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This change fixes a bug that occurs if you use KDE with CONTACT_MAP as the input variables. (#1441)
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‎regtest/gridtools/rt-vary-nkernels/Makefile‎

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include ../../scripts/test.make

‎regtest/gridtools/rt-vary-nkernels/config‎

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type=driver
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plumed_modules=adjmat
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# this is to test a different name
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arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt %8.4f" # --debug-forces forces.num"

‎regtest/gridtools/rt-vary-nkernels/grid.grid.reference‎

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#! FIELDS ux uy uz avkde davkde_ux davkde_uy davkde_uz
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#! SET nbins 144
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0.1176 -0.9931 0.0000 0.0936 0.1994 -0.8329 0.0066
4+
-0.1497 -0.9792 -0.1372 0.0825 -0.1550 -0.7078 -0.0705
5+
0.0228 -0.9653 0.2602 0.0803 0.0608 -0.6820 0.1594
6+
0.1874 -0.9514 -0.2444 0.0861 0.2115 -0.7491 -0.0953
7+
-0.3427 -0.9375 0.0606 0.0997 -0.4062 -0.8402 0.0160
8+
0.3234 -0.9236 0.2057 0.1026 0.3544 -0.8905 0.0896
9+
-0.1078 -0.9097 -0.4010 0.0757 -0.0996 -0.6007 -0.2740
10+
-0.2048 -0.8958 0.3944 0.0747 -0.1225 -0.5926 0.2483
11+
0.4428 -0.8819 -0.1617 0.1077 0.4518 -0.9289 -0.0376
12+
-0.4589 -0.8681 -0.1894 0.1014 -0.4691 -0.8282 -0.0814
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0.2204 -0.8542 0.4710 0.0803 0.1287 -0.6283 0.3257
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0.1623 -0.8403 -0.5173 0.0662 0.0458 -0.5065 -0.2826
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-0.4872 -0.8264 0.2823 0.0853 -0.3939 -0.6843 0.0840
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0.5694 -0.8125 0.1252 0.1041 0.4859 -0.8714 0.0291
17+
-0.3461 -0.7986 -0.4923 0.0778 -0.2126 -0.5759 -0.3339
18+
-0.0797 -0.7847 0.6147 0.0868 -0.0156 -0.6179 0.5299
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0.4871 -0.7708 -0.4105 0.0641 0.2624 -0.5033 -0.1089
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-0.6529 -0.7569 -0.0270 0.1066 -0.6000 -0.8265 -0.0113
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0.4744 -0.7431 0.4721 0.0630 0.2061 -0.4707 0.1922
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-0.0316 -0.7292 -0.6836 0.0801 -0.0829 -0.5446 -0.5129
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-0.4478 -0.7153 0.5366 0.0575 -0.1690 -0.3940 0.2370
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0.7064 -0.7014 -0.0950 0.0846 0.4634 -0.6415 -0.0188
25+
-0.5961 -0.6875 -0.4147 0.0673 -0.3150 -0.4688 -0.1661
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0.1622 -0.6736 0.7211 0.0841 0.0480 -0.5515 0.5625
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0.3736 -0.6597 -0.6520 0.0487 0.1112 -0.2770 -0.2714
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-0.7274 -0.6458 0.2320 0.0760 -0.4654 -0.5198 0.0395
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0.7036 -0.6319 0.3251 0.0582 0.3221 -0.3837 0.0753
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-0.3035 -0.6181 -0.7252 0.0784 -0.1675 -0.4632 -0.5252
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-0.2697 -0.6042 0.7498 0.0726 -0.0855 -0.4057 0.5096
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0.7145 -0.5903 -0.3755 0.0518 0.3043 -0.3059 -0.0942
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-0.7902 -0.5764 -0.2083 0.0738 -0.4928 -0.4292 -0.0471
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0.4472 -0.5625 0.6954 0.0571 0.1595 -0.2664 0.3734
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0.1416 -0.5486 -0.8240 0.0656 0.0274 -0.3135 -0.4869
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-0.6681 -0.5347 0.5174 0.0459 -0.2452 -0.2105 0.1738
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0.8507 -0.5208 0.0705 0.0681 0.5071 -0.3003 0.0120
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0.0042 -0.4931 0.8700 0.0802 -0.0090 -0.4019 0.6066
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0.5897 -0.4792 -0.6501 0.0495 0.2371 -0.1353 -0.3200
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0.3213 -0.3819 0.8666 0.0729 0.2104 -0.1942 0.5737
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0.3506 -0.3681 -0.8612 0.0760 0.2557 -0.1185 -0.6351
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-0.8451 -0.3542 0.4005 0.0562 -0.4415 -0.1167 0.1249
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0.8986 -0.3403 0.2770 0.0696 0.6036 -0.0990 0.0891
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-0.4779 -0.3264 -0.8155 0.0860 -0.3833 -0.1486 -0.6720
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-0.1994 -0.3125 0.9287 0.0840 -0.1934 -0.1728 0.7077
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0.7781 -0.2986 -0.5527 0.0560 0.3673 -0.0685 -0.2996
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0.6239 -0.2708 0.7330 0.0815 0.4463 -0.0547 0.6141
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0.0352 -0.2569 -0.9658 0.0759 0.0599 -0.1238 -0.6500
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0.1353 -0.2014 0.9701 0.0765 0.1112 -0.1014 0.6476
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0.5571 -0.1875 -0.8090 0.0984 0.4625 -0.0445 -0.8200
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-0.9597 -0.1736 0.2208 0.0989 -0.9338 -0.0529 0.0534
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0.8589 -0.1597 0.4866 0.0755 0.5826 -0.0230 0.3222
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-0.3053 -0.1458 -0.9410 0.0919 -0.3473 -0.0719 -0.7675
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-0.4114 -0.1319 0.9019 0.1112 -0.4501 -0.0369 0.9640
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0.9141 -0.1181 -0.3878 0.0764 0.6712 -0.0233 -0.1542
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-0.9375 -0.1042 -0.3320 0.0928 -0.8353 -0.0271 -0.1616
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0.4676 -0.0903 0.8793 0.1072 0.5277 -0.0156 0.8780
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0.2494 -0.0764 -0.9654 0.1049 0.3463 -0.0261 -0.9298
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-0.8368 -0.0625 0.5439 0.0688 -0.4923 -0.0080 0.3395
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0.9852 -0.0486 0.1644 0.1204 1.1599 -0.0062 0.0593
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-0.6158 -0.0347 -0.7872 0.1119 -0.6225 -0.0194 -0.8796
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-0.0777 -0.0208 0.9968 0.0878 -0.1515 -0.0097 0.7795
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0.7307 -0.0069 -0.6826 0.0839 0.4759 -0.0069 -0.6182
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-0.9999 0.0069 0.0098 0.1334 -1.3032 -0.0033 -0.0038
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0.7438 0.0208 0.6681 0.0969 0.6037 0.0117 0.6815
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-0.0971 0.0347 -0.9947 0.0801 -0.0789 0.0132 -0.6974
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-0.6000 0.0486 0.7986 0.1064 -0.5190 0.0159 0.8823
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0.9810 0.0625 -0.1834 0.1148 1.1071 0.0194 -0.0435
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-0.8465 0.0764 -0.5269 0.0815 -0.6037 0.0070 -0.4061
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0.2679 0.0903 0.9592 0.0902 0.3121 0.0463 0.7616
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0.4498 0.1042 -0.8871 0.1138 0.4818 0.0246 -0.9828
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-0.9294 0.1181 0.3497 0.0819 -0.7406 0.0234 0.1252
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0.9199 0.1319 0.3693 0.0863 0.7530 0.0328 0.1930
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-0.4280 0.1458 -0.8919 0.0997 -0.4637 0.0380 -0.8199
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-0.2862 0.1597 0.9448 0.1022 -0.3538 0.0520 0.8991
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0.8472 0.1736 -0.5021 0.0636 0.4789 0.0331 -0.2587
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-0.9614 0.1875 -0.2015 0.1009 -0.9530 0.0411 -0.0696
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0.5711 0.2014 0.7958 0.1005 0.5277 0.0704 0.7914
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0.1160 0.2153 -0.9696 0.0846 0.1622 0.1122 -0.7318
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-0.7381 0.2292 0.6345 0.0674 -0.3976 0.0483 0.4560
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0.9695 0.2431 0.0306 0.1091 1.0313 0.0943 0.0125
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-0.6916 0.2569 -0.6750 0.0775 -0.4582 0.0447 -0.5508
94+
0.0538 0.2708 0.9611 0.0738 0.0365 0.1438 0.6208
95+
0.6070 0.2847 -0.7420 0.0753 0.3607 0.0633 -0.5924
96+
-0.9446 0.2986 0.1365 0.0886 -0.8234 0.0918 0.0278
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0.7850 0.3125 0.5349 0.0648 0.4352 0.0854 0.3348
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-0.2164 0.3264 -0.9201 0.0743 -0.1583 0.1829 -0.6011
99+
-0.4595 0.3403 0.8204 0.0786 -0.3235 0.0900 0.6501
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0.8881 0.3542 -0.2929 0.0677 0.5746 0.1402 -0.0693
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-0.8478 0.3681 -0.3817 0.0580 -0.4574 0.1006 -0.1464
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0.3651 0.3819 0.8490 0.0804 0.2822 0.2197 0.6250
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0.3024 0.3958 -0.8671 0.0789 0.2031 0.2075 -0.6423
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-0.8033 0.4097 0.4322 0.0495 -0.3551 0.1289 0.1501
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0.8781 0.4236 0.2223 0.0725 0.5884 0.2186 0.0588
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-0.4937 0.4375 -0.7516 0.0633 -0.2530 0.1587 -0.4662
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-0.1426 0.4514 0.8809 0.0681 -0.0717 0.2350 0.5419
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0.6945 0.4653 -0.5488 0.0461 0.2589 0.1507 -0.2159
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-0.8754 0.4792 -0.0639 0.0697 -0.5551 0.2453 -0.0118
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0.5970 0.4931 0.6328 0.0604 0.2722 0.2174 0.3732
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-0.0126 0.5069 -0.8619 0.0810 0.0039 0.4192 -0.6073
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-0.5674 0.5208 0.6378 0.0469 -0.2141 0.1593 0.2842
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0.8406 0.5347 -0.0862 0.0790 0.5782 0.4009 -0.0111
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-0.6709 0.5486 -0.4989 0.0463 -0.2451 0.2111 -0.1776
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0.1559 0.5625 0.8120 0.0792 0.1234 0.4393 0.5672
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0.4285 0.5764 -0.6958 0.0575 0.1412 0.2758 -0.3817
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-0.7764 0.5903 0.2209 0.0629 -0.4007 0.3767 0.0448
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0.7125 0.6042 0.3569 0.0633 0.3679 0.3881 0.1100
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-0.2805 0.6181 -0.7344 0.0719 -0.0885 0.4262 -0.4856
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-0.2852 0.6319 0.7206 0.0542 -0.0712 0.2900 0.3556
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0.6867 0.6458 -0.3337 0.0645 0.3730 0.4379 -0.0699
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-0.7203 0.6597 -0.2144 0.0700 -0.3936 0.4951 -0.0407
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0.3799 0.6736 0.6340 0.0737 0.1832 0.4703 0.4347
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0.1455 0.6875 -0.7115 0.0846 0.0359 0.5543 -0.5686
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-0.5770 0.7014 0.4184 0.0570 -0.2682 0.4143 0.1059
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0.6943 0.7153 0.0797 0.0991 0.5778 0.7411 0.0206
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-0.4486 0.7292 -0.5168 0.0613 -0.1748 0.4416 -0.2331
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-0.0179 0.7431 0.6690 0.0767 0.0624 0.5262 0.4806
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0.4541 0.7569 -0.4699 0.0621 0.2129 0.4569 -0.1902
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-0.6359 0.7708 0.0387 0.1003 -0.5036 0.8177 0.0083
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0.4817 0.7847 0.3901 0.0786 0.3186 0.5996 0.1930
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-0.0890 0.7986 -0.5952 0.0873 -0.0405 0.6328 -0.5118
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-0.3259 0.8125 0.4833 0.0611 -0.1514 0.4767 0.1817
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0.5475 0.8264 -0.1316 0.1055 0.5452 0.8520 -0.0269
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-0.4743 0.8403 -0.2626 0.0935 -0.3803 0.7865 -0.0861
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0.1653 0.8542 0.4930 0.0792 0.1337 0.5971 0.3749
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0.2016 0.8681 -0.4537 0.0747 0.0984 0.5752 -0.3082
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-0.4321 0.8819 0.1883 0.1041 -0.4301 0.8971 0.0453
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0.4203 0.8958 0.1443 0.1034 0.4654 0.8550 0.0651
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-0.1985 0.9097 -0.3647 0.0842 -0.1712 0.6956 -0.2302
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-0.0923 0.9236 0.3721 0.0732 -0.0647 0.6046 0.1992
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0.2899 0.9375 -0.1925 0.0873 0.2960 0.7325 -0.0801
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-0.3043 0.9514 -0.0477 0.1128 -0.4028 0.9962 -0.0238
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0.1630 0.9653 0.2042 0.0810 0.1649 0.6853 0.1115
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0.0138 0.9792 -0.2026 0.0803 -0.0267 0.6914 -0.1150
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-0.0852 0.9931 0.0811 0.0889 -0.1513 0.7880 0.0297

‎regtest/gridtools/rt-vary-nkernels/plumed.dat‎

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cmap: CONTACT_MATRIX GROUP=1-800 COMPONENTS SWITCH={RATIONAL D_0=0.4 R_0=0.15 NN=6 MM=10 D_MAX=0.75}
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dmap: CUSTOM ARG=cmap.x,cmap.y,cmap.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
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ux: CUSTOM ARG=cmap.x,dmap FUNC=x/y PERIODIC=NO
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uy: CUSTOM ARG=cmap.y,dmap FUNC=x/y PERIODIC=NO
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uz: CUSTOM ARG=cmap.z,dmap FUNC=x/y PERIODIC=NO
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skde: SPHERICAL_KDE ARG=ux,uy,uz CONCENTRATION=10 HEIGHTS=cmap.w GRID_BIN=144
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nbonds: SUM ARG=cmap.w PERIODIC=NO
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nskde: CUSTOM ARG=skde,nbonds FUNC=x/y PERIODIC=NO
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oneb: ONES SIZE=1
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nframes: ACCUMULATE ARG=oneb STRIDE=1
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akde: ACCUMULATE ARG=nskde STRIDE=1
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avkde: CUSTOM ARG=akde,nframes FUNC=x/y PERIODIC=NO
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DUMPGRID ARG=avkde FILE=grid.grid STRIDE=5 FMT=%8.4f
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