#-----------------------------------------------Some settings----------------------------------------------------------------------- dimension 3 boundary p p f units metal atom_style atomic variable a equal 4.06 # lattice size variable nx equal 3 # system duplicate in x & y direction variable nz equal 5 # system duplicate in x direction variable c_fe equal 0.008 # concentration of iron variable step_eq equal 4000 lattice fcc ${a} lattice fcc 4.06 Lattice spacing in x,y,z = 4.06 4.06 4.06 region r1 block 0 ${nx} 0 ${nx} -${nz} 0 #units box region r1 block 0 3 0 ${nx} -${nz} 0 region r1 block 0 3 0 3 -${nz} 0 region r1 block 0 3 0 3 -5 0 region r2 block 0 ${nx} 0 ${nx} -6 1 # make box larget to prevent atoms on wall face region r2 block 0 3 0 ${nx} -6 1 region r2 block 0 3 0 3 -6 1 create_box 5 r2 Created orthogonal box = (0 0 -24.36) to (12.18 12.18 4.06) 2 by 2 by 6 MPI processor grid create_atoms 1 region r1 Created 198 atoms Time spent = 0.00062119 secs variable zI equal zlo variable zH equal zhi variable Lz equal lz #-----------------------------------------------potential ---------------------------------------------------------------------- pair_style meam/c pair_coeff * * library.meam Al Cu Fe Mg Si Al-Cu-Fe-Mg-Si.meam Al Cu Fe Mg Si neighbor 0.3 bin neigh_modify delay 1 #---------------------------------------------- Initialize ---------------------------------------------------------------------- velocity all create 300 4928459 dist gaussian run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 1 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65, bins = 5 5 11 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 8.607 | 8.624 | 8.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -650.50999 0 -642.87072 -9413.5585 Loop time of 8.32827e-06 on 24 procs for 0 steps with 198 atoms 113.1% CPU use with 24 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.328e-06 | | |100.00 Nlocal: 8.25 ave 14 max 4 min Histogram: 4 4 0 0 0 12 0 0 0 4 Nghost: 162.417 ave 215 max 91 min Histogram: 8 0 0 0 0 0 0 8 0 8 Neighs: 156.75 ave 294 max 16 min Histogram: 4 0 2 2 0 4 8 0 0 4 FullNghs: 313.5 ave 588 max 100 min Histogram: 8 0 0 0 0 12 0 0 0 4 Total # of neighbors = 7524 Ave neighs/atom = 38 Neighbor list builds = 0 Dangerous builds = 0 variable step equal 30000 variable v_lo equal ${Lz}*0.5/(${step}*0.002) variable v_lo equal 28.42*0.5/(${step}*0.002) variable v_lo equal 28.42*0.5/(30000*0.002) variable v_hi equal -${Lz}*0.5/(${step}*0.002) variable v_hi equal -28.42*0.5/(${step}*0.002) variable v_hi equal -28.42*0.5/(30000*0.002) variable linear_lo equal vdisplace(${zI},${v_lo}) variable linear_lo equal vdisplace(-24.36,${v_lo}) variable linear_lo equal vdisplace(-24.36,0.236833333333333) variable linear_hi equal vdisplace(${zH},${v_hi}) variable linear_hi equal vdisplace(4.06,${v_hi}) variable linear_hi equal vdisplace(4.06,-0.236833333333333) #---------------------------------------------- Simulation ------------------------------------------------------------------ fix f3 all npt temp 300 300 0.1 x 0 0 1.0 y 0 0 1 drag 1.0 fix wallhi all wall/lj126 zlo v_linear_lo 4.0 4.0 2.5 fix walllo all wall/lj126 zhi v_linear_hi 4.0 4.0 2.5 #---------------------------------------------- output ---------------------------------------------------------------------- dump d1 all atom 1000 compression_step.lammpstrj dump_modify d1 image yes thermo 1000 thermo_style custom step ke pe press lx ly lz pxx pyy pzz run ${step} run 30000 Per MPI rank memory allocation (min/avg/max) = 9.608 | 9.625 | 9.64 Mbytes Step KinEng PotEng Press Lx Ly Lz Pxx Pyy Pzz 0 7.6392746 -650.50999 -9413.5585 12.18 12.18 28.42 -11967.777 -11960.251 -4312.6478 1000 7.820194 -643.40206 6237.5802 12.085471 12.127597 28.42 4706.2858 3346.1076 10660.347 2000 7.7440042 -643.04421 -803.09661 12.139826 12.170599 28.42 -2045.5918 -2920.4301 2556.732 3000 7.8925054 -643.20869 786.7776 12.11608 12.161241 28.42 378.32171 -1148.0517 3130.0628 4000 7.8157654 -643.08568 3413.9904 12.079667 12.105849 28.42 2538.9482 2455.7125 5247.3106 5000 7.6975426 -643.02383 -2151.9124 12.118654 12.159658 28.42 -3151.385 -3679.3052 374.95305 6000 8.0299079 -643.30911 2671.2928 12.108236 12.071537 28.42 1328.6455 2643.7503 4041.4827 7000 7.7985099 -643.02726 -2978.9436 12.143986 12.122379 28.42 -3934.7183 -4117.4212 -884.69133 8000 7.746233 -643.06364 1439.1423 12.087154 12.071605 28.42 831.18484 1956.5382 1529.7038 9000 7.6897774 -642.96316 36.898684 12.098967 12.07307 28.42 58.872743 244.63712 -192.81381 10000 7.9710423 -643.26397 -2003.4959 12.109156 12.066954 28.42 -2424.4851 -1087.6126 -2498.39 11000 7.9182251 -643.21072 -1137.2981 12.087996 12.061811 28.42 -184.46689 -744.8084 -2482.619 12000 7.4211633 -642.63787 -582.1693 12.080111 12.053602 28.42 -246.20735 100.06814 -1600.3687 13000 7.3892051 -642.6271 697.17116 12.082088 12.059888 28.42 1411.9426 430.38346 249.18741 14000 7.061011 -642.39836 -1682.3495 12.093979 12.065977 28.42 -1559.2894 -1380.186 -2107.573 ERROR: Lost atoms: original 198 current 180 (src/thermo.cpp:441) Last command: run ${step}