From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Thu Jul 06 2006 - 13:52:00 CDT
Hi,
I am getting close to getting my force output script correct. However, I
am now running into problems. I need to write the file in some sort of
binary format. It is going to be too big to write in ASCII.
In my example here, I have 192 atoms I am trying to write out fx,fy,and fz
for. I want to put them in some sort of dcd similar format, so I am
trying to do
fx(i), i = 1, numatoms
fy(i), i = 1, numatoms
fz(i), i = 1, numatoms
So the way I am currently trying to do this is with three 'for' loops.
This might be slow, but I am just trying to get it done for now.
I can write out the ASCII file fine, but when I try binary, I think I am
having trouble converting to strings. I am using 'f' which is supposed to
be single-precision floating point in the machine's native representation.
My error is
Reason: FATAL ERROR: expected floating-point number but got "$0.627131146684"
while executing
"binary format f $fx"
(procedure "calcforces" line 16)
invoked from within
"calcforces"
It is putting a $ sign in front for some reason.
Thanks in advance for any help.
Here is my script.
tclforces on
tclForcesScript {
# The IDS of the atoms
set numatoms 192
for {set i 1} {$i < $numatoms} {incr i 1} {
addatom $i
}
proc calcforces {} {
set filename "forces.txt"
set fileID [open $filename "a"]
set filename_check "forces_check.txt"
set fileID_check [open $filename_check "a"]
global numatoms
loadtotalforces p
for {set i 0} {$i < $numatoms} {incr i 1} {
if {[array exists p]} {
set f $p($i)
set fx $[lindex $f 0]
set outBinData $[binary format f $fx]
fconfigure $fileID -translation binary
puts -nonewline $fileID $outBinData
puts $fileID_check $p($i)
loadtotalforces p
for {set i 0} {$i < $numatoms} {incr i 1} {
if {[array exists p]} {
set f $p($i)
set fx $[lindex $f 0]
set outBinData $[binary format f $fx]
fconfigure $fileID -translation binary
puts -nonewline $fileID $outBinData
puts $fileID_check $p($i)
}
}
for {set i 0} {$i < $numatoms} {incr i 1} {
if {[array exists p]} {
set f $p($i)
set fy $[lindex $f 0]
set outBinData $[binary format f $fy]
fconfigure $fileID -translation binary
puts -nonewline $fileID $outBinData
}
}
for {set i 0} {$i < $numatoms} {incr i 1} {
if {[array exists p]} {
set f $p($i)
set fz $[lindex $f 0]
set outBinData $[binary format f $fz]
fconfigure $fileID -translation binary
puts -nonewline $fileID $outBinData
}
}
close $fileID
close $fileID_check
}
}
--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------
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