[gmx-developers] version3.1.3*: Fatal error: Atomtype not found!
Mehmet Suezen
suzen at theochem.tu-muenchen.de
Fri May 3 13:38:11 CEST 2002
Dear Gromacs Team,
I've faced the same problem before (cf. mailing list) in 3.0.5 but in
that case it was
about dimension of c[] in push_nbt of toppush.c. Here again I couln'd
figure our what is
the problem. I've checked carefully MAXFORCEPARAMS or any array bounds
that may cause
*(at->atamname[i]) points to somewhere else at a2type() in topitils.c.
*Since parameter
storage changed a bit. And xutils.c is added, somehow.
I'm attaching a print statements form different functions. What could be
the reason?
Any idea will be appriciated or hint, how did you test in the
development phase?
for a new pair force field.
Have a nice day.
cheers,
mehmet
-------------- next part --------------
:-) G R O M A C S (-:
Grunge ROck MAChoS
:-) VERSION 3.1.3 (-:
Copyright (c) 1991-2002, University of Groningen, The Netherlands
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) ./grompp_d (double precision) (-:
creating statusfile for 1 node...
calling /lib/cpp...
processing topology...
===========================================
= **read_topol src/kernel/topio.c =======
= =======
= =======
===========================================
= push_at() src/kernel/toppush.c =======
= =======
= =======
nb_funct at push_at is 15
F_BHAMLJ at push_at is 15
at->nr at push_at is 0
line Si 28.0855 2.4 A 0.0 0.0 0.0 0.0 0.0 at push_at is -1073748428
line at F_BHAMLJ Si 28.0855 2.4 A 0.0 0.0 0.0 0.0 0.0 at push_at is -1073775116
here we are ! toppush push_at F_BHAMLJ
here we are ! toppush push_at type Si
here we are ! toppush push_at &m -1.993703
here we are ! toppush push_at &q -1.968251
here we are ! toppush push_at m 28.085500
here we are ! toppush push_at q 2.400000
here we are ! toppush push_at ptype A
here we are ! toppush push_at &c[0] 2.400001
here we are ! toppush push_at &c[1] -1.993703
here we are ! toppush push_at &c[2] 2.400001
here we are ! toppush push_at &c[3] -1.993703
here we are ! toppush push_at &c[4] 2.400001
here we are ! toppush push_at c[0] 0.000000
here we are ! toppush push_at c[1] 0.000000
here we are ! toppush push_at c[2] 0.000000
here we are ! toppush push_at c[3] 0.000000
here we are ! toppush push_at c[4] 0.000000
mr.gromacs filling arrays in push_at type Si
mr.gromacs filling arrays in push_at at->atomname[nr] Si at nr 0
===========================================
= push_at() src/kernel/toppush.c =======
= =======
= =======
nb_funct at push_at is 15
F_BHAMLJ at push_at is 15
at->nr at push_at is 1
line O 15.9999 -1.2 A 0.0 0.0 0.0 0.0 0.0 at push_at is -1073748428
line at F_BHAMLJ O 15.9999 -1.2 A 0.0 0.0 0.0 0.0 0.0 at push_at is -1073775116
here we are ! toppush push_at F_BHAMLJ
here we are ! toppush push_at type O
here we are ! toppush push_at &m -1.993703
here we are ! toppush push_at &q -1.968251
here we are ! toppush push_at m 15.999900
here we are ! toppush push_at q -1.200000
here we are ! toppush push_at ptype A
here we are ! toppush push_at &c[0] -1.200001
here we are ! toppush push_at &c[1] -1.993703
here we are ! toppush push_at &c[2] -1.200001
here we are ! toppush push_at &c[3] -1.993703
here we are ! toppush push_at &c[4] -1.200001
here we are ! toppush push_at c[0] 0.000000
here we are ! toppush push_at c[1] 0.000000
here we are ! toppush push_at c[2] 0.000000
here we are ! toppush push_at c[3] 0.000000
here we are ! toppush push_at c[4] 0.000000
mr.gromacs filling arrays in push_at type O
mr.gromacs filling arrays in push_at at->atomname[nr] O at nr 1
pline in topio d_nonbond_params Si Si 3 8417e+7 152.207 2248.11508e-6 1.2768e+3 0.04
*atype->atomname[i] Si at i 0 in topio
*atype->atomname[i] O at i 1 in topio
===========================================
= push_nbt() src/kernel/toppush.c =======
= =======
= =======
ftpe in push_nbt 15
NRFP(ftype) 5
pline push_nbt Si Si 3 8417e+7 152.207 2248.11508e-6 1.2768e+3 0.04
here in side NRFPftype 5
here in side NRFP(ftype) 5 AFTER READING pline
nrfp 5
c is 84170000000.000000 at i 0
cr is 84170000000.000000 at i 0
c is 152.207000 at i 1
cr is 152.207000 at i 1
c is 0.002248 at i 2
cr is 0.002248 at i 2
c is 1276.800000 at i 3
cr is 1276.800000 at i 3
c is 0.040000 at i 4
cr is 0.040000 at i 4
a0 Si
a1 Si
*atype->atomname[i] Si at i 0 in push_nbt
*atype->atomname[i] O at i 1 in push_nbt
===========================================
= a2type() src/kernel/toputil.c =======
= =======
= =======
here just before screw up atomname[i] Si at increment i 0
here just before screw up atomname[i] O at increment i 1
-------------------------------------------
i 0 and at>nr 2 and str Si
-------------------------------------------
ai 0
===========================================
= a2type() src/kernel/toputil.c =======
= =======
= =======
here just before screw up atomname[i] Si at increment i 0
here just before screw up atomname[i] O at increment i 1
-------------------------------------------
i 0 and at>nr 2 and str Si
-------------------------------------------
aj 0
pline in topio d_nonbond_params O O 3 169512.294 28.464078 20718.904e-6 0.04613 0.22
*atype->atomname[i] Si at i 0 in topio
*atype->atomname[i] O at i 1 in topio
===========================================
= push_nbt() src/kernel/toppush.c =======
= =======
= =======
ftpe in push_nbt 15
NRFP(ftype) 5
pline push_nbt O O 3 169512.294 28.464078 20718.904e-6 0.04613 0.22
here in side NRFPftype 5
here in side NRFP(ftype) 5 AFTER READING pline
nrfp 5
c is 169512.294000 at i 0
cr is 169512.294000 at i 0
c is 28.464078 at i 1
cr is 28.464078 at i 1
c is 0.020719 at i 2
cr is 0.020719 at i 2
c is 0.046130 at i 3
cr is 0.046130 at i 3
c is 0.220000 at i 4
cr is 0.220000 at i 4
a0 O
a1 O
*atype->atomname[i] Si at i 0 in push_nbt
*atype->atomname[i] O at i 1 in push_nbt
===========================================
= a2type() src/kernel/toputil.c =======
= =======
= =======
here just before screw up atomname[i] Si at increment i 0
here just before screw up atomname[i] O at increment i 1
fucking i 0 fucking atatomname[i] Si at at2type and at->nr 2
-------------------------------------------
i 1 and at>nr 2 and str O
-------------------------------------------
ai 1
===========================================
= a2type() src/kernel/toputil.c =======
= =======
= =======
here just before screw up atomname[i] Si at increment i 0
here just before screw up atomname[i] O at increment i 1
fucking i 0 fucking atatomname[i] Si at at2type and at->nr 2
-------------------------------------------
i 1 and at>nr 2 and str O
-------------------------------------------
aj 1
pline in topio d_nonbond_params Si O 3 1034469.617 47.95933 6824.8429e-6 1.0834 0.13
*atype->atomname[i] Si at i 0 in topio
*atype->atomname[i] )\???(??`f1 at i 1 in topio
===========================================
= push_nbt() src/kernel/toppush.c =======
= =======
= =======
ftpe in push_nbt 15
NRFP(ftype) 5
pline push_nbt Si O 3 1034469.617 47.95933 6824.8429e-6 1.0834 0.13
here in side NRFPftype 5
here in side NRFP(ftype) 5 AFTER READING pline
nrfp 5
c is 1034469.617000 at i 0
cr is 1034469.617000 at i 0
c is 47.959330 at i 1
cr is 47.959330 at i 1
c is 0.006825 at i 2
cr is 0.006825 at i 2
c is 1.083400 at i 3
cr is 1.083400 at i 3
c is 0.130000 at i 4
cr is 0.130000 at i 4
a0 Si
a1 O
*atype->atomname[i] Si at i 0 in push_nbt
*atype->atomname[i] )\???(??`f1 at i 1 in push_nbt
===========================================
= a2type() src/kernel/toputil.c =======
= =======
= =======
here just before screw up atomname[i] Si at increment i 0
here just before screw up atomname[i] )\???(??`f1 at increment i 1
-------------------------------------------
i 0 and at>nr 2 and str Si
-------------------------------------------
ai 0
===========================================
= a2type() src/kernel/toputil.c =======
= =======
= =======
here just before screw up atomname[i] Si at increment i 0
here just before screw up atomname[i] )\???(??`f1 at increment i 1
fucking i 0 fucking atatomname[i] Si at at2type and at->nr 2
fucking i 1 fucking atatomname[i] )\???(??`f1 at at2type and at->nr 2
-------------------------------------------
i 2 and at>nr 2 and str O
-------------------------------------------
More information about the gromacs.org_gmx-developers
mailing list