diff --git a/examples/kim/data.VOH b/examples/kim/data.VOH new file mode 100644 index 0000000000..c093705adc --- /dev/null +++ b/examples/kim/data.VOH @@ -0,0 +1,118 @@ +# VOH example + +100 atoms +4 atom types + +0 25.000 xlo xhi +0 25.000 ylo yhi +0 25.000 zlo zhi + +Masses + +1 1.0080 +2 12.0107 +3 15.9994 +4 50.9415 + +Atoms + + 1 2 0.0 12.35333 12.56112 11.08925 + 2 4 0.0 12.32916 12.62071 13.13099 + 3 3 0.0 14.09425 12.56218 13.76130 + 4 3 0.0 11.42814 11.10330 13.76732 + 5 3 0.0 11.63260 13.89286 13.64097 + 6 1 0.0 10.61647 11.29221 14.30535 + 7 1 0.0 14.38026 13.34626 14.29055 + 8 1 0.0 11.32479 12.58820 10.70253 + 9 1 0.0 12.90918 13.42567 10.69612 + 10 1 0.0 12.84043 11.63643 10.74688 + 11 2 0.0 0.93670 23.74637 24.45218 + 12 4 0.0 2.18151 24.36876 0.94725 + 13 3 0.0 3.93452 24.44779 0.28384 + 14 3 0.0 2.13668 23.10529 2.33362 + 15 3 0.0 1.76108 0.74666 1.48323 + 16 1 0.0 1.82070 23.45305 3.20745 + 17 1 0.0 4.35555 0.34186 0.31083 + 18 1 0.0 24.90472 23.68735 24.82586 + 19 1 0.0 0.97611 24.45631 23.61244 + 20 1 0.0 1.24583 22.75250 24.09589 + 21 2 0.0 2.25730 12.18969 18.74792 + 22 4 0.0 0.67140 13.31162 19.37385 + 23 3 0.0 0.71106 13.43250 21.24545 + 24 3 0.0 24.08603 12.44025 18.87949 + 25 3 0.0 0.70486 14.71920 18.75808 + 26 1 0.0 23.49516 12.95430 18.26686 + 27 1 0.0 0.79723 14.34808 21.60818 + 28 1 0.0 2.24383 12.10285 17.65239 + 29 1 0.0 3.19860 12.66607 19.06030 + 30 1 0.0 2.20214 11.18299 19.18774 + 31 2 0.0 9.32237 8.16220 23.74501 + 32 4 0.0 9.41775 7.26178 21.91463 + 33 3 0.0 8.54752 8.34565 20.65588 + 34 3 0.0 8.50942 5.62151 22.00137 + 35 3 0.0 10.87539 7.02683 21.48455 + 36 1 0.0 9.06507 4.82324 21.80615 + 37 1 0.0 9.11458 8.67119 19.91477 + 38 1 0.0 9.82196 7.53487 24.49616 + 39 1 0.0 9.81855 9.14254 23.70532 + 40 1 0.0 8.27176 8.30387 24.03831 + 41 2 0.0 9.10113 13.98748 23.44281 + 42 4 0.0 8.84954 12.89163 21.73780 + 43 3 0.0 10.01387 13.54293 20.42005 + 44 3 0.0 7.08992 13.11522 21.12954 + 45 3 0.0 9.12937 11.39982 21.99065 + 46 1 0.0 6.55309 12.28287 21.08224 + 47 1 0.0 10.67858 12.89258 20.08249 + 48 1 0.0 8.42108 13.62252 24.22498 + 49 1 0.0 10.13926 13.89766 23.79639 + 50 1 0.0 8.88118 15.04646 23.24289 + 51 2 0.0 17.73225 3.40708 8.28945 + 52 4 0.0 18.49877 5.29835 8.37599 + 53 3 0.0 19.48472 5.62627 6.81505 + 54 3 0.0 19.66498 5.40961 9.84118 + 55 3 0.0 17.38120 6.34466 8.51889 + 56 1 0.0 19.41208 6.07779 10.52927 + 57 1 0.0 19.15960 6.37609 6.25924 + 58 1 0.0 17.15579 3.19557 9.20103 + 59 1 0.0 17.07197 3.31049 7.41454 + 60 1 0.0 18.54903 2.67524 8.20436 + 61 2 0.0 5.18346 20.97409 24.28840 + 62 4 0.0 7.06396 20.17968 24.34847 + 63 3 0.0 7.63220 19.82889 22.59578 + 64 3 0.0 7.00272 18.55243 0.28036 + 65 3 0.0 8.05085 21.13715 0.03620 + 66 1 0.0 7.56109 18.51690 1.09952 + 67 1 0.0 8.44257 20.31624 22.30833 + 68 1 0.0 4.83239 21.17976 0.30904 + 69 1 0.0 5.19182 21.91237 23.71419 + 70 1 0.0 4.49282 20.26573 23.80772 + 71 2 0.0 21.82701 12.79861 20.63056 + 72 4 0.0 21.27646 11.09990 19.63611 + 73 3 0.0 19.52930 10.64327 20.13923 + 74 3 0.0 22.41924 9.70346 20.14638 + 75 3 0.0 21.34556 11.30206 18.11274 + 76 1 0.0 22.94464 9.30084 19.40876 + 77 1 0.0 18.86743 10.62817 19.40629 + 78 1 0.0 22.85378 13.07853 20.35349 + 79 1 0.0 21.14666 13.62206 20.37063 + 80 1 0.0 21.78702 12.62668 21.71522 + 81 2 0.0 4.84801 10.63893 5.85720 + 82 4 0.0 2.99668 11.06158 5.10490 + 83 3 0.0 3.09505 11.09458 3.23258 + 84 3 0.0 2.48053 12.76555 5.69567 + 85 3 0.0 1.96195 10.01780 5.55634 + 86 1 0.0 1.65323 12.78746 6.24245 + 87 1 0.0 2.52753 10.43264 2.76734 + 88 1 0.0 4.80984 10.62196 6.95551 + 89 1 0.0 5.18492 9.65688 5.49273 + 90 1 0.0 5.56737 11.40648 5.53568 + 91 2 0.0 13.58126 9.47098 19.40329 + 92 4 0.0 14.17691 10.17243 21.22692 + 93 3 0.0 14.44428 12.02521 21.10583 + 94 3 0.0 15.81206 9.37183 21.67632 + 95 3 0.0 13.12907 9.86545 22.30960 + 96 1 0.0 15.80034 8.83149 22.50703 + 97 1 0.0 13.87232 12.57457 21.69672 + 98 1 0.0 13.42563 8.38456 19.45392 + 99 1 0.0 12.63978 9.95672 19.10431 + 100 1 0.0 14.35123 9.68789 18.64825 diff --git a/examples/kim/in.kim.VOH.simulator.model b/examples/kim/in.kim.VOH.simulator.model new file mode 100644 index 0000000000..3803ceceba --- /dev/null +++ b/examples/kim/in.kim.VOH.simulator.model @@ -0,0 +1,24 @@ +# REAX potential for VOH system +# ..... + +units real +atom_style charge + +kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 + +read_data data.VOH + +kim_style define NULL H C O V + +neighbor 2 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq +fix 3 all temp/berendsen 500.0 500.0 100.0 + +timestep 0.25 + +#dump 1 all atom 30 dump.reax.voh + +run 300 diff --git a/examples/kim/in.kim.ex_si_1.simulator_model b/examples/kim/in.kim.ex_si_1.simulator_model new file mode 100644 index 0000000000..03f9c25a33 --- /dev/null +++ b/examples/kim/in.kim.ex_si_1.simulator_model @@ -0,0 +1,69 @@ + +units metal +kim_style init ex_sim_model_Si_mod_tersoff + +atom_style atomic +atom_modify map array +boundary p p p + +# temperatures +variable tlo equal 1800.0 +variable thi equal 2400.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 +create_box 1 myreg +create_atoms 1 region myreg + +mass 1 28.06 + +group Si type 1 + +velocity all create ${thi} 5287286 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +delete_atoms group del +kim_style define ex_sim_model_Si_mod_tersoff Si + +thermo 10 + +fix 1 all nve +fix 2 all langevin ${thi} ${thi} 0.1 48278 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +run 100 + diff --git a/examples/kim/in.kim.ex_si_2.simulator_model b/examples/kim/in.kim.ex_si_2.simulator_model new file mode 100644 index 0000000000..18efd94222 --- /dev/null +++ b/examples/kim/in.kim.ex_si_2.simulator_model @@ -0,0 +1,69 @@ + +units metal +kim_style init ex_sim_model_Si_mod_tersoff + +atom_style atomic +atom_modify map array +boundary p p p + +# temperatures +variable tlo equal 1800.0 +variable thi equal 2400.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 +create_box 1 myreg +create_atoms 1 region myreg + +mass 1 28.06 + +group Si type 1 + +velocity all create ${thi} 5287286 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +delete_atoms group del +kim_style define NULL Si + +thermo 10 + +fix 1 all nve +fix 2 all langevin ${thi} ${thi} 0.1 48278 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +run 100 + diff --git a/examples/kim/in.kim.simulator-model b/examples/kim/in.kim.lj.simulator-model similarity index 88% rename from examples/kim/in.kim.simulator-model rename to examples/kim/in.kim.lj.simulator-model index 1e6e9dec89..21d60a48d9 100644 --- a/examples/kim/in.kim.simulator-model +++ b/examples/kim/in.kim.lj.simulator-model @@ -16,18 +16,19 @@ variable zz equal 20*$z units metal atom_style atomic +newton on lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 2 box +create_box 1 box create_atoms 1 box #pair_style lj/cut 8.1500 #pair_coeff 1 1 0.0104 3.4000 -kim_style define ex_sim_model_Si_mod_tersoff Si Si +kim_style define LennardJones_Ar Ar -mass * 39.95 +mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin