(31ae0b54) · Commits · 郑智淋 / lammps

examples/reax/AB/README

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Original line number	Diff line number	Diff line
		Disclaimer: Using these force fields for systems they
		have not been explicitly trained against may produce
		unrealistic results. Please see the README file in
		each subdirectory for more detailed information.

		Ammonia Borane:

		The follow information is reproduced from:

		"Weismiller, M.R.; van Duin, A.C.T.; Lee, J.;
		Yetter, R.A. J. Phys. Chem. A 2010, 114, 5485-5492"

		- QM data were generated describing the single and
		(if relevant) double and triple bond dissociation
		for all B/N/O/H combinations. These data were used
		to derive initial ReaxFF bond parameters, and all
		calculations were performed using DFT with the B3LYP
		functional and the Pople 6-311G** basis set.

		- The training set was then extended with QM data
		describing angular distortions in a set of small
		AB-related (AB = H3N-BH3) molecules. These data
		were used to derive the initial ReaxFF angular
		parameters.

		- The training set was extended with reaction barriers
		for key reaction steps such as H2 release
		from AB, dimerization of H2B-NH2 and reaction
		energies associated with H2 release from AB and with AB
		oxidation.

examples/reax/AB/data.AB

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Original line number	Diff line number	Diff line
		# 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

examples/reax/AB/ffield.reax.AB

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Original line number	Diff line number	Diff line
		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

examples/reax/AB/in.AB

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Original line number	Diff line number	Diff line
		# 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 H B N

		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

examples/reax/AB/lmp_control

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Original line number	Diff line number	Diff line
		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

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