diff --git a/examples/reax/AB/data.AB b/examples/reax/AB/data.AB new file mode 100644 index 000000000..11cf7f7b8 --- /dev/null +++ b/examples/reax/AB/data.AB @@ -0,0 +1,121 @@ +# Ammonia Borane + +104 atoms +3 atom types + +0 25.000 xlo xhi +0 25.000 ylo yhi +0 25.000 zlo zhi + +Masses + +1 1.0080 +2 10.8117 +3 14.0067 + +Atoms + + 1 3 0.0 21.58564 10.86619 4.70885 + 2 1 0.0 21.19760 9.94446 4.74054 + 3 1 0.0 21.14376 11.32383 5.48963 + 4 1 0.0 22.52969 10.72323 5.03709 + 5 2 0.0 21.33003 11.52202 3.17801 + 6 1 0.0 20.16015 11.81000 3.18142 + 7 1 0.0 22.10959 12.43989 3.23920 + 8 1 0.0 21.67217 10.56122 2.52638 + 9 3 0.0 4.24143 19.61017 3.81309 + 10 1 0.0 3.56235 19.79503 4.54088 + 11 1 0.0 3.71635 19.01681 3.17657 + 12 1 0.0 4.26467 20.49478 3.31128 + 13 2 0.0 5.67609 18.91643 4.40855 + 14 1 0.0 5.24445 17.78451 4.37952 + 15 1 0.0 6.37233 19.23409 3.46283 + 16 1 0.0 6.25149 19.12579 5.47206 + 17 3 0.0 0.89462 7.91396 14.99527 + 18 1 0.0 0.72479 8.43031 15.83903 + 19 1 0.0 1.24806 8.61493 14.37633 + 20 1 0.0 1.70866 7.41947 15.22380 + 21 2 0.0 24.55492 6.97703 14.54765 + 22 1 0.0 24.03223 6.60612 15.57703 + 23 1 0.0 23.92498 7.80225 13.92379 + 24 1 0.0 0.02583 6.09167 13.87354 + 25 3 0.0 4.66465 16.82677 16.99192 + 26 1 0.0 4.62534 16.28658 16.13848 + 27 1 0.0 3.74455 16.70664 17.37073 + 28 1 0.0 5.23064 16.24589 17.59551 + 29 2 0.0 5.02445 18.47393 16.97100 + 30 1 0.0 4.62973 18.72985 18.08626 + 31 1 0.0 6.20730 18.68932 16.81563 + 32 1 0.0 4.32199 18.83556 16.05590 + 33 3 0.0 7.48903 15.88476 18.79121 + 34 1 0.0 8.31121 15.49673 19.21568 + 35 1 0.0 6.87045 15.09772 18.76578 + 36 1 0.0 7.10399 16.44296 19.54910 + 37 2 0.0 7.93310 16.32894 17.23434 + 38 1 0.0 8.43068 15.30470 16.80480 + 39 1 0.0 6.95342 16.67000 16.59839 + 40 1 0.0 8.73737 17.23060 17.31825 + 41 3 0.0 19.55405 16.45468 3.81603 + 42 1 0.0 19.01196 16.26900 4.64950 + 43 1 0.0 18.84178 16.63550 3.12282 + 44 1 0.0 19.92571 17.37229 3.99337 + 45 2 0.0 20.78058 15.38170 3.37516 + 46 1 0.0 21.31391 15.94910 2.45252 + 47 1 0.0 21.43655 15.29867 4.38599 + 48 1 0.0 20.19343 14.37495 3.05930 + 49 3 0.0 11.25650 13.93863 6.50513 + 50 1 0.0 10.47802 13.34119 6.29339 + 51 1 0.0 10.88883 14.52507 7.24873 + 52 1 0.0 11.88104 13.31764 7.00803 + 53 2 0.0 11.80335 14.65105 5.07290 + 54 1 0.0 10.81860 15.20998 4.64424 + 55 1 0.0 12.62637 15.36828 5.60115 + 56 1 0.0 12.23749 13.81655 4.31005 + 57 3 0.0 14.12278 18.92964 16.18553 + 58 1 0.0 13.86785 18.29885 16.93515 + 59 1 0.0 14.63200 19.65592 16.67737 + 60 1 0.0 14.85867 18.42143 15.71710 + 61 2 0.0 12.82506 19.32328 15.17366 + 62 1 0.0 12.30690 18.24359 15.00075 + 63 1 0.0 12.09247 20.11034 15.72994 + 64 1 0.0 13.40632 19.74074 14.20032 + 65 3 0.0 7.15975 7.91772 21.87223 + 66 1 0.0 6.94095 8.85484 22.14906 + 67 1 0.0 7.14577 7.42244 22.75116 + 68 1 0.0 6.30154 7.60932 21.43191 + 69 2 0.0 8.65756 7.96870 21.10184 + 70 1 0.0 9.23138 8.64523 21.92967 + 71 1 0.0 9.14659 6.87844 20.90953 + 72 1 0.0 8.38539 8.53998 20.07235 + 73 3 0.0 3.60275 6.07904 14.47750 + 74 1 0.0 3.06913 6.82785 14.81958 + 75 1 0.0 4.31760 6.55009 13.96420 + 76 1 0.0 4.08183 5.77530 15.28947 + 77 2 0.0 2.92592 4.66779 13.85448 + 78 1 0.0 3.93110 4.13782 13.43914 + 79 1 0.0 2.38889 4.03886 14.73441 + 80 1 0.0 2.16003 5.04498 12.99309 + 81 3 0.0 19.85292 10.63565 14.28476 + 82 1 0.0 20.41401 10.45720 13.46284 + 83 1 0.0 19.71088 11.63033 14.24389 + 84 1 0.0 18.94474 10.27406 14.01871 + 85 2 0.0 20.47644 10.22299 15.80000 + 86 1 0.0 20.56662 9.01697 15.78854 + 87 1 0.0 21.53177 10.81320 15.70304 + 88 1 0.0 19.76851 10.65037 16.68948 + 89 3 0.0 9.35755 2.14123 0.37265 + 90 1 0.0 9.85587 2.70547 1.05361 + 91 1 0.0 9.77467 2.42073 24.50548 + 92 1 0.0 9.75048 1.22190 0.52235 + 93 2 0.0 7.67209 2.24069 0.25918 + 94 1 0.0 7.61413 3.39707 24.90925 + 95 1 0.0 7.02283 1.51970 24.53256 + 96 1 0.0 7.45770 2.01651 1.43307 + 97 3 0.0 14.57295 16.09372 1.38098 + 98 1 0.0 14.96678 16.71455 2.07503 + 99 1 0.0 14.15675 16.73222 0.71986 + 100 1 0.0 15.38847 15.76347 0.88832 + 101 2 0.0 13.58777 14.84818 1.95819 + 102 1 0.0 14.21056 14.18883 2.76070 + 103 1 0.0 12.64767 15.42497 2.46003 + 104 1 0.0 13.37239 14.31125 0.90033 diff --git a/examples/reax/AB/dump.reax.ab b/examples/reax/AB/dump.reax.ab new file mode 100644 index 000000000..e326eef96 --- /dev/null +++ b/examples/reax/AB/dump.reax.ab @@ -0,0 +1,11413 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +104 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +89 3 0.374302 0.0856492 0.014906 +90 1 0.394235 0.108219 0.0421444 +92 1 0.390019 0.048876 0.020894 +93 2 0.306884 0.0896276 0.0103672 +96 1 0.298308 0.0806604 0.0573228 +1 3 0.863426 0.434648 0.188354 +2 1 0.847904 0.397778 0.189622 +3 1 0.84575 0.452953 0.219585 +4 1 0.901188 0.428929 0.201484 +5 2 0.853201 0.460881 0.12712 +6 1 0.806406 0.4724 0.127257 +7 1 0.884384 0.497596 0.129568 +8 1 0.866887 0.422449 0.101055 +24 1 0.0010332 0.243667 0.554942 +73 3 0.14411 0.243162 0.5791 +76 1 0.163273 0.231012 0.611579 +77 2 0.117037 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+98 1 0.66029 0.642212 0.108345 +99 1 0.646741 0.649194 0.0484533 +100 1 0.647049 0.59216 0.0752395 +101 2 0.570286 0.625981 0.102198 +102 1 0.56824 0.602723 0.144861 +104 1 0.544888 0.609728 0.0638165 +42 1 0.736977 0.701964 0.132696 +41 3 0.729716 0.670374 0.156386 +43 1 0.746149 0.68024 0.191513 +44 1 0.692429 0.66973 0.162 +46 1 0.723957 0.580048 0.141198 +47 1 0.742176 0.63458 0.0832717 +45 2 0.751866 0.615655 0.127012 +48 1 0.797208 0.602229 0.135619 +9 3 0.179713 0.784468 0.157837 +10 1 0.152532 0.790877 0.185629 +11 1 0.160623 0.75919 0.129589 +12 1 0.184667 0.820038 0.139363 +13 2 0.236955 0.752514 0.172274 +15 1 0.281041 0.782442 0.173093 +51 1 0.499339 0.602886 0.251569 +52 1 0.437816 0.607647 0.260176 +55 1 0.452532 0.513825 0.258528 +25 3 0.182969 0.696131 0.711226 +26 1 0.170395 0.691717 0.746833 +27 1 0.197665 0.662436 0.700289 +28 1 0.150566 0.696058 0.688756 +29 2 0.219652 0.738613 0.681142 +32 1 0.211761 0.708193 0.634849 +31 1 0.269883 0.735637 0.677619 +37 2 0.344294 0.651143 0.698574 +39 1 0.374657 0.658569 0.66013 +40 1 0.339423 0.694639 0.723581 +33 3 0.283766 0.625712 0.713672 +34 1 0.255098 0.648473 0.70257 +36 1 0.264106 0.587563 0.708991 +38 1 0.369305 0.616614 0.722941 +58 1 0.582789 0.739727 0.632363 +59 1 0.534424 0.7383 0.673158 +30 1 0.211871 0.786798 0.686087 +62 1 0.468224 0.755966 0.627648 +60 1 0.569806 0.790691 0.667959 +63 1 0.505268 0.826164 0.596961 +57 3 0.551378 0.761472 0.644721 +61 2 0.502543 0.779607 0.601776 +64 1 0.514867 0.754287 0.56088 +35 1 0.283941 0.628137 0.752587 diff --git a/examples/reax/AB/ffield.reax.AB b/examples/reax/AB/ffield.reax.AB new file mode 100644 index 000000000..a74519388 --- /dev/null +++ b/examples/reax/AB/ffield.reax.AB @@ -0,0 +1,151 @@ +Reactive MD-force field for Ammonia Borane: Weismiller, M.R.; van Duin, A.C.T.; Lee, J.; Yetter, R.A. J. Phys. Chem. A 2010, 114, 5485-5492 + 39 ! Number of general parameters + 50.0000 !Overcoordination parameter + 9.4514 !Overcoordination parameter + 56.6636 !Valency angle conjugation parameter + 3.0000 !Triple bond stabilisation parameter + 6.5000 !Triple bond stabilisation parameter + 50.0000 !C2-correction + 1.0701 !Undercoordination parameter + 15.0000 !Triple bond stabilisation parameter + 11.9083 !Undercoordination parameter + 13.3822 !Undercoordination parameter + -24.6710 !Triple bond stabilization energy + 0.0000 !Lower Taper-radius + 10.0000 !Upper Taper-radius + 2.8793 !Not used + 33.8667 !Valency undercoordination + 5.8971 !Valency angle/lone pair parameter + 1.0563 !Valency angle + 2.0384 !Valency angle parameter + 6.1431 !Not used + 6.9290 !Double bond/angle parameter + 0.3989 !Double bond/angle parameter: overcoord + 3.9954 !Double bond/angle parameter: overcoord + -2.4837 !Not used + 5.8374 !Torsion/BO parameter + 10.0000 !Torsion overcoordination + 1.8820 !Torsion overcoordination + -1.2327 !Conjugation 0 (not used) + 2.1861 !Conjugation + 1.5591 !vdWaals shielding + 0.0100 !Cutoff for bond order (*100) + 0.7151 !Valency angle conjugation parameter + 2.7425 !Overcoordination parameter + 12.5819 !Overcoordination parameter + 2.1533 !Valency/lone pair parameter + 0.5000 !Not used + 20.0000 !Not used + 5.0000 !Molecular energy (not used) + 0.0000 !Molecular energy (not used) + 1.4155 !Valency angle conjugation parameter + 5 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. + cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. + ov/un;val1;n.u.;val3,vval4 + H 0.6867 1.0000 1.0080 1.3525 0.0616 0.7492 -0.1000 1.0000 + 9.3858 5.0013 1.0000 0.0000 121.1250 6.5362 7.0327 1.0000 + -0.1000 0.0000 59.5599 6.1752 4.8714 0.0009 1.0698 0.0000 + -15.7683 2.1504 1.0338 1.0000 2.8793 0.6000 0.1000 10.0000 + O 1.5423 2.0000 15.9990 2.0514 0.0880 1.0184 1.2611 6.0000 + 10.2186 7.7719 4.0000 29.5271 116.0768 8.5000 7.5530 2.0000 + 0.9909 16.0134 68.6129 42.5068 1.4404 0.0713 0.9745 0.0000 + -3.5965 2.5000 1.0493 4.0000 2.9225 1.4000 0.1000 12.0000 + N 1.5520 3.0000 14.0000 1.7695 0.1375 1.0000 1.2641 5.0000 + 10.0677 7.6886 4.0000 27.4217 100.0000 8.1308 7.0000 2.0000 + 1.0972 29.9200 -2.3700 2.5862 2.7645 2.6432 0.9745 0.0000 + -6.4340 2.6491 1.0183 4.0000 2.8793 1.4000 0.1000 10.0000 + B 1.3484 3.0000 10.8110 1.8276 0.0500 0.9088 1.0000 3.0000 + 12.4662 2.6721 3.0000 7.2404 80.0000 6.8775 6.7020 0.0000 + -1.3000 0.0000 -2.3700 4.0943 6.8208 1.0943 0.0000 0.0000 + -3.6082 1.8000 1.0564 3.0000 2.8413 1.4000 0.1000 12.0000 + X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000 + 10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000 + -0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000 + -11.0000 2.7466 1.0338 6.2998 2.8793 1.0000 0.1000 10.0000 + 10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr + 1 1 165.7021 0.0000 0.0000 -0.8238 0.0000 1.0000 6.0000 0.3597 + 6.5603 1.0000 0.0000 1.0000 -0.0113 5.6991 0.0000 0.0000 + 2 2 83.4125 192.4592 40.0000 -1.1375 -0.1210 1.0000 22.4755 0.9926 + 0.7782 -0.5000 7.0000 1.0000 -0.1796 6.6205 1.0000 0.0000 + 2 3 144.4207 110.3672 54.8984 0.7380 -0.1832 1.0000 17.1494 0.5521 + 1.1003 -0.4323 6.4197 1.0000 -0.2384 4.7532 1.0000 0.0000 + 3 3 104.5870 85.8215 151.8152 -0.9395 -0.2820 1.0000 12.0357 1.0000 + 0.3279 -0.4426 8.2367 1.0000 -0.1884 5.6414 1.0000 0.0000 + 1 2 207.7908 0.0000 0.0000 -0.8770 0.0000 1.0000 6.0000 0.4021 + 1.1523 1.0000 0.0000 0.0000 -0.0570 5.3078 0.0000 0.0000 + 1 3 231.8918 0.0000 0.0000 -0.7398 0.0000 1.0000 6.0000 0.4224 + 9.1469 1.0000 0.0000 1.0000 -0.0491 5.7202 0.0000 0.0000 + 1 4 177.4103 0.0000 0.0000 -0.4601 -0.3000 1.0000 25.0000 0.4971 + 9.2806 0.0000 0.0000 1.0000 -0.0722 5.1245 1.0000 0.0000 + 3 4 143.9715 94.2037 0.0000 0.2868 -0.2500 1.0000 25.0000 0.1083 + 0.5585 -0.2935 10.2737 1.0000 -0.1650 6.5248 1.0000 0.0000 + 4 4 109.1015 0.0000 0.0000 1.0000 -0.2500 1.0000 25.0000 0.1000 + 0.8313 -0.2000 15.0000 1.0000 -0.0691 5.0065 1.0000 0.0000 + 2 4 235.2369 114.6973 0.0000 -0.9000 -0.2500 1.0000 25.0000 0.5534 + 0.5237 -0.2746 13.4037 1.0000 -0.0898 6.0651 1.0000 0.0000 + 6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 1 2 0.0422 1.8000 10.3041 0.8950 -1.0000 -1.0000 + 1 3 0.0367 1.6470 10.5106 0.9496 -1.0000 -1.0000 + 2 3 0.1102 1.9459 10.1207 1.2076 1.0927 1.0039 + 1 4 0.0526 1.5010 11.2019 1.1648 -1.0000 -1.0000 + 3 4 0.0564 1.7000 10.7561 1.4037 1.2073 -1.0000 + 2 4 0.0960 2.1711 10.3073 1.3579 1.2435 -1.0000 +40 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2;val(bo) + 1 1 1 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 2 2 2 90.0000 16.3789 2.2172 -10.0000 0.4537 0.0000 1.3765 + 2 2 3 81.8855 14.7823 5.2059 0.0000 0.4537 0.0000 1.0783 + 3 2 3 74.9511 45.0000 1.7305 0.0000 0.4537 0.0000 1.0783 + 1 2 2 70.9309 45.0568 7.5000 0.0000 2.0000 0.0000 1.0500 + 1 2 3 77.8084 44.9886 1.4470 0.0000 0.2904 0.0000 1.0500 + 1 2 1 79.2872 14.5680 2.0061 0.0000 0.5136 0.0000 1.3652 + 2 3 2 80.6417 45.0000 1.1167 -30.2047 1.7772 0.0000 1.0500 + 2 3 3 76.8384 45.0000 1.1304 -0.9193 1.7772 0.0000 1.0500 + 3 3 3 73.9146 20.6158 3.9104 0.0000 1.7772 0.0000 1.0500 + 1 3 2 84.8524 44.1822 1.7374 0.0000 0.0780 0.0000 1.0369 + 1 3 3 72.7618 24.2550 2.3034 0.0000 0.1000 0.0000 1.0400 + 1 3 1 85.5836 27.9831 4.0538 0.0000 0.7544 0.0000 1.2487 + 2 1 2 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 2 1 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 3 1 3 0.0000 5.0000 2.0000 0.0000 0.0000 0.0000 1.0400 + 1 1 2 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 1 3 0.0000 10.0019 1.0000 0.0000 0.0000 0.0000 1.0400 + 1 3 4 55.0000 14.9131 0.5290 0.0000 0.1000 0.0000 1.0400 + 1 4 1 62.5987 14.6089 2.3811 0.0000 3.0000 0.0000 3.0000 + 1 4 3 55.0000 2.5000 0.1000 0.0000 0.1000 0.0000 2.2627 + 1 4 4 55.0000 32.2012 4.7029 0.0000 3.0000 0.0000 1.0400 + 3 4 3 72.3075 38.0571 4.2562 0.0000 1.1083 0.0000 1.3861 + 4 3 4 50.0000 30.8700 0.8444 0.0000 3.0000 0.0000 1.0576 + 3 1 4 0.0000 9.6980 1.0000 0.0000 1.0000 0.0000 1.0400 + 1 1 4 0.0000 5.0019 1.0000 0.0000 0.0000 0.0000 1.5000 + 1 2 4 72.5977 9.2973 0.7810 0.0000 2.0787 0.0000 3.0000 + 1 4 2 65.0000 23.9782 6.0000 0.0000 3.0000 0.0000 1.6585 + 2 4 2 50.0000 25.3190 6.0000 0.0000 3.0000 35.0000 3.0000 + 4 2 4 60.2683 34.0172 6.0000 0.0000 3.0000 0.0000 1.0400 + 2 1 4 0.0000 2.5000 0.1000 0.0000 1.6740 0.0000 2.8604 + 2 4 3 67.1161 39.5652 6.0000 0.0000 3.0000 0.0000 1.6555 + 2 2 4 90.0000 50.0000 1.5928 0.0000 1.4924 0.0000 1.0400 + 2 3 4 70.0000 30.0000 2.0000 0.0000 1.0000 0.0000 1.2500 + 3 2 4 70.0000 30.0000 2.0000 0.0000 1.0000 0.0000 1.2500 + 4 1 4 0.0000 5.0000 1.0000 0.0000 1.0000 0.0000 1.0400 + 3 4 4 50.0000 40.0000 6.0000 0.0000 3.0000 0.0000 1.0400 + 3 3 4 70.0000 40.0000 4.0000 0.0000 1.0000 0.0000 1.2500 + 4 4 4 70.0000 35.0000 3.0000 0.0000 1.5000 0.0000 1.0100 + 2 4 4 70.0000 20.0000 4.0000 0.0000 1.0000 0.0000 1.2500 + 10 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 0 1 1 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 1 2 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 2 2 0 0.0002 150.0000 0.3000 -5.0000 0.0000 0.0000 0.0000 + 0 1 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 2 3 0 1.3934 72.0073 -0.2804 -9.0000 -2.0000 0.0000 0.0000 + 0 3 3 0 -2.0000 24.4048 -0.1617 -3.3327 -2.0000 0.0000 0.0000 + 0 3 4 0 -2.0000 19.3351 0.3228 -5.4735 0.0000 0.0000 0.0000 + 0 4 4 0 0.2500 50.0000 0.3000 -7.5000 0.0000 0.0000 0.0000 + 0 2 4 0 -1.9522 50.0000 -0.5000 -2.5000 0.0000 0.0000 0.0000 + 4 2 2 4 2.0000 75.0000 0.3000 -5.0000 0.0000 0.0000 0.0000 + 4 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 2 1 2 2.0347 -2.5000 3.0000 15.0000 + 2 1 3 2.0000 -2.5000 3.0000 15.0000 + 3 1 2 2.0000 -2.5000 3.0000 15.0000 + 3 1 3 2.0000 -2.5002 3.0000 15.0000 diff --git a/examples/reax/AB/in.AB b/examples/reax/AB/in.AB new file mode 100644 index 000000000..a7f1ae33e --- /dev/null +++ b/examples/reax/AB/in.AB @@ -0,0 +1,23 @@ +# REAX potential for Nitroamines system +# ..... + +units real + +atom_style charge +read_data data.AB + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AB 1 4 3 + +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.ab + +run 3000 diff --git a/examples/reax/AB/lmp_control b/examples/reax/AB/lmp_control new file mode 100644 index 000000000..c5d98968a --- /dev/null +++ b/examples/reax/AB/lmp_control @@ -0,0 +1,17 @@ +simulation_name AB_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title AB ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/AB/log.reaxc.ab.18Feb11.linux.1 b/examples/reax/AB/log.reaxc.ab.18Feb11.linux.1 new file mode 100644 index 000000000..ebb5926b2 --- /dev/null +++ b/examples/reax/AB/log.reaxc.ab.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for Nitroamines system +# ..... + +units real + +atom_style charge +read_data data.AB + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 processor grid + 104 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AB 1 4 3 + +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.ab + +run 3000 +Memory usage per processor = 3.16337 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -8505.1809 0 -8505.1809 -670.77434 + 3000 506.01502 -8413.974 0 -8258.6156 622.75341 +Loop time of 37.4245 on 1 procs for 3000 steps with 104 atoms + +Pair time (%) = 34.2758 (91.5863) +Neigh time (%) = 0.118505 (0.316651) +Comm time (%) = 0.0524154 (0.140056) +Outpt time (%) = 0.0176296 (0.0471071) +Other time (%) = 2.96023 (7.90985) + +Nlocal: 104 ave 104 max 104 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 698 ave 698 max 698 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2868 ave 2868 max 2868 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2868 +Ave neighs/atom = 27.5769 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/AB/log.reaxc.ab.18Feb11.linux.4 b/examples/reax/AB/log.reaxc.ab.18Feb11.linux.4 new file mode 100644 index 000000000..d99be23fa --- /dev/null +++ b/examples/reax/AB/log.reaxc.ab.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for Nitroamines system +# ..... + +units real + +atom_style charge +read_data data.AB + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 processor grid + 104 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AB 1 4 3 + +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.ab + +run 3000 +Memory usage per processor = 3.13024 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -8505.1809 0 -8505.1809 -670.77434 + 3000 554.67987 -8433.2315 0 -8262.9318 274.36558 +Loop time of 46.2095 on 4 procs for 3000 steps with 104 atoms + +Pair time (%) = 27.0956 (58.6364) +Neigh time (%) = 0.034441 (0.0745323) +Comm time (%) = 1.26853 (2.74517) +Outpt time (%) = 0.0193296 (0.0418304) +Other time (%) = 17.7916 (38.502) + +Nlocal: 26 ave 34 max 14 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 418 ave 449 max 369 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 857.75 ave 1158 max 469 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 3431 +Ave neighs/atom = 32.9904 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/AB/param.qeq b/examples/reax/AB/param.qeq new file mode 100644 index 000000000..187c4b64a --- /dev/null +++ b/examples/reax/AB/param.qeq @@ -0,0 +1,3 @@ +1 6.5362 14.0654 0.7492 +2 6.8775 13.4040 0.9088 +3 8.1308 14.0000 1.0000 diff --git a/examples/reax/Au_O/data.AuO b/examples/reax/Au_O/data.AuO new file mode 100644 index 000000000..0a8127df0 --- /dev/null +++ b/examples/reax/Au_O/data.AuO @@ -0,0 +1,976 @@ +# AuO example + +960 atoms +2 atom types + +0 26.15618 xlo xhi +0 21.54252 ylo yhi +0 24.00246 zlo zhi + +Masses + +1 15.9994 +2 196.9665 + +Atoms + + 1 2 0.0 0.77942 3.90147 0.45327 + 2 2 0.0 0.77942 3.90147 4.45368 + 3 2 0.0 0.77942 3.90147 8.45409 + 4 2 0.0 0.77942 3.90147 12.45450 + 5 2 0.0 0.77942 3.90147 16.45491 + 6 2 0.0 0.77942 3.90147 20.45532 + 7 2 0.0 0.77942 14.67273 0.45327 + 8 2 0.0 0.77942 14.67273 4.45368 + 9 2 0.0 0.77942 14.67273 8.45409 + 10 2 0.0 0.77942 14.67273 12.45450 + 11 2 0.0 0.77942 14.67273 16.45491 + 12 2 0.0 0.77942 14.67273 20.45532 + 13 2 0.0 13.85751 3.90147 0.45327 + 14 2 0.0 13.85751 3.90147 4.45368 + 15 2 0.0 13.85751 3.90147 8.45409 + 16 2 0.0 13.85751 3.90147 12.45450 + 17 2 0.0 13.85751 3.90147 16.45491 + 18 2 0.0 13.85751 3.90147 20.45532 + 19 2 0.0 13.85751 14.67273 0.45327 + 20 2 0.0 13.85751 14.67273 4.45368 + 21 2 0.0 13.85751 14.67273 8.45409 + 22 2 0.0 13.85751 14.67273 12.45450 + 23 2 0.0 13.85751 14.67273 16.45491 + 24 2 0.0 13.85751 14.67273 20.45532 + 25 2 0.0 5.87820 1.58345 0.45499 + 26 2 0.0 5.87820 1.58345 4.45540 + 27 2 0.0 5.87820 1.58345 8.45581 + 28 2 0.0 5.87820 1.58345 12.45622 + 29 2 0.0 5.87820 1.58345 16.45663 + 30 2 0.0 5.87820 1.58345 20.45704 + 31 2 0.0 5.87820 12.35471 0.45499 + 32 2 0.0 5.87820 12.35471 4.45540 + 33 2 0.0 5.87820 12.35471 8.45581 + 34 2 0.0 5.87820 12.35471 12.45622 + 35 2 0.0 5.87820 12.35471 16.45663 + 36 2 0.0 5.87820 12.35471 20.45704 + 37 2 0.0 18.95629 1.58345 0.45499 + 38 2 0.0 18.95629 1.58345 4.45540 + 39 2 0.0 18.95629 1.58345 8.45581 + 40 2 0.0 18.95629 1.58345 12.45622 + 41 2 0.0 18.95629 1.58345 16.45663 + 42 2 0.0 18.95629 1.58345 20.45704 + 43 2 0.0 18.95629 12.35471 0.45499 + 44 2 0.0 18.95629 12.35471 4.45540 + 45 2 0.0 18.95629 12.35471 8.45581 + 46 2 0.0 18.95629 12.35471 12.45622 + 47 2 0.0 18.95629 12.35471 16.45663 + 48 2 0.0 18.95629 12.35471 20.45704 + 49 2 0.0 7.31156 9.28890 0.45901 + 50 2 0.0 7.31156 9.28890 4.45942 + 51 2 0.0 7.31156 9.28890 8.45983 + 52 2 0.0 7.31156 9.28890 12.46024 + 53 2 0.0 7.31156 9.28890 16.46065 + 54 2 0.0 7.31156 9.28890 20.46106 + 55 2 0.0 7.31156 20.06016 0.45901 + 56 2 0.0 7.31156 20.06016 4.45942 + 57 2 0.0 7.31156 20.06016 8.45983 + 58 2 0.0 7.31156 20.06016 12.46024 + 59 2 0.0 7.31156 20.06016 16.46065 + 60 2 0.0 7.31156 20.06016 20.46106 + 61 2 0.0 20.38965 9.28890 0.45901 + 62 2 0.0 20.38965 9.28890 4.45942 + 63 2 0.0 20.38965 9.28890 8.45983 + 64 2 0.0 20.38965 9.28890 12.46024 + 65 2 0.0 20.38965 9.28890 16.46065 + 66 2 0.0 20.38965 9.28890 20.46106 + 67 2 0.0 20.38965 20.06016 0.45901 + 68 2 0.0 20.38965 20.06016 4.45942 + 69 2 0.0 20.38965 20.06016 8.45983 + 70 2 0.0 20.38965 20.06016 12.46024 + 71 2 0.0 20.38965 20.06016 16.46065 + 72 2 0.0 20.38965 20.06016 20.46106 + 73 2 0.0 12.41979 6.96450 0.45374 + 74 2 0.0 12.41979 6.96450 4.45415 + 75 2 0.0 12.41979 6.96450 8.45456 + 76 2 0.0 12.41979 6.96450 12.45497 + 77 2 0.0 12.41979 6.96450 16.45538 + 78 2 0.0 12.41979 6.96450 20.45579 + 79 2 0.0 12.41979 17.73576 0.45374 + 80 2 0.0 12.41979 17.73576 4.45415 + 81 2 0.0 12.41979 17.73576 8.45456 + 82 2 0.0 12.41979 17.73576 12.45497 + 83 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0.34611 +477 1 0.911296 0.771388 0.346799 +524 1 0.751693 0.752149 0.29638 +525 1 0.751693 0.752149 0.463047 +596 1 0.786345 0.856773 0.30437 +597 1 0.786345 0.856773 0.471036 +620 1 0.967616 0.898324 0.303906 +621 1 0.967616 0.898324 0.470573 +740 1 0.843162 0.733195 0.264277 +741 1 0.843162 0.733195 0.430944 +957 1 0.876982 0.876825 0.339543 +16 2 0.529515 0.181057 0.518711 +17 2 0.529515 0.181057 0.685378 +40 2 0.725064 0.0731096 0.518988 +41 2 0.725064 0.0731096 0.685655 +112 2 0.599885 0.306049 0.560784 +113 2 0.599885 0.306049 0.727451 +232 2 0.725264 0.323195 0.60222 +304 2 0.600306 0.0563738 0.643676 +328 2 0.654516 0.198344 0.644051 +400 1 0.591938 0.23286 0.514139 +401 1 0.591938 0.23286 0.680806 +424 1 0.661502 0.0216783 0.51301 +425 1 0.661502 0.0216783 0.679677 +496 1 0.500913 0.00210369 0.633168 +544 1 0.538424 0.108082 0.639395 +568 1 0.716454 0.146861 0.638191 +712 1 0.66325 0.272351 0.596452 +784 1 0.50249 0.252483 0.547487 +785 1 0.50249 0.252483 0.714154 +928 1 0.628243 0.125913 0.506026 +929 1 0.628243 0.125913 0.672692 +88 2 0.975269 0.323193 0.519006 +89 2 0.975269 0.323193 0.685672 +160 2 0.849963 0.0559887 0.560457 +161 2 0.849963 0.0559887 0.727124 +184 2 0.904524 0.198419 0.560729 +185 2 0.904524 0.198419 0.727395 +256 2 0.779738 0.18158 0.602351 +280 2 0.974908 0.0734979 0.602245 +352 2 0.84993 0.306078 0.644016 +472 1 0.911296 0.271388 0.513465 +473 1 0.911296 0.271388 0.680132 +520 1 0.751693 0.252149 0.629714 +664 1 0.877828 0.129484 0.590187 +736 1 0.843162 0.233195 0.59761 +760 1 0.911302 0.0229038 0.595435 +808 1 0.751813 0.00288763 0.547475 +809 1 0.751813 0.00288763 0.714142 +880 1 0.787702 0.10677 0.554519 +881 1 0.787702 0.10677 0.721186 +904 1 0.96818 0.146923 0.555598 +905 1 0.96818 0.146923 0.722264 +46 2 0.725064 0.57311 0.518988 +47 2 0.725064 0.57311 0.685655 +136 2 0.654215 0.448294 0.560337 +137 2 0.654215 0.448294 0.727003 +208 2 0.529323 0.43111 0.602087 +310 2 0.600306 0.556374 0.643676 +430 1 0.661502 0.521678 0.51301 +431 1 0.661502 0.521678 0.679677 +502 1 0.500913 0.502104 0.633168 +550 1 0.538424 0.608082 0.639395 +574 1 0.716454 0.646861 0.638191 +640 1 0.627357 0.377193 0.589382 +688 1 0.591721 0.482951 0.597128 +832 1 0.537259 0.35806 0.555666 +833 1 0.537259 0.35806 0.722333 +856 1 0.717067 0.395245 0.554485 +857 1 0.717067 0.395245 0.721152 +934 1 0.628243 0.625913 0.506026 +935 1 0.628243 0.625913 0.672692 +64 2 0.77947 0.43145 0.519038 +65 2 0.77947 0.43145 0.685705 +166 2 0.849963 0.555989 0.560457 +167 2 0.849963 0.555989 0.727124 +286 2 0.974908 0.573498 0.602245 +376 2 0.904102 0.448368 0.644203 +448 1 0.843057 0.482227 0.512776 +449 1 0.843057 0.482227 0.679443 +592 1 0.786345 0.356773 0.637703 +616 1 0.967616 0.398324 0.63724 +670 1 0.877828 0.629484 0.590187 +766 1 0.911302 0.522904 0.595435 +814 1 0.751813 0.502888 0.547475 +815 1 0.751813 0.502888 0.714142 +886 1 0.787702 0.60677 0.554519 +887 1 0.787702 0.60677 0.721186 +910 1 0.96818 0.646923 0.555598 +911 1 0.96818 0.646923 0.722264 +952 1 0.876982 0.376825 0.506209 +953 1 0.876982 0.376825 0.672876 +22 2 0.529515 0.681057 0.518711 +23 2 0.529515 0.681057 0.685378 +118 2 0.599885 0.806049 0.560784 +119 2 0.599885 0.806049 0.727451 +142 2 0.654215 0.948294 0.560337 +143 2 0.654215 0.948294 0.727003 +214 2 0.529323 0.93111 0.602087 +238 2 0.725264 0.823195 0.60222 +334 2 0.654516 0.698344 0.644051 +406 1 0.591938 0.73286 0.514139 +407 1 0.591938 0.73286 0.680806 +646 1 0.627357 0.877193 0.589382 +694 1 0.591721 0.982951 0.597128 +718 1 0.66325 0.772351 0.596452 +790 1 0.50249 0.752483 0.547487 +791 1 0.50249 0.752483 0.714154 +838 1 0.537259 0.85806 0.555666 +839 1 0.537259 0.85806 0.722333 +862 1 0.717067 0.895245 0.554485 +863 1 0.717067 0.895245 0.721152 +70 2 0.77947 0.93145 0.519038 +71 2 0.77947 0.93145 0.685705 +94 2 0.975269 0.823193 0.519006 +95 2 0.975269 0.823193 0.685672 +190 2 0.904524 0.698419 0.560729 +191 2 0.904524 0.698419 0.727395 +262 2 0.779738 0.68158 0.602351 +358 2 0.84993 0.806078 0.644016 +382 2 0.904102 0.948368 0.644203 +454 1 0.843057 0.982227 0.512776 +455 1 0.843057 0.982227 0.679443 +478 1 0.911296 0.771388 0.513465 +479 1 0.911296 0.771388 0.680132 +526 1 0.751693 0.752149 0.629714 +598 1 0.786345 0.856773 0.637703 +622 1 0.967616 0.898324 0.63724 +742 1 0.843162 0.733195 0.59761 +958 1 0.876982 0.876825 0.506209 +959 1 0.876982 0.876825 0.672876 +18 2 0.529515 0.181057 0.852044 +42 2 0.725064 0.0731096 0.852321 +114 2 0.599885 0.306049 0.894117 +233 2 0.725264 0.323195 0.768887 +234 2 0.725264 0.323195 0.935554 +305 2 0.600306 0.0563738 0.810343 +306 2 0.600306 0.0563738 0.977009 +329 2 0.654516 0.198344 0.810718 +330 2 0.654516 0.198344 0.977384 +402 1 0.591938 0.23286 0.847472 +426 1 0.661502 0.0216783 0.846344 +497 1 0.500913 0.00210369 0.799835 +498 1 0.500913 0.00210369 0.966501 +545 1 0.538424 0.108082 0.806061 +546 1 0.538424 0.108082 0.972728 +569 1 0.716454 0.146861 0.804857 +570 1 0.716454 0.146861 0.971524 +713 1 0.66325 0.272351 0.763119 +714 1 0.66325 0.272351 0.929785 +786 1 0.50249 0.252483 0.880821 +930 1 0.628243 0.125913 0.839359 +90 2 0.975269 0.323193 0.852339 +162 2 0.849963 0.0559887 0.893791 +186 2 0.904524 0.198419 0.894062 +257 2 0.779738 0.18158 0.769017 +258 2 0.779738 0.18158 0.935684 +281 2 0.974908 0.0734979 0.768912 +282 2 0.974908 0.0734979 0.935578 +353 2 0.84993 0.306078 0.810683 +354 2 0.84993 0.306078 0.97735 +474 1 0.911296 0.271388 0.846799 +521 1 0.751693 0.252149 0.79638 +522 1 0.751693 0.252149 0.963047 +665 1 0.877828 0.129484 0.756854 +666 1 0.877828 0.129484 0.923521 +737 1 0.843162 0.233195 0.764277 +738 1 0.843162 0.233195 0.930944 +761 1 0.911302 0.0229038 0.762101 +762 1 0.911302 0.0229038 0.928768 +810 1 0.751813 0.00288763 0.880808 +882 1 0.787702 0.10677 0.887852 +906 1 0.96818 0.146923 0.888931 +48 2 0.725064 0.57311 0.852321 +138 2 0.654215 0.448294 0.89367 +209 2 0.529323 0.43111 0.768754 +210 2 0.529323 0.43111 0.93542 +311 2 0.600306 0.556374 0.810343 +312 2 0.600306 0.556374 0.977009 +432 1 0.661502 0.521678 0.846344 +503 1 0.500913 0.502104 0.799835 +504 1 0.500913 0.502104 0.966501 +551 1 0.538424 0.608082 0.806061 +552 1 0.538424 0.608082 0.972728 +575 1 0.716454 0.646861 0.804857 +576 1 0.716454 0.646861 0.971524 +641 1 0.627357 0.377193 0.756049 +642 1 0.627357 0.377193 0.922715 +689 1 0.591721 0.482951 0.763795 +690 1 0.591721 0.482951 0.930461 +834 1 0.537259 0.35806 0.889 +858 1 0.717067 0.395245 0.887819 +936 1 0.628243 0.625913 0.839359 +66 2 0.77947 0.43145 0.852372 +168 2 0.849963 0.555989 0.893791 +287 2 0.974908 0.573498 0.768912 +288 2 0.974908 0.573498 0.935578 +377 2 0.904102 0.448368 0.81087 +378 2 0.904102 0.448368 0.977537 +450 1 0.843057 0.482227 0.84611 +593 1 0.786345 0.356773 0.80437 +594 1 0.786345 0.356773 0.971036 +617 1 0.967616 0.398324 0.803906 +618 1 0.967616 0.398324 0.970573 +671 1 0.877828 0.629484 0.756854 +672 1 0.877828 0.629484 0.923521 +767 1 0.911302 0.522904 0.762101 +768 1 0.911302 0.522904 0.928768 +816 1 0.751813 0.502888 0.880808 +888 1 0.787702 0.60677 0.887852 +912 1 0.96818 0.646923 0.888931 +954 1 0.876982 0.376825 0.839543 +24 2 0.529515 0.681057 0.852044 +120 2 0.599885 0.806049 0.894117 +144 2 0.654215 0.948294 0.89367 +215 2 0.529323 0.93111 0.768754 +216 2 0.529323 0.93111 0.93542 +239 2 0.725264 0.823195 0.768887 +240 2 0.725264 0.823195 0.935554 +335 2 0.654516 0.698344 0.810718 +336 2 0.654516 0.698344 0.977384 +408 1 0.591938 0.73286 0.847472 +647 1 0.627357 0.877193 0.756049 +648 1 0.627357 0.877193 0.922715 +695 1 0.591721 0.982951 0.763794 +696 1 0.591721 0.982951 0.930461 +719 1 0.66325 0.772351 0.763119 +720 1 0.66325 0.772351 0.929785 +792 1 0.50249 0.752483 0.880821 +840 1 0.537259 0.85806 0.889 +864 1 0.717067 0.895245 0.887819 +72 2 0.77947 0.93145 0.852372 +96 2 0.975269 0.823193 0.852339 +192 2 0.904524 0.698419 0.894062 +263 2 0.779738 0.68158 0.769017 +264 2 0.779738 0.68158 0.935684 +359 2 0.84993 0.806078 0.810683 +360 2 0.84993 0.806078 0.97735 +383 2 0.904102 0.948368 0.81087 +384 2 0.904102 0.948368 0.977537 +456 1 0.843057 0.982227 0.84611 +480 1 0.911296 0.771388 0.846799 +527 1 0.751693 0.752149 0.79638 +528 1 0.751693 0.752149 0.963047 +599 1 0.786345 0.856773 0.80437 +600 1 0.786345 0.856773 0.971036 +623 1 0.967616 0.898324 0.803906 +624 1 0.967616 0.898324 0.970573 +743 1 0.843162 0.733195 0.764277 +744 1 0.843162 0.733195 0.930944 +960 1 0.876982 0.876825 0.839543 diff --git a/examples/reax/Au_O/ffield.reax.AuO b/examples/reax/Au_O/ffield.reax.AuO new file mode 100644 index 000000000..e258b733b --- /dev/null +++ b/examples/reax/Au_O/ffield.reax.AuO @@ -0,0 +1,105 @@ +Reactive MD-force field: Au-Au: Keith, J. A. et al. Phys Rev B 2010, 81, 235404; Joshi, K. et al., J. Mat. Chem 2010, 20, 10431-10437 + 39 ! Number of general parameters + 50.0000 !Overcoordination parameter + 9.5469 !Overcoordination parameter + 26.5405 !Valency angle conjugation parameter + 1.7224 !Triple bond stabilisation parameter + 6.8702 !Triple bond stabilisation parameter + 60.4850 !C2-correction + 1.0588 !Undercoordination parameter + 4.6000 !Triple bond stabilisation parameter + 12.1176 !Undercoordination parameter + 13.3056 !Undercoordination parameter + -60.5044 !Triple bond stabilization energy + 0.0000 !Lower Taper-radius + 10.0000 !Upper Taper-radius + 2.8793 !Not used + 33.8667 !Valency undercoordination + 6.0891 !Valency angle/lone pair parameter + 1.0563 !Valency angle + 2.0384 !Valency angle parameter + 6.1431 !Not used + 6.9290 !Double bond/angle parameter + 0.3989 !Double bond/angle parameter: overcoord + 3.9954 !Double bond/angle parameter: overcoord + -2.4837 !Not used + 5.7796 !Torsion/BO parameter + 10.0000 !Torsion overcoordination + 1.9487 !Torsion overcoordination + -1.2327 !Conjugation 0 (not used) + 2.1645 !Conjugation + 1.5591 !vdWaals shielding + 0.1000 !Cutoff for bond order (*100) + 2.1365 !Valency angle conjugation parameter + 0.6991 !Overcoordination parameter + 50.0000 !Overcoordination parameter + 1.8512 !Valency/lone pair parameter + 0.5000 !Not used + 20.0000 !Not used + 5.0000 !Molecular energy (not used) + 0.0000 !Molecular energy (not used) + 2.6962 !Valency angle conjugation parameter + 3 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. + cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. + ov/un;val1;n.u.;val3,vval4 + H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000 + 8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000 + -0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000 + -19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 + O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000 + 9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000 + 0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000 + -3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 + Au 2.0074 1.0000 196.9665 2.1413 0.3730 0.9623 -1.0000 1.0000 + 12.1061 2.1635 1.0000 0.0000 0.0000 6.0000 5.6481 0.0000 + -1.0000 0.0000 92.5070 6.2293 5.2294 0.1542 0.8563 0.0000 + -24.8303 2.9867 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000 + 6 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr + 1 1 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300 + 6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000 + 2 2 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 + 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 + 1 2 160.0000 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5626 + 1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000 + 1 3 100.1691 0.0000 0.0000 -0.2641 0.0000 1.0000 6.0000 0.1273 + 8.0163 1.0000 0.0000 1.0000 -0.1717 9.3297 0.0000 0.0000 + 2 3 120.1812 0.0000 0.0000 -0.0090 -0.2000 1.0000 16.0000 0.1884 + 0.0577 -0.2000 15.0000 1.0000 -0.1541 6.1034 1.0000 0.0000 + 3 3 142.6814 0.0000 0.0000 -0.0100 -0.2000 0.0000 16.0000 0.3663 + 0.2903 -0.2000 15.0000 1.0000 -0.1517 5.2066 0.0000 0.0000 + 3 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 1 2 0.0283 1.2885 10.9190 0.9215 -1.0000 -1.0000 + 1 3 0.1644 1.3669 12.0930 1.7000 -1.0000 -1.0000 + 2 3 0.1645 1.8867 9.8430 1.6576 -1.0000 -1.0000 + 17 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2;val(bo) + 1 1 1 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 2 2 2 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783 + 1 2 2 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680 + 1 2 1 85.8000 9.8453 2.2720 0.0000 2.8635 0.0000 1.5800 + 2 1 2 0.0000 15.0000 2.8900 0.0000 0.0000 0.0000 2.8774 + 1 1 2 0.0000 8.5744 3.0000 0.0000 0.0000 0.0000 1.0421 + 1 1 3 0.0000 1.0000 1.0000 0.0000 1.0001 0.0000 1.2500 + 1 3 1 90.0000 20.0000 1.0000 0.0000 1.0000 0.0000 1.2500 + 3 1 3 0.0000 10.0000 1.0000 0.0000 1.0000 0.0000 1.2500 + 1 3 3 80.0000 10.0000 1.0000 0.0000 1.0000 0.0000 1.2500 + 1 2 3 70.0000 10.0000 1.0000 0.0000 1.0500 0.0000 1.2500 + 2 1 3 0.0000 5.0000 2.0000 0.0000 1.0000 0.0000 1.2500 + 1 3 2 30.0000 10.0000 2.0000 0.0000 1.0000 0.0000 1.2500 + 2 2 3 80.3915 36.3302 1.5083 0.0000 1.0000 0.0000 1.5506 + 2 3 2 14.1302 7.6175 6.2730 0.0000 0.5000 0.0000 1.0917 + 3 2 3 0.1000 2.8512 8.0000 0.0000 0.5000 0.0000 1.0000 + 2 3 3 6.7044 15.5303 0.5696 0.0000 0.1000 0.0000 1.5220 + 9 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 1 2 2 1 2.5000 -4.0000 0.9000 -2.5000 -1.0000 0.0000 0.0000 + 1 2 2 2 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 0.0000 0.0000 + 2 2 2 2 -2.5000 -4.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 + 0 1 1 0 0.0000 0.0000 0.0000 0.0000 -1.2327 0.0000 0.0000 + 0 1 2 0 0.0000 0.1000 0.0200 -2.5415 -1.2327 0.0000 0.0000 + 0 2 2 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 + 1 2 3 3 0.0000 0.0100 0.0100 -5.0000 0.0000 0.0000 0.0000 + 1 2 2 3 0.0000 0.0000 0.0000 -5.0000 0.0000 0.0000 0.0000 + 3 2 2 3 0.0000 0.0000 0.0000 -5.0000 0.0000 0.0000 0.0000 + 1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 2 1 2 2.1200 -3.5800 1.4500 19.5000 diff --git a/examples/reax/Au_O/in.AuO b/examples/reax/Au_O/in.AuO new file mode 100644 index 000000000..2e385f8c9 --- /dev/null +++ b/examples/reax/Au_O/in.AuO @@ -0,0 +1,23 @@ +# REAX potential for AuO system +# ..... + +units real + +atom_style charge +read_data data.AuO + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AuO 2 3 + +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.auo + +run 100 diff --git a/examples/reax/Au_O/lmp_control b/examples/reax/Au_O/lmp_control new file mode 100644 index 000000000..d24ae0a05 --- /dev/null +++ b/examples/reax/Au_O/lmp_control @@ -0,0 +1,17 @@ +simulation_name AuO_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title AuO ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.1 b/examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.1 new file mode 100644 index 000000000..ebc1f9f85 --- /dev/null +++ b/examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for AuO system +# ..... + +units real + +atom_style charge +read_data data.AuO + orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025) + 1 by 1 by 1 processor grid + 960 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AuO 2 3 + +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.auo + +run 100 +Memory usage per processor = 9.86232 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -72201.565 0 -72201.565 -129.89248 + 100 68.887452 -72075.82 0 -71878.898 22598.806 +Loop time of 47.9321 on 1 procs for 100 steps with 960 atoms + +Pair time (%) = 41.9124 (87.4412) +Neigh time (%) = 0.252858 (0.527534) +Comm time (%) = 0.0153484 (0.0320212) +Outpt time (%) = 0.00529695 (0.0110509) +Other time (%) = 5.74621 (11.9882) + +Nlocal: 960 ave 960 max 960 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6708 ave 6708 max 6708 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 369164 ave 369164 max 369164 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369164 +Ave neighs/atom = 384.546 +Neighbor list builds = 10 +Dangerous builds = 0 diff --git a/examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.4 b/examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.4 new file mode 100644 index 000000000..b0dbf9745 --- /dev/null +++ b/examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for AuO system +# ..... + +units real + +atom_style charge +read_data data.AuO + orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025) + 2 by 1 by 2 processor grid + 960 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.AuO 2 3 + +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.auo + +run 100 +Memory usage per processor = 5.18368 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -72201.565 0 -72201.565 -129.90134 + 100 68.887528 -72075.82 0 -71878.899 22598.686 +Loop time of 42.8697 on 4 procs for 100 steps with 960 atoms + +Pair time (%) = 37.8474 (88.2849) +Neigh time (%) = 0.0749036 (0.174724) +Comm time (%) = 1.0132 (2.36345) +Outpt time (%) = 0.00368738 (0.00860138) +Other time (%) = 3.93044 (9.16835) + +Nlocal: 240 ave 240 max 240 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3981 ave 3981 max 3981 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 105988 ave 105988 max 105988 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 423952 +Ave neighs/atom = 441.617 +Neighbor list builds = 10 +Dangerous builds = 0 diff --git a/examples/reax/Au_O/param.qeq b/examples/reax/Au_O/param.qeq new file mode 100644 index 000000000..87dee369f --- /dev/null +++ b/examples/reax/Au_O/param.qeq @@ -0,0 +1,2 @@ +1 8.5000 16.6244 1.0898 +2 6.0000 11.2962 0.9623 diff --git a/examples/reax/CHO/data.CHO b/examples/reax/CHO/data.CHO new file mode 100644 index 000000000..74e16ac92 --- /dev/null +++ b/examples/reax/CHO/data.CHO @@ -0,0 +1,122 @@ +# CHO example + +105 atoms +3 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 + +Atoms + + 1 2 0.0 10.67229 14.36836 12.47166 + 2 1 0.0 11.02446 14.91550 13.35233 + 3 1 0.0 11.02446 14.91549 11.59096 + 4 1 0.0 9.57932 14.41980 12.47166 + 5 2 0.0 11.17534 12.87608 12.47165 + 6 1 0.0 10.79792 12.33546 13.34037 + 7 1 0.0 10.79790 12.33545 11.60294 + 8 2 0.0 12.75013 12.93134 12.47163 + 9 1 0.0 13.13241 13.47175 11.60486 + 10 1 0.0 13.13241 13.47210 13.33818 + 11 2 0.0 13.22294 11.42815 12.47199 + 12 1 0.0 12.83858 10.89166 11.60377 + 13 1 0.0 12.83959 10.89255 13.34119 + 14 2 0.0 14.79762 11.45137 12.47107 + 15 1 0.0 15.21044 10.43808 12.47354 + 16 1 0.0 15.19550 11.96345 11.58877 + 17 1 0.0 15.19648 11.96815 13.35018 + 18 2 0.0 0.24250 0.91354 1.10383 + 19 1 0.0 0.97225 1.67509 1.39797 + 20 1 0.0 24.87363 1.18825 0.11010 + 21 1 0.0 24.39847 0.98637 1.79630 + 22 2 0.0 0.86944 24.46895 1.11508 + 23 1 0.0 1.21047 24.19771 2.11484 + 24 1 0.0 0.12679 23.71752 0.84453 + 25 2 0.0 2.06454 24.48829 0.08825 + 26 1 0.0 1.72846 24.75977 24.08683 + 27 1 0.0 2.80951 0.23920 0.35408 + 28 2 0.0 2.67036 23.03401 0.12171 + 29 1 0.0 1.92204 22.28680 24.85503 + 30 1 0.0 3.00638 22.76782 1.12450 + 31 2 0.0 3.87027 23.02208 24.10132 + 32 1 0.0 4.35176 22.04072 24.06515 + 33 1 0.0 3.54082 23.26189 23.08511 + 34 1 0.0 4.63935 23.75310 24.37121 + 35 2 0.0 1.37929 14.62909 17.52744 + 36 1 0.0 1.08393 15.52196 18.08818 + 37 1 0.0 2.47385 14.59977 17.52258 + 38 1 0.0 1.05260 14.77122 16.49293 + 39 2 0.0 0.76275 13.31937 18.14786 + 40 1 0.0 24.67295 13.35030 18.12450 + 41 1 0.0 1.04396 12.44064 17.56651 + 42 2 0.0 1.30113 13.22425 19.62581 + 43 1 0.0 2.39107 13.19385 19.65447 + 44 1 0.0 1.02336 14.10169 20.21106 + 45 2 0.0 0.66878 11.90830 20.21883 + 46 1 0.0 0.94960 11.03396 19.63080 + 47 1 0.0 24.57945 11.94426 20.18968 + 48 2 0.0 1.19125 11.78568 21.69954 + 49 1 0.0 0.79365 10.89123 22.18875 + 50 1 0.0 2.28374 11.72162 21.74071 + 51 1 0.0 0.89616 12.64769 22.30679 + 52 2 0.0 11.41750 7.16471 22.76002 + 53 1 0.0 11.74866 7.28340 21.72336 + 54 1 0.0 11.72154 8.06612 23.30055 + 55 1 0.0 11.97469 6.32478 23.18558 + 56 2 0.0 9.86319 6.92474 22.85179 + 57 1 0.0 9.57626 6.01094 22.33031 + 58 1 0.0 9.54930 6.78307 23.88660 + 59 2 0.0 9.17390 8.18942 22.21244 + 60 1 0.0 9.45849 9.10599 22.73021 + 61 1 0.0 9.48557 8.33580 21.17777 + 62 2 0.0 7.62459 7.92132 22.31840 + 63 1 0.0 7.31756 7.77569 23.35472 + 64 1 0.0 7.34468 7.00469 21.79795 + 65 2 0.0 6.90692 9.17258 21.68631 + 66 1 0.0 5.81845 9.06496 21.71809 + 67 1 0.0 7.15914 10.09632 22.21721 + 68 1 0.0 7.18992 9.31630 20.63835 + 69 2 0.0 4.69047 14.13340 23.48572 + 70 1 0.0 4.95366 15.17281 23.26391 + 71 1 0.0 5.39163 13.78010 24.24888 + 72 1 0.0 4.87514 13.55000 22.57874 + 73 2 0.0 3.19477 13.99798 23.95930 + 74 1 0.0 2.50599 14.33002 23.18163 + 75 1 0.0 2.93803 12.95591 24.15345 + 76 2 0.0 3.05322 14.87431 0.26136 + 77 1 0.0 3.74058 14.54651 1.04202 + 78 1 0.0 3.30993 15.91730 0.07257 + 79 2 0.0 1.55058 14.71961 0.71013 + 80 1 0.0 1.29864 13.67531 0.89801 + 81 1 0.0 0.86725 15.05003 24.92701 + 82 2 0.0 1.37850 15.58633 2.01380 + 83 1 0.0 0.35341 15.53527 2.39297 + 84 1 0.0 2.04062 15.24695 2.81709 + 85 1 0.0 1.60704 16.64178 1.83261 + 86 3 0.0 8.51658 13.05007 22.43728 + 87 3 0.0 9.43965 13.72051 21.88842 + 88 3 0.0 18.16518 4.73455 8.81928 + 89 3 0.0 18.65469 4.57291 7.66370 + 90 3 0.0 6.43553 20.34119 24.80049 + 91 3 0.0 6.44898 20.31621 23.53493 + 92 3 0.0 21.90539 11.54301 19.82384 + 93 3 0.0 20.76137 11.61918 20.36007 + 94 3 0.0 3.42232 11.07545 5.77130 + 95 3 0.0 3.88671 10.95299 4.60048 + 96 3 0.0 11.93988 4.94134 20.86058 + 97 3 0.0 12.98804 5.47798 20.39555 + 98 3 0.0 14.08646 9.50799 20.80806 + 99 3 0.0 14.09449 10.68237 20.33642 + 100 3 0.0 3.45246 19.93144 16.38965 + 101 3 0.0 2.86282 19.60263 15.31936 + 102 3 0.0 12.85008 21.95287 13.63796 + 103 3 0.0 12.06593 21.16486 14.24238 + 104 3 0.0 24.47055 7.42219 14.24997 + 105 3 0.0 24.43181 7.37102 12.98624 diff --git a/examples/reax/CHO/dump.reax.cho b/examples/reax/CHO/dump.reax.cho new file mode 100644 index 000000000..15f75d620 --- /dev/null +++ b/examples/reax/CHO/dump.reax.cho @@ -0,0 +1,11514 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +18 2 0.0097 0.0365416 0.0441532 +19 1 0.03889 0.0670036 0.0559188 +27 1 0.11238 0.009568 0.0141632 +20 1 0.994945 0.04753 0.004404 +21 1 0.975939 0.0394548 0.071852 +94 3 0.136893 0.443018 0.230852 +95 3 0.155468 0.43812 0.184019 +88 3 0.726607 0.189382 0.352771 +89 3 0.746188 0.182916 0.306548 +7 1 0.431916 0.493418 0.464118 +11 2 0.528918 0.457126 0.49888 +12 1 0.513543 0.435666 0.464151 +14 2 0.591905 0.458055 0.498843 +15 1 0.608418 0.417523 0.498942 +16 1 0.60782 0.478538 0.463551 +41 1 0.0417584 0.497626 0.70266 +6 1 0.431917 0.493418 0.533615 +13 1 0.513584 0.435702 0.533648 +17 1 0.607859 0.478726 0.534007 +104 3 0.978822 0.296888 0.569999 +105 3 0.977272 0.294841 0.51945 +57 1 0.38305 0.240438 0.893212 +96 3 0.477595 0.197654 0.834423 +97 3 0.519522 0.219119 0.815822 +45 2 0.0267512 0.476332 0.808753 +46 1 0.037984 0.441358 0.785232 +48 2 0.04765 0.471427 0.867982 +49 1 0.031746 0.435649 0.88755 +50 1 0.0913496 0.468865 0.869628 +66 1 0.232738 0.362598 0.868724 +52 2 0.4567 0.286588 0.910401 +53 1 0.469946 0.291336 0.868934 +54 1 0.468862 0.322645 0.932022 +55 1 0.478988 0.252991 0.927423 +56 2 0.394528 0.27699 0.914072 +58 1 0.381972 0.271323 0.955464 +59 2 0.366956 0.327577 0.888498 +60 1 0.37834 0.36424 0.909208 +61 1 0.379423 0.333432 0.847111 +62 2 0.304984 0.316853 0.892736 +63 1 0.292702 0.311028 0.934189 +64 1 0.293787 0.280188 0.871918 +65 2 0.276277 0.366903 0.867452 +67 1 0.286366 0.403853 0.888688 +68 1 0.287597 0.372652 0.825534 +98 3 0.563458 0.38032 0.832322 +99 3 0.56378 0.427295 0.813457 +47 1 0.983178 0.47777 0.807587 +92 3 0.876216 0.46172 0.792954 +93 3 0.830455 0.464767 0.814403 +76 2 0.122129 0.594972 0.0104544 +77 1 0.149623 0.58186 0.0416808 +78 1 0.132397 0.636692 0.0029028 +79 2 0.0620232 0.588784 0.0284052 +80 1 0.0519456 0.547012 0.0359204 +82 2 0.05514 0.623453 0.080552 +83 1 0.0141364 0.621411 0.0957188 +84 1 0.0816248 0.609878 0.112684 +85 1 0.0642816 0.665671 0.0733044 +22 2 0.0347776 0.978758 0.0446032 +23 1 0.0484188 0.967908 0.0845936 +24 1 0.0050716 0.948701 0.0337812 +25 2 0.0825816 0.979532 0.00353 +28 2 0.106814 0.92136 0.0048684 +30 1 0.120255 0.910713 0.04498 +1 2 0.426892 0.574734 0.498866 +3 1 0.440978 0.59662 0.463638 +4 1 0.383173 0.576792 0.498866 +5 2 0.447014 0.515043 0.498866 +8 2 0.510005 0.517254 0.498865 +9 1 0.525296 0.53887 0.464194 +35 2 0.0551716 0.585164 0.701098 +36 1 0.0433572 0.620878 0.723527 +37 1 0.098954 0.583991 0.700903 +38 1 0.042104 0.590849 0.659717 +39 2 0.03051 0.532775 0.725914 +2 1 0.440978 0.59662 0.534093 +10 1 0.525296 0.538884 0.533527 +40 1 0.986918 0.534012 0.72498 +100 3 0.138098 0.797258 0.655586 +101 3 0.114513 0.784105 0.612774 +103 3 0.482637 0.846594 0.569695 +102 3 0.514003 0.878115 0.545518 +42 2 0.0520452 0.52897 0.785032 +43 1 0.0956428 0.527754 0.786179 +44 1 0.0409344 0.564068 0.808442 +51 1 0.0358464 0.505908 0.892272 +69 2 0.187619 0.565336 0.939429 +70 1 0.198146 0.606912 0.930556 +71 1 0.215665 0.551204 0.969955 +72 1 0.195006 0.542 0.90315 +73 2 0.127791 0.559919 0.958372 +74 1 0.10024 0.573201 0.927265 +75 1 0.117521 0.518236 0.966138 +81 1 0.03469 0.602001 0.99708 +86 3 0.340663 0.522003 0.897491 +87 3 0.377586 0.54882 0.875537 +26 1 0.0691384 0.990391 0.963473 +29 1 0.0768816 0.891472 0.994201 +31 2 0.154811 0.920883 0.964053 +32 1 0.17407 0.881629 0.962606 +33 1 0.141633 0.930476 0.923404 +34 1 0.185574 0.950124 0.974848 +90 3 0.257421 0.813648 0.99202 +91 3 0.257959 0.812648 0.941397 +ITEM: TIMESTEP +30 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +18 2 0.00937076 0.0367917 0.0443399 +19 1 0.0392865 0.0666041 0.0560555 +27 1 0.112563 0.00869584 0.0157483 +20 1 0.995044 0.046987 0.00418757 +21 1 0.975607 0.0410635 0.0715217 +94 3 0.136905 0.443042 0.230771 +95 3 0.155436 0.438172 0.184016 +88 3 0.726616 0.189381 0.352736 +89 3 0.74617 0.182922 0.306584 +7 1 0.432546 0.49359 0.46375 +11 2 0.529406 0.457042 0.498886 +12 1 0.513495 0.43632 0.463792 +14 2 0.592271 0.457773 0.498847 +15 1 0.610023 0.41801 0.498881 +16 1 0.607272 0.478632 0.463344 +41 1 0.0421444 0.497487 0.703117 +6 1 0.432565 0.49359 0.533993 +13 1 0.513596 0.436404 0.534069 +17 1 0.607264 0.478699 0.534314 +104 3 0.97883 0.296901 0.569972 +105 3 0.97728 0.294852 0.519499 +57 1 0.38383 0.240944 0.89213 +96 3 0.477609 0.197521 0.8343 +97 3 0.519401 0.219055 0.815887 +45 2 0.0267941 0.476208 0.809243 +46 1 0.0382293 0.441644 0.784969 +48 2 0.0476202 0.471178 0.868322 +49 1 0.0323999 0.43591 0.888843 +50 1 0.0913082 0.469252 0.869307 +66 1 0.232481 0.364312 0.868032 +52 2 0.457165 0.286744 0.910597 +53 1 0.469443 0.292128 0.868703 +54 1 0.468567 0.322924 0.932203 +55 1 0.480711 0.253459 0.92637 +56 2 0.395135 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0.854408 +50 1 0.95282 0.535368 0.906732 +29 1 0.12731 0.921296 0.954705 +28 2 0.137982 0.964559 0.959312 +26 1 0.0507442 0.981841 0.946923 +78 1 0.201169 0.616784 0.987952 +49 1 0.942638 0.508002 0.844021 +3 1 0.520738 0.638528 0.504693 +ITEM: TIMESTEP +2970 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +18 2 0.0271211 0.00547178 0.0566292 +19 1 0.0352751 0.0489413 0.0594742 +89 3 0.734009 0.18896 0.314292 +88 3 0.705338 0.207829 0.351511 +12 1 0.507904 0.466333 0.478926 +84 1 0.167615 0.496404 0.000860222 +104 3 0.0212602 0.354642 0.608371 +13 1 0.481615 0.458185 0.538382 +17 1 0.576006 0.455538 0.583226 +11 2 0.51683 0.476489 0.520259 +15 1 0.571648 0.406801 0.531412 +14 2 0.569847 0.45015 0.539817 +105 3 0.00624109 0.335504 0.563969 +92 3 0.837218 0.483643 0.75088 +96 3 0.29031 0.107485 0.837369 +97 3 0.254295 0.112089 0.872438 +86 3 0.932126 0.327781 0.957539 +93 3 0.877043 0.497541 0.778384 +32 1 0.169422 0.0364745 0.911169 +83 1 0.157693 0.490291 0.929116 +87 3 0.980464 0.313803 0.96197 +27 1 0.0863677 0.0384258 0.968604 +53 1 0.381688 0.403818 0.916379 +57 1 0.491176 0.370359 0.944033 +66 1 0.630942 0.382835 0.861856 +52 2 0.423519 0.418376 0.916809 +54 1 0.428034 0.436648 0.955554 +56 2 0.465449 0.370981 0.908591 +58 1 0.448081 0.331593 0.909445 +59 2 0.494736 0.378763 0.853583 +60 1 0.502569 0.338418 0.837486 +61 1 0.470641 0.400731 0.822928 +62 2 0.548768 0.405976 0.867749 +63 1 0.55583 0.41569 0.911258 +64 1 0.555268 0.442594 0.845968 +65 2 0.592856 0.361149 0.85496 +67 1 0.59225 0.326822 0.884608 +68 1 0.586725 0.348787 0.814974 +99 3 0.605649 0.462063 0.71061 +98 3 0.586825 0.423063 0.736383 +55 1 0.422847 0.450544 0.885996 +16 1 0.605369 0.468848 0.521629 +37 1 0.10406 0.495898 0.829888 +44 1 0.0435445 0.495764 0.785794 +69 2 0.288692 0.66493 0.0148331 +94 3 0.21362 0.525292 0.121279 +21 1 0.0225991 0.991838 0.0997717 +90 3 0.145637 0.728596 0.0130775 +70 1 0.250464 0.687424 0.0179586 +95 3 0.173818 0.545406 0.0972364 +22 2 0.0753001 0.973769 0.0303044 +23 1 0.110284 0.976909 0.0583447 +24 1 0.0670676 0.93143 0.0273629 +7 1 0.463192 0.559381 0.472513 +72 1 0.320488 0.693458 0.00314802 +20 1 0.988495 0.999765 0.0379375 +71 1 0.296236 0.65252 0.0554148 +91 3 0.11219 0.706549 0.0440088 +77 1 0.233765 0.582563 0.0354768 +35 2 0.122206 0.535298 0.82263 +36 1 0.120605 0.557281 0.860759 +9 1 0.562465 0.551955 0.510256 +38 1 0.164855 0.529008 0.810838 +101 3 0.0950047 0.756943 0.679357 +100 3 0.0755312 0.724177 0.645988 +2 1 0.49616 0.63043 0.571079 +1 2 0.48791 0.624726 0.527985 +4 1 0.454299 0.650772 0.517018 +5 2 0.47488 0.564525 0.514196 +6 1 0.437806 0.551094 0.532982 +10 1 0.533806 0.543678 0.576508 +8 2 0.527388 0.536842 0.53294 +103 3 0.481813 0.753961 0.538526 +102 3 0.490962 0.803433 0.544283 +39 2 0.0920276 0.564703 0.776519 +41 1 0.107338 0.556051 0.735274 +40 1 0.0969868 0.608611 0.781288 +42 2 0.0352003 0.539717 0.790542 +43 1 0.00290578 0.549542 0.7627 +33 1 0.201019 0.97449 0.893691 +81 1 0.233787 0.552613 0.911207 +73 2 0.288327 0.615381 0.975333 +74 1 0.293413 0.625635 0.933435 +75 1 0.322846 0.589253 0.979172 +80 1 0.260512 0.508478 0.954693 +46 1 0.0371353 0.58915 0.864549 +82 2 0.17199 0.516621 0.961837 +31 2 0.163248 0.993189 0.906447 +25 2 0.0858536 0.99314 0.972792 +45 2 0.0206012 0.55189 0.849953 +48 2 0.958514 0.544055 0.862723 +79 2 0.230191 0.539354 0.953425 +47 1 0.0413449 0.522758 0.876101 +85 1 0.143956 0.550044 0.963195 +34 1 0.136564 0.986955 0.871135 +30 1 0.168524 0.961513 0.991631 +76 2 0.233972 0.588565 0.991159 +51 1 0.93576 0.577393 0.845822 +50 1 0.949853 0.541396 0.904993 +29 1 0.132825 0.922829 0.945398 +28 2 0.140923 0.964185 0.957793 +26 1 0.0521312 0.976612 0.950496 +78 1 0.200026 0.614825 0.980652 +49 1 0.94228 0.507101 0.843066 +3 1 0.524178 0.639248 0.507073 +ITEM: TIMESTEP +3000 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +18 2 0.0264154 0.00547536 0.0588956 +19 1 0.0343961 0.0480093 0.0568907 +20 1 0.989047 0.000454696 0.0355724 +89 3 0.733753 0.189111 0.314529 +88 3 0.705118 0.208073 0.351422 +12 1 0.515383 0.468567 0.477936 +104 3 0.0219499 0.355414 0.608732 +105 3 0.00674738 0.336128 0.564711 +13 1 0.484723 0.459936 0.544771 +17 1 0.573734 0.454057 0.584702 +11 2 0.517763 0.474293 0.521004 +15 1 0.574194 0.403611 0.533075 +14 2 0.570973 0.447283 0.541182 +99 3 0.602383 0.465021 0.708681 +98 3 0.589079 0.422937 0.734138 +16 1 0.604685 0.468063 0.521807 +97 3 0.249948 0.109137 0.871974 +32 1 0.181185 0.0326172 0.916216 +27 1 0.0876796 0.0347384 0.968968 +34 1 0.130601 0.00356754 0.876611 +96 3 0.288432 0.10886 0.839147 +83 1 0.161711 0.481893 0.929153 +37 1 0.108887 0.495741 0.839288 +44 1 0.0353841 0.494242 0.788502 +84 1 0.170439 0.493352 0.999416 +53 1 0.385902 0.396449 0.916328 +57 1 0.493783 0.370755 0.94413 +52 2 0.424678 0.416201 0.91196 +54 1 0.429308 0.445686 0.945752 +56 2 0.467013 0.368996 0.909801 +58 1 0.445128 0.331695 0.909483 +59 2 0.497129 0.376933 0.856103 +61 1 0.47402 0.401462 0.829145 +55 1 0.42443 0.438862 0.875719 +66 1 0.635955 0.381623 0.860721 +60 1 0.50511 0.339211 0.834851 +62 2 0.551873 0.408135 0.865876 +63 1 0.551364 0.428147 0.904 +64 1 0.557349 0.44037 0.836499 +65 2 0.594695 0.36428 0.859343 +67 1 0.590837 0.333387 0.888817 +68 1 0.595953 0.343565 0.819619 +92 3 0.834725 0.484022 0.752479 +86 3 0.929145 0.32792 0.955512 +93 3 0.877382 0.497028 0.776369 +87 3 0.975626 0.309936 0.964414 +94 3 0.212566 0.525249 0.122672 +90 3 0.144098 0.730198 0.0147625 +95 3 0.176605 0.546477 0.0941241 +77 1 0.232081 0.577639 0.0324452 +91 3 0.111133 0.704535 0.0428872 +69 2 0.291747 0.667973 0.0152501 +70 1 0.252095 0.686964 0.0160459 +72 1 0.321744 0.699796 0.00753098 +71 1 0.300144 0.653146 0.0557279 +21 1 0.0189145 0.994092 0.100593 +22 2 0.0731487 0.973469 0.0324809 +23 1 0.10794 0.979752 0.0573955 +24 1 0.0650735 0.930316 0.0340481 +7 1 0.470226 0.563919 0.471576 +100 3 0.0757659 0.726941 0.644352 +41 1 0.108135 0.545249 0.742992 +2 1 0.495881 0.631615 0.571337 +1 2 0.487564 0.628209 0.528192 +4 1 0.456582 0.659031 0.518067 +5 2 0.474163 0.568825 0.514411 +6 1 0.440972 0.554694 0.537963 +9 1 0.562766 0.5524 0.513872 +10 1 0.534072 0.543081 0.575547 +8 2 0.526201 0.536705 0.532792 +3 1 0.524707 0.639613 0.507381 +101 3 0.0946882 0.756665 0.680486 +103 3 0.481911 0.752155 0.537957 +102 3 0.49045 0.801431 0.544218 +35 2 0.121998 0.535307 0.826846 +36 1 0.120006 0.562403 0.861143 +38 1 0.164613 0.532753 0.819755 +39 2 0.0907763 0.562247 0.777928 +40 1 0.0919969 0.605147 0.776546 +42 2 0.0350699 0.537588 0.789747 +43 1 0.00477948 0.548618 0.761042 +81 1 0.230192 0.548838 0.909627 +46 1 0.0331954 0.59091 0.862035 +82 2 0.172648 0.513294 0.959969 +45 2 0.0210181 0.551113 0.851147 +79 2 0.229282 0.537933 0.952026 +47 1 0.0376608 0.52262 0.878893 +85 1 0.141469 0.544507 0.959622 +76 2 0.236264 0.589607 0.990282 +78 1 0.19993 0.616056 0.983465 +73 2 0.291334 0.617688 0.978089 +74 1 0.292576 0.629255 0.936322 +75 1 0.32408 0.592758 0.989224 +80 1 0.259169 0.508712 0.961744 +48 2 0.959833 0.545818 0.859475 +51 1 0.937399 0.578029 0.839123 +50 1 0.949082 0.549475 0.902339 +49 1 0.944729 0.506622 0.845565 +33 1 0.196462 0.973326 0.882978 +31 2 0.164335 0.994403 0.904316 +25 2 0.0878704 0.991498 0.972405 +30 1 0.171247 0.963737 0.98573 +29 1 0.138907 0.922846 0.94514 +28 2 0.142243 0.964439 0.95457 +26 1 0.057267 0.983305 0.942056 diff --git a/examples/reax/CHO/ffield.reax.cho b/examples/reax/CHO/ffield.reax.cho new file mode 100755 index 000000000..948773c92 --- /dev/null +++ b/examples/reax/CHO/ffield.reax.cho @@ -0,0 +1,123 @@ +Reactive MD-force field c/h/o combustion force field: Chenoweth, K.; van Duin, A.C.T.; Goddard, W.A. J. Phys. Chem. A 2008, 112, 1040-1053. + 39 ! Number of general parameters + 50.0000 !p(boc1) + 9.5469 !p(boc2) + 26.5405 !p(coa2) + 1.5105 !p(trip4) + 6.6630 !p(trip3) + 70.0000 !kc2 + 1.0588 !p(ovun6) + 4.6000 !p(trip2) + 12.1176 !p(ovun7) + 13.3056 !p(ovun8) + -70.1292 !p(trip1) + 0.0000 !Lower Taper-radius (swa) + 10.0000 !Upper Taper-radius (swb) + 0.0000 !not used + 33.8667 !p(val7) + 6.0891 !p(lp1) + 1.0563 !p(val9) + 2.0384 !p(val10) + 6.1431 !not used + 6.9290 !p(pen2) + 0.3989 !p(pen3) + 3.9954 !p(pen4) + 0.0000 !not used + 5.7796 !p(tor2) + 10.0000 !p(tor3) + 1.9487 !p(tor4) + 0.0000 !not used + 2.1645 !p(cot2) + 1.5591 !p(vdW1) + 0.1000 !Cutoff for bond order*100 (cutoff) + 2.1365 !p(coa4) + 0.6991 !p(ovun4) + 50.0000 !p(ovun3) + 1.8512 !p(val8) + 0.0000 !not used + 0.0000 !not used + 0.0000 !not used + 0.0000 !not used + 2.6962 !p(coa3) + 3 ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma;ro(pi);Val(e) + alfa;gamma(w);Val(angle);p(ovun5);n.u.;chiEEM;etaEEM;n.u. + ro(pipi);p(lp2);Heat increment;p(boc4);p(boc3);p(boc5),n.u.;n.u. + p(ovun2);p(val3);n.u.;Val(boc);p(val5);n.u.;n.u.;n.u. + C 1.3825 4.0000 12.0000 1.9133 0.1853 0.9000 1.1359 4.0000 + 9.7602 2.1346 4.0000 33.2433 79.5548 5.8678 7.0000 0.0000 + 1.2104 0.0000 199.0303 8.6991 34.7289 13.3894 0.8563 0.0000 + -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 + H 0.7853 1.0000 1.0080 1.5904 0.0419 1.0206 -0.1000 1.0000 + 9.3557 5.0518 1.0000 0.0000 121.1250 5.3200 7.4366 1.0000 + -0.1000 0.0000 62.4879 1.9771 3.3517 0.7571 1.0698 0.0000 + -15.7683 2.1488 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 + O 1.2477 2.0000 15.9990 1.9236 0.0904 1.0503 1.0863 6.0000 + 10.2127 7.7719 4.0000 36.9573 116.0768 8.5000 8.9989 2.0000 + 0.9088 1.0003 60.8726 20.4140 3.3754 0.2702 0.9745 0.0000 + -3.6141 2.7025 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 + 6 ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(bo5);13corr;n.u.;p(bo6),p(ovun1) + p(be2);p(bo3);p(bo4);n.u.;p(bo1);p(bo2) + 1 1 156.5953 100.0397 80.0000 -0.8157 -0.4591 1.0000 37.7369 0.4235 + 0.4527 -0.1000 9.2605 1.0000 -0.0750 6.8316 1.0000 0.0000 + 1 2 170.2316 0.0000 0.0000 -0.5931 0.0000 1.0000 6.0000 0.7140 + 5.2267 1.0000 0.0000 1.0000 -0.0500 6.8315 0.0000 0.0000 + 2 2 156.0973 0.0000 0.0000 -0.1377 0.0000 1.0000 6.0000 0.8240 + 2.9907 1.0000 0.0000 1.0000 -0.0593 4.8358 0.0000 0.0000 + 1 3 160.4802 105.1693 23.3059 -0.3873 -0.1613 1.0000 10.8851 1.0000 + 0.5341 -0.3174 7.0303 1.0000 -0.1463 5.2913 0.0000 0.0000 + 3 3 60.1463 176.6202 51.1430 -0.2802 -0.1244 1.0000 29.6439 0.9114 + 0.2441 -0.1239 7.6487 1.0000 -0.1302 6.2919 1.0000 0.0000 + 2 3 180.4373 0.0000 0.0000 -0.8074 0.0000 1.0000 6.0000 0.5514 + 1.2490 1.0000 0.0000 1.0000 -0.0657 5.0451 0.0000 0.0000 + 3 ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);ro(pi);ro(pipi) + 1 2 0.1219 1.4000 9.8442 1.1203 -1.0000 -1.0000 + 2 3 0.0344 1.6800 10.3247 0.9013 -1.0000 -1.0000 + 1 3 0.1131 1.8523 9.8442 1.2775 1.1342 1.0621 + 18 ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);p(val7);p(pen1);p(val4) + 1 1 1 67.2326 22.0695 1.6286 0.0000 1.7959 15.4141 1.8089 + 1 1 2 65.2527 14.3185 6.2977 0.0000 0.5645 0.0000 1.1530 + 2 1 2 70.0840 25.3540 3.4508 0.0000 0.0050 0.0000 3.0000 + 1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400 + 2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 1 1 3 49.5561 7.3771 4.9568 0.0000 0.7533 15.9906 1.0010 + 3 1 3 77.1171 39.8746 2.5403 -24.3902 1.7740 -42.9758 2.1240 + 2 1 3 65.0000 14.2057 4.8649 0.0000 0.3504 0.0000 1.7185 + 1 3 1 74.3994 44.7500 0.7982 0.0000 3.0000 0.0000 1.0528 + 1 3 3 77.9854 36.6201 2.0201 0.0000 0.7434 67.0264 3.0000 + 3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783 + 1 3 2 71.5018 21.7062 0.4735 0.0000 0.5186 0.0000 1.1793 + 2 3 3 84.9468 23.3540 1.5057 0.0000 2.6374 0.0000 1.3023 + 2 3 2 77.0645 10.4737 1.2895 0.0000 0.9924 0.0000 1.1043 + 1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400 + 3 2 3 0.0000 0.0148 6.0000 0.0000 0.0000 0.0000 1.0400 + 2 2 3 0.0000 9.7025 6.0000 0.0000 0.0000 0.0000 1.0400 + 26 ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);n.u;n.u. + 1 1 1 1 -0.2500 11.5822 0.1879 -4.7057 -2.2047 0.0000 0.0000 + 1 1 1 2 -0.2500 31.2596 0.1709 -4.6391 -1.9002 0.0000 0.0000 + 2 1 1 2 -0.1770 30.0252 0.4340 -5.0019 -2.0697 0.0000 0.0000 + 1 1 1 3 -0.7098 22.2951 0.0060 -2.5000 -2.1688 0.0000 0.0000 + 2 1 1 3 -0.3568 22.6472 0.6045 -4.0088 -1.0000 0.0000 0.0000 + 3 1 1 3 -0.0528 6.8150 0.7498 -5.0913 -1.0000 0.0000 0.0000 + 1 1 3 1 2.0007 25.5641 -0.0608 -2.6456 -1.1766 0.0000 0.0000 + 1 1 3 2 -1.1953 42.1545 -1.0000 -8.0821 -1.0000 0.0000 0.0000 + 2 1 3 1 -0.9284 34.3952 0.7285 -2.5440 -2.4641 0.0000 0.0000 + 2 1 3 2 -2.5000 79.6980 1.0000 -3.5697 -2.7501 0.0000 0.0000 + 1 1 3 3 -0.0179 5.0603 -0.1894 -2.5000 -2.0399 0.0000 0.0000 + 2 1 3 3 -0.5583 80.0000 1.0000 -4.4000 -3.0000 0.0000 0.0000 + 3 1 3 1 -2.5000 76.0427 -0.0141 -3.7586 -2.9000 0.0000 0.0000 + 3 1 3 2 0.0345 78.9586 -0.6810 -4.1777 -3.0000 0.0000 0.0000 + 3 1 3 3 -2.5000 66.3525 0.3986 -3.0293 -3.0000 0.0000 0.0000 + 1 3 3 1 2.5000 -0.5332 1.0000 -3.5096 -2.9000 0.0000 0.0000 + 1 3 3 2 -2.5000 3.3219 0.7180 -5.2021 -2.9330 0.0000 0.0000 + 2 3 3 2 2.2500 -6.2288 1.0000 -2.6189 -1.0000 0.0000 0.0000 + 1 3 3 3 0.0531 -17.3983 1.0000 -2.5000 -2.1584 0.0000 0.0000 + 2 3 3 3 0.4723 -12.4144 -1.0000 -2.5000 -1.0000 0.0000 0.0000 + 3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 + 0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000 + 0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 + 1 ! Nr of hydrogen bonds. at1;at2;at3;r(hb);p(hb1);p(hb2);p(hb3) + 3 2 3 1.9682 -4.4628 1.7976 3.0000 diff --git a/examples/reax/CHO/in.CHO b/examples/reax/CHO/in.CHO new file mode 100644 index 000000000..17c71843a --- /dev/null +++ b/examples/reax/CHO/in.CHO @@ -0,0 +1,23 @@ +# REAX potential for CHO system +# ..... + +units real + +atom_style charge +read_data data.CHO + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.cho 2 1 3 + +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.cho + +run 3000 diff --git a/examples/reax/CHO/lmp_control b/examples/reax/CHO/lmp_control new file mode 100644 index 000000000..6db169bf7 --- /dev/null +++ b/examples/reax/CHO/lmp_control @@ -0,0 +1,17 @@ +simulation_name CHO_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title CHO ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/CHO/log.reaxc.cho.18Feb11.linux.1 b/examples/reax/CHO/log.reaxc.cho.18Feb11.linux.1 new file mode 100644 index 000000000..b4b88bad9 --- /dev/null +++ b/examples/reax/CHO/log.reaxc.cho.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for CHO system +# ..... + +units real + +atom_style charge +read_data data.CHO + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.CHO 2 1 3 + +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.cho + +run 3000 +Memory usage per processor = 3.1747 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10226.557 0 -10226.557 -106.0975 + 3000 547.35519 -10170.009 0 -10000.327 72.598622 +Loop time of 33.0127 on 1 procs for 3000 steps with 105 atoms + +Pair time (%) = 29.6315 (89.7579) +Neigh time (%) = 0.106584 (0.322859) +Comm time (%) = 0.0486262 (0.147295) +Outpt time (%) = 0.0179088 (0.0542483) +Other time (%) = 3.20809 (9.71774) + +Nlocal: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 643 ave 643 max 643 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4237 ave 4237 max 4237 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4237 +Ave neighs/atom = 40.3524 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/CHO/log.reaxc.cho.18Feb11.linux.4 b/examples/reax/CHO/log.reaxc.cho.18Feb11.linux.4 new file mode 100644 index 000000000..4e7a3d3a6 --- /dev/null +++ b/examples/reax/CHO/log.reaxc.cho.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for CHO system +# ..... + +units real + +atom_style charge +read_data data.CHO + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.cho 2 1 3 + +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.cho + +run 3000 +Memory usage per processor = 3.12825 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10226.557 0 -10226.557 -106.09743 + 3000 547.67802 -10170.116 0 -10000.334 62.805642 +Loop time of 38.7423 on 4 procs for 3000 steps with 105 atoms + +Pair time (%) = 22.397 (57.8101) +Neigh time (%) = 0.0308624 (0.0796607) +Comm time (%) = 1.92916 (4.97947) +Outpt time (%) = 0.0171081 (0.0441586) +Other time (%) = 14.3682 (37.0867) + +Nlocal: 26.25 ave 45 max 6 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 380.75 ave 495 max 261 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 1269.5 ave 2197 max 179 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 5078 +Ave neighs/atom = 48.3619 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/CHO/param.qeq b/examples/reax/CHO/param.qeq new file mode 100644 index 000000000..c863880d0 --- /dev/null +++ b/examples/reax/CHO/param.qeq @@ -0,0 +1,3 @@ +1 5.3200 14.8732 1.0206 +2 5.8678 14.0000 0.9000 +3 8.5000 17.9978 1.0503 diff --git a/examples/reax/Fe_O_H/data.FeOH3 b/examples/reax/Fe_O_H/data.FeOH3 new file mode 100644 index 000000000..aa2138e86 --- /dev/null +++ b/examples/reax/Fe_O_H/data.FeOH3 @@ -0,0 +1,122 @@ +# FeOH3 example + +105 atoms +3 atom types + +0 25.000 xlo xhi +0 25.000 ylo yhi +0 25.000 zlo zhi + +Masses + +1 1.0080 +2 15.9994 +3 55.8450 + +Atoms + + 1 3 0.0 14.63130 11.53919 10.02566 + 2 2 0.0 14.66818 11.64433 8.31385 + 3 2 0.0 13.19732 11.59171 10.97982 + 4 2 0.0 16.09606 11.79339 10.90520 + 5 1 0.0 15.37579 11.57108 7.64798 + 6 1 0.0 13.03522 11.61430 11.93898 + 7 1 0.0 16.34568 11.57890 11.82994 + 8 3 0.0 4.23334 23.22931 22.91765 + 9 2 0.0 3.17949 22.76642 21.63236 + 10 2 0.0 3.72561 23.54563 24.52094 + 11 2 0.0 5.92362 23.49124 22.55535 + 12 1 0.0 3.33529 22.57874 20.68991 + 13 1 0.0 4.19726 23.80080 0.33508 + 14 1 0.0 6.68129 23.69266 23.13075 + 15 3 0.0 3.09410 12.02471 16.65602 + 16 2 0.0 4.53790 11.22867 16.12595 + 17 2 0.0 1.98216 12.79921 15.59862 + 18 2 0.0 2.94350 12.44420 18.32254 + 19 1 0.0 5.24401 10.77330 16.61803 + 20 1 0.0 1.10176 13.19382 15.77157 + 21 1 0.0 2.24435 12.85961 18.85529 + 22 3 0.0 11.46014 6.57998 19.54155 + 23 2 0.0 11.41247 7.36935 21.07367 + 24 2 0.0 12.10967 5.02110 19.27082 + 25 2 0.0 10.74290 7.40346 18.15014 + 26 1 0.0 11.04310 8.22526 21.35875 + 27 1 0.0 12.23932 4.47293 18.47557 + 28 1 0.0 10.67373 7.10685 17.22712 + 29 3 0.0 11.08460 12.33864 19.28104 + 30 2 0.0 11.34836 13.23119 20.73896 + 31 2 0.0 9.92831 11.10473 19.09894 + 32 2 0.0 12.09164 12.69825 17.89278 + 33 1 0.0 11.96775 13.94859 20.96031 + 34 1 0.0 9.68067 10.50031 18.37427 + 35 1 0.0 12.10206 12.31962 16.99755 + 36 3 0.0 16.30156 8.77946 9.35117 + 37 2 0.0 14.89172 7.88636 9.75359 + 38 2 0.0 16.88966 9.02164 7.73765 + 39 2 0.0 17.49737 9.08373 10.64053 + 40 1 0.0 14.48147 7.61584 10.59321 + 41 1 0.0 17.67137 9.46163 7.36999 + 42 1 0.0 18.17147 9.79838 10.64156 + 43 3 0.0 5.13212 13.69884 22.13154 + 44 2 0.0 5.48279 12.35370 23.11195 + 45 2 0.0 5.09394 13.69454 20.44390 + 46 2 0.0 4.66841 15.19478 22.89478 + 47 1 0.0 5.62303 12.19015 24.06195 + 48 1 0.0 4.81388 14.30156 19.73513 + 49 1 0.0 4.45081 16.06980 22.52921 + 50 3 0.0 20.66764 3.98511 5.60363 + 51 2 0.0 19.99184 2.40263 5.50286 + 52 2 0.0 20.51708 5.02486 6.95773 + 53 2 0.0 21.60880 4.57878 4.24996 + 54 1 0.0 20.00878 1.72191 4.80697 + 55 1 0.0 20.82035 5.93286 7.13931 + 56 1 0.0 22.07480 5.42038 4.11310 + 57 3 0.0 8.85743 19.34284 21.52754 + 58 2 0.0 7.27070 20.01992 21.47027 + 59 2 0.0 9.69182 18.97544 22.97169 + 60 2 0.0 9.65070 18.93927 20.02944 + 61 1 0.0 6.71593 20.32474 20.72955 + 62 1 0.0 10.56063 18.57499 23.16295 + 63 1 0.0 10.51934 18.54777 19.83721 + 64 3 0.0 23.51972 10.47305 17.25322 + 65 2 0.0 23.97098 11.96260 18.04948 + 66 2 0.0 24.54307 9.59907 16.22117 + 67 2 0.0 21.90294 9.84477 17.50180 + 68 1 0.0 23.46396 12.52267 18.66351 + 69 1 0.0 24.45997 8.77863 15.69939 + 70 1 0.0 21.46999 9.04903 17.14619 + 71 3 0.0 5.60291 10.17273 2.44803 + 72 2 0.0 7.16694 9.77649 3.07411 + 73 2 0.0 4.24384 10.54236 3.41008 + 74 2 0.0 5.39786 10.28750 0.72616 + 75 1 0.0 8.00942 9.55137 2.64434 + 76 1 0.0 3.31957 10.78047 3.20702 + 77 1 0.0 4.62129 10.42132 0.15716 + 78 3 0.0 16.37311 9.22286 18.09708 + 79 2 0.0 15.78190 8.64503 16.57376 + 80 2 0.0 16.64835 8.23357 19.45928 + 81 2 0.0 16.63400 10.94106 18.29447 + 82 1 0.0 15.62322 9.10143 15.72854 + 83 1 0.0 16.95513 8.40601 20.36893 + 84 1 0.0 16.95257 11.45993 19.05240 + 85 3 0.0 5.28764 18.69912 13.31319 + 86 2 0.0 5.98620 20.03778 12.47788 + 87 2 0.0 5.53460 18.35154 14.97223 + 88 2 0.0 4.20516 17.64051 12.43642 + 89 1 0.0 5.91944 20.34771 11.55794 + 90 1 0.0 5.23156 17.63037 15.55409 + 91 1 0.0 3.72069 16.84340 12.70885 + 92 3 0.0 14.77099 20.78362 11.41422 + 93 2 0.0 14.16229 20.18810 9.91169 + 94 2 0.0 15.97692 21.98487 11.56211 + 95 2 0.0 14.12859 20.12000 12.89882 + 96 1 0.0 13.48968 19.51852 9.69561 + 97 1 0.0 16.41268 22.41296 12.32187 + 98 1 0.0 14.32168 20.31720 13.83061 + 99 3 0.0 1.41350 6.47339 10.98887 + 100 2 0.0 3.11373 6.73061 10.88875 + 101 2 0.0 0.51986 6.36995 12.45155 + 102 2 0.0 0.51098 6.26826 9.49521 + 103 1 0.0 3.72376 6.83273 10.13691 + 104 1 0.0 24.57790 6.21134 12.64347 + 105 1 0.0 24.56896 6.08899 9.34052 diff --git a/examples/reax/Fe_O_H/dump.reax.feoh b/examples/reax/Fe_O_H/dump.reax.feoh new file mode 100644 index 000000000..f4d912d96 --- /dev/null +++ b/examples/reax/Fe_O_H/dump.reax.feoh @@ -0,0 +1,11514 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +50 3 0.826706 0.159404 0.224145 +51 2 0.799674 0.0961052 0.220114 +53 2 0.864352 0.183151 0.169998 +54 1 0.800351 0.0688764 0.192279 +56 1 0.882992 0.216815 0.164524 +71 3 0.224116 0.406909 0.0979212 +73 2 0.169754 0.421694 0.136403 +74 2 0.215914 0.4115 0.0290464 +76 1 0.132783 0.431219 0.128281 +77 1 0.184852 0.416853 0.0062864 +72 2 0.286678 0.39106 0.122964 +75 1 0.320377 0.382055 0.105774 +52 2 0.820683 0.200994 0.278309 +55 1 0.832814 0.237314 0.285572 +105 1 0.982758 0.24356 0.373621 +99 3 0.05654 0.258936 0.439555 +100 2 0.124549 0.269224 0.43555 +101 2 0.0207944 0.254798 0.498062 +102 2 0.0204392 0.25073 0.379808 +103 1 0.14895 0.273309 0.405476 +1 3 0.585252 0.461568 0.401026 +2 2 0.586727 0.465773 0.332554 +3 2 0.527893 0.463668 0.439193 +4 2 0.643842 0.471736 0.436208 +5 1 0.615032 0.462843 0.305919 +6 1 0.521409 0.464572 0.477559 +7 1 0.653827 0.463156 0.473198 +36 3 0.652062 0.351178 0.374047 +37 2 0.595669 0.315454 0.390144 +38 2 0.675586 0.360866 0.309506 +39 2 0.699895 0.363349 0.425621 +40 1 0.579259 0.304634 0.423728 +41 1 0.706855 0.378465 0.2948 +42 1 0.726859 0.391935 0.425662 +27 1 0.489573 0.178917 0.739023 +104 1 0.983116 0.248454 0.505739 +15 3 0.123764 0.480988 0.666241 +16 2 0.181516 0.449147 0.645038 +18 2 0.11774 0.497768 0.732902 +19 1 0.20976 0.430932 0.664721 +25 2 0.429716 0.296138 0.726006 +28 1 0.426949 0.284274 0.689085 +34 1 0.387227 0.420012 0.734971 +35 1 0.484082 0.492785 0.679902 +78 3 0.654924 0.368914 0.723883 +79 2 0.631276 0.345801 0.66295 +81 2 0.66536 0.437642 0.731779 +82 1 0.624929 0.364057 0.629142 +64 3 0.940789 0.418922 0.690129 +65 2 0.958839 0.478504 0.721979 +66 2 0.981723 0.383963 0.648847 +67 2 0.876118 0.393791 0.700072 +69 1 0.978399 0.351145 0.627976 +70 1 0.8588 0.361961 0.685848 +24 2 0.484387 0.200844 0.770833 +44 2 0.219312 0.494148 0.924478 +47 1 0.224921 0.487606 0.962478 +22 3 0.458406 0.263199 0.781662 +23 2 0.456499 0.294774 0.842947 +26 1 0.441724 0.32901 0.85435 +29 3 0.443384 0.493546 0.771242 +31 2 0.397132 0.444189 0.763958 +80 2 0.665934 0.329343 0.778371 +83 1 0.678205 0.33624 0.814757 +84 1 0.678103 0.458397 0.762096 +13 1 0.16789 0.952032 0.0134032 +88 2 0.168206 0.70562 0.497457 +86 2 0.239448 0.801511 0.499115 +89 1 0.236778 0.813908 0.462318 +92 3 0.59084 0.831345 0.456569 +93 2 0.566492 0.807524 0.396468 +94 2 0.639077 0.879395 0.462484 +96 1 0.539587 0.780741 0.387824 +97 1 0.656507 0.896518 0.492875 +17 2 0.0792864 0.511968 0.623945 +20 1 0.0440704 0.527753 0.630863 +85 3 0.211506 0.747965 0.532528 +87 2 0.221384 0.734062 0.598889 +90 1 0.209262 0.705215 0.622164 +91 1 0.148828 0.673736 0.508354 +32 2 0.483666 0.50793 0.715711 +68 1 0.938558 0.500907 0.74654 +95 2 0.565144 0.8048 0.515953 +98 1 0.572867 0.812688 0.553224 +21 1 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0.742241 +23 2 0.424344 0.241466 0.780504 +80 2 0.597133 0.320082 0.72283 +28 1 0.491786 0.27458 0.881019 +48 1 0.277907 0.464204 0.861067 +22 3 0.493119 0.245623 0.782152 +26 1 0.398636 0.244498 0.81002 +34 1 0.536851 0.469609 0.805561 +45 2 0.250067 0.472623 0.884593 +4 2 0.576796 0.540185 0.433845 +13 1 0.188023 0.934765 0.0176754 +2 2 0.565886 0.513139 0.340988 +93 2 0.579001 0.797441 0.400691 +7 1 0.5674 0.57607 0.4297 +94 2 0.61915 0.882256 0.457706 +96 1 0.586576 0.812072 0.365896 +97 1 0.634475 0.899499 0.425773 +92 3 0.591037 0.821631 0.466881 +89 1 0.202144 0.808226 0.46829 +5 1 0.59905 0.536654 0.332729 +91 1 0.230105 0.643432 0.499417 +88 2 0.235866 0.675434 0.520386 +85 3 0.193796 0.734138 0.536871 +87 2 0.170504 0.735535 0.602056 +16 2 0.153524 0.575001 0.650879 +15 3 0.112467 0.514906 0.650493 +19 1 0.15533 0.604953 0.675109 +20 1 0.139076 0.517641 0.556928 +57 3 0.338548 0.774213 0.842688 +32 2 0.4708 0.513307 0.689428 +90 1 0.169605 0.711277 0.631755 +29 3 0.461586 0.517578 0.758166 +95 2 0.56721 0.789482 0.526046 +98 1 0.533558 0.778761 0.539178 +47 1 0.302617 0.579465 0.971732 +43 3 0.229475 0.51517 0.93373 +46 2 0.157005 0.533747 0.933317 +44 2 0.266509 0.572125 0.958539 +30 2 0.397504 0.512498 0.791915 +17 2 0.108791 0.51444 0.584649 +63 1 0.39607 0.725587 0.777397 +60 2 0.368268 0.721439 0.805058 +62 1 0.317262 0.790946 0.936671 +8 3 0.183515 0.912813 0.920938 +9 2 0.146487 0.944422 0.871652 +10 2 0.169892 0.939582 0.983021 +11 2 0.21924 0.861653 0.894724 +12 1 0.150997 0.938653 0.832164 +58 2 0.319059 0.826202 0.803196 +59 2 0.337545 0.774314 0.906872 +61 1 0.282792 0.83943 0.792169 +14 1 0.215897 0.825372 0.881801 +49 1 0.141311 0.570281 0.935756 +86 2 0.209238 0.793021 0.503521 +35 1 0.458348 0.534072 0.659531 +31 2 0.520185 0.502935 0.793964 +21 1 0.0804591 0.51093 0.742423 +ITEM: TIMESTEP +3000 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +50 3 0.837135 0.170603 0.228523 +53 2 0.834986 0.187196 0.159099 +56 1 0.830163 0.220935 0.142754 +71 3 0.235249 0.442015 0.100875 +73 2 0.216709 0.419402 0.036978 +76 1 0.185631 0.432622 0.015883 +75 1 0.170037 0.432983 0.172847 +72 2 0.207996 0.433435 0.159633 +74 2 0.290216 0.489797 0.0867333 +77 1 0.321601 0.480261 0.0669815 +102 2 0.00873168 0.237727 0.387044 +51 2 0.793563 0.123621 0.258601 +54 1 0.793727 0.098728 0.288038 +105 1 0.977054 0.225059 0.370596 +52 2 0.889435 0.184378 0.269345 +55 1 0.901424 0.169365 0.30379 +99 3 0.0270464 0.259069 0.451654 +100 2 0.0812176 0.306629 0.446271 +103 1 0.0796431 0.33654 0.420171 +38 2 0.64873 0.360058 0.352708 +6 1 0.586101 0.386099 0.424675 +37 2 0.690352 0.355453 0.45982 +40 1 0.705656 0.386917 0.477146 +41 1 0.624182 0.35137 0.322218 +1 3 0.562001 0.482163 0.404527 +36 3 0.674304 0.319685 0.40309 +3 2 0.575044 0.419752 0.427007 +39 2 0.71476 0.276521 0.362326 +42 1 0.739835 0.276202 0.33626 +101 2 0.0079016 0.244244 0.516812 +27 1 0.525785 0.1781 0.718441 +24 2 0.526756 0.209087 0.743356 +104 1 0.991394 0.211751 0.531503 +18 2 0.0921014 0.482886 0.708051 +68 1 0.0118359 0.436672 0.68158 +20 1 0.13107 0.498765 0.555187 +21 1 0.0724545 0.499202 0.735872 +84 1 0.712333 0.383879 0.735144 +78 3 0.621327 0.376011 0.692982 +79 2 0.604868 0.389231 0.627602 +81 2 0.678817 0.399319 0.728201 +82 1 0.600877 0.364963 0.596738 +80 2 0.594984 0.321606 0.721729 +64 3 0.915846 0.396779 0.662702 +65 2 0.975597 0.433763 0.689087 +66 2 0.925097 0.363926 0.603981 +67 2 0.862338 0.409643 0.704203 +69 1 0.945804 0.334213 0.590707 +70 1 0.84388 0.443036 0.715096 +23 2 0.425466 0.240581 0.779742 +22 3 0.493848 0.245851 0.782395 +26 1 0.39745 0.244324 0.807125 +45 2 0.248993 0.475916 0.883722 +33 1 0.364126 0.499251 0.779261 +28 1 0.491727 0.270127 0.881994 +48 1 0.276683 0.462402 0.862344 +83 1 0.595899 0.301994 0.755848 +25 2 0.513223 0.272117 0.850991 +34 1 0.531633 0.472566 0.812577 +13 1 0.185602 0.93306 0.0182693 +91 1 0.227471 0.645139 0.499262 +4 2 0.576705 0.542455 0.432913 +2 2 0.56811 0.514012 0.339509 +7 1 0.575623 0.579435 0.438022 +5 1 0.585227 0.546856 0.328553 +89 1 0.196242 0.802741 0.467344 +93 2 0.578599 0.795518 0.40056 +94 2 0.619603 0.8836 0.458831 +96 1 0.582158 0.815344 0.366815 +97 1 0.633141 0.898086 0.424594 +92 3 0.59104 0.821379 0.46688 +88 2 0.237193 0.676977 0.519961 +85 3 0.193444 0.733151 0.537335 +87 2 0.169535 0.736431 0.602486 +16 2 0.151622 0.575082 0.650207 +15 3 0.113286 0.515276 0.6514 +19 1 0.149901 0.607215 0.67208 +90 1 0.165837 0.708724 0.629336 +17 2 0.10762 0.516036 0.583186 +32 2 0.471525 0.515662 0.689166 +35 1 0.451865 0.529409 0.659466 +86 2 0.209877 0.792726 0.503323 +95 2 0.567357 0.789961 0.52577 +98 1 0.532793 0.776829 0.536687 +43 3 0.229911 0.514524 0.934356 +46 2 0.157758 0.535857 0.929315 +49 1 0.138893 0.569073 0.933337 +29 3 0.461683 0.516986 0.757739 +47 1 0.304428 0.577963 0.969498 +44 2 0.267698 0.569452 0.961727 +30 2 0.398301 0.511999 0.791517 +63 1 0.400421 0.718369 0.785621 +60 2 0.367931 0.721655 0.806062 +31 2 0.520925 0.505636 0.79324 +8 3 0.184055 0.913087 0.921022 +9 2 0.147983 0.943285 0.872029 +10 2 0.169542 0.939905 0.983065 +11 2 0.218368 0.859778 0.894821 +12 1 0.145754 0.940359 0.832767 +14 1 0.207465 0.823052 0.884153 +57 3 0.337917 0.774092 0.84205 +62 1 0.316707 0.790286 0.935818 +58 2 0.32005 0.827377 0.802312 +59 2 0.3371 0.774147 0.905957 +61 1 0.285256 0.839046 0.787431 diff --git a/examples/reax/Fe_O_H/ffield.reax.Fe_O_C_H b/examples/reax/Fe_O_H/ffield.reax.Fe_O_C_H new file mode 100644 index 000000000..c3b46afec --- /dev/null +++ b/examples/reax/Fe_O_H/ffield.reax.Fe_O_C_H @@ -0,0 +1,160 @@ +Reactive MD-force field: Fe/O/water: Aryanpour, M.; van Duin, A. C. T.; Kubicki, J. D. J. Phys. Chem. A 2010, 114, 6298-6307 + 39 ! Number of general parameters + 50.0000 !Overcoordination parameter + 9.5469 !Overcoordination parameter + 1.6725 !Valency angle conjugation parameter + 1.7224 !Triple bond stabilisation parameter + 6.8702 !Triple bond stabilisation parameter + 60.4850 !C2-correction + 1.0588 !Undercoordination parameter + 4.6000 !Triple bond stabilisation parameter + 12.1176 !Undercoordination parameter + 13.3056 !Undercoordination parameter + -55.1978 !Triple bond stabilization energy + 0.0000 !Lower Taper-radius + 10.0000 !Upper Taper-radius + 2.8793 !Not used + 33.8667 !Valency undercoordination + 6.0891 !Valency angle/lone pair parameter + 1.0563 !Valency angle + 2.0384 !Valency angle parameter + 6.1431 !Not used + 6.9290 !Double bond/angle parameter + 0.3989 !Double bond/angle parameter: overcoord + 3.9954 !Double bond/angle parameter: overcoord + -2.4837 !Not used + 5.7796 !Torsion/BO parameter + 10.0000 !Torsion overcoordination + 1.9487 !Torsion overcoordination + -1.2327 !Conjugation 0 (not used) + 2.1645 !Conjugation + 1.5591 !vdWaals shielding + 0.1000 !Cutoff for bond order (*100) + 1.7602 !Valency angle conjugation parameter + 0.6991 !Overcoordination parameter + 50.0000 !Overcoordination parameter + 1.8512 !Valency/lone pair parameter + 0.5000 !Not used + 20.0000 !Not used + 5.0000 !Molecular energy (not used) + 0.0000 !Molecular energy (not used) + 0.7903 !Valency angle conjugation parameter + 4 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. + cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. + ov/un;val1;n.u.;val3,vval4 + C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000 + 9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000 + 1.2114 0.0000 202.6057 8.9539 34.9289 13.5366 0.8563 0.0000 + -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 + H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000 + 8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000 + -0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000 + -19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 + O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000 + 9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000 + 0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000 + -3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 + Fe 1.9506 3.0000 55.8450 2.0308 0.1274 0.7264 -1.0000 3.0000 + 11.0534 2.2637 3.0000 0.0000 18.3725 1.2457 7.3021 0.0000 + -1.2000 0.0000 66.4838 30.0000 1.0000 0.0000 0.8563 0.0000 + -16.2040 2.7917 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000 + 10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr + 1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147 + 0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000 + 1 2 169.4760 0.0000 0.0000 -0.6083 0.0000 1.0000 6.0000 0.7652 + 5.2290 1.0000 0.0000 1.0000 -0.0500 6.9136 0.0000 0.0000 + 2 2 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300 + 6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000 + 1 3 164.4303 82.6772 60.8077 -0.3739 -0.2351 1.0000 10.5036 1.0000 + 0.4475 -0.2288 7.0250 1.0000 -0.1363 4.8734 0.0000 0.0000 + 3 3 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 + 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 + 2 3 160.0000 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5626 + 1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000 + 1 4 133.0514 0.0000 0.0000 1.0000 -0.3000 1.0000 36.0000 0.0673 + 0.2350 -0.3500 15.0000 1.0000 -0.1143 4.5217 1.0000 0.0000 + 2 4 105.0054 0.0000 0.0000 -0.0717 0.0000 0.0000 6.0000 0.0505 + 0.1000 1.0000 0.0000 1.0000 -0.1216 4.5062 0.0000 0.0000 + 3 4 65.7713 0.0000 0.0000 0.1366 -0.3000 1.0000 36.0000 0.0494 + 0.9495 -0.3500 15.0000 1.0000 -0.0555 7.9897 1.0000 0.0000 + 4 4 38.7471 0.0000 0.0000 0.3595 -0.2000 0.0000 16.0000 0.2749 + 1.0000 -0.2000 15.0000 1.0000 -0.0771 6.4477 0.0000 0.0000 + 6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 1 2 0.1239 1.4004 9.8467 1.1210 -1.0000 -1.0000 + 2 3 0.0283 1.2885 10.9190 0.9215 -1.0000 -1.0000 + 1 3 0.1345 1.8422 9.7725 1.2835 1.1576 1.0637 + 1 4 0.1358 1.8293 10.0425 1.6096 -1.0000 -1.0000 + 2 4 0.0640 1.6974 11.5167 1.3517 -1.0000 -1.0000 + 3 4 0.0846 1.4284 10.0808 1.8339 -1.0000 -1.0000 + 37 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 + 1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244 + 1 1 2 65.7758 14.5234 6.2481 0.0000 0.5665 0.0000 1.6255 + 2 1 2 70.2607 25.2202 3.7312 0.0000 0.0050 0.0000 2.7500 + 1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400 + 2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 1 1 3 53.9517 7.8968 2.6122 0.0000 3.0000 58.6562 1.0338 + 3 1 3 76.9627 44.2852 2.4177 -25.3063 1.6334 -50.0000 2.7392 + 2 1 3 65.0000 16.3141 5.2730 0.0000 0.4448 0.0000 1.4077 + 1 3 1 72.6199 42.5510 0.7205 0.0000 2.9294 0.0000 1.3096 + 1 3 3 81.9029 32.2258 1.7397 0.0000 0.9888 68.1072 1.7777 + 3 3 3 80.7324 30.4554 0.9953 0.0000 3.0000 50.0000 1.0783 + 1 3 2 70.1101 13.1217 4.4734 0.0000 0.8433 0.0000 3.0000 + 2 3 3 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680 + 2 3 2 85.8000 9.8453 2.2720 0.0000 2.8635 0.0000 1.5800 + 1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400 + 3 2 3 0.0000 15.0000 2.8900 0.0000 0.0000 0.0000 2.8774 + 2 2 3 0.0000 8.5744 3.0000 0.0000 0.0000 0.0000 1.0421 + 1 4 1 29.1655 3.3035 0.2000 0.0000 1.1221 0.0000 1.0562 + 1 1 4 59.8697 2.8115 1.9262 0.0000 0.7602 0.0000 1.4056 + 1 4 4 25.4591 15.9430 0.9664 0.0000 2.2242 0.0000 1.1088 + 4 1 4 88.6279 26.0015 1.0328 0.0000 0.2361 0.0000 2.0576 + 2 1 4 47.3695 16.9204 4.1052 0.0000 0.1000 0.0000 1.0050 + 2 4 2 34.1965 6.6782 6.5943 0.0000 1.3895 0.0000 1.5365 + 2 2 4 0.1000 30.0000 3.4094 0.0000 2.4379 0.0000 1.5166 + 4 2 4 0.0000 8.2994 5.7832 0.0000 2.9873 0.0000 1.7716 + 2 4 4 21.2590 6.5954 0.9951 0.0000 2.8006 0.0000 1.0000 + 2 4 4 180.0000 -6.9970 24.3956 0.0000 0.7878 0.0000 1.3672 + 1 3 4 90.0000 12.8684 1.4601 0.0000 0.8757 0.0000 1.0000 + 3 1 4 18.8567 24.3753 3.9647 0.0000 0.1000 0.0000 1.5314 + 3 4 3 79.7335 0.0100 0.1392 0.0000 0.4968 0.0000 2.1948 + 4 3 4 57.6787 4.8566 2.5768 0.0000 0.7552 0.0000 1.0000 + 2 3 4 59.4556 10.2025 0.7481 0.0000 1.4521 0.0000 1.0000 + 3 3 4 73.6721 32.6330 1.7223 0.0000 1.0221 0.0000 1.4351 + 3 4 4 65.7545 5.6268 4.0645 0.0000 1.7794 0.0000 2.6730 + 3 2 4 0.0000 4.6026 2.5343 0.0000 0.7284 0.0000 1.1051 + 2 4 3 34.0653 20.1868 4.7461 0.0000 0.1000 0.0000 1.6752 + 29 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000 + 1 1 1 2 -0.2500 29.2131 0.2945 -4.9581 -2.1802 0.0000 0.0000 + 2 1 1 2 -0.2500 31.2081 0.4539 -4.8923 -2.2677 0.0000 0.0000 + 1 1 1 3 1.2799 20.7787 -0.5249 -2.5000 -1.0000 0.0000 0.0000 + 2 1 1 3 1.9159 19.8113 0.7914 -4.6995 -1.0000 0.0000 0.0000 + 3 1 1 3 -1.4477 16.6853 0.6461 -4.9622 -1.0000 0.0000 0.0000 + 1 1 3 1 0.4816 19.6316 -0.0057 -2.5000 -1.0000 0.0000 0.0000 + 1 1 3 2 1.2044 80.0000 -0.3139 -6.1481 -1.0000 0.0000 0.0000 + 2 1 3 1 -2.5000 31.0191 0.6165 -2.7733 -2.9807 0.0000 0.0000 + 2 1 3 2 -2.4875 70.8145 0.7582 -4.2274 -3.0000 0.0000 0.0000 + 1 1 3 3 -0.3566 10.0000 0.0816 -2.6110 -1.9631 0.0000 0.0000 + 2 1 3 3 -1.4383 80.0000 1.0000 -3.6877 -2.8000 0.0000 0.0000 + 3 1 3 1 -1.1390 78.0747 -0.0964 -4.5172 -3.0000 0.0000 0.0000 + 3 1 3 2 -2.5000 70.3345 -1.0000 -5.5315 -3.0000 0.0000 0.0000 + 3 1 3 3 -2.0234 80.0000 0.1684 -3.1568 -2.6174 0.0000 0.0000 + 1 3 3 1 1.1637 -17.3637 0.5459 -3.6005 -2.6938 0.0000 0.0000 + 1 3 3 2 -2.1289 12.8382 1.0000 -5.6657 -2.9759 0.0000 0.0000 + 2 3 3 2 2.5000 -22.9397 0.6991 -3.3961 -1.0000 0.0000 0.0000 + 1 3 3 3 2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 + 2 3 3 3 -2.5000 -2.5103 -1.0000 -2.5000 -1.0000 0.0000 0.0000 + 3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 + 0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000 + 0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 + 1 1 3 3 -0.0002 20.1851 0.1601 -9.0000 -2.0000 0.0000 0.0000 + 1 3 3 1 0.0002 80.0000 -1.5000 -4.4848 -2.0000 0.0000 0.0000 + 3 1 3 3 -0.1583 20.0000 1.5000 -9.0000 -2.0000 0.0000 0.0000 + 1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 3 2 3 2.1200 -3.5800 1.4500 19.5000 diff --git a/examples/reax/Fe_O_H/in.FeOH3 b/examples/reax/Fe_O_H/in.FeOH3 new file mode 100644 index 000000000..2a7e13fb9 --- /dev/null +++ b/examples/reax/Fe_O_H/in.FeOH3 @@ -0,0 +1,23 @@ +# REAX potential for Fe/O/H system +# ..... + +units real + +atom_style charge +read_data data.FeOH3 + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.Fe_O_C_H 2 3 4 + +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.feoh + +run 3000 diff --git a/examples/reax/Fe_O_H/lmp_control b/examples/reax/Fe_O_H/lmp_control new file mode 100644 index 000000000..779c7da7e --- /dev/null +++ b/examples/reax/Fe_O_H/lmp_control @@ -0,0 +1,17 @@ +simulation_name FeOH3_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title Fe_OH3 ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.1 b/examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.1 new file mode 100644 index 000000000..19e0ac656 --- /dev/null +++ b/examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for Fe/O/H system +# ..... + +units real + +atom_style charge +read_data data.FeOH3 + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.Fe_O_C_H 2 3 4 + +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.feoh + +run 3000 +Memory usage per processor = 3.16114 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -9715.3326 0 -9715.3326 -139.61126 + 3000 527.2578 -9636.206 0 -9472.7539 63.147298 +Loop time of 26.1413 on 1 procs for 3000 steps with 105 atoms + +Pair time (%) = 23.9754 (91.7144) +Neigh time (%) = 0.122616 (0.46905) +Comm time (%) = 0.048074 (0.1839) +Outpt time (%) = 0.018285 (0.0699468) +Other time (%) = 1.97698 (7.56267) + +Nlocal: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 647 ave 647 max 647 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3389 ave 3389 max 3389 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3389 +Ave neighs/atom = 32.2762 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.4 b/examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.4 new file mode 100644 index 000000000..0870be4be --- /dev/null +++ b/examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for Fe/O/H system +# ..... + +units real + +atom_style charge +read_data data.FeOH3 + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.Fe_O_C_H 2 3 4 + +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.feoh + +run 3000 +Memory usage per processor = 3.2417 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -9715.3326 0 -9715.3326 -139.61126 + 3000 528.17911 -9636.1936 0 -9472.4559 115.66644 +Loop time of 32.2966 on 4 procs for 3000 steps with 105 atoms + +Pair time (%) = 20.3011 (62.8582) +Neigh time (%) = 0.0376834 (0.116679) +Comm time (%) = 1.54638 (4.78805) +Outpt time (%) = 0.0282907 (0.0875967) +Other time (%) = 10.3832 (32.1495) + +Nlocal: 26.25 ave 34 max 12 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 406.5 ave 460 max 347 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 1108.5 ave 1418 max 452 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 4434 +Ave neighs/atom = 42.2286 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/Fe_O_H/param.qeq b/examples/reax/Fe_O_H/param.qeq new file mode 100644 index 000000000..f8c1b9353 --- /dev/null +++ b/examples/reax/Fe_O_H/param.qeq @@ -0,0 +1,3 @@ +1 3.7248 19.2186 0.8203 +2 8.5000 16.6244 1.0898 +3 1.2457 14.6042 0.7264 diff --git a/examples/reax/RDX/data.RDX b/examples/reax/RDX/data.RDX new file mode 100644 index 000000000..e7b327cd6 --- /dev/null +++ b/examples/reax/RDX/data.RDX @@ -0,0 +1,123 @@ +# RDX example + +105 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 14.0067 + +Atoms + + 1 2 0.0 14.70747 14.63296 9.00078 + 2 4 0.0 14.75209 14.82706 10.48551 + 3 2 0.0 16.08626 14.66861 11.14801 + 4 4 0.0 17.12170 13.78716 10.51955 + 5 2 0.0 17.04682 13.61313 9.03355 + 6 4 0.0 15.72698 13.75678 8.33970 + 7 4 0.0 13.70357 13.95851 11.17372 + 8 4 0.0 17.16997 12.43180 11.21817 + 9 4 0.0 15.13478 12.38723 8.02188 + 10 3 0.0 12.62896 13.62099 10.53217 + 11 3 0.0 13.83977 13.66206 12.42825 + 12 3 0.0 16.82023 12.33906 12.46289 + 13 3 0.0 17.66680 11.40779 10.59764 + 14 3 0.0 15.92308 11.37429 7.84061 + 15 3 0.0 13.85940 12.27085 7.82144 + 16 1 0.0 13.68156 14.38512 8.65830 + 17 1 0.0 14.86042 15.64132 8.56730 + 18 1 0.0 16.53138 15.68341 11.16029 + 19 1 0.0 15.97457 14.44920 12.22991 + 20 1 0.0 17.69011 14.41034 8.61081 + 21 1 0.0 17.57332 12.69163 8.70975 + 22 2 0.0 3.36149 0.85818 22.25391 + 23 4 0.0 4.29015 1.45411 23.26712 + 24 2 0.0 5.74921 1.45638 22.92772 + 25 4 0.0 6.29203 0.41356 21.99929 + 26 2 0.0 5.33619 24.83726 21.00015 + 27 4 0.0 3.87094 24.81178 21.31073 + 28 4 0.0 4.05868 0.83226 24.64084 + 29 4 0.0 6.98470 24.30334 22.78351 + 30 4 0.0 3.44230 23.42075 21.76753 + 31 3 0.0 2.89169 0.35364 24.93982 + 32 3 0.0 4.99347 0.89125 0.53699 + 33 3 0.0 7.50875 24.56580 23.93971 + 34 3 0.0 7.14388 23.13739 22.23984 + 35 3 0.0 4.09644 22.38053 21.35482 + 36 3 0.0 2.36102 23.28086 22.46865 + 37 1 0.0 2.40372 0.54739 22.72003 + 38 1 0.0 3.04434 1.70393 21.61188 + 39 1 0.0 5.93246 2.42528 22.42195 + 40 1 0.0 6.37424 1.54698 23.84001 + 41 1 0.0 5.43492 0.47260 20.09754 + 42 1 0.0 5.68639 23.85112 20.63130 + 43 2 0.0 5.15008 14.27075 16.08622 + 44 4 0.0 4.09420 15.20855 16.58603 + 45 2 0.0 3.92027 15.30093 18.07104 + 46 4 0.0 4.29094 14.13174 18.93110 + 47 2 0.0 5.34851 13.21298 18.40049 + 48 4 0.0 5.54406 13.09043 16.92035 + 49 4 0.0 2.75847 14.92758 15.90470 + 50 4 0.0 3.04761 13.34492 19.33408 + 51 4 0.0 4.88840 11.81712 16.39491 + 52 3 0.0 2.74084 14.40258 14.71964 + 53 3 0.0 1.65772 15.32101 16.46502 + 54 3 0.0 1.90378 13.94960 19.41349 + 55 3 0.0 3.16329 12.10774 19.70337 + 56 3 0.0 4.75708 10.79296 17.17883 + 57 3 0.0 4.57293 11.72857 15.14074 + 58 1 0.0 4.95906 13.97394 15.03430 + 59 1 0.0 6.06811 14.88424 15.99204 + 60 1 0.0 4.58442 16.12697 18.39458 + 61 1 0.0 2.91579 15.69160 18.33484 + 62 1 0.0 6.30641 13.60900 18.79230 + 63 1 0.0 5.29326 12.21519 18.88294 + 64 2 0.0 13.05017 9.27453 21.06302 + 65 4 0.0 13.22363 8.73253 19.67727 + 66 2 0.0 12.46841 9.42196 18.58256 + 67 4 0.0 11.19480 10.14168 18.90515 + 68 2 0.0 11.05337 10.66891 20.30016 + 69 4 0.0 11.78824 9.99842 21.42019 + 70 4 0.0 12.95863 7.23041 19.64978 + 71 4 0.0 9.98593 9.29169 18.52622 + 72 4 0.0 10.85140 9.08952 22.20989 + 73 3 0.0 13.15446 6.52488 20.71943 + 74 3 0.0 12.65239 6.65389 18.52986 + 75 3 0.0 10.08724 8.42350 17.56895 + 76 3 0.0 8.83919 9.52316 19.08441 + 77 3 0.0 9.58446 9.35972 22.25629 + 78 3 0.0 11.34338 8.12396 22.92120 + 79 1 0.0 13.30695 8.51270 21.82781 + 80 1 0.0 13.86236 10.01731 21.19243 + 81 1 0.0 13.15621 10.19964 18.19477 + 82 1 0.0 12.34371 8.75964 17.70106 + 83 1 0.0 11.44941 11.70333 20.26572 + 84 1 0.0 9.98790 10.83504 20.56091 + 85 2 0.0 19.51848 5.12365 5.80007 + 86 4 0.0 19.97495 6.54940 5.74510 + 87 2 0.0 20.89012 6.92320 4.61959 + 88 4 0.0 21.76730 5.87657 4.00380 + 89 2 0.0 21.28205 4.46126 4.07818 + 90 4 0.0 20.37198 4.05135 5.19524 + 91 4 0.0 20.56721 6.97708 7.08440 + 92 4 0.0 23.19172 5.98569 4.53905 + 93 4 0.0 21.14957 3.30814 6.27705 + 94 3 0.0 20.17218 6.39776 8.17469 + 95 3 0.0 21.37277 7.99145 7.13448 + 96 3 0.0 23.63632 7.13187 4.95003 + 97 3 0.0 23.98190 4.96020 4.47319 + 98 3 0.0 22.22095 2.65104 5.95961 + 99 3 0.0 20.67169 3.24305 7.48024 + 100 1 0.0 19.18861 4.84621 6.82250 + 101 1 0.0 18.56668 5.09719 5.23312 + 102 1 0.0 20.22614 7.26910 3.80257 + 103 1 0.0 21.46600 7.84127 4.85745 + 104 1 0.0 20.69928 4.30046 3.14942 + 105 1 0.0 22.11866 3.74259 3.95659 diff --git a/examples/reax/RDX/dump.reax.rdx b/examples/reax/RDX/dump.reax.rdx new file mode 100644 index 000000000..a3bce5a27 --- /dev/null +++ b/examples/reax/RDX/dump.reax.rdx @@ -0,0 +1,11514 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +32 3 0.199739 0.03565 0.0214796 +101 1 0.742667 0.203888 0.209325 +85 2 0.780739 0.204946 0.232003 +88 4 0.870692 0.235063 0.160152 +89 2 0.851282 0.17845 0.163127 +90 4 0.814879 0.162054 0.20781 +92 4 0.927669 0.239428 0.181562 +97 3 0.959276 0.198408 0.178928 +98 3 0.888838 0.106042 0.238384 +104 1 0.827971 0.172018 0.125977 +105 1 0.884746 0.149704 0.158264 +86 4 0.798998 0.261976 0.229804 +87 2 0.835605 0.276928 0.184784 +96 3 0.945453 0.285275 0.198001 +102 1 0.809046 0.290764 0.152103 +103 1 0.85864 0.313651 0.194298 +93 4 0.845983 0.132326 0.251082 +99 3 0.826868 0.129722 0.29921 +100 1 0.767544 0.193848 0.2729 +8 4 0.686799 0.497272 0.448727 +9 4 0.605391 0.495489 0.320875 +12 3 0.672809 0.493562 0.498516 +13 3 0.706672 0.456312 0.423906 +14 3 0.636923 0.454972 0.313624 +15 3 0.554376 0.490834 0.312858 +91 4 0.822688 0.279083 0.283376 +94 3 0.806887 0.25591 0.326988 +95 3 0.854911 0.319658 0.285379 +51 4 0.195536 0.472685 0.655796 +56 3 0.190283 0.431718 0.687153 +57 3 0.182917 0.469143 0.60563 +66 2 0.498736 0.376878 0.743302 +71 4 0.399437 0.371668 0.741049 +75 3 0.40349 0.33694 0.702758 +82 1 0.493748 0.350386 0.708042 +74 3 0.506096 0.266156 0.741194 +81 1 0.526248 0.407986 0.727791 +22 2 0.13446 0.0343272 0.890156 +23 4 0.171606 0.0581644 0.930685 +24 2 0.229968 0.0582552 0.917109 +28 4 0.162347 0.0332904 0.985634 +31 3 0.115668 0.0141456 0.997593 +37 1 0.0961488 0.0218956 0.908801 +38 1 0.121774 0.0681572 0.864475 +39 1 0.237298 0.0970112 0.896878 +41 1 0.217397 0.018904 0.803902 +25 4 0.251681 0.0165424 0.879972 +40 1 0.25497 0.0618792 0.9536 +55 3 0.126532 0.48431 0.788135 +63 1 0.21173 0.488608 0.755318 +67 4 0.447792 0.405667 0.756206 +68 2 0.442135 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+96 3 0.934719 0.249826 0.123069 +102 1 0.83038 0.338984 0.184502 +103 1 0.887675 0.319658 0.213733 +101 1 0.738424 0.272996 0.251164 +85 2 0.777058 0.257315 0.265241 +98 3 0.867294 0.154754 0.254742 +93 4 0.817681 0.167009 0.267183 +99 3 0.791681 0.134975 0.298901 +100 1 0.765935 0.246217 0.306367 +95 3 0.872213 0.262985 0.323617 +9 4 0.621497 0.44816 0.35011 +13 3 0.626963 0.40892 0.492886 +14 3 0.569449 0.44839 0.345129 +15 3 0.648741 0.405654 0.339838 +21 1 0.681621 0.435175 0.430453 +94 3 0.868608 0.355594 0.318354 +5 2 0.678583 0.478345 0.423692 +6 4 0.649656 0.496585 0.37444 +20 1 0.721504 0.485763 0.417168 +4 4 0.660137 0.499396 0.476613 +51 4 0.0863871 0.486232 0.612165 +57 3 0.0415857 0.461639 0.619183 +48 4 0.135821 0.455514 0.628542 +63 1 0.0790484 0.430611 0.687143 +47 2 0.123681 0.429944 0.681716 +62 1 0.12774 0.386329 0.676836 +46 4 0.152416 0.449152 0.731079 +59 1 0.204877 0.48514 0.589314 +74 3 0.410444 0.399451 0.656417 +70 4 0.408073 0.391429 0.707591 +82 1 0.500246 0.440832 0.705341 +12 3 0.64078 0.461441 0.564049 +31 3 0.119173 0.0478196 0.976433 +22 2 0.161629 0.0385132 0.860038 +23 4 0.189936 0.0536962 0.910701 +24 2 0.248942 0.04972 0.912338 +28 4 0.16538 0.0298931 0.961829 +38 1 0.177998 0.0687433 0.832989 +39 1 0.262212 0.0910527 0.90862 +37 1 0.11718 0.0394293 0.861857 +40 1 0.260406 0.0326291 0.951775 +25 4 0.276691 0.0165309 0.869657 +33 3 0.361567 0.00179309 0.909985 +61 1 0.221056 0.485397 0.762179 +71 4 0.516419 0.491328 0.789787 +45 2 0.209796 0.463783 0.725084 +79 1 0.399119 0.338018 0.788855 +73 3 0.366832 0.405734 0.734982 +69 4 0.467552 0.354178 0.838452 +72 4 0.426964 0.343815 0.882742 +77 3 0.402705 0.384923 0.902705 +78 3 0.429956 0.298845 0.908314 +84 1 0.472652 0.43096 0.864213 +64 2 0.443897 0.340058 0.785214 +66 2 0.501406 0.410335 0.737765 +81 1 0.533052 0.380255 0.728096 +67 4 0.522201 0.429315 0.789345 +68 2 0.499561 0.405611 0.839884 +83 1 0.535376 0.394294 0.867536 +80 1 0.44793 0.295084 0.782516 +65 4 0.458004 0.368697 0.734208 +43 2 0.184666 0.490959 0.627944 +60 1 0.236582 0.430742 0.734299 +8 4 0.644313 0.454047 0.512766 +44 4 0.223652 0.492419 0.673914 +50 4 0.120718 0.493583 0.758547 +10 3 0.5046 0.58144 0.462383 +1 2 0.61495 0.545785 0.375001 +2 4 0.593694 0.564088 0.427474 +3 2 0.613612 0.539392 0.477673 +11 3 0.512281 0.534045 0.385559 +17 1 0.640033 0.578093 0.361667 +16 1 0.582514 0.542387 0.345589 +7 4 0.532825 0.554152 0.429205 +18 1 0.630876 0.573957 0.498686 +34 3 0.302537 0.933755 0.916584 +55 3 0.0768548 0.510052 0.736875 +41 1 0.256964 0.981118 0.795436 +49 4 0.238447 0.549781 0.685243 +52 3 0.254657 0.579442 0.647228 +53 3 0.231613 0.56877 0.733638 +58 1 0.163997 0.5289 0.633461 +56 3 0.0910161 0.527413 0.579624 +29 4 0.31474 0.981746 0.901203 +19 1 0.580701 0.520228 0.502676 +75 3 0.466235 0.507215 0.790303 +42 1 0.251233 0.935576 0.844903 +54 3 0.143637 0.52044 0.796557 +26 2 0.242721 0.979511 0.837541 +27 4 0.183518 0.98884 0.833354 +30 4 0.152066 0.939447 0.851106 +35 3 0.0997368 0.943459 0.848747 +36 3 0.172775 0.891719 0.849188 +76 3 0.555393 0.524221 0.795812 +32 3 0.190728 0.992515 0.987341 +ITEM: TIMESTEP +3000 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +89 2 0.812256 0.214001 0.180699 +90 4 0.784368 0.205751 0.233818 +97 3 0.929736 0.214209 0.205635 +104 1 0.78073 0.217058 0.149067 +105 1 0.828459 0.175765 0.164674 +92 4 0.907154 0.237252 0.165829 +96 3 0.933387 0.24901 0.121944 +88 4 0.849858 0.258688 0.169618 +87 2 0.846923 0.305412 0.206755 +102 1 0.826225 0.340609 0.185497 +103 1 0.885562 0.329607 0.210161 +98 3 0.866936 0.156855 0.255633 +93 4 0.817684 0.16724 0.266754 +99 3 0.792083 0.136856 0.299688 +100 1 0.776473 0.246355 0.306574 +101 1 0.736618 0.271511 0.252987 +9 4 0.62216 0.448851 0.348433 +13 3 0.625619 0.407988 0.493214 +14 3 0.57071 0.443811 0.349623 +15 3 0.649027 0.404293 0.34126 +21 1 0.678732 0.432685 0.422214 +5 2 0.679185 0.478208 0.423621 +6 4 0.650622 0.496395 0.374243 +20 1 0.719826 0.495104 0.422615 +4 4 0.658946 0.4989 0.476252 +91 4 0.853077 0.309618 0.305587 +86 4 0.815595 0.303161 0.25821 +85 2 0.778025 0.256508 0.263008 +95 3 0.872857 0.264428 0.322687 +94 3 0.869075 0.354962 0.32418 +51 4 0.0861667 0.486662 0.610379 +57 3 0.0399191 0.46251 0.615954 +48 4 0.136803 0.455726 0.628518 +63 1 0.0807216 0.437684 0.691848 +47 2 0.123408 0.430229 0.680843 +62 1 0.126674 0.387022 0.678495 +46 4 0.150921 0.44648 0.731873 +59 1 0.206516 0.486794 0.590164 +45 2 0.208325 0.461337 0.725403 +43 2 0.18393 0.492245 0.628411 +60 1 0.235676 0.423901 0.727354 +44 4 0.22161 0.49141 0.674792 +74 3 0.408251 0.400406 0.655931 +70 4 0.406263 0.393062 0.707152 +82 1 0.494472 0.438571 0.703233 +73 3 0.364501 0.408642 0.733629 +66 2 0.498442 0.41205 0.736326 +65 4 0.455518 0.370298 0.735519 +12 3 0.638495 0.461947 0.564177 +81 1 0.527748 0.381462 0.727402 +8 4 0.644327 0.451494 0.513641 +31 3 0.117731 0.0474902 0.977784 +22 2 0.166834 0.0381978 0.859974 +23 4 0.189168 0.0562602 0.91233 +24 2 0.248542 0.0506487 0.911441 +28 4 0.16544 0.0328262 0.963007 +38 1 0.173413 0.0704263 0.830131 +37 1 0.122742 0.0411723 0.863386 +39 1 0.265496 0.0914643 0.908695 +40 1 0.263746 0.0413662 0.953663 +25 4 0.276334 0.0161296 0.870744 +33 3 0.363182 0.000971603 0.908345 +61 1 0.223853 0.481536 0.76147 +50 4 0.121046 0.49221 0.75914 +79 1 0.397519 0.341829 0.793253 +69 4 0.467798 0.354803 0.836635 +72 4 0.427548 0.34347 0.88233 +77 3 0.402204 0.384104 0.901947 +78 3 0.428635 0.298064 0.907788 +84 1 0.469373 0.435312 0.85719 +64 2 0.441011 0.339602 0.785787 +68 2 0.499375 0.405326 0.838334 +80 1 0.454935 0.299611 0.776404 +71 4 0.518492 0.49109 0.789307 +67 4 0.521694 0.431759 0.787571 +83 1 0.529675 0.405674 0.870762 +10 3 0.502755 0.579625 0.463179 +1 2 0.616985 0.54613 0.376031 +2 4 0.593213 0.56443 0.428203 +3 2 0.613655 0.537074 0.477575 +11 3 0.513141 0.535757 0.385151 +17 1 0.639909 0.580275 0.358552 +16 1 0.582058 0.538841 0.347691 +7 4 0.533666 0.55669 0.427329 +55 3 0.0778788 0.513341 0.739323 +49 4 0.240703 0.548309 0.686809 +53 3 0.234248 0.567708 0.733772 +58 1 0.170851 0.534566 0.621654 +56 3 0.0918536 0.527032 0.579827 +52 3 0.255978 0.577585 0.645478 +19 1 0.579616 0.527141 0.504068 +18 1 0.624996 0.57274 0.503319 +54 3 0.145857 0.516635 0.797133 +75 3 0.470762 0.507937 0.797042 +76 3 0.559376 0.524084 0.794278 +26 2 0.242143 0.978956 0.836939 +27 4 0.183274 0.98779 0.832323 +30 4 0.151029 0.938341 0.850019 +35 3 0.0998967 0.942329 0.850284 +36 3 0.17578 0.892816 0.847166 +32 3 0.18801 0.992296 0.98637 +34 3 0.301954 0.933303 0.915971 +41 1 0.262572 0.976769 0.795871 +29 4 0.316531 0.980555 0.899812 +42 1 0.252705 0.93661 0.844156 diff --git a/examples/reax/RDX/ffield.reax.rdx b/examples/reax/RDX/ffield.reax.rdx new file mode 100644 index 000000000..84e22bba6 --- /dev/null +++ b/examples/reax/RDX/ffield.reax.rdx @@ -0,0 +1,156 @@ +Reactive MD-force field nitramines (RDX/HMX/TATB/PETN): Strachan, A.; et al. Phys. Rev. Lett. 2003, 91, 098301 + 39 ! Number of general parameters + 50.0000 !Overcoordination parameter + 9.4514 !Overcoordination parameter + 30.0000 !Valency angle conjugation parameter + 216.4305 !Triple bond stabilisation parameter + 12.4838 !Triple bond stabilisation parameter + 0.0000 !C2-correction + 1.0701 !Undercoordination parameter + 7.5000 !Triple bond stabilisation parameter + 11.9083 !Undercoordination parameter + 13.3822 !Undercoordination parameter + -10.4637 !Triple bond stabilization energy + 0.0000 !Lower Taper-radius + 10.0000 !Upper Taper-radius + 2.8793 !Not used + 33.8667 !Valency undercoordination + 3.5895 !Valency angle/lone pair parameter + 1.0563 !Valency angle + 2.0384 !Valency angle parameter + 6.1431 !Not used + 6.9290 !Double bond/angle parameter + 0.0283 !Double bond/angle parameter: overcoord + 0.0570 !Double bond/angle parameter: overcoord + -2.4837 !Not used + 5.8374 !Torsion/BO parameter + 10.0000 !Torsion overcoordination + 1.8820 !Torsion overcoordination + -1.2327 !Conjugation 0 (not used) + 2.1861 !Conjugation + 1.5591 !vdWaals shielding + 0.0100 !Cutoff for bond order (*100) + 5.2216 !Valency angle conjugation parameter + 3.4021 !Overcoordination parameter + 38.5241 !Overcoordination parameter + 2.1533 !Valency/lone pair parameter + 0.5000 !Not used + 20.0000 !Not used + 5.0000 !Molecular energy (not used) + 2.0000 !Version number + 6.5560 !Valency angle conjugation parameter + 4 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. + cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. + ov/un;val1;n.u.;val3,vval4 + C 1.3742 4.0000 12.0000 1.9684 0.1723 0.8712 1.2385 4.0000 + 9.4606 2.1346 4.0000 31.0823 79.5548 5.7254 6.9235 0.0000 + 1.2104 0.0000 183.7012 5.7419 33.3951 11.9957 0.8563 0.0000 + -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 + H 0.6867 1.0000 1.0080 1.3525 0.0616 0.8910 -0.1000 1.0000 + 9.3858 5.0013 1.0000 0.0000 121.1250 3.8446 10.0839 1.0000 + -0.1000 0.0000 58.4228 3.8461 3.2540 1.0000 1.0698 0.0000 + -15.7683 2.1504 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 + O 1.3142 2.0000 15.9990 1.9741 0.0880 0.8712 1.1139 6.0000 + 10.2186 7.7719 4.0000 29.5271 116.0768 8.5000 7.1412 2.0000 + 0.9909 14.9473 69.2812 9.1371 1.6258 0.1863 0.9745 0.0000 + -3.5965 2.5000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 + N 1.2450 3.0000 14.0000 1.9951 0.1088 1.0512 1.1911 5.0000 + 9.9303 7.8431 4.0000 32.4758 100.0000 6.7768 6.8035 2.0000 + 1.0636 0.1045 128.0119 2.1604 2.9464 2.5181 0.9745 0.0000 + -4.0959 2.0047 1.0183 4.0000 2.8793 0.0000 0.0000 0.0000 + 10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr + 1 1 141.9346 113.4487 67.6027 0.1554 -0.3045 1.0000 30.4515 0.4283 + 0.0801 -0.2113 8.5395 1.0000 -0.0933 6.6967 1.0000 0.0000 + 1 2 163.6889 0.0000 0.0000 -0.4525 0.0000 1.0000 6.0000 0.5921 + 12.1053 1.0000 0.0000 1.0000 -0.0097 8.6351 0.0000 0.0000 + 2 2 169.8421 0.0000 0.0000 -0.3591 0.0000 1.0000 6.0000 0.7503 + 9.3119 1.0000 0.0000 1.0000 -0.0169 5.9406 0.0000 0.0000 + 1 3 164.0476 117.4881 72.1261 -0.6031 -0.1795 1.0000 14.9755 0.5413 + 1.2626 -0.3063 7.0000 1.0000 -0.1588 4.5000 0.0000 0.0000 + 3 3 110.4748 155.6441 40.0000 0.1150 -0.1054 1.0000 28.5221 0.2000 + 0.9590 -0.2635 8.5715 1.0000 -0.1007 6.8548 1.0000 0.0000 + 1 4 130.7147 175.2276 97.2523 -0.0368 -0.4942 1.0000 26.7545 0.5133 + 0.3296 -0.3653 7.0000 1.0000 -0.1171 5.1025 1.0000 0.0000 + 3 4 85.4950 114.0081 70.1453 0.5778 -0.1070 1.0000 16.6611 0.2339 + 0.3474 -0.1948 8.3762 1.0000 -0.1089 5.8148 1.0000 0.0000 + 4 4 157.7518 67.1322 160.9732 -0.5869 -0.1824 1.0000 12.0000 0.7136 + 0.8204 -0.1657 10.6490 1.0000 -0.0967 4.5976 1.0000 0.0000 + 2 3 224.3076 0.0000 0.0000 -0.6280 0.0000 1.0000 6.0000 1.0000 + 5.0050 1.0000 0.0000 1.0000 -0.0512 5.1982 0.0000 0.0000 + 2 4 212.1772 0.0000 0.0000 -0.3585 0.0000 1.0000 6.0000 0.3316 + 10.4316 1.0000 0.0000 1.0000 -0.0658 6.4545 0.0000 0.0000 + 6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 1 2 0.0464 1.8296 10.1311 1.0029 -1.0000 -1.0000 + 2 3 0.0375 1.7275 10.8037 0.8813 -1.0000 -1.0000 + 2 4 0.0509 1.7672 10.4261 0.9990 -1.0000 -1.0000 + 1 3 0.1036 1.8869 9.5668 1.3590 1.1099 1.1534 + 1 4 0.1971 1.7356 10.0734 1.2754 1.2113 1.1172 + 3 4 0.0535 1.6709 10.8180 1.2968 1.1416 1.0167 + 42 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 + 1 1 1 74.0317 32.2712 0.9501 0.0000 0.1780 10.5736 1.0400 + 1 1 2 70.6558 14.3658 5.3224 0.0000 0.0058 0.0000 1.0400 + 2 1 2 76.7339 14.4217 3.3631 0.0000 0.0127 0.0000 1.0400 + 1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400 + 2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 1 1 3 65.3104 6.3897 7.5000 0.0000 0.2000 10.0000 1.8525 + 3 1 3 71.9855 28.5708 6.4252 0.0000 0.2000 0.0000 1.8525 + 1 1 4 65.8892 45.0000 1.6598 0.0000 0.2000 10.0000 1.8525 + 3 1 4 73.1057 25.8227 4.2145 0.0000 0.2000 0.0000 1.8525 + 4 1 4 65.8759 40.9838 2.4369 0.0000 0.2000 0.0000 1.8525 + 2 1 3 56.3039 17.3681 5.3095 0.0000 0.9110 0.0000 1.0400 + 2 1 4 71.5505 11.1820 3.7129 0.0000 0.9110 0.0000 1.0400 + 1 2 4 0.0000 0.0019 6.3000 0.0000 0.0000 0.0000 1.0400 + 1 3 1 72.3642 37.8942 1.1566 0.0000 0.7472 0.0000 1.2639 + 1 3 3 90.0000 45.0000 0.5719 0.0000 0.7472 0.0000 1.2639 + 1 3 4 70.4313 14.4055 7.1593 0.0000 0.7472 0.0000 1.2639 + 3 3 3 83.8833 23.3345 2.3433 -10.0000 0.7472 0.0000 1.2639 + 3 3 4 84.0407 45.0000 1.0695 0.0000 0.7472 0.0000 1.2639 + 4 3 4 73.9966 24.4410 5.2760 0.0000 0.7472 0.0000 1.2639 + 1 3 2 89.1394 37.0874 0.3849 0.0000 3.0000 0.0000 1.2618 + 2 3 3 80.7068 5.0854 5.7151 0.0000 3.0000 0.0000 1.2618 + 2 3 4 76.0238 45.0000 0.8637 0.0000 3.0000 0.0000 1.2618 + 2 3 2 82.3474 13.5165 3.4896 0.0000 0.3596 0.0000 1.3307 + 1 4 1 68.4330 19.3525 2.1625 0.0000 1.7325 0.0000 1.0440 + 1 4 3 86.2893 37.5587 1.2660 0.0000 1.7325 0.0000 1.0440 + 1 4 4 74.2404 12.0547 7.5000 0.0000 1.7325 0.0000 1.0440 + 3 4 3 78.5566 43.8492 1.3351 -26.1471 1.7325 40.0000 1.0440 + 3 4 4 77.4239 33.7297 1.7944 -0.9193 1.7325 0.0000 1.0440 + 4 4 4 64.9107 17.5558 7.5000 0.0000 1.7325 0.0000 1.0440 + 1 4 2 90.0000 32.0540 0.7195 0.0000 0.5355 0.0000 2.5279 + 2 4 3 84.1185 45.0000 1.3826 0.0000 0.5355 0.0000 2.5279 + 2 4 4 78.7133 24.6250 3.8202 0.0000 0.5355 0.0000 2.5279 + 2 4 2 56.3036 14.1532 3.3914 0.0000 0.2000 0.0000 2.1689 + 1 2 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 3 2 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 3 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 4 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 2 2 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 17 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 1 1 1 1 0.0000 48.4194 0.3163 -8.6506 -1.7255 0.0000 0.0000 + 1 1 1 2 0.0000 63.3484 0.2210 -8.8401 -1.8081 0.0000 0.0000 + 2 1 1 2 0.0000 45.2741 0.4171 -6.9800 -1.2359 0.0000 0.0000 + 0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 1 3 0 -0.0002 85.8794 0.3236 -3.8134 -2.0000 0.0000 0.0000 + 0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 3 3 0 -0.9667 116.4743 0.0002 -4.9422 0.0000 0.0000 0.0000 + 0 1 4 0 -0.0069 150.0000 0.4891 -7.4921 -2.0000 0.0000 0.0000 + 0 2 4 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 3 4 0 1.6745 56.6301 -0.0008 -4.5064 -2.0000 0.0000 0.0000 + 0 4 4 0 1.1253 75.3447 0.0080 -9.0000 -2.0000 0.0000 0.0000 + 0 1 1 0 0.0930 18.5962 0.0002 -9.0000 -1.0000 0.0000 0.0000 + 4 1 4 4 -2.0000 20.8732 -1.5000 -9.0000 -2.0000 0.0000 0.0000 + 1 1 3 3 -0.0002 21.5452 0.1727 -9.0000 -2.0000 0.0000 0.0000 + 1 3 3 1 0.0002 79.3777 -1.5000 -5.2139 -2.0000 0.0000 0.0000 + 3 1 3 3 -1.3476 22.4932 1.5000 -9.0000 -2.0000 0.0000 0.0000 + 4 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 3 2 3 2.0000 -5.0000 3.0000 3.0000 + 3 2 4 1.7753 -5.0000 3.0000 3.0000 + 4 2 3 1.3884 -5.0000 3.0000 3.0000 + 4 2 4 1.6953 -4.0695 3.0000 3.0000 diff --git a/examples/reax/RDX/in.RDX b/examples/reax/RDX/in.RDX new file mode 100644 index 000000000..bdab6de56 --- /dev/null +++ b/examples/reax/RDX/in.RDX @@ -0,0 +1,23 @@ +# REAX potential for high energy CHON systems +# ..... + +units real + +atom_style charge +read_data data.RDX + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.rdx 2 1 3 4 + +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.rdx + +run 3000 diff --git a/examples/reax/RDX/lmp_control b/examples/reax/RDX/lmp_control new file mode 100644 index 000000000..c729255b4 --- /dev/null +++ b/examples/reax/RDX/lmp_control @@ -0,0 +1,17 @@ +simulation_name RDX_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title RDX ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.1 b/examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.1 new file mode 100644 index 000000000..7551bc891 --- /dev/null +++ b/examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for high energy CHON systems +# ..... + +units real + +atom_style charge +read_data data.RDX + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.rdx 2 1 3 4 + +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.rdx + +run 3000 +Memory usage per processor = 3.16963 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10197.932 0 -10197.932 38.347492 + 3000 507.54195 -10090.701 0 -9933.3613 548.17543 +Loop time of 49.7786 on 1 procs for 3000 steps with 105 atoms + +Pair time (%) = 47.1977 (94.8153) +Neigh time (%) = 0.111814 (0.224622) +Comm time (%) = 0.0492859 (0.0990101) +Outpt time (%) = 0.0182638 (0.0366901) +Other time (%) = 2.40152 (4.8244) + +Nlocal: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 645 ave 645 max 645 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3063 ave 3063 max 3063 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3063 +Ave neighs/atom = 29.1714 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.4 b/examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.4 new file mode 100644 index 000000000..b71c00f96 --- /dev/null +++ b/examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for high energy CHON systems +# ..... + +units real + +atom_style charge +read_data data.RDX + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.rdx 2 1 3 4 + +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.rdx + +run 3000 +Memory usage per processor = 3.12657 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10197.932 0 -10197.932 38.347492 + 3000 507.16511 -10090.577 0 -9933.3534 520.87142 +Loop time of 52.5856 on 4 procs for 3000 steps with 105 atoms + +Pair time (%) = 35.3037 (67.1356) +Neigh time (%) = 0.0323967 (0.0616075) +Comm time (%) = 1.76248 (3.35164) +Outpt time (%) = 0.0193251 (0.0367498) +Other time (%) = 15.4678 (29.4144) + +Nlocal: 26.25 ave 46 max 8 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 399.5 ave 512 max 288 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 1011.25 ave 1818 max 421 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 4045 +Ave neighs/atom = 38.5238 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/RDX/param.qeq b/examples/reax/RDX/param.qeq new file mode 100644 index 000000000..e515b3a7b --- /dev/null +++ b/examples/reax/RDX/param.qeq @@ -0,0 +1,4 @@ +1 3.8446 20.1678 0.8910 +2 5.7254 13.8470 0.8712 +3 8.5000 14.2824 0.8712 +4 6.7768 13.6070 1.0512 diff --git a/examples/reax/README b/examples/reax/README new file mode 100644 index 000000000..20e2856cf --- /dev/null +++ b/examples/reax/README @@ -0,0 +1,25 @@ +This directory contains input files for two ReaxFF +simulations (RDX and TATB crystals) using a +generic hydrocarbon ReaxFF parameter file. +Input files based on pair_style reax and pair_style +reax/c are provided. + +In addition, each subdirectory +contains validated parameter files for a particular +published version of ReaxFF. In all cases, the examples +use pair_style reax/c. + +CHO: Reactive MD-force field c/h/o combustion force field +This version requires tripflag = 0 and hbnewflag = 1 + +AB: Reactive MD-force field for Ammonia Borane: Weismiller, M.R.; van Duin, A.C.T.; Lee, J.; Yetter, R.A. J. Phys. Chem. A 2010, 114, 5485-5492 + +Au_O: Reactive MD-force field: Au-Au: Keith, J. A. et al. Phys Rev B 2010, 81, 235404; Joshi, K. et al., J. Mat. Chem 2010, 20, 10431-10437 + +Fe_O_C_H: Reactive MD-force field: Fe/O/water: Aryanpour, M.; van Duin, A. C. T.; Kubicki, J. D. J. Phys. Chem. A 2010, 114, 6298-6307 + +RDX: Reactive MD-force field nitramines (RDX/HMX/TATB/PETN): Strachan, A.; et al. Phys. Rev. Lett. 2003, 91, 098301 + +V_O_H: Reactive MD-force field: V/O/C/H potential: Chenoweth, K.; et al. J. Phys. Chem. C, 2008, 112, 14645-14654. + +Zn_O_H: Reactive MD-force field: water/zinc: Raymand, D.; van Duin A.C.T.; Baudin M.; Hermannson K. Surface Science 2008, 602, 1020-1031. diff --git a/examples/reax/V_O_H/data.VOH b/examples/reax/V_O_H/data.VOH new file mode 100644 index 000000000..c093705ad --- /dev/null +++ b/examples/reax/V_O_H/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/reax/V_O_H/dump.reax.voh b/examples/reax/V_O_H/dump.reax.voh new file mode 100644 index 000000000..edf82f6a2 --- /dev/null +++ b/examples/reax/V_O_H/dump.reax.voh @@ -0,0 +1,11009 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +100 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +15 3 0.0704432 0.0298664 0.0593292 +17 1 0.174222 0.0136744 0.0124332 +81 2 0.19392 0.425557 0.234288 +82 4 0.119867 0.442463 0.204196 +83 3 0.123802 0.443783 0.129303 +85 3 0.078478 0.400712 0.222254 +87 1 0.101101 0.417306 0.110694 +89 1 0.207397 0.386275 0.219709 +90 1 0.222695 0.456259 0.221427 +51 2 0.70929 0.136283 0.331578 +52 4 0.739951 0.211934 0.33504 +58 1 0.686232 0.127823 0.368041 +59 1 0.682879 0.13242 0.296582 +60 1 0.741961 0.10701 0.328174 +53 3 0.779389 0.225051 0.272602 +54 3 0.786599 0.216384 0.393647 +56 1 0.776483 0.243112 0.421171 +88 1 0.192394 0.424878 0.27822 +10 1 0.513617 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0.396377 0.887573 +34 3 0.398268 0.210493 0.920551 +36 1 0.425852 0.191885 0.900385 +44 3 0.311502 0.453368 0.850598 +31 2 0.417134 0.334952 0.958129 +32 4 0.382845 0.282937 0.904726 +33 3 0.308448 0.293368 0.894786 +35 3 0.414995 0.29798 0.852705 +37 1 0.3009 0.311982 0.861301 +74 3 0.790243 0.456771 0.868351 +39 1 0.45377 0.349696 0.939155 +40 1 0.389918 0.368388 0.965307 +21 2 0.176761 0.479503 0.584129 +46 1 0.29518 0.440131 0.886373 +99 1 0.588361 0.474825 0.723813 +72 4 0.727422 0.464921 0.910355 +91 2 0.553758 0.449871 0.729436 +92 4 0.546777 0.430347 0.809691 +93 3 0.557803 0.485987 0.860067 +94 3 0.588363 0.374004 0.835134 +95 3 0.49028 0.410753 0.823553 +96 1 0.568304 0.339328 0.841849 +76 1 0.78367 0.462596 0.829211 +8 1 0.542749 0.419891 0.529716 +73 3 0.681669 0.401924 0.908923 +47 1 0.440437 0.476885 0.848753 +38 1 0.42705 0.31351 0.99502 +97 1 0.52769 0.496127 0.882709 +78 1 0.791702 0.482395 0.988688 +1 2 0.525686 0.447748 0.500605 +26 1 0.0530143 0.4914 0.695067 +24 3 0.0865873 0.499716 0.673981 +84 3 0.109472 0.512384 0.233582 +86 1 0.0706057 0.521982 0.241397 +64 3 0.30026 0.748784 0.0171242 +66 1 0.30931 0.755858 0.0558158 +12 4 0.111903 0.957678 0.0228878 +14 3 0.121211 0.899547 0.0706779 +16 1 0.14714 0.908576 0.101847 +70 1 0.17069 0.817534 0.00973111 +65 3 0.275523 0.857056 0.011402 +19 1 0.00777142 0.952622 0.0226337 +5 3 0.476867 0.55679 0.498419 +22 4 0.154228 0.516184 0.655984 +25 3 0.152608 0.580524 0.65787 +75 3 0.691886 0.506714 0.882468 +67 1 0.33027 0.840179 0.909542 +2 4 0.491775 0.51104 0.539035 +6 1 0.394604 0.513217 0.564773 +3 3 0.537318 0.542802 0.590724 +7 1 0.538539 0.581691 0.588046 +62 4 0.268033 0.804605 0.977834 +27 1 0.234211 0.530688 0.719429 +79 1 0.754122 0.538089 0.980823 +41 2 0.315911 0.581058 0.82334 +42 4 0.349326 0.518509 0.862548 +43 3 0.419287 0.507269 0.83575 +69 1 0.174558 0.759911 0.968134 +48 1 0.279482 0.568099 0.802896 +49 1 0.305986 0.61257 0.851771 +50 1 0.34472 0.596086 0.794259 +45 3 0.35277 0.533396 0.921899 +63 3 0.304875 0.811639 0.911849 +20 1 0.0295336 0.989557 0.966931 +11 2 0.036906 0.953995 0.991004 +23 3 0.208364 0.503263 0.70609 +61 2 0.187578 0.800828 0.973083 +17 1 0.199452 0.977153 0.973372 +13 3 0.167642 0.956612 0.971757 +18 1 0.0327094 0.918279 0.966136 +68 1 0.172902 0.824887 0.939374 +ITEM: TIMESTEP +3000 +ITEM: NUMBER OF ATOMS +100 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +15 3 0.118452 0.0103452 0.0546761 +57 1 0.786793 0.232143 0.245758 +81 2 0.191871 0.412821 0.247666 +82 4 0.122817 0.440789 0.214386 +83 3 0.117641 0.433907 0.139503 +85 3 0.0725481 0.411904 0.235424 +87 1 0.0904154 0.413872 0.120802 +90 1 0.21854 0.398276 0.216122 +80 1 0.710776 0.494762 0.0169684 +78 1 0.773411 0.458301 0.00565982 +51 2 0.700656 0.127122 0.334629 +52 4 0.74112 0.198403 0.330318 +58 1 0.722778 0.100187 0.361005 +59 1 0.659973 0.133648 0.351026 +60 1 0.697718 0.109233 0.294789 +55 3 0.70404 0.247294 0.323002 +53 3 0.788908 0.204885 0.272603 +54 3 0.778979 0.215557 0.394123 +88 1 0.211062 0.446027 0.268811 +89 1 0.183186 0.380204 0.276379 +9 1 0.495031 0.426942 0.476756 +10 1 0.558406 0.461034 0.475624 +56 1 0.770683 0.253252 0.407262 +30 1 0.161957 0.49713 0.550904 +28 1 0.224601 0.486568 0.580142 +29 1 0.176371 0.437342 0.588738 +21 2 0.181494 0.481589 0.5872 +24 3 0.0835207 0.494707 0.671478 +26 1 0.0602711 0.473124 0.685763 +4 3 0.427491 0.495584 0.57657 +100 1 0.563412 0.414401 0.705579 +98 1 0.516429 0.467621 0.71448 +99 1 0.586511 0.480345 0.723378 +91 2 0.554141 0.450655 0.728908 +8 1 0.540979 0.419998 0.531547 +1 2 0.525531 0.447775 0.501432 +34 3 0.398975 0.210917 0.921243 +36 1 0.430678 0.191214 0.906532 +44 3 0.31079 0.453344 0.850873 +31 2 0.417205 0.333924 0.958522 +32 4 0.382789 0.282813 0.904988 +33 3 0.307905 0.292154 0.895184 +35 3 0.415624 0.296722 0.854158 +37 1 0.299015 0.309625 0.860401 +39 1 0.45341 0.35387 0.940398 +40 1 0.388655 0.365247 0.97092 +46 1 0.294286 0.435571 0.882231 +95 3 0.488784 0.411272 0.820863 +47 1 0.434625 0.473659 0.853115 +38 1 0.429413 0.312739 0.994168 +71 2 0.745152 0.490257 0.989839 +77 1 0.652744 0.396638 0.884597 +72 4 0.725074 0.464843 0.911976 +92 4 0.545821 0.431172 0.808709 +93 3 0.556958 0.486072 0.861833 +94 3 0.589844 0.374815 0.835789 +96 1 0.571221 0.340928 0.841988 +73 3 0.686776 0.40208 0.904792 +97 1 0.521172 0.493639 0.87887 +74 3 0.789627 0.462589 0.871773 +76 1 0.781331 0.466102 0.832573 +84 3 0.11009 0.513016 0.233669 +86 1 0.069901 0.521672 0.237227 +64 3 0.300799 0.748044 0.0158663 +12 4 0.112196 0.957959 0.023059 +14 3 0.121803 0.900049 0.0710882 +16 1 0.145974 0.905891 0.103281 +70 1 0.167465 0.814914 0.00949788 +19 1 0.00600159 0.953009 0.0227352 +66 1 0.305188 0.756537 0.0553972 +65 3 0.274699 0.856894 0.0116968 +5 3 0.477981 0.55543 0.497224 +22 4 0.157056 0.516526 0.652185 +25 3 0.154083 0.580717 0.657721 +27 1 0.240143 0.527293 0.709013 +23 3 0.20597 0.505508 0.709605 +2 4 0.491548 0.51182 0.539098 +6 1 0.395488 0.512566 0.565588 +3 3 0.536435 0.54279 0.591192 +7 1 0.542833 0.581442 0.594014 +41 2 0.317963 0.581326 0.820714 +42 4 0.349302 0.518571 0.86286 +43 3 0.418756 0.506691 0.83668 +48 1 0.28348 0.566834 0.797977 +49 1 0.304796 0.613119 0.84939 +50 1 0.348201 0.598022 0.792744 +45 3 0.352086 0.534908 0.921824 +75 3 0.691069 0.506088 0.882328 +79 1 0.762163 0.529564 0.987894 +69 1 0.176868 0.756524 0.966753 +20 1 0.029765 0.989358 0.965564 +11 2 0.0365677 0.95433 0.990887 +61 2 0.186896 0.799421 0.972234 +17 1 0.200571 0.97629 0.972805 +13 3 0.167886 0.954988 0.971649 +18 1 0.0338374 0.918054 0.966767 +68 1 0.172266 0.822062 0.937981 +67 1 0.325489 0.843912 0.911459 +62 4 0.267997 0.8053 0.977943 +63 3 0.306199 0.810272 0.911769 diff --git a/examples/reax/V_O_H/ffield.reax.V_O_C_H b/examples/reax/V_O_H/ffield.reax.V_O_C_H new file mode 100644 index 000000000..75f2aa668 --- /dev/null +++ b/examples/reax/V_O_H/ffield.reax.V_O_C_H @@ -0,0 +1,166 @@ +Reactive MD-force field: V/O/C/H potential: Chenoweth, K.; et al. J. Phys. Chem. C, 2008, 112, 14645-14654. + 39 ! Number of general parameters + 50.0000 !Overcoordination parameter + 9.5469 !Overcoordination parameter + 26.5405 !Valency angle conjugation parameter + 1.5105 !Triple bond stabilisation parameter + 6.6630 !Triple bond stabilisation parameter + 0.0000 !C2-correction + 1.0588 !Undercoordination parameter + 4.6000 !Triple bond stabilisation parameter + 12.1176 !Undercoordination parameter + 13.3056 !Undercoordination parameter + -70.1292 !Triple bond stabilization energy + 0.0000 !Lower Taper-radius + 10.0000 !Upper Taper-radius + 2.8793 !Not used + 33.8667 !Valency undercoordination + 6.0891 !Valency angle/lone pair parameter + 1.0563 !Valency angle + 2.0384 !Valency angle parameter + 6.1431 !Not used + 6.9290 !Double bond/angle parameter + 0.3989 !Double bond/angle parameter: overcoord + 3.9954 !Double bond/angle parameter: overcoord + -2.4837 !Not used + 5.7796 !Torsion/BO parameter + 10.0000 !Torsion overcoordination + 1.9487 !Torsion overcoordination + -1.2327 !Conjugation 0 (not used) + 2.1645 !Conjugation + 1.5591 !vdWaals shielding + 0.1000 !Cutoff for bond order (*100) + 2.1365 !Valency angle conjugation parameter + 0.6991 !Overcoordination parameter + 50.0000 !Overcoordination parameter + 1.8512 !Valency/lone pair parameter + 0.5000 !Not used + 20.0000 !Not used + 5.0000 !Molecular energy (not used) + 0.0000 !Molecular energy (not used) + 2.6962 !Valency angle conjugation parameter + 5 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. + cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. + ov/un;val1;n.u.;val3,vval4 + C 1.3825 4.0000 12.0000 1.9133 0.1853 0.9000 1.1359 4.0000 + 9.7602 2.1346 4.0000 33.2433 79.5548 5.8678 7.0000 0.0000 + 1.2104 0.0000 199.0303 8.6991 34.7289 13.3894 0.8563 0.0000 + -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 + H 0.7853 1.0000 1.0080 1.5904 0.0419 1.0206 -0.1000 1.0000 + 9.3557 5.0518 1.0000 0.0000 121.1250 5.3200 7.4366 1.0000 + -0.1000 0.0000 62.4879 1.9771 3.3517 0.7571 1.0698 0.0000 + -15.7683 2.1488 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 + O 1.2477 2.0000 15.9990 1.9236 0.0904 1.0503 1.0863 6.0000 + 10.2127 7.7719 4.0000 36.9573 116.0768 8.5000 8.9989 2.0000 + 0.9088 1.0003 60.8726 20.4140 3.3754 0.2702 0.9745 0.0000 + -3.6141 2.7025 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 + V 2.3008 3.0000 50.9415 1.8842 0.2471 0.5518 0.1000 5.0000 + 12.3750 5.2538 3.0000 0.0000 0.0000 2.1056 5.4975 0.0000 + -1.0000 0.0000 117.6300 23.2444 6.5966 1.0000 0.8563 0.0000 + -3.2973 2.3344 1.0338 6.0000 3.6411 0.0000 0.0000 0.0000 + X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000 + 10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000 + -0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000 + -11.0000 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000 + 10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr + 1 1 156.5953 100.0397 80.0000 -0.8157 -0.4591 1.0000 37.7369 0.4235 + 0.4527 -0.1000 9.2605 1.0000 -0.0750 6.8316 1.0000 0.0000 + 1 2 170.2316 0.0000 0.0000 -0.5931 0.0000 1.0000 6.0000 0.7140 + 5.2267 1.0000 0.0000 1.0000 -0.0500 6.8315 0.0000 0.0000 + 2 2 156.0973 0.0000 0.0000 -0.1377 0.0000 1.0000 6.0000 0.8240 + 2.9907 1.0000 0.0000 1.0000 -0.0593 4.8358 0.0000 0.0000 + 1 3 160.4802 105.1693 23.3059 -0.3873 -0.1613 1.0000 10.8851 1.0000 + 0.5341 -0.3174 7.0303 1.0000 -0.1463 5.2913 0.0000 0.0000 + 3 3 60.1463 176.6202 51.1430 -0.2802 -0.1244 1.0000 29.6439 0.9114 + 0.2441 -0.1239 7.6487 1.0000 -0.1302 6.2919 1.0000 0.0000 + 2 3 180.4373 0.0000 0.0000 -0.8074 0.0000 1.0000 6.0000 0.5514 + 1.2490 1.0000 0.0000 1.0000 -0.0657 5.0451 0.0000 0.0000 + 4 4 36.0707 0.0000 0.0000 0.1764 -0.3000 0.0000 16.0000 0.1020 + 0.0350 -0.3000 16.0000 1.0000 -0.0587 8.4813 0.0000 0.0000 + 3 4 137.8828 56.4570 0.0000 0.0310 -0.3000 1.0000 36.0000 0.2355 + 0.7943 -0.2977 15.9401 1.0000 -0.1952 5.0015 1.0000 0.0000 + 2 4 112.6739 0.0000 0.0000 0.1669 -0.3000 0.0000 36.0000 0.0751 + -0.4510 -0.2500 20.0000 1.0000 -0.0822 6.4179 0.0000 0.0000 + 1 4 130.2004 0.0000 0.0000 -0.3153 -0.3000 1.0000 36.0000 0.6315 + 0.9750 -0.2500 20.0000 1.0000 -0.1203 6.5055 1.0000 0.0000 + 6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 1 2 0.1219 1.4000 9.8442 1.1203 -1.0000 -1.0000 + 2 3 0.0344 1.6800 10.3247 0.9013 -1.0000 -1.0000 + 1 3 0.1131 1.8523 9.8442 1.2775 1.1342 1.0621 + 1 4 0.1005 1.7015 12.0291 1.8429 -1.0000 -1.0000 + 2 4 0.1211 1.6565 10.7328 1.4538 -1.0000 -1.0000 + 3 4 0.0807 1.9659 10.0132 1.6500 1.5900 -1.0000 +35 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 + 1 1 1 67.2326 22.0695 1.6286 0.0000 1.7959 15.4141 1.8089 + 1 1 2 65.2527 14.3185 6.2977 0.0000 0.5645 0.0000 1.1530 + 2 1 2 70.0840 25.3540 3.4508 0.0000 0.0050 0.0000 3.0000 + 1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400 + 1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400 + 2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 1 1 3 49.5561 7.3771 4.9568 0.0000 0.7533 15.9906 1.0010 + 3 1 3 77.1171 39.8746 2.5403 -24.3902 1.7740 -42.9758 2.1240 + 2 1 3 65.0000 14.2057 4.8649 0.0000 0.3504 0.0000 1.7185 + 1 3 1 74.3994 44.7500 0.7982 0.0000 3.0000 0.0000 1.0528 + 1 3 3 77.9854 36.6201 2.0201 0.0000 0.7434 67.0264 3.0000 + 3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783 + 1 3 2 71.5018 21.7062 0.4735 0.0000 0.5186 0.0000 1.1793 + 2 3 3 84.9468 23.3540 1.5057 0.0000 2.6374 0.0000 1.3023 + 2 3 2 77.0645 10.4737 1.2895 0.0000 0.9924 0.0000 1.1043 + 1 2 3 0.0000 5.0000 3.0000 0.0000 1.0000 0.0000 1.5000 + 3 2 3 0.0000 0.0148 6.0000 0.0000 0.0000 0.0000 1.0400 + 2 2 3 0.0000 9.7025 6.0000 0.0000 0.0000 0.0000 1.0400 + 3 4 3 68.9780 25.4118 1.8941 0.0000 2.6245 0.0000 1.0010 + 4 3 4 57.5689 6.3911 5.0236 0.0000 1.0358 0.0000 2.5634 + 3 3 4 54.0069 6.0419 1.1089 0.0000 2.7213 0.0000 1.5000 + 1 3 4 67.7243 5.1160 5.6779 0.0000 1.0536 0.0000 1.0010 + 2 3 4 100.0000 12.7432 1.5773 0.0000 1.3885 0.0000 3.8809 + 3 4 4 22.6212 4.2523 3.3011 0.0000 1.1185 0.0000 2.2035 + 1 1 4 70.0000 14.3983 2.0000 0.0000 1.0000 0.0000 1.2000 + 2 1 4 70.0000 7.0700 2.0000 0.0000 1.0000 0.0000 1.2000 + 3 1 4 70.8486 39.9493 1.8219 0.0000 1.0000 0.0000 1.1696 + 1 2 4 0.0000 5.0000 2.0000 0.0000 1.0000 0.0000 1.2000 + 2 2 4 0.0000 9.0000 2.0000 0.0000 1.0000 0.0000 1.2000 + 3 2 4 0.0000 5.9843 1.8885 0.0000 1.0000 0.0000 1.2456 + 1 4 1 70.0000 23.6766 1.0000 0.0000 1.0000 0.0000 1.2000 + 1 4 2 70.0000 6.0546 1.0000 0.0000 1.0000 0.0000 1.2000 + 1 4 3 64.7486 23.1702 3.0204 0.0000 1.0000 0.0000 1.0937 + 2 4 2 65.0000 11.6200 1.0000 0.0000 1.0000 0.0000 1.2000 + 2 4 3 60.4260 22.5101 3.6090 0.0000 1.0000 0.0000 1.2953 + 33 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 1 1 1 1 -0.2500 11.5822 0.1879 -4.7057 -2.2047 0.0000 0.0000 + 1 1 1 2 -0.2500 31.2596 0.1709 -4.6391 -1.9002 0.0000 0.0000 + 2 1 1 2 -0.1770 30.0252 0.4340 -5.0019 -2.0697 0.0000 0.0000 + 1 1 1 3 -0.7098 22.2951 0.0060 -2.5000 -2.1688 0.0000 0.0000 + 2 1 1 3 -0.3568 22.6472 0.6045 -4.0088 -1.0000 0.0000 0.0000 + 3 1 1 3 -0.0528 6.8150 0.7498 -5.0913 -1.0000 0.0000 0.0000 + 1 1 3 1 2.0007 25.5641 -0.0608 -2.6456 -1.1766 0.0000 0.0000 + 1 1 3 2 -1.1953 42.1545 -1.0000 -8.0821 -1.0000 0.0000 0.0000 + 2 1 3 1 -0.9284 34.3952 0.7285 -2.5440 -2.4641 0.0000 0.0000 + 2 1 3 2 -2.5000 79.6980 1.0000 -3.5697 -2.7501 0.0000 0.0000 + 1 1 3 3 -0.0179 5.0603 -0.1894 -2.5000 -2.0399 0.0000 0.0000 + 2 1 3 3 -0.5583 80.0000 1.0000 -4.4000 -3.0000 0.0000 0.0000 + 3 1 3 1 -2.5000 76.0427 -0.0141 -3.7586 -2.9000 0.0000 0.0000 + 3 1 3 2 0.0345 78.9586 -0.6810 -4.1777 -3.0000 0.0000 0.0000 + 3 1 3 3 -2.5000 66.3525 0.3986 -3.0293 -3.0000 0.0000 0.0000 + 1 3 3 1 2.5000 -0.5332 1.0000 -3.5096 -2.9000 0.0000 0.0000 + 1 3 3 2 -2.5000 3.3219 0.7180 -5.2021 -2.9330 0.0000 0.0000 + 2 3 3 2 2.2500 -6.2288 1.0000 -2.6189 -1.0000 0.0000 0.0000 + 1 3 3 3 0.0531 -17.3983 1.0000 -2.5000 -2.1584 0.0000 0.0000 + 2 3 3 3 0.4723 -12.4144 -1.0000 -2.5000 -1.0000 0.0000 0.0000 + 3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 + 0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 + 0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000 + 0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 + 2 3 4 3 0.6439 21.4220 -0.6344 -5.5022 0.0000 0.0000 0.0000 + 1 3 4 3 -0.5000 26.4579 -1.0000 -6.1063 0.0000 0.0000 0.0000 + 1 1 3 4 -0.5000 5.9300 -1.0000 -6.1328 0.0000 0.0000 0.0000 + 2 1 3 4 1.5000 13.6826 0.1478 -2.9478 0.0000 0.0000 0.0000 + 4 3 3 4 -0.0641 59.7588 -1.0000 -3.5975 0.0000 0.0000 0.0000 + 3 3 4 3 1.5000 50.0000 0.3000 -4.5000 0.0000 0.0000 0.0000 + 4 3 4 3 0.0000 0.0000 0.0000 -9.0000 0.0000 0.0000 0.0000 + 1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 3 2 3 2.1082 -2.5000 3.0000 23.0000 diff --git a/examples/reax/V_O_H/in.VOH b/examples/reax/V_O_H/in.VOH new file mode 100644 index 000000000..16eb547fc --- /dev/null +++ b/examples/reax/V_O_H/in.VOH @@ -0,0 +1,23 @@ +# REAX potential for VOH system +# ..... + +units real + +atom_style charge +read_data data.VOH + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.V_O_C_H 2 1 3 4 + +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 3000 diff --git a/examples/reax/V_O_H/lmp_control b/examples/reax/V_O_H/lmp_control new file mode 100644 index 000000000..735540053 --- /dev/null +++ b/examples/reax/V_O_H/lmp_control @@ -0,0 +1,17 @@ +simulation_name VOH_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title VOH ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.1 b/examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.1 new file mode 100644 index 000000000..4c515ef1e --- /dev/null +++ b/examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for VOH system +# ..... + +units real + +atom_style charge +read_data data.VOH + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 processor grid + 100 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.V_O_C_H 2 1 3 4 + +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 3000 +Memory usage per processor = 3.16753 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10246.814 0 -10246.814 42.527005 + 3000 519.62589 -10195.211 0 -10041.869 -789.30523 +Loop time of 31.6405 on 1 procs for 3000 steps with 100 atoms + +Pair time (%) = 28.9498 (91.4959) +Neigh time (%) = 0.111138 (0.351253) +Comm time (%) = 0.0515051 (0.162782) +Outpt time (%) = 0.0176251 (0.0557042) +Other time (%) = 2.51046 (7.93434) + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 602 ave 602 max 602 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3385 ave 3385 max 3385 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3385 +Ave neighs/atom = 33.85 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.4 b/examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.4 new file mode 100644 index 000000000..29f8dbe00 --- /dev/null +++ b/examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for VOH system +# ..... + +units real + +atom_style charge +read_data data.VOH + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 processor grid + 100 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.V_O_C_H 2 1 3 4 + +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 3000 +Memory usage per processor = 3.12726 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10246.814 0 -10246.814 42.527008 + 3000 507.60452 -10189.859 0 -10040.064 -433.64486 +Loop time of 35.267 on 4 procs for 3000 steps with 100 atoms + +Pair time (%) = 21.3274 (60.4741) +Neigh time (%) = 0.0317798 (0.090112) +Comm time (%) = 1.31544 (3.72995) +Outpt time (%) = 0.018347 (0.0520231) +Other time (%) = 12.574 (35.6538) + +Nlocal: 25 ave 38 max 11 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 371.25 ave 453 max 285 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 1087 ave 1787 max 421 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 4348 +Ave neighs/atom = 43.48 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/V_O_H/param.qeq b/examples/reax/V_O_H/param.qeq new file mode 100644 index 000000000..cad819b91 --- /dev/null +++ b/examples/reax/V_O_H/param.qeq @@ -0,0 +1,4 @@ +1 5.3200 14.8732 1.0206 +2 5.8678 14.0000 0.9000 +3 8.5000 17.9978 1.0503 +4 2.1056 10.9950 0.5518 diff --git a/examples/reax/Zn_O_H/data.ZnOH2 b/examples/reax/Zn_O_H/data.ZnOH2 new file mode 100644 index 000000000..af14cfb5b --- /dev/null +++ b/examples/reax/Zn_O_H/data.ZnOH2 @@ -0,0 +1,122 @@ +# ZnOH2 example + +105 atoms +3 atom types + +0 25.000 xlo xhi +0 25.000 ylo yhi +0 25.000 zlo zhi + +Masses + +1 1.0080 +2 15.9990 +3 65.3900 + +Atoms + + 1 3 0.0 12.11798 12.78280 12.46474 + 2 2 0.0 12.30416 12.56916 14.37979 + 3 2 0.0 12.12265 12.63171 10.53701 + 4 1 0.0 12.91874 13.12536 14.81289 + 5 1 0.0 12.65934 11.96727 10.15577 + 6 3 0.0 1.58040 24.31298 0.61068 + 7 2 0.0 2.91627 24.72949 1.95019 + 8 2 0.0 0.48945 23.71942 24.12667 + 9 1 0.0 3.61429 0.29759 1.69671 + 10 1 0.0 0.67172 22.87315 23.77336 + 11 3 0.0 1.38189 13.21679 18.93974 + 12 2 0.0 24.75026 14.03116 19.59558 + 13 2 0.0 2.72553 11.96082 18.36057 + 14 1 0.0 24.80232 14.58872 20.34549 + 15 1 0.0 2.72772 11.12684 18.78223 + 16 3 0.0 10.28220 7.25838 22.67157 + 17 2 0.0 9.71575 6.56657 20.82008 + 18 2 0.0 9.54424 8.41704 24.03481 + 19 1 0.0 9.49644 7.16185 20.12191 + 20 1 0.0 8.69705 8.28870 24.40622 + 21 3 0.0 8.77480 12.96987 22.47649 + 22 2 0.0 8.66515 12.00764 20.79751 + 23 2 0.0 9.22897 14.11643 23.96904 + 24 1 0.0 9.35719 12.11042 20.17651 + 25 1 0.0 8.94019 15.00536 23.93842 + 26 3 0.0 14.01728 9.20480 11.81342 + 27 2 0.0 15.54778 10.36845 11.59125 + 28 2 0.0 12.30605 8.39415 12.20116 + 29 1 0.0 16.34372 10.11892 12.01518 + 30 1 0.0 11.75428 8.82781 12.82011 + 31 3 0.0 3.31959 14.28210 24.72110 + 32 2 0.0 2.70076 15.80638 23.69735 + 33 2 0.0 3.57881 12.68952 0.78967 + 34 1 0.0 2.87681 16.65260 24.05533 + 35 1 0.0 2.95652 12.53609 1.47088 + 36 3 0.0 18.02652 4.79906 8.51043 + 37 2 0.0 18.94853 6.50297 8.53165 + 38 2 0.0 17.36977 2.99183 8.29669 + 39 1 0.0 19.03997 6.96466 7.72300 + 40 1 0.0 17.99667 2.29846 8.31262 + 41 3 0.0 6.52020 20.57673 24.60168 + 42 2 0.0 8.21127 19.64145 24.44360 + 43 2 0.0 4.74514 21.32679 24.40734 + 44 1 0.0 8.80366 19.92974 23.77942 + 45 1 0.0 4.09966 20.76648 24.02713 + 46 3 0.0 21.56715 11.68831 19.78805 + 47 2 0.0 21.06032 10.04683 18.89933 + 48 2 0.0 21.59033 13.26327 20.91213 + 49 1 0.0 20.14609 9.92081 18.74583 + 50 1 0.0 22.11031 13.23728 21.68877 + 51 3 0.0 3.46476 10.81470 5.54977 + 52 2 0.0 1.81531 11.35666 4.68960 + 53 2 0.0 5.26606 10.43021 6.14328 + 54 1 0.0 1.58282 10.91371 3.89945 + 55 1 0.0 5.91838 11.07051 5.94665 + 56 3 0.0 11.47463 5.52361 20.53283 + 57 2 0.0 12.03967 6.22280 22.37265 + 58 2 0.0 11.86155 4.50111 18.90066 + 59 1 0.0 12.85331 6.71281 22.45500 + 60 1 0.0 12.46688 3.79830 18.92313 + 61 3 0.0 13.84325 9.73776 20.81219 + 62 2 0.0 14.64076 10.58418 22.35938 + 63 2 0.0 13.28566 9.07063 19.08653 + 64 1 0.0 14.24006 11.36576 22.68132 + 65 1 0.0 13.82499 9.29075 18.35388 + 66 3 0.0 3.56971 19.75123 16.14741 + 67 2 0.0 2.61000 18.27004 16.94796 + 68 2 0.0 4.24529 21.22096 15.08479 + 69 1 0.0 2.45624 17.51671 16.41547 + 70 1 0.0 3.64162 21.89789 14.85702 + 71 3 0.0 12.89964 21.66576 13.71630 + 72 2 0.0 13.40113 22.26753 15.48824 + 73 2 0.0 12.08396 20.91476 12.13021 + 74 1 0.0 13.39875 21.63410 16.17637 + 75 1 0.0 11.19771 21.15305 11.95014 + 76 3 0.0 24.61573 7.23215 13.93967 + 77 2 0.0 22.71382 6.90606 14.01512 + 78 2 0.0 1.48982 7.78336 13.53204 + 79 1 0.0 22.29828 6.44977 13.31505 + 80 1 0.0 1.65344 8.71176 13.33278 + 81 3 0.0 17.88434 8.12367 3.54514 + 82 2 0.0 19.27721 9.14063 4.42293 + 83 2 0.0 16.79998 6.83289 2.59685 + 84 1 0.0 19.51530 9.96222 4.04489 + 85 1 0.0 17.23105 6.25138 2.00467 + 86 3 0.0 9.87871 1.60680 24.83330 + 87 2 0.0 9.85901 1.39615 22.90756 + 88 2 0.0 9.46800 1.80406 1.71444 + 89 1 0.0 9.43925 2.06388 22.40490 + 90 1 0.0 8.80208 1.25329 2.07177 + 91 3 0.0 0.78894 6.68436 23.75692 + 92 2 0.0 1.91858 5.41167 24.68689 + 93 2 0.0 24.59213 7.68039 22.60451 + 94 1 0.0 2.54601 4.94359 24.17511 + 95 1 0.0 23.78283 7.26758 22.38117 + 96 3 0.0 3.18381 6.68568 13.82109 + 97 2 0.0 2.57422 5.10796 14.84012 + 98 2 0.0 4.95907 7.17379 13.16284 + 99 1 0.0 2.10641 5.31182 15.62965 + 100 1 0.0 5.47671 6.53998 12.70878 + 101 3 0.0 8.53378 12.86625 3.93332 + 102 2 0.0 10.16990 12.00286 4.50825 + 103 2 0.0 6.71801 13.53392 3.83669 + 104 1 0.0 10.20734 11.07072 4.44278 + 105 1 0.0 6.37259 13.93509 4.60760 diff --git a/examples/reax/Zn_O_H/dump.reax.znoh b/examples/reax/Zn_O_H/dump.reax.znoh new file mode 100644 index 000000000..13d5f5513 --- /dev/null +++ b/examples/reax/Zn_O_H/dump.reax.znoh @@ -0,0 +1,11514 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +9 1 0.144572 0.0119036 0.0678684 +88 2 0.37872 0.0721624 0.0685776 +90 1 0.352083 0.0501316 0.0828708 +51 3 0.13859 0.432588 0.221991 +52 2 0.0726124 0.454266 0.187584 +53 2 0.210642 0.417208 0.245731 +54 1 0.0633128 0.436548 0.155978 +55 1 0.236735 0.44282 0.237866 +102 2 0.406796 0.480114 0.18033 +104 1 0.408294 0.442829 0.177711 +81 3 0.715374 0.324947 0.141806 +83 2 0.671999 0.273316 0.103874 +85 1 0.689242 0.250055 0.0801868 +82 2 0.771088 0.365625 0.176917 +84 1 0.780612 0.398489 0.161796 +36 3 0.721061 0.191962 0.340417 +38 2 0.694791 0.119673 0.331868 +40 1 0.719867 0.0919384 0.332505 +28 2 0.492242 0.335766 0.488046 +5 1 0.506374 0.478691 0.406231 +26 3 0.560691 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0.259156 0.87643 +18 2 0.455225 0.368951 0.909564 +19 1 0.37718 0.227097 0.892635 +20 1 0.440464 0.400156 0.921344 +30 1 0.565103 0.335507 0.569827 +63 2 0.48326 0.31149 0.786835 +23 2 0.274713 0.454325 0.979421 +65 1 0.505478 0.313095 0.755755 +61 3 0.5247 0.346771 0.865295 +62 2 0.576872 0.391639 0.898613 +64 1 0.602557 0.417252 0.88587 +49 1 0.928531 0.439843 0.787173 +50 1 0.733256 0.462501 0.814973 +47 2 0.906395 0.427598 0.814219 +46 3 0.832608 0.446309 0.826185 +48 2 0.756427 0.442722 0.83654 +28 2 0.584495 0.330481 0.537776 +31 3 0.154834 0.517752 0.0416014 +101 3 0.340366 0.511859 0.0952121 +103 2 0.304577 0.54028 0.159086 +105 1 0.326918 0.557871 0.181874 +9 1 0.0891554 0.995902 0.11546 +6 3 0.116476 0.954575 0.0286619 +32 2 0.206354 0.58165 0.0376368 +54 1 0.117797 0.506687 0.232121 +5 1 0.523258 0.575591 0.409205 +3 2 0.517286 0.571857 0.44582 +75 1 0.444272 0.795993 0.495482 +102 2 0.400738 0.508916 0.0347901 +34 1 0.242929 0.57544 0.0402528 +52 2 0.107481 0.50137 0.196563 +67 2 0.132882 0.728602 0.631065 +69 1 0.126473 0.706965 0.601353 +14 1 0.02546 0.608988 0.695638 +42 2 0.221073 0.743107 0.989632 +12 2 0.046204 0.619125 0.724521 +66 3 0.162253 0.799963 0.619402 +68 2 0.187287 0.870042 0.598384 +70 1 0.18245 0.897821 0.623169 +71 3 0.500066 0.854164 0.555135 +72 2 0.539554 0.909863 0.592437 +74 1 0.575502 0.903265 0.599956 +11 3 0.0811413 0.554151 0.754571 +24 1 0.425245 0.523876 0.917895 +44 1 0.194575 0.718105 0.981491 +41 3 0.215275 0.816713 0.958426 +8 2 0.101982 0.890738 0.986124 +45 1 0.156066 0.892851 0.946067 +10 1 0.0686518 0.888065 0.968571 +43 2 0.188347 0.881569 0.927234 +22 2 0.390085 0.535354 0.921601 +73 2 0.480071 0.797387 0.50653 +4 1 0.428132 0.520634 0.546137 +13 2 0.119963 0.502634 0.797609 +ITEM: TIMESTEP +2970 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +88 2 0.401887 0.0434819 0.0085462 +90 1 0.382628 0.0355478 0.0396455 +51 3 0.153761 0.454898 0.156021 +1 3 0.495468 0.498252 0.471131 +53 2 0.236207 0.455515 0.175758 +7 2 0.111657 0.00522929 0.0871486 +55 1 0.255013 0.490998 0.171481 +35 1 0.144168 0.41872 0.061926 +33 2 0.124283 0.443234 0.0839459 +39 1 0.667148 0.251459 0.252195 +29 1 0.536907 0.424825 0.407323 +81 3 0.714031 0.317399 0.164353 +83 2 0.658687 0.26499 0.180726 +85 1 0.62849 0.264425 0.158359 +82 2 0.788661 0.331747 0.147979 +84 1 0.812823 0.327018 0.176165 +36 3 0.729247 0.207474 0.318482 +38 2 0.752163 0.141899 0.352267 +40 1 0.780727 0.123238 0.336752 +37 2 0.692533 0.26272 0.278957 +27 2 0.539531 0.440482 0.443401 +26 3 0.569609 0.38132 0.48447 +97 2 0.0774114 0.195745 0.579882 +99 1 0.103663 0.167802 0.594525 +78 2 0.0483907 0.325504 0.550667 +80 1 0.0521086 0.353726 0.522257 +96 3 0.103172 0.268698 0.558365 +98 2 0.180763 0.290196 0.539871 +100 1 0.192682 0.265012 0.514927 +25 1 0.255231 0.447796 0.946776 +2 2 0.439209 0.495652 0.5228 +15 1 0.124846 0.470842 0.779911 +76 3 0.976108 0.292204 0.560426 +77 2 0.91456 0.242782 0.564746 +79 1 0.879556 0.254963 0.558506 +92 2 0.000327133 0.211923 0.908884 +94 1 0.0233155 0.192727 0.886452 +56 3 0.413725 0.254188 0.804239 +86 3 0.390887 0.113077 0.976045 +87 2 0.380933 0.187211 0.954689 +89 1 0.347082 0.19873 0.972238 +58 2 0.399741 0.205006 0.750054 +60 1 0.425404 0.180394 0.748097 +59 1 0.533816 0.238511 0.910202 +95 1 0.0526133 0.359206 0.990249 +93 2 0.0429686 0.35345 0.954509 +91 3 0.0262947 0.281577 0.93224 +21 3 0.341967 0.492426 0.968177 +57 2 0.525534 0.269349 0.929358 +16 3 0.446321 0.289855 0.932823 +17 2 0.388916 0.259805 0.879092 +18 2 0.454092 0.369512 0.909592 +19 1 0.382616 0.224837 0.893094 +20 1 0.443605 0.408146 0.921358 +30 1 0.560043 0.32495 0.563081 +63 2 0.486121 0.309383 0.790282 +23 2 0.275537 0.452272 0.978858 +65 1 0.508465 0.32158 0.763569 +61 3 0.523811 0.346581 0.865458 +62 2 0.57775 0.393519 0.895048 +64 1 0.610923 0.395225 0.875674 +49 1 0.925442 0.446848 0.790096 +50 1 0.736305 0.457055 0.807189 +47 2 0.90633 0.425545 0.814562 +46 3 0.83225 0.445983 0.826835 +48 2 0.75545 0.442382 0.83594 +28 2 0.588081 0.332049 0.538589 +31 3 0.155503 0.517315 0.0408064 +101 3 0.339034 0.511954 0.093848 +103 2 0.302741 0.540068 0.159799 +105 1 0.31861 0.556472 0.189934 +9 1 0.0874406 0.997365 0.114557 +6 3 0.116919 0.95467 0.0290933 +32 2 0.207091 0.580917 0.0406126 +54 1 0.12156 0.511029 0.230685 +5 1 0.529651 0.575348 0.411235 +3 2 0.517834 0.572215 0.446434 +75 1 0.443764 0.794441 0.497343 +102 2 0.404869 0.507924 0.0332954 +34 1 0.243965 0.577851 0.0446123 +52 2 0.109912 0.50285 0.196043 +104 1 0.438849 0.500126 0.046243 +67 2 0.134964 0.728305 0.630516 +69 1 0.125762 0.70764 0.600752 +14 1 0.0217311 0.61651 0.697593 +42 2 0.21856 0.743083 0.988188 +12 2 0.0489217 0.622035 0.722204 +66 3 0.161958 0.800159 0.619293 +68 2 0.18825 0.869806 0.597753 +70 1 0.186186 0.896899 0.623524 +71 3 0.499949 0.854077 0.555195 +72 2 0.539203 0.909763 0.592077 +74 1 0.575288 0.903153 0.599325 +11 3 0.0807705 0.553834 0.755368 +24 1 0.421171 0.523277 0.930408 +44 1 0.18616 0.724236 0.987803 +41 3 0.215716 0.816428 0.958438 +8 2 0.102956 0.890597 0.987521 +45 1 0.154012 0.892475 0.944087 +10 1 0.0769154 0.890195 0.960071 +43 2 0.187259 0.879518 0.925232 +22 2 0.387001 0.536358 0.920532 +73 2 0.479867 0.796904 0.506882 +4 1 0.419873 0.528389 0.526104 +13 2 0.122507 0.504711 0.797065 +ITEM: TIMESTEP +3000 +ITEM: NUMBER OF ATOMS +105 +ITEM: BOX BOUNDS +0 25 +0 25 +0 25 +ITEM: ATOMS id type xs ys zs +7 2 0.111071 0.00573817 0.0867629 +88 2 0.402409 0.0432832 0.00610523 +90 1 0.385956 0.035522 0.038706 +51 3 0.153883 0.455224 0.156505 +53 2 0.236578 0.455337 0.173351 +35 1 0.139442 0.410167 0.0671443 +33 2 0.127504 0.443132 0.0826264 +55 1 0.262888 0.484741 0.176459 +81 3 0.714259 0.316948 0.16486 +83 2 0.65911 0.264282 0.182807 +85 1 0.625164 0.269294 0.167303 +82 2 0.788061 0.332559 0.146895 +84 1 0.812317 0.324834 0.174352 +36 3 0.728936 0.207728 0.317931 +38 2 0.752746 0.142446 0.35228 +40 1 0.784681 0.127327 0.340381 +1 3 0.495849 0.498303 0.471249 +39 1 0.665107 0.253011 0.251394 +29 1 0.516298 0.425243 0.410627 +37 2 0.692462 0.262213 0.277736 +27 2 0.540766 0.441195 0.438687 +26 3 0.569418 0.381085 0.484809 +97 2 0.0776243 0.195734 0.581231 +99 1 0.0974242 0.163927 0.578647 +58 2 0.40044 0.20691 0.745916 +60 1 0.431562 0.189514 0.737316 +77 2 0.916245 0.242727 0.564331 +79 1 0.88024 0.248844 0.567846 +78 2 0.0488391 0.327486 0.549364 +80 1 0.0510011 0.35758 0.529926 +96 3 0.102211 0.268187 0.558433 +98 2 0.180519 0.290927 0.539965 +100 1 0.193263 0.263521 0.51547 +2 2 0.435233 0.497413 0.523439 +30 1 0.562523 0.312653 0.55434 +28 2 0.591332 0.333004 0.54028 +76 3 0.976133 0.292119 0.560482 +94 1 0.0207882 0.194875 0.883095 +86 3 0.391088 0.113754 0.975971 +87 2 0.377473 0.18925 0.954199 +89 1 0.363948 0.214711 0.979124 +19 1 0.380849 0.221058 0.906677 +59 1 0.527211 0.234007 0.916384 +92 2 0.99947 0.213325 0.907787 +25 1 0.248274 0.46513 0.956244 +15 1 0.113614 0.470802 0.790024 +95 1 0.0464654 0.360279 0.992074 +93 2 0.0431813 0.353544 0.955327 +91 3 0.0265856 0.281636 0.932145 +56 3 0.412821 0.254291 0.804419 +21 3 0.342072 0.492697 0.969134 +16 3 0.446424 0.289056 0.933506 +17 2 0.389336 0.260214 0.882448 +18 2 0.452632 0.370544 0.909426 +20 1 0.452715 0.405941 0.921119 +63 2 0.489257 0.307482 0.796194 +23 2 0.276206 0.450346 0.977518 +57 2 0.528238 0.268099 0.931241 +65 1 0.503514 0.323813 0.765579 +61 3 0.522528 0.346021 0.865435 +62 2 0.580321 0.395737 0.890877 +64 1 0.608699 0.376435 0.876092 +50 1 0.736827 0.449973 0.802453 +49 1 0.922787 0.451768 0.795042 +47 2 0.906227 0.423906 0.814659 +46 3 0.831935 0.445533 0.827548 +48 2 0.754447 0.442377 0.834967 +31 3 0.156221 0.516744 0.0404309 +32 2 0.206697 0.579285 0.0434063 +54 1 0.125109 0.516288 0.229439 +34 1 0.243358 0.576753 0.0496867 +52 2 0.111758 0.504941 0.196379 +101 3 0.338204 0.512149 0.0921673 +103 2 0.300406 0.539132 0.159884 +105 1 0.312854 0.551912 0.193795 +102 2 0.406104 0.506627 0.0331529 +104 1 0.439969 0.500664 0.0480927 +9 1 0.0857662 0.999043 0.113589 +6 3 0.117266 0.954779 0.0295887 +5 1 0.536267 0.575041 0.414536 +3 2 0.518143 0.571942 0.447109 +75 1 0.443417 0.792544 0.498773 +67 2 0.137096 0.728012 0.629944 +69 1 0.125067 0.709362 0.599718 +14 1 0.0195906 0.626734 0.700902 +12 2 0.0520481 0.623181 0.720427 +4 1 0.415259 0.525861 0.509136 +66 3 0.161654 0.800336 0.619196 +68 2 0.189201 0.869553 0.597173 +70 1 0.19018 0.896399 0.623078 +71 3 0.49988 0.853985 0.555221 +73 2 0.479527 0.796447 0.507305 +72 2 0.538769 0.909676 0.59182 +74 1 0.575133 0.903306 0.598485 +42 2 0.215912 0.743742 0.986484 +11 3 0.080243 0.554041 0.756009 +44 1 0.181621 0.730411 0.995002 +13 2 0.124898 0.505865 0.796017 +24 1 0.420767 0.537862 0.932421 +22 2 0.384241 0.536279 0.920004 +41 3 0.216155 0.81589 0.958501 +8 2 0.104284 0.890294 0.988144 +45 1 0.152547 0.886 0.94166 +10 1 0.0846283 0.895534 0.956542 +43 2 0.186004 0.877888 0.92338 diff --git a/examples/reax/Zn_O_H/ffield.reax.ZnOH b/examples/reax/Zn_O_H/ffield.reax.ZnOH new file mode 100644 index 000000000..00d22a00c --- /dev/null +++ b/examples/reax/Zn_O_H/ffield.reax.ZnOH @@ -0,0 +1,97 @@ +Reactive MD-force field: water/zinc: Raymand, D.; van Duin A.C.T.; Baudin M.; Hermannson K. Surface Science 2008, 602, 1020-1031. + 39 ! Number of general parameters + 50.0000 !Overcoordination parameter + 9.5469 !Overcoordination parameter + 26.5405 !Valency angle conjugation parameter + 1.7224 !Triple bond stabilisation parameter + 6.8702 !Triple bond stabilisation parameter + 60.4850 !C2-correction + 1.0588 !Undercoordination parameter + 4.6000 !Triple bond stabilisation parameter + 12.1176 !Undercoordination parameter + 13.3056 !Undercoordination parameter + -70.5044 !Triple bond stabilization energy + 0.0000 !Lower Taper-radius + 10.0000 !Upper Taper-radius + 2.8793 !Not used + 33.8667 !Valency undercoordination + 6.0891 !Valency angle/lone pair parameter + 1.0563 !Valency angle + 2.0384 !Valency angle parameter + 6.1431 !Not used + 6.9290 !Double bond/angle parameter + 0.3989 !Double bond/angle parameter: overcoord + 3.9954 !Double bond/angle parameter: overcoord + -2.4837 !Not used + 5.7796 !Torsion/BO parameter + 10.0000 !Torsion overcoordination + 1.9487 !Torsion overcoordination + -1.2327 !Conjugation 0 (not used) + 2.1645 !Conjugation + 1.5591 !vdWaals shielding + 0.1000 !Cutoff for bond order (*100) + 2.1365 !Valency angle conjugation parameter + 0.6991 !Overcoordination parameter + 50.0000 !Overcoordination parameter + 1.8512 !Valency/lone pair parameter + 0.5000 !Not used + 20.0000 !Not used + 5.0000 !Molecular energy (not used) + 0.0000 !Molecular energy (not used) + 2.6962 !Valency angle conjugation parameter + 4 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. + cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. + ov/un;val1;n.u.;val3,vval4 + H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000 + 8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000 + -0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000 + -19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 + O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000 + 9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000 + 0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000 + -3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 + Zn 1.8862 2.0000 65.3900 1.9200 0.2998 0.4828 -1.6836 2.0000 + 11.5134 18.3776 2.0000 0.0078 0.0000 2.0219 5.7915 0.0000 + -1.2000 0.0000 266.4838 5.3430 10.1260 0.7590 0.0000 0.0000 + -3.0614 2.1158 1.0338 6.2998 2.5791 0.0000 0.0000 0.0000 + X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000 + 10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000 + -0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000 + -11.0000 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000 + 6 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr + 1 1 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300 + 6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000 + 2 2 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 + 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 + 1 2 160.0000 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5626 + 1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000 + 1 3 0.0000 0.0000 0.0000 0.0000 -0.5000 1.0000 50.0000 0.5000 + 0.5000 -0.5000 30.0000 1.0000 -0.2000 8.0000 0.0000 0.0000 + 2 3 159.9755 0.0000 0.0000 -0.4548 -0.5000 0.0000 35.0000 0.0375 + 1.3099 -0.5000 25.0000 0.0000 -0.4787 4.6717 0.0000 0.0000 + 3 3 38.4643 0.0000 0.0000 -0.6944 -0.2000 0.0000 16.0000 0.2129 + 0.5059 -0.2000 15.0000 0.0000 -0.0814 6.0333 0.0000 0.0000 + 3 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 1 2 0.0283 1.2885 10.9190 0.9215 -1.0000 -1.0000 + 2 3 0.2744 2.1414 9.7703 1.9804 -1.0000 -1.0000 + 1 3 0.0987 1.8227 12.0654 0.1000 -1.0000 -1.0000 +11 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 + 1 1 1 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 + 2 2 2 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783 + 1 2 2 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680 + 1 2 1 85.8000 9.8453 2.2720 0.0000 2.8635 0.0000 1.5800 + 2 1 2 0.0000 15.0000 2.8900 0.0000 0.0000 0.0000 2.8774 + 1 1 2 0.0000 8.5744 3.0000 0.0000 0.0000 0.0000 1.0421 + 1 2 3 77.5446 9.9016 2.3157 0.0000 0.4543 0.0000 2.3770 + 2 3 2 10.8790 38.9915 0.7072 0.0000 2.0000 0.0000 2.6162 + 3 2 3 37.5284 32.3525 0.2657 0.0000 0.4403 0.0000 1.1000 + 2 3 3 16.9624 30.3241 0.2697 0.0000 2.0000 0.0000 3.0708 + 2 2 3 60.0000 20.0000 0.5000 0.0000 1.0000 0.0000 2.0000 + 3 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 1 2 2 1 2.2500 -6.2288 1.0000 -2.6189 -1.0000 0.0000 0.0000 + 1 2 2 2 0.4723 -12.4144 -1.0000 -2.5000 -1.0000 0.0000 0.0000 + 2 2 2 2 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 + 1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 2 1 2 2.1200 -3.5800 1.4500 19.5000 diff --git a/examples/reax/Zn_O_H/in.ZnOH2 b/examples/reax/Zn_O_H/in.ZnOH2 new file mode 100644 index 000000000..fe4c3395a --- /dev/null +++ b/examples/reax/Zn_O_H/in.ZnOH2 @@ -0,0 +1,23 @@ +# REAX potential for ZnOH2 system +# ..... + +units real + +atom_style charge +read_data data.ZnOH2 + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.ZnOH 1 2 3 + +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.znoh + +run 3000 diff --git a/examples/reax/Zn_O_H/lmp_control b/examples/reax/Zn_O_H/lmp_control new file mode 100644 index 000000000..0fb44fe86 --- /dev/null +++ b/examples/reax/Zn_O_H/lmp_control @@ -0,0 +1,17 @@ +simulation_name ZnOH2_example ! output files will carry this name + their specific ext + +tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation +energy_update_freq 1 + +nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A +hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions +bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs +thb_cutoff 0.001 ! cutoff value for three body interactions + +write_freq 1 ! write trajectory after so many steps +traj_title ZnOH2 ! (no white spaces) +atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file +atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file +atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file +bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file +angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file diff --git a/examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.1 b/examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.1 new file mode 100644 index 000000000..81ecd5686 --- /dev/null +++ b/examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.1 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for ZnOH2 system +# ..... + +units real + +atom_style charge +read_data data.ZnOH2 + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.ZnOH 1 2 3 + +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.znoh + +run 3000 +Memory usage per processor = 3.1717 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -7900.2668 0 -7900.2668 60.076093 + 3000 546.29009 -7937.7702 0 -7768.418 -754.7834 +Loop time of 21.5906 on 1 procs for 3000 steps with 105 atoms + +Pair time (%) = 19.4307 (89.9965) +Neigh time (%) = 0.120478 (0.558014) +Comm time (%) = 0.0459824 (0.212974) +Outpt time (%) = 0.0180607 (0.0836508) +Other time (%) = 1.9753 (9.14891) + +Nlocal: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 649 ave 649 max 649 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3959 ave 3959 max 3959 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3959 +Ave neighs/atom = 37.7048 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.4 b/examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.4 new file mode 100644 index 000000000..d9cf3c835 --- /dev/null +++ b/examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.4 @@ -0,0 +1,50 @@ +LAMMPS (18 Jan 2011) +# REAX potential for ZnOH2 system +# ..... + +units real + +atom_style charge +read_data data.ZnOH2 + orthogonal box = (0 0 0) to (25 25 25) + 1 by 2 by 2 processor grid + 105 atoms + +pair_style reax/c lmp_control +pair_coeff * * ffield.reax.ZnOH 1 2 3 + +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.znoh + +run 3000 +Memory usage per processor = 3.12752 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -7900.2668 0 -7900.2668 60.076093 + 3000 548.4473 -7938.3751 0 -7768.3542 -811.9332 +Loop time of 24.5601 on 4 procs for 3000 steps with 105 atoms + +Pair time (%) = 14.946 (60.855) +Neigh time (%) = 0.0340881 (0.138795) +Comm time (%) = 1.40431 (5.71784) +Outpt time (%) = 0.0192205 (0.0782589) +Other time (%) = 8.15644 (33.2101) + +Nlocal: 26.25 ave 45 max 15 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 399 ave 509 max 295 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Neighs: 1146.25 ave 2055 max 700 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 4585 +Ave neighs/atom = 43.6667 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/reax/Zn_O_H/param.qeq b/examples/reax/Zn_O_H/param.qeq new file mode 100644 index 000000000..9cf803518 --- /dev/null +++ b/examples/reax/Zn_O_H/param.qeq @@ -0,0 +1,3 @@ +1 3.7248 19.2186 0.8203 +2 8.5000 16.6244 1.0898 +3 2.0219 11.5830 0.4828 diff --git a/examples/reax/bonds.reax.tatb b/examples/reax/bonds.reax.tatb deleted file mode 100644 index 4c7af471b..000000000 --- a/examples/reax/bonds.reax.tatb +++ /dev/null @@ -1,784 +0,0 @@ -# Timestep 0 -# -# Number of particles 384 -# -# Max.number of bonds per atom 3 with coarse bond order cutoff 0.300 -# Particle connection table and bond orders -# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q - 1 1 3 2 6 13 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 2 1 3 1 3 14 0 1.324 1.345 1.300 3.969 0.000 0.193 - 3 1 3 2 4 15 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 4 1 3 3 5 16 0 1.336 1.306 1.324 3.967 0.000 0.196 - 5 1 3 4 6 17 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 6 1 3 1 5 18 0 1.332 1.317 1.318 3.967 0.000 0.191 - 7 2 1 14 0 0.873 1.075 0.000 0.366 - 8 2 1 14 0 0.897 1.056 0.000 0.386 - 9 2 1 16 0 0.905 1.051 0.000 0.379 - 10 2 2 16 23 0 0.838 0.267 1.105 0.000 0.385 - 11 2 2 18 24 0 0.868 0.216 1.083 0.000 0.377 - 12 2 1 18 0 0.881 1.069 0.000 0.386 - 13 4 3 1 20 19 0 1.109 1.198 1.197 3.504 0.165 0.344 - 14 4 3 2 7 8 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 15 4 3 3 21 22 0 1.083 1.211 1.214 3.508 0.160 0.371 - 16 4 3 4 9 10 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 17 4 3 5 23 24 0 1.143 1.171 1.190 3.504 0.165 0.341 - 18 4 3 6 11 12 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 19 3 1 13 0 1.197 1.393 2.000 -0.381 - 20 3 1 13 0 1.198 1.407 2.000 -0.413 - 21 3 1 15 0 1.211 1.378 2.000 -0.375 - 22 3 1 15 0 1.214 1.368 2.000 -0.399 - 23 3 2 10 17 0 0.267 1.171 1.446 2.000 -0.388 - 24 3 2 11 17 0 0.216 1.190 1.413 2.000 -0.411 - 25 1 3 30 26 37 0 1.332 1.324 1.109 3.767 0.000 -0.073 - 26 1 3 25 27 38 0 1.324 1.345 1.300 3.969 0.000 0.193 - 27 1 3 26 28 39 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 28 1 3 27 29 40 0 1.336 1.306 1.324 3.967 0.000 0.196 - 29 1 3 28 30 41 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 30 1 3 25 29 42 0 1.332 1.317 1.318 3.967 0.000 0.191 - 31 2 1 38 0 0.873 1.075 0.000 0.366 - 32 2 1 38 0 0.897 1.056 0.000 0.386 - 33 2 1 40 0 0.905 1.051 0.000 0.379 - 34 2 2 47 40 0 0.267 0.838 1.105 0.000 0.385 - 35 2 2 42 48 0 0.868 0.216 1.083 0.000 0.377 - 36 2 1 42 0 0.881 1.069 0.000 0.386 - 37 4 3 25 43 44 0 1.109 1.197 1.198 3.504 0.165 0.344 - 38 4 3 26 32 31 0 1.300 0.897 0.873 3.070 0.966 -0.469 - 39 4 3 27 45 46 0 1.083 1.211 1.214 3.508 0.160 0.371 - 40 4 3 28 33 34 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 41 4 3 29 47 48 0 1.143 1.171 1.190 3.504 0.165 0.341 - 42 4 3 30 35 36 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 43 3 1 37 0 1.197 1.393 2.000 -0.381 - 44 3 1 37 0 1.198 1.407 2.000 -0.413 - 45 3 1 39 0 1.211 1.378 2.000 -0.375 - 46 3 1 39 0 1.214 1.368 2.000 -0.399 - 47 3 2 34 41 0 0.267 1.171 1.446 2.000 -0.388 - 48 3 2 35 41 0 0.216 1.190 1.413 2.000 -0.411 - 49 1 3 50 54 61 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 50 1 3 49 51 62 0 1.324 1.345 1.300 3.969 0.000 0.193 - 51 1 3 50 52 63 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 52 1 3 51 53 64 0 1.336 1.306 1.324 3.967 0.000 0.196 - 53 1 3 52 54 65 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 54 1 3 49 53 66 0 1.332 1.317 1.318 3.967 0.000 0.191 - 55 2 1 62 0 0.873 1.075 0.000 0.366 - 56 2 1 62 0 0.897 1.056 0.000 0.386 - 57 2 1 64 0 0.905 1.051 0.000 0.379 - 58 2 2 64 71 0 0.838 0.267 1.105 0.000 0.385 - 59 2 2 66 72 0 0.868 0.216 1.083 0.000 0.377 - 60 2 1 66 0 0.881 1.069 0.000 0.386 - 62 4 3 50 55 56 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 63 4 3 51 69 70 0 1.083 1.211 1.214 3.508 0.160 0.371 - 64 4 3 52 57 58 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 65 4 3 53 71 72 0 1.143 1.171 1.190 3.504 0.165 0.341 - 66 4 3 54 59 60 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 69 3 1 63 0 1.211 1.378 2.000 -0.375 - 70 3 1 63 0 1.214 1.368 2.000 -0.399 - 71 3 2 58 65 0 0.267 1.171 1.446 2.000 -0.388 - 72 3 2 59 65 0 0.216 1.190 1.413 2.000 -0.411 - 73 1 3 78 74 85 0 1.332 1.324 1.109 3.767 0.000 -0.073 - 74 1 3 73 75 86 0 1.324 1.345 1.300 3.969 0.000 0.193 - 75 1 3 74 76 87 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 76 1 3 75 77 88 0 1.336 1.306 1.324 3.967 0.000 0.196 - 77 1 3 76 78 89 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 78 1 3 73 77 90 0 1.332 1.317 1.318 3.967 0.000 0.191 - 79 2 1 86 0 0.873 1.075 0.000 0.366 - 80 2 1 86 0 0.897 1.056 0.000 0.386 - 81 2 1 88 0 0.905 1.051 0.000 0.379 - 82 2 2 95 88 0 0.267 0.838 1.105 0.000 0.385 - 83 2 2 90 96 0 0.868 0.216 1.083 0.000 0.377 - 84 2 1 90 0 0.881 1.069 0.000 0.386 - 85 4 3 73 91 92 0 1.109 1.197 1.198 3.504 0.165 0.344 - 86 4 3 74 80 79 0 1.300 0.897 0.873 3.070 0.966 -0.469 - 87 4 3 75 93 94 0 1.083 1.211 1.214 3.508 0.160 0.371 - 88 4 3 76 81 82 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 89 4 3 77 95 96 0 1.143 1.171 1.190 3.504 0.165 0.341 - 90 4 3 78 83 84 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 91 3 1 85 0 1.197 1.393 2.000 -0.381 - 92 3 1 85 0 1.198 1.407 2.000 -0.413 - 93 3 1 87 0 1.211 1.378 2.000 -0.375 - 94 3 1 87 0 1.214 1.368 2.000 -0.399 - 95 3 2 82 89 0 0.267 1.171 1.446 2.000 -0.388 - 96 3 2 83 89 0 0.216 1.190 1.413 2.000 -0.411 - 97 1 3 98 102 109 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 98 1 3 97 99 110 0 1.324 1.345 1.300 3.969 0.000 0.193 - 99 1 3 98 100 111 0 1.345 1.337 1.083 3.767 0.000 -0.060 - 100 1 3 99 101 112 0 1.337 1.306 1.324 3.967 0.000 0.196 - 101 1 3 100 113 102 0 1.306 1.143 1.317 3.769 0.000 -0.063 - 102 1 3 97 101 114 0 1.332 1.317 1.318 3.967 0.000 0.191 - 103 2 1 110 0 0.873 1.075 0.000 0.366 - 104 2 1 110 0 0.897 1.056 0.000 0.386 - 105 2 1 112 0 0.905 1.051 0.000 0.379 - 106 2 2 119 112 0 0.267 0.838 1.105 0.000 0.385 - 107 2 2 114 120 0 0.868 0.216 1.083 0.000 0.377 - 108 2 1 114 0 0.881 1.069 0.000 0.386 - 109 4 3 116 97 115 0 1.198 1.109 1.197 3.504 0.165 0.344 - 110 4 3 103 104 98 0 0.873 0.897 1.300 3.070 0.966 -0.469 - 111 4 3 99 117 118 0 1.083 1.211 1.214 3.508 0.160 0.371 - 112 4 3 100 105 106 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 113 4 3 101 119 120 0 1.143 1.171 1.190 3.504 0.165 0.341 - 114 4 3 102 107 108 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 115 3 1 109 0 1.197 1.393 2.000 -0.381 - 116 3 1 109 0 1.198 1.407 2.000 -0.413 - 117 3 1 111 0 1.211 1.378 2.000 -0.375 - 118 3 1 111 0 1.214 1.368 2.000 -0.399 - 119 3 2 106 113 0 0.267 1.171 1.446 2.000 -0.388 - 120 3 2 107 113 0 0.216 1.190 1.413 2.000 -0.411 - 121 1 3 126 122 133 0 1.332 1.324 1.109 3.767 0.000 -0.073 - 122 1 3 121 123 134 0 1.324 1.345 1.300 3.969 0.000 0.193 - 123 1 3 122 124 135 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 124 1 3 123 125 136 0 1.336 1.306 1.324 3.967 0.000 0.196 - 125 1 3 124 126 137 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 126 1 3 121 125 138 0 1.332 1.317 1.318 3.967 0.000 0.191 - 127 2 1 134 0 0.873 1.075 0.000 0.366 - 128 2 1 134 0 0.897 1.056 0.000 0.386 - 129 2 1 136 0 0.905 1.051 0.000 0.379 - 130 2 2 143 136 0 0.267 0.838 1.105 0.000 0.385 - 131 2 2 138 144 0 0.868 0.216 1.083 0.000 0.377 - 132 2 1 138 0 0.881 1.069 0.000 0.386 - 133 4 3 121 139 140 0 1.109 1.197 1.198 3.504 0.165 0.344 - 134 4 3 122 127 128 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 135 4 3 123 141 142 0 1.083 1.211 1.214 3.508 0.160 0.371 - 136 4 3 124 129 130 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 137 4 3 125 143 144 0 1.143 1.171 1.190 3.504 0.165 0.341 - 138 4 3 126 131 132 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 139 3 1 133 0 1.197 1.393 2.000 -0.381 - 140 3 1 133 0 1.198 1.407 2.000 -0.413 - 141 3 1 135 0 1.211 1.378 2.000 -0.375 - 142 3 1 135 0 1.214 1.368 2.000 -0.399 - 143 3 2 130 137 0 0.267 1.171 1.446 2.000 -0.388 - 144 3 2 131 137 0 0.216 1.190 1.413 2.000 -0.411 - 145 1 3 146 150 157 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 146 1 3 145 147 158 0 1.324 1.345 1.300 3.969 0.000 0.193 - 147 1 3 146 148 159 0 1.345 1.337 1.083 3.767 0.000 -0.060 - 148 1 3 147 149 160 0 1.337 1.306 1.324 3.967 0.000 0.196 - 149 1 3 148 161 150 0 1.306 1.143 1.317 3.769 0.000 -0.063 - 150 1 3 145 149 162 0 1.332 1.317 1.318 3.967 0.000 0.191 - 151 2 1 158 0 0.873 1.075 0.000 0.366 - 152 2 1 158 0 0.897 1.056 0.000 0.386 - 153 2 1 160 0 0.905 1.051 0.000 0.379 - 154 2 2 167 160 0 0.267 0.838 1.105 0.000 0.385 - 155 2 2 168 162 0 0.216 0.868 1.083 0.000 0.377 - 156 2 1 162 0 0.881 1.069 0.000 0.386 - 158 4 3 151 152 146 0 0.873 0.897 1.300 3.070 0.966 -0.469 - 159 4 3 147 165 166 0 1.083 1.211 1.214 3.508 0.160 0.371 - 160 4 3 148 153 154 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 161 4 3 149 167 168 0 1.143 1.171 1.190 3.504 0.165 0.341 - 162 4 3 150 155 156 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 165 3 1 159 0 1.211 1.378 2.000 -0.375 - 166 3 1 159 0 1.214 1.368 2.000 -0.399 - 167 3 2 154 161 0 0.267 1.171 1.446 2.000 -0.388 - 168 3 2 155 161 0 0.216 1.190 1.413 2.000 -0.411 - 169 1 3 174 170 181 0 1.332 1.324 1.109 3.767 0.000 -0.073 - 170 1 3 169 171 182 0 1.324 1.345 1.300 3.969 0.000 0.193 - 171 1 3 170 172 183 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 172 1 3 171 173 184 0 1.336 1.306 1.324 3.967 0.000 0.196 - 173 1 3 172 174 185 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 174 1 3 169 173 186 0 1.332 1.317 1.318 3.967 0.000 0.191 - 175 2 1 182 0 0.873 1.075 0.000 0.366 - 176 2 1 182 0 0.897 1.056 0.000 0.386 - 177 2 1 184 0 0.905 1.051 0.000 0.379 - 178 2 2 191 184 0 0.267 0.838 1.105 0.000 0.385 - 179 2 2 186 192 0 0.868 0.216 1.083 0.000 0.377 - 180 2 1 186 0 0.881 1.069 0.000 0.386 - 181 4 3 169 187 188 0 1.109 1.197 1.198 3.504 0.165 0.344 - 182 4 3 170 175 176 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 183 4 3 171 189 190 0 1.083 1.211 1.214 3.508 0.160 0.371 - 184 4 3 172 177 178 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 185 4 3 173 191 192 0 1.143 1.171 1.190 3.504 0.165 0.341 - 186 4 3 174 179 180 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 187 3 1 181 0 1.197 1.393 2.000 -0.381 - 188 3 1 181 0 1.198 1.407 2.000 -0.413 - 189 3 1 183 0 1.211 1.378 2.000 -0.375 - 190 3 1 183 0 1.214 1.368 2.000 -0.399 - 191 3 2 178 185 0 0.267 1.171 1.446 2.000 -0.388 - 192 3 2 179 185 0 0.216 1.190 1.413 2.000 -0.411 - 193 1 3 194 198 205 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 194 1 3 193 195 206 0 1.324 1.345 1.300 3.969 0.000 0.193 - 195 1 3 194 196 207 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 196 1 3 195 197 208 0 1.336 1.306 1.324 3.967 0.000 0.196 - 197 1 3 196 198 209 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 198 1 3 193 197 210 0 1.332 1.317 1.318 3.967 0.000 0.191 - 199 2 1 206 0 0.873 1.075 0.000 0.366 - 200 2 1 206 0 0.897 1.056 0.000 0.386 - 201 2 1 208 0 0.905 1.051 0.000 0.379 - 202 2 2 208 215 0 0.838 0.267 1.105 0.000 0.385 - 203 2 2 210 216 0 0.868 0.216 1.083 0.000 0.377 - 204 2 1 210 0 0.881 1.069 0.000 0.386 - 205 4 3 212 193 211 0 1.198 1.109 1.197 3.504 0.165 0.344 - 206 4 3 199 200 194 0 0.873 0.897 1.300 3.070 0.966 -0.469 - 207 4 3 195 213 214 0 1.083 1.211 1.214 3.508 0.160 0.371 - 208 4 3 196 201 202 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 209 4 3 197 215 216 0 1.143 1.171 1.190 3.504 0.165 0.341 - 210 4 3 198 203 204 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 211 3 1 205 0 1.197 1.393 2.000 -0.381 - 212 3 1 205 0 1.198 1.407 2.000 -0.413 - 213 3 1 207 0 1.211 1.378 2.000 -0.375 - 214 3 1 207 0 1.214 1.368 2.000 -0.399 - 215 3 2 202 209 0 0.267 1.171 1.446 2.000 -0.388 - 216 3 2 203 209 0 0.216 1.190 1.413 2.000 -0.411 - 217 1 3 218 222 229 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 218 1 3 217 219 230 0 1.324 1.345 1.300 3.969 0.000 0.193 - 219 1 3 218 220 231 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 220 1 3 219 221 232 0 1.336 1.306 1.324 3.967 0.000 0.196 - 221 1 3 220 222 233 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 222 1 3 217 221 234 0 1.332 1.317 1.318 3.967 0.000 0.191 - 223 2 1 230 0 0.873 1.075 0.000 0.366 - 224 2 1 230 0 0.897 1.056 0.000 0.386 - 225 2 1 232 0 0.905 1.051 0.000 0.379 - 226 2 2 239 232 0 0.267 0.838 1.105 0.000 0.385 - 227 2 2 234 240 0 0.868 0.216 1.083 0.000 0.377 - 228 2 1 234 0 0.881 1.069 0.000 0.386 - 229 4 3 217 235 236 0 1.109 1.197 1.198 3.504 0.165 0.344 - 230 4 3 218 223 224 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 231 4 3 219 237 238 0 1.083 1.211 1.214 3.508 0.160 0.371 - 232 4 3 225 226 220 0 0.905 0.838 1.324 3.068 0.968 -0.443 - 233 4 3 221 239 240 0 1.143 1.171 1.190 3.504 0.165 0.341 - 234 4 3 222 227 228 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 235 3 1 229 0 1.197 1.393 2.000 -0.381 - 236 3 1 229 0 1.198 1.407 2.000 -0.413 - 237 3 1 231 0 1.211 1.378 2.000 -0.375 - 238 3 1 231 0 1.214 1.368 2.000 -0.399 - 239 3 2 233 226 0 1.171 0.267 1.446 2.000 -0.388 - 240 3 2 227 233 0 0.216 1.190 1.413 2.000 -0.411 - 241 1 3 242 246 253 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 242 1 3 241 243 254 0 1.324 1.345 1.300 3.969 0.000 0.193 - 243 1 3 242 244 255 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 244 1 3 243 245 256 0 1.336 1.306 1.324 3.967 0.000 0.196 - 245 1 3 244 246 257 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 246 1 3 241 245 258 0 1.332 1.317 1.318 3.967 0.000 0.191 - 247 2 1 254 0 0.873 1.075 0.000 0.366 - 248 2 1 254 0 0.897 1.056 0.000 0.386 - 249 2 1 256 0 0.905 1.051 0.000 0.379 - 250 2 2 256 263 0 0.838 0.267 1.105 0.000 0.385 - 251 2 2 258 264 0 0.868 0.216 1.083 0.000 0.377 - 252 2 1 258 0 0.881 1.069 0.000 0.386 - 254 4 3 247 248 242 0 0.873 0.897 1.300 3.070 0.966 -0.469 - 255 4 3 243 261 262 0 1.083 1.211 1.214 3.508 0.160 0.371 - 256 4 3 244 249 250 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 257 4 3 245 263 264 0 1.143 1.171 1.190 3.504 0.165 0.341 - 258 4 3 246 251 252 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 261 3 1 255 0 1.211 1.378 2.000 -0.375 - 262 3 1 255 0 1.214 1.368 2.000 -0.399 - 263 3 2 250 257 0 0.267 1.171 1.446 2.000 -0.388 - 264 3 2 251 257 0 0.216 1.190 1.413 2.000 -0.411 - 265 1 3 266 270 277 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 266 1 3 265 267 278 0 1.324 1.345 1.300 3.969 0.000 0.193 - 267 1 3 266 268 279 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 268 1 3 267 269 280 0 1.336 1.306 1.324 3.967 0.000 0.196 - 269 1 3 268 270 281 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 270 1 3 265 269 282 0 1.332 1.317 1.318 3.967 0.000 0.191 - 271 2 1 278 0 0.873 1.075 0.000 0.366 - 272 2 1 278 0 0.897 1.056 0.000 0.386 - 273 2 1 280 0 0.905 1.051 0.000 0.379 - 274 2 2 287 280 0 0.267 0.838 1.105 0.000 0.385 - 275 2 2 282 288 0 0.868 0.216 1.083 0.000 0.377 - 276 2 1 282 0 0.881 1.069 0.000 0.386 - 277 4 3 265 283 284 0 1.109 1.197 1.198 3.504 0.165 0.344 - 278 4 3 266 271 272 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 279 4 3 267 285 286 0 1.083 1.211 1.214 3.508 0.160 0.371 - 280 4 3 273 274 268 0 0.905 0.838 1.324 3.068 0.968 -0.443 - 281 4 3 269 287 288 0 1.143 1.171 1.190 3.504 0.165 0.341 - 282 4 3 270 275 276 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 283 3 1 277 0 1.197 1.393 2.000 -0.381 - 284 3 1 277 0 1.198 1.407 2.000 -0.413 - 285 3 1 279 0 1.211 1.378 2.000 -0.375 - 286 3 1 279 0 1.214 1.368 2.000 -0.399 - 287 3 2 281 274 0 1.171 0.267 1.446 2.000 -0.388 - 288 3 2 275 281 0 0.216 1.190 1.413 2.000 -0.411 - 289 1 3 290 294 301 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 290 1 3 289 291 302 0 1.324 1.345 1.300 3.969 0.000 0.193 - 291 1 3 290 303 292 0 1.345 1.083 1.337 3.767 0.000 -0.060 - 292 1 3 291 293 304 0 1.337 1.306 1.324 3.967 0.000 0.196 - 293 1 3 292 294 305 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 294 1 3 289 293 306 0 1.332 1.317 1.318 3.967 0.000 0.191 - 295 2 1 302 0 0.873 1.075 0.000 0.366 - 296 2 1 302 0 0.897 1.056 0.000 0.386 - 297 2 1 304 0 0.905 1.051 0.000 0.379 - 298 2 2 311 304 0 0.267 0.838 1.105 0.000 0.385 - 299 2 2 312 306 0 0.216 0.868 1.083 0.000 0.377 - 300 2 1 306 0 0.881 1.069 0.000 0.386 - 301 4 3 289 308 307 0 1.109 1.198 1.197 3.504 0.165 0.344 - 302 4 3 290 295 296 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 303 4 3 291 309 310 0 1.083 1.211 1.214 3.508 0.160 0.371 - 304 4 3 292 297 298 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 305 4 3 293 311 312 0 1.143 1.171 1.190 3.504 0.165 0.341 - 306 4 3 294 299 300 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 307 3 1 301 0 1.197 1.393 2.000 -0.381 - 308 3 1 301 0 1.198 1.407 2.000 -0.413 - 309 3 1 303 0 1.211 1.378 2.000 -0.375 - 310 3 1 303 0 1.214 1.368 2.000 -0.399 - 311 3 2 298 305 0 0.267 1.171 1.446 2.000 -0.388 - 312 3 2 299 305 0 0.216 1.190 1.413 2.000 -0.411 - 313 1 3 314 318 325 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 314 1 3 313 315 326 0 1.324 1.345 1.300 3.969 0.000 0.193 - 315 1 3 314 316 327 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 316 1 3 315 317 328 0 1.336 1.306 1.324 3.967 0.000 0.196 - 317 1 3 316 318 329 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 318 1 3 313 317 330 0 1.332 1.317 1.318 3.967 0.000 0.191 - 319 2 1 326 0 0.873 1.075 0.000 0.366 - 320 2 1 326 0 0.897 1.056 0.000 0.386 - 321 2 1 328 0 0.905 1.051 0.000 0.379 - 322 2 2 335 328 0 0.267 0.838 1.105 0.000 0.385 - 323 2 2 330 336 0 0.868 0.216 1.083 0.000 0.377 - 324 2 1 330 0 0.881 1.069 0.000 0.386 - 325 4 3 313 331 332 0 1.109 1.197 1.198 3.504 0.165 0.344 - 326 4 3 314 320 319 0 1.300 0.897 0.873 3.070 0.966 -0.469 - 327 4 3 315 333 334 0 1.083 1.211 1.214 3.508 0.160 0.371 - 328 4 3 321 322 316 0 0.905 0.838 1.324 3.068 0.968 -0.443 - 329 4 3 317 335 336 0 1.143 1.171 1.190 3.504 0.165 0.341 - 330 4 3 318 323 324 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 331 3 1 325 0 1.197 1.393 2.000 -0.381 - 332 3 1 325 0 1.198 1.407 2.000 -0.413 - 333 3 1 327 0 1.211 1.378 2.000 -0.375 - 334 3 1 327 0 1.214 1.368 2.000 -0.399 - 335 3 2 329 322 0 1.171 0.267 1.446 2.000 -0.388 - 336 3 2 323 329 0 0.216 1.190 1.413 2.000 -0.411 - 337 1 3 338 342 349 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 338 1 3 337 339 350 0 1.324 1.345 1.300 3.969 0.000 0.193 - 339 1 3 338 351 340 0 1.345 1.083 1.337 3.767 0.000 -0.060 - 340 1 3 339 341 352 0 1.337 1.306 1.324 3.967 0.000 0.196 - 341 1 3 340 342 353 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 342 1 3 337 341 354 0 1.332 1.317 1.318 3.967 0.000 0.191 - 343 2 1 350 0 0.873 1.075 0.000 0.366 - 344 2 1 350 0 0.897 1.056 0.000 0.386 - 345 2 1 352 0 0.905 1.051 0.000 0.379 - 346 2 2 352 359 0 0.838 0.267 1.105 0.000 0.385 - 347 2 2 360 354 0 0.216 0.868 1.083 0.000 0.377 - 348 2 1 354 0 0.881 1.069 0.000 0.386 - 350 4 3 338 343 344 0 1.300 0.873 0.897 3.070 0.966 -0.469 - 351 4 3 339 357 358 0 1.083 1.211 1.214 3.508 0.160 0.371 - 352 4 3 340 345 346 0 1.324 0.905 0.838 3.068 0.968 -0.443 - 353 4 3 341 360 359 0 1.143 1.190 1.171 3.504 0.165 0.341 - 354 4 3 342 347 348 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 357 3 1 351 0 1.211 1.378 2.000 -0.375 - 358 3 1 351 0 1.214 1.368 2.000 -0.399 - 359 3 2 346 353 0 0.267 1.171 1.446 2.000 -0.388 - 360 3 2 347 353 0 0.216 1.190 1.413 2.000 -0.411 - 361 1 3 362 366 373 0 1.324 1.332 1.109 3.767 0.000 -0.073 - 362 1 3 361 363 374 0 1.324 1.345 1.300 3.969 0.000 0.193 - 363 1 3 362 364 375 0 1.345 1.336 1.083 3.767 0.000 -0.060 - 364 1 3 363 365 376 0 1.336 1.306 1.324 3.967 0.000 0.196 - 365 1 3 364 366 377 0 1.306 1.317 1.143 3.769 0.000 -0.063 - 366 1 3 361 365 378 0 1.332 1.317 1.318 3.967 0.000 0.191 - 367 2 1 374 0 0.873 1.075 0.000 0.366 - 368 2 1 374 0 0.897 1.056 0.000 0.386 - 369 2 1 376 0 0.905 1.051 0.000 0.379 - 370 2 2 383 376 0 0.267 0.838 1.105 0.000 0.385 - 371 2 2 378 384 0 0.868 0.216 1.083 0.000 0.377 - 372 2 1 378 0 0.881 1.069 0.000 0.386 - 373 4 3 361 379 380 0 1.109 1.197 1.198 3.504 0.165 0.344 - 374 4 3 362 368 367 0 1.300 0.897 0.873 3.070 0.966 -0.469 - 375 4 3 363 381 382 0 1.083 1.211 1.214 3.508 0.160 0.371 - 376 4 3 369 370 364 0 0.905 0.838 1.324 3.068 0.968 -0.443 - 377 4 3 365 383 384 0 1.143 1.171 1.190 3.504 0.165 0.341 - 378 4 3 366 371 372 0 1.318 0.868 0.881 3.067 0.969 -0.438 - 379 3 1 373 0 1.197 1.393 2.000 -0.381 - 380 3 1 373 0 1.198 1.407 2.000 -0.413 - 381 3 1 375 0 1.211 1.378 2.000 -0.375 - 382 3 1 375 0 1.214 1.368 2.000 -0.399 - 383 3 2 377 370 0 1.171 0.267 1.446 2.000 -0.388 - 384 3 2 371 377 0 0.216 1.190 1.413 2.000 -0.411 - 61 4 3 49 68 67 0 1.109 1.198 1.197 3.504 0.165 0.344 - 67 3 1 61 0 1.197 1.393 2.000 -0.381 - 68 3 1 61 0 1.198 1.407 2.000 -0.413 - 157 4 3 164 145 163 0 1.198 1.109 1.197 3.504 0.165 0.344 - 163 3 1 157 0 1.197 1.393 2.000 -0.381 - 164 3 1 157 0 1.198 1.407 2.000 -0.413 - 253 4 3 260 241 259 0 1.198 1.109 1.197 3.504 0.165 0.344 - 259 3 1 253 0 1.197 1.393 2.000 -0.381 - 260 3 1 253 0 1.198 1.407 2.000 -0.413 - 349 4 3 337 356 355 0 1.109 1.198 1.197 3.504 0.165 0.344 - 355 3 1 349 0 1.197 1.393 2.000 -0.381 - 356 3 1 349 0 1.198 1.407 2.000 -0.413 -# -# Timestep 25 -# -# Number of particles 384 -# -# Max.number of bonds per atom 3 with coarse bond order cutoff 0.300 -# Particle connection table and bond orders -# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q - 1 1 3 2 6 13 0 1.321 1.328 1.129 3.783 0.000 -0.075 - 2 1 3 1 3 14 0 1.321 1.341 1.325 3.987 0.000 0.190 - 3 1 3 2 4 15 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 4 1 3 3 5 16 0 1.333 1.303 1.350 3.985 0.000 0.194 - 5 1 3 4 6 17 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 6 1 3 1 5 18 0 1.328 1.313 1.344 3.985 0.000 0.188 - 7 2 2 14 20 0 0.855 0.269 1.123 0.000 0.366 - 8 2 2 14 21 0 0.878 0.236 1.114 0.000 0.387 - 9 2 2 16 22 0 0.885 0.232 1.116 0.000 0.380 - 10 2 2 16 23 0 0.827 0.291 1.118 0.000 0.385 - 11 2 2 18 24 0 0.852 0.273 1.124 0.000 0.377 - 12 2 2 18 19 0 0.862 0.262 1.125 0.000 0.387 - 13 4 3 1 20 19 0 1.129 1.232 1.231 3.591 0.083 0.362 - 14 4 3 2 7 8 0 1.325 0.855 0.878 3.058 0.977 -0.457 - 15 4 3 3 21 22 0 1.103 1.245 1.247 3.595 0.081 0.390 - 16 4 3 4 9 10 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 17 4 3 5 23 24 0 1.161 1.206 1.224 3.591 0.084 0.359 - 18 4 3 6 11 12 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 19 3 2 12 13 0 0.262 1.231 1.504 2.000 -0.395 - 20 3 2 7 13 0 0.269 1.232 1.511 2.000 -0.426 - 21 3 2 8 15 0 0.236 1.245 1.491 2.000 -0.389 - 22 3 2 9 15 0 0.232 1.247 1.489 2.000 -0.415 - 23 3 2 10 17 0 0.291 1.206 1.508 2.000 -0.397 - 24 3 2 11 17 0 0.273 1.224 1.507 2.000 -0.422 - 25 1 3 30 26 37 0 1.328 1.321 1.129 3.783 0.000 -0.075 - 26 1 3 25 27 38 0 1.321 1.341 1.325 3.987 0.000 0.190 - 27 1 3 26 28 39 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 28 1 3 27 29 40 0 1.333 1.303 1.350 3.985 0.000 0.194 - 29 1 3 28 30 41 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 30 1 3 25 29 42 0 1.328 1.313 1.344 3.985 0.000 0.188 - 31 2 2 44 38 0 0.269 0.855 1.123 0.000 0.366 - 32 2 2 38 45 0 0.878 0.236 1.114 0.000 0.387 - 33 2 2 40 46 0 0.885 0.232 1.116 0.000 0.380 - 34 2 2 47 40 0 0.291 0.827 1.118 0.000 0.385 - 35 2 2 42 48 0 0.852 0.273 1.124 0.000 0.377 - 36 2 2 42 43 0 0.862 0.262 1.125 0.000 0.387 - 37 4 3 25 43 44 0 1.129 1.231 1.232 3.591 0.083 0.362 - 38 4 3 26 32 31 0 1.325 0.878 0.855 3.058 0.977 -0.457 - 39 4 3 27 45 46 0 1.103 1.245 1.247 3.595 0.081 0.390 - 40 4 3 28 33 34 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 41 4 3 29 47 48 0 1.161 1.206 1.224 3.591 0.084 0.359 - 42 4 3 30 35 36 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 43 3 2 36 37 0 0.262 1.231 1.504 2.000 -0.395 - 44 3 2 31 37 0 0.269 1.232 1.511 2.000 -0.426 - 45 3 2 32 39 0 0.236 1.245 1.491 2.000 -0.389 - 46 3 2 33 39 0 0.232 1.247 1.489 2.000 -0.415 - 47 3 2 34 41 0 0.291 1.206 1.508 2.000 -0.397 - 48 3 2 35 41 0 0.273 1.224 1.507 2.000 -0.422 - 49 1 3 50 54 61 0 1.321 1.328 1.129 3.783 0.000 -0.075 - 50 1 3 49 51 62 0 1.321 1.341 1.325 3.987 0.000 0.190 - 51 1 3 50 52 63 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 52 1 3 51 53 64 0 1.333 1.303 1.350 3.985 0.000 0.194 - 53 1 3 52 54 65 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 54 1 3 49 53 66 0 1.328 1.313 1.344 3.985 0.000 0.188 - 55 2 2 62 68 0 0.855 0.269 1.123 0.000 0.366 - 56 2 2 62 69 0 0.878 0.236 1.114 0.000 0.387 - 57 2 2 64 70 0 0.885 0.232 1.116 0.000 0.380 - 58 2 2 64 71 0 0.827 0.291 1.118 0.000 0.385 - 59 2 2 66 72 0 0.852 0.273 1.124 0.000 0.377 - 60 2 2 66 67 0 0.862 0.262 1.125 0.000 0.387 - 62 4 3 50 55 56 0 1.325 0.855 0.878 3.058 0.977 -0.457 - 63 4 3 51 69 70 0 1.103 1.245 1.247 3.595 0.081 0.390 - 64 4 3 52 57 58 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 65 4 3 53 71 72 0 1.161 1.206 1.224 3.591 0.084 0.359 - 66 4 3 54 59 60 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 69 3 2 56 63 0 0.236 1.245 1.491 2.000 -0.389 - 70 3 2 57 63 0 0.232 1.247 1.489 2.000 -0.415 - 71 3 2 58 65 0 0.291 1.206 1.508 2.000 -0.397 - 72 3 2 59 65 0 0.273 1.224 1.507 2.000 -0.422 - 73 1 3 78 74 85 0 1.328 1.321 1.129 3.783 0.000 -0.075 - 74 1 3 73 75 86 0 1.321 1.341 1.325 3.987 0.000 0.190 - 75 1 3 74 76 87 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 76 1 3 75 77 88 0 1.333 1.303 1.350 3.985 0.000 0.194 - 77 1 3 76 78 89 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 78 1 3 73 77 90 0 1.328 1.313 1.344 3.985 0.000 0.188 - 79 2 2 92 86 0 0.269 0.855 1.123 0.000 0.366 - 80 2 2 86 93 0 0.878 0.236 1.114 0.000 0.387 - 81 2 2 88 94 0 0.885 0.232 1.116 0.000 0.380 - 82 2 2 95 88 0 0.291 0.827 1.118 0.000 0.385 - 83 2 2 90 96 0 0.852 0.273 1.124 0.000 0.377 - 84 2 2 90 91 0 0.862 0.262 1.125 0.000 0.387 - 85 4 3 73 91 92 0 1.129 1.231 1.232 3.591 0.083 0.362 - 86 4 3 74 80 79 0 1.325 0.878 0.855 3.058 0.977 -0.457 - 87 4 3 75 93 94 0 1.103 1.245 1.247 3.595 0.081 0.390 - 88 4 3 76 81 82 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 89 4 3 77 95 96 0 1.161 1.206 1.224 3.591 0.084 0.359 - 90 4 3 78 83 84 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 91 3 2 84 85 0 0.262 1.231 1.504 2.000 -0.395 - 92 3 2 79 85 0 0.269 1.232 1.511 2.000 -0.426 - 93 3 2 80 87 0 0.236 1.245 1.491 2.000 -0.389 - 94 3 2 81 87 0 0.232 1.247 1.489 2.000 -0.415 - 95 3 2 82 89 0 0.291 1.206 1.508 2.000 -0.397 - 96 3 2 83 89 0 0.273 1.224 1.507 2.000 -0.422 - 97 1 3 109 98 102 0 1.129 1.321 1.328 3.783 0.000 -0.075 - 98 1 3 99 97 110 0 1.341 1.321 1.325 3.987 0.000 0.190 - 99 1 3 98 100 111 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 100 1 3 99 101 112 0 1.333 1.303 1.350 3.985 0.000 0.194 - 101 1 3 100 113 102 0 1.303 1.161 1.313 3.784 0.000 -0.066 - 102 1 3 101 114 97 0 1.313 1.344 1.328 3.985 0.000 0.188 - 103 2 2 110 116 0 0.855 0.269 1.123 0.000 0.366 - 104 2 2 110 117 0 0.878 0.236 1.114 0.000 0.387 - 105 2 2 112 118 0 0.885 0.232 1.116 0.000 0.380 - 106 2 2 119 112 0 0.291 0.827 1.118 0.000 0.385 - 107 2 2 114 120 0 0.852 0.273 1.124 0.000 0.377 - 108 2 2 114 115 0 0.862 0.262 1.125 0.000 0.387 - 109 4 3 97 116 115 0 1.129 1.232 1.231 3.591 0.083 0.362 - 110 4 3 103 104 98 0 0.855 0.878 1.325 3.058 0.977 -0.457 - 111 4 3 99 117 118 0 1.103 1.245 1.247 3.595 0.081 0.390 - 112 4 3 100 105 106 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 113 4 3 101 119 120 0 1.161 1.206 1.224 3.591 0.084 0.359 - 114 4 3 102 107 108 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 115 3 2 109 108 0 1.231 0.262 1.504 2.000 -0.395 - 116 3 2 103 109 0 0.269 1.232 1.511 2.000 -0.426 - 117 3 2 111 104 0 1.245 0.236 1.491 2.000 -0.389 - 118 3 2 105 111 0 0.232 1.247 1.489 2.000 -0.415 - 119 3 2 106 113 0 0.291 1.206 1.508 2.000 -0.397 - 120 3 2 107 113 0 0.273 1.224 1.507 2.000 -0.422 - 121 1 3 126 122 133 0 1.328 1.321 1.129 3.783 0.000 -0.075 - 122 1 3 121 123 134 0 1.321 1.341 1.325 3.987 0.000 0.190 - 123 1 3 122 124 135 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 124 1 3 123 125 136 0 1.333 1.303 1.350 3.985 0.000 0.194 - 125 1 3 124 126 137 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 126 1 3 121 125 138 0 1.328 1.313 1.344 3.985 0.000 0.188 - 127 2 2 134 140 0 0.855 0.269 1.123 0.000 0.366 - 128 2 2 134 141 0 0.878 0.236 1.114 0.000 0.387 - 129 2 2 136 142 0 0.885 0.232 1.116 0.000 0.380 - 130 2 2 143 136 0 0.291 0.827 1.118 0.000 0.385 - 131 2 2 138 144 0 0.852 0.273 1.124 0.000 0.377 - 132 2 2 138 139 0 0.862 0.262 1.125 0.000 0.387 - 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151 2 2 158 164 0 0.855 0.269 1.123 0.000 0.366 - 152 2 2 158 165 0 0.878 0.236 1.114 0.000 0.387 - 153 2 2 160 166 0 0.885 0.232 1.116 0.000 0.380 - 154 2 2 167 160 0 0.291 0.827 1.118 0.000 0.385 - 155 2 2 168 162 0 0.273 0.852 1.124 0.000 0.377 - 156 2 2 162 163 0 0.862 0.262 1.125 0.000 0.387 - 158 4 3 151 152 146 0 0.855 0.878 1.325 3.058 0.977 -0.457 - 159 4 3 147 165 166 0 1.103 1.245 1.247 3.595 0.081 0.390 - 160 4 3 148 153 154 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 161 4 3 149 167 168 0 1.161 1.206 1.224 3.591 0.084 0.359 - 162 4 3 150 155 156 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 165 3 2 159 152 0 1.245 0.236 1.491 2.000 -0.389 - 166 3 2 153 159 0 0.232 1.247 1.489 2.000 -0.415 - 167 3 2 154 161 0 0.291 1.206 1.508 2.000 -0.397 - 168 3 2 155 161 0 0.273 1.224 1.507 2.000 -0.422 - 169 1 3 174 170 181 0 1.328 1.321 1.129 3.783 0.000 -0.075 - 170 1 3 169 171 182 0 1.321 1.341 1.325 3.987 0.000 0.190 - 171 1 3 170 172 183 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 172 1 3 171 173 184 0 1.333 1.303 1.350 3.985 0.000 0.194 - 173 1 3 172 174 185 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 174 1 3 169 173 186 0 1.328 1.313 1.344 3.985 0.000 0.188 - 175 2 2 182 188 0 0.855 0.269 1.123 0.000 0.366 - 176 2 2 182 189 0 0.878 0.236 1.114 0.000 0.387 - 177 2 2 184 190 0 0.885 0.232 1.116 0.000 0.380 - 178 2 2 191 184 0 0.291 0.827 1.118 0.000 0.385 - 179 2 2 186 192 0 0.852 0.273 1.124 0.000 0.377 - 180 2 2 186 187 0 0.862 0.262 1.125 0.000 0.387 - 181 4 3 169 187 188 0 1.129 1.231 1.232 3.591 0.083 0.362 - 182 4 3 170 175 176 0 1.325 0.855 0.878 3.058 0.977 -0.457 - 183 4 3 171 189 190 0 1.103 1.245 1.247 3.595 0.081 0.390 - 184 4 3 172 177 178 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 185 4 3 173 191 192 0 1.161 1.206 1.224 3.591 0.084 0.359 - 186 4 3 174 179 180 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 187 3 2 180 181 0 0.262 1.231 1.504 2.000 -0.395 - 188 3 2 175 181 0 0.269 1.232 1.511 2.000 -0.426 - 189 3 2 176 183 0 0.236 1.245 1.491 2.000 -0.389 - 190 3 2 177 183 0 0.232 1.247 1.489 2.000 -0.415 - 191 3 2 178 185 0 0.291 1.206 1.508 2.000 -0.397 - 192 3 2 179 185 0 0.273 1.224 1.507 2.000 -0.422 - 193 1 3 205 194 198 0 1.129 1.321 1.328 3.783 0.000 -0.075 - 194 1 3 195 193 206 0 1.341 1.321 1.325 3.987 0.000 0.190 - 195 1 3 194 196 207 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 196 1 3 195 197 208 0 1.333 1.303 1.350 3.985 0.000 0.194 - 197 1 3 196 198 209 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 198 1 3 197 193 210 0 1.313 1.328 1.344 3.985 0.000 0.188 - 199 2 2 206 212 0 0.855 0.269 1.123 0.000 0.366 - 200 2 2 206 213 0 0.878 0.236 1.114 0.000 0.387 - 201 2 2 214 208 0 0.232 0.885 1.116 0.000 0.380 - 202 2 2 208 215 0 0.827 0.291 1.118 0.000 0.385 - 203 2 2 210 216 0 0.852 0.273 1.124 0.000 0.377 - 204 2 2 210 211 0 0.862 0.262 1.125 0.000 0.387 - 205 4 3 193 212 211 0 1.129 1.232 1.231 3.591 0.083 0.362 - 206 4 3 199 200 194 0 0.855 0.878 1.325 3.058 0.977 -0.457 - 207 4 3 195 213 214 0 1.103 1.245 1.247 3.595 0.081 0.390 - 208 4 3 196 201 202 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 209 4 3 197 215 216 0 1.161 1.206 1.224 3.591 0.084 0.359 - 210 4 3 198 203 204 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 211 3 2 205 204 0 1.231 0.262 1.504 2.000 -0.395 - 212 3 2 199 205 0 0.269 1.232 1.511 2.000 -0.426 - 213 3 2 207 200 0 1.245 0.236 1.491 2.000 -0.389 - 214 3 2 201 207 0 0.232 1.247 1.489 2.000 -0.415 - 215 3 2 202 209 0 0.291 1.206 1.508 2.000 -0.397 - 216 3 2 203 209 0 0.273 1.224 1.507 2.000 -0.422 - 217 1 3 218 222 229 0 1.321 1.328 1.129 3.783 0.000 -0.075 - 218 1 3 217 219 230 0 1.321 1.341 1.325 3.987 0.000 0.190 - 219 1 3 218 220 231 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 220 1 3 219 221 232 0 1.333 1.303 1.350 3.985 0.000 0.194 - 221 1 3 220 222 233 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 222 1 3 217 221 234 0 1.328 1.313 1.344 3.985 0.000 0.188 - 223 2 2 230 236 0 0.855 0.269 1.123 0.000 0.366 - 224 2 2 230 237 0 0.878 0.236 1.114 0.000 0.387 - 225 2 2 232 238 0 0.885 0.232 1.116 0.000 0.380 - 226 2 2 239 232 0 0.291 0.827 1.118 0.000 0.385 - 227 2 2 234 240 0 0.852 0.273 1.124 0.000 0.377 - 228 2 2 234 235 0 0.862 0.262 1.125 0.000 0.387 - 229 4 3 217 235 236 0 1.129 1.231 1.232 3.591 0.083 0.362 - 230 4 3 218 223 224 0 1.325 0.855 0.878 3.058 0.977 -0.457 - 231 4 3 219 237 238 0 1.103 1.245 1.247 3.595 0.081 0.390 - 232 4 3 225 226 220 0 0.885 0.827 1.350 3.061 0.974 -0.433 - 233 4 3 221 239 240 0 1.161 1.206 1.224 3.591 0.084 0.359 - 234 4 3 222 227 228 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 235 3 2 228 229 0 0.262 1.231 1.504 2.000 -0.395 - 236 3 2 223 229 0 0.269 1.232 1.511 2.000 -0.426 - 237 3 2 231 224 0 1.245 0.236 1.491 2.000 -0.389 - 238 3 2 225 231 0 0.232 1.247 1.489 2.000 -0.415 - 239 3 2 233 226 0 1.206 0.291 1.508 2.000 -0.397 - 240 3 2 227 233 0 0.273 1.224 1.507 2.000 -0.422 - 241 1 3 253 242 246 0 1.129 1.321 1.328 3.783 0.000 -0.075 - 242 1 3 243 241 254 0 1.341 1.321 1.325 3.987 0.000 0.190 - 243 1 3 242 244 255 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 244 1 3 243 245 256 0 1.333 1.303 1.350 3.985 0.000 0.194 - 245 1 3 244 246 257 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 246 1 3 245 241 258 0 1.313 1.328 1.344 3.985 0.000 0.188 - 247 2 2 254 260 0 0.855 0.269 1.123 0.000 0.366 - 248 2 2 254 261 0 0.878 0.236 1.114 0.000 0.387 - 249 2 2 262 256 0 0.232 0.885 1.116 0.000 0.380 - 250 2 2 256 263 0 0.827 0.291 1.118 0.000 0.385 - 251 2 2 258 264 0 0.852 0.273 1.124 0.000 0.377 - 252 2 2 258 259 0 0.862 0.262 1.125 0.000 0.387 - 254 4 3 247 248 242 0 0.855 0.878 1.325 3.058 0.977 -0.457 - 255 4 3 243 261 262 0 1.103 1.245 1.247 3.595 0.081 0.390 - 256 4 3 244 249 250 0 1.350 0.885 0.827 3.061 0.974 -0.433 - 257 4 3 245 263 264 0 1.161 1.206 1.224 3.591 0.084 0.359 - 258 4 3 246 251 252 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 261 3 2 255 248 0 1.245 0.236 1.491 2.000 -0.389 - 262 3 2 249 255 0 0.232 1.247 1.489 2.000 -0.415 - 263 3 2 250 257 0 0.291 1.206 1.508 2.000 -0.397 - 264 3 2 251 257 0 0.273 1.224 1.507 2.000 -0.422 - 265 1 3 266 270 277 0 1.321 1.328 1.129 3.783 0.000 -0.075 - 266 1 3 265 267 278 0 1.321 1.341 1.325 3.987 0.000 0.190 - 267 1 3 266 268 279 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 268 1 3 267 269 280 0 1.333 1.303 1.350 3.985 0.000 0.194 - 269 1 3 268 270 281 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 270 1 3 265 269 282 0 1.328 1.313 1.344 3.985 0.000 0.188 - 271 2 2 278 284 0 0.855 0.269 1.123 0.000 0.366 - 272 2 2 278 285 0 0.878 0.236 1.114 0.000 0.387 - 273 2 2 280 286 0 0.885 0.232 1.116 0.000 0.380 - 274 2 2 287 280 0 0.291 0.827 1.118 0.000 0.385 - 275 2 2 282 288 0 0.852 0.273 1.124 0.000 0.377 - 276 2 2 282 283 0 0.862 0.262 1.125 0.000 0.387 - 277 4 3 265 283 284 0 1.129 1.231 1.232 3.591 0.083 0.362 - 278 4 3 266 271 272 0 1.325 0.855 0.878 3.058 0.977 -0.457 - 279 4 3 267 285 286 0 1.103 1.245 1.247 3.595 0.081 0.390 - 280 4 3 273 274 268 0 0.885 0.827 1.350 3.061 0.974 -0.433 - 281 4 3 269 287 288 0 1.161 1.206 1.224 3.591 0.084 0.359 - 282 4 3 270 275 276 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 283 3 2 276 277 0 0.262 1.231 1.504 2.000 -0.395 - 284 3 2 271 277 0 0.269 1.232 1.511 2.000 -0.426 - 285 3 2 279 272 0 1.245 0.236 1.491 2.000 -0.389 - 286 3 2 273 279 0 0.232 1.247 1.489 2.000 -0.415 - 287 3 2 281 274 0 1.206 0.291 1.508 2.000 -0.397 - 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306 4 3 294 299 300 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 307 3 2 300 301 0 0.262 1.231 1.504 2.000 -0.395 - 308 3 2 295 301 0 0.269 1.232 1.511 2.000 -0.426 - 309 3 2 296 303 0 0.236 1.245 1.491 2.000 -0.389 - 310 3 2 297 303 0 0.232 1.247 1.489 2.000 -0.415 - 311 3 2 298 305 0 0.291 1.206 1.508 2.000 -0.397 - 312 3 2 299 305 0 0.273 1.224 1.507 2.000 -0.422 - 313 1 3 314 318 325 0 1.321 1.328 1.129 3.783 0.000 -0.075 - 314 1 3 313 315 326 0 1.321 1.341 1.325 3.987 0.000 0.190 - 315 1 3 314 316 327 0 1.341 1.333 1.103 3.783 0.000 -0.063 - 316 1 3 315 317 328 0 1.333 1.303 1.350 3.985 0.000 0.194 - 317 1 3 316 318 329 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 318 1 3 313 317 330 0 1.328 1.313 1.344 3.985 0.000 0.188 - 319 2 2 332 326 0 0.269 0.855 1.123 0.000 0.366 - 320 2 2 326 333 0 0.878 0.236 1.114 0.000 0.387 - 321 2 2 328 334 0 0.885 0.232 1.116 0.000 0.380 - 322 2 2 335 328 0 0.291 0.827 1.118 0.000 0.385 - 323 2 2 330 336 0 0.852 0.273 1.124 0.000 0.377 - 324 2 2 330 331 0 0.862 0.262 1.125 0.000 0.387 - 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365 1 3 364 366 377 0 1.303 1.313 1.161 3.784 0.000 -0.066 - 366 1 3 361 365 378 0 1.328 1.313 1.344 3.985 0.000 0.188 - 367 2 2 380 374 0 0.269 0.855 1.123 0.000 0.366 - 368 2 2 374 381 0 0.878 0.236 1.114 0.000 0.387 - 369 2 2 376 382 0 0.885 0.232 1.116 0.000 0.380 - 370 2 2 383 376 0 0.291 0.827 1.118 0.000 0.385 - 371 2 2 378 384 0 0.852 0.273 1.124 0.000 0.377 - 372 2 2 378 379 0 0.862 0.262 1.125 0.000 0.387 - 373 4 3 361 379 380 0 1.129 1.231 1.232 3.591 0.083 0.362 - 374 4 3 362 368 367 0 1.325 0.878 0.855 3.058 0.977 -0.457 - 375 4 3 363 381 382 0 1.103 1.245 1.247 3.595 0.081 0.390 - 376 4 3 369 370 364 0 0.885 0.827 1.350 3.061 0.974 -0.433 - 377 4 3 365 383 384 0 1.161 1.206 1.224 3.591 0.084 0.359 - 378 4 3 366 371 372 0 1.344 0.852 0.862 3.058 0.977 -0.427 - 379 3 2 372 373 0 0.262 1.231 1.504 2.000 -0.395 - 380 3 2 367 373 0 0.269 1.232 1.511 2.000 -0.426 - 381 3 2 375 368 0 1.245 0.236 1.491 2.000 -0.389 - 382 3 2 369 375 0 0.232 1.247 1.489 2.000 -0.415 - 383 3 2 377 370 0 1.206 0.291 1.508 2.000 -0.397 - 384 3 2 371 377 0 0.273 1.224 1.507 2.000 -0.422 - 61 4 3 49 68 67 0 1.129 1.232 1.231 3.591 0.083 0.362 - 67 3 2 60 61 0 0.262 1.231 1.504 2.000 -0.395 - 68 3 2 55 61 0 0.269 1.232 1.511 2.000 -0.426 - 157 4 3 145 164 163 0 1.129 1.232 1.231 3.591 0.083 0.362 - 163 3 2 157 156 0 1.231 0.262 1.504 2.000 -0.395 - 164 3 2 151 157 0 0.269 1.232 1.511 2.000 -0.426 - 253 4 3 241 260 259 0 1.129 1.232 1.231 3.591 0.083 0.362 - 259 3 2 253 252 0 1.231 0.262 1.504 2.000 -0.395 - 260 3 2 247 253 0 0.269 1.232 1.511 2.000 -0.426 - 349 4 3 337 356 355 0 1.129 1.232 1.231 3.591 0.083 0.362 - 355 3 2 348 349 0 0.262 1.231 1.504 2.000 -0.395 - 356 3 2 343 349 0 0.269 1.232 1.511 2.000 -0.426 -#