xtcfile from cli

Author: mlund

src/icoscan.rs

@@ -68,6 +68,7 @@ pub fn do_icoscan(
     temperature: &f64,
     pmf_file: &PathBuf,
     disktable: &Option<PathBuf>,
+    xtcfile: &Option<PathBuf>,
 ) -> std::result::Result<(), anyhow::Error> {
     let table = Table6D::from_resolution(rmin, rmax, dr, angle_resolution)?;
     let n_vertices = table.get(rmin)?.get(0.0)?.len();
@@ -118,34 +119,36 @@ pub fn do_icoscan(
         });
 
     // Write oriented structures to trajectory file
-    log::info!("Writing trajectory file traj.xtc");
-    let mut traj = xdrfile::XTCTrajectory::open_write("traj.xtc")?;
-    let mut frame_cnt: usize = 0;
-    let n = r_and_omega.len();
-    r_and_omega
-        .into_iter()
-        .progress_count(n as u64)
-        .for_each(|(r, omega)| {
-            table
-                .get_icospheres(r, omega) // remaining 4D
-                .expect("invalid (r, omega) value")
-                .flat_iter()
-                .for_each(|(pos_a, pos_b, _data_b)| {
-                    let (oriented_a, oriented_b) =
-                        orient_structures(r, omega, *pos_a, *pos_b, &ref_a, &ref_b);
-                    let mut frame = xdrfile::Frame::new();
-                    frame.step = frame_cnt;
-                    frame.time = frame_cnt as f32;
-                    frame_cnt += 1;
-                    frame.coords = oriented_a
-                        .pos
-                        .iter()
-                        .chain(oriented_b.pos.iter())
-                        .map(|&p| [p.x as f32, p.y as f32, p.z as f32])
-                        .collect();
-                    traj.write(&frame).expect("Failed to write XTC frame");
-                });
-        });
+    if let Some(xtcfile) = xtcfile {
+        log::info!("Writing trajectory file {}", xtcfile.display());
+        let mut traj = xdrfile::XTCTrajectory::open_write(xtcfile)?;
+        let mut frame_cnt: usize = 0;
+        let n = r_and_omega.len();
+        r_and_omega
+            .into_iter()
+            .progress_count(n as u64)
+            .for_each(|(r, omega)| {
+                table
+                    .get_icospheres(r, omega) // remaining 4D
+                    .expect("invalid (r, omega) value")
+                    .flat_iter()
+                    .for_each(|(pos_a, pos_b, _data_b)| {
+                        let (oriented_a, oriented_b) =
+                            orient_structures(r, omega, *pos_a, *pos_b, &ref_a, &ref_b);
+                        let mut frame = xdrfile::Frame::new();
+                        frame.step = frame_cnt;
+                        frame.time = frame_cnt as f32;
+                        frame_cnt += 1;
+                        frame.coords = oriented_a
+                            .pos
+                            .iter()
+                            .chain(oriented_b.pos.iter())
+                            .map(|&p| [p.x as f32, p.y as f32, p.z as f32])
+                            .collect();
+                        traj.write(&frame).expect("Failed to write XTC frame");
+                    });
+            });
+    }
 
     // Partition function contribution for single (r, omega) point
     // i.e. averaged over 4D angular space
@@ -163,7 +166,7 @@ pub fn do_icoscan(
     if let Some(savetable) = disktable {
         log::info!("Saving 6D table to {}", savetable.display());
         let mut stream = faunus::aux::open_compressed(savetable)?;
-        for r in distances.iter() {
+        for r in distances.iter().progress_count(distances.len() as u64) {
             table.stream_angular_space(*r, &mut stream)?;
         }
     }

src/main.rs

@@ -125,6 +125,9 @@ enum Commands {
         /// Save table to disk (use .gz suffix for compression)
         #[arg(long)]
         savetable: Option<PathBuf>,
+        /// Export XTC file with all poses
+        #[arg(long)]
+        xtcfile: Option<PathBuf>,
     },
 }
 
@@ -144,6 +147,7 @@ fn do_scan(cmd: &Commands) -> Result<()> {
         fixed_dielectric,
         pmf_file,
         savetable,
+        xtcfile,
     } = cmd
     else {
         bail!("Unknown command");
@@ -175,11 +179,13 @@ fn do_scan(cmd: &Commands) -> Result<()> {
     );
     let ref_a = Structure::from_xyz(mol1, topology.atomkinds())?;
     let ref_b = Structure::from_xyz(mol2, topology.atomkinds())?;
-    let mut xyz_file = File::create("confout.xyz")?;
-    ref_a
-        .clone()
-        .add(ref_b.clone())
-        .to_xyz(&mut xyz_file, topology.atomkinds())?;
+    if xtcfile.is_some() {
+        log::info!("Exporting merged XYZ file with both initial structures: confout.xyz");
+        ref_a
+            .clone()
+            .add(ref_b.clone())
+            .to_xyz(&mut File::create("confout.xyz")?, topology.atomkinds())?;
+    }
 
     info!("{}", medium);
     info!(
@@ -216,6 +222,7 @@ fn do_scan(cmd: &Commands) -> Result<()> {
         temperature,
         pmf_file,
         savetable,
+        xtcfile,
     )
 }