VMD-L Mailing List

From: Bharat Sharma (bharatsolbridge_at_gmail.com)
Date: Fri Mar 27 2015 - 11:10:26 CDT

Hello Felipe and Josh,

Thank you for your reply. Yes, atomselection is the most memory consumption
part in my case. I deleted and it will save some memory.

Thank your for the suggestions.

Bharat

On Fri, Mar 27, 2015 at 9:49 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> You have an atomselection inside the inner loop. That's gonna be a huge
> penalty in performance (atomselects are fast, but they aren't THAT fast),
> and there isn't a "$sel delete" statement, so you will run yourself out of
> memory as old atomselections are still stored. Here is how I would do it:
>
> set sel [atomselect top "whatever the selection needs to be" frame 0]
> set ixyz [$sel get {x y z}]
> for {set f 0} { $f < [molinfo top get numframes] } { incr f } {
> $sel frame $f
> set nxyz [$sel get {x y z}]
> set msd 0.0
> for {set i 0} { $i < [llength $nxyz]} { incr i } {
> set tmp [veclength2 [vecsub $nxyz $ixyz]]
> set msd [expr $msd +$tmp]
> }
> #Put your saving stuff here
> }
>
> Notice I'm only updating a single atomselection, which should save you a
> bunch of time.
>
> -Josh Vermaas
>
>
> On 3/27/15 6:33 AM, Bharat Sharma wrote:
>
> Hello Everyone,
> I am trying to calculate MSD using following script. I just realize that
> it need a lot of memory to complete the calculation for reasonably good
> size of system. I think the most time consuming part is calculating MSD and
> putting in to an array.
>
> Here is my script. Can anyone help me to play my code to save some
> memory?
>
> Appreciate you suggestions.
>
> Thank you.
>
> Bharat
>
> Here is the scripts (I am only showing some parts of the blocks, please
> ignore some syntax errors coming from missing braces)
>
> ---------------------------------------------------------------------------------------------
> for {set k [expr $i]} {$k <[expr $i+$msdlength]} {incr k} {
> set msd 0.0
> foreach idx $idxlist {
>
> set sel [atomselect top "index $idx"]
> $sel frame $i
> set ref [measure center $sel]
> $sel frame [expr $k]
> set poslist [measure center $sel]
> set msd [expr $msd + [veclength2 [vecsub $ref $poslist]]]
> }
> # change
> set msdarray($i,$k) [expr $msd]
>
> }
>
>
>
> for {set l 0} {$l <$msdlength} {incr l} {
>
> for {set m 0} {$m <$msdlength} {incr m} {
> set search [lsearch $missing_i $m]
> if {$search == -1} {
> set sum($l) [expr $sum($l)+$msdarray($m,[expr $m+$l])]
> }
> }
> set t [expr $l * 0.0025* $step]
>
> # change
> puts $msdfile "$count00 $t [expr $sum($l)/$count00]"
> }
>
>
> -----------------------------------------------------------------------------------------------
>
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