From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Aug 11 2010 - 06:57:27 CDT
Hi,
Just in case someone is willing to fix the CHARMM part of reading NAMD coor
files. I figured out that the code is not portabele between 32/64Bit more then
to figure out the problem is beyond may lacking C skills.
Everything I found out so far is documented in the CHARMM-Forum:
http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24987
http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=25078
It looks as if the CHARMM Devs are not very eager to fix this bug.
I don't know how much work it is to fix the variable declaration (I guess it
is some INT <-> LONG Problem) but if has the time, will and guts to mess with
this code I would appreciate it very much since I occasionately would like to
read a coor file instead of reding the coordinate set from a whole DCD.
I'll shortly summarize my findings:
The following check fails compiled for 64Bit:
/* checking if the number of atoms is the same
printf("checking if the number of atoms is the same\n");
if ( n != (*ptr_natom)) {
printf("number of atoms does not match; in psf %d, in file %d ; exiting...
\n", n, *ptr_natom);
free(filename);
*ptr_ier = -1;
return;
}*/
--->
number of atoms does not match; in psf 68120, in file 68120 ; exiting..
<---
Commenting out the above check, makes the following loop infinite:
printf("read in coordinates\n");
for (i = 0; i < n; i++) {
printf("read in coordinates. Atom %d of %d \n", i, n);
fread(x++,sizeof(double),1,fp);
fread(y++,sizeof(double),1,fp);
fread(z++,sizeof(double),1,fp);
}
printf("done reading coordinates\n");
---->
[...]
read in coordinates. Atom 10961940 of 68120
read in coordinates. Atom 10961941 of 68120
[...]
<----
What is weird:
i,n and ptr_natom ar all declared as LONG:
#ifdef i8
#define INT long
#else
#define INT int
#endif
I know it is some extraordinary request... fixing some code of a competitive
program ;-)
Cheers
Bjoern
-- Bjoern Olausson Martin-Luther-Universität Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:01 CST