From: Gadi Oron (gadi_at_proteologics.com)
Date: Sun Apr 18 2004 - 01:51:42 CDT
Hi,
On Thu, 2004-04-15 at 22:13, Cheri M Turman wrote:
> Hi all,
> I had this problem earlier but I got distracted and I am just now
> getting back to it. Jim Philips advised me to use the new script with
> xmgrace, which is what I am currently using. I no longer get the
...
I've revised the namdplot script to work with gnuplot instead of
xmgrace. I find it better since closing the plot window does not require
confirmation. It is a complete rewrite in bash instead of csh, so it
might work better.
A second variant I've written plots the same variable from 2 runs
together.
A third script is great for those who work over slow connection. It
displays the plot in the text window.
All these files are attached to this email. Hope it helps.
- Gadi
-- ================= Gadi ORON, PhD -o- Proteologics ====================== ========== gadi/at/proteologics.com ========== +972 8 9475666 ========== A 'full' life in my experience is usually full only of other people's demands. ****************************************************************************** This e-mail message, together with any attachments, contains information of Proteologics, Ltd (Rehovot, Israel) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named in this message. If you are not the intended recipient, please notify us immediately and do not disclose, distribute, or retain this e-mail or any part of it. Proteologics, Ltd reserves the right to monitor all e-mail communications through its network. ** eSafe scanned this email for viruses, vandals and malicious content. ** ******************************************************************************
#!/bin/tcsh
# Written in 1999 by Jim Phillips, Theoretical Biophysics Group,
# Beckman Institute, University of Illinois at Urbana-Champaign.
if ( $#argv < 1 ) then
echo "Usage: $0 [zero] [diff] [from <first>] [to <last>] [<yfield> [<yfield> ...] [vs <xfield>]] <file1> <file2>"
exit -1
endif
set titles = `awk '/^ETITLE:/ { print; exit }' $argv[$#argv]`
echo $titles
if ( $#argv < 2 ) then
echo "Usage: $0 [zero] [diff] [from <first>] [to <last>] [<yfield> [<yfield> ...] [vs <xfield>]] <file>"
exit -1
endif
if ( $1 == zero ) then
set zero = 1
shift argv
else
set zero = 0
endif
if ( $1 == diff ) then
set zero = 1
set diff = 1
shift argv
else
set diff = 0
endif
if ( $1 == from ) then
shift argv
set first_step = $1
shift argv
else
set first_step = 0
endif
if ( $1 == to ) then
shift argv
set last_step = $1
shift argv
else
set last_step = 0
endif
set ytargets =
while ( $#argv > 2 && $1 != vs )
@ pos = 1
foreach t ( $titles )
if ( $t == $1 ) set ytargets = ( $ytargets $pos )
@ pos++
end
shift argv
end
if ( $#ytargets == 0 ) exit -1
set xtarget = 2
if ( $1 == vs ) then
shift argv
@ pos = 1
foreach t ( $titles )
if ( $t == $1 ) set xtarget = $pos
@ pos++
end
shift argv
endif
set file = ($argv[1] $argv[2])
set ytitle =
foreach y ( $ytargets )
set ytitle = ( $ytitle $titles[$y] )
end
set xtitle = $titles[$xtarget]
echo Plotting $ytitle vs $xtitle
set title = "Comparing 1: $file[1] to 2: $file[2]"
set open = '{'
set close = '}'
set dollar = '$'
if ( $zero ) then
set prog = "BEGIN $open zset = 0 $close"
else
set prog = ""
endif
if ( $first_step ) then
set prog = "$prog ${dollar}2 < $first_step $open next $close ;"
endif
if ( $last_step ) then
set prog = "$prog ${dollar}2 > $last_step $open next $close ;"
endif
if ( $zero ) then
set subtitle = "change from initial value"
set prog = "$prog zset == 0 $open zset = 1;"
foreach y ( $ytargets )
set prog = "$prog z$y = $dollar$y;"
end
set prog = "$prog $close"
set prog = "$prog $open print $dollar$xtarget"
foreach y ( $ytargets )
set prog = "$prog, $dollar$y - z$y"
end
set prog = "$prog $close"
if ( $diff ) then
set subtitle = "running backward difference"
set prog = "$prog $open"
foreach y ( $ytargets )
set prog = "$prog z$y = $dollar$y;"
end
set prog = "$prog $close"
endif
else
set subtitle = ""
set prog = "$prog $open print $dollar$xtarget"
foreach y ( $ytargets )
set prog = "$prog, $dollar$y"
end
set prog = "$prog $close"
endif
set quote = '"'
set p_subtitle = "SUBTITLE $quote$subtitle$quote"
set tmpfile = (/tmp/namdplot.$USER.$$.1.tmp /tmp/namdplot.$USER.$$.2.tmp)
set p_cmd = 0
foreach i (1 2)
@ pos = 2
foreach t ( $ytitle )
if ( "$p_cmd" == "0" ) then
set p_cmd = "plot $quote$tmpfile[$i]$quote u 1:$pos t $quote$t ($i)$quote"
else
set p_cmd = "$p_cmd, $quote$tmpfile[$i]$quote u 1:$pos t $quote$t ($i)$quote"
endif
@ pos++
end
grep '^ENERGY:' $file[$i] | grep -v '[a-z]' | awk "$prog" > $tmpfile[$i]
end
#xmgrace \
# -pexec "LEGEND on" \
# -pexec "$l_cmd[1]" \
# -pexec "$l_cmd[2]" \
# -pexec "$l_cmd[3]" \
# -pexec "$l_cmd[4]" \
# -pexec "$l_cmd[5]" \
# -pexec "$l_cmd[6]" \
# -pexec "$l_cmd[7]" \
# -pexec "$l_cmd[8]" \
# -pexec "$l_cmd[9]" \
# -pexec "$l_cmd[10]" \
# -pexec "$p_title" -pexec "$p_subtitle" -pexec "$p_xaxis" \
# -pexec "XAXIS TICKLABEL FORMAT DECIMAL" -pexec "XAXIS TICKLABEL PREC 0" \
# -pexec "YAXIS TICKLABEL FORMAT DECIMAL" -pexec "YAXIS TICKLABEL PREC 0" \
# -autoscale xy -remove -nxy $tmpfile &
echo \
set term x11\; \
set mouse\; \
set title $quote$title$quote\; \
set xlabel $quote$xtitle$quote\; \
$p_cmd\; \
| gnuplot -persist
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