From dd567c0c0f5fa7a922ad62b841da1108fb3318a4 Mon Sep 17 00:00:00 2001 From: Ken-ichi Nomura Date: Wed, 9 Jan 2019 04:47:00 -0800 Subject: [PATCH] added examples removed polyethylene.xyz --- examples/1-reaxff/Makefile | 10 ++ examples/1-reaxff/ffield | 219 ++++++++++++++++++++++++++++ examples/1-reaxff/input.xyz | 14 ++ examples/1-reaxff/rxmd.in | 9 ++ examples/2-reaxff-dc/Makefile | 10 ++ examples/2-reaxff-dc/ffield | 219 ++++++++++++++++++++++++++++ examples/2-reaxff-dc/input.xyz | 14 ++ examples/2-reaxff-dc/rxmd.in | 9 ++ examples/3-reaxpq+/Makefile | 10 ++ examples/3-reaxpq+/ffield | 219 ++++++++++++++++++++++++++++ examples/3-reaxpq+/input.xyz | 14 ++ examples/3-reaxpq+/pqeq1.par | 15 ++ examples/3-reaxpq+/rxmd.in | 9 ++ examples/4-reaxpq+-efield/Makefile | 10 ++ examples/4-reaxpq+-efield/ffield | 219 ++++++++++++++++++++++++++++ examples/4-reaxpq+-efield/input.xyz | 14 ++ examples/4-reaxpq+-efield/pqeq1.par | 15 ++ examples/4-reaxpq+-efield/rxmd.in | 9 ++ init/polyethylene.xyz | 14 -- 19 files changed, 1038 insertions(+), 14 deletions(-) create mode 100644 examples/1-reaxff/Makefile create mode 100644 examples/1-reaxff/ffield create mode 100644 examples/1-reaxff/input.xyz create mode 100644 examples/1-reaxff/rxmd.in create mode 100644 examples/2-reaxff-dc/Makefile create mode 100644 examples/2-reaxff-dc/ffield create mode 100644 examples/2-reaxff-dc/input.xyz create mode 100644 examples/2-reaxff-dc/rxmd.in create mode 100644 examples/3-reaxpq+/Makefile create mode 100644 examples/3-reaxpq+/ffield create mode 100644 examples/3-reaxpq+/input.xyz create mode 100644 examples/3-reaxpq+/pqeq1.par create mode 100644 examples/3-reaxpq+/rxmd.in create mode 100644 examples/4-reaxpq+-efield/Makefile create mode 100644 examples/4-reaxpq+-efield/ffield create mode 100644 examples/4-reaxpq+-efield/input.xyz create mode 100644 examples/4-reaxpq+-efield/pqeq1.par create mode 100644 examples/4-reaxpq+-efield/rxmd.in delete mode 100644 init/polyethylene.xyz diff --git a/examples/1-reaxff/Makefile b/examples/1-reaxff/Makefile new file mode 100644 index 0000000..cd9ca5a --- /dev/null +++ b/examples/1-reaxff/Makefile @@ -0,0 +1,10 @@ +set: + cp -v ../../init/geninit . + cp -v ../../rxmd . + ./geninit -i input.xyz -f ffield -o DAT/ -mc 2 3 5 + +run: + mpirun -np 1 ./rxmd + +clean: + rm -fv geninit* rxmd DAT/* diff --git a/examples/1-reaxff/ffield b/examples/1-reaxff/ffield new file mode 100644 index 0000000..a5199d8 --- /dev/null +++ b/examples/1-reaxff/ffield @@ -0,0 +1,219 @@ +Reactive MD-force field: nitramines (RDX/HMX/TATB/PETN) + 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) + 0.0000 !Molecular energy (not used) + 6.5560 !Valency angle conjugation parameter + 7 ! 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 + S 1.9647 2.0000 32.0600 2.0783 0.2176 1.0336 1.5386 6.0000 + 9.9676 5.0812 4.0000 35.1648 112.1416 6.5000 8.2545 2.0000 + 1.4703 9.4922 70.0338 8.5146 28.0801 8.5010 0.9745 0.0000 + -10.0773 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000 + Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000 + 11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000 + -1.0000 0.0000 126.5331 6.4918 8.5961 0.2368 0.8563 0.0000 + -3.8112 3.1873 1.0338 4.0000 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 4.0000 2.8793 0.0000 0.0000 0.0000 + 18 ! 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 + 1 5 128.7959 56.4134 39.0716 0.0688 -0.4463 1.0000 31.1766 0.4530 + 0.1955 -0.3587 6.2148 1.0000 -0.0770 6.6386 1.0000 0.0000 + 2 5 128.6090 0.0000 0.0000 -0.5555 0.0000 1.0000 6.0000 0.4721 + 10.8735 1.0000 0.0000 1.0000 -0.0242 9.1937 1.0000 0.0000 + 3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000 + 0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000 + 4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000 + 0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000 + 5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000 + 0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000 + 6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583 + 0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000 + 2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256 + 17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000 + 3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764 + 1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000 + 10 ! 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 + 2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000 + 3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000 + 1 5 0.1408 1.8161 9.9393 1.7986 1.3021 1.4031 + 2 5 0.0895 1.6239 10.0104 1.4640 -1.0000 -1.0000 + 62 ! 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 + 1 1 5 74.4180 33.4273 1.7018 0.1463 0.5000 0.0000 1.6178 + 1 5 1 79.7037 28.2036 1.7073 0.1463 0.5000 0.0000 1.6453 + 2 1 5 63.3289 29.4225 2.1326 0.0000 0.5000 0.0000 3.0000 + 1 5 2 85.9449 38.3109 1.2492 0.0000 0.5000 0.0000 1.1000 + 1 5 5 85.6645 40.0000 2.9274 0.1463 0.5000 0.0000 1.3830 + 2 5 2 83.8555 5.1317 0.4377 0.0000 0.5000 0.0000 3.0000 + 2 5 5 97.0064 32.1121 2.0242 0.0000 0.5000 0.0000 2.8568 + 6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241 + 2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400 + 2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400 + 3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400 + 2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400 + 3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400 + 6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400 + 2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400 + 3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400 + 2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400 + 6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400 + 3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400 + 2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 23 ! 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 + 0 1 5 0 4.0885 78.7058 0.1174 -2.1639 0.0000 0.0000 0.0000 + 0 5 5 0 -0.0170 -56.0786 0.6132 -2.2092 0.0000 0.0000 0.0000 + 0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000 + 0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000 + 0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 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 + 9 ! 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 + 3 2 5 2.6644 -3.0000 3.0000 3.0000 + 4 2 5 4.0476 -3.0000 3.0000 3.0000 + 5 2 3 2.1126 -4.5790 3.0000 3.0000 + 5 2 4 2.2066 -5.7038 3.0000 3.0000 + 5 2 5 1.9461 -4.0000 3.0000 3.0000 diff --git a/examples/1-reaxff/input.xyz b/examples/1-reaxff/input.xyz new file mode 100644 index 0000000..82df2e1 --- /dev/null +++ b/examples/1-reaxff/input.xyz @@ -0,0 +1,14 @@ +12 "Poly(ethylene), C.W.Bunn (1939) Trans.Faraday Soc. 35:482-" +7.40000 4.93000 2.53400 90.000 90.000 90.000 +C 0.038000000 0.935000000 0.250000000 +C 0.962000000 0.065000000 0.750000000 +C 0.462000000 0.435000000 0.750000000 +C 0.538000000 0.565000000 0.250000000 +H 0.197000000 0.970000000 0.250000000 +H 0.803000000 0.030000000 0.750000000 +H 0.303000000 0.470000000 0.750000000 +H 0.697000000 0.530000000 0.250000000 +H 0.018000000 0.722000000 0.250000000 +H 0.982000000 0.278000000 0.750000000 +H 0.482000000 0.222000000 0.750000000 +H 0.518000000 0.778000000 0.250000000 diff --git a/examples/1-reaxff/rxmd.in b/examples/1-reaxff/rxmd.in new file mode 100644 index 0000000..d9fd298 --- /dev/null +++ b/examples/1-reaxff/rxmd.in @@ -0,0 +1,9 @@ +1 +0.25 100
+300 1.0 100 +100 10 +1 1 1 +1 500 1.d-7 1 +1.0 2.0 +.false. .false. .false. .false. +1.d-6 diff --git a/examples/2-reaxff-dc/Makefile b/examples/2-reaxff-dc/Makefile new file mode 100644 index 0000000..053b43b --- /dev/null +++ b/examples/2-reaxff-dc/Makefile @@ -0,0 +1,10 @@ +set: + cp -v ../../init/geninit . + cp -v ../../rxmd . + ./geninit -i input.xyz -f ffield -o DAT/ -mc 4 3 5 -v 2 1 1 + +run: + mpirun -np 2 ./rxmd + +clean: + rm -fv geninit* rxmd DAT/* diff --git a/examples/2-reaxff-dc/ffield b/examples/2-reaxff-dc/ffield new file mode 100644 index 0000000..a5199d8 --- /dev/null +++ b/examples/2-reaxff-dc/ffield @@ -0,0 +1,219 @@ +Reactive MD-force field: nitramines (RDX/HMX/TATB/PETN) + 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) + 0.0000 !Molecular energy (not used) + 6.5560 !Valency angle conjugation parameter + 7 ! 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 + S 1.9647 2.0000 32.0600 2.0783 0.2176 1.0336 1.5386 6.0000 + 9.9676 5.0812 4.0000 35.1648 112.1416 6.5000 8.2545 2.0000 + 1.4703 9.4922 70.0338 8.5146 28.0801 8.5010 0.9745 0.0000 + -10.0773 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000 + Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000 + 11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000 + -1.0000 0.0000 126.5331 6.4918 8.5961 0.2368 0.8563 0.0000 + -3.8112 3.1873 1.0338 4.0000 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 4.0000 2.8793 0.0000 0.0000 0.0000 + 18 ! 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 + 1 5 128.7959 56.4134 39.0716 0.0688 -0.4463 1.0000 31.1766 0.4530 + 0.1955 -0.3587 6.2148 1.0000 -0.0770 6.6386 1.0000 0.0000 + 2 5 128.6090 0.0000 0.0000 -0.5555 0.0000 1.0000 6.0000 0.4721 + 10.8735 1.0000 0.0000 1.0000 -0.0242 9.1937 1.0000 0.0000 + 3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000 + 0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000 + 4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000 + 0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000 + 5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000 + 0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000 + 6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583 + 0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000 + 2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256 + 17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000 + 3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764 + 1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000 + 10 ! 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 + 2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000 + 3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000 + 1 5 0.1408 1.8161 9.9393 1.7986 1.3021 1.4031 + 2 5 0.0895 1.6239 10.0104 1.4640 -1.0000 -1.0000 + 62 ! 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 + 1 1 5 74.4180 33.4273 1.7018 0.1463 0.5000 0.0000 1.6178 + 1 5 1 79.7037 28.2036 1.7073 0.1463 0.5000 0.0000 1.6453 + 2 1 5 63.3289 29.4225 2.1326 0.0000 0.5000 0.0000 3.0000 + 1 5 2 85.9449 38.3109 1.2492 0.0000 0.5000 0.0000 1.1000 + 1 5 5 85.6645 40.0000 2.9274 0.1463 0.5000 0.0000 1.3830 + 2 5 2 83.8555 5.1317 0.4377 0.0000 0.5000 0.0000 3.0000 + 2 5 5 97.0064 32.1121 2.0242 0.0000 0.5000 0.0000 2.8568 + 6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241 + 2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400 + 2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400 + 3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400 + 2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400 + 3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400 + 6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400 + 2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400 + 3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400 + 2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400 + 6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400 + 3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400 + 2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 23 ! 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 + 0 1 5 0 4.0885 78.7058 0.1174 -2.1639 0.0000 0.0000 0.0000 + 0 5 5 0 -0.0170 -56.0786 0.6132 -2.2092 0.0000 0.0000 0.0000 + 0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000 + 0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000 + 0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 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 + 9 ! 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 + 3 2 5 2.6644 -3.0000 3.0000 3.0000 + 4 2 5 4.0476 -3.0000 3.0000 3.0000 + 5 2 3 2.1126 -4.5790 3.0000 3.0000 + 5 2 4 2.2066 -5.7038 3.0000 3.0000 + 5 2 5 1.9461 -4.0000 3.0000 3.0000 diff --git a/examples/2-reaxff-dc/input.xyz b/examples/2-reaxff-dc/input.xyz new file mode 100644 index 0000000..82df2e1 --- /dev/null +++ b/examples/2-reaxff-dc/input.xyz @@ -0,0 +1,14 @@ +12 "Poly(ethylene), C.W.Bunn (1939) Trans.Faraday Soc. 35:482-" +7.40000 4.93000 2.53400 90.000 90.000 90.000 +C 0.038000000 0.935000000 0.250000000 +C 0.962000000 0.065000000 0.750000000 +C 0.462000000 0.435000000 0.750000000 +C 0.538000000 0.565000000 0.250000000 +H 0.197000000 0.970000000 0.250000000 +H 0.803000000 0.030000000 0.750000000 +H 0.303000000 0.470000000 0.750000000 +H 0.697000000 0.530000000 0.250000000 +H 0.018000000 0.722000000 0.250000000 +H 0.982000000 0.278000000 0.750000000 +H 0.482000000 0.222000000 0.750000000 +H 0.518000000 0.778000000 0.250000000 diff --git a/examples/2-reaxff-dc/rxmd.in b/examples/2-reaxff-dc/rxmd.in new file mode 100644 index 0000000..7c8ef63 --- /dev/null +++ b/examples/2-reaxff-dc/rxmd.in @@ -0,0 +1,9 @@ +1 +0.25 100
+300 1.0 100 +100 10 +2 1 1 +1 500 1.d-7 1 +1.0 2.0 +.false. .false. .false. .false. +1.d-6 diff --git a/examples/3-reaxpq+/Makefile b/examples/3-reaxpq+/Makefile new file mode 100644 index 0000000..0534c6b --- /dev/null +++ b/examples/3-reaxpq+/Makefile @@ -0,0 +1,10 @@ +set: + cp -v ../../init/geninit . + cp -v ../../rxmd . + ./geninit -i input.xyz -f ffield -o DAT/ -mc 2 3 5 + +run: + mpirun -np 1 ./rxmd --pqeq pqeq1.par + +clean: + rm -fv geninit* rxmd DAT/* diff --git a/examples/3-reaxpq+/ffield b/examples/3-reaxpq+/ffield new file mode 100644 index 0000000..a5199d8 --- /dev/null +++ b/examples/3-reaxpq+/ffield @@ -0,0 +1,219 @@ +Reactive MD-force field: nitramines (RDX/HMX/TATB/PETN) + 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) + 0.0000 !Molecular energy (not used) + 6.5560 !Valency angle conjugation parameter + 7 ! 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 + S 1.9647 2.0000 32.0600 2.0783 0.2176 1.0336 1.5386 6.0000 + 9.9676 5.0812 4.0000 35.1648 112.1416 6.5000 8.2545 2.0000 + 1.4703 9.4922 70.0338 8.5146 28.0801 8.5010 0.9745 0.0000 + -10.0773 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000 + Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000 + 11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000 + -1.0000 0.0000 126.5331 6.4918 8.5961 0.2368 0.8563 0.0000 + -3.8112 3.1873 1.0338 4.0000 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 4.0000 2.8793 0.0000 0.0000 0.0000 + 18 ! 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 + 1 5 128.7959 56.4134 39.0716 0.0688 -0.4463 1.0000 31.1766 0.4530 + 0.1955 -0.3587 6.2148 1.0000 -0.0770 6.6386 1.0000 0.0000 + 2 5 128.6090 0.0000 0.0000 -0.5555 0.0000 1.0000 6.0000 0.4721 + 10.8735 1.0000 0.0000 1.0000 -0.0242 9.1937 1.0000 0.0000 + 3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000 + 0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000 + 4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000 + 0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000 + 5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000 + 0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000 + 6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583 + 0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000 + 2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256 + 17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000 + 3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764 + 1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000 + 10 ! 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 + 2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000 + 3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000 + 1 5 0.1408 1.8161 9.9393 1.7986 1.3021 1.4031 + 2 5 0.0895 1.6239 10.0104 1.4640 -1.0000 -1.0000 + 62 ! 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 + 1 1 5 74.4180 33.4273 1.7018 0.1463 0.5000 0.0000 1.6178 + 1 5 1 79.7037 28.2036 1.7073 0.1463 0.5000 0.0000 1.6453 + 2 1 5 63.3289 29.4225 2.1326 0.0000 0.5000 0.0000 3.0000 + 1 5 2 85.9449 38.3109 1.2492 0.0000 0.5000 0.0000 1.1000 + 1 5 5 85.6645 40.0000 2.9274 0.1463 0.5000 0.0000 1.3830 + 2 5 2 83.8555 5.1317 0.4377 0.0000 0.5000 0.0000 3.0000 + 2 5 5 97.0064 32.1121 2.0242 0.0000 0.5000 0.0000 2.8568 + 6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241 + 2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400 + 2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400 + 3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400 + 2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400 + 3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400 + 6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400 + 2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400 + 3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400 + 2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400 + 6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400 + 3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400 + 2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 23 ! 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 + 0 1 5 0 4.0885 78.7058 0.1174 -2.1639 0.0000 0.0000 0.0000 + 0 5 5 0 -0.0170 -56.0786 0.6132 -2.2092 0.0000 0.0000 0.0000 + 0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000 + 0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000 + 0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 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 + 9 ! 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 + 3 2 5 2.6644 -3.0000 3.0000 3.0000 + 4 2 5 4.0476 -3.0000 3.0000 3.0000 + 5 2 3 2.1126 -4.5790 3.0000 3.0000 + 5 2 4 2.2066 -5.7038 3.0000 3.0000 + 5 2 5 1.9461 -4.0000 3.0000 3.0000 diff --git a/examples/3-reaxpq+/input.xyz b/examples/3-reaxpq+/input.xyz new file mode 100644 index 0000000..82df2e1 --- /dev/null +++ b/examples/3-reaxpq+/input.xyz @@ -0,0 +1,14 @@ +12 "Poly(ethylene), C.W.Bunn (1939) Trans.Faraday Soc. 35:482-" +7.40000 4.93000 2.53400 90.000 90.000 90.000 +C 0.038000000 0.935000000 0.250000000 +C 0.962000000 0.065000000 0.750000000 +C 0.462000000 0.435000000 0.750000000 +C 0.538000000 0.565000000 0.250000000 +H 0.197000000 0.970000000 0.250000000 +H 0.803000000 0.030000000 0.750000000 +H 0.303000000 0.470000000 0.750000000 +H 0.697000000 0.530000000 0.250000000 +H 0.018000000 0.722000000 0.250000000 +H 0.982000000 0.278000000 0.750000000 +H 0.482000000 0.222000000 0.750000000 +H 0.518000000 0.778000000 0.250000000 diff --git a/examples/3-reaxpq+/pqeq1.par b/examples/3-reaxpq+/pqeq1.par new file mode 100644 index 0000000..e80278d --- /dev/null +++ b/examples/3-reaxpq+/pqeq1.par @@ -0,0 +1,15 @@ +################################################################ +# +# Polarizable Charge Equilibration (PQEq1) Parameter Set +# +# contacts: +# Saber Naserifar, naseri@caltech.edu +# William A. Goddard III, wag@wag.caltech.edu +# +# +################################################################ +#E P Xo Jo Z Rc Rs Ks +################################################################ +NPARMS 2 + C 1 5.50813 9.81186 1.000000 0.75900 0.75900 198.84054 + H 1 4.72484 15.57338 1.000000 0.37100 0.37100 2037.20061 diff --git a/examples/3-reaxpq+/rxmd.in b/examples/3-reaxpq+/rxmd.in new file mode 100644 index 0000000..d9fd298 --- /dev/null +++ b/examples/3-reaxpq+/rxmd.in @@ -0,0 +1,9 @@ +1 +0.25 100
+300 1.0 100 +100 10 +1 1 1 +1 500 1.d-7 1 +1.0 2.0 +.false. .false. .false. .false. +1.d-6 diff --git a/examples/4-reaxpq+-efield/Makefile b/examples/4-reaxpq+-efield/Makefile new file mode 100644 index 0000000..11c8696 --- /dev/null +++ b/examples/4-reaxpq+-efield/Makefile @@ -0,0 +1,10 @@ +set: + cp -v ../../init/geninit . + cp -v ../../rxmd . + ./geninit -i input.xyz -f ffield -o DAT/ -mc 2 3 5 + +run: + mpirun -np 1 ./rxmd --pqeq pqeq1.par -e 1 0.01 + +clean: + rm -fv geninit* rxmd DAT/* diff --git a/examples/4-reaxpq+-efield/ffield b/examples/4-reaxpq+-efield/ffield new file mode 100644 index 0000000..a5199d8 --- /dev/null +++ b/examples/4-reaxpq+-efield/ffield @@ -0,0 +1,219 @@ +Reactive MD-force field: nitramines (RDX/HMX/TATB/PETN) + 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) + 0.0000 !Molecular energy (not used) + 6.5560 !Valency angle conjugation parameter + 7 ! 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 + S 1.9647 2.0000 32.0600 2.0783 0.2176 1.0336 1.5386 6.0000 + 9.9676 5.0812 4.0000 35.1648 112.1416 6.5000 8.2545 2.0000 + 1.4703 9.4922 70.0338 8.5146 28.0801 8.5010 0.9745 0.0000 + -10.0773 2.7466 1.0338 6.2998 2.8793 0.0000 0.0000 0.0000 + Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000 + 11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000 + -1.0000 0.0000 126.5331 6.4918 8.5961 0.2368 0.8563 0.0000 + -3.8112 3.1873 1.0338 4.0000 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 4.0000 2.8793 0.0000 0.0000 0.0000 + 18 ! 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 + 1 5 128.7959 56.4134 39.0716 0.0688 -0.4463 1.0000 31.1766 0.4530 + 0.1955 -0.3587 6.2148 1.0000 -0.0770 6.6386 1.0000 0.0000 + 2 5 128.6090 0.0000 0.0000 -0.5555 0.0000 1.0000 6.0000 0.4721 + 10.8735 1.0000 0.0000 1.0000 -0.0242 9.1937 1.0000 0.0000 + 3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000 + 0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000 + 4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000 + 0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000 + 5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000 + 0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000 + 6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583 + 0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000 + 2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256 + 17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000 + 3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764 + 1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000 + 10 ! 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 + 2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000 + 3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000 + 1 5 0.1408 1.8161 9.9393 1.7986 1.3021 1.4031 + 2 5 0.0895 1.6239 10.0104 1.4640 -1.0000 -1.0000 + 62 ! 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 + 1 1 5 74.4180 33.4273 1.7018 0.1463 0.5000 0.0000 1.6178 + 1 5 1 79.7037 28.2036 1.7073 0.1463 0.5000 0.0000 1.6453 + 2 1 5 63.3289 29.4225 2.1326 0.0000 0.5000 0.0000 3.0000 + 1 5 2 85.9449 38.3109 1.2492 0.0000 0.5000 0.0000 1.1000 + 1 5 5 85.6645 40.0000 2.9274 0.1463 0.5000 0.0000 1.3830 + 2 5 2 83.8555 5.1317 0.4377 0.0000 0.5000 0.0000 3.0000 + 2 5 5 97.0064 32.1121 2.0242 0.0000 0.5000 0.0000 2.8568 + 6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241 + 2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400 + 2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400 + 3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400 + 2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400 + 3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400 + 6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400 + 2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400 + 3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400 + 2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400 + 6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400 + 3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400 + 2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 + 23 ! 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 + 0 1 5 0 4.0885 78.7058 0.1174 -2.1639 0.0000 0.0000 0.0000 + 0 5 5 0 -0.0170 -56.0786 0.6132 -2.2092 0.0000 0.0000 0.0000 + 0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000 + 0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000 + 0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 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 + 9 ! 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 + 3 2 5 2.6644 -3.0000 3.0000 3.0000 + 4 2 5 4.0476 -3.0000 3.0000 3.0000 + 5 2 3 2.1126 -4.5790 3.0000 3.0000 + 5 2 4 2.2066 -5.7038 3.0000 3.0000 + 5 2 5 1.9461 -4.0000 3.0000 3.0000 diff --git a/examples/4-reaxpq+-efield/input.xyz b/examples/4-reaxpq+-efield/input.xyz new file mode 100644 index 0000000..82df2e1 --- /dev/null +++ b/examples/4-reaxpq+-efield/input.xyz @@ -0,0 +1,14 @@ +12 "Poly(ethylene), C.W.Bunn (1939) Trans.Faraday Soc. 35:482-" +7.40000 4.93000 2.53400 90.000 90.000 90.000 +C 0.038000000 0.935000000 0.250000000 +C 0.962000000 0.065000000 0.750000000 +C 0.462000000 0.435000000 0.750000000 +C 0.538000000 0.565000000 0.250000000 +H 0.197000000 0.970000000 0.250000000 +H 0.803000000 0.030000000 0.750000000 +H 0.303000000 0.470000000 0.750000000 +H 0.697000000 0.530000000 0.250000000 +H 0.018000000 0.722000000 0.250000000 +H 0.982000000 0.278000000 0.750000000 +H 0.482000000 0.222000000 0.750000000 +H 0.518000000 0.778000000 0.250000000 diff --git a/examples/4-reaxpq+-efield/pqeq1.par b/examples/4-reaxpq+-efield/pqeq1.par new file mode 100644 index 0000000..e80278d --- /dev/null +++ b/examples/4-reaxpq+-efield/pqeq1.par @@ -0,0 +1,15 @@ +################################################################ +# +# Polarizable Charge Equilibration (PQEq1) Parameter Set +# +# contacts: +# Saber Naserifar, naseri@caltech.edu +# William A. Goddard III, wag@wag.caltech.edu +# +# +################################################################ +#E P Xo Jo Z Rc Rs Ks +################################################################ +NPARMS 2 + C 1 5.50813 9.81186 1.000000 0.75900 0.75900 198.84054 + H 1 4.72484 15.57338 1.000000 0.37100 0.37100 2037.20061 diff --git a/examples/4-reaxpq+-efield/rxmd.in b/examples/4-reaxpq+-efield/rxmd.in new file mode 100644 index 0000000..d9fd298 --- /dev/null +++ b/examples/4-reaxpq+-efield/rxmd.in @@ -0,0 +1,9 @@ +1 +0.25 100
+300 1.0 100 +100 10 +1 1 1 +1 500 1.d-7 1 +1.0 2.0 +.false. .false. .false. .false. +1.d-6 diff --git a/init/polyethylene.xyz b/init/polyethylene.xyz deleted file mode 100644 index 9cb39e8..0000000 --- a/init/polyethylene.xyz +++ /dev/null @@ -1,14 +0,0 @@ -12 " Poly(ethylene), C.W.Bunn (1939) Trans.Faraday Soc. 35:482-" -7.4000 4.9300 2.5340 90.0000 90.0000 90.0000 - C 0.281200 4.609550 0.633500 - C 7.118800 0.320450 1.900500 - C 3.418800 2.144550 1.900500 - C 3.981200 2.785450 0.633500 - H 1.457800 4.782100 0.633500 - H 5.942200 0.147900 1.900500 - H 2.242200 2.317100 1.900500 - H 5.157800 2.612900 0.633500 - H 0.133200 3.559460 0.633500 - H 7.266800 1.370540 1.900500 - H 3.566800 1.094460 1.900500 - H 3.833200 3.835540 0.633500