From ad0c32d0d833daeb86093d8229e5de9a3594c0d0 Mon Sep 17 00:00:00 2001
From: martinachondo <acho.martin@gmail.com>
Date: Sun, 2 Jun 2024 22:47:45 -0400
Subject: [PATCH] Run Simulation Function

---
 xppbe/Model/pbj_utils/pbj_interface.py |  2 +-
 xppbe/Scripts                          | 13 +++----------
 xppbe/__init__.py                      |  9 +++++++++
 3 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/xppbe/Model/pbj_utils/pbj_interface.py b/xppbe/Model/pbj_utils/pbj_interface.py
index 0162424..2483de0 100644
--- a/xppbe/Model/pbj_utils/pbj_interface.py
+++ b/xppbe/Model/pbj_utils/pbj_interface.py
@@ -33,4 +33,4 @@ def calculate_potential_ens(self, atom_name = ["H"], mesh_dx = 1.0, mesh_length
     
     def calculate_solvation_energy(self):
         self.simulation.calculate_solvation_energy()
-        return self.simulation.solutes[0].results['solvation_energy']
+        return self.simulation.solutes[0].results['electrostatic_solvation_energy']
diff --git a/xppbe/Scripts b/xppbe/Scripts
index 97da156..0b8f95d 100644
--- a/xppbe/Scripts
+++ b/xppbe/Scripts
@@ -18,21 +18,15 @@ function Allrun() {
     fi
 
     PYTHON_CODE="
-import os
-import sys
-from xppbe import Simulation
+import os,sys
+from xppbe import RunSimulation
 
 yaml_path = os.path.abspath(sys.argv[1])
-
 results_path = '${results_path%/results}'
 plot_pbj = '--pbj' in sys.argv
 plot_mesh = '--mesh' in sys.argv
 
-sim = Simulation(yaml_path, results_path=results_path)
-sim.create_simulation()
-sim.adapt_model()
-sim.solve_model()
-sim.postprocessing(mesh=plot_mesh, pbj=plot_pbj)
+RunSimulation(yaml_path,results_path,(plot_mesh,plot_pbj))
     "
 
     sims_count=0
@@ -130,7 +124,6 @@ function SimsStatus() {
 if [[ "$current_dir" == "$main_dir" ]]; then
     sims_path="$main_dir/simulations_list"
     results_path="$main_dir/results"
-    pbj_flag='--pbj'
 fi
 
 for arg in "$@"; do
diff --git a/xppbe/__init__.py b/xppbe/__init__.py
index 31a87bd..0bee5fb 100644
--- a/xppbe/__init__.py
+++ b/xppbe/__init__.py
@@ -5,6 +5,15 @@
 xppbe_path = os.path.dirname(os.path.abspath(__file__))
 scripts_path = os.path.join(xppbe_path,'Scripts')
 
+
+def RunSimulation(yaml_path,results_path,plot_flags):
+    plot_mesh,plot_pbj = plot_flags
+    sim = Simulation(yaml_path, results_path=results_path)
+    sim.create_simulation()
+    sim.adapt_model()
+    sim.solve_model()
+    sim.postprocessing(mesh=plot_mesh, pbj=plot_pbj)
+
 def Allrun(sims_path, results_path, plot_mesh=False, plot_pbj=False):
     sims_path = os.path.abspath(sims_path)
     results_path = os.path.abspath(results_path)