From 583455b021fd56c6c92cbb5bcb467ba641a5a074 Mon Sep 17 00:00:00 2001
From: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Fri, 13 Dec 2024 09:55:39 +0000
Subject: [PATCH] Add warning for velocity set on init

---
 janus_core/calculations/md.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/janus_core/calculations/md.py b/janus_core/calculations/md.py
index 2e37dc48..8f85e383 100644
--- a/janus_core/calculations/md.py
+++ b/janus_core/calculations/md.py
@@ -1569,7 +1569,11 @@ def __init__(
         (ensemble_kwargs,) = none_to_dict(ensemble_kwargs)
 
         # Velocity distribution must be non-zero before dynamics is set
-        self._set_velocity_distribution()
+        if np.isclose(self.struct.get_kinetic_energy(), 0.0, rtol=0, atol=1e-12):
+            if self.logger:
+                self.logger.warning("Velocities modified during Bussi initialisation")
+            self._set_velocity_distribution()
+
         self.dyn = Bussi(
             self.struct,
             timestep=self.timestep,