Dear Sir
I am trying to simulate core-shell Ti-TiO2 using comb3 potential. I am also using charge equilibration. Below I have given my log file output with error message. this type of error is new to me. Can anybody help me about this?
LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
units metal # set ‘metal’ units (Angstrom,ps timescale)
dimension 3
boundary p p p # periodic BCs
atom_style charge
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
----------------------- ATOM DEFINITION ----------------------------
read_data core.lmp
orthogonal box = (0 0 0) to (165 165 165)
2 by 2 by 4 MPI processor grid
reading atoms …
174300 atoms
read_data CPU = 0.191665 secs
write_dump all atom all_atom.lammpstrj
WARNING: Calling write_dump before a full system init. (src/write_dump.cpp:80)
mass 1 47.86700000
group type1 type 1
75572 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 15.99900000
group type2 type 2
98728 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
------------------Define Interatomic Potential -----------------
pair_style comb3 polar_off
pair_coeff * * ffield.TiO.comb3 Ti O
Reading potential file ffield.TiO.comb3 with DATE: 2014-02-01
Groups
region rinterior sphere 82.5 82.5 82.5 72.5 # define inner box region used for simulation domain
region rexterior sphere 82.5 82.5 82.5 68.5 side out # define thermostat region outside of simulation domain
region outer intersect 2 rinterior rexterior
group interior region rinterior # define group called ‘interior’ comprised of region ‘rinterior’
129124 atoms in group interior
group exterior region rexterior
69068 atoms in group exterior
group heatsink region outer
23892 atoms in group heatsink
compute kin all ke/atom
compute pot all pe/atom
thermo 100
thermo_style custom step temp etotal pe ke evdwl ecoul press vol c_q1 c_q2
thermo_modify lost warn line one flush yes
velocity all create 300 87287
Recoil atom
group PKA id == 101051
1 atoms in group PKA
velocity PKA set 5000 NULL NULL
fix charge all qeq/comb 1 0.0001 file fq.out
dump 1 interior custom 100 test_interior.dump mass type xs ys zs id type q c_kin c_pot c_charge1 c_charge2
dump 2 all custom 100 test_all.dump mass type xs ys zs id type q c_kin c_pot c_charge1 c_charge2
dump 3 PKA custom 100 PKA_traj.dump mass type xs ys zs id type q c_kin c_pot c_charge1 c_charge2