fix_deposit help

Hello everybody,

i'm trying to perform a trial deposition simulation but I
get a segmentation fault error:

[MacBook-Pro-di-Domenico:19290] *** Process received signal ***
[MacBook-Pro-di-Domenico:19290] Signal: Segmentation fault: 11 (11)
[MacBook-Pro-di-Domenico:19290] Signal code: Address not mapped (1)
[MacBook-Pro-di-Domenico:19290] Failing at address: 0x7f963db8c5dc
[MacBook-Pro-di-Domenico:19290] *** End of error message ***

I attached the input files.

Could someone help me to fix this ?

Thanks to everybody
Domenico

pentacene_final.in (985 Bytes)

pentacene_final.data (12.5 KB)

pentacene_template (11.9 KB)

Hello everybody,

i'm trying to perform a trial deposition simulation but I
get a segmentation fault error:

[MacBook-Pro-di-Domenico:19290] *** Process received signal ***
[MacBook-Pro-di-Domenico:19290] Signal: Segmentation fault: 11 (11)
[MacBook-Pro-di-Domenico:19290] Signal code: Address not mapped (1)
[MacBook-Pro-di-Domenico:19290] Failing at address: 0x7f963db8c5dc
[MacBook-Pro-di-Domenico:19290] *** End of error message ***

I attached the input files.

Could someone help me to fix this ?

yes. this is a genuine bug.

thanks a *lot* for providing a simple and complete(!) input example.
when adding a molecule from a template, dihedral and improper
information is added incompletely.

you need to apply the attached patch or replace your version of
molecule.cpp with the attached one and recompile. the is, of course,
relative to the latest git/svn version.

you also will need to reduce your timestep or use fix shake. 1fs is
too large for unconstrained hydrogens.

axel.

lammps-molecule-dihedral-bugfix.diff.gz (432 Bytes)

molecule.cpp.gz (7.75 KB)

Hello everybody,
i have two problems in my trial simulation using fix_deposit:
1)The inserted molecules seems to not interact between each others;
2)The inserted molecules seems to not have the initial velocity that I set in the fix_deposit command (vz=-1.0)

could someone help me to fix these problems ?

I attached the input files.

Thanks everybody,
Domenico

pentacene_final.in (1.16 KB)

pentacene_template (14.6 KB)

pentacene_final_due.data (23.8 KB)

Hello everybody,
i have two problems in my trial simulation using fix_deposit:
1)The inserted molecules seems to not interact between each others;
2)The inserted molecules seems to not have the initial velocity that I set
in the fix_deposit command (vz=-1.0)

could someone help me to fix these problems ?

I attached the input files.

you input doesn't work with the/my current version of LAMMPS (14 Feb 2014-ICMS):

fix 1 all deposit 50 2 1000 34254 region ins id max near
10.0 attempt 10 vx -1.0 1.0 vy -1.0 1.0 vz -1.0 -1.0 mol penta units
box shake 4
WARNING: Molecule has bond topology but no special bond settings
(../molecule.cpp:1036)
fix 3 all nvt temp 300.0 300.0 200.0
fix 4 all shake 1e-5 5000 0 b 2 mol penta
ERROR: Fix shake molecule template must have shake info (../fix_shake.cpp:171)

got this change as well

thanks,
Steve