(8e8151fe) · Commits · 郑智淋 / lammps

examples/reax/AuO/README

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		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.

		Au/O

		The follow information is reproduced from
		"Keith, J. A.; Fantauzzi, D.; Jacob, T.;
		van Duin, A. C. T. Phys Rev B 2010, 81, 235404"

		- The force field optimization involved parameterization
		of the fcc, bcc, ideal-hcp, sc, diamond, and a15 bulk phases of Au.
		For these phases the ReaxFF force field gives good
		agreement for the binding energy, volume of minimum
		energy, and curvature of the binding well around the
		minimum compared to the QM calculations used
		for parameterization.

examples/reax/AuO/data.AuO

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File added.

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examples/reax/AuO/ffield.reax.AuO

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Original line number	Diff line number	Diff line
		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

examples/reax/AuO/in.AuO

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Original line number	Diff line number	Diff line
		# 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 O Au

		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

examples/reax/AuO/lmp_control

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Original line number	Diff line number	Diff line
		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

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