Dear all user
I want to simulate 405600 atoms with GB that equilibrate at 300 kelvin with timestep 0.001 ps for 10000 run
When I do that with cluster, it lost atoms. When I do this simulation with smaller timestep it lost atoms again. Please let me how can I correct my simulation
units metal
atom_style atomic
boundary p p f
region all block 0 157.48216 0 166.00077 -0.01 192.35334 side in units box
create_box 2 all
Created orthogonal box = (0 0 -0.01) to (157.482 166.001 192.353)
1 by 1 by 31 MPI processor grid read_dump dump.eff 1471 x y z box yes add yes replace yes format native
orthogonal box = (0 0 0) to (157.482 166.001 192.353)
0 atoms before read
405600 atoms in snapshot
0 atoms purged
0 atoms replaced
0 atoms trimmed
405600 atoms added
405600 atoms after read
reset_timestep 0
group REGION region all
405600 atoms in group REGION
mass 1 55.845
pair_style eam/fs
pair_coeff * * Fe_mm.eam.fs Fe
velocity all create 300.0 43454 rot yes dist gaussian
fix 1 all nvt temp 300 300 1
thermo 10
thermo_style custom step elapsed cpu temp pe etotal press vol
timestep 0.001
dump atom all custom 10000 gbfe.eff id type x y z vx vy vz
restart 2500 tempfe.restart
run 10000
Memory usage per processor = 12.4368 Mbytes
Step Elapsed CPU Temp PotEng TotEng Press Volume
0 0 0 300 -1613304.3 -1597575.9 -6121.3998 5028524.7
10 10 5.7689662 269.7682 -1611718.5 -1597575.2 -5497.2843 5028524.7
20 20 11.335278 199.78427 -1608047.5 -1597573.3 -4680.0929 5028524.7 … … 1840 1840 1071.0102 381.07867 -1617790.2 -1597811.1 3866.7187 5028524.7
1850 1850 1076.3437 381.89671 -1617844.4 -1597822.4 4091.4655 5028524.7
1860 1860 1083.2227 382.35829 -1617880 -1597833.8 4357.4499 5028524.7
1870 1870 1089.5128 382.39267 -1617893.3 -1597845.3 4683.1844 5028524.7
1880 1880 1094.3024 382.2469 -1617897.1 -1597856.7 5029.3625 5028524.7
1890 1890 1099.7497 382.62562 -1617928.5 -1597868.3 5341.4546 5028524.7
1900 1900 1106.4883 383.72929 -1617998 -1597879.9 5583.8742 5028524.7
1910 1910 1112.1996 384.81319 -1618066.5 -1597891.6 5806.6998 5028524.7
1920 1920 1116.8349 385.20028 -1618098.6 -1597903.4 6075.4488 5028524.7
1930 1930 1124.4218 385.03755 -1618101.9 -1597915.2 6398.8468 5028524.7
1940 1940 1131.393 384.94377 -1618108.8 -1597927.1 6727.5212 5028524.7
1950 1950 1137.1276 385.22341 -1618135.4 -1597939 7020.6747 5028524.7
ERROR: Lost atoms: original 405600 current 405599 (…/thermo.cpp:389)
Thanks
Best