# This is the control script for LAMMPS. 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 pair_style lj/class2/coul/long 12 pair_modify mix sixthpower pair_modify tail yes bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0 box tilt large read_data structure.dat include parameters.dat neighbor 2.0 bin neigh_modify delay 0 every 1 check yes kspace_style pppm 0.00001 variable R equal 0.00198722 variable sysvol equal vol variable sysmass equal mass(all)/6.0221367e+23 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 movable union all group fixed subtract all movable 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] # # Subsets # group subset_Li id 1 2 3 4 5 6 7 8 9 10 group subset_Li id 11 12 13 14 15 16 17 18 19 20 group subset_Li id 21 22 23 24 25 26 27 28 29 30 group subset_Li id 31 32 33 34 35 36 37 38 39 40 group subset_Li id 41 42 43 44 45 46 47 48 49 50 group subset_Li id 51 52 53 54 55 56 57 58 59 60 group subset_Li id 61 62 63 64 65 66 67 68 69 70 group subset_Li id 71 72 73 74 75 76 77 78 79 80 group subset_Li id 81 82 83 84 85 86 87 88 89 90 group subset_Li id 91 92 93 94 95 96 97 98 99 100 group subset_Li id 101 102 103 104 105 106 107 108 109 110 group subset_Li id 111 112 113 114 115 116 117 118 119 120 group subset_Li id 121 122 123 124 125 126 127 128 129 130 group subset_Li id 131 132 133 134 135 136 137 138 139 140 group subset_Li id 141 142 143 144 145 146 147 148 149 150 group subset_Li id 151 152 153 154 155 156 157 158 159 160 group subset_Li id 161 162 163 164 165 166 167 168 169 170 group subset_Li id 171 172 173 174 175 176 177 group subset_Cl id 178 179 180 181 182 183 184 185 186 187 group subset_Cl id 188 189 190 191 192 193 194 195 196 197 group subset_Cl id 198 199 200 201 202 203 204 205 206 207 group subset_Cl id 208 209 210 211 212 213 214 215 216 217 group subset_Cl id 218 219 220 221 222 223 224 225 226 227 group subset_Cl id 228 229 230 231 232 233 234 235 236 237 group subset_Cl id 238 239 240 241 242 243 244 245 246 247 group subset_Cl id 248 249 250 251 252 253 254 255 256 257 group subset_Cl id 258 259 260 261 262 263 264 265 266 267 group subset_Cl id 268 269 270 271 272 273 274 275 276 277 group subset_Cl id 278 279 280 281 282 283 284 285 286 287 group subset_Cl id 288 289 290 291 292 293 294 295 296 297 group subset_Cl id 298 299 300 301 302 303 304 305 306 307 group subset_Cl id 308 309 310 311 312 313 314 315 316 317 group subset_Cl id 318 319 320 321 322 323 324 325 326 327 group subset_Cl id 328 329 330 331 332 333 334 335 336 337 group subset_Cl id 338 339 340 341 342 343 344 345 346 347 group subset_Cl id 348 349 350 351 352 353 354 group subset_O(H2O) id 355 358 361 364 367 370 373 376 379 382 group subset_O(H2O) id 385 388 391 394 397 400 403 406 409 412 group subset_O(H2O) id 415 418 421 424 427 430 433 436 439 442 group subset_O(H2O) id 445 448 451 454 457 460 463 466 469 472 group subset_O(H2O) id 475 478 481 484 487 490 493 496 499 502 group subset_O(H2O) id 505 508 511 514 517 520 523 526 529 532 group subset_O(H2O) id 535 538 541 544 547 550 553 556 559 562 group subset_O(H2O) id 565 568 571 574 577 580 583 586 589 592 group subset_O(H2O) id 595 598 601 604 607 610 613 616 619 622 group subset_O(H2O) id 625 628 631 634 637 640 643 646 649 652 group subset_O(H2O) id 655 658 661 664 667 670 673 676 679 682 group subset_O(H2O) id 685 688 691 694 697 700 703 706 709 712 group subset_O(H2O) id 715 718 721 724 727 730 733 736 739 742 group subset_O(H2O) id 745 748 751 754 757 760 763 766 769 772 group subset_O(H2O) id 775 778 781 784 787 790 793 796 799 802 group subset_O(H2O) id 805 808 811 814 817 820 823 826 829 832 group subset_O(H2O) id 835 838 841 844 847 850 853 856 859 862 group subset_O(H2O) id 865 868 871 874 877 880 883 886 889 892 group subset_O(H2O) id 895 898 901 904 907 910 913 916 919 922 group subset_O(H2O) id 925 928 931 934 937 940 943 946 949 952 group subset_O(H2O) id 955 958 961 964 967 970 973 976 979 982 group subset_O(H2O) id 985 988 991 994 997 1000 1003 1006 1009 1012 group subset_O(H2O) id 1015 1018 1021 1024 1027 1030 1033 1036 1039 1042 group subset_O(H2O) id 1045 1048 1051 1054 1057 1060 1063 1066 1069 1072 group subset_O(H2O) id 1075 1078 1081 1084 1087 1090 1093 1096 1099 1102 group subset_O(H2O) id 1105 1108 1111 1114 1117 1120 1123 1126 1129 1132 group subset_O(H2O) id 1135 1138 1141 1144 1147 1150 1153 1156 1159 1162 group subset_O(H2O) id 1165 1168 1171 1174 1177 1180 1183 1186 1189 1192 group subset_O(H2O) id 1195 1198 1201 1204 1207 1210 1213 1216 1219 1222 group subset_O(H2O) id 1225 1228 1231 1234 1237 1240 1243 1246 1249 1252 group subset_O(H2O) id 1255 1258 1261 1264 1267 1270 1273 1276 1279 1282 group subset_O(H2O) id 1285 1288 1291 1294 1297 1300 1303 1306 1309 1312 group subset_O(H2O) id 1315 1318 1321 1324 1327 1330 1333 1336 1339 1342 group subset_O(H2O) id 1345 1348 1351 1354 1357 1360 1363 1366 1369 1372 group subset_O(H2O) id 1375 1378 1381 1384 1387 1390 1393 1396 1399 1402 group subset_O(H2O) id 1405 1408 1411 1414 1417 1420 1423 1426 1429 1432 group subset_O(H2O) id 1435 1438 1441 1444 1447 1450 1453 1456 1459 1462 group subset_O(H2O) id 1465 1468 1471 1474 1477 1480 1483 1486 1489 1492 group subset_O(H2O) id 1495 1498 1501 1504 1507 1510 1513 1516 1519 1522 group subset_O(H2O) id 1525 1528 1531 1534 1537 1540 1543 1546 1549 1552 group subset_O(H2O) id 1555 1558 1561 1564 1567 1570 1573 1576 1579 1582 group subset_O(H2O) id 1585 1588 1591 1594 1597 1600 1603 1606 1609 1612 group subset_O(H2O) id 1615 1618 1621 1624 1627 1630 1633 1636 1639 1642 group subset_O(H2O) id 1645 1648 1651 1654 1657 1660 1663 1666 1669 1672 group subset_O(H2O) id 1675 1678 1681 1684 1687 1690 1693 1696 1699 1702 group subset_O(H2O) id 1705 1708 1711 1714 1717 1720 1723 1726 1729 1732 group subset_O(H2O) id 1735 1738 1741 1744 1747 1750 1753 1756 1759 1762 group subset_O(H2O) id 1765 1768 1771 1774 1777 1780 1783 1786 1789 1792 group subset_O(H2O) id 1795 1798 1801 1804 1807 1810 1813 1816 1819 1822 group subset_O(H2O) id 1825 1828 1831 1834 1837 1840 1843 1846 1849 1852 group subset_O(H2O) id 1855 1858 1861 1864 1867 1870 1873 1876 1879 1882 group subset_O(H2O) id 1885 1888 1891 1894 1897 1900 1903 1906 1909 1912 group subset_O(H2O) id 1915 1918 1921 1924 1927 1930 1933 1936 1939 1942 group subset_O(H2O) id 1945 1948 1951 1954 1957 1960 1963 1966 1969 1972 group subset_O(H2O) id 1975 1978 1981 1984 1987 1990 1993 1996 1999 2002 group subset_O(H2O) id 2005 2008 2011 2014 2017 2020 2023 2026 2029 2032 group subset_O(H2O) id 2035 2038 2041 2044 2047 2050 2053 2056 2059 2062 group subset_O(H2O) id 2065 2068 2071 2074 2077 2080 2083 2086 2089 2092 group subset_O(H2O) id 2095 2098 2101 2104 2107 2110 2113 2116 2119 2122 group subset_O(H2O) id 2125 2128 2131 2134 2137 2140 2143 2146 2149 2152 group subset_O(H2O) id 2155 2158 2161 2164 2167 2170 2173 2176 2179 2182 group subset_O(H2O) id 2185 2188 2191 2194 2197 2200 2203 2206 2209 2212 group subset_O(H2O) id 2215 2218 2221 2224 2227 2230 2233 2236 2239 2242 group subset_O(H2O) id 2245 2248 2251 2254 2257 2260 2263 2266 2269 2272 group subset_O(H2O) id 2275 2278 2281 2284 2287 2290 2293 2296 2299 2302 group subset_O(H2O) id 2305 2308 2311 2314 2317 2320 2323 2326 2329 2332 group subset_O(H2O) id 2335 2338 2341 2344 2347 2350 2353 2356 2359 2362 group subset_O(H2O) id 2365 2368 2371 2374 2377 2380 2383 2386 2389 2392 group subset_O(H2O) id 2395 2398 2401 2404 2407 2410 2413 2416 2419 2422 group subset_O(H2O) id 2425 2428 2431 2434 2437 2440 2443 2446 2449 2452 group subset_O(H2O) id 2455 2458 2461 2464 2467 2470 2473 2476 2479 2482 group subset_O(H2O) id 2485 2488 2491 2494 2497 2500 2503 2506 2509 2512 group subset_O(H2O) id 2515 2518 2521 2524 2527 2530 2533 2536 2539 2542 group subset_O(H2O) id 2545 2548 2551 2554 2557 2560 2563 2566 2569 2572 group subset_O(H2O) id 2575 2578 2581 2584 2587 2590 2593 2596 2599 2602 group subset_O(H2O) id 2605 2608 2611 2614 2617 2620 2623 2626 2629 2632 group subset_O(H2O) id 2635 2638 2641 2644 2647 2650 2653 2656 2659 2662 group subset_O(H2O) id 2665 2668 2671 2674 2677 2680 2683 2686 2689 2692 group subset_O(H2O) id 2695 2698 2701 2704 2707 2710 2713 2716 2719 2722 group subset_O(H2O) id 2725 2728 2731 2734 2737 2740 2743 2746 2749 2752 group subset_O(H2O) id 2755 2758 2761 2764 2767 2770 2773 2776 2779 2782 group subset_O(H2O) id 2785 2788 2791 2794 2797 2800 2803 2806 2809 2812 group subset_O(H2O) id 2815 2818 2821 2824 2827 2830 2833 2836 2839 2842 group subset_O(H2O) id 2845 2848 2851 2854 2857 2860 2863 2866 2869 2872 group subset_O(H2O) id 2875 2878 2881 2884 2887 2890 2893 2896 2899 2902 group subset_O(H2O) id 2905 2908 2911 2914 2917 2920 2923 2926 2929 2932 group subset_O(H2O) id 2935 2938 2941 2944 2947 2950 2953 2956 2959 2962 group subset_O(H2O) id 2965 2968 2971 2974 2977 2980 2983 2986 2989 2992 group subset_O(H2O) id 2995 2998 3001 3004 3007 3010 3013 3016 3019 3022 group subset_O(H2O) id 3025 3028 3031 3034 3037 3040 3043 3046 3049 3052 group subset_O(H2O) id 3055 3058 3061 3064 3067 3070 3073 3076 3079 3082 group subset_O(H2O) id 3085 3088 3091 3094 3097 3100 3103 3106 3109 3112 group subset_O(H2O) id 3115 3118 3121 3124 3127 3130 3133 3136 3139 3142 group subset_O(H2O) id 3145 3148 3151 3154 3157 3160 3163 3166 3169 3172 group subset_O(H2O) id 3175 3178 3181 3184 3187 3190 3193 3196 3199 3202 group subset_O(H2O) id 3205 3208 3211 3214 3217 3220 3223 3226 3229 3232 group subset_O(H2O) id 3235 3238 3241 3244 3247 3250 3253 3256 3259 3262 group subset_O(H2O) id 3265 3268 3271 3274 3277 3280 3283 3286 3289 3292 group subset_O(H2O) id 3295 3298 3301 3304 3307 3310 3313 3316 3319 3322 group subset_O(H2O) id 3325 3328 3331 3334 3337 3340 3343 3346 3349 3352 group subset_O(H2O) id 3355 3358 3361 3364 3367 3370 3373 3376 3379 3382 group subset_O(H2O) id 3385 3388 3391 3394 3397 3400 3403 3406 3409 3412 group subset_O(H2O) id 3415 3418 3421 3424 3427 3430 3433 3436 3439 3442 group subset_O(H2O) id 3445 3448 3451 3454 3457 3460 3463 3466 3469 3472 group subset_O(H2O) id 3475 3478 3481 3484 3487 3490 3493 3496 3499 3502 group subset_O(H2O) id 3505 3508 3511 3514 3517 3520 3523 3526 3529 3532 group subset_O(H2O) id 3535 3538 3541 3544 3547 3550 3553 3556 3559 3562 group subset_O(H2O) id 3565 3568 3571 3574 3577 3580 3583 3586 3589 3592 group subset_O(H2O) id 3595 3598 3601 3604 3607 3610 3613 3616 3619 3622 group subset_O(H2O) id 3625 3628 3631 3634 3637 3640 3643 3646 3649 3652 group subset_O(H2O) id 3655 3658 3661 3664 3667 3670 3673 3676 3679 3682 group subset_O(H2O) id 3685 3688 3691 3694 3697 3700 3703 3706 3709 3712 group subset_O(H2O) id 3715 3718 3721 3724 3727 3730 3733 3736 3739 3742 group subset_O(H2O) id 3745 3748 3751 3754 3757 3760 3763 3766 3769 3772 group subset_O(H2O) id 3775 3778 3781 3784 3787 3790 3793 3796 3799 3802 group subset_O(H2O) id 3805 3808 3811 3814 3817 3820 3823 3826 3829 3832 group subset_O(H2O) id 3835 3838 3841 3844 3847 3850 3853 3856 3859 3862 group subset_O(H2O) id 3865 3868 3871 3874 3877 3880 3883 3886 3889 3892 group subset_O(H2O) id 3895 3898 3901 3904 3907 3910 3913 3916 3919 3922 group subset_O(H2O) id 3925 3928 3931 3934 3937 3940 3943 3946 3949 3952 group subset_O(H2O) id 3955 3958 3961 3964 3967 3970 3973 3976 3979 3982 group subset_O(H2O) id 3985 3988 3991 3994 3997 4000 4003 4006 4009 4012 group subset_O(H2O) id 4015 4018 4021 4024 4027 4030 4033 4036 4039 4042 group subset_O(H2O) id 4045 4048 4051 4054 4057 4060 4063 4066 4069 4072 group subset_O(H2O) id 4075 4078 4081 4084 4087 4090 4093 4096 4099 4102 group subset_O(H2O) id 4105 4108 4111 4114 4117 4120 4123 4126 4129 4132 group subset_O(H2O) id 4135 4138 4141 4144 4147 4150 4153 4156 4159 4162 group subset_O(H2O) id 4165 4168 4171 4174 4177 4180 4183 4186 4189 4192 group subset_O(H2O) id 4195 4198 4201 4204 4207 4210 4213 4216 4219 4222 group subset_O(H2O) id 4225 4228 4231 4234 4237 4240 4243 4246 4249 4252 group subset_O(H2O) id 4255 4258 4261 4264 4267 4270 4273 4276 4279 4282 group subset_O(H2O) id 4285 4288 4291 4294 4297 4300 4303 4306 4309 4312 group subset_O(H2O) id 4315 4318 4321 4324 4327 4330 4333 4336 4339 4342 group subset_O(H2O) id 4345 4348 4351 4354 4357 4360 4363 4366 4369 4372 group subset_O(H2O) id 4375 4378 4381 4384 4387 4390 4393 4396 4399 4402 group subset_O(H2O) id 4405 4408 4411 4414 4417 4420 4423 4426 4429 4432 group subset_O(H2O) id 4435 4438 4441 4444 4447 4450 4453 4456 4459 4462 group subset_O(H2O) id 4465 4468 4471 4474 4477 4480 4483 4486 4489 4492 group subset_O(H2O) id 4495 4498 4501 4504 4507 4510 4513 4516 4519 4522 group subset_O(H2O) id 4525 4528 4531 4534 4537 4540 4543 4546 4549 4552 group subset_O(H2O) id 4555 4558 4561 4564 4567 4570 4573 4576 4579 4582 group subset_O(H2O) id 4585 4588 4591 4594 4597 4600 4603 4606 4609 4612 group subset_O(H2O) id 4615 4618 4621 4624 4627 4630 4633 4636 4639 4642 group subset_O(H2O) id 4645 4648 4651 4654 4657 4660 4663 4666 4669 4672 group subset_O(H2O) id 4675 4678 4681 4684 4687 4690 4693 4696 4699 4702 group subset_O(H2O) id 4705 4708 4711 4714 4717 4720 4723 4726 4729 4732 group subset_O(H2O) id 4735 4738 4741 4744 4747 4750 4753 4756 4759 4762 group subset_O(H2O) id 4765 4768 4771 4774 4777 4780 4783 4786 4789 4792 group subset_O(H2O) id 4795 4798 4801 4804 4807 4810 4813 4816 4819 4822 group subset_O(H2O) id 4825 4828 4831 4834 4837 4840 4843 4846 4849 4852 group subset_O(H2O) id 4855 4858 4861 4864 4867 4870 4873 4876 4879 4882 group subset_O(H2O) id 4885 4888 4891 4894 4897 4900 4903 4906 4909 4912 group subset_O(H2O) id 4915 4918 4921 4924 4927 4930 4933 4936 4939 4942 group subset_O(H2O) id 4945 4948 4951 4954 4957 4960 4963 4966 4969 4972 group subset_O(H2O) id 4975 4978 4981 4984 4987 4990 4993 4996 4999 5002 group subset_O(H2O) id 5005 5008 5011 5014 5017 5020 5023 5026 5029 5032 group subset_O(H2O) id 5035 5038 5041 5044 5047 5050 5053 5056 5059 5062 group subset_O(H2O) id 5065 5068 5071 5074 5077 5080 5083 5086 5089 5092 group subset_O(H2O) id 5095 5098 5101 5104 5107 5110 5113 5116 5119 5122 group subset_O(H2O) id 5125 5128 5131 5134 5137 5140 5143 5146 5149 5152 group subset_O(H2O) id 5155 5158 5161 5164 5167 5170 5173 5176 5179 5182 group subset_O(H2O) id 5185 5188 5191 5194 5197 5200 5203 5206 5209 5212 group subset_O(H2O) id 5215 5218 5221 5224 5227 5230 5233 5236 5239 5242 group subset_O(H2O) id 5245 5248 5251 5254 5257 5260 5263 5266 5269 5272 group subset_O(H2O) id 5275 5278 5281 5284 5287 5290 5293 5296 5299 5302 group subset_O(H2O) id 5305 5308 5311 5314 5317 5320 5323 5326 5329 5332 group subset_O(H2O) id 5335 5338 5341 5344 5347 5350 5353 5356 5359 5362 group subset_O(H2O) id 5365 5368 5371 5374 5377 5380 5383 5386 5389 5392 group subset_O(H2O) id 5395 5398 5401 5404 5407 5410 group subset_H(H2O) id 356 357 359 360 362 363 365 366 368 369 group subset_H(H2O) id 371 372 374 375 377 378 380 381 383 384 group subset_H(H2O) id 386 387 389 390 392 393 395 396 398 399 group subset_H(H2O) id 401 402 404 405 407 408 410 411 413 414 group subset_H(H2O) id 416 417 419 420 422 423 425 426 428 429 group subset_H(H2O) id 431 432 434 435 437 438 440 441 443 444 group subset_H(H2O) id 446 447 449 450 452 453 455 456 458 459 group subset_H(H2O) id 461 462 464 465 467 468 470 471 473 474 group subset_H(H2O) id 476 477 479 480 482 483 485 486 488 489 group subset_H(H2O) id 491 492 494 495 497 498 500 501 503 504 group subset_H(H2O) id 506 507 509 510 512 513 515 516 518 519 group subset_H(H2O) id 521 522 524 525 527 528 530 531 533 534 group subset_H(H2O) id 536 537 539 540 542 543 545 546 548 549 group subset_H(H2O) id 551 552 554 555 557 558 560 561 563 564 group subset_H(H2O) id 566 567 569 570 572 573 575 576 578 579 group subset_H(H2O) id 581 582 584 585 587 588 590 591 593 594 group subset_H(H2O) id 596 597 599 600 602 603 605 606 608 609 group subset_H(H2O) id 611 612 614 615 617 618 620 621 623 624 group subset_H(H2O) id 626 627 629 630 632 633 635 636 638 639 group subset_H(H2O) id 641 642 644 645 647 648 650 651 653 654 group subset_H(H2O) id 656 657 659 660 662 663 665 666 668 669 group subset_H(H2O) id 671 672 674 675 677 678 680 681 683 684 group subset_H(H2O) id 686 687 689 690 692 693 695 696 698 699 group subset_H(H2O) id 701 702 704 705 707 708 710 711 713 714 group subset_H(H2O) id 716 717 719 720 722 723 725 726 728 729 group subset_H(H2O) id 731 732 734 735 737 738 740 741 743 744 group subset_H(H2O) id 746 747 749 750 752 753 755 756 758 759 group subset_H(H2O) id 761 762 764 765 767 768 770 771 773 774 group subset_H(H2O) id 776 777 779 780 782 783 785 786 788 789 group subset_H(H2O) id 791 792 794 795 797 798 800 801 803 804 group subset_H(H2O) id 806 807 809 810 812 813 815 816 818 819 group subset_H(H2O) id 821 822 824 825 827 828 830 831 833 834 group subset_H(H2O) id 836 837 839 840 842 843 845 846 848 849 group subset_H(H2O) id 851 852 854 855 857 858 860 861 863 864 group subset_H(H2O) id 866 867 869 870 872 873 875 876 878 879 group subset_H(H2O) id 881 882 884 885 887 888 890 891 893 894 group subset_H(H2O) id 896 897 899 900 902 903 905 906 908 909 group subset_H(H2O) id 911 912 914 915 917 918 920 921 923 924 group subset_H(H2O) id 926 927 929 930 932 933 935 936 938 939 group subset_H(H2O) id 941 942 944 945 947 948 950 951 953 954 group subset_H(H2O) id 956 957 959 960 962 963 965 966 968 969 group subset_H(H2O) id 971 972 974 975 977 978 980 981 983 984 group subset_H(H2O) id 986 987 989 990 992 993 995 996 998 999 group subset_H(H2O) id 1001 1002 1004 1005 1007 1008 1010 1011 1013 1014 group subset_H(H2O) id 1016 1017 1019 1020 1022 1023 1025 1026 1028 1029 group subset_H(H2O) id 1031 1032 1034 1035 1037 1038 1040 1041 1043 1044 group subset_H(H2O) id 1046 1047 1049 1050 1052 1053 1055 1056 1058 1059 group subset_H(H2O) id 1061 1062 1064 1065 1067 1068 1070 1071 1073 1074 group subset_H(H2O) id 1076 1077 1079 1080 1082 1083 1085 1086 1088 1089 group subset_H(H2O) id 1091 1092 1094 1095 1097 1098 1100 1101 1103 1104 group subset_H(H2O) id 1106 1107 1109 1110 1112 1113 1115 1116 1118 1119 group subset_H(H2O) id 1121 1122 1124 1125 1127 1128 1130 1131 1133 1134 group subset_H(H2O) id 1136 1137 1139 1140 1142 1143 1145 1146 1148 1149 group subset_H(H2O) id 1151 1152 1154 1155 1157 1158 1160 1161 1163 1164 group subset_H(H2O) id 1166 1167 1169 1170 1172 1173 1175 1176 1178 1179 group subset_H(H2O) id 1181 1182 1184 1185 1187 1188 1190 1191 1193 1194 group subset_H(H2O) id 1196 1197 1199 1200 1202 1203 1205 1206 1208 1209 group subset_H(H2O) id 1211 1212 1214 1215 1217 1218 1220 1221 1223 1224 group subset_H(H2O) id 1226 1227 1229 1230 1232 1233 1235 1236 1238 1239 group subset_H(H2O) id 1241 1242 1244 1245 1247 1248 1250 1251 1253 1254 group subset_H(H2O) id 1256 1257 1259 1260 1262 1263 1265 1266 1268 1269 group subset_H(H2O) id 1271 1272 1274 1275 1277 1278 1280 1281 1283 1284 group subset_H(H2O) id 1286 1287 1289 1290 1292 1293 1295 1296 1298 1299 group subset_H(H2O) id 1301 1302 1304 1305 1307 1308 1310 1311 1313 1314 group subset_H(H2O) id 1316 1317 1319 1320 1322 1323 1325 1326 1328 1329 group subset_H(H2O) id 1331 1332 1334 1335 1337 1338 1340 1341 1343 1344 group subset_H(H2O) id 1346 1347 1349 1350 1352 1353 1355 1356 1358 1359 group subset_H(H2O) id 1361 1362 1364 1365 1367 1368 1370 1371 1373 1374 group subset_H(H2O) id 1376 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1994 1995 1997 1998 2000 2001 2003 2004 group subset_H(H2O) id 2006 2007 2009 2010 2012 2013 2015 2016 2018 2019 group subset_H(H2O) id 2021 2022 2024 2025 2027 2028 2030 2031 2033 2034 group subset_H(H2O) id 2036 2037 2039 2040 2042 2043 2045 2046 2048 2049 group subset_H(H2O) id 2051 2052 2054 2055 2057 2058 2060 2061 2063 2064 group subset_H(H2O) id 2066 2067 2069 2070 2072 2073 2075 2076 2078 2079 group subset_H(H2O) id 2081 2082 2084 2085 2087 2088 2090 2091 2093 2094 group subset_H(H2O) id 2096 2097 2099 2100 2102 2103 2105 2106 2108 2109 group subset_H(H2O) id 2111 2112 2114 2115 2117 2118 2120 2121 2123 2124 group subset_H(H2O) id 2126 2127 2129 2130 2132 2133 2135 2136 2138 2139 group subset_H(H2O) id 2141 2142 2144 2145 2147 2148 2150 2151 2153 2154 group subset_H(H2O) id 2156 2157 2159 2160 2162 2163 2165 2166 2168 2169 group subset_H(H2O) id 2171 2172 2174 2175 2177 2178 2180 2181 2183 2184 group subset_H(H2O) id 2186 2187 2189 2190 2192 2193 2195 2196 2198 2199 group 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2609 2610 2612 2613 2615 2616 2618 2619 group subset_H(H2O) id 2621 2622 2624 2625 2627 2628 2630 2631 2633 2634 group subset_H(H2O) id 2636 2637 2639 2640 2642 2643 2645 2646 2648 2649 group subset_H(H2O) id 2651 2652 2654 2655 2657 2658 2660 2661 2663 2664 group subset_H(H2O) id 2666 2667 2669 2670 2672 2673 2675 2676 2678 2679 group subset_H(H2O) id 2681 2682 2684 2685 2687 2688 2690 2691 2693 2694 group subset_H(H2O) id 2696 2697 2699 2700 2702 2703 2705 2706 2708 2709 group subset_H(H2O) id 2711 2712 2714 2715 2717 2718 2720 2721 2723 2724 group subset_H(H2O) id 2726 2727 2729 2730 2732 2733 2735 2736 2738 2739 group subset_H(H2O) id 2741 2742 2744 2745 2747 2748 2750 2751 2753 2754 group subset_H(H2O) id 2756 2757 2759 2760 2762 2763 2765 2766 2768 2769 group subset_H(H2O) id 2771 2772 2774 2775 2777 2778 2780 2781 2783 2784 group subset_H(H2O) id 2786 2787 2789 2790 2792 2793 2795 2796 2798 2799 group subset_H(H2O) id 2801 2802 2804 2805 2807 2808 2810 2811 2813 2814 group 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3021 3023 3024 group subset_H(H2O) id 3026 3027 3029 3030 3032 3033 3035 3036 3038 3039 group subset_H(H2O) id 3041 3042 3044 3045 3047 3048 3050 3051 3053 3054 group subset_H(H2O) id 3056 3057 3059 3060 3062 3063 3065 3066 3068 3069 group subset_H(H2O) id 3071 3072 3074 3075 3077 3078 3080 3081 3083 3084 group subset_H(H2O) id 3086 3087 3089 3090 3092 3093 3095 3096 3098 3099 group subset_H(H2O) id 3101 3102 3104 3105 3107 3108 3110 3111 3113 3114 group subset_H(H2O) id 3116 3117 3119 3120 3122 3123 3125 3126 3128 3129 group subset_H(H2O) id 3131 3132 3134 3135 3137 3138 3140 3141 3143 3144 group subset_H(H2O) id 3146 3147 3149 3150 3152 3153 3155 3156 3158 3159 group subset_H(H2O) id 3161 3162 3164 3165 3167 3168 3170 3171 3173 3174 group subset_H(H2O) id 3176 3177 3179 3180 3182 3183 3185 3186 3188 3189 group subset_H(H2O) id 3191 3192 3194 3195 3197 3198 3200 3201 3203 3204 group subset_H(H2O) id 3206 3207 3209 3210 3212 3213 3215 3216 3218 3219 group subset_H(H2O) id 3221 3222 3224 3225 3227 3228 3230 3231 3233 3234 group subset_H(H2O) id 3236 3237 3239 3240 3242 3243 3245 3246 3248 3249 group subset_H(H2O) id 3251 3252 3254 3255 3257 3258 3260 3261 3263 3264 group subset_H(H2O) id 3266 3267 3269 3270 3272 3273 3275 3276 3278 3279 group subset_H(H2O) id 3281 3282 3284 3285 3287 3288 3290 3291 3293 3294 group subset_H(H2O) id 3296 3297 3299 3300 3302 3303 3305 3306 3308 3309 group subset_H(H2O) id 3311 3312 3314 3315 3317 3318 3320 3321 3323 3324 group subset_H(H2O) id 3326 3327 3329 3330 3332 3333 3335 3336 3338 3339 group subset_H(H2O) id 3341 3342 3344 3345 3347 3348 3350 3351 3353 3354 group subset_H(H2O) id 3356 3357 3359 3360 3362 3363 3365 3366 3368 3369 group subset_H(H2O) id 3371 3372 3374 3375 3377 3378 3380 3381 3383 3384 group subset_H(H2O) id 3386 3387 3389 3390 3392 3393 3395 3396 3398 3399 group subset_H(H2O) id 3401 3402 3404 3405 3407 3408 3410 3411 3413 3414 group subset_H(H2O) id 3416 3417 3419 3420 3422 3423 3425 3426 3428 3429 group 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3636 3638 3639 group subset_H(H2O) id 3641 3642 3644 3645 3647 3648 3650 3651 3653 3654 group subset_H(H2O) id 3656 3657 3659 3660 3662 3663 3665 3666 3668 3669 group subset_H(H2O) id 3671 3672 3674 3675 3677 3678 3680 3681 3683 3684 group subset_H(H2O) id 3686 3687 3689 3690 3692 3693 3695 3696 3698 3699 group subset_H(H2O) id 3701 3702 3704 3705 3707 3708 3710 3711 3713 3714 group subset_H(H2O) id 3716 3717 3719 3720 3722 3723 3725 3726 3728 3729 group subset_H(H2O) id 3731 3732 3734 3735 3737 3738 3740 3741 3743 3744 group subset_H(H2O) id 3746 3747 3749 3750 3752 3753 3755 3756 3758 3759 group subset_H(H2O) id 3761 3762 3764 3765 3767 3768 3770 3771 3773 3774 group subset_H(H2O) id 3776 3777 3779 3780 3782 3783 3785 3786 3788 3789 group subset_H(H2O) id 3791 3792 3794 3795 3797 3798 3800 3801 3803 3804 group subset_H(H2O) id 3806 3807 3809 3810 3812 3813 3815 3816 3818 3819 group subset_H(H2O) id 3821 3822 3824 3825 3827 3828 3830 3831 3833 3834 group subset_H(H2O) id 3836 3837 3839 3840 3842 3843 3845 3846 3848 3849 group subset_H(H2O) id 3851 3852 3854 3855 3857 3858 3860 3861 3863 3864 group subset_H(H2O) id 3866 3867 3869 3870 3872 3873 3875 3876 3878 3879 group subset_H(H2O) id 3881 3882 3884 3885 3887 3888 3890 3891 3893 3894 group subset_H(H2O) id 3896 3897 3899 3900 3902 3903 3905 3906 3908 3909 group subset_H(H2O) id 3911 3912 3914 3915 3917 3918 3920 3921 3923 3924 group subset_H(H2O) id 3926 3927 3929 3930 3932 3933 3935 3936 3938 3939 group subset_H(H2O) id 3941 3942 3944 3945 3947 3948 3950 3951 3953 3954 group subset_H(H2O) id 3956 3957 3959 3960 3962 3963 3965 3966 3968 3969 group subset_H(H2O) id 3971 3972 3974 3975 3977 3978 3980 3981 3983 3984 group subset_H(H2O) id 3986 3987 3989 3990 3992 3993 3995 3996 3998 3999 group subset_H(H2O) id 4001 4002 4004 4005 4007 4008 4010 4011 4013 4014 group subset_H(H2O) id 4016 4017 4019 4020 4022 4023 4025 4026 4028 4029 group subset_H(H2O) id 4031 4032 4034 4035 4037 4038 4040 4041 4043 4044 group 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4251 4253 4254 group subset_H(H2O) id 4256 4257 4259 4260 4262 4263 4265 4266 4268 4269 group subset_H(H2O) id 4271 4272 4274 4275 4277 4278 4280 4281 4283 4284 group subset_H(H2O) id 4286 4287 4289 4290 4292 4293 4295 4296 4298 4299 group subset_H(H2O) id 4301 4302 4304 4305 4307 4308 4310 4311 4313 4314 group subset_H(H2O) id 4316 4317 4319 4320 4322 4323 4325 4326 4328 4329 group subset_H(H2O) id 4331 4332 4334 4335 4337 4338 4340 4341 4343 4344 group subset_H(H2O) id 4346 4347 4349 4350 4352 4353 4355 4356 4358 4359 group subset_H(H2O) id 4361 4362 4364 4365 4367 4368 4370 4371 4373 4374 group subset_H(H2O) id 4376 4377 4379 4380 4382 4383 4385 4386 4388 4389 group subset_H(H2O) id 4391 4392 4394 4395 4397 4398 4400 4401 4403 4404 group subset_H(H2O) id 4406 4407 4409 4410 4412 4413 4415 4416 4418 4419 group subset_H(H2O) id 4421 4422 4424 4425 4427 4428 4430 4431 4433 4434 group subset_H(H2O) id 4436 4437 4439 4440 4442 4443 4445 4446 4448 4449 group subset_H(H2O) id 4451 4452 4454 4455 4457 4458 4460 4461 4463 4464 group subset_H(H2O) id 4466 4467 4469 4470 4472 4473 4475 4476 4478 4479 group subset_H(H2O) id 4481 4482 4484 4485 4487 4488 4490 4491 4493 4494 group subset_H(H2O) id 4496 4497 4499 4500 4502 4503 4505 4506 4508 4509 group subset_H(H2O) id 4511 4512 4514 4515 4517 4518 4520 4521 4523 4524 group subset_H(H2O) id 4526 4527 4529 4530 4532 4533 4535 4536 4538 4539 group subset_H(H2O) id 4541 4542 4544 4545 4547 4548 4550 4551 4553 4554 group subset_H(H2O) id 4556 4557 4559 4560 4562 4563 4565 4566 4568 4569 group subset_H(H2O) id 4571 4572 4574 4575 4577 4578 4580 4581 4583 4584 group subset_H(H2O) id 4586 4587 4589 4590 4592 4593 4595 4596 4598 4599 group subset_H(H2O) id 4601 4602 4604 4605 4607 4608 4610 4611 4613 4614 group subset_H(H2O) id 4616 4617 4619 4620 4622 4623 4625 4626 4628 4629 group subset_H(H2O) id 4631 4632 4634 4635 4637 4638 4640 4641 4643 4644 group subset_H(H2O) id 4646 4647 4649 4650 4652 4653 4655 4656 4658 4659 group subset_H(H2O) id 4661 4662 4664 4665 4667 4668 4670 4671 4673 4674 group subset_H(H2O) id 4676 4677 4679 4680 4682 4683 4685 4686 4688 4689 group subset_H(H2O) id 4691 4692 4694 4695 4697 4698 4700 4701 4703 4704 group subset_H(H2O) id 4706 4707 4709 4710 4712 4713 4715 4716 4718 4719 group subset_H(H2O) id 4721 4722 4724 4725 4727 4728 4730 4731 4733 4734 group subset_H(H2O) id 4736 4737 4739 4740 4742 4743 4745 4746 4748 4749 group subset_H(H2O) id 4751 4752 4754 4755 4757 4758 4760 4761 4763 4764 group subset_H(H2O) id 4766 4767 4769 4770 4772 4773 4775 4776 4778 4779 group subset_H(H2O) id 4781 4782 4784 4785 4787 4788 4790 4791 4793 4794 group subset_H(H2O) id 4796 4797 4799 4800 4802 4803 4805 4806 4808 4809 group subset_H(H2O) id 4811 4812 4814 4815 4817 4818 4820 4821 4823 4824 group subset_H(H2O) id 4826 4827 4829 4830 4832 4833 4835 4836 4838 4839 group subset_H(H2O) id 4841 4842 4844 4845 4847 4848 4850 4851 4853 4854 group subset_H(H2O) id 4856 4857 4859 4860 4862 4863 4865 4866 4868 4869 group subset_H(H2O) id 4871 4872 4874 4875 4877 4878 4880 4881 4883 4884 group subset_H(H2O) id 4886 4887 4889 4890 4892 4893 4895 4896 4898 4899 group subset_H(H2O) id 4901 4902 4904 4905 4907 4908 4910 4911 4913 4914 group subset_H(H2O) id 4916 4917 4919 4920 4922 4923 4925 4926 4928 4929 group subset_H(H2O) id 4931 4932 4934 4935 4937 4938 4940 4941 4943 4944 group subset_H(H2O) id 4946 4947 4949 4950 4952 4953 4955 4956 4958 4959 group subset_H(H2O) id 4961 4962 4964 4965 4967 4968 4970 4971 4973 4974 group subset_H(H2O) id 4976 4977 4979 4980 4982 4983 4985 4986 4988 4989 group subset_H(H2O) id 4991 4992 4994 4995 4997 4998 5000 5001 5003 5004 group subset_H(H2O) id 5006 5007 5009 5010 5012 5013 5015 5016 5018 5019 group subset_H(H2O) id 5021 5022 5024 5025 5027 5028 5030 5031 5033 5034 group subset_H(H2O) id 5036 5037 5039 5040 5042 5043 5045 5046 5048 5049 group subset_H(H2O) id 5051 5052 5054 5055 5057 5058 5060 5061 5063 5064 group subset_H(H2O) id 5066 5067 5069 5070 5072 5073 5075 5076 5078 5079 group subset_H(H2O) id 5081 5082 5084 5085 5087 5088 5090 5091 5093 5094 group subset_H(H2O) id 5096 5097 5099 5100 5102 5103 5105 5106 5108 5109 group subset_H(H2O) id 5111 5112 5114 5115 5117 5118 5120 5121 5123 5124 group subset_H(H2O) id 5126 5127 5129 5130 5132 5133 5135 5136 5138 5139 group subset_H(H2O) id 5141 5142 5144 5145 5147 5148 5150 5151 5153 5154 group subset_H(H2O) id 5156 5157 5159 5160 5162 5163 5165 5166 5168 5169 group subset_H(H2O) id 5171 5172 5174 5175 5177 5178 5180 5181 5183 5184 group subset_H(H2O) id 5186 5187 5189 5190 5192 5193 5195 5196 5198 5199 group subset_H(H2O) id 5201 5202 5204 5205 5207 5208 5210 5211 5213 5214 group subset_H(H2O) id 5216 5217 5219 5220 5222 5223 5225 5226 5228 5229 group subset_H(H2O) id 5231 5232 5234 5235 5237 5238 5240 5241 5243 5244 group subset_H(H2O) id 5246 5247 5249 5250 5252 5253 5255 5256 5258 5259 group subset_H(H2O) id 5261 5262 5264 5265 5267 5268 5270 5271 5273 5274 group subset_H(H2O) id 5276 5277 5279 5280 5282 5283 5285 5286 5288 5289 group subset_H(H2O) id 5291 5292 5294 5295 5297 5298 5300 5301 5303 5304 group subset_H(H2O) id 5306 5307 5309 5310 5312 5313 5315 5316 5318 5319 group subset_H(H2O) id 5321 5322 5324 5325 5327 5328 5330 5331 5333 5334 group subset_H(H2O) id 5336 5337 5339 5340 5342 5343 5345 5346 5348 5349 group subset_H(H2O) id 5351 5352 5354 5355 5357 5358 5360 5361 5363 5364 group subset_H(H2O) id 5366 5367 5369 5370 5372 5373 5375 5376 5378 5379 group subset_H(H2O) id 5381 5382 5384 5385 5387 5388 5390 5391 5393 5394 group subset_H(H2O) id 5396 5397 5399 5400 5402 5403 5405 5406 5408 5409 group subset_H(H2O) id 5411 5412 log 2.2_Minimization.out #------------------------------------------------------------------------------- # Stage 2.2: Minimization #------------------------------------------------------------------------------- min_style cg min_modify dmax 0.05 line fast reset_timestep 0 thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz dump sci all custom 3000 2.2.xyz id mol type q xs ys zs thermo 100 minimize 0.0 1.0 3000 10000 undump sci log 2.3_Velocities.out #------------------------------------------------------------------------------- # Stage 2.3: Set the initial velocities for $T #------------------------------------------------------------------------------- velocity all create 298.2 72489 dist gaussian mom yes rot no log 2.4_NPT.out #------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 1 b 1 reset_timestep 0 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 npt temp 298.2 298.2 100 iso 0.9869233 0.9869233 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1 fix 3 movable ave/time 200 1 200 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 undump sci restart 0 dump sci all custom 2000000 2.4.xyz id mol type q xs ys zs run 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken