From 3377e3454b3d35b3e0244c01996f5c2c1026230d Mon Sep 17 00:00:00 2001
From: jzhang <39238584+jzhang-github@users.noreply.github.com>
Date: Tue, 19 Dec 2023 13:26:41 +0800
Subject: [PATCH] fix a bug in `AgatCalculator`

This bug will not affect model predictions and relaxed structures.
---
 .spyproject/config/workspace.ini | 2 +-
 agat/app/app.py                  | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.spyproject/config/workspace.ini b/.spyproject/config/workspace.ini
index f59f9d28..b46ba9fc 100644
--- a/.spyproject/config/workspace.ini
+++ b/.spyproject/config/workspace.ini
@@ -4,7 +4,7 @@ save_data_on_exit = True
 save_history = True
 save_non_project_files = False
 project_type = 'empty-project-type'
-recent_files = ['agat\\test\\test.py', 'agat\\test\\test_graph_build_method.py']
+recent_files = ['agat\\test\\test.py']
 
 [main]
 version = 0.2.0
diff --git a/agat/app/app.py b/agat/app/app.py
index b0cda6fd..081695df 100644
--- a/agat/app/app.py
+++ b/agat/app/app.py
@@ -104,6 +104,9 @@ def calculate(self, atoms=None, properties=None, system_changes=['positions', 'n
         if properties is None:
             properties = self.implemented_properties
 
+        if atoms is not None:
+            self.atoms = atoms.copy()
+
         # read graph
         graph, info = self.cg.get_graph(atoms)
         graph = graph.to(self.device)