From f0458e8280e7ad3a0db4ecee5ed669592998b0e8 Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Thu, 30 Nov 2023 21:41:51 -0500
Subject: [PATCH] Fix vibration animation

Fixes #1445 - animation would "wiggle" from previous frames
Optimization steps are now cleared before vibrational modes added

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 avogadro/core/molecule.cpp             | 8 +++++++-
 avogadro/core/molecule.h               | 5 +++++
 avogadro/qtplugins/spectra/spectra.cpp | 3 ++-
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/avogadro/core/molecule.cpp b/avogadro/core/molecule.cpp
index e064e8ca44..f82d5a3b44 100644
--- a/avogadro/core/molecule.cpp
+++ b/avogadro/core/molecule.cpp
@@ -81,7 +81,8 @@ void Molecule::readProperties(const Molecule& other)
   m_label = other.m_label;
   m_colors = other.m_colors;
   // merge data maps by iterating through other's map
-  for (auto it = other.m_data.constBegin(); it != other.m_data.constEnd(); ++it) {
+  for (auto it = other.m_data.constBegin(); it != other.m_data.constEnd();
+       ++it) {
     // even if we have the same key, we want to overwrite
     m_data.setValue(it->first, it->second);
   }
@@ -1218,6 +1219,11 @@ bool Molecule::setCoordinate3d(int coord)
   return false;
 }
 
+void Molecule::clearCoordinate3d()
+{
+  m_coordinates3d.clear();
+}
+
 Array<Vector3> Molecule::coordinate3d(int index) const
 {
   return m_coordinates3d[index];
diff --git a/avogadro/core/molecule.h b/avogadro/core/molecule.h
index a242be6ed7..cf05ca2ba3 100644
--- a/avogadro/core/molecule.h
+++ b/avogadro/core/molecule.h
@@ -553,6 +553,11 @@ class AVOGADROCORE_EXPORT Molecule
   Array<Vector3> coordinate3d(int index) const;
   bool setCoordinate3d(const Array<Vector3>& coords, int index);
 
+  /**
+   * Clear coordinate sets (except the default set)
+   */
+  void clearCoordinate3d();
+
   /**
    * Timestep property is used when molecular dynamics trajectories are read
    */
diff --git a/avogadro/qtplugins/spectra/spectra.cpp b/avogadro/qtplugins/spectra/spectra.cpp
index d3e1341a7d..09c7e25ee3 100644
--- a/avogadro/qtplugins/spectra/spectra.cpp
+++ b/avogadro/qtplugins/spectra/spectra.cpp
@@ -139,10 +139,11 @@ void Spectra::setMode(int mode)
       m_molecule->setForceVector(atom, v);
       ++atom;
     }
-    m_molecule->emitChanged(QtGui::Molecule::Atoms | QtGui::Molecule::Added);
+    // m_molecule->emitChanged(QtGui::Molecule::Atoms | QtGui::Molecule::Added);
 
     int frames = 5; // TODO: needs an option
     int frameCounter = 0;
+    m_molecule->clearCoordinate3d();
     m_molecule->setCoordinate3d(atomPositions, frameCounter++);
 
     // Current coords + displacement.