# This is the control script for LAMMPS. Run LAMMPS on GPU
echo both
log 2.1_Initialize.out
#-------------------------------------------------------------------------------
# Stage 2.1: Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units real
boundary p p p
atom_style full
atom_modify map array
box tilt large
read_data structure.dat
pair_style reax/c NULL checkqeq no safezone 10.0 mincap 1000
pair_coeff * * parameters.dat N Si
variable R equal 0.00198722
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+023
variable sysdensity equal v_sysmass/v_sysvol/1.0e-24
variable coulomb equal ecoul+elong
variable etotal equal etotal
variable pe equal pe
variable ke equal ke
variable evdwl equal evdwl
variable epair equal epair
variable ebond equal ebond
variable eangle equal eangle
variable edihed equal edihed
variable eimp equal eimp
variable lx equal lx
variable ly equal ly
variable lz equal lz
variable Nthermo equal 0
variable cella equal lx
variable cellb equal sqrt(ly*ly+xy*xy)
variable cellc equal sqrt(lz*lz+xz*xz+yz*yz)
variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc))
variable cellbeta equal acos(xz/v_cellc)
variable cellgamma equal acos(xy/v_cellb)
variable p equal press
variable pxx equal pxx
variable pyy equal pyy
variable pzz equal pzz
variable pyz equal pyz
variable pxz equal pxz
variable pxy equal pxy
variable sxx equal -pxx
variable syy equal -pyy
variable szz equal -pzz
variable syz equal -pyz
variable sxz equal -pxz
variable sxy equal -pxy
variable fmax equal fmax
variable fnorm equal fnorm
variable time equal step*dt+0.000001
variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz)
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo_modify flush yes
#
# Set up the fixed and movable groups
#
group fixed id 1 3 5 6 7 8 9 10 11 12
group fixed id 16 17 19 21 23 24 25 26 27 28
group fixed id 30 32 33 35 37 38 39 40 41 42
group fixed id 43 44 48 49 51 53 55 56 57 58
group fixed id 59 60 62 64 65 67 69 70 71 72
group fixed id 73 74 75 76 80 81 83 85 87 88
group fixed id 89 90 91 92 94 96 97 99 101 102
group fixed id 103 104 105 106 107 108 112 113 115 117
group fixed id 119 120 121 122 123 124 126 128 129 131
group fixed id 133 134 135 136 137 138 139 140 144 145
group fixed id 147 149 151 152 153 154 155 156 158 160
group fixed id 161 163 165 166 167 168 169 170 171 172
group fixed id 176 177 179 181 183 184 185 186 187 188
group fixed id 190 192 193 195 197 198 199 200 201 202
group fixed id 203 204 208 209 211 213 215 216 217 218
group fixed id 219 220 222 224 225 227 229 230 231 232
group fixed id 233 234 235 236 240 241 243 245 247 248
group fixed id 249 250 251 252 254 256 257 259 261 262
group fixed id 263 264 265 266 267 268 272 273 275 277
group fixed id 279 280 281 282 283 284 286 288 289 291
group fixed id 293 294 295 296 297 298 299 300 304 305
group fixed id 307 309 311 312 313 314 315 316 318 320
group fixed id 321 323 325 326 327 328 329 330 331 332
group fixed id 336 337 339 341 343 344 345 346 347 348
group fixed id 350 352 353 355 357 358 359 360 361 362
group fixed id 363 364 368 369 371 373 375 376 377 378
group fixed id 379 380 382 384 385 387 389 390 391 392
group fixed id 393 394 395 396 400 401 403 405 407 408
group fixed id 409 410 411 412 414 416 417 419 421 422
group fixed id 423 424 425 426 427 428 432 433 435 437
group fixed id 439 440 441 442 443 444 446 448 449 451
group fixed id 453 454 455 456 457 458 459 460 464 465
group fixed id 467 469 471 472 473 474 475 476 478 480
group fixed id 481 483 485 486 487 488 489 490 491 492
group fixed id 496 497 499 501 503 504 505 506 507 508
group fixed id 510 512 513 515 517 518 519 520 521 522
group fixed id 523 524 528 529 531 533 535 536 537 538
group fixed id 539 540 542 544 545 547 549 550 551 552
group fixed id 553 554 555 556 560 561 563 565 567 568
group fixed id 569 570 571 572 574 576 577 579 581 582
group fixed id 583 584 585 586 587 588 592 593 595 597
group fixed id 599 600 601 602 603 604 606 608 609 611
group fixed id 613 614 615 616 617 618 619 620 624 625
group fixed id 627 629 631 632 633 634 635 636 638 640
group fixed id 641 643 645 646 647 648 649 650 651 652
group fixed id 656 657 659 661 663 664 665 666 667 668
group fixed id 670 672 673 675 677 678 679 680 681 682
group fixed id 683 684 688 689 691 693 695 696 697 698
group fixed id 699 700 702 704 705 707 709 710 711 712
group fixed id 713 714 715 716 720 721 723 725 727 728
group fixed id 729 730 731 732 734 736 737 739 741 742
group fixed id 743 744 745 746 747 748 752 753 755 757
group fixed id 759 760 761 762 763 764 766 768 769 771
group fixed id 773 774 775 776 777 778 779 780 784 785
group fixed id 787 789 791 792 793 794 795 796 798 800
group fixed id 801 803 805 806 807 808 809 810 811 812
group fixed id 816 817 819 821 823 824 825 826 827 828
group fixed id 830 832 833 835 837 838 839 840 841 842
group fixed id 843 844 848 849 851 853 855 856 857 858
group fixed id 859 860 862 864 865 867 869 870 871 872
group fixed id 873 874 875 876 880 881 883 885 887 888
group fixed id 889 890 891 892 894 896 897 899 901 902
group fixed id 903 904 905 906 907 908 912 913 915 917
group fixed id 919 920 921 922 923 924 926 928 929 931
group fixed id 933 934 935 936 937 938 939 940 944 945
group fixed id 947 949 951 952 953 954 955 956 958 960
group fixed id 961 963 965 966 967 968 969 970 971 972
group fixed id 976 977 979 981 983 984 985 986 987 988
group fixed id 990 992 993 995 997 998 999 1000 1001 1002
group fixed id 1003 1004 1008 1009 1011 1013 1015 1016 1017 1018
group fixed id 1019 1020 1022 1024 1025 1027 1029 1030 1031 1032
group fixed id 1033 1034 1035 1036 1040 1041 1043 1045 1047 1048
group fixed id 1049 1050 1051 1052 1054 1056 1057 1059 1061 1062
group fixed id 1063 1064 1065 1066 1067 1068 1072 1073 1075 1077
group fixed id 1079 1080 1081 1082 1083 1084 1086 1088 1089 1091
group fixed id 1093 1094 1095 1096 1097 1098 1099 1100 1104 1105
group fixed id 1107 1109 1111 1112 1113 1114 1115 1116 1118 1120
group fixed id 1121 1123 1125 1126 1127 1128 1129 1130 1131 1132
group fixed id 1136 1137 1139 1141 1143 1144 1145 1146 1147 1148
group fixed id 1150 1152 1153 1155 1157 1158 1159 1160 1161 1162
group fixed id 1163 1164 1168 1169 1171 1173 1175 1176 1177 1178
group fixed id 1179 1180 1182 1184 1185 1187 1189 1190 1191 1192
group fixed id 1193 1194 1195 1196 1200 1201 1203 1205 1207 1208
group fixed id 1209 1210 1211 1212 1214 1216 1217 1219 1221 1222
group fixed id 1223 1224 1225 1226 1227 1228 1232 1233 1235 1237
group fixed id 1239 1240 1241 1242 1243 1244 1246 1248 1249 1251
group fixed id 1253 1254 1255 1256 1257 1258 1259 1260 1264 1265
group fixed id 1267 1269 1271 1272 1273 1274 1275 1276 1278 1280
group fixed id 1281 1283 1296 1297 1299 1312 1313 1315 1328 1329
group fixed id 1331 1344 1345 1347 1360 1361 1363 1376 1377 1379
group fixed id 1392 1393 1395 1408 1409 1411 1424 1425 1427 1440
group fixed id 1441 1443 1456 1457 1459 1472 1473 1475 1488 1489
group fixed id 1491 1504 1505 1507 1520 1521 1523 1536 1537 1539
group fixed id 1552 1553 1555 1568 1569 1571 1584 1585 1587 1600
group fixed id 1601 1603 1616 1617 1619 1632 1633 1635 1648 1649
group fixed id 1651 1664 1665 1667 1680 1681 1683 1696 1697 1699
group fixed id 1712 1713 1715 1728 1729 1731 1744 1745 1747 1760
group fixed id 1761 1763 1776 1777 1779 1792 1793 1795 1808 1809
group fixed id 1811 1824 1825 1827 1840 1841 1843 1856 1857 1859
group fixed id 1872 1873 1875 1888 1889 1891 1904 1905 1907 1920
group fixed id 1921 1923 1936 1937 1939 1952 1953 1955 1968 1969
group fixed id 1971 1984 1985 1987 2000 2001 2003 2016 2017 2019
group fixed id 2032 2033 2035 2048 2049 2050 2053 2054 2055 2058
group fixed id 2059 2060 2063 2064 2065 2068 2069 2070 2073 2074
group fixed id 2075 2078 2079 2080 2083 2084 2085 2088 2089 2090
group fixed id 2093 2094 2095 2098 2099 2100 2103 2104 2105 2108
group fixed id 2109 2110 2113 2114 2115 2118 2119 2120 2123 2124
group fixed id 2125 2128 2129 2130 2133 2134 2135 2138 2139 2140
group fixed id 2143 2144 2145 2148 2149 2150 2153 2154 2155 2158
group fixed id 2159 2160 2163 2164 2165 2168 2169 2170 2173 2174
group fixed id 2175 2178 2179 2180 2183 2184 2185 2188 2189 2190
group fixed id 2193 2194 2195 2198 2199 2200 2203 2204 2205 2208
group fixed id 2209 2210 2213 2214 2215 2218 2219 2220 2223 2224
group fixed id 2225 2228 2229 2230 2233 2234 2235 2238 2239 2240
group fixed id 2243 2244 2245 2248 2249 2250 2253 2254 2255 2258
group fixed id 2259 2260 2263 2264 2265 2268 2269 2270 2273 2274
group fixed id 2275 2278 2279 2280 2283 2284 2285 2288 2289 2290
group fixed id 2293 2294 2295 2298 2299 2300 2303 2304 2305 2308
group fixed id 2309 2310 2313 2314 2315 2318 2319 2320 2323 2324
group fixed id 2325 2328 2329 2330 2333 2334 2335 2338 2339 2340
group fixed id 2343 2344 2345 2348 2349 2350 2353 2354 2355 2358
group fixed id 2359 2360 2363 2364 2365 2368 2369 2370 2373 2374
group fixed id 2375 2378 2379 2380 2383 2384 2385 2388 2389 2390
group fixed id 2393 2394 2395 2398 2399 2400 2403 2404 2405 2408
group fixed id 2409 2410 2413 2414 2415 2418 2419 2420 2423 2424
group fixed id 2425 2428 2429 2430 2433 2434 2435 2438 2439 2440
group fixed id 2443 2444 2445 2448 2449 2450 2453 2454 2455 2458
group fixed id 2459 2460 2463 2464 2465 2468 2469 2470 2473 2474
group fixed id 2475 2478 2479 2480 2483 2484 2485 2488 2489 2490
group fixed id 2493 2494 2495 2498 2499 2500 2503 2504 2505 2508
group fixed id 2509 2510 2513 2514 2515 2518 2519 2520 2523 2524
group fixed id 2525 2528 2529 2530 2533 2534 2535 2538 2539 2540
group fixed id 2543 2544 2545 2548 2549 2550 2553 2554 2555 2558
group fixed id 2559 2560 2563 2564 2565 2568 2569 2570 2573 2574
group fixed id 2575 2578 2579 2580 2583 2584 2585 2588 2589 2590
group fixed id 2593 2594 2595 2598 2599 2600 2603 2604 2605 2608
group fixed id 2609 2610 2613 2614 2615 2618 2619 2620 2623 2624
group fixed id 2625 2628 2629 2630 2633 2634 2635 2638 2639 2640
group fixed id 2643 2644 2645 2648 2649 2650 2653 2654 2655 2658
group fixed id 2659 2660 2663 2664 2665 2668 2669 2670 2673 2674
group fixed id 2675 2678 2679 2680 2683 2684 2685 2688 2689 2691
group fixed id 2699 2700 2702 2710 2711 2713 2721 2722 2724 2732
group fixed id 2733 2735 2743 2744 2746 2754 2755 2757 2765 2766
group fixed id 2768 2776 2777 2779 2787 2788 2790 2798 2799 2801
group fixed id 2809 2810 2812 2820 2821 2823 2831 2832 2834 2842
group fixed id 2843 2845 2853 2854 2856 2864 2865 2867 2880 2881
group fixed id 2883 2896 2897 2899 2912 2913 2915 2928 2929 2931
group fixed id 2944 2945 2947 2960 2961 2963 2976 2977 2979 2992
group fixed id 2993 2995 3008 3009 3011 3024 3025 3027 3040 3041
group fixed id 3043 3056 3057 3059 3072 3073 3075 3088 3089 3091
group fixed id 3104 3105 3107 3120 3121 3123 3136 3137 3139 3152
group fixed id 3153 3155 3168 3169 3171 3184 3185 3187 3200 3201
group fixed id 3203 3216 3217 3219 3232 3233 3235 3248 3249 3251
group fixed id 3264 3265 3267 3280 3281 3283 3296 3297 3299 3312
group fixed id 3313 3315 3328 3329 3331 3344 3345 3347 3360 3361
group fixed id 3363 3376 3377 3379 3382 3384 3386 3388 3390 3392
group fixed id 3393 3395 3398 3400 3402 3404 3406 3408 3409 3411
group fixed id 3414 3416 3418 3420 3422 3424 3425 3427 3430 3432
group fixed id 3434 3436 3438 3440 3441 3443 3446 3448 3450 3452
group fixed id 3454 3456 3457 3459 3462 3464 3466 3468 3470 3472
group fixed id 3473 3475 3478 3480 3482 3484 3486 3488 3489 3491
group fixed id 3494 3496 3498 3500 3502 3504 3505 3507 3510 3512
group fixed id 3514 3516 3518 3520 3521 3523 3526 3528 3530 3532
group fixed id 3534 3536 3537 3539 3542 3544 3546 3548 3550 3552
group fixed id 3553 3555 3558 3560 3562 3564 3566 3568 3569 3571
group fixed id 3574 3576 3578 3580 3582 3584 3585 3587 3590 3592
group fixed id 3594 3596 3598 3600 3601 3603 3606 3608 3610 3612
group fixed id 3614 3616 3617 3619 3622 3624 3626 3628 3630 3632
group fixed id 3633 3635 3637 3638 3639 3640 3641 3642 3643 3644
group fixed id 3646 3648 3649 3651 3653 3654 3655 3656 3657 3658
group fixed id 3659 3660 3662 3664 3665 3667 3669 3670 3671 3672
group fixed id 3673 3674 3675 3676 3678 3680 3681 3683 3685 3686
group fixed id 3687 3688 3689 3690 3691 3692 3694 3696 3697 3699
group fixed id 3701 3702 3703 3704 3705 3706 3707 3708 3710 3712
group fixed id 3713 3715 3717 3718 3719 3720 3721 3722 3723 3724
group fixed id 3726 3728 3729 3731 3733 3734 3735 3736 3737 3738
group fixed id 3739 3740 3742 3744 3745 3747 3749 3750 3751 3752
group fixed id 3753 3754 3755 3756 3758 3760 3761 3763 3765 3766
group fixed id 3767 3768 3769 3770 3771 3772 3774 3776 3777 3779
group fixed id 3781 3782 3783 3784 3785 3786 3787 3788 3790 3792
group fixed id 3793 3795 3797 3798 3799 3800 3801 3802 3803 3804
group fixed id 3806 3808 3809 3811 3813 3814 3815 3816 3817 3818
group fixed id 3819 3820 3822 3824 3825 3827 3829 3830 3831 3832
group fixed id 3833 3834 3835 3836 3838 3840 3841 3843 3845 3846
group fixed id 3847 3848 3849 3850 3851 3852 3854 3856 3857 3859
group fixed id 3861 3862 3863 3864 3865 3866 3867 3868 3870 3872
group fixed id 3873 3875 3877 3878 3879 3880 3881 3882 3883 3884
group fixed id 3886 3888 3889 3891 3893 3894 3895 3896 3897 3898
group fixed id 3899 3900 3902 3904 3905 3907 3909 3910 3911 3912
group fixed id 3913 3914 3915 3916 3918 3920 3921 3923 3925 3926
group fixed id 3927 3928 3929 3930 3931 3932 3934 3936 3937 3939
group fixed id 3941 3942 3943 3944 3945 3946 3947 3948 3950 3952
group fixed id 3953 3955 3957 3958 3959 3960 3961 3962 3963 3964
group fixed id 3966 3968 3969 3971 3973 3974 3975 3976 3977 3978
group fixed id 3979 3980 3982 3984 3985 3987 3989 3990 3991 3992
group fixed id 3993 3994 3995 3996 3998 4000 4001 4003 4005 4006
group fixed id 4007 4008 4009 4010 4011 4012 4014 4016 4017 4019
group fixed id 4021 4022 4023 4024 4025 4026 4027 4028 4030 4032
group fixed id 4033 4035 4037 4038 4039 4040 4041 4042 4043 4044
group fixed id 4046 4048 4049 4051 4053 4054 4055 4056 4057 4058
group fixed id 4059 4060 4062 4064 4065 4067 4069 4070 4071 4072
group fixed id 4073 4074 4075 4076 4078 4080 4081 4083 4085 4086
group fixed id 4087 4088 4089 4090 4091 4092 4094 4096 4097 4099
group fixed id 4101 4102 4103 4104 4105 4106 4107 4108 4110 4112
group fixed id 4113 4115 4117 4118 4119 4120 4121 4122 4123 4124
group fixed id 4126 4128 4129 4131 4133 4134 4135 4136 4137 4138
group fixed id 4139 4140 4142 4144 4145 4147 4149 4150 4151 4152
group fixed id 4153 4154 4155 4156 4158 4160 4161 4163 4165 4166
group fixed id 4167 4168 4169 4170 4171 4172 4174 4176 4177 4179
group fixed id 4181 4182 4183 4184 4185 4186 4187 4188 4190 4192
group fixed id 4193 4195 4197 4198 4199 4200 4201 4202 4203 4204
group fixed id 4206 4208 4209 4211 4213 4214 4215 4216 4217 4218
group fixed id 4219 4220 4222 4224 4225 4227 4229 4230 4231 4232
group fixed id 4233 4234 4235 4236 4238 4240 4241 4243 4245 4246
group fixed id 4247 4248 4249 4250 4251 4252 4254 4256 4257 4259
group fixed id 4261 4262 4263 4264 4265 4266 4267 4268 4270 4272
group fixed id 4273 4275 4277 4278 4279 4280 4281 4282 4283 4284
group fixed id 4286 4288 4289 4291 4293 4294 4295 4296 4297 4298
group fixed id 4299 4300 4302 4304 4305 4307 4309 4310 4311 4312
group fixed id 4313 4314 4315 4316 4318 4320 4321 4323 4325 4326
group fixed id 4327 4328 4329 4330 4331 4332 4334 4336 4337 4339
group fixed id 4341 4342 4343 4344 4345 4346 4347 4348 4350 4352
group fixed id 4353 4355 4357 4358 4359 4360 4361 4362 4363 4364
group fixed id 4366 4368 4369 4371 4373 4374 4375 4376 4377 4378
group fixed id 4379 4380 4382 4384 4385 4387 4389 4390 4391 4392
group fixed id 4393 4394 4395 4396 4398 4400 4401 4403 4405 4406
group fixed id 4407 4408 4409 4410 4411 4412 4414 4416 4417 4419
group fixed id 4421 4422 4423 4424 4425 4426 4427 4428 4430 4432
group fixed id 4433 4435 4437 4438 4439 4440 4441 4442 4443 4444
group fixed id 4446 4448 4449 4451 4453 4454 4455 4456 4457 4458
group fixed id 4459 4460 4462 4464 4465 4467 4469 4470 4471 4472
group fixed id 4473 4474 4475 4476 4478 4480 4481 4483 4485 4486
group fixed id 4487 4488 4489 4490 4491 4492 4494 4496 4497 4499
group fixed id 4501 4502 4503 4504 4505 4506 4507 4508 4510 4512
group fixed id 4513 4515 4517 4518 4519 4520 4521 4522 4523 4524
group fixed id 4526 4528 4529 4531 4533 4534 4535 4536 4537 4538
group fixed id 4539 4540 4542 4544 4545 4547 4549 4550 4551 4552
group fixed id 4553 4554 4555 4556 4558 4560 4561 4563 4565 4566
group fixed id 4567 4568 4569 4570 4571 4572 4574 4576 4577 4579
group fixed id 4581 4582 4583 4584 4585 4586 4587 4588 4590 4592
group fixed id 4593 4595 4597 4598 4599 4600 4601 4602 4603 4604
group fixed id 4606 4608 4609 4611 4613 4614 4615 4616 4617 4618
group fixed id 4619 4620 4622 4624 4625 4627 4629 4630 4631 4632
group fixed id 4633 4634 4635 4636 4638 4640 4641 4643 4645 4646
group fixed id 4647 4648 4649 4650 4651 4652 4654 4656
group movable subtract all fixed
compute sum_f1 movable reduce sum fx fy fz
variable sum_fx equal c_sum_f1[1]
variable sum_fy equal c_sum_f1[2]
variable sum_fz equal c_sum_f1[3]
uncompute thermo_temp
compute thermo_temp movable temp
#
# Subsets
#
group subset_thermostat id 1 3 5 6 7 8 9 10 11 12
group subset_thermostat id 16 17 19 21 23 24 25 26 27 28
group subset_thermostat id 30 32 33 35 37 38 39 40 41 42
group subset_thermostat id 43 44 48 49 51 53 55 56 57 58
group subset_thermostat id 59 60 62 64 65 67 69 70 71 72
group subset_thermostat id 73 74 75 76 80 81 83 85 87 88
group subset_thermostat id 89 90 91 92 94 96 97 99 101 102
group subset_thermostat id 103 104 105 106 107 108 112 113 115 117
group subset_thermostat id 119 120 121 122 123 124 126 128 129 131
group subset_thermostat id 133 134 135 136 137 138 139 140 144 145
group subset_thermostat id 147 149 151 152 153 154 155 156 158 160
group subset_thermostat id 161 163 165 166 167 168 169 170 171 172
group subset_thermostat id 176 177 179 181 183 184 185 186 187 188
group subset_thermostat id 190 192 193 195 197 198 199 200 201 202
group subset_thermostat id 203 204 208 209 211 213 215 216 217 218
group subset_thermostat id 219 220 222 224 225 227 229 230 231 232
group subset_thermostat id 233 234 235 236 240 241 243 245 247 248
group subset_thermostat id 249 250 251 252 254 256 257 259 261 262
group subset_thermostat id 263 264 265 266 267 268 272 273 275 277
group subset_thermostat id 279 280 281 282 283 284 286 288 289 291
group subset_thermostat id 293 294 295 296 297 298 299 300 304 305
group subset_thermostat id 307 309 311 312 313 314 315 316 318 320
group subset_thermostat id 321 323 325 326 327 328 329 330 331 332
group subset_thermostat id 336 337 339 341 343 344 345 346 347 348
group subset_thermostat id 350 352 353 355 357 358 359 360 361 362
group subset_thermostat id 363 364 368 369 371 373 375 376 377 378
group subset_thermostat id 379 380 382 384 385 387 389 390 391 392
group subset_thermostat id 393 394 395 396 400 401 403 405 407 408
group subset_thermostat id 409 410 411 412 414 416 417 419 421 422
group subset_thermostat id 423 424 425 426 427 428 432 433 435 437
group subset_thermostat id 439 440 441 442 443 444 446 448 449 451
group subset_thermostat id 453 454 455 456 457 458 459 460 464 465
group subset_thermostat id 467 469 471 472 473 474 475 476 478 480
group subset_thermostat id 481 483 485 486 487 488 489 490 491 492
group subset_thermostat id 496 497 499 501 503 504 505 506 507 508
group subset_thermostat id 510 512 513 515 517 518 519 520 521 522
group subset_thermostat id 523 524 528 529 531 533 535 536 537 538
group subset_thermostat id 539 540 542 544 545 547 549 550 551 552
group subset_thermostat id 553 554 555 556 560 561 563 565 567 568
group subset_thermostat id 569 570 571 572 574 576 577 579 581 582
group subset_thermostat id 583 584 585 586 587 588 592 593 595 597
group subset_thermostat id 599 600 601 602 603 604 606 608 609 611
group subset_thermostat id 613 614 615 616 617 618 619 620 624 625
group subset_thermostat id 627 629 631 632 633 634 635 636 638 640
group subset_thermostat id 641 643 645 646 647 648 649 650 651 652
group subset_thermostat id 656 657 659 661 663 664 665 666 667 668
group subset_thermostat id 670 672 673 675 677 678 679 680 681 682
group subset_thermostat id 683 684 688 689 691 693 695 696 697 698
group subset_thermostat id 699 700 702 704 705 707 709 710 711 712
group subset_thermostat id 713 714 715 716 720 721 723 725 727 728
group subset_thermostat id 729 730 731 732 734 736 737 739 741 742
group subset_thermostat id 743 744 745 746 747 748 752 753 755 757
group subset_thermostat id 759 760 761 762 763 764 766 768 769 771
group subset_thermostat id 773 774 775 776 777 778 779 780 784 785
group subset_thermostat id 787 789 791 792 793 794 795 796 798 800
group subset_thermostat id 801 803 805 806 807 808 809 810 811 812
group subset_thermostat id 816 817 819 821 823 824 825 826 827 828
group subset_thermostat id 830 832 833 835 837 838 839 840 841 842
group subset_thermostat id 843 844 848 849 851 853 855 856 857 858
group subset_thermostat id 859 860 862 864 865 867 869 870 871 872
group subset_thermostat id 873 874 875 876 880 881 883 885 887 888
group subset_thermostat id 889 890 891 892 894 896 897 899 901 902
group subset_thermostat id 903 904 905 906 907 908 912 913 915 917
group subset_thermostat id 919 920 921 922 923 924 926 928 929 931
group subset_thermostat id 933 934 935 936 937 938 939 940 944 945
group subset_thermostat id 947 949 951 952 953 954 955 956 958 960
group subset_thermostat id 961 963 965 966 967 968 969 970 971 972
group subset_thermostat id 976 977 979 981 983 984 985 986 987 988
group subset_thermostat id 990 992 993 995 997 998 999 1000 1001 1002
group subset_thermostat id 1003 1004 1008 1009 1011 1013 1015 1016 1017 1018
group subset_thermostat id 1019 1020 1022 1024 1025 1027 1029 1030 1031 1032
group subset_thermostat id 1033 1034 1035 1036 1040 1041 1043 1045 1047 1048
group subset_thermostat id 1049 1050 1051 1052 1054 1056 1057 1059 1061 1062
group subset_thermostat id 1063 1064 1065 1066 1067 1068 1072 1073 1075 1077
group subset_thermostat id 1079 1080 1081 1082 1083 1084 1086 1088 1089 1091
group subset_thermostat id 1093 1094 1095 1096 1097 1098 1099 1100 1104 1105
group subset_thermostat id 1107 1109 1111 1112 1113 1114 1115 1116 1118 1120
group subset_thermostat id 1121 1123 1125 1126 1127 1128 1129 1130 1131 1132
group subset_thermostat id 1136 1137 1139 1141 1143 1144 1145 1146 1147 1148
group subset_thermostat id 1150 1152 1153 1155 1157 1158 1159 1160 1161 1162
group subset_thermostat id 1163 1164 1168 1169 1171 1173 1175 1176 1177 1178
group subset_thermostat id 1179 1180 1182 1184 1185 1187 1189 1190 1191 1192
group subset_thermostat id 1193 1194 1195 1196 1200 1201 1203 1205 1207 1208
group subset_thermostat id 1209 1210 1211 1212 1214 1216 1217 1219 1221 1222
group subset_thermostat id 1223 1224 1225 1226 1227 1228 1232 1233 1235 1237
group subset_thermostat id 1239 1240 1241 1242 1243 1244 1246 1248 1249 1251
group subset_thermostat id 1253 1254 1255 1256 1257 1258 1259 1260 1264 1265
group subset_thermostat id 1267 1269 1271 1272 1273 1274 1275 1276 1278 1280
group subset_thermostat id 1281 1283 1296 1297 1299 1312 1313 1315 1328 1329
group subset_thermostat id 1331 1344 1345 1347 1360 1361 1363 1376 1377 1379
group subset_thermostat id 1392 1393 1395 1408 1409 1411 1424 1425 1427 1440
group subset_thermostat id 1441 1443 1456 1457 1459 1472 1473 1475 1488 1489
group subset_thermostat id 1491 1504 1505 1507 1520 1521 1523 1536 1537 1539
group subset_thermostat id 1552 1553 1555 1568 1569 1571 1584 1585 1587 1600
group subset_thermostat id 1601 1603 1616 1617 1619 1632 1633 1635 1648 1649
group subset_thermostat id 1651 1664 1665 1667 1680 1681 1683 1696 1697 1699
group subset_thermostat id 1712 1713 1715 1728 1729 1731 1744 1745 1747 1760
group subset_thermostat id 1761 1763 1776 1777 1779 1792 1793 1795 1808 1809
group subset_thermostat id 1811 1824 1825 1827 1840 1841 1843 1856 1857 1859
group subset_thermostat id 1872 1873 1875 1888 1889 1891 1904 1905 1907 1920
group subset_thermostat id 1921 1923 1936 1937 1939 1952 1953 1955 1968 1969
group subset_thermostat id 1971 1984 1985 1987 2000 2001 2003 2016 2017 2019
group subset_thermostat id 2032 2033 2035 2048 2049 2050 2053 2054 2055 2058
group subset_thermostat id 2059 2060 2063 2064 2065 2068 2069 2070 2073 2074
group subset_thermostat id 2075 2078 2079 2080 2083 2084 2085 2088 2089 2090
group subset_thermostat id 2093 2094 2095 2098 2099 2100 2103 2104 2105 2108
group subset_thermostat id 2109 2110 2113 2114 2115 2118 2119 2120 2123 2124
group subset_thermostat id 2125 2128 2129 2130 2133 2134 2135 2138 2139 2140
group subset_thermostat id 2143 2144 2145 2148 2149 2150 2153 2154 2155 2158
group subset_thermostat id 2159 2160 2163 2164 2165 2168 2169 2170 2173 2174
group subset_thermostat id 2175 2178 2179 2180 2183 2184 2185 2188 2189 2190
group subset_thermostat id 2193 2194 2195 2198 2199 2200 2203 2204 2205 2208
group subset_thermostat id 2209 2210 2213 2214 2215 2218 2219 2220 2223 2224
group subset_thermostat id 2225 2228 2229 2230 2233 2234 2235 2238 2239 2240
group subset_thermostat id 2243 2244 2245 2248 2249 2250 2253 2254 2255 2258
group subset_thermostat id 2259 2260 2263 2264 2265 2268 2269 2270 2273 2274
group subset_thermostat id 2275 2278 2279 2280 2283 2284 2285 2288 2289 2290
group subset_thermostat id 2293 2294 2295 2298 2299 2300 2303 2304 2305 2308
group subset_thermostat id 2309 2310 2313 2314 2315 2318 2319 2320 2323 2324
group subset_thermostat id 2325 2328 2329 2330 2333 2334 2335 2338 2339 2340
group subset_thermostat id 2343 2344 2345 2348 2349 2350 2353 2354 2355 2358
group subset_thermostat id 2359 2360 2363 2364 2365 2368 2369 2370 2373 2374
group subset_thermostat id 2375 2378 2379 2380 2383 2384 2385 2388 2389 2390
group subset_thermostat id 2393 2394 2395 2398 2399 2400 2403 2404 2405 2408
group subset_thermostat id 2409 2410 2413 2414 2415 2418 2419 2420 2423 2424
group subset_thermostat id 2425 2428 2429 2430 2433 2434 2435 2438 2439 2440
group subset_thermostat id 2443 2444 2445 2448 2449 2450 2453 2454 2455 2458
group subset_thermostat id 2459 2460 2463 2464 2465 2468 2469 2470 2473 2474
group subset_thermostat id 2475 2478 2479 2480 2483 2484 2485 2488 2489 2490
group subset_thermostat id 2493 2494 2495 2498 2499 2500 2503 2504 2505 2508
group subset_thermostat id 2509 2510 2513 2514 2515 2518 2519 2520 2523 2524
group subset_thermostat id 2525 2528 2529 2530 2533 2534 2535 2538 2539 2540
group subset_thermostat id 2543 2544 2545 2548 2549 2550 2553 2554 2555 2558
group subset_thermostat id 2559 2560 2563 2564 2565 2568 2569 2570 2573 2574
group subset_thermostat id 2575 2578 2579 2580 2583 2584 2585 2588 2589 2590
group subset_thermostat id 2593 2594 2595 2598 2599 2600 2603 2604 2605 2608
group subset_thermostat id 2609 2610 2613 2614 2615 2618 2619 2620 2623 2624
group subset_thermostat id 2625 2628 2629 2630 2633 2634 2635 2638 2639 2640
group subset_thermostat id 2643 2644 2645 2648 2649 2650 2653 2654 2655 2658
group subset_thermostat id 2659 2660 2663 2664 2665 2668 2669 2670 2673 2674
group subset_thermostat id 2675 2678 2679 2680 2683 2684 2685 2688 2689 2691
group subset_thermostat id 2699 2700 2702 2710 2711 2713 2721 2722 2724 2732
group subset_thermostat id 2733 2735 2743 2744 2746 2754 2755 2757 2765 2766
group subset_thermostat id 2768 2776 2777 2779 2787 2788 2790 2798 2799 2801
group subset_thermostat id 2809 2810 2812 2820 2821 2823 2831 2832 2834 2842
group subset_thermostat id 2843 2845 2853 2854 2856 2864 2865 2867 2880 2881
group subset_thermostat id 2883 2896 2897 2899 2912 2913 2915 2928 2929 2931
group subset_thermostat id 2944 2945 2947 2960 2961 2963 2976 2977 2979 2992
group subset_thermostat id 2993 2995 3008 3009 3011 3024 3025 3027 3040 3041
group subset_thermostat id 3043 3056 3057 3059 3072 3073 3075 3088 3089 3091
group subset_thermostat id 3104 3105 3107 3120 3121 3123 3136 3137 3139 3152
group subset_thermostat id 3153 3155 3168 3169 3171 3184 3185 3187 3200 3201
group subset_thermostat id 3203 3216 3217 3219 3232 3233 3235 3248 3249 3251
group subset_thermostat id 3264 3265 3267 3280 3281 3283 3296 3297 3299 3312
group subset_thermostat id 3313 3315 3328 3329 3331 3344 3345 3347 3360 3361
group subset_thermostat id 3363 3376 3377 3379 3382 3384 3386 3388 3390 3392
group subset_thermostat id 3393 3395 3398 3400 3402 3404 3406 3408 3409 3411
group subset_thermostat id 3414 3416 3418 3420 3422 3424 3425 3427 3430 3432
group subset_thermostat id 3434 3436 3438 3440 3441 3443 3446 3448 3450 3452
group subset_thermostat id 3454 3456 3457 3459 3462 3464 3466 3468 3470 3472
group subset_thermostat id 3473 3475 3478 3480 3482 3484 3486 3488 3489 3491
group subset_thermostat id 3494 3496 3498 3500 3502 3504 3505 3507 3510 3512
group subset_thermostat id 3514 3516 3518 3520 3521 3523 3526 3528 3530 3532
group subset_thermostat id 3534 3536 3537 3539 3542 3544 3546 3548 3550 3552
group subset_thermostat id 3553 3555 3558 3560 3562 3564 3566 3568 3569 3571
group subset_thermostat id 3574 3576 3578 3580 3582 3584 3585 3587 3590 3592
group subset_thermostat id 3594 3596 3598 3600 3601 3603 3606 3608 3610 3612
group subset_thermostat id 3614 3616 3617 3619 3622 3624 3626 3628 3630 3632
group subset_thermostat id 3633 3635 3637 3638 3639 3640 3641 3642 3643 3644
group subset_thermostat id 3646 3648 3649 3651 3653 3654 3655 3656 3657 3658
group subset_thermostat id 3659 3660 3662 3664 3665 3667 3669 3670 3671 3672
group subset_thermostat id 3673 3674 3675 3676 3678 3680 3681 3683 3685 3686
group subset_thermostat id 3687 3688 3689 3690 3691 3692 3694 3696 3697 3699
group subset_thermostat id 3701 3702 3703 3704 3705 3706 3707 3708 3710 3712
group subset_thermostat id 3713 3715 3717 3718 3719 3720 3721 3722 3723 3724
group subset_thermostat id 3726 3728 3729 3731 3733 3734 3735 3736 3737 3738
group subset_thermostat id 3739 3740 3742 3744 3745 3747 3749 3750 3751 3752
group subset_thermostat id 3753 3754 3755 3756 3758 3760 3761 3763 3765 3766
group subset_thermostat id 3767 3768 3769 3770 3771 3772 3774 3776 3777 3779
group subset_thermostat id 3781 3782 3783 3784 3785 3786 3787 3788 3790 3792
group subset_thermostat id 3793 3795 3797 3798 3799 3800 3801 3802 3803 3804
group subset_thermostat id 3806 3808 3809 3811 3813 3814 3815 3816 3817 3818
group subset_thermostat id 3819 3820 3822 3824 3825 3827 3829 3830 3831 3832
group subset_thermostat id 3833 3834 3835 3836 3838 3840 3841 3843 3845 3846
group subset_thermostat id 3847 3848 3849 3850 3851 3852 3854 3856 3857 3859
group subset_thermostat id 3861 3862 3863 3864 3865 3866 3867 3868 3870 3872
group subset_thermostat id 3873 3875 3877 3878 3879 3880 3881 3882 3883 3884
group subset_thermostat id 3886 3888 3889 3891 3893 3894 3895 3896 3897 3898
group subset_thermostat id 3899 3900 3902 3904 3905 3907 3909 3910 3911 3912
group subset_thermostat id 3913 3914 3915 3916 3918 3920 3921 3923 3925 3926
group subset_thermostat id 3927 3928 3929 3930 3931 3932 3934 3936 3937 3939
group subset_thermostat id 3941 3942 3943 3944 3945 3946 3947 3948 3950 3952
group subset_thermostat id 3953 3955 3957 3958 3959 3960 3961 3962 3963 3964
group subset_thermostat id 3966 3968 3969 3971 3973 3974 3975 3976 3977 3978
group subset_thermostat id 3979 3980 3982 3984 3985 3987 3989 3990 3991 3992
group subset_thermostat id 3993 3994 3995 3996 3998 4000 4001 4003 4005 4006
group subset_thermostat id 4007 4008 4009 4010 4011 4012 4014 4016 4017 4019
group subset_thermostat id 4021 4022 4023 4024 4025 4026 4027 4028 4030 4032
group subset_thermostat id 4033 4035 4037 4038 4039 4040 4041 4042 4043 4044
group subset_thermostat id 4046 4048 4049 4051 4053 4054 4055 4056 4057 4058
group subset_thermostat id 4059 4060 4062 4064 4065 4067 4069 4070 4071 4072
group subset_thermostat id 4073 4074 4075 4076 4078 4080 4081 4083 4085 4086
group subset_thermostat id 4087 4088 4089 4090 4091 4092 4094 4096 4097 4099
group subset_thermostat id 4101 4102 4103 4104 4105 4106 4107 4108 4110 4112
group subset_thermostat id 4113 4115 4117 4118 4119 4120 4121 4122 4123 4124
group subset_thermostat id 4126 4128 4129 4131 4133 4134 4135 4136 4137 4138
group subset_thermostat id 4139 4140 4142 4144 4145 4147 4149 4150 4151 4152
group subset_thermostat id 4153 4154 4155 4156 4158 4160 4161 4163 4165 4166
group subset_thermostat id 4167 4168 4169 4170 4171 4172 4174 4176 4177 4179
group subset_thermostat id 4181 4182 4183 4184 4185 4186 4187 4188 4190 4192
group subset_thermostat id 4193 4195 4197 4198 4199 4200 4201 4202 4203 4204
group subset_thermostat id 4206 4208 4209 4211 4213 4214 4215 4216 4217 4218
group subset_thermostat id 4219 4220 4222 4224 4225 4227 4229 4230 4231 4232
group subset_thermostat id 4233 4234 4235 4236 4238 4240 4241 4243 4245 4246
group subset_thermostat id 4247 4248 4249 4250 4251 4252 4254 4256 4257 4259
group subset_thermostat id 4261 4262 4263 4264 4265 4266 4267 4268 4270 4272
group subset_thermostat id 4273 4275 4277 4278 4279 4280 4281 4282 4283 4284
group subset_thermostat id 4286 4288 4289 4291 4293 4294 4295 4296 4297 4298
group subset_thermostat id 4299 4300 4302 4304 4305 4307 4309 4310 4311 4312
group subset_thermostat id 4313 4314 4315 4316 4318 4320 4321 4323 4325 4326
group subset_thermostat id 4327 4328 4329 4330 4331 4332 4334 4336 4337 4339
group subset_thermostat id 4341 4342 4343 4344 4345 4346 4347 4348 4350 4352
group subset_thermostat id 4353 4355 4357 4358 4359 4360 4361 4362 4363 4364
group subset_thermostat id 4366 4368 4369 4371 4373 4374 4375 4376 4377 4378
group subset_thermostat id 4379 4380 4382 4384 4385 4387 4389 4390 4391 4392
group subset_thermostat id 4393 4394 4395 4396 4398 4400 4401 4403 4405 4406
group subset_thermostat id 4407 4408 4409 4410 4411 4412 4414 4416 4417 4419
group subset_thermostat id 4421 4422 4423 4424 4425 4426 4427 4428 4430 4432
group subset_thermostat id 4433 4435 4437 4438 4439 4440 4441 4442 4443 4444
group subset_thermostat id 4446 4448 4449 4451 4453 4454 4455 4456 4457 4458
group subset_thermostat id 4459 4460 4462 4464 4465 4467 4469 4470 4471 4472
group subset_thermostat id 4473 4474 4475 4476 4478 4480 4481 4483 4485 4486
group subset_thermostat id 4487 4488 4489 4490 4491 4492 4494 4496 4497 4499
group subset_thermostat id 4501 4502 4503 4504 4505 4506 4507 4508 4510 4512
group subset_thermostat id 4513 4515 4517 4518 4519 4520 4521 4522 4523 4524
group subset_thermostat id 4526 4528 4529 4531 4533 4534 4535 4536 4537 4538
group subset_thermostat id 4539 4540 4542 4544 4545 4547 4549 4550 4551 4552
group subset_thermostat id 4553 4554 4555 4556 4558 4560 4561 4563 4565 4566
group subset_thermostat id 4567 4568 4569 4570 4571 4572 4574 4576 4577 4579
group subset_thermostat id 4581 4582 4583 4584 4585 4586 4587 4588 4590 4592
group subset_thermostat id 4593 4595 4597 4598 4599 4600 4601 4602 4603 4604
group subset_thermostat id 4606 4608 4609 4611 4613 4614 4615 4616 4617 4618
group subset_thermostat id 4619 4620 4622 4624 4625 4627 4629 4630 4631 4632
group subset_thermostat id 4633 4634 4635 4636 4638 4640 4641 4643 4645 4646
group subset_thermostat id 4647 4648 4649 4650 4651 4652 4654 4656
group subset_N_atom id 4657
log 2.2_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.2: Set the initial velocities for $T
#-------------------------------------------------------------------------------
velocity movable create 300 72489 dist gaussian mom yes rot no
velocity fixed set 0.0 0.0 0.0
log 2.3_Deposition.out
#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 100 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_N_atom id 4657
delete_atoms group deposition_atoms_N_atom
molecule depositing_species_N_atom deposition_N_atom.dat
region deposition_region_N_atom block EDGE EDGE EDGE EDGE 50 60 units box
region evaporation_region block EDGE EDGE EDGE EDGE 90 EDGE units box
group evaporation_group dynamic all region evaporation_region every 1000
uncompute thermo_temp
compute thermo_temp movable temp
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
fix 1 movable nve
fix 2 evaporation_group reax/c/species 1 1 1000 removed_fragments.out element N Si terse yes
fix 3 all evaporate 1000 1000 evaporation_region 1 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 401 tally yes
fix 4 movable ave/time 1 50000 50000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_averages.txt off 1
fix 5 movable ave/time 50000000 1 50000000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_instantaneous.txt
fix 6 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix deposition_N_atom_1 deposition_atoms_N_atom deposit 500 0 1000 1 region deposition_region_N_atom mol depositing_species_N_atom vz -0.10564503102330547 -0.12912170458404001 vx 0.020697854830212851 -0.020697854830212851 vy 0.020697854830212851 -0.020697854830212851 near 1.50 id next units box
fix deposition_N_atom_2 deposition_atoms_N_atom nve
dump trj all custom 50000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_N_atom deposition_atoms_N_atom custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
timestep 0.2
run 500000
write_dump all xyz final_2.3.xyz modify element N Si
undump trj
unfix trjE
undump trj_N_atom
write_dump deposition_atoms_N_atom custom 2.3.deposited_1.xyz id mol type q xs ys zs
restart 0
dump sci all custom 500000 2.3.xyz id mol type q xs ys zs
run 0
undump sci
unfix 1
unfix 2
unfix 3
unfix 4
unfix 5
unfix 6
unfix deposition_N_atom_1
unfix deposition_N_atom_2
unfix dlan