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log.lammps
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LAMMPS (3 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
atom_modify map array
dimension 3
boundary p p f
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region 1 block 0 10 0 10 1 50 units lattice
region 3 cylinder z 5.0 5.0 2.0 0 50 units lattice
region centerslice block 3 5 0 10 1 100 units lattice
region todump block 0 10 0 10 52 100 units lattice
read_data microporSi50percent_1010100.csv
orthogonal box = (0 0 0) to (54.3 54.3 543)
1 by 1 by 1 MPI processor grid
reading atoms ...
19699 atoms
read_data CPU = 0.0553367 secs
group allatoms type 1
19699 atoms in group allatoms
group centeratoms1 region 3
2246 atoms in group centeratoms1
variable Nn equal count(all,todump)
mass 1 28.0
pair_style tersoff
pair_coeff * * Si.tersoff Si
Reading potential file Si.tersoff with DATE: 2007-10-25
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
thermo 10
thermo_modify lost ignore flush yes
velocity allatoms create 300 12345
fix 2 all nve
fix 3 all ave/time 1 1 1 v_Nn file outputs/NPs_flux_output300nm1Jcm210fs0.5por10nmsize
compute coord all coord/atom cutoff 2.6
dump 8 all movie 2 outputs/3d300nm1Jcm210fs0.5por10nmsize.mpg c_coord type zoom 1.0 adiam 2.2 axes yes 0.8 0.02 view 60 -30 size 2048 2048
dump 9 all movie 2 outputs/flat300nm1Jcm210fs0.5por10nmsize.mpg c_coord type zoom 1.6 adiam 2.2 axes yes 0.8 0.02 view 90 0 size 2048 2048
dump 12 all movie 2 outputs/slice300nm1Jcm210fs0.5por10nmsize.mpg c_coord type zoom 1.0 adiam 2.2 axes yes 0.8 0.02 view 60 -30 size 2048 2048
dump 13 all movie 2 outputs/flatslice300nm1Jcm210fs0.5por10nmsize.mpg c_coord type zoom 1.6 adiam 2.2 axes yes 0.8 0.02 view 90 0 size 2048 2048
dump_modify 8 amap 1 6 cf 0.0 3 min blue 0.6 yellow max green
dump_modify 9 amap 1 6 cf 0.0 3 min blue 0.6 yellow max green
dump_modify 12 amap 1 6 cf 0.0 3 min blue 0.6 yellow max green region centerslice
dump_modify 13 amap 1 6 cf 0.0 3 min blue 0.6 yellow max green region centerslice
run 100
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.7
ghost atom cutoff = 3.7
binsize = 1.85, bins = 30 30 294
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) compute coord/atom, occasional, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
ERROR on proc 0: Support for writing movies not included (src/dump_movie.cpp:52)
Last command: run 100