Change int* to tagint*

examples/PACKAGES/pod/Ta/Ta_compute.pod

@@ -3,7 +3,7 @@
 # initialize simulation
 
 variable 	nsteps index 0
-variable 	nrep equal 1
+variable 	nrep equal 2
 variable 	a equal 2.0
 units		metal
 
@@ -30,12 +30,23 @@ variable 	rcutfac equal 6.0
 pair_style 	zero ${rcutfac}
 pair_coeff 	* *
 
-# calculate global POD descriptors and their derivatives
-compute gdd all pod/gdd Ta_param.pod "" "" C C
+# set up per-atom computes
+
+compute ld all pod/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
+compute dd all podd/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
+
+# set up compute snap generating global array
+
+compute gdd all pod/gdd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
 fix 		gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector
 
-# calculate per-atom POD descriptors and their derivatives
-compute ldd all pod/ldd Ta_param.pod "" "" C C
+compute ldd all pod/ldd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
 fix 		ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector
 
+dump 		mydump_ld all custom 1000 dump_ld id c_ld[*]
+dump 		mydump_dd all custom 1000 dump_dd id c_dd[*]
 
+variable sample_ld1 equal C_ld[1][10]  # Arbitrary local descriptor
+fix ldprint all print 1 "${sample_ld1}" file sample_ld.txt
+
+run             ${nsteps}

examples/PACKAGES/pod/Ta/dump_ld

@@ -0,0 +1,25 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+16
+ITEM: BOX BOUNDS pp pp pp
+0.0000000000000000e+00 4.0000000000000000e+00
+0.0000000000000000e+00 4.0000000000000000e+00
+0.0000000000000000e+00 4.0000000000000000e+00
+ITEM: ATOMS id c_ld[1] c_ld[2] c_ld[3] c_ld[4] c_ld[5] c_ld[6] c_ld[7] c_ld[8] c_ld[9] c_ld[10] c_ld[11] c_ld[12] c_ld[13] c_ld[14] c_ld[15] c_ld[16] c_ld[17] c_ld[18] c_ld[19] c_ld[20] c_ld[21] c_ld[22] c_ld[23] c_ld[24] c_ld[25] c_ld[26] c_ld[27] c_ld[28] c_ld[29] c_ld[30] c_ld[31] c_ld[32] c_ld[33] c_ld[34] c_ld[35] c_ld[36] c_ld[37] c_ld[38] c_ld[39] c_ld[40] c_ld[41] c_ld[42] c_ld[43] c_ld[44] c_ld[45] c_ld[46] c_ld[47] c_ld[48] c_ld[49] c_ld[50] c_ld[51] c_ld[52] c_ld[53] c_ld[54] c_ld[55] c_ld[56] c_ld[57] c_ld[58] c_ld[59] c_ld[60] c_ld[61] c_ld[62] c_ld[63] c_ld[64] c_ld[65] c_ld[66] c_ld[67] c_ld[68] c_ld[69] c_ld[70] c_ld[71] c_ld[72] c_ld[73] c_ld[74] c_ld[75] c_ld[76] c_ld[77] c_ld[78] c_ld[79] c_ld[80] c_ld[81] c_ld[82] c_ld[83] c_ld[84] c_ld[85] c_ld[86] c_ld[87] c_ld[88] c_ld[89] c_ld[90] c_ld[91] c_ld[92] c_ld[93] c_ld[94] c_ld[95] c_ld[96] c_ld[97] c_ld[98] c_ld[99] c_ld[100] c_ld[101] c_ld[102] c_ld[103] c_ld[104] c_ld[105] c_ld[106] c_ld[107] c_ld[108] c_ld[109] c_ld[110] c_ld[111] c_ld[112] c_ld[113] c_ld[114] c_ld[115] c_ld[116] c_ld[117] c_ld[118] c_ld[119] c_ld[120] c_ld[121] c_ld[122]
+1 4.49503 10.9496 -9.51513 9.76683 -18.2757 5.06405 39.8529 0.114405 13.3216 0.134392 8.07812 236.479 0.110188 78.9295 0.193969 47.5315 178.577 1.65132 59.8012 1.7958 36.4171 188.149 1.6524 63.4702 2.14313 38.4147 658.786 0.886907 220.671 1.19001 132.84 353.335 1.01431 118.109 0.341942 1.19152 0.342292 39.5941 5107.23 2.37973 1704.64 0.821219 4.18914 0.816552 569.718 -3351.46 -30.9914 -1122.33 -10.8333 -33.7029 -10.4267 -377.565 3624.52 31.8319 1222.7 10.4135 41.2855 10.8783 417.427 3132.67 18588.6 4.37096 10.6474 -9.25251 9.49726 -17.7713 4.92428 38.7529 0.111247 12.9539 0.130682 7.85516 229.952 0.107147 76.751 0.188615 46.2196 173.648 1.60574 58.1507 1.74623 35.412 182.956 1.60679 61.7184 2.08398 37.3544 640.603 0.862428 214.58 1.15717 129.173 343.583 0.986318 114.85 0.332504 1.15863 0.332844 38.5013 4966.27 2.31405 1657.59 0.798553 4.07352 0.794015 553.993 -3258.96 -30.136 -1091.35 -10.5343 -32.7726 -10.1389 -367.144 3524.48 30.9534 1188.95 10.1261 40.146 10.578 405.906 3046.2 18075.5
+2 4.51943 10.6538 -10.1605 9.64074 -17.0469 5.67958 40.284 0.214448 13.5432 0.307119 8.22367 223.86 0.212115 74.7829 0.253561 45.019 203.609 2.03963 67.9955 1.77758 41.5817 183.31 4.66792 61.8587 3.45837 38.3103 573.136 1.90355 191.523 1.31909 115.239 359.072 1.91149 120.718 0.664993 2.73751 0.691926 40.9172 4703.78 4.457 1571.35 1.49225 5.32787 1.47773 526.051 -4080.16 -40.8725 -1362.58 -13.7097 -35.6214 -13.4691 -455.876 3485.48 88.7564 1176.19 31.7132 65.7578 31.4138 401.989 3200.6 17785.8 4.39409 10.3583 -9.87872 9.37336 -16.5741 5.52206 39.1668 0.208501 13.1676 0.298601 7.99559 217.651 0.206232 72.7088 0.246529 43.7704 197.962 1.98306 66.1097 1.72828 40.4285 178.226 4.53846 60.1431 3.36245 37.2478 557.241 1.85075 186.212 1.2825 112.043 349.114 1.85848 117.37 0.64655 2.66159 0.672736 39.7824 4573.32 4.33339 1527.77 1.45087 5.18011 1.43674 511.461 -3967 -39.7389 -1324.79 -13.3294 -34.6335 -13.0956 -443.232 3388.81 86.2948 1143.57 30.8337 63.9341 30.5426 390.84 3111.83 17292.6
+3 4.60187 10.9376 -8.98069 9.74094 -18.2912 4.81709 41.7766 0.192115 13.9403 0.150262 8.44855 235.997 0.0754332 78.7109 0.128212 47.3399 159.105 2.76723 53.161 1.72279 32.911 187.183 1.97007 62.594 2.19639 37.7061 660.009 1.92675 220.436 1.25478 132.585 379.255 1.74406 126.553 0.563025 1.36411 0.58104 42.2741 5092.03 1.6276 1698.32 0.52917 2.76639 0.549626 566.758 -2818.75 -49.0251 -941.818 -16.8877 -30.5214 -16.591 -315.413 3596.92 37.857 1202.81 13.1353 42.2061 12.8434 403.516 3442.94 19449.2 4.4763 10.6391 -8.73564 9.47514 -17.7921 4.68565 40.6366 0.186873 13.56 0.146162 8.21802 229.557 0.0733749 76.5632 0.124713 46.0481 154.763 2.69172 51.7104 1.67578 32.013 182.075 1.91631 60.8861 2.13646 36.6772 641.999 1.87417 214.422 1.22054 128.968 368.906 1.69647 123.1 0.547662 1.32688 0.565185 41.1205 4953.08 1.58319 1651.98 0.51473 2.6909 0.534628 551.293 -2741.84 -47.6874 -916.119 -16.4269 -29.6886 -16.1382 -306.806 3498.77 36.824 1169.99 12.7769 41.0544 12.493 392.505 3349 18918.5
+4 4.23332 10.8904 -11.0027 9.19336 -17.428 5.98028 35.3478 0.0192613 11.7994 0.110296 7.12078 233.929 0.0296453 78.0637 0.292684 46.9542 238.781 0.555149 79.86 0.768454 48.2347 166.705 1.23131 56.1338 1.1659 34.3831 599.096 0.500109 200.879 1.01622 121.618 295.15 0.16083 98.5239 0.0523567 0.920957 0.0508645 32.9346 5024.88 0.636793 1676.84 0.20866 6.28697 0.217915 560.206 -5182.02 -12.0478 -1733.12 -4.25423 -16.677 -3.9841 -581.52 3022.89 22.3276 1017.88 8.07185 21.1415 7.48522 346.095 2464.47 16309.7 4.11657 10.59 -10.6993 8.93982 -16.9474 5.81535 34.3729 0.0187301 11.474 0.107254 6.9244 227.477 0.0288277 75.9108 0.284612 45.6593 232.195 0.539838 77.6576 0.747261 46.9045 162.107 1.19735 54.5857 1.13375 33.4348 582.573 0.486317 195.339 0.988197 118.264 287.01 0.156395 95.8067 0.0509127 0.895558 0.0494617 32.0263 4886.3 0.619231 1630.59 0.202905 6.11358 0.211905 544.756 -5039.1 -11.7156 -1685.32 -4.1369 -16.217 -3.87423 -565.482 2939.52 21.7118 989.812 7.84923 20.5585 7.27879 336.55 2396.5 15859.9
+5 4.31258 10.934 -10.5487 9.15107 -17.9446 5.88523 36.6862 0.0158009 12.2486 0.075257 7.39145 235.822 0.0211404 78.6831 0.188062 47.2972 219.497 1.02406 73.5984 1.21474 44.583 165.185 2.48683 55.2132 1.77457 33.2971 635.178 2.12192 212.201 2.03986 127.941 312.081 0.134415 104.196 0.0452344 0.640195 0.0454229 34.845 5086.16 0.455953 1697.02 0.15729 4.05609 0.161461 566.761 -4567.27 -21.3086 -1531.43 -7.13475 -25.2762 -7.05036 -516.319 2981.75 44.8896 996.65 15.6495 32.0326 15.2019 334.014 2654.81 17065.3 4.1942 10.6338 -10.2592 8.89987 -17.452 5.72368 35.6791 0.0153672 11.9124 0.0731912 7.18855 229.349 0.0205601 76.5232 0.1829 45.9989 213.472 0.995953 71.5781 1.18139 43.3592 160.651 2.41856 53.6976 1.72585 32.3831 617.742 2.06367 206.376 1.98387 124.429 303.515 0.130725 101.336 0.0439927 0.622621 0.044176 33.8885 4946.55 0.443437 1650.44 0.152973 3.94475 0.157029 551.203 -4441.89 -20.7237 -1489.39 -6.9389 -24.5823 -6.85683 -502.146 2899.9 43.6574 969.292 15.2199 31.1533 14.7846 324.845 2581.93 16596.9
+6 4.50673 10.9356 -9.47393 9.54877 -18.1586 5.10538 40.0632 0.136767 13.4178 0.133502 8.13535 235.887 0.0958326 78.7369 0.17742 47.4151 177.044 1.95914 59.3807 1.50419 36.3874 179.853 1.55397 60.0841 2.18171 36.3246 650.409 0.307592 217.275 0.907229 130.862 356.147 1.21581 119.279 0.409523 1.18679 0.413083 40.1376 5088.22 2.06717 1698.4 0.702671 3.82705 0.692145 567.678 -3308.53 -36.6114 -1109.68 -11.6111 -28.1096 -12.1846 -374.403 3387.56 29.2693 1131.7 9.71345 41.0929 9.75169 378.914 3166.01 18641.1 4.3829 10.6351 -9.21362 9.2864 -17.6597 4.9651 38.9624 0.133009 13.0491 0.129834 7.91182 229.405 0.0931994 76.5735 0.172545 46.1123 172.18 1.90531 57.7492 1.46286 35.3876 174.911 1.51127 58.4332 2.12176 35.3265 632.538 0.299141 211.305 0.882302 127.267 346.361 1.1824 116.002 0.39827 1.15418 0.401733 39.0348 4948.42 2.01037 1651.74 0.683364 3.7219 0.673127 552.08 -3217.62 -35.6055 -1079.19 -11.292 -27.3372 -11.8498 -364.115 3294.48 28.4651 1100.6 9.44656 39.9638 9.48374 368.503 3079.02 18128.9
+7 4.45432 10.9846 -9.68605 9.05207 -18.5817 5.63187 39.1442 0.0934148 13.0864 0.148189 7.92204 238.052 0.0706752 79.4665 0.296013 47.7977 185.097 1.1399 62.0234 0.87225 38.104 161.659 0.831017 54.0089 0.99937 32.5378 681.202 3.99333 227.232 2.884 136.688 343.996 0.820922 115.002 0.278226 1.30227 0.276356 38.556 5158.95 1.53164 1722.16 0.514437 6.41505 0.50335 575.741 -3537.13 -21.783 -1185.24 -7.41091 -16.6684 -7.21183 -399.197 2887.05 14.841 964.536 4.8496 17.8476 5.00775 322.977 3023.01 18384.2 4.3336 10.6869 -9.42356 8.80676 -18.0781 5.47925 38.0834 0.0908833 12.7317 0.144173 7.70735 231.601 0.0687599 77.3129 0.287991 46.5024 180.081 1.109 60.3425 0.848612 37.0714 157.278 0.808496 52.5452 0.972287 31.656 662.741 3.88511 221.074 2.80584 132.984 334.674 0.798675 111.885 0.270686 1.26698 0.268866 37.5111 5019.14 1.49013 1675.49 0.500496 6.2412 0.489709 560.138 -3441.27 -21.1926 -1153.12 -7.21007 -16.2166 -7.01639 -388.379 2808.81 14.4388 938.396 4.71817 17.3639 4.87204 314.224 2941.09 17886
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+9 4.40538 10.5898 -10.8079 9.96778 -17.2881 6.11061 38.2712 0.162506 12.8629 0.214595 7.86846 221.147 0.260034 73.9095 0.234692 44.4909 230.348 1.74814 76.9616 2.08091 46.5457 195.931 6.25936 66.9007 4.69967 41.2642 589.39 0.449804 197.909 0.84872 119.649 332.477 1.41175 111.745 0.50332 1.86426 0.524311 37.8644 4618.21 5.43028 1543.45 1.79042 4.90108 1.78573 517.153 -4909.42 -37.2582 -1640.29 -12.3309 -44.3505 -11.9858 -549.296 3851.3 123.037 1315.03 47.3641 92.3786 45.1867 459.935 2888.35 16690.1 4.28201 10.2932 -10.5052 9.68864 -16.804 5.93948 37.1994 0.157955 12.5027 0.208585 7.6481 214.954 0.252751 71.8396 0.22812 43.245 223.897 1.69919 74.8064 2.02264 45.2422 190.444 6.08407 65.0272 4.56806 40.1086 572.884 0.437208 192.367 0.824952 116.298 323.166 1.37222 108.615 0.489224 1.81206 0.509628 36.8041 4488.88 5.27821 1500.23 1.74028 4.76382 1.73572 502.67 -4771.93 -36.2148 -1594.35 -11.9856 -43.1085 -11.6501 -533.913 3743.44 119.591 1278.2 46.0376 89.7916 43.9212 447.055 2807.46 16222.7
+10 4.50594 10.8915 -9.55195 9.65284 -17.7806 5.04756 40.0455 0.0507701 13.4174 0.20445 8.12717 233.967 0.0234821 78.1422 0.367235 47.0078 179.956 0.479218 60.5411 0.973057 37.463 183.778 2.29185 61.5429 1.86998 37.4124 623.555 0.944803 208.61 1.82189 125.797 355.895 0.451208 119.244 0.1559 1.817 0.147449 40.1525 5026.01 0.504434 1678.63 0.171232 7.88882 0.171573 561.717 -3390.32 -9.02832 -1140.58 -3.15841 -18.3321 -3.08051 -387.206 3498.89 43.6338 1171.7 14.7433 35.602 14.6093 394.149 3162.93 18479.5 4.38132 10.5902 -9.28777 9.38586 -17.2888 4.90796 38.9379 0.0493659 13.0463 0.198795 7.90239 227.496 0.0228326 75.9809 0.357078 45.7076 174.979 0.465963 58.8666 0.946144 36.4268 178.695 2.22846 59.8408 1.81826 36.3776 606.309 0.918671 202.84 1.7715 122.317 346.052 0.438728 115.946 0.151588 1.76674 0.143371 39.0419 4887 0.490483 1632.2 0.166496 7.67063 0.166828 546.181 -3296.55 -8.77862 -1109.03 -3.07105 -17.8251 -2.99531 -376.497 3402.12 42.427 1139.29 14.3355 34.6173 14.2053 383.248 3075.45 17968.4
+11 4.48993 10.6274 -10.4336 9.72103 -16.8017 5.88229 39.7606 0.201311 13.3626 0.299864 8.1616 222.754 0.129822 74.4558 0.244233 44.8101 214.706 1.35096 71.8596 1.5182 43.9076 186.379 6.17036 63.2283 4.76521 38.8782 556.775 3.72796 186.489 2.70096 112.357 352.101 1.78271 118.333 0.623308 2.65545 0.653349 40.0878 4669.03 2.72112 1560.62 0.87729 5.11923 0.892669 523.099 -4418.27 -27.8003 -1478.75 -9.0183 -31.242 -9.25826 -496.97 3573.41 118.303 1212.26 43.6248 91.3624 42.7357 418.48 3118.03 17468.4 4.36557 10.333 -10.1446 9.45178 -16.3363 5.71936 38.6594 0.195735 12.9925 0.291558 7.93554 216.585 0.126226 72.3935 0.237468 43.569 208.759 1.31354 69.8692 1.47615 42.6915 181.217 5.99945 61.477 4.63322 37.8014 541.353 3.6247 181.324 2.62615 109.245 342.348 1.73333 115.055 0.606044 2.5819 0.635253 38.9775 4539.71 2.64575 1517.4 0.852991 4.97744 0.867944 508.61 -4295.9 -27.0303 -1437.79 -8.76852 -30.3766 -9.00183 -483.205 3474.44 115.026 1178.69 42.4165 88.8319 41.5521 406.889 3031.67 16984.6
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+13 4.18953 10.8855 -11.2192 9.15184 -17.8149 6.25476 34.6207 0.00843489 11.5528 0.0909255 6.96027 233.722 0.0304736 77.9326 0.265742 46.8415 248.274 0.623702 82.8497 0.916373 49.8288 165.205 2.3438 55.2091 2.34557 33.4253 625.997 0.910981 209.24 2.01355 126.169 286.093 0.0697028 95.4678 0.0232267 0.751374 0.0254634 31.8916 5018.25 0.654299 1673.29 0.217953 5.70575 0.218572 558.126 -5494.13 -13.8021 -1833.41 -4.57662 -20.2787 -4.49197 -612.483 2982.21 42.3092 996.61 14.3101 42.3411 13.9083 333.873 2364.16 15960.3 4.0741 10.5856 -10.9101 8.89971 -17.3241 6.08243 33.6669 0.00820251 11.2345 0.0884204 6.76851 227.283 0.029634 75.7855 0.25842 45.551 241.434 0.606519 80.5671 0.891127 48.456 160.653 2.27923 53.6881 2.28095 32.5044 608.751 0.885883 203.475 1.95807 122.693 278.211 0.0677825 92.8376 0.0225868 0.730674 0.0247619 31.013 4880 0.636273 1627.19 0.211949 5.54855 0.21255 542.75 -5342.76 -13.4219 -1782.9 -4.45053 -19.72 -4.36821 -595.609 2900.04 41.1436 969.152 13.9159 41.1746 13.5252 324.675 2299.03 15520.6
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examples/PACKAGES/pod/Ta/pod.gdd.dat

@@ -1,3 +1,53 @@
 # Time-averaged data for fix gdd
 # TimeStep Number-of-rows
 # Row c_gdd[1] c_gdd[2] c_gdd[3] c_gdd[4] c_gdd[5] c_gdd[6] c_gdd[7] c_gdd[8] c_gdd[9] c_gdd[10] c_gdd[11] c_gdd[12] c_gdd[13] c_gdd[14] c_gdd[15] c_gdd[16] c_gdd[17] c_gdd[18] c_gdd[19] c_gdd[20] c_gdd[21] c_gdd[22] c_gdd[23] c_gdd[24] c_gdd[25] c_gdd[26] c_gdd[27] c_gdd[28] c_gdd[29] c_gdd[30] c_gdd[31] c_gdd[32] c_gdd[33] c_gdd[34] c_gdd[35] c_gdd[36] c_gdd[37] c_gdd[38] c_gdd[39] c_gdd[40] c_gdd[41] c_gdd[42] c_gdd[43] c_gdd[44] c_gdd[45] c_gdd[46] c_gdd[47] c_gdd[48] c_gdd[49] c_gdd[50] c_gdd[51] c_gdd[52] c_gdd[53] c_gdd[54] c_gdd[55] c_gdd[56] c_gdd[57] c_gdd[58] c_gdd[59] c_gdd[60] c_gdd[61] c_gdd[62] c_gdd[63] c_gdd[64] c_gdd[65] c_gdd[66] c_gdd[67] c_gdd[68] c_gdd[69] c_gdd[70] c_gdd[71] c_gdd[72] c_gdd[73] c_gdd[74] c_gdd[75] c_gdd[76] c_gdd[77] c_gdd[78] c_gdd[79] c_gdd[80] c_gdd[81] c_gdd[82] c_gdd[83] c_gdd[84] c_gdd[85] c_gdd[86] c_gdd[87] c_gdd[88] c_gdd[89] c_gdd[90] c_gdd[91] c_gdd[92] c_gdd[93] c_gdd[94] c_gdd[95] c_gdd[96] c_gdd[97] c_gdd[98] c_gdd[99] c_gdd[100] c_gdd[101] c_gdd[102] c_gdd[103] c_gdd[104] c_gdd[105] c_gdd[106] c_gdd[107] c_gdd[108] c_gdd[109] c_gdd[110] c_gdd[111] c_gdd[112] c_gdd[113] c_gdd[114] c_gdd[115] c_gdd[116] c_gdd[117] c_gdd[118] c_gdd[119] c_gdd[120] c_gdd[121] c_gdd[122] c_gdd[123]
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examples/PACKAGES/pod/Ta/sample_ld.txt

@@ -0,0 +1,2 @@
+# Fix print output for fix ldprint
+0.134391735306588