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


From: Myatnoe Suukyi <myatnoesuukyi@...444...>
Date: Tue, 26 Sep 2017 16:07:35 +0100

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