From 48e1a4ba1986986dd2dbbd3dc95b81e2a728ca58 Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Sun, 8 Sep 2024 11:15:31 -0400
Subject: [PATCH 1/2] Small patch to parsing XYZ trajectories to handle ORCA 6
 separators

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 avogadro/io/xyzformat.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/avogadro/io/xyzformat.cpp b/avogadro/io/xyzformat.cpp
index 8c042da5e4..64a3988f2b 100644
--- a/avogadro/io/xyzformat.cpp
+++ b/avogadro/io/xyzformat.cpp
@@ -129,8 +129,12 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
 
   // Do we have an animation?
   size_t numAtoms2;
-  if (getline(inStream, buffer) && (numAtoms2 = lexicalCast<int>(buffer)) &&
-      numAtoms == numAtoms2) {
+  // check if the next frame has the same number of atoms
+  getline(inStream, buffer); // should be the number of atoms
+  if (buffer[0] == '<')
+    getline(inStream, buffer); // Orca 6 prints ">" separators instead
+
+  if ((numAtoms2 = lexicalCast<int>(buffer)) && numAtoms == numAtoms2) {
     getline(inStream, buffer); // Skip the blank
     mol.setCoordinate3d(mol.atomPositions3d(), 0);
     int coordSet = 1;

From 2b50616acc3f5826613a169c226f52b350ffe870 Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Fri, 13 Sep 2024 15:53:57 -0400
Subject: [PATCH 2/2] Fixup to read all of Orca trajectory

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 avogadro/io/xyzformat.cpp | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/avogadro/io/xyzformat.cpp b/avogadro/io/xyzformat.cpp
index 64a3988f2b..3ed855ef94 100644
--- a/avogadro/io/xyzformat.cpp
+++ b/avogadro/io/xyzformat.cpp
@@ -14,8 +14,7 @@
 #include <nlohmann/json.hpp>
 
 #include <iomanip>
-#include <istream>
-#include <ostream>
+#include <iostream>
 #include <sstream>
 #include <string>
 
@@ -131,8 +130,9 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
   size_t numAtoms2;
   // check if the next frame has the same number of atoms
   getline(inStream, buffer); // should be the number of atoms
-  if (buffer[0] == '<')
-    getline(inStream, buffer); // Orca 6 prints ">" separators instead
+  if (buffer.size() == 0 || buffer[0] == '>') {
+    getline(inStream, buffer); // Orca 6 prints ">" separators
+  }
 
   if ((numAtoms2 = lexicalCast<int>(buffer)) && numAtoms == numAtoms2) {
     getline(inStream, buffer); // Skip the blank
@@ -144,6 +144,11 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
 
       for (size_t i = 0; i < numAtoms; ++i) {
         getline(inStream, buffer);
+        if (inStream.eof()) {
+          numAtoms2 = 0;
+          break; // break this inner loop
+        }
+
         vector<string> tokens(split(buffer, ' '));
         if (tokens.size() < 4) {
           appendError("Not enough tokens in this line: " + buffer);
@@ -157,9 +162,21 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
 
       mol.setCoordinate3d(positions, coordSet++);
 
-      if (!getline(inStream, buffer)) {
+      if (getline(inStream, buffer)) {
+        if (inStream.eof()) {
+          numAtoms2 = 0;
+          break; // break this inner loop
+        }
+
+        if (buffer.size() == 0 || buffer[0] == '>')
+          getline(inStream, buffer); // Orca 6 prints ">" separators
+        if (inStream.eof()) {
+          numAtoms2 = 0;
+          break; // break this inner loop
+        }
+
         numAtoms2 = lexicalCast<int>(buffer);
-        if (numAtoms == numAtoms2)
+        if (numAtoms != numAtoms2)
           break;
       }