# 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/cut 9.5 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 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_O(H2O) id 1 4 7 10 13 16 19 22 25 28 group subset_O(H2O) id 31 34 37 40 43 46 49 52 55 58 group subset_O(H2O) id 61 64 67 70 73 76 79 82 85 88 group subset_O(H2O) id 91 94 97 100 103 106 109 112 115 118 group subset_O(H2O) id 121 124 127 130 133 136 139 142 145 148 group subset_O(H2O) id 151 154 157 160 163 166 169 172 175 178 group subset_O(H2O) id 181 184 187 190 193 196 199 202 205 208 group subset_O(H2O) id 211 214 217 220 223 226 229 232 235 238 group subset_O(H2O) id 241 244 247 250 253 256 259 262 265 268 group subset_O(H2O) id 271 274 277 280 283 286 289 292 295 298 group subset_O(H2O) id 301 304 307 310 313 316 319 322 325 328 group subset_O(H2O) id 331 334 337 340 343 346 349 352 355 358 group subset_O(H2O) id 361 364 367 370 373 376 379 382 385 388 group subset_O(H2O) id 391 394 397 400 403 406 409 412 415 418 group subset_O(H2O) id 421 424 427 430 433 436 439 442 445 448 group subset_O(H2O) id 451 454 457 460 463 466 469 472 475 478 group subset_O(H2O) id 481 484 487 490 493 496 499 502 505 508 group subset_O(H2O) id 511 514 517 520 523 526 529 532 535 538 group subset_O(H2O) id 541 544 547 550 553 556 559 562 565 568 group subset_O(H2O) id 571 574 577 580 583 586 589 592 595 598 group subset_O(H2O) id 601 604 607 610 613 616 619 622 625 628 group subset_O(H2O) id 631 634 637 640 643 646 649 652 655 658 group subset_O(H2O) id 661 664 667 670 673 676 679 682 685 688 group subset_O(H2O) id 691 694 697 700 703 706 709 712 715 718 group subset_O(H2O) id 721 724 727 730 733 736 739 742 745 748 group subset_O(H2O) id 751 754 757 760 763 766 769 772 775 778 group subset_O(H2O) id 781 784 787 790 793 796 799 802 805 808 group subset_O(H2O) id 811 814 817 820 823 826 829 832 835 838 group subset_O(H2O) id 841 844 847 850 853 856 859 862 865 868 group subset_O(H2O) id 871 874 877 880 883 886 889 892 895 898 group subset_O(H2O) id 901 904 907 910 913 916 919 922 925 928 group subset_O(H2O) id 931 934 937 940 943 946 949 952 955 958 group subset_O(H2O) id 961 964 967 970 973 976 979 982 985 988 group subset_O(H2O) id 991 994 997 1000 1003 1006 1009 1012 1015 1018 group subset_O(H2O) id 1021 1024 1027 1030 1033 1036 1039 1042 1045 1048 group subset_O(H2O) id 1051 1054 1057 1060 1063 1066 1069 1072 1075 1078 group subset_O(H2O) id 1081 1084 1087 1090 1093 1096 1099 1102 1105 1108 group subset_O(H2O) id 1111 1114 1117 1120 1123 1126 1129 1132 1135 1138 group subset_O(H2O) id 1141 1144 1147 1150 1153 1156 1159 1162 1165 1168 group subset_O(H2O) id 1171 1174 1177 1180 1183 1186 1189 1192 1195 1198 group subset_O(H2O) id 1201 1204 1207 1210 1213 1216 1219 1222 1225 1228 group subset_O(H2O) id 1231 1234 1237 1240 1243 1246 1249 1252 1255 1258 group subset_O(H2O) id 1261 1264 1267 1270 1273 1276 1279 1282 1285 1288 group subset_O(H2O) id 1291 1294 1297 1300 1303 1306 1309 1312 1315 1318 group subset_O(H2O) id 1321 1324 1327 1330 1333 1336 1339 1342 1345 1348 group subset_O(H2O) id 1351 1354 1357 1360 1363 1366 1369 1372 1375 1378 group subset_O(H2O) id 1381 1384 1387 1390 1393 1396 1399 1402 1405 1408 group subset_O(H2O) id 1411 1414 1417 1420 1423 1426 1429 1432 1435 1438 group subset_O(H2O) id 1441 1444 1447 1450 1453 1456 1459 1462 1465 1468 group subset_O(H2O) id 1471 1474 1477 1480 1483 1486 1489 1492 1495 1498 group subset_O(H2O) id 1501 1504 1507 1510 1513 1516 1519 1522 1525 1528 group subset_O(H2O) id 1531 1534 1537 1540 1543 1546 1549 1552 1555 1558 group subset_O(H2O) id 1561 1564 1567 1570 1573 1576 1579 1582 1585 1588 group subset_O(H2O) id 1591 1594 1597 1600 1603 1606 1609 1612 1615 1618 group subset_O(H2O) id 1621 1624 1627 1630 1633 1636 1639 1642 1645 1648 group subset_O(H2O) id 1651 1654 1657 1660 1663 1666 1669 1672 1675 1678 group subset_O(H2O) id 1681 1684 1687 1690 1693 1696 1699 1702 1705 1708 group subset_O(H2O) id 1711 1714 1717 1720 1723 1726 1729 1732 1735 1738 group subset_O(H2O) id 1741 1744 1747 1750 1753 1756 1759 1762 1765 1768 group subset_O(H2O) id 1771 1774 1777 1780 1783 1786 1789 1792 1795 1798 group subset_O(H2O) id 1801 1804 1807 1810 1813 1816 1819 1822 1825 1828 group subset_O(H2O) id 1831 1834 1837 1840 1843 1846 1849 1852 1855 1858 group subset_O(H2O) id 1861 1864 1867 1870 1873 1876 1879 1882 1885 1888 group subset_O(H2O) id 1891 1894 1897 1900 1903 1906 1909 1912 1915 1918 group subset_O(H2O) id 1921 1924 1927 1930 1933 1936 1939 1942 1945 1948 group subset_O(H2O) id 1951 1954 1957 1960 1963 1966 1969 1972 1975 1978 group subset_O(H2O) id 1981 1984 1987 1990 1993 1996 1999 2002 2005 2008 group subset_O(H2O) id 2011 2014 2017 2020 2023 2026 2029 2032 2035 2038 group subset_O(H2O) id 2041 2044 2047 2050 2053 2056 2059 2062 2065 2068 group subset_O(H2O) id 2071 2074 2077 2080 2083 2086 2089 2092 2095 2098 group subset_O(H2O) id 2101 2104 2107 2110 2113 2116 2119 2122 2125 2128 group subset_O(H2O) id 2131 2134 2137 2140 2143 2146 2149 2152 2155 2158 group subset_O(H2O) id 2161 2164 2167 2170 2173 2176 2179 2182 2185 2188 group subset_O(H2O) id 2191 2194 2197 2200 2203 2206 2209 2212 2215 2218 group subset_O(H2O) id 2221 2224 2227 2230 2233 2236 2239 2242 2245 2248 group subset_O(H2O) id 2251 2254 2257 2260 2263 2266 2269 2272 2275 2278 group subset_O(H2O) id 2281 2284 2287 2290 2293 2296 2299 2302 2305 2308 group subset_O(H2O) id 2311 2314 2317 2320 2323 2326 2329 2332 2335 2338 group subset_O(H2O) id 2341 2344 2347 2350 2353 2356 2359 2362 2365 2368 group subset_O(H2O) id 2371 2374 2377 2380 2383 2386 2389 2392 2395 2398 group subset_O(H2O) id 2401 2404 2407 2410 2413 2416 2419 2422 2425 2428 group subset_O(H2O) id 2431 2434 2437 2440 2443 2446 2449 2452 2455 2458 group subset_O(H2O) id 2461 2464 2467 2470 2473 2476 2479 2482 2485 2488 group subset_O(H2O) id 2491 2494 2497 2500 2503 2506 2509 2512 2515 2518 group subset_O(H2O) id 2521 2524 2527 2530 2533 2536 2539 2542 2545 2548 group subset_O(H2O) id 2551 2554 2557 2560 2563 2566 2569 2572 2575 2578 group subset_O(H2O) id 2581 2584 2587 2590 2593 2596 2599 2602 2605 2608 group subset_O(H2O) id 2611 2614 2617 2620 2623 2626 2629 2632 2635 2638 group subset_O(H2O) id 2641 2644 2647 2650 2653 2656 2659 2662 2665 2668 group subset_O(H2O) id 2671 2674 2677 2680 2683 2686 2689 2692 2695 2698 group subset_O(H2O) id 2701 2704 2707 2710 2713 2716 2719 2722 2725 2728 group subset_O(H2O) id 2731 2734 2737 2740 2743 2746 2749 2752 2755 2758 group subset_O(H2O) id 2761 2764 2767 2770 2773 2776 2779 2782 2785 2788 group subset_O(H2O) id 2791 2794 2797 2800 2803 2806 2809 2812 2815 2818 group subset_O(H2O) id 2821 2824 2827 2830 2833 2836 2839 2842 2845 2848 group subset_O(H2O) id 2851 2854 2857 2860 2863 2866 2869 2872 2875 2878 group subset_O(H2O) id 2881 2884 2887 2890 2893 2896 2899 2902 2905 2908 group subset_O(H2O) id 2911 2914 2917 2920 2923 2926 2929 2932 2935 2938 group subset_O(H2O) id 2941 2944 2947 2950 2953 2956 2959 2962 2965 2968 group subset_O(H2O) id 2971 2974 2977 2980 2983 2986 2989 2992 2995 2998 group subset_H(H2O) id 2 3 5 6 8 9 11 12 14 15 group subset_H(H2O) id 17 18 20 21 23 24 26 27 29 30 group subset_H(H2O) id 32 33 35 36 38 39 41 42 44 45 group subset_H(H2O) id 47 48 50 51 53 54 56 57 59 60 group subset_H(H2O) id 62 63 65 66 68 69 71 72 74 75 group subset_H(H2O) id 77 78 80 81 83 84 86 87 89 90 group subset_H(H2O) id 92 93 95 96 98 99 101 102 104 105 group subset_H(H2O) id 107 108 110 111 113 114 116 117 119 120 group subset_H(H2O) id 122 123 125 126 128 129 131 132 134 135 group subset_H(H2O) id 137 138 140 141 143 144 146 147 149 150 group subset_H(H2O) id 152 153 155 156 158 159 161 162 164 165 group subset_H(H2O) id 167 168 170 171 173 174 176 177 179 180 group subset_H(H2O) id 182 183 185 186 188 189 191 192 194 195 group subset_H(H2O) id 197 198 200 201 203 204 206 207 209 210 group subset_H(H2O) id 212 213 215 216 218 219 221 222 224 225 group subset_H(H2O) id 227 228 230 231 233 234 236 237 239 240 group subset_H(H2O) id 242 243 245 246 248 249 251 252 254 255 group subset_H(H2O) id 257 258 260 261 263 264 266 267 269 270 group subset_H(H2O) id 272 273 275 276 278 279 281 282 284 285 group subset_H(H2O) id 287 288 290 291 293 294 296 297 299 300 group subset_H(H2O) id 302 303 305 306 308 309 311 312 314 315 group subset_H(H2O) id 317 318 320 321 323 324 326 327 329 330 group subset_H(H2O) id 332 333 335 336 338 339 341 342 344 345 group subset_H(H2O) id 347 348 350 351 353 354 356 357 359 360 group subset_H(H2O) id 362 363 365 366 368 369 371 372 374 375 group subset_H(H2O) id 377 378 380 381 383 384 386 387 389 390 group subset_H(H2O) id 392 393 395 396 398 399 401 402 404 405 group subset_H(H2O) id 407 408 410 411 413 414 416 417 419 420 group subset_H(H2O) id 422 423 425 426 428 429 431 432 434 435 group subset_H(H2O) id 437 438 440 441 443 444 446 447 449 450 group subset_H(H2O) id 452 453 455 456 458 459 461 462 464 465 group subset_H(H2O) id 467 468 470 471 473 474 476 477 479 480 group subset_H(H2O) id 482 483 485 486 488 489 491 492 494 495 group subset_H(H2O) id 497 498 500 501 503 504 506 507 509 510 group subset_H(H2O) id 512 513 515 516 518 519 521 522 524 525 group subset_H(H2O) id 527 528 530 531 533 534 536 537 539 540 group subset_H(H2O) id 542 543 545 546 548 549 551 552 554 555 group subset_H(H2O) id 557 558 560 561 563 564 566 567 569 570 group subset_H(H2O) id 572 573 575 576 578 579 581 582 584 585 group subset_H(H2O) id 587 588 590 591 593 594 596 597 599 600 group subset_H(H2O) id 602 603 605 606 608 609 611 612 614 615 group subset_H(H2O) id 617 618 620 621 623 624 626 627 629 630 group subset_H(H2O) id 632 633 635 636 638 639 641 642 644 645 group subset_H(H2O) id 647 648 650 651 653 654 656 657 659 660 group subset_H(H2O) id 662 663 665 666 668 669 671 672 674 675 group subset_H(H2O) id 677 678 680 681 683 684 686 687 689 690 group subset_H(H2O) id 692 693 695 696 698 699 701 702 704 705 group subset_H(H2O) id 707 708 710 711 713 714 716 717 719 720 group subset_H(H2O) id 722 723 725 726 728 729 731 732 734 735 group subset_H(H2O) id 737 738 740 741 743 744 746 747 749 750 group subset_H(H2O) id 752 753 755 756 758 759 761 762 764 765 group subset_H(H2O) id 767 768 770 771 773 774 776 777 779 780 group subset_H(H2O) id 782 783 785 786 788 789 791 792 794 795 group subset_H(H2O) id 797 798 800 801 803 804 806 807 809 810 group subset_H(H2O) id 812 813 815 816 818 819 821 822 824 825 group subset_H(H2O) id 827 828 830 831 833 834 836 837 839 840 group subset_H(H2O) id 842 843 845 846 848 849 851 852 854 855 group subset_H(H2O) id 857 858 860 861 863 864 866 867 869 870 group subset_H(H2O) id 872 873 875 876 878 879 881 882 884 885 group subset_H(H2O) id 887 888 890 891 893 894 896 897 899 900 group subset_H(H2O) id 902 903 905 906 908 909 911 912 914 915 group subset_H(H2O) id 917 918 920 921 923 924 926 927 929 930 group subset_H(H2O) id 932 933 935 936 938 939 941 942 944 945 group subset_H(H2O) id 947 948 950 951 953 954 956 957 959 960 group subset_H(H2O) id 962 963 965 966 968 969 971 972 974 975 group subset_H(H2O) id 977 978 980 981 983 984 986 987 989 990 group subset_H(H2O) id 992 993 995 996 998 999 1001 1002 1004 1005 group subset_H(H2O) id 1007 1008 1010 1011 1013 1014 1016 1017 1019 1020 group subset_H(H2O) id 1022 1023 1025 1026 1028 1029 1031 1032 1034 1035 group subset_H(H2O) id 1037 1038 1040 1041 1043 1044 1046 1047 1049 1050 group subset_H(H2O) id 1052 1053 1055 1056 1058 1059 1061 1062 1064 1065 group subset_H(H2O) id 1067 1068 1070 1071 1073 1074 1076 1077 1079 1080 group subset_H(H2O) id 1082 1083 1085 1086 1088 1089 1091 1092 1094 1095 group subset_H(H2O) id 1097 1098 1100 1101 1103 1104 1106 1107 1109 1110 group subset_H(H2O) id 1112 1113 1115 1116 1118 1119 1121 1122 1124 1125 group subset_H(H2O) id 1127 1128 1130 1131 1133 1134 1136 1137 1139 1140 group subset_H(H2O) id 1142 1143 1145 1146 1148 1149 1151 1152 1154 1155 group subset_H(H2O) id 1157 1158 1160 1161 1163 1164 1166 1167 1169 1170 group subset_H(H2O) id 1172 1173 1175 1176 1178 1179 1181 1182 1184 1185 group subset_H(H2O) id 1187 1188 1190 1191 1193 1194 1196 1197 1199 1200 group subset_H(H2O) id 1202 1203 1205 1206 1208 1209 1211 1212 1214 1215 group subset_H(H2O) id 1217 1218 1220 1221 1223 1224 1226 1227 1229 1230 group subset_H(H2O) id 1232 1233 1235 1236 1238 1239 1241 1242 1244 1245 group subset_H(H2O) id 1247 1248 1250 1251 1253 1254 1256 1257 1259 1260 group subset_H(H2O) id 1262 1263 1265 1266 1268 1269 1271 1272 1274 1275 group subset_H(H2O) id 1277 1278 1280 1281 1283 1284 1286 1287 1289 1290 group subset_H(H2O) id 1292 1293 1295 1296 1298 1299 1301 1302 1304 1305 group subset_H(H2O) id 1307 1308 1310 1311 1313 1314 1316 1317 1319 1320 group subset_H(H2O) id 1322 1323 1325 1326 1328 1329 1331 1332 1334 1335 group subset_H(H2O) id 1337 1338 1340 1341 1343 1344 1346 1347 1349 1350 group subset_H(H2O) id 1352 1353 1355 1356 1358 1359 1361 1362 1364 1365 group subset_H(H2O) id 1367 1368 1370 1371 1373 1374 1376 1377 1379 1380 group subset_H(H2O) id 1382 1383 1385 1386 1388 1389 1391 1392 1394 1395 group subset_H(H2O) id 1397 1398 1400 1401 1403 1404 1406 1407 1409 1410 group subset_H(H2O) id 1412 1413 1415 1416 1418 1419 1421 1422 1424 1425 group subset_H(H2O) id 1427 1428 1430 1431 1433 1434 1436 1437 1439 1440 group subset_H(H2O) id 1442 1443 1445 1446 1448 1449 1451 1452 1454 1455 group subset_H(H2O) id 1457 1458 1460 1461 1463 1464 1466 1467 1469 1470 group subset_H(H2O) id 1472 1473 1475 1476 1478 1479 1481 1482 1484 1485 group subset_H(H2O) id 1487 1488 1490 1491 1493 1494 1496 1497 1499 1500 group subset_H(H2O) id 1502 1503 1505 1506 1508 1509 1511 1512 1514 1515 group subset_H(H2O) id 1517 1518 1520 1521 1523 1524 1526 1527 1529 1530 group subset_H(H2O) id 1532 1533 1535 1536 1538 1539 1541 1542 1544 1545 group subset_H(H2O) id 1547 1548 1550 1551 1553 1554 1556 1557 1559 1560 group subset_H(H2O) id 1562 1563 1565 1566 1568 1569 1571 1572 1574 1575 group subset_H(H2O) id 1577 1578 1580 1581 1583 1584 1586 1587 1589 1590 group subset_H(H2O) id 1592 1593 1595 1596 1598 1599 1601 1602 1604 1605 group subset_H(H2O) id 1607 1608 1610 1611 1613 1614 1616 1617 1619 1620 group subset_H(H2O) id 1622 1623 1625 1626 1628 1629 1631 1632 1634 1635 group subset_H(H2O) id 1637 1638 1640 1641 1643 1644 1646 1647 1649 1650 group subset_H(H2O) id 1652 1653 1655 1656 1658 1659 1661 1662 1664 1665 group subset_H(H2O) id 1667 1668 1670 1671 1673 1674 1676 1677 1679 1680 group subset_H(H2O) id 1682 1683 1685 1686 1688 1689 1691 1692 1694 1695 group subset_H(H2O) id 1697 1698 1700 1701 1703 1704 1706 1707 1709 1710 group subset_H(H2O) id 1712 1713 1715 1716 1718 1719 1721 1722 1724 1725 group subset_H(H2O) id 1727 1728 1730 1731 1733 1734 1736 1737 1739 1740 group subset_H(H2O) id 1742 1743 1745 1746 1748 1749 1751 1752 1754 1755 group subset_H(H2O) id 1757 1758 1760 1761 1763 1764 1766 1767 1769 1770 group subset_H(H2O) id 1772 1773 1775 1776 1778 1779 1781 1782 1784 1785 group subset_H(H2O) id 1787 1788 1790 1791 1793 1794 1796 1797 1799 1800 group subset_H(H2O) id 1802 1803 1805 1806 1808 1809 1811 1812 1814 1815 group subset_H(H2O) id 1817 1818 1820 1821 1823 1824 1826 1827 1829 1830 group subset_H(H2O) id 1832 1833 1835 1836 1838 1839 1841 1842 1844 1845 group subset_H(H2O) id 1847 1848 1850 1851 1853 1854 1856 1857 1859 1860 group subset_H(H2O) id 1862 1863 1865 1866 1868 1869 1871 1872 1874 1875 group subset_H(H2O) id 1877 1878 1880 1881 1883 1884 1886 1887 1889 1890 group subset_H(H2O) id 1892 1893 1895 1896 1898 1899 1901 1902 1904 1905 group subset_H(H2O) id 1907 1908 1910 1911 1913 1914 1916 1917 1919 1920 group subset_H(H2O) id 1922 1923 1925 1926 1928 1929 1931 1932 1934 1935 group subset_H(H2O) id 1937 1938 1940 1941 1943 1944 1946 1947 1949 1950 group subset_H(H2O) id 1952 1953 1955 1956 1958 1959 1961 1962 1964 1965 group subset_H(H2O) id 1967 1968 1970 1971 1973 1974 1976 1977 1979 1980 group subset_H(H2O) id 1982 1983 1985 1986 1988 1989 1991 1992 1994 1995 group subset_H(H2O) id 1997 1998 2000 2001 2003 2004 2006 2007 2009 2010 group subset_H(H2O) id 2012 2013 2015 2016 2018 2019 2021 2022 2024 2025 group subset_H(H2O) id 2027 2028 2030 2031 2033 2034 2036 2037 2039 2040 group subset_H(H2O) id 2042 2043 2045 2046 2048 2049 2051 2052 2054 2055 group subset_H(H2O) id 2057 2058 2060 2061 2063 2064 2066 2067 2069 2070 group subset_H(H2O) id 2072 2073 2075 2076 2078 2079 2081 2082 2084 2085 group subset_H(H2O) id 2087 2088 2090 2091 2093 2094 2096 2097 2099 2100 group subset_H(H2O) id 2102 2103 2105 2106 2108 2109 2111 2112 2114 2115 group subset_H(H2O) id 2117 2118 2120 2121 2123 2124 2126 2127 2129 2130 group subset_H(H2O) id 2132 2133 2135 2136 2138 2139 2141 2142 2144 2145 group subset_H(H2O) id 2147 2148 2150 2151 2153 2154 2156 2157 2159 2160 group subset_H(H2O) id 2162 2163 2165 2166 2168 2169 2171 2172 2174 2175 group subset_H(H2O) id 2177 2178 2180 2181 2183 2184 2186 2187 2189 2190 group subset_H(H2O) id 2192 2193 2195 2196 2198 2199 2201 2202 2204 2205 group subset_H(H2O) id 2207 2208 2210 2211 2213 2214 2216 2217 2219 2220 group subset_H(H2O) id 2222 2223 2225 2226 2228 2229 2231 2232 2234 2235 group subset_H(H2O) id 2237 2238 2240 2241 2243 2244 2246 2247 2249 2250 group subset_H(H2O) id 2252 2253 2255 2256 2258 2259 2261 2262 2264 2265 group subset_H(H2O) id 2267 2268 2270 2271 2273 2274 2276 2277 2279 2280 group subset_H(H2O) id 2282 2283 2285 2286 2288 2289 2291 2292 2294 2295 group subset_H(H2O) id 2297 2298 2300 2301 2303 2304 2306 2307 2309 2310 group subset_H(H2O) id 2312 2313 2315 2316 2318 2319 2321 2322 2324 2325 group subset_H(H2O) id 2327 2328 2330 2331 2333 2334 2336 2337 2339 2340 group subset_H(H2O) id 2342 2343 2345 2346 2348 2349 2351 2352 2354 2355 group subset_H(H2O) id 2357 2358 2360 2361 2363 2364 2366 2367 2369 2370 group subset_H(H2O) id 2372 2373 2375 2376 2378 2379 2381 2382 2384 2385 group subset_H(H2O) id 2387 2388 2390 2391 2393 2394 2396 2397 2399 2400 group subset_H(H2O) id 2402 2403 2405 2406 2408 2409 2411 2412 2414 2415 group subset_H(H2O) id 2417 2418 2420 2421 2423 2424 2426 2427 2429 2430 group subset_H(H2O) id 2432 2433 2435 2436 2438 2439 2441 2442 2444 2445 group subset_H(H2O) id 2447 2448 2450 2451 2453 2454 2456 2457 2459 2460 group subset_H(H2O) id 2462 2463 2465 2466 2468 2469 2471 2472 2474 2475 group subset_H(H2O) id 2477 2478 2480 2481 2483 2484 2486 2487 2489 2490 group subset_H(H2O) id 2492 2493 2495 2496 2498 2499 2501 2502 2504 2505 group subset_H(H2O) id 2507 2508 2510 2511 2513 2514 2516 2517 2519 2520 group subset_H(H2O) id 2522 2523 2525 2526 2528 2529 2531 2532 2534 2535 group subset_H(H2O) id 2537 2538 2540 2541 2543 2544 2546 2547 2549 2550 group subset_H(H2O) id 2552 2553 2555 2556 2558 2559 2561 2562 2564 2565 group subset_H(H2O) id 2567 2568 2570 2571 2573 2574 2576 2577 2579 2580 group subset_H(H2O) id 2582 2583 2585 2586 2588 2589 2591 2592 2594 2595 group subset_H(H2O) id 2597 2598 2600 2601 2603 2604 2606 2607 2609 2610 group subset_H(H2O) id 2612 2613 2615 2616 2618 2619 2621 2622 2624 2625 group subset_H(H2O) id 2627 2628 2630 2631 2633 2634 2636 2637 2639 2640 group subset_H(H2O) id 2642 2643 2645 2646 2648 2649 2651 2652 2654 2655 group subset_H(H2O) id 2657 2658 2660 2661 2663 2664 2666 2667 2669 2670 group subset_H(H2O) id 2672 2673 2675 2676 2678 2679 2681 2682 2684 2685 group subset_H(H2O) id 2687 2688 2690 2691 2693 2694 2696 2697 2699 2700 group subset_H(H2O) id 2702 2703 2705 2706 2708 2709 2711 2712 2714 2715 group subset_H(H2O) id 2717 2718 2720 2721 2723 2724 2726 2727 2729 2730 group subset_H(H2O) id 2732 2733 2735 2736 2738 2739 2741 2742 2744 2745 group subset_H(H2O) id 2747 2748 2750 2751 2753 2754 2756 2757 2759 2760 group subset_H(H2O) id 2762 2763 2765 2766 2768 2769 2771 2772 2774 2775 group subset_H(H2O) id 2777 2778 2780 2781 2783 2784 2786 2787 2789 2790 group subset_H(H2O) id 2792 2793 2795 2796 2798 2799 2801 2802 2804 2805 group subset_H(H2O) id 2807 2808 2810 2811 2813 2814 2816 2817 2819 2820 group subset_H(H2O) id 2822 2823 2825 2826 2828 2829 2831 2832 2834 2835 group subset_H(H2O) id 2837 2838 2840 2841 2843 2844 2846 2847 2849 2850 group subset_H(H2O) id 2852 2853 2855 2856 2858 2859 2861 2862 2864 2865 group subset_H(H2O) id 2867 2868 2870 2871 2873 2874 2876 2877 2879 2880 group subset_H(H2O) id 2882 2883 2885 2886 2888 2889 2891 2892 2894 2895 group subset_H(H2O) id 2897 2898 2900 2901 2903 2904 2906 2907 2909 2910 group subset_H(H2O) id 2912 2913 2915 2916 2918 2919 2921 2922 2924 2925 group subset_H(H2O) id 2927 2928 2930 2931 2933 2934 2936 2937 2939 2940 group subset_H(H2O) id 2942 2943 2945 2946 2948 2949 2951 2952 2954 2955 group subset_H(H2O) id 2957 2958 2960 2961 2963 2964 2966 2967 2969 2970 group subset_H(H2O) id 2972 2973 2975 2976 2978 2979 2981 2982 2984 2985 group subset_H(H2O) id 2987 2988 2990 2991 2993 2994 2996 2997 2999 3000 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 1000 2.2.xyz id mol type q xs ys zs thermo 100 minimize 0.0 1.0 1000 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 atm #------------------------------------------------------------------------------- # 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 1 1 100 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 log 2.5_NVT.out #------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 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 file 2.5_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_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 undump sci restart 0 dump sci all custom 2000000 2.5.xyz id mol type q xs ys zs run 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out #------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 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 v_surfacetension file 2.6_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_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension file 2.6_instantaneous.txt restart 2000000 2.6.restart dump sci all custom 200000 2.6.xyz id mol type q xs ys zs timestep 1 run 2000000 undump sci restart 0 dump sci all custom 2000000 2.6.xyz id mol type q xs ys zs run 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken