolysis/reaction.py
+++ b/src/homolysis/reaction.py
@@ -33,6 +33,8 @@ def get_recipe_collection(self, files: TaskFiles):
         # Initialization of filepaths
         files.input["itp"] = self.config.itp
         files.input["edis"] = self.config.edis
+        frequency_factor = self.config.arrhenius_equation.frequency_factor
+        temperature = self.config.arrhenius_equation.temperature
 
         # Initialization of objects from files
         distances = read_distances_dat(files.input["plumed_out"])
@@ -78,7 +80,7 @@ def get_recipe_collection(self, files: TaskFiles):
             #     f"plumedid: {plumedid}, atomids: {atomnrs}, atomtypes: {atomtypes}, b0: {b0}, kb: {kb}, E_dis: {E_dis}"
             # )
 
-            k_avg, _ = morse_transition_rate([sum(dists) / len(dists)], b0, E_dis, kb)
+            k_avg, _ = morse_transition_rate([sum(dists) / len(dists)], b0, E_dis, kb,frequency_factor,temperature)
             # averaging distances works here because we typically have
             # one conformational state per calculation
 
diff --git a/tests/test_default_reactions.py b/tests/test_default_reactions.py
index 775221d..bc5f4d1 100644
--- a/tests/test_default_reactions.py
+++ b/tests/test_default_reactions.py
@@ -140,12 +140,12 @@ def test_morse_transition_rate(homolysis_files):
         [
             0.00000000e00,
             0.00000000e00,
-            5.79066994e-41,
-            2.51010748e-11,
-            3.59809866e-03,
-            2.17080461e-01,
-            2.88000000e-01,
-            2.88000000e-01,
+            1.01587680e-40, 
+            2.89436858e-11,
+            3.69638684e-03, 
+            2.17458162e-01, 
+            2.88000000e-01, 
+            2.88000000e-01
         ]
     )
     fs_ref = np.asarray(