Tutorial#
In this tutorial, the molecular dynamics (MD) in
metal organic framework named CALF-20 and water system
will be used as an example. Note that, the trajectory alpha.4000
was calculated without equilibration and sampled only 4000 steps with 1 fs of timestep.
Therefore, the values obtained from present tutorial are not important.
For more details, see [our CALF-20 paper].
Figure 1 The example of CALF-20 structure with water loading will be used in this tutorial#
Mean square displacement#
The input example for MSD calculation is shown in input.msd file.
First, calculation mode is selected mode='msd', following by specifying a path to trajectory.
The important tags for averaging can specified by
mdstep, bufferinterval, nbuffer and nstepskip.
Here, buffer length is determined
(mdstep - nstepskip) - nbuffer * bufferinterval.
Time interval dt between neighnoring snapshots is 100 fs.
For &msd namelist, the evaluation on the specified groups, only water molecules, will be done.
For ecah group, a center of mass (COM) will be computed.
Therefore, each group must contain only 1 water molecule.
The projection of the displacement on
the axis \(\vec{u}=(0,1,1)\) will be obtained.
Rather than specify the cartesian vector,
we define the center of the first pore in fractional scale 0.25 0.25 0.25 as
the beginning point and the center of the second pore 0.25 0.50 0.50 as the ending point.
Therefore, a vector connecting between 2 pore centers will be a our reference axis.
&control
mode = "msd"
dumpfile = "../dump.1"
mdstep = 10000
bufferinterval = 1000
nbuffer = 5
nstepskip = 2000
dt = 100
ntype = 7
writeunwrap = "xsf"
/
&msd
groupmol = .TRUE.
decomposemol = .FALSE.
project = 0.25 0.25 0.25 0.25 0.50 0.50
logfile = "log.dat"
/
C H N O Zn H O
768 512 768 512 256 256 128
12.011 1.008 14.007 15.999 65.38 1.008 15.999
128
3 2817 2818 3073
3 2819 2820 3074
3 2821 2822 3075
3 2823 2824 3076
3 2825 2826 3077
3 2827 2828 3078
3 2829 2830 3079
3 2831 2832 3080
3 2833 2834 3081
3 2835 2836 3082
3 2837 2838 3083
3 2839 2840 3084
3 2841 2842 3085
3 2843 2844 3086
3 2845 2846 3087
3 2847 2848 3088
3 2849 2850 3089
3 2851 2852 3090
3 2853 2854 3091
3 2855 2856 3092
3 2857 2858 3093
3 2859 2860 3094
3 2861 2862 3095
3 2863 2864 3096
3 2865 2866 3097
3 2867 2868 3098
3 2869 2870 3099
3 2871 2872 3100
3 2873 2874 3101
3 2875 2876 3102
3 2877 2878 3103
3 2879 2880 3104
3 2881 2882 3105
3 2883 2884 3106
3 2885 2886 3107
3 2887 2888 3108
3 2889 2890 3109
3 2891 2892 3110
3 2893 2894 3111
3 2895 2896 3112
3 2897 2898 3113
3 2899 2900 3114
3 2901 2902 3115
3 2903 2904 3116
3 2905 2906 3117
3 2907 2908 3118
3 2909 2910 3119
3 2911 2912 3120
3 2913 2914 3121
3 2915 2916 3122
3 2917 2918 3123
3 2919 2920 3124
3 2921 2922 3125
3 2923 2924 3126
3 2925 2926 3127
3 2927 2928 3128
3 2929 2930 3129
3 2931 2932 3130
3 2933 2934 3131
3 2935 2936 3132
3 2937 2938 3133
3 2939 2940 3134
3 2941 2942 3135
3 2943 2944 3136
3 2945 2946 3137
3 2947 2948 3138
3 2949 2950 3139
3 2951 2952 3140
3 2953 2954 3141
3 2955 2956 3142
3 2957 2958 3143
3 2959 2960 3144
3 2961 2962 3145
3 2963 2964 3146
3 2965 2966 3147
3 2967 2968 3148
3 2969 2970 3149
3 2971 2972 3150
3 2973 2974 3151
3 2975 2976 3152
3 2977 2978 3153
3 2979 2980 3154
3 2981 2982 3155
3 2983 2984 3156
3 2985 2986 3157
3 2987 2988 3158
3 2989 2990 3159
3 2991 2992 3160
3 2993 2994 3161
3 2995 2996 3162
3 2997 2998 3163
3 2999 3000 3164
3 3001 3002 3165
3 3003 3004 3166
3 3005 3006 3167
3 3007 3008 3168
3 3009 3010 3169
3 3011 3012 3170
3 3013 3014 3171
3 3015 3016 3172
3 3017 3018 3173
3 3019 3020 3174
3 3021 3022 3175
3 3023 3024 3176
3 3025 3026 3177
3 3027 3028 3178
3 3029 3030 3179
3 3031 3032 3180
3 3033 3034 3181
3 3035 3036 3182
3 3037 3038 3183
3 3039 3040 3184
3 3041 3042 3185
3 3043 3044 3186
3 3045 3046 3187
3 3047 3048 3188
3 3049 3050 3189
3 3051 3052 3190
3 3053 3054 3191
3 3055 3056 3192
3 3057 3058 3193
3 3059 3060 3194
3 3061 3062 3195
3 3063 3064 3196
3 3065 3066 3197
3 3067 3068 3198
3 3069 3070 3199
3 3071 3072 3200
Here, when group of waters is specified, only water molecules will be calculated as shown in Figure below.
Figure 2 The example of water groups used in MSD calculations#
The execution is simple.
$ ./a.out intput.msd
One can get the output files.
Total_xyz.datcontains the MSD decompsed in X, Y and Z axisTotal_sum.datcontains total MSDTotal_axis.datcontains the projected MSD on the specified axisunwrap_trajectory.xsfcontains the unwraped trajectory including all atomsunwrap_groups.xsfcontains the unwraped trajectory including only atoms in groups and their center of massunwrap_disp_*.xsfcontains the trajcetory of center of mass used in each buffer
The example MSD can be plotted as shown in following figure.
Figure 3 MSD calculated on center of mass of each water molecule#
The important aspect of unwrap_disp_*.xsf file is that it contains the velocity imformation as vectors.
One can visualize and perform the further analysis using these vectors.
Figure 4 The example of center of mass of each water group used in MSD calculations. The vectors represent the velocity of each center of mass.#
Intermittent bond autocorrelation#
The input example for MSD calculation is shown in input.bond_correlation file.
The first set mode='bond_correlation' following by specifying a path to dump file.
The important tags for averaging is specify by
mdstep, bufferinterval, nbuffer and nstepskip.
Time interval between neighnoring snapshots is 100 fs.
For &bond_correlation namelist, the evaluation on whole atoms will be done.
In this tutorial, we are interested in the correlation of Zn-water bond.
Thus, atomic index 5 for Zn and atomic index 7 for water oxygen will be focused.
Here, the criteria for bond is 2.5 Å
Input#
&control
mode = "bond_correlation"
dumpfile = "../dump.1"
mdstep = 10000
bufferinterval = 300
nbuffer = 25
nstepskip = 1
dt = 100
ntype = 7
writeunwrap = "xsf"
/
&bond_correlation
groupmol = .FALSE.
decomposemol = .FALSE.
bondpair = 4 6
bondtreshold = 2.0
autocorrfile = "auto.bond.4.6"
/
C H N O Zn H O
768 512 768 512 256 256 128
12.011 1.008 14.007 15.999 65.38 1.008 15.999
The execution is simple.
$ ./a.out input.bond_correlation
One can get the output files.
auto.bondcontains bond autocorrelation function
In this example, we calculated the antocorrelation function on \(O_F-H_w\), \(Zn_F-O_w\) and \(O_w-O_w\) as shown in figure below. We can clearly see that waters \(O_w-O_w\) are making cluster with long lifetime, while \(O_F-H_w\) and \(Zn_F-O_w\) interaction do not persist longer than 100 ps.
Figure 5 The bond autocorrelation function showing the lifetime of the bonds of interest#
Angle autocorrelation#
The input example for MSD calculation is shown in input.angle_correlation file.
The first set mode='angle_correlation' following by specifying a path to dump file.
The important tags for averaging is specify by
mdstep, bufferinterval, nbuffer and nstepskip.
Time interval between neighnoring snapshots is 100 fs.
For &angle_correlation namelist, the evaluation on the specified groups will be done.
For ecah group, five atoms for 2 planes definition are required.
The first atomic index represent the center atoms. The second and the third are the definition of
plane A, while the forth and the fifth are the definition of plane B.
Note that, the order second to fifth will be count the clockwise direction around the center (first atom).
The specification required an external script to control.
In this tutorial we are focusing on the openess of the Zn metal node in CALF-20 where the first plane is defined by the O-Zn-O plane (O is oxalate oxygen), while the second plane is defined by the N-Zn-N plane (N is triazole nitrogen).
Figure 6 The molecular groups specified by atomic index below the namelist. The vectors operators will be computed within each node. The vectors shown in this figure is an example of normal vector of O-Zn-O plane.#
Figure 7 The molecular group specified by atomic index below the namelist. The vectors operators will be computed within each node. The vectors shown in this figure is an example of normal vector of O-Zn-O plane.#
Input#
&control
mode = "angle_correlation"
dumpfile = "../dump.1"
mdstep = 10000
bufferinterval = 1000
nbuffer = 5
nstepskip = 2000
dt = 100
ntype = 7
writeunwrap = "xsf"
/
&angle_correlation
groupmol = .TRUE.
decomposemol = .FALSE.
functype = 1
logfile = "log.angle.1"
autocorrfile = "auto.angle.1"
/
C H N O Zn H O
768 512 768 512 256 256 128
12.011 1.008 14.007 15.999 65.38 1.008 15.999
256
5 2561 2199 2049 1287 1497
5 2562 2056 2122 1396 1282
5 2563 2069 2051 1285 1307
5 2564 2054 2060 1298 1284
5 2565 2207 2057 1299 1509
5 2566 2064 2050 1288 1294
5 2567 2077 2059 1297 1319
5 2568 2116 2062 1296 1382
5 2569 2065 2055 1281 1311
5 2570 2072 2138 1420 1306
5 2571 2181 2067 1309 1475
5 2572 2076 2070 1308 1322
5 2573 2073 2063 1293 1323
5 2574 2080 2066 1312 1318
5 2575 2189 2075 1321 1487
5 2576 2132 2078 1320 1406
5 2577 2081 2231 1545 1335
5 2578 2154 2088 1330 1444
5 2579 2101 2083 1333 1355
5 2580 2092 2086 1332 1346
5 2581 2239 2089 1347 1557
5 2582 2082 2096 1342 1336
5 2583 2109 2091 1345 1367
5 2584 2094 2148 1430 1344
5 2585 2087 2097 1359 1329
5 2586 2104 2170 1468 1354
5 2587 2213 2099 1357 1523
5 2588 2108 2102 1356 1370
5 2589 2095 2105 1371 1341
5 2590 2112 2098 1360 1366
5 2591 2221 2107 1369 1535
5 2592 2164 2110 1368 1454
5 2593 2263 2113 1383 1593
5 2594 2120 2058 1300 1378
5 2595 2115 2133 1403 1381
5 2596 2118 2124 1394 1380
5 2597 2271 2121 1395 1605
5 2598 2114 2128 1390 1384
5 2599 2141 2123 1393 1415
5 2600 2126 2052 1286 1392
5 2601 2129 2119 1377 1407
5 2602 2074 2136 1402 1324
5 2603 2131 2245 1571 1405
5 2604 2140 2134 1404 1418
5 2605 2137 2127 1389 1419
5 2606 2144 2130 1408 1414
5 2607 2139 2253 1583 1417
5 2608 2142 2068 1310 1416
5 2609 2295 2145 1431 1641
5 2610 2152 2090 1348 1426
5 2611 2165 2147 1429 1451
5 2612 2150 2156 1442 1428
5 2613 2303 2153 1443 1653
5 2614 2146 2160 1438 1432
5 2615 2155 2173 1463 1441
5 2616 2084 2158 1440 1334
5 2617 2161 2151 1425 1455
5 2618 2106 2168 1450 1372
5 2619 2163 2277 1619 1453
5 2620 2172 2166 1452 1466
5 2621 2169 2159 1437 1467
5 2622 2176 2162 1456 1462
5 2623 2285 2171 1465 1631
5 2624 2100 2174 1464 1358
5 2625 2071 2177 1305 1479
5 2626 2250 2184 1474 1588
5 2627 2179 2197 1499 1477
5 2628 2182 2188 1490 1476
5 2629 2079 2185 1317 1491
5 2630 2178 2192 1486 1480
5 2631 2187 2205 1511 1489
5 2632 2244 2190 1488 1574
5 2633 2193 2183 1473 1503
5 2634 2266 2200 1498 1612
5 2635 2195 2053 1283 1501
5 2636 2198 2204 1514 1500
5 2637 2191 2201 1485 1515
5 2638 2208 2194 1504 1510
5 2639 2203 2061 1295 1513
5 2640 2260 2206 1512 1598
5 2641 2209 2103 1353 1527
5 2642 2282 2216 1522 1636
5 2643 2229 2211 1525 1547
5 2644 2220 2214 1524 1538
5 2645 2111 2217 1539 1365
5 2646 2224 2210 1528 1534
5 2647 2237 2219 1537 1559
5 2648 2222 2276 1622 1536
5 2649 2225 2215 1521 1551
5 2650 2298 2232 1546 1660
5 2651 2227 2085 1331 1549
5 2652 2236 2230 1548 1562
5 2653 2233 2223 1533 1563
5 2654 2240 2226 1552 1558
5 2655 2235 2093 1343 1561
5 2656 2238 2292 1646 1560
5 2657 2241 2135 1401 1575
5 2658 2186 2248 1570 1492
5 2659 2261 2243 1573 1595
5 2660 2252 2246 1572 1586
5 2661 2143 2249 1587 1413
5 2662 2242 2256 1582 1576
5 2663 2269 2251 1585 1607
5 2664 2254 2180 1478 1584
5 2665 2247 2257 1599 1569
5 2666 2264 2202 1516 1594
5 2667 2117 2259 1597 1379
5 2668 2262 2268 1610 1596
5 2669 2265 2255 1581 1611
5 2670 2258 2272 1606 1600
5 2671 2125 2267 1609 1391
5 2672 2270 2196 1502 1608
5 2673 2273 2167 1449 1623
5 2674 2218 2280 1618 1540
5 2675 2275 2293 1643 1621
5 2676 2284 2278 1620 1634
5 2677 2175 2281 1635 1461
5 2678 2288 2274 1624 1630
5 2679 2301 2283 1633 1655
5 2680 2286 2212 1526 1632
5 2681 2289 2279 1617 1647
5 2682 2234 2296 1642 1564
5 2683 2149 2291 1645 1427
5 2684 2300 2294 1644 1658
5 2685 2287 2297 1659 1629
5 2686 2304 2290 1648 1654
5 2687 2299 2157 1439 1657
5 2688 2228 2302 1656 1550
5 2689 2305 2455 1881 1671
5 2690 2312 2378 1780 1666
5 2691 2307 2325 1691 1669
5 2692 2316 2310 1668 1682
5 2693 2313 2463 1893 1683
5 2694 2306 2320 1678 1672
5 2695 2333 2315 1681 1703
5 2696 2372 2318 1680 1766
5 2697 2321 2311 1665 1695
5 2698 2328 2394 1804 1690
5 2699 2323 2437 1859 1693
5 2700 2326 2332 1706 1692
5 2701 2329 2319 1677 1707
5 2702 2336 2322 1696 1702
5 2703 2331 2445 1871 1705
5 2704 2334 2388 1790 1704
5 2705 2337 2487 1929 1719
5 2706 2410 2344 1714 1828
5 2707 2339 2357 1739 1717
5 2708 2348 2342 1716 1730
5 2709 2495 2345 1731 1941
5 2710 2338 2352 1726 1720
5 2711 2365 2347 1729 1751
5 2712 2350 2404 1814 1728
5 2713 2353 2343 1713 1743
5 2714 2426 2360 1738 1852
5 2715 2355 2469 1907 1741
5 2716 2358 2364 1754 1740
5 2717 2351 2361 1755 1725
5 2718 2368 2354 1744 1750
5 2719 2477 2363 1753 1919
5 2720 2420 2366 1752 1838
5 2721 2369 2519 1977 1767
5 2722 2314 2376 1762 1684
5 2723 2389 2371 1765 1787
5 2724 2374 2380 1778 1764
5 2725 2377 2527 1989 1779
5 2726 2370 2384 1774 1768
5 2727 2379 2397 1799 1777
5 2728 2382 2308 1670 1776
5 2729 2375 2385 1791 1761
5 2730 2392 2330 1708 1786
5 2731 2501 2387 1789 1955
5 2732 2390 2396 1802 1788
5 2733 2393 2383 1773 1803
5 2734 2400 2386 1792 1798
5 2735 2395 2509 1967 1801
5 2736 2398 2324 1694 1800
5 2737 2401 2551 2025 1815
5 2738 2346 2408 1810 1732
5 2739 2421 2403 1813 1835
5 2740 2406 2412 1826 1812
5 2741 2409 2559 2037 1827
5 2742 2402 2416 1822 1816
5 2743 2411 2429 1847 1825
5 2744 2414 2340 1718 1824
5 2745 2417 2407 1809 1839
5 2746 2424 2362 1756 1834
5 2747 2533 2419 1837 2003
5 2748 2422 2428 1850 1836
5 2749 2415 2425 1851 1821
5 2750 2432 2418 1840 1846
5 2751 2427 2541 2015 1849
5 2752 2430 2356 1742 1848
5 2753 2327 2433 1863 1689
5 2754 2440 2506 1972 1858
5 2755 2435 2453 1883 1861
5 2756 2438 2444 1874 1860
5 2757 2441 2335 1701 1875
5 2758 2434 2448 1870 1864
5 2759 2461 2443 1873 1895
5 2760 2446 2500 1958 1872
5 2761 2439 2449 1887 1857
5 2762 2522 2456 1882 1996
5 2763 2309 2451 1885 1667
5 2764 2454 2460 1898 1884
5 2765 2447 2457 1899 1869
5 2766 2464 2450 1888 1894
5 2767 2459 2317 1679 1897
5 2768 2462 2516 1982 1896
5 2769 2465 2359 1737 1911
5 2770 2472 2538 2020 1906
5 2771 2485 2467 1909 1931
5 2772 2476 2470 1908 1922
5 2773 2367 2473 1923 1749
5 2774 2480 2466 1912 1918
5 2775 2475 2493 1943 1921
5 2776 2532 2478 1920 2006
5 2777 2471 2481 1935 1905
5 2778 2488 2554 2044 1930
5 2779 2341 2483 1933 1715
5 2780 2492 2486 1932 1946
5 2781 2479 2489 1947 1917
5 2782 2496 2482 1936 1942
5 2783 2491 2349 1727 1945
5 2784 2548 2494 1944 2030
5 2785 2497 2391 1785 1959
5 2786 2442 2504 1954 1876
5 2787 2499 2517 1979 1957
5 2788 2502 2508 1970 1956
5 2789 2399 2505 1971 1797
5 2790 2512 2498 1960 1966
5 2791 2507 2525 1991 1969
5 2792 2510 2436 1862 1968
5 2793 2513 2503 1953 1983
5 2794 2458 2520 1978 1900
5 2795 2515 2373 1763 1981
5 2796 2518 2524 1994 1980
5 2797 2521 2511 1965 1995
5 2798 2528 2514 1984 1990
5 2799 2381 2523 1993 1775
5 2800 2526 2452 1886 1992
5 2801 2423 2529 2007 1833
5 2802 2536 2474 1924 2002
5 2803 2549 2531 2005 2027
5 2804 2540 2534 2004 2018
5 2805 2431 2537 2019 1845
5 2806 2544 2530 2008 2014
5 2807 2557 2539 2039 2017
5 2808 2542 2468 1910 2016
5 2809 2545 2535 2001 2031
5 2810 2490 2552 2026 1948
5 2811 2547 2405 1811 2029
5 2812 2556 2550 2028 2042
5 2813 2553 2543 2013 2043
5 2814 2560 2546 2032 2038
5 2815 2555 2413 1823 2041
5 2816 2484 2558 2040 1934
The execution is simple.
$ ./a.out input.angle_correlation
Figure 8 The geometry index of ecah node as a function of time#
Figure 9 The angle measured by 2 different schemes as a a function of time#
Figure 10 The autocorrelation function for each parameters (2 geometry indices and 2 angle scheme)#
Dipole-derivative autocorrelation#
Input#
&control
mode = "dipole_correlation"
dumpfile = "../dump.1"
mdstep = 100000
bufferinterval = 14000
nbuffer = 5
nstepskip = 1
dt = 1
ntype = 261
writeunwrap = "xsf"
/
&dipole_correlation
groupmol = .TRUE.
decomposemol = .FALSE.
logfile = "log.dat"
autocorrfile = "autocorrelation.water.tip4p"
/
F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C F C H N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S N S O Zn H O
8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 512 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 8 4 512 256 256 128
0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1111 0.5119 0.1281 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.16505 -0.2756 -0.5151 0.6456 0.52 -1.04
128
3 2817 2818 3073
3 2819 2820 3074
3 2821 2822 3075
3 2823 2824 3076
3 2825 2826 3077
3 2827 2828 3078
3 2829 2830 3079
3 2831 2832 3080
3 2833 2834 3081
3 2835 2836 3082
3 2837 2838 3083
3 2839 2840 3084
3 2841 2842 3085
3 2843 2844 3086
3 2845 2846 3087
3 2847 2848 3088
3 2849 2850 3089
3 2851 2852 3090
3 2853 2854 3091
3 2855 2856 3092
3 2857 2858 3093
3 2859 2860 3094
3 2861 2862 3095
3 2863 2864 3096
3 2865 2866 3097
3 2867 2868 3098
3 2869 2870 3099
3 2871 2872 3100
3 2873 2874 3101
3 2875 2876 3102
3 2877 2878 3103
3 2879 2880 3104
3 2881 2882 3105
3 2883 2884 3106
3 2885 2886 3107
3 2887 2888 3108
3 2889 2890 3109
3 2891 2892 3110
3 2893 2894 3111
3 2895 2896 3112
3 2897 2898 3113
3 2899 2900 3114
3 2901 2902 3115
3 2903 2904 3116
3 2905 2906 3117
3 2907 2908 3118
3 2909 2910 3119
3 2911 2912 3120
3 2913 2914 3121
3 2915 2916 3122
3 2917 2918 3123
3 2919 2920 3124
3 2921 2922 3125
3 2923 2924 3126
3 2925 2926 3127
3 2927 2928 3128
3 2929 2930 3129
3 2931 2932 3130
3 2933 2934 3131
3 2935 2936 3132
3 2937 2938 3133
3 2939 2940 3134
3 2941 2942 3135
3 2943 2944 3136
3 2945 2946 3137
3 2947 2948 3138
3 2949 2950 3139
3 2951 2952 3140
3 2953 2954 3141
3 2955 2956 3142
3 2957 2958 3143
3 2959 2960 3144
3 2961 2962 3145
3 2963 2964 3146
3 2965 2966 3147
3 2967 2968 3148
3 2969 2970 3149
3 2971 2972 3150
3 2973 2974 3151
3 2975 2976 3152
3 2977 2978 3153
3 2979 2980 3154
3 2981 2982 3155
3 2983 2984 3156
3 2985 2986 3157
3 2987 2988 3158
3 2989 2990 3159
3 2991 2992 3160
3 2993 2994 3161
3 2995 2996 3162
3 2997 2998 3163
3 2999 3000 3164
3 3001 3002 3165
3 3003 3004 3166
3 3005 3006 3167
3 3007 3008 3168
3 3009 3010 3169
3 3011 3012 3170
3 3013 3014 3171
3 3015 3016 3172
3 3017 3018 3173
3 3019 3020 3174
3 3021 3022 3175
3 3023 3024 3176
3 3025 3026 3177
3 3027 3028 3178
3 3029 3030 3179
3 3031 3032 3180
3 3033 3034 3181
3 3035 3036 3182
3 3037 3038 3183
3 3039 3040 3184
3 3041 3042 3185
3 3043 3044 3186
3 3045 3046 3187
3 3047 3048 3188
3 3049 3050 3189
3 3051 3052 3190
3 3053 3054 3191
3 3055 3056 3192
3 3057 3058 3193
3 3059 3060 3194
3 3061 3062 3195
3 3063 3064 3196
3 3065 3066 3197
3 3067 3068 3198
3 3069 3070 3199
3 3071 3072 3200
The execution is simple.
$ ./a.out input.dipole_correlation
Figure 11 The IR spectra of water loaded CALF-20, where the concentration is ranging from 0 - 1.0 H2O/unit cell (u.c.)#
Velocity autocorrelation#
Input#
The input is resemble to the dipole correlation calculation, therefore, the example is not provided here. The execution is simple.
$ ./a.out input.velocity_correlation
Figure 11 The IR spectra of water loaded CALF-20, where the concentration is ranging from 0 - 1.0 H2O/unit cell (u.c.)#