WIP: Numerical sorting of all types

topoangles.tcl

@@ -29,7 +29,7 @@ proc ::TopoTools::angleinfo {infotype sel {flag none}} {
 
         numangles      { return $numangles }
         numangletypes  { return [array size angletypes] }
-        angletypenames { return [lsort -ascii [array names angletypes]] }
+        angletypenames { return [lsort -integer [array names angletypes]] }
         getanglelist   { return $anglelist }
         default        { return "bug! shoot the programmer?"}
     }

topobonds.tcl

@@ -37,7 +37,7 @@ proc ::TopoTools::bondinfo {infotype sel {flag none}} {
     switch $infotype {
         numbonds      { return $numbonds }
         numbondtypes  { return [array size bondtypes] }
-        bondtypenames { return [lsort -ascii [array names bondtypes]] }
+        bondtypenames { return [lsort -integer [array names bondtypes]] }
         getbondlist   { return $bidxlist }
         default       { return "bug? shoot the programmer!"}
     }

topodihedrals.tcl

@@ -30,7 +30,7 @@ proc ::TopoTools::dihedralinfo {infotype sel {flag none}} {
 
         numdihedrals      { return $numdihedrals }
         numdihedraltypes  { return [array size dihedraltypes] }
-        dihedraltypenames { return [lsort -ascii [array names dihedraltypes]] }
+        dihedraltypenames { return [lsort -integer [array names dihedraltypes]] }
         getdihedrallist   { return $dihedrallist }
         default        { return "bug! shoot the programmer?"}
     }

topoimpropers.tcl

@@ -30,7 +30,7 @@ proc ::TopoTools::improperinfo {infotype sel {flag none}} {
 
         numimpropers      { return $numimpropers }
         numimpropertypes  { return [array size impropertypes] }
-        impropertypenames { return [lsort -ascii [array names impropertypes]] }
+        impropertypenames { return [lsort -integer [array names impropertypes]] }
         getimproperlist   { return $improperlist }
         default        { return "bug! shoot the programmer?"}
     }

topolammps.tcl

@@ -4,6 +4,11 @@
 #
 # Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2022,2023 by Axel Kohlmeyer <akohlmey@gmail.com>
 # $Id: topolammps.tcl,v 1.47 2023/04/21 05:41:03 johns Exp $
+#
+# FIXED VERSION: Changed all atom type sorting from -ascii to -integer
+# to preserve numerical order (1,2,3...10,11,12,13) instead of 
+# alphabetical order (1,10,11,12,13,2,3,4,5,6,7,8,9)
+# Fix date: 2026-02-05
 
 # high level subroutines for LAMMPS support.
 #
@@ -243,9 +248,9 @@ proc ::TopoTools::readlammpsdata {filename style {flags none}} {
     # apply masses. Atoms section sets a default of 1.0.
     # since the Masses section can appear before the Atoms section
     # we have to set it here after the parsing.
-    if {[llength atommasses] > 0} {
+    if {[llength $atommasses] > 0} {
         # we have type labels, but masses are indexed by numeric type
-        if {([lindex $atommasses 0] == 1) && ([llength atomlabels] > 0)} {
+        if {([lindex $atommasses 0] == 1) && ([llength $atomlabels] > 0)} {
             foreach {t m} $atommasses {d l} $atomlabels {
                 set msel [atomselect $mol "type '$l'"]
                 $msel set mass $m
@@ -883,7 +888,8 @@ proc ::TopoTools::writelammpsdata {mol filename typelabels style sel {flags none
     set lammps(angles)        [angleinfo    numangles    $sel]
     set lammps(dihedrals)     [dihedralinfo numdihedrals $sel]
     set lammps(impropers)     [improperinfo numimpropers $sel]
-    set lammps(atomtypes)     [llength [lsort -ascii -unique [$sel get {type}]]]
+    # FIXED: Changed from -ascii to -integer for numerical sorting
+    set lammps(atomtypes)     [llength [lsort -integer -unique [$sel get {type}]]]
     set lammps(bondtypes)     [bondinfo     numbondtypes     $sel]
     set lammps(angletypes)    [angleinfo    numangletypes    $sel]
     set lammps(dihedraltypes) [dihedralinfo numdihedraltypes $sel]
@@ -1074,7 +1080,8 @@ proc ::TopoTools::writelammpslabelmaps {fp sel flags} {
     array set lammps $flags
 
     if {$lammps(atomtypes) > 0} {
-        set typemap [lsort -unique -ascii [$sel get type]]
+        # FIXED: Changed from -ascii to -integer for numerical sorting
+        set typemap [lsort -unique -integer [$sel get type]]
         set typeid 1
 
         puts $fp " Atom Type Labels\n"
@@ -1129,7 +1136,8 @@ proc ::TopoTools::writelammpslabelmaps {fp sel flags} {
 proc ::TopoTools::writelammpsmasses {fp sel typelabels} {
 
     # first run the checks and build list of masses
-    set typemap  [lsort -unique -ascii [$sel get type]]
+    # FIXED: Changed from -ascii to -integer for numerical sorting
+    set typemap  [lsort -unique -integer [$sel get type]]
     set masslist {}
     set mol [$sel molid]
     set selstr [$sel text]
@@ -1166,12 +1174,14 @@ proc ::TopoTools::writelammpsatoms {fp sel style typelabels} {
     vmdcon -info "writing LAMMPS Atoms section in style '$style'."
 
     puts $fp " Atoms # $style\n"
-    set typemap [lsort -unique -ascii [$sel get type]]
+    # FIXED: Changed from -ascii to -integer for numerical sorting
+    set typemap [lsort -unique -integer [$sel get type]]
     set resmap  [lsort -unique -integer [$sel get resid]]
     set atomid 0
     foreach adat [$sel get {type resid charge x y z resname mass radius}] {
         lassign $adat type resid charge x y z resname mass radius
-        set atomtype [lsearch -sorted -ascii $typemap $type]
+        # FIXED: Changed from -ascii to -integer for numerical search
+        set atomtype [lsearch -sorted -integer $typemap $type]
         set resid    [lsearch -sorted -integer $resmap $resid]
         incr atomid
         incr atomtype
@@ -1264,7 +1274,7 @@ proc ::TopoTools::writelammpsbonds {fp sel atomidmap typelabels} {
         if {$typelabels} {
             puts $fp [format "%d %s %d %d" $bondid $t $at1 $at2]
         } else {
-            set type [lsearch -ascii $bondtypes $t]
+            set type [lsearch -integer $bondtypes $t]
 
             # go from 0-based to 1-based indexing and write out
             incr type
@@ -1295,7 +1305,7 @@ proc ::TopoTools::writelammpsangles {fp sel atomidmap typelabels} {
         if {$typelabels} {
             puts $fp [format "%d %s %d %d %d" $angleid $t $at1 $at2 $at3]
         } else {
-            set type [lsearch -ascii $angletypes $t]
+            set type [lsearch -integer $angletypes $t]
 
             # go from 0-based to 1-based indexing and write out
             incr type
@@ -1327,7 +1337,7 @@ proc ::TopoTools::writelammpsdihedrals {fp sel atomidmap typelabels} {
         if {$typelabels} {
             puts $fp [format "%d %s %d %d %d %d" $dihedralid $t $at1 $at2 $at3 $at4]
         } else {
-            set type [lsearch -ascii $dihedraltypes $t]
+            set type [lsearch -integer $dihedraltypes $t]
 
             # go from 0-based to 1-based indexing and write out
             incr type
@@ -1359,7 +1369,7 @@ proc ::TopoTools::writelammpsimpropers {fp sel atomidmap typelabels} {
         if {$typelabels} {
             puts $fp [format "%d %s %d %d %d %d" $improperid $t $at1 $at2 $at3 $at4]
         } else {
-            set type [lsearch -ascii $impropertypes $t]
+            set type [lsearch -integer $impropertypes $t]
 
             # go from 0-based to 1-based indexing and write out
             incr type
@@ -1397,7 +1407,8 @@ proc ::TopoTools::writelammpscoeffhint {fp sel typelabels type} {
         atoms {
             puts $fp "\# Pair Coeffs\n\#"
             set aid 1
-            set atlist [lsort -ascii -unique [$sel get {type}]]
+            # FIXED: Changed from -ascii to -integer for numerical sorting
+            set atlist [lsort -integer -unique [$sel get {type}]]
             foreach at $atlist {
                 if {$typelabels} {
                     puts $fp "\# $at"
@@ -1462,4 +1473,4 @@ proc ::TopoTools::writelammpscoeffhint {fp sel typelabels type} {
     }
     puts $fp ""
     return
-}
+}