VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Aug 04 2016 - 03:31:05 CDT

Hi!

I would advise to delete all the atomselection you create in the inner
loop. So put at the end of the frame loop:

$H3O delete
$SeO3 delete
$REST delete

and also for all the inner loops delete the atom selection that you have
made (h30, seo3, rest).

Best,
Ajasja

On 4 August 2016 at 07:56, Sangkha Borah <sborah53_at_gmail.com> wrote:

> Dear all,
>
> I need some help to improve my script. Though the script works but is very
> slow. In fact it runs with desired speed initially but becomes terribly
> slow afterwards. I guess the script is not able to deallocate the memory
> during the process. The script simply finds some selections and prints in
> some order.
>
>
> ###################################################
> mol new TRAJECTORY.xyz type xyz first 0 last -1 step 1 waitfor all
> package require pbctools
> pbc set {12.42 12.42 12.42} -all
> animate goto 0
> set mol [molinfo top]
> set nf [molinfo $mol get numframes]
> set ox [atomselect $mol {name O and not index 1 2 3}]
> set all [atomselect $mol {name H O}]
> set out [open "TRAJ-SORTED.xyz" w]
>
> foreach i [$ox get index] {
> set sel($i) [atomselect $mol "pbwithin 1.30 of index $i"]
> }
>
>
> for {set n 0} {$n < $nf} {incr n} {
> foreach i [$ox get index] {
> $all frame $n
> $ox frame $n
> $sel($i) frame $n
> $sel($i) update
> set num [$sel($i) num]
> if {$num ==2} {
> puts $out "183"
> puts $out "$n"
> set H3O [atomselect $mol "index [$sel($i) get index]"]
> set SeO3 [atomselect $mol "index 0 1 2 3"]
> set REST [atomselect $mol "not index [$H3O get index] [$SeO3 get
> index]"]
>
> foreach iH3O [$H3O get index] {
> set h3o [atomselect $mol "index $iH3O"]
> $h3o frame $n
> puts $out "[$h3o get name] [$h3o get x] [$h3o get y] [$h3o get z]"
> }
>
> foreach iSeO3 [$SeO3 get index] {
> set seo3 [atomselect $mol "index $iSeO3"]
> $seo3 frame $n
> puts $out "[$seo3 get name] [$seo3 get x] [$seo3 get y] [$seo3 get z]"
> }
>
> foreach iREST [$REST get index] {
> set rest [atomselect $mol "index $iREST"]
> $rest frame $n
> puts $out "[$rest get name] [$rest get x] [$rest get y] [$rest get z]"
> }
>
>
> }
> }
> }
> # clean up selections
> foreach i [$ox get index] {
> $sel($i) delete
> }
> $ox delete
> $all delete
> unset ox all sel i n
> exit
>
> ############################################################
>
> Best,
> --
> Sangkha Borah
> Email-sborah53_at_gmail.com
> IIT Guwahati, India
>