From c11caf45095d96aeb2a1477ce78d6e0c03ea7505 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Sun, 23 Jun 2019 10:34:43 -0500 Subject: [PATCH] update kim examples to temp. current state of code --- examples/kim/data.VOH | 118 ---------------------- examples/kim/in.kim.VOH.simulator_model | 23 ----- examples/kim/in.kim.ex_si.simulator_model | 69 ------------- examples/kim/in.kim.lj.simulator_model | 10 +- 4 files changed, 2 insertions(+), 218 deletions(-) delete mode 100644 examples/kim/data.VOH delete mode 100644 examples/kim/in.kim.VOH.simulator_model delete mode 100644 examples/kim/in.kim.ex_si.simulator_model diff --git a/examples/kim/data.VOH b/examples/kim/data.VOH deleted file mode 100644 index c093705adc..0000000000 --- a/examples/kim/data.VOH +++ /dev/null @@ -1,118 +0,0 @@ -# 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 deleted file mode 100644 index 8696cf265a..0000000000 --- a/examples/kim/in.kim.VOH.simulator_model +++ /dev/null @@ -1,23 +0,0 @@ -# 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 H C O V - -neighbor 2 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -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.simulator_model b/examples/kim/in.kim.ex_si.simulator_model deleted file mode 100644 index 2f9e79ef4e..0000000000 --- a/examples/kim/in.kim.ex_si.simulator_model +++ /dev/null @@ -1,69 +0,0 @@ - -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 Si - -thermo 10 - -fix 1 all nve -fix 2 all langevin ${thi} ${thi} 0.1 48278 - -timestep 1.0e-3 -neighbor 1.0 bin -neigh_modify every 1 delay 10 check yes - -run 100 - diff --git a/examples/kim/in.kim.lj.simulator_model b/examples/kim/in.kim.lj.simulator_model index 01ee5aa64c..cb7a2e14ed 100644 --- a/examples/kim/in.kim.lj.simulator_model +++ b/examples/kim/in.kim.lj.simulator_model @@ -14,9 +14,7 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -echo both -#kim_style model LennardJones_Ar metal -kim_style model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode +kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode newton on lattice fcc 4.4300 @@ -24,10 +22,7 @@ region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -kim_style setup Au +kim_interactions Au mass 1 39.95 velocity all create 200.0 232345 loop geom @@ -36,6 +31,5 @@ neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100