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Re: [lammps-users] segmentation fault (core dumped)
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Re: [lammps-users] segmentation fault (core dumped)


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 27 Sep 2017 09:25:19 -0400

On Tue, Sep 26, 2017 at 11:07 AM, Myatnoe Suukyi via lammps-users
<lammps-users@lists.sourceforge.net> wrote:
> Dear Steve and Friends,
> I am a new to Lammps. I am trying to simulate graphene and octane system. I
> ask my system to compute the temperature and the pressure of octanes in the
> flow and I am getting the error of segmentation fault (core dumped) . I

a segmentation fault is a very unspecific error message and can have
many causes including hardware issues.
with certain MPI libraries, you will get a segfault under all
circumstances, where you have an input error. so check your output
more carefully.

> enclosed my Lammps Script and many thanks in advance for your help and time.

please clean up your input and remove all commands that are commented
out and also remove those not required to cause the segfault.
at the very least you should *always* report which version of LAMMPS
you are using and on what platform you are running.
also try with as small a system as possible. that way you can also
provide the data file to the mailing list and people can actually try
to reproduce it.
with the limited information you provide, it is impossible to give any
meaningful advice.

axel.

> Best regards,
> suu
>
>
> #bla
> #from system.in.init - moltemplate
> units  real
> atom_style  full
> dimension               3
> boundary                p p p
>
> #
>     bond_style hybrid harmonic
>     angle_style hybrid harmonic
>     dihedral_style hybrid opls charmm
> #    improper_style hybrid harmonic
> #    pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/cut 25.0
> #    the above combination does not seem to work
>     pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut 10.0
> #    pair_style hybrid lj/cut/coul/long 10.0 10.0
>     pair_modify mix geometric
>     special_bonds lj/coul 0.0 0.0 0.5
>     kspace_style pppm 0.0001
> #
> read_data "10nmgraphene.data"
> #
> # for graphene
> #pair_style              lj/cut/coul/cut 25.0
> #    pair_coeff 1 1 lj/cut/coul/cut 0.086 3.4
> #!!!!!
>     pair_coeff  1 1 lj/cut/coul/long 0.086 3.4
>     bond_coeff  1 harmonic 24.0610 1.0
>     angle_coeff  1 harmonic 1.9474 109.47
>     dihedral_coeff  1 charmm 3.1 2 180 0.0
> #
> # for octane
> #
>     pair_coeff 2 2 lj/cut/coul/long 0.066 3.5
>     pair_coeff 3 3 lj/cut/coul/long 0.066 3.5
>     pair_coeff 4 4 lj/cut/coul/long 0.03 2.5
>     pair_coeff 5 5 lj/cut/coul/long 0.026290630975 2.5
> #
>     bond_coeff 2 harmonic 268.0 1.529
>     bond_coeff 3 harmonic 340.0 1.09
> #
>     angle_coeff 2 harmonic 58.35 112.7
>     angle_coeff 3 harmonic 33.0 107.8
>     angle_coeff 4 harmonic 37.5 110.7
> #
>     dihedral_coeff 2 opls 0.0 0.0 0.3 0.0
>     dihedral_coeff 3 opls 0.0 0.0 0.3 0.0
>     dihedral_coeff 4 opls 0.6446926386 -0.2143420172 0.1782194073 0.0
> # do I need this? yes, apparantly
> #    improper_coeff 1 harmonic 10.5 180.0
> #    improper_coeff 2 harmonic 10.5 180.0
> #    improper_coeff 3 harmonic 2.5 180.0
> #    improper_coeff 4 harmonic 15.0 180.0
> #    improper_coeff 5 harmonic 2.5 180.0
> #
>     set type 2 charge -0.222  # "Alkane CH3- (LOPLS CT_CH3)"
>     set type 3 charge -0.148  # "Alkane -CH2- (LOPLS CT_CH2)"
>     set type 4 charge 0.074  # "Alkane H-C CH3 (LOPLS HC_CH3)"
>     set type 5 charge 0.074  # "Alkane H-C CH2 (LOPLS HC_CH2)"
> #
>     set type 1 charge 0.0
> #
> #octane graphene interaction
> #pair_style              lj/cut/coul/cut 25.0
> #    pair_coeff 1 2 lj/cut/coul/long 0.01 3.5
> #    pair_coeff 1 3 lj/cut/coul/long 0.01 3.5
> #    pair_coeff 1 4 lj/cut/coul/long 0.01 3.5
> #    pair_coeff 1 5 lj/cut/coul/long 0.01 3.5
>     pair_coeff 1 2 lj/cut 0.4 2.0
>     pair_coeff 1 3 lj/cut 0.4 2.0
>     pair_coeff 1 4 lj/cut 0.4 2.0
>     pair_coeff 1 5 lj/cut 0.4 2.0
> neighbor 5.0 bin
> neigh_modify delay 0 every 1 check yes page 600000 one 60000
>
>
> timestep        0.25
>
> dump            1 all custom 1000 traj_nvt.lammpstrj1 id mol type x y z ix
> iy iz
> #
> #velocity        all create 100.0 482748
> fix  1 all nve
> #fix             2 all temp/rescale 100 100.0 100.0 1.0 1.0
> group           sheet type 1
> velocity        sheet set 0.0 0.0 0.0
> fix 3 sheet setforce 0.0 0.0 0.0
>
> group flow type 2 3 4 5
> fix             4 flow addforce 0.0 0.0 0.0
> velocity flow create 100.0 482748
> fix 5 flow temp/rescale  100 100.0 100.0 1.0 1.0
>
> compute  1 flow stress/atom
> compute  p flow reduce sum c_1[1] c_1[2] c_1[3]
> variable  press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
> thermo_style  custom step time temp v_press
> #compute 2 flow temp
>
> #compute  3 all  ke/atom
>
> #
> thermo                  100
> #thermo_style            multi
> #
> run             2500000
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.