Fixed a panic when writing groups of atoms not starting with index 0 into XTC/TRR files

Author: Ladme

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "groan_rs"
 description = "Gromacs Analysis Library for Rust"
-version = "0.11.0"
+version = "0.11.1"
 license = "MIT"
 edition = "2021"
 authors = ["Ladislav Bartos"]

src/io/trr_io.rs

@@ -491,17 +491,17 @@ impl PrivateTrajWrite for TrrWriter {
         let iterator =
             AtomIterator::new(system.get_atoms(), self.group.get_atoms(), system.get_box());
 
-        for atom in iterator {
+        for (i, atom) in iterator.enumerate() {
             if let Some(pos) = atom.get_position() {
-                coordinates[atom.get_index()] = [pos.x, pos.y, pos.z];
+                coordinates[i] = [pos.x, pos.y, pos.z];
             }
 
             if let Some(vel) = atom.get_velocity() {
-                velocities[atom.get_index()] = [vel.x, vel.y, vel.z];
+                velocities[i] = [vel.x, vel.y, vel.z];
             }
 
             if let Some(force) = atom.get_force() {
-                forces[atom.get_index()] = [force.x, force.y, force.z]
+                forces[i] = [force.x, force.y, force.z]
             }
         }
 

src/io/xtc_io/mod.rs

@@ -304,9 +304,9 @@ mod xtc_write {
             let iterator =
                 AtomIterator::new(system.get_atoms(), self.group.get_atoms(), system.get_box());
             let mut coordinates = vec![[0.0, 0.0, 0.0]; n_atoms];
-            for atom in iterator {
+            for (i, atom) in iterator.enumerate() {
                 if let Some(pos) = atom.get_position() {
-                    coordinates[atom.get_index()] = [pos.x, pos.y, pos.z];
+                    coordinates[i] = [pos.x, pos.y, pos.z];
                 }
             }