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Merge pull request #771 from stanmoore1/reax_example 

Add ReaxFF Example
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examples/reax/HNS/README.txt 0 → 100644
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# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
Authors: Mitchell Wood, Stan Moore, and Aidan Thompson, Sandia National Labs
Date: 2017-10-17
Questions: Mitchell Wood, mitwood@sandia.gov
---------ReaxFF Benchmark Files---------
1) in.reaxc.hns
2) data.hns-equil
3) ffield.reax.hns
---------File Description---------
1) LAMMPS input file for this test.
The file is read line by line looking for keywords to set up this run.
It will read in the configuration given by the argument of the read_data command, which is supplied in this distribution.
The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
*There are four free varaibles in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
*The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
*The number of timesteps taken is controlled by the 'run' command given the value of $t
It is worth noting that these four free variables can be set at the command line when the simulation is invoked rather than editing the file by hand prior to each run.
Example syntax:
lmp_serial -in in.reaxc.hns -v x 2 -v y 2 -v z 2 -v t 100
2) LAMMPS Data file for crystalline HNS
This file matches the LAMMPS data format, more information about this data structure can be found at lammps.sandia.gov
This particular data file is of the energetic material Hexanitrostilbene (HNS) with atom_style charge (id type q x y z).
The file contains eight molecules (2 unit cells).
Chemical Name: Hexanitrostilbene
Molecule Composition: C14H6N6O12
IUPAC Name: 1,3,5-Trinitro-2-[2-(2,4,6-trinitrophenyl)ethenyl]benzene
Phyical Properties (Gerard F., Hardy A. Acta Cryst. (1988) 1283-1287)
Density: 1.741 g/cc
Crystal Structure: Monoclinic P2(1)/c
Molecules per Unit Cell: 4
Lattice Constants: a=22.326
b=5.5706
c=14.667
beta=110.04 deg
3) ReaxFF force field file.
Details about this particular parameterization can be found in T.-R. Shan, R. R. Wixom, A. P. Thompson, "Atomistic Simulation of Nanoscale Void-Enhanced Initiation in Hexanitrostilbene", Proc. 15th International Detonation Symposium, pp. 962-969, SAND Number: SAND2014-15518J
examples/reax/HNS/data.hns-equil 0 → 100644
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examples/reax/HNS/ffield.reax.hns 0 → 100644
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Reactive MD-force field: c/h/o/s/f/cl Jan30_2012
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)
-60.1292 !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)
4 ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma
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 55.0000 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
N 1.6157 3.0000 14.0000 1.9376 0.1203 1.0000 1.2558 5.0000
9.4267 26.8500 4.0000 8.6294 100.0000 7.6099 7.7500 2.0000
1.0439 0.1000 119.9837 1.7640 2.7409 2.3814 0.9745 0.0000
-6.5798 4.4843 1.0183 4.0000 2.8793 0.0000 0.0000 0.0000
10 ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(b
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
1 4 175.7446 131.3190 132.3859 -0.5827 -0.2709 1.0000 29.9009 0.8400
1.9511 -0.2103 7.4487 1.0000 -0.1150 5.8717 1.0000 0.0000
2 4 161.1063 0.0000 0.0000 -0.1387 0.0000 1.0000 6.0000 0.7276
0.6127 1.0000 0.0000 1.0000 -0.0395 7.2218 0.0000 0.0000
3 4 86.0536 180.5864 40.0000 1.0000 -0.4462 1.0000 34.9336 0.2000
0.8154 -0.2175 7.0255 1.0000 -0.1937 5.2140 1.0000 0.0000
4 4 134.6492 66.2329 149.2707 -0.7228 -0.1000 1.0000 19.0850 1.0000
0.6060 -0.2050 9.7308 1.0000 -0.1791 5.8008 1.0000 0.0000
6 ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);r
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 0.1398 1.9263 10.1847 1.4778 1.1446 1.1216
2 4 0.0480 2.3000 9.0050 1.0156 -1.0000 -1.0000
3 4 0.0942 1.9531 10.3265 1.3018 1.0984 1.0125
40 ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);
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
1 1 4 61.6894 9.9742 3.5920 0.0000 5.0000 50.0000 2.2098
3 1 4 67.5853 29.6915 1.8611 0.0000 3.0000 0.0000 1.5926
4 1 4 53.0437 35.9280 1.7824 0.0000 5.0000 0.0000 4.0000
2 1 4 66.9313 25.8025 3.5718 0.0000 0.0600 0.0000 1.0946
1 3 4 71.7246 38.5022 1.1738 0.0000 1.6310 0.0000 1.2782
3 3 4 83.0764 35.5413 1.4072 0.0000 1.6310 0.0000 1.1439
4 3 4 79.3317 40.0000 2.3424 0.0000 1.6310 0.0000 1.0061
2 3 4 81.0695 40.0000 2.0285 0.0000 0.1218 0.0000 1.4477
1 4 1 68.9764 14.3404 1.9702 0.0000 1.3606 0.0000 1.0000
1 4 3 76.1086 35.0355 1.0724 0.0000 1.6777 0.0000 1.6071
1 4 4 81.8917 25.7475 0.7287 0.0000 2.0100 0.0000 1.9350
3 4 3 80.1274 24.7547 1.7946 -10.0963 1.6777 0.0000 3.2815
3 4 4 83.6527 36.3627 1.0967 -0.9193 1.6777 0.0000 1.0000
4 4 4 90.0000 44.3028 1.6659 0.0000 0.7529 0.0000 1.2398
1 4 2 76.9847 29.2262 0.9407 0.0000 0.0300 0.0000 2.6196
2 4 3 85.4080 40.0000 1.7549 0.0000 0.0222 0.0000 1.0774
2 4 4 83.5658 40.0000 1.3540 0.0000 0.0222 0.0000 2.6397
2 4 2 58.0387 1.1862 3.9770 0.0000 0.0222 0.0000 1.0000
1 2 4 0.0000 0.0019 6.3000 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
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
31 ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);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
0 1 4 0 -0.5473 25.3808 0.9931 -4.3407 -3.0000 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 2.0000 71.9948 -0.8805 -6.1274 -2.7831 0.0000 0.0000
0 4 4 0 2.0000 90.0000 -0.7837 -9.0000 -2.0000 0.0000 0.0000
4 1 4 4 -2.0000 90.0000 -0.0279 -7.5866 -0.1000 0.0000 0.0000
4 ! Nr of hydrogen bonds. at1;at2;at3;r(hb);p(hb1);p(hb2);p(hb3
3 2 3 2.0000 -2.0000 1.5000 19.5000
3 2 4 1.9000 -2.0000 1.7976 19.0000
4 2 3 1.9000 -2.0000 1.7976 19.0000
4 2 4 1.9000 -2.0000 1.7976 19.0000
examples/reax/HNS/in.reaxc.hns 0 → 100644
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# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
# See README for more info
units real
atom_style charge
atom_modify sort 100 0.0 # optional
dimension 3
boundary p p p
box tilt large
read_data data.hns-equil
replicate $x $y $z bbox
pair_style reax/c NULL
pair_coeff * * ffield.reax.hns C H O N
compute reax all pair reax/c
neighbor 1.0 bin
neigh_modify every 20 delay 0 check no
timestep 0.1
thermo_style custom step temp pe press evdwl ecoul vol
thermo_modify norm yes
thermo 100
velocity all create 300.0 41279 loop geom
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
run 100
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