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Fix VMD script bugs: pbctools + atomselect segfault #29

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Fix VMD script bugs: pbctools + atomselect segfault #29

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13 changes: 8 additions & 5 deletions faunus/src/topology/io/psf.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -281,6 +281,7 @@ pub fn write_vmd_script(
writeln!(w, "mol load psf {psf_file} {traj_ext} {trajectory_file}")?;
writeln!(w, "mol modstyle 0 top VDW 1.0 12.0")?;
writeln!(w, "mol modcolor 0 top Charge")?;
writeln!(w, "package require pbctools")?;
writeln!(w, "pbc box")?;

let present: std::collections::BTreeSet<usize> = groups
Expand Down Expand Up @@ -412,14 +413,15 @@ fn write_vmd_charges_callback(w: &mut impl Write, charges_file: &str) -> anyhow:
}
writeln!(w, "close $_fp")?;
writeln!(w)?;
// Persistent selection avoids create/delete on every frame, which segfaults VMD 1.9.3
writeln!(w, r#"set _charge_sel [atomselect top "all"]"#)?;
writeln!(w)?;
writeln!(w, "proc faunus_update_charges {{args}} {{")?;
writeln!(w, " global vmd_frame charge_data")?;
writeln!(w, " global vmd_frame charge_data _charge_sel")?;
writeln!(w, " set f $vmd_frame(0)")?;
writeln!(w, " if {{$f >= [llength $charge_data]}} return")?;
writeln!(w, " set charges [lindex $charge_data $f]")?;
writeln!(w, r#" set _all [atomselect top "all"]"#)?;
writeln!(w, " $_all set charge $charges")?;
writeln!(w, " $_all delete")?;
writeln!(w, " $_charge_sel frame $f")?;
writeln!(w, " $_charge_sel set charge [lindex $charge_data $f]")?;
writeln!(w, "}}")?;
writeln!(w)?;
writeln!(w, "if {{[llength $charge_data] > 0}} {{")?;
Expand Down Expand Up @@ -509,6 +511,7 @@ system:
std::fs::remove_file(&tcl_path).ok();

assert!(content.contains("mol load psf traj.psf xtc traj.xtc"));
assert!(content.contains("package require pbctools"));
assert!(content.contains("pbc box"));
// A has sigma=4.0, so radius=2.0
assert!(content.contains("type A"));
Expand Down