QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters2' [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [I] RUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 18:53:15 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 2 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 16 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=3456 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.037037037037037 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.12962962962963 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.7037037037e-02 -0.0000000000e+00 -1.2962962963e-01 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=4.649934e+01 pxpb=0.000000e+00 pypb=7.159042e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 436 need remove atom 438 need remove atom 440 need remove atom 441 need remove atom 541 need remove atom 544 need remove atom 546 need remove atom 548 need remove atom 549 need remove atom 559 need remove atom 649 need remove atom 652 need remove atom 654 need remove atom 656 need remove atom 657 need remove atom 667 need remove atom 757 need remove atom 760 need remove atom 762 need remove atom 764 need remove atom 765 need remove atom 775 need remove atom 865 need remove atom 868 need remove atom 870 need remove atom 872 need remove atom 873 need remove atom 883 need remove atom 973 need remove atom 976 need remove atom 978 need remove atom 980 need remove atom 981 need remove atom 991 need remove atom 1081 need remove atom 1084 need remove atom 1086 need remove atom 1088 need remove atom 1089 need remove atom 1099 need remove atom 1189 need remove atom 1192 need remove atom 1194 need remove atom 1196 need remove atom 1197 need remove atom 1207 need remove atom 1297 need remove atom 1315 need remove atom 2364 need remove atom 2367 need remove atom 2472 need remove atom 2475 need remove atom 2580 need remove atom 2583 need remove atom 2688 need remove atom 2691 need remove atom 2796 need remove atom 2799 need remove atom 2904 need remove atom 2907 need remove atom 3012 need remove atom 3015 need remove atom 3120 need remove atom 3123 [I] need removenum=64 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.5122253199e-01 1.0912600846e-01 -3.3453083836e-01 dub= -3.6844519215e-01 1.0912866165e-01 3.4111007297e-01 duc= 3.5122350700e-01 -1.1058437348e-01 -3.3453190610e-01 [I] overall tilt ux= -7.1966772414e-01 2.6531902521e-06 6.7564091133e-01 uy= 9.7500543794e-07 -2.1971038194e-01 -1.0677439892e-06 [I] storedr[0]= -1.4507987583e-02 -4.1659287100e-04 -4.4120699675e-03 [I] originally 3456 atoms [I] insert 0 atoms [I] now 3456 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3456 atoms [I] remove 64 atoms [I] now 3392 atoms [I] NP=3392 n=3392 [I] ASSIGN finalcnfile = dipole_1.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 18:53:16 2023 CPU time spent: 0.293212 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 18:57:23 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 23 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=7452 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.024691358024691 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.12962962962963 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.4691358025e-02 -0.0000000000e+00 -1.2962962963e-01 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=6.974901e+01 pxpb=0.000000e+00 pypb=1.029112e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3174 need remove atom 3177 need remove atom 3179 need remove atom 3187 need remove atom 3189 need remove atom 3192 need remove atom 3194 need remove atom 3205 need remove atom 3282 need remove atom 3285 need remove atom 3287 need remove atom 3295 need remove atom 3297 need remove atom 3300 need remove atom 3302 need remove atom 3313 need remove atom 3390 need remove atom 3393 need remove atom 3395 need remove atom 3403 need remove atom 3405 need remove atom 3408 need remove atom 3410 need remove atom 3421 need remove atom 3498 need remove atom 3501 need remove atom 3503 need remove atom 3511 need remove atom 3513 need remove atom 3516 need remove atom 3518 need remove atom 3529 need remove atom 3606 need remove atom 3609 need remove atom 3611 need remove atom 3619 need remove atom 3621 need remove atom 3624 need remove atom 3626 need remove atom 3637 need remove atom 3714 need remove atom 3717 need remove atom 3719 need remove atom 3727 need remove atom 3729 need remove atom 3732 need remove atom 3734 need remove atom 3745 need remove atom 3822 need remove atom 3825 need remove atom 3827 need remove atom 3835 need remove atom 3837 need remove atom 3840 need remove atom 3842 need remove atom 3853 need remove atom 3930 need remove atom 3933 need remove atom 3935 need remove atom 3943 need remove atom 3945 need remove atom 3948 need remove atom 3950 need remove atom 3961 need remove atom 4038 need remove atom 4041 need remove atom 4043 need remove atom 4051 need remove atom 4053 need remove atom 4056 need remove atom 4058 need remove atom 4069 need remove atom 4146 need remove atom 4149 need remove atom 4151 need remove atom 4159 need remove atom 4161 need remove atom 4164 need remove atom 4166 need remove atom 4177 need remove atom 4254 need remove atom 4257 need remove atom 4259 need remove atom 4267 need remove atom 4269 need remove atom 4272 need remove atom 4274 need remove atom 4285 need remove atom 4375 need remove atom 4377 need remove atom 4380 need remove atom 4382 [I] need removenum=92 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4747892631e-01 1.1039928634e-01 -3.2833040682e-01 dub= -3.6430706710e-01 1.1040149044e-01 3.3399054097e-01 duc= 3.4747993485e-01 -1.1176492405e-01 -3.2833146445e-01 [I] overall tilt ux= -7.1178599342e-01 2.2041030051e-06 6.6232094779e-01 uy= 1.0085307218e-06 -2.2216421039e-01 -1.0576304339e-06 [I] storedr[0]= -3.9217039009e-02 -5.8374348681e-04 -5.6186315896e-02 [I] originally 7452 atoms [I] insert 0 atoms [I] now 7452 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7452 atoms [I] remove 92 atoms [I] now 7360 atoms [I] NP=7360 n=7360 [I] ASSIGN finalcnfile = dipole_1.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 18:57:24 2023 CPU time spent: 0.625613 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 19:00:45 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 23 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=14904 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.024691358024691 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.064814814814815 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.4691358025e-02 -0.0000000000e+00 -6.4814814815e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=6.974901e+01 pxpb=0.000000e+00 pypb=1.029112e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 6306 need remove atom 6309 need remove atom 6311 need remove atom 6319 need remove atom 6321 need remove atom 6324 need remove atom 6326 need remove atom 6337 need remove atom 6414 need remove atom 6417 need remove atom 6419 need remove atom 6427 need remove atom 6429 need remove atom 6432 need remove atom 6434 need remove atom 6445 need remove atom 6522 need remove atom 6525 need remove atom 6527 need remove atom 6535 need remove atom 6537 need remove atom 6540 need remove atom 6542 need remove atom 6553 need remove atom 6630 need remove atom 6633 need remove atom 6635 need remove atom 6643 need remove atom 6645 need remove atom 6648 need remove atom 6650 need remove atom 6661 need remove atom 6738 need remove atom 6741 need remove atom 6743 need remove atom 6751 need remove atom 6753 need remove atom 6756 need remove atom 6758 need remove atom 6769 need remove atom 6846 need remove atom 6849 need remove atom 6851 need remove atom 6859 need remove atom 6861 need remove atom 6864 need remove atom 6866 need remove atom 6877 need remove atom 6954 need remove atom 6957 need remove atom 6959 need remove atom 6967 need remove atom 6969 need remove atom 6972 need remove atom 6974 need remove atom 6985 need remove atom 7062 need remove atom 7065 need remove atom 7067 need remove atom 7075 need remove atom 7077 need remove atom 7080 need remove atom 7082 need remove atom 7093 need remove atom 7170 need remove atom 7173 need remove atom 7175 need remove atom 7183 need remove atom 7185 need remove atom 7188 need remove atom 7190 need remove atom 7201 need remove atom 7278 need remove atom 7281 need remove atom 7283 need remove atom 7291 need remove atom 7293 need remove atom 7296 need remove atom 7298 need remove atom 7309 need remove atom 7386 need remove atom 7389 need remove atom 7391 need remove atom 7399 need remove atom 7401 need remove atom 7404 need remove atom 7406 need remove atom 7417 need remove atom 7494 need remove atom 7497 need remove atom 7499 need remove atom 7507 need remove atom 7509 need remove atom 7512 need remove atom 7514 need remove atom 7525 need remove atom 7602 need remove atom 7605 need remove atom 7607 need remove atom 7615 need remove atom 7617 need remove atom 7620 need remove atom 7622 need remove atom 7633 need remove atom 7710 need remove atom 7713 need remove atom 7715 need remove atom 7723 need remove atom 7725 need remove atom 7728 need remove atom 7730 need remove atom 7741 need remove atom 7818 need remove atom 7821 need remove atom 7823 need remove atom 7831 need remove atom 7833 need remove atom 7836 need remove atom 7838 need remove atom 7849 need remove atom 7926 need remove atom 7929 need remove atom 7931 need remove atom 7939 need remove atom 7941 need remove atom 7944 need remove atom 7946 need remove atom 7957 need remove atom 8034 need remove atom 8037 need remove atom 8039 need remove atom 8047 need remove atom 8049 need remove atom 8052 need remove atom 8054 need remove atom 8065 need remove atom 8142 need remove atom 8145 need remove atom 8147 need remove atom 8155 need remove atom 8157 need remove atom 8160 need remove atom 8162 need remove atom 8173 need remove atom 8250 need remove atom 8253 need remove atom 8255 need remove atom 8263 need remove atom 8265 need remove atom 8268 need remove atom 8270 need remove atom 8281 need remove atom 8358 need remove atom 8361 need remove atom 8363 need remove atom 8371 need remove atom 8373 need remove atom 8376 need remove atom 8378 need remove atom 8389 need remove atom 8466 need remove atom 8469 need remove atom 8471 need remove atom 8479 need remove atom 8481 need remove atom 8484 need remove atom 8486 need remove atom 8497 need remove atom 8574 need remove atom 8577 need remove atom 8579 need remove atom 8587 need remove atom 8589 need remove atom 8592 need remove atom 8594 need remove atom 8605 need remove atom 8695 need remove atom 8697 need remove atom 8700 need remove atom 8702 need remove atom 8803 need remove atom 8805 need remove atom 8808 need remove atom 8810 [I] need removenum=184 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4747892631e-01 1.1039928634e-01 -3.2833040682e-01 dub= -3.6430706710e-01 1.1040149044e-01 3.3399054097e-01 duc= 3.4747993485e-01 -1.1176492405e-01 -3.2833146445e-01 [I] overall tilt ux= -7.1178599342e-01 2.2041030051e-06 6.6232094779e-01 uy= 1.0085307218e-06 -2.2216421039e-01 -1.0576304339e-06 [I] storedr[0]= -3.9217039009e-02 -5.8374348681e-04 -5.6186315896e-02 [I] originally 14904 atoms [I] insert 0 atoms [I] now 14904 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 14904 atoms [I] remove 184 atoms [I] now 14720 atoms [I] NP=14720 n=14720 [I] ASSIGN finalcnfile = dipole_1.8.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.8.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.8.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 19:00:47 2023 CPU time spent: 1.241916 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 19:09:14 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 4 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 31 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=26784 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.018518518518519 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.064814814814815 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.8518518519e-02 -0.0000000000e+00 -6.4814814815e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=9.299868e+01 pxpb=0.000000e+00 pypb=1.387064e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 8424 need remove atom 8425 need remove atom 8428 need remove atom 8430 need remove atom 8432 need remove atom 8433 need remove atom 8441 need remove atom 8443 need remove atom 8532 need remove atom 8533 need remove atom 8536 need remove atom 8538 need remove atom 8540 need remove atom 8541 need remove atom 8549 need remove atom 8551 need remove atom 8640 need remove atom 8641 need remove atom 8644 need remove atom 8646 need remove atom 8648 need remove atom 8649 need remove atom 8657 need remove atom 8659 need remove atom 8748 need remove atom 8749 need remove atom 8752 need remove atom 8754 need remove atom 8756 need remove atom 8757 need remove atom 8765 need remove atom 8767 need remove atom 8856 need remove atom 8857 need remove atom 8860 need remove atom 8862 need remove atom 8864 need remove atom 8865 need remove atom 8873 need remove atom 8875 need remove atom 8964 need remove atom 8965 need remove atom 8968 need remove atom 8970 need remove atom 8972 need remove atom 8973 need remove atom 8981 need remove atom 8983 need remove atom 9072 need remove atom 9073 need remove atom 9076 need remove atom 9078 need remove atom 9080 need remove atom 9081 need remove atom 9089 need remove atom 9091 need remove atom 9180 need remove atom 9181 need remove atom 9184 need remove atom 9186 need remove atom 9188 need remove atom 9189 need remove atom 9197 need remove atom 9199 need remove atom 9288 need remove atom 9289 need remove atom 9292 need remove atom 9294 need remove atom 9296 need remove atom 9297 need remove atom 9305 need remove atom 9307 need remove atom 9396 need remove atom 9397 need remove atom 9400 need remove atom 9402 need remove atom 9404 need remove atom 9405 need remove atom 9413 need remove atom 9415 need remove atom 9504 need remove atom 9505 need remove atom 9508 need remove atom 9510 need remove atom 9512 need remove atom 9513 need remove atom 9521 need remove atom 9523 need remove atom 9612 need remove atom 9613 need remove atom 9616 need remove atom 9618 need remove atom 9620 need remove atom 9621 need remove atom 9629 need remove atom 9631 need remove atom 9720 need remove atom 9721 need remove atom 9724 need remove atom 9726 need remove atom 9728 need remove atom 9729 need remove atom 9737 need remove atom 9739 need remove atom 9828 need remove atom 9829 need remove atom 9832 need remove atom 9834 need remove atom 9836 need remove atom 9837 need remove atom 9845 need remove atom 9847 need remove atom 9936 need remove atom 9937 need remove atom 9940 need remove atom 9942 need remove atom 9944 need remove atom 9945 need remove atom 9953 need remove atom 9955 need remove atom 10044 need remove atom 10045 need remove atom 10048 need remove atom 10050 need remove atom 10052 need remove atom 10053 need remove atom 10061 need remove atom 10063 need remove atom 10152 need remove atom 10153 need remove atom 10156 need remove atom 10158 need remove atom 10160 need remove atom 10161 need remove atom 10169 need remove atom 10171 need remove atom 10260 need remove atom 10261 need remove atom 10264 need remove atom 10266 need remove atom 10268 need remove atom 10269 need remove atom 10277 need remove atom 10279 need remove atom 10368 need remove atom 10369 need remove atom 10372 need remove atom 10374 need remove atom 10376 need remove atom 10377 need remove atom 10385 need remove atom 10387 need remove atom 10476 need remove atom 10477 need remove atom 10480 need remove atom 10482 need remove atom 10484 need remove atom 10485 need remove atom 10493 need remove atom 10495 need remove atom 10584 need remove atom 10585 need remove atom 10588 need remove atom 10590 need remove atom 10592 need remove atom 10593 need remove atom 10601 need remove atom 10603 need remove atom 10692 need remove atom 10693 need remove atom 10696 need remove atom 10698 need remove atom 10700 need remove atom 10701 need remove atom 10709 need remove atom 10711 need remove atom 10800 need remove atom 10801 need remove atom 10804 need remove atom 10806 need remove atom 10808 need remove atom 10809 need remove atom 10817 need remove atom 10819 need remove atom 10908 need remove atom 10909 need remove atom 10912 need remove atom 10914 need remove atom 10916 need remove atom 10917 need remove atom 10925 need remove atom 10927 need remove atom 11016 need remove atom 11017 need remove atom 11020 need remove atom 11022 need remove atom 11024 need remove atom 11025 need remove atom 11033 need remove atom 11035 need remove atom 11124 need remove atom 11125 need remove atom 11128 need remove atom 11130 need remove atom 11132 need remove atom 11133 need remove atom 11141 need remove atom 11143 need remove atom 11232 need remove atom 11233 need remove atom 11236 need remove atom 11238 need remove atom 11240 need remove atom 11241 need remove atom 11249 need remove atom 11251 need remove atom 11340 need remove atom 11341 need remove atom 11344 need remove atom 11346 need remove atom 11348 need remove atom 11349 need remove atom 11357 need remove atom 11359 need remove atom 11448 need remove atom 11449 need remove atom 11452 need remove atom 11454 need remove atom 11456 need remove atom 11457 need remove atom 11465 need remove atom 11467 need remove atom 11556 need remove atom 11557 need remove atom 11560 need remove atom 11562 need remove atom 11564 need remove atom 11565 need remove atom 11573 need remove atom 11575 need remove atom 11664 need remove atom 11665 need remove atom 11681 need remove atom 11683 need remove atom 11772 need remove atom 11773 need remove atom 11789 need remove atom 11791 [I] need removenum=248 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4844542040e-01 1.1007629836e-01 -3.2991451039e-01 dub= -3.6538050937e-01 1.1007862195e-01 3.3581059357e-01 duc= 3.4844642064e-01 -1.1146553898e-01 -3.2991557089e-01 [I] overall tilt ux= -7.1382592977e-01 2.3235950791e-06 6.6572510397e-01 uy= 1.0002423446e-06 -2.2154183734e-01 -1.0605001303e-06 [I] storedr[0]= -3.6783898504e-02 -6.6925514165e-04 -5.7546015659e-02 [I] originally 26784 atoms [I] insert 0 atoms [I] now 26784 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 26784 atoms [I] remove 248 atoms [I] now 26536 atoms [I] NP=26536 n=26536 [I] ASSIGN finalcnfile = dipole_2.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 19:09:17 2023 CPU time spent: 2.266367 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 19:16:31 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 5 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 39 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=42120 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.014814814814815 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.064814814814815 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.4814814815e-02 -0.0000000000e+00 -6.4814814815e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=1.162484e+02 pxpb=0.000000e+00 pypb=1.745016e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 19051 need remove atom 19053 need remove atom 19063 need remove atom 19065 need remove atom 19068 need remove atom 19070 need remove atom 19079 need remove atom 19081 need remove atom 19159 need remove atom 19161 need remove atom 19171 need remove atom 19173 need remove atom 19176 need remove atom 19178 need remove atom 19187 need remove atom 19189 need remove atom 19267 need remove atom 19269 need remove atom 19279 need remove atom 19281 need remove atom 19284 need remove atom 19286 need remove atom 19295 need remove atom 19297 need remove atom 19375 need remove atom 19377 need remove atom 19387 need remove atom 19389 need remove atom 19392 need remove atom 19394 need remove atom 19403 need remove atom 19405 need remove atom 19483 need remove atom 19485 need remove atom 19495 need remove atom 19497 need remove atom 19500 need remove atom 19502 need remove atom 19511 need remove atom 19513 need remove atom 19591 need remove atom 19593 need remove atom 19603 need remove atom 19605 need remove atom 19608 need remove atom 19610 need remove atom 19619 need remove atom 19621 need remove atom 19699 need remove atom 19701 need remove atom 19711 need remove atom 19713 need remove atom 19716 need remove atom 19718 need remove atom 19727 need remove atom 19729 need remove atom 19807 need remove atom 19809 need remove atom 19819 need remove atom 19821 need remove atom 19824 need remove atom 19826 need remove atom 19835 need remove atom 19837 need remove atom 19915 need remove atom 19917 need remove atom 19927 need remove atom 19929 need remove atom 19932 need remove atom 19934 need remove atom 19943 need remove atom 19945 need remove atom 20023 need remove atom 20025 need remove atom 20035 need remove atom 20037 need remove atom 20040 need remove atom 20042 need remove atom 20051 need remove atom 20053 need remove atom 20131 need remove atom 20133 need remove atom 20143 need remove atom 20145 need remove atom 20148 need remove atom 20150 need remove atom 20159 need remove atom 20161 need remove atom 20239 need remove atom 20241 need remove atom 20251 need remove atom 20253 need remove atom 20256 need remove atom 20258 need remove atom 20267 need remove atom 20269 need remove atom 20347 need remove atom 20349 need remove atom 20359 need remove atom 20361 need remove atom 20364 need remove atom 20366 need remove atom 20375 need remove atom 20377 need remove atom 20455 need remove atom 20457 need remove atom 20467 need remove atom 20469 need remove atom 20472 need remove atom 20474 need remove atom 20483 need remove atom 20485 need remove atom 20563 need remove atom 20565 need remove atom 20575 need remove atom 20577 need remove atom 20580 need remove atom 20582 need remove atom 20591 need remove atom 20593 need remove atom 20671 need remove atom 20673 need remove atom 20683 need remove atom 20685 need remove atom 20688 need remove atom 20690 need remove atom 20699 need remove atom 20701 need remove atom 20779 need remove atom 20781 need remove atom 20791 need remove atom 20793 need remove atom 20796 need remove atom 20798 need remove atom 20807 need remove atom 20809 need remove atom 20887 need remove atom 20889 need remove atom 20899 need remove atom 20901 need remove atom 20904 need remove atom 20906 need remove atom 20915 need remove atom 20917 need remove atom 20995 need remove atom 20997 need remove atom 21007 need remove atom 21009 need remove atom 21012 need remove atom 21014 need remove atom 21023 need remove atom 21025 need remove atom 21103 need remove atom 21105 need remove atom 21115 need remove atom 21117 need remove atom 21120 need remove atom 21122 need remove atom 21131 need remove atom 21133 need remove atom 21211 need remove atom 21213 need remove atom 21223 need remove atom 21225 need remove atom 21228 need remove atom 21230 need remove atom 21239 need remove atom 21241 need remove atom 21319 need remove atom 21321 need remove atom 21331 need remove atom 21333 need remove atom 21336 need remove atom 21338 need remove atom 21347 need remove atom 21349 need remove atom 21427 need remove atom 21429 need remove atom 21439 need remove atom 21441 need remove atom 21444 need remove atom 21446 need remove atom 21455 need remove atom 21457 need remove atom 21535 need remove atom 21537 need remove atom 21547 need remove atom 21549 need remove atom 21552 need remove atom 21554 need remove atom 21563 need remove atom 21565 need remove atom 21643 need remove atom 21645 need remove atom 21655 need remove atom 21657 need remove atom 21660 need remove atom 21662 need remove atom 21671 need remove atom 21673 need remove atom 21751 need remove atom 21753 need remove atom 21763 need remove atom 21765 need remove atom 21768 need remove atom 21770 need remove atom 21779 need remove atom 21781 need remove atom 21859 need remove atom 21861 need remove atom 21871 need remove atom 21873 need remove atom 21876 need remove atom 21878 need remove atom 21887 need remove atom 21889 need remove atom 21967 need remove atom 21969 need remove atom 21979 need remove atom 21981 need remove atom 21984 need remove atom 21986 need remove atom 21995 need remove atom 21997 need remove atom 22075 need remove atom 22077 need remove atom 22087 need remove atom 22089 need remove atom 22092 need remove atom 22094 need remove atom 22103 need remove atom 22105 need remove atom 22183 need remove atom 22185 need remove atom 22195 need remove atom 22197 need remove atom 22200 need remove atom 22202 need remove atom 22211 need remove atom 22213 need remove atom 22291 need remove atom 22293 need remove atom 22303 need remove atom 22305 need remove atom 22308 need remove atom 22310 need remove atom 22319 need remove atom 22321 need remove atom 22399 need remove atom 22401 need remove atom 22411 need remove atom 22413 need remove atom 22416 need remove atom 22418 need remove atom 22427 need remove atom 22429 need remove atom 22507 need remove atom 22509 need remove atom 22519 need remove atom 22521 need remove atom 22524 need remove atom 22526 need remove atom 22535 need remove atom 22537 need remove atom 22615 need remove atom 22617 need remove atom 22627 need remove atom 22629 need remove atom 22632 need remove atom 22634 need remove atom 22643 need remove atom 22645 need remove atom 22723 need remove atom 22725 need remove atom 22735 need remove atom 22737 need remove atom 22740 need remove atom 22742 need remove atom 22751 need remove atom 22753 need remove atom 22831 need remove atom 22833 need remove atom 22843 need remove atom 22845 need remove atom 22848 need remove atom 22850 need remove atom 22859 need remove atom 22861 need remove atom 22939 need remove atom 22941 need remove atom 22951 need remove atom 22953 need remove atom 22956 need remove atom 22958 need remove atom 22967 need remove atom 22969 need remove atom 23047 need remove atom 23049 need remove atom 23059 need remove atom 23061 need remove atom 23064 need remove atom 23066 need remove atom 23075 need remove atom 23077 need remove atom 23167 need remove atom 23169 need remove atom 23172 need remove atom 23174 need remove atom 23275 need remove atom 23277 need remove atom 23280 need remove atom 23282 [I] need removenum=312 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4901530139e-01 1.0988396925e-01 -3.3085392325e-01 dub= -3.6601182016e-01 1.0988636219e-01 3.3688958271e-01 duc= 3.4901629663e-01 -1.1128723612e-01 -3.3085498536e-01 [I] overall tilt ux= -7.1502712155e-01 2.3929357866e-06 6.6774350596e-01 uy= 9.9523526065e-07 -2.2117120538e-01 -1.0621099676e-06 [I] storedr[0]= -3.2546725583e-02 -6.9803391721e-04 -5.1414047718e-02 [I] originally 42120 atoms [I] insert 0 atoms [I] now 42120 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 42120 atoms [I] remove 312 atoms [I] now 41808 atoms [I] NP=41808 n=41808 [I] ASSIGN finalcnfile = dipole_3.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 19:16:35 2023 CPU time spent: 3.542706 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 19:32:07 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 5 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 39 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=63180 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.014814814814815 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.04320987654321 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.4814814815e-02 -0.0000000000e+00 -4.3209876543e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=1.162484e+02 pxpb=0.000000e+00 pypb=1.745016e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 28555 need remove atom 28557 need remove atom 28567 need remove atom 28569 need remove atom 28572 need remove atom 28574 need remove atom 28583 need remove atom 28585 need remove atom 28663 need remove atom 28665 need remove atom 28675 need remove atom 28677 need remove atom 28680 need remove atom 28682 need remove atom 28691 need remove atom 28693 need remove atom 28771 need remove atom 28773 need remove atom 28783 need remove atom 28785 need remove atom 28788 need remove atom 28790 need remove atom 28799 need remove atom 28801 need remove atom 28879 need remove atom 28881 need remove atom 28891 need remove atom 28893 need remove atom 28896 need remove atom 28898 need remove atom 28907 need remove atom 28909 need remove atom 28987 need remove atom 28989 need remove atom 28999 need remove atom 29001 need remove atom 29004 need remove atom 29006 need remove atom 29015 need remove atom 29017 need remove atom 29095 need remove atom 29097 need remove atom 29107 need remove atom 29109 need remove atom 29112 need remove atom 29114 need remove atom 29123 need remove atom 29125 need remove atom 29203 need remove atom 29205 need remove atom 29215 need remove atom 29217 need remove atom 29220 need remove atom 29222 need remove atom 29231 need remove atom 29233 need remove atom 29311 need remove atom 29313 need remove atom 29323 need remove atom 29325 need remove atom 29328 need remove atom 29330 need remove atom 29339 need remove atom 29341 need remove atom 29419 need remove atom 29421 need remove atom 29431 need remove atom 29433 need remove atom 29436 need remove atom 29438 need remove atom 29447 need remove atom 29449 need remove atom 29527 need remove atom 29529 need remove atom 29539 need remove atom 29541 need remove atom 29544 need remove atom 29546 need remove atom 29555 need remove atom 29557 need remove atom 29635 need remove atom 29637 need remove atom 29647 need remove atom 29649 need remove atom 29652 need remove atom 29654 need remove atom 29663 need remove atom 29665 need remove atom 29743 need remove atom 29745 need remove atom 29755 need remove atom 29757 need remove atom 29760 need remove atom 29762 need remove atom 29771 need remove atom 29773 need remove atom 29851 need remove atom 29853 need remove atom 29863 need remove atom 29865 need remove atom 29868 need remove atom 29870 need remove atom 29879 need remove atom 29881 need remove atom 29959 need remove atom 29961 need remove atom 29971 need remove atom 29973 need remove atom 29976 need remove atom 29978 need remove atom 29987 need remove atom 29989 need remove atom 30067 need remove atom 30069 need remove atom 30079 need remove atom 30081 need remove atom 30084 need remove atom 30086 need remove atom 30095 need remove atom 30097 need remove atom 30175 need remove atom 30177 need remove atom 30187 need remove atom 30189 need remove atom 30192 need remove atom 30194 need remove atom 30203 need remove atom 30205 need remove atom 30283 need remove atom 30285 need remove atom 30295 need remove atom 30297 need remove atom 30300 need remove atom 30302 need remove atom 30311 need remove atom 30313 need remove atom 30391 need remove atom 30393 need remove atom 30403 need remove atom 30405 need remove atom 30408 need remove atom 30410 need remove atom 30419 need remove atom 30421 need remove atom 30499 need remove atom 30501 need remove atom 30511 need remove atom 30513 need remove atom 30516 need remove atom 30518 need remove atom 30527 need remove atom 30529 need remove atom 30607 need remove atom 30609 need remove atom 30619 need remove atom 30621 need remove atom 30624 need remove atom 30626 need remove atom 30635 need remove atom 30637 need remove atom 30715 need remove atom 30717 need remove atom 30727 need remove atom 30729 need remove atom 30732 need remove atom 30734 need remove atom 30743 need remove atom 30745 need remove atom 30823 need remove atom 30825 need remove atom 30835 need remove atom 30837 need remove atom 30840 need remove atom 30842 need remove atom 30851 need remove atom 30853 need remove atom 30931 need remove atom 30933 need remove atom 30943 need remove atom 30945 need remove atom 30948 need remove atom 30950 need remove atom 30959 need remove atom 30961 need remove atom 31039 need remove atom 31041 need remove atom 31051 need remove atom 31053 need remove atom 31056 need remove atom 31058 need remove atom 31067 need remove atom 31069 need remove atom 31147 need remove atom 31149 need remove atom 31159 need remove atom 31161 need remove atom 31164 need remove atom 31166 need remove atom 31175 need remove atom 31177 need remove atom 31255 need remove atom 31257 need remove atom 31267 need remove atom 31269 need remove atom 31272 need remove atom 31274 need remove atom 31283 need remove atom 31285 need remove atom 31363 need remove atom 31365 need remove atom 31375 need remove atom 31377 need remove atom 31380 need remove atom 31382 need remove atom 31391 need remove atom 31393 need remove atom 31471 need remove atom 31473 need remove atom 31483 need remove atom 31485 need remove atom 31488 need remove atom 31490 need remove atom 31499 need remove atom 31501 need remove atom 31579 need remove atom 31581 need remove atom 31591 need remove atom 31593 need remove atom 31596 need remove atom 31598 need remove atom 31607 need remove atom 31609 need remove atom 31687 need remove atom 31689 need remove atom 31699 need remove atom 31701 need remove atom 31704 need remove atom 31706 need remove atom 31715 need remove atom 31717 need remove atom 31795 need remove atom 31797 need remove atom 31807 need remove atom 31809 need remove atom 31812 need remove atom 31814 need remove atom 31823 need remove atom 31825 need remove atom 31903 need remove atom 31905 need remove atom 31915 need remove atom 31917 need remove atom 31920 need remove atom 31922 need remove atom 31931 need remove atom 31933 need remove atom 32011 need remove atom 32013 need remove atom 32023 need remove atom 32025 need remove atom 32028 need remove atom 32030 need remove atom 32039 need remove atom 32041 need remove atom 32119 need remove atom 32121 need remove atom 32131 need remove atom 32133 need remove atom 32136 need remove atom 32138 need remove atom 32147 need remove atom 32149 need remove atom 32227 need remove atom 32229 need remove atom 32239 need remove atom 32241 need remove atom 32244 need remove atom 32246 need remove atom 32255 need remove atom 32257 need remove atom 32335 need remove atom 32337 need remove atom 32347 need remove atom 32349 need remove atom 32352 need remove atom 32354 need remove atom 32363 need remove atom 32365 need remove atom 32443 need remove atom 32445 need remove atom 32455 need remove atom 32457 need remove atom 32460 need remove atom 32462 need remove atom 32471 need remove atom 32473 need remove atom 32551 need remove atom 32553 need remove atom 32563 need remove atom 32565 need remove atom 32568 need remove atom 32570 need remove atom 32579 need remove atom 32581 need remove atom 32659 need remove atom 32661 need remove atom 32671 need remove atom 32673 need remove atom 32676 need remove atom 32678 need remove atom 32687 need remove atom 32689 need remove atom 32767 need remove atom 32769 need remove atom 32779 need remove atom 32781 need remove atom 32784 need remove atom 32786 need remove atom 32795 need remove atom 32797 need remove atom 32875 need remove atom 32877 need remove atom 32887 need remove atom 32889 need remove atom 32892 need remove atom 32894 need remove atom 32903 need remove atom 32905 need remove atom 32983 need remove atom 32985 need remove atom 32995 need remove atom 32997 need remove atom 33000 need remove atom 33002 need remove atom 33011 need remove atom 33013 need remove atom 33091 need remove atom 33093 need remove atom 33103 need remove atom 33105 need remove atom 33108 need remove atom 33110 need remove atom 33119 need remove atom 33121 need remove atom 33199 need remove atom 33201 need remove atom 33211 need remove atom 33213 need remove atom 33216 need remove atom 33218 need remove atom 33227 need remove atom 33229 need remove atom 33307 need remove atom 33309 need remove atom 33319 need remove atom 33321 need remove atom 33324 need remove atom 33326 need remove atom 33335 need remove atom 33337 need remove atom 33415 need remove atom 33417 need remove atom 33427 need remove atom 33429 need remove atom 33432 need remove atom 33434 need remove atom 33443 need remove atom 33445 need remove atom 33523 need remove atom 33525 need remove atom 33535 need remove atom 33537 need remove atom 33540 need remove atom 33542 need remove atom 33551 need remove atom 33553 need remove atom 33631 need remove atom 33633 need remove atom 33643 need remove atom 33645 need remove atom 33648 need remove atom 33650 need remove atom 33659 need remove atom 33661 need remove atom 33739 need remove atom 33741 need remove atom 33751 need remove atom 33753 need remove atom 33756 need remove atom 33758 need remove atom 33767 need remove atom 33769 need remove atom 33847 need remove atom 33849 need remove atom 33859 need remove atom 33861 need remove atom 33864 need remove atom 33866 need remove atom 33875 need remove atom 33877 need remove atom 33955 need remove atom 33957 need remove atom 33967 need remove atom 33969 need remove atom 33972 need remove atom 33974 need remove atom 33983 need remove atom 33985 need remove atom 34063 need remove atom 34065 need remove atom 34075 need remove atom 34077 need remove atom 34080 need remove atom 34082 need remove atom 34091 need remove atom 34093 need remove atom 34171 need remove atom 34173 need remove atom 34183 need remove atom 34185 need remove atom 34188 need remove atom 34190 need remove atom 34199 need remove atom 34201 need remove atom 34279 need remove atom 34281 need remove atom 34291 need remove atom 34293 need remove atom 34296 need remove atom 34298 need remove atom 34307 need remove atom 34309 need remove atom 34387 need remove atom 34389 need remove atom 34399 need remove atom 34401 need remove atom 34404 need remove atom 34406 need remove atom 34415 need remove atom 34417 need remove atom 34495 need remove atom 34497 need remove atom 34507 need remove atom 34509 need remove atom 34512 need remove atom 34514 need remove atom 34523 need remove atom 34525 need remove atom 34603 need remove atom 34605 need remove atom 34615 need remove atom 34617 need remove atom 34620 need remove atom 34622 need remove atom 34631 need remove atom 34633 need remove atom 34723 need remove atom 34725 need remove atom 34728 need remove atom 34730 need remove atom 34831 need remove atom 34833 need remove atom 34836 need remove atom 34838 need remove atom 34939 need remove atom 34941 need remove atom 34944 need remove atom 34946 [I] need removenum=468 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4901530139e-01 1.0988396925e-01 -3.3085392325e-01 dub= -3.6601182016e-01 1.0988636219e-01 3.3688958271e-01 duc= 3.4901629663e-01 -1.1128723612e-01 -3.3085498536e-01 [I] overall tilt ux= -7.1502712155e-01 2.3929357866e-06 6.6774350596e-01 uy= 9.9523526065e-07 -2.2117120538e-01 -1.0621099676e-06 [I] storedr[0]= -3.2546725583e-02 -6.9803391721e-04 -5.1414047718e-02 [I] originally 63180 atoms [I] insert 0 atoms [I] now 63180 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 63180 atoms [I] remove 468 atoms [I] now 62712 atoms [I] NP=62712 n=62712 [I] ASSIGN finalcnfile = dipole_3.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 19:32:13 2023 CPU time spent: 5.336329 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 19:57:56 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 6 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 47 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=91368 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.012345679012346 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.04320987654321 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.2345679012e-02 -0.0000000000e+00 -4.3209876543e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=1.394980e+02 pxpb=0.000000e+00 pypb=2.102969e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 34344 need remove atom 34345 need remove atom 34346 need remove atom 34348 need remove atom 34351 need remove atom 34352 need remove atom 34361 need remove atom 34363 need remove atom 34452 need remove atom 34453 need remove atom 34454 need remove atom 34456 need remove atom 34459 need remove atom 34460 need remove atom 34469 need remove atom 34471 need remove atom 34560 need remove atom 34561 need remove atom 34562 need remove atom 34564 need remove atom 34567 need remove atom 34568 need remove atom 34577 need remove atom 34579 need remove atom 34668 need remove atom 34669 need remove atom 34670 need remove atom 34672 need remove atom 34675 need remove atom 34676 need remove atom 34685 need remove atom 34687 need remove atom 34776 need remove atom 34777 need remove atom 34778 need remove atom 34780 need remove atom 34783 need remove atom 34784 need remove atom 34793 need remove atom 34795 need remove atom 34884 need remove atom 34885 need remove atom 34886 need remove atom 34888 need remove atom 34891 need remove atom 34892 need remove atom 34901 need remove atom 34903 need remove atom 34992 need remove atom 34993 need remove atom 34994 need remove atom 34996 need remove atom 34999 need remove atom 35000 need remove atom 35009 need remove atom 35011 need remove atom 35100 need remove atom 35101 need remove atom 35102 need remove atom 35104 need remove atom 35107 need remove atom 35108 need remove atom 35117 need remove atom 35119 need remove atom 35208 need remove atom 35209 need remove atom 35210 need remove atom 35212 need remove atom 35215 need remove atom 35216 need remove atom 35225 need remove atom 35227 need remove atom 35316 need remove atom 35317 need remove atom 35318 need remove atom 35320 need remove atom 35323 need remove atom 35324 need remove atom 35333 need remove atom 35335 need remove atom 35424 need remove atom 35425 need remove atom 35426 need remove atom 35428 need remove atom 35431 need remove atom 35432 need remove atom 35441 need remove atom 35443 need remove atom 35532 need remove atom 35533 need remove atom 35534 need remove atom 35536 need remove atom 35539 need remove atom 35540 need remove atom 35549 need remove atom 35551 need remove atom 35640 need remove atom 35641 need remove atom 35642 need remove atom 35644 need remove atom 35647 need remove atom 35648 need remove atom 35657 need remove atom 35659 need remove atom 35748 need remove atom 35749 need remove atom 35750 need remove atom 35752 need remove atom 35755 need remove atom 35756 need remove atom 35765 need remove atom 35767 need remove atom 35856 need remove atom 35857 need remove atom 35858 need remove atom 35860 need remove atom 35863 need remove atom 35864 need remove atom 35873 need remove atom 35875 need remove atom 35964 need remove atom 35965 need remove atom 35966 need remove atom 35968 need remove atom 35971 need remove atom 35972 need remove atom 35981 need remove atom 35983 need remove atom 36072 need remove atom 36073 need remove atom 36074 need remove atom 36076 need remove atom 36079 need remove atom 36080 need remove atom 36089 need remove atom 36091 need remove atom 36180 need remove atom 36181 need remove atom 36182 need remove atom 36184 need remove atom 36187 need remove atom 36188 need remove atom 36197 need remove atom 36199 need remove atom 36288 need remove atom 36289 need remove atom 36290 need remove atom 36292 need remove atom 36295 need remove atom 36296 need remove atom 36305 need remove atom 36307 need remove atom 36396 need remove atom 36397 need remove atom 36398 need remove atom 36400 need remove atom 36403 need remove atom 36404 need remove atom 36413 need remove atom 36415 need remove atom 36504 need remove atom 36505 need remove atom 36506 need remove atom 36508 need remove atom 36511 need remove atom 36512 need remove atom 36521 need remove atom 36523 need remove atom 36612 need remove atom 36613 need remove atom 36614 need remove atom 36616 need remove atom 36619 need remove atom 36620 need remove atom 36629 need remove atom 36631 need remove atom 36720 need remove atom 36721 need remove atom 36722 need remove atom 36724 need remove atom 36727 need remove atom 36728 need remove atom 36737 need remove atom 36739 need remove atom 36828 need remove atom 36829 need remove atom 36830 need remove atom 36832 need remove atom 36835 need remove atom 36836 need remove atom 36845 need remove atom 36847 need remove atom 36936 need remove atom 36937 need remove atom 36938 need remove atom 36940 need remove atom 36943 need remove atom 36944 need remove atom 36953 need remove atom 36955 need remove atom 37044 need remove atom 37045 need remove atom 37046 need remove atom 37048 need remove atom 37051 need remove atom 37052 need remove atom 37061 need remove atom 37063 need remove atom 37152 need remove atom 37153 need remove atom 37154 need remove atom 37156 need remove atom 37159 need remove atom 37160 need remove atom 37169 need remove atom 37171 need remove atom 37260 need remove atom 37261 need remove atom 37262 need remove atom 37264 need remove atom 37267 need remove atom 37268 need remove atom 37277 need remove atom 37279 need remove atom 37368 need remove atom 37369 need remove atom 37370 need remove atom 37372 need remove atom 37375 need remove atom 37376 need remove atom 37385 need remove atom 37387 need remove atom 37476 need remove atom 37477 need remove atom 37478 need remove atom 37480 need remove atom 37483 need remove atom 37484 need remove atom 37493 need remove atom 37495 need remove atom 37584 need remove atom 37585 need remove atom 37586 need remove atom 37588 need remove atom 37591 need remove atom 37592 need remove atom 37601 need remove atom 37603 need remove atom 37692 need remove atom 37693 need remove atom 37694 need remove atom 37696 need remove atom 37699 need remove atom 37700 need remove atom 37709 need remove atom 37711 need remove atom 37800 need remove atom 37801 need remove atom 37802 need remove atom 37804 need remove atom 37807 need remove atom 37808 need remove atom 37817 need remove atom 37819 need remove atom 37908 need remove atom 37909 need remove atom 37910 need remove atom 37912 need remove atom 37915 need remove atom 37916 need remove atom 37925 need remove atom 37927 need remove atom 38016 need remove atom 38017 need remove atom 38018 need remove atom 38020 need remove atom 38023 need remove atom 38024 need remove atom 38033 need remove atom 38035 need remove atom 38124 need remove atom 38125 need remove atom 38126 need remove atom 38128 need remove atom 38131 need remove atom 38132 need remove atom 38141 need remove atom 38143 need remove atom 38232 need remove atom 38233 need remove atom 38234 need remove atom 38236 need remove atom 38239 need remove atom 38240 need remove atom 38249 need remove atom 38251 need remove atom 38340 need remove atom 38341 need remove atom 38342 need remove atom 38344 need remove atom 38347 need remove atom 38348 need remove atom 38357 need remove atom 38359 need remove atom 38448 need remove atom 38449 need remove atom 38450 need remove atom 38452 need remove atom 38455 need remove atom 38456 need remove atom 38465 need remove atom 38467 need remove atom 38556 need remove atom 38557 need remove atom 38558 need remove atom 38560 need remove atom 38563 need remove atom 38564 need remove atom 38573 need remove atom 38575 need remove atom 38664 need remove atom 38665 need remove atom 38666 need remove atom 38668 need remove atom 38671 need remove atom 38672 need remove atom 38681 need remove atom 38683 need remove atom 38772 need remove atom 38773 need remove atom 38774 need remove atom 38776 need remove atom 38779 need remove atom 38780 need remove atom 38789 need remove atom 38791 need remove atom 38880 need remove atom 38881 need remove atom 38882 need remove atom 38884 need remove atom 38887 need remove atom 38888 need remove atom 38897 need remove atom 38899 need remove atom 38988 need remove atom 38989 need remove atom 38990 need remove atom 38992 need remove atom 38995 need remove atom 38996 need remove atom 39005 need remove atom 39007 need remove atom 39096 need remove atom 39097 need remove atom 39098 need remove atom 39100 need remove atom 39103 need remove atom 39104 need remove atom 39113 need remove atom 39115 need remove atom 39204 need remove atom 39205 need remove atom 39206 need remove atom 39208 need remove atom 39211 need remove atom 39212 need remove atom 39221 need remove atom 39223 need remove atom 39312 need remove atom 39313 need remove atom 39314 need remove atom 39316 need remove atom 39319 need remove atom 39320 need remove atom 39329 need remove atom 39331 need remove atom 39420 need remove atom 39421 need remove atom 39422 need remove atom 39424 need remove atom 39427 need remove atom 39428 need remove atom 39437 need remove atom 39439 need remove atom 39528 need remove atom 39529 need remove atom 39530 need remove atom 39532 need remove atom 39535 need remove atom 39536 need remove atom 39545 need remove atom 39547 need remove atom 39636 need remove atom 39637 need remove atom 39638 need remove atom 39640 need remove atom 39643 need remove atom 39644 need remove atom 39653 need remove atom 39655 need remove atom 39744 need remove atom 39745 need remove atom 39746 need remove atom 39748 need remove atom 39751 need remove atom 39752 need remove atom 39761 need remove atom 39763 need remove atom 39852 need remove atom 39853 need remove atom 39854 need remove atom 39856 need remove atom 39859 need remove atom 39860 need remove atom 39869 need remove atom 39871 need remove atom 39960 need remove atom 39961 need remove atom 39962 need remove atom 39964 need remove atom 39967 need remove atom 39968 need remove atom 39977 need remove atom 39979 need remove atom 40068 need remove atom 40069 need remove atom 40070 need remove atom 40072 need remove atom 40075 need remove atom 40076 need remove atom 40085 need remove atom 40087 need remove atom 40176 need remove atom 40177 need remove atom 40178 need remove atom 40180 need remove atom 40183 need remove atom 40184 need remove atom 40193 need remove atom 40195 need remove atom 40284 need remove atom 40285 need remove atom 40286 need remove atom 40288 need remove atom 40291 need remove atom 40292 need remove atom 40301 need remove atom 40303 need remove atom 40392 need remove atom 40393 need remove atom 40394 need remove atom 40396 need remove atom 40399 need remove atom 40400 need remove atom 40409 need remove atom 40411 need remove atom 40500 need remove atom 40501 need remove atom 40502 need remove atom 40504 need remove atom 40507 need remove atom 40508 need remove atom 40517 need remove atom 40519 need remove atom 40608 need remove atom 40609 need remove atom 40610 need remove atom 40612 need remove atom 40615 need remove atom 40616 need remove atom 40625 need remove atom 40627 need remove atom 40716 need remove atom 40717 need remove atom 40718 need remove atom 40720 need remove atom 40723 need remove atom 40724 need remove atom 40733 need remove atom 40735 need remove atom 40824 need remove atom 40825 need remove atom 40826 need remove atom 40828 need remove atom 40831 need remove atom 40832 need remove atom 40841 need remove atom 40843 need remove atom 40932 need remove atom 40933 need remove atom 40934 need remove atom 40936 need remove atom 40939 need remove atom 40940 need remove atom 40949 need remove atom 40951 need remove atom 41040 need remove atom 41041 need remove atom 41042 need remove atom 41044 need remove atom 41047 need remove atom 41048 need remove atom 41057 need remove atom 41059 need remove atom 41148 need remove atom 41149 need remove atom 41150 need remove atom 41152 need remove atom 41155 need remove atom 41156 need remove atom 41165 need remove atom 41167 need remove atom 41256 need remove atom 41257 need remove atom 41258 need remove atom 41260 need remove atom 41263 need remove atom 41264 need remove atom 41273 need remove atom 41275 need remove atom 41364 need remove atom 41365 need remove atom 41366 need remove atom 41368 need remove atom 41371 need remove atom 41372 need remove atom 41381 need remove atom 41383 need remove atom 41472 need remove atom 41473 need remove atom 41474 need remove atom 41476 need remove atom 41479 need remove atom 41480 need remove atom 41489 need remove atom 41491 need remove atom 41580 need remove atom 41581 need remove atom 41582 need remove atom 41584 need remove atom 41587 need remove atom 41588 need remove atom 41597 need remove atom 41599 need remove atom 41688 need remove atom 41689 need remove atom 41690 need remove atom 41692 need remove atom 41695 need remove atom 41696 need remove atom 41705 need remove atom 41707 need remove atom 41796 need remove atom 41797 need remove atom 41813 need remove atom 41815 need remove atom 41904 need remove atom 41905 need remove atom 41921 need remove atom 41923 need remove atom 42012 need remove atom 42013 need remove atom 42029 need remove atom 42031 [I] need removenum=564 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4939112869e-01 1.0975637090e-01 -3.3147565453e-01 dub= -3.6642748651e-01 1.0975880910e-01 3.3760354034e-01 duc= 3.4939212058e-01 -1.1116893239e-01 -3.3147671767e-01 [I] overall tilt ux= -7.1581861520e-01 2.4381970545e-06 6.6907919487e-01 uy= 9.9188455605e-07 -2.2092530328e-01 -1.0631375026e-06 [I] storedr[0]= -2.9075794307e-02 -7.0993952649e-04 -4.4986217088e-02 [I] originally 91368 atoms [I] insert 0 atoms [I] now 91368 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 91368 atoms [I] remove 564 atoms [I] now 90804 atoms [I] NP=90804 n=90804 [I] ASSIGN finalcnfile = dipole_4.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 19:58:04 2023 CPU time spent: 7.725107 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 20:30:00 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 7 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 55 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=124740 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.010582010582011 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.04320987654321 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.0582010582e-02 -0.0000000000e+00 -4.3209876543e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=1.627477e+02 pxpb=0.000000e+00 pypb=2.460921e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 58039 need remove atom 58041 need remove atom 58049 need remove atom 58051 need remove atom 58054 need remove atom 58056 need remove atom 58067 need remove atom 58069 need remove atom 58147 need remove atom 58149 need remove atom 58157 need remove atom 58159 need remove atom 58162 need remove atom 58164 need remove atom 58175 need remove atom 58177 need remove atom 58255 need remove atom 58257 need remove atom 58265 need remove atom 58267 need remove atom 58270 need remove atom 58272 need remove atom 58283 need remove atom 58285 need remove atom 58363 need remove atom 58365 need remove atom 58373 need remove atom 58375 need remove atom 58378 need remove atom 58380 need remove atom 58391 need remove atom 58393 need remove atom 58471 need remove atom 58473 need remove atom 58481 need remove atom 58483 need remove atom 58486 need remove atom 58488 need remove atom 58499 need remove atom 58501 need remove atom 58579 need remove atom 58581 need remove atom 58589 need remove atom 58591 need remove atom 58594 need remove atom 58596 need remove atom 58607 need remove atom 58609 need remove atom 58687 need remove atom 58689 need remove atom 58697 need remove atom 58699 need remove atom 58702 need remove atom 58704 need remove atom 58715 need remove atom 58717 need remove atom 58795 need remove atom 58797 need remove atom 58805 need remove atom 58807 need remove atom 58810 need remove atom 58812 need remove atom 58823 need remove atom 58825 need remove atom 58903 need remove atom 58905 need remove atom 58913 need remove atom 58915 need remove atom 58918 need remove atom 58920 need remove atom 58931 need remove atom 58933 need remove atom 59011 need remove atom 59013 need remove atom 59021 need remove atom 59023 need remove atom 59026 need remove atom 59028 need remove atom 59039 need remove atom 59041 need remove atom 59119 need remove atom 59121 need remove atom 59129 need remove atom 59131 need remove atom 59134 need remove atom 59136 need remove atom 59147 need remove atom 59149 need remove atom 59227 need remove atom 59229 need remove atom 59237 need remove atom 59239 need remove atom 59242 need remove atom 59244 need remove atom 59255 need remove atom 59257 need remove atom 59335 need remove atom 59337 need remove atom 59345 need remove atom 59347 need remove atom 59350 need remove atom 59352 need remove atom 59363 need remove atom 59365 need remove atom 59443 need remove atom 59445 need remove atom 59453 need remove atom 59455 need remove atom 59458 need remove atom 59460 need remove atom 59471 need remove atom 59473 need remove atom 59551 need remove atom 59553 need remove atom 59561 need remove atom 59563 need remove atom 59566 need remove atom 59568 need remove atom 59579 need remove atom 59581 need remove atom 59659 need remove atom 59661 need remove atom 59669 need remove atom 59671 need remove atom 59674 need remove atom 59676 need remove atom 59687 need remove atom 59689 need remove atom 59767 need remove atom 59769 need remove atom 59777 need remove atom 59779 need remove atom 59782 need remove atom 59784 need remove atom 59795 need remove atom 59797 need remove atom 59875 need remove atom 59877 need remove atom 59885 need remove atom 59887 need remove atom 59890 need remove atom 59892 need remove atom 59903 need remove atom 59905 need remove atom 59983 need remove atom 59985 need remove atom 59993 need remove atom 59995 need remove atom 59998 need remove atom 60000 need remove atom 60011 need remove atom 60013 need remove atom 60091 need remove atom 60093 need remove atom 60101 need remove atom 60103 need remove atom 60106 need remove atom 60108 need remove atom 60119 need remove atom 60121 need remove atom 60199 need remove atom 60201 need remove atom 60209 need remove atom 60211 need remove atom 60214 need remove atom 60216 need remove atom 60227 need remove atom 60229 need remove atom 60307 need remove atom 60309 need remove atom 60317 need remove atom 60319 need remove atom 60322 need remove atom 60324 need remove atom 60335 need remove atom 60337 need remove atom 60415 need remove atom 60417 need remove atom 60425 need remove atom 60427 need remove atom 60430 need remove atom 60432 need remove atom 60443 need remove atom 60445 need remove atom 60523 need remove atom 60525 need remove atom 60533 need remove atom 60535 need remove atom 60538 need remove atom 60540 need remove atom 60551 need remove atom 60553 need remove atom 60631 need remove atom 60633 need remove atom 60641 need remove atom 60643 need remove atom 60646 need remove atom 60648 need remove atom 60659 need remove atom 60661 need remove atom 60739 need remove atom 60741 need remove atom 60749 need remove atom 60751 need remove atom 60754 need remove atom 60756 need remove atom 60767 need remove atom 60769 need remove atom 60847 need remove atom 60849 need remove atom 60857 need remove atom 60859 need remove atom 60862 need remove atom 60864 need remove atom 60875 need remove atom 60877 need remove atom 60955 need remove atom 60957 need remove atom 60965 need remove atom 60967 need remove atom 60970 need remove atom 60972 need remove atom 60983 need remove atom 60985 need remove atom 61063 need remove atom 61065 need remove atom 61073 need remove atom 61075 need remove atom 61078 need remove atom 61080 need remove atom 61091 need remove atom 61093 need remove atom 61171 need remove atom 61173 need remove atom 61181 need remove atom 61183 need remove atom 61186 need remove atom 61188 need remove atom 61199 need remove atom 61201 need remove atom 61279 need remove atom 61281 need remove atom 61289 need remove atom 61291 need remove atom 61294 need remove atom 61296 need remove atom 61307 need remove atom 61309 need remove atom 61387 need remove atom 61389 need remove atom 61397 need remove atom 61399 need remove atom 61402 need remove atom 61404 need remove atom 61415 need remove atom 61417 need remove atom 61495 need remove atom 61497 need remove atom 61505 need remove atom 61507 need remove atom 61510 need remove atom 61512 need remove atom 61523 need remove atom 61525 need remove atom 61603 need remove atom 61605 need remove atom 61613 need remove atom 61615 need remove atom 61618 need remove atom 61620 need remove atom 61631 need remove atom 61633 need remove atom 61711 need remove atom 61713 need remove atom 61721 need remove atom 61723 need remove atom 61726 need remove atom 61728 need remove atom 61739 need remove atom 61741 need remove atom 61819 need remove atom 61821 need remove atom 61829 need remove atom 61831 need remove atom 61834 need remove atom 61836 need remove atom 61847 need remove atom 61849 need remove atom 61927 need remove atom 61929 need remove atom 61937 need remove atom 61939 need remove atom 61942 need remove atom 61944 need remove atom 61955 need remove atom 61957 need remove atom 62035 need remove atom 62037 need remove atom 62045 need remove atom 62047 need remove atom 62050 need remove atom 62052 need remove atom 62063 need remove atom 62065 need remove atom 62143 need remove atom 62145 need remove atom 62153 need remove atom 62155 need remove atom 62158 need remove atom 62160 need remove atom 62171 need remove atom 62173 need remove atom 62251 need remove atom 62253 need remove atom 62261 need remove atom 62263 need remove atom 62266 need remove atom 62268 need remove atom 62279 need remove atom 62281 need remove atom 62359 need remove atom 62361 need remove atom 62369 need remove atom 62371 need remove atom 62374 need remove atom 62376 need remove atom 62387 need remove atom 62389 need remove atom 62467 need remove atom 62469 need remove atom 62477 need remove atom 62479 need remove atom 62482 need remove atom 62484 need remove atom 62495 need remove atom 62497 need remove atom 62575 need remove atom 62577 need remove atom 62585 need remove atom 62587 need remove atom 62590 need remove atom 62592 need remove atom 62603 need remove atom 62605 need remove atom 62683 need remove atom 62685 need remove atom 62693 need remove atom 62695 need remove atom 62698 need remove atom 62700 need remove atom 62711 need remove atom 62713 need remove atom 62791 need remove atom 62793 need remove atom 62801 need remove atom 62803 need remove atom 62806 need remove atom 62808 need remove atom 62819 need remove atom 62821 need remove atom 62899 need remove atom 62901 need remove atom 62909 need remove atom 62911 need remove atom 62914 need remove atom 62916 need remove atom 62927 need remove atom 62929 need remove atom 63007 need remove atom 63009 need remove atom 63017 need remove atom 63019 need remove atom 63022 need remove atom 63024 need remove atom 63035 need remove atom 63037 need remove atom 63115 need remove atom 63117 need remove atom 63125 need remove atom 63127 need remove atom 63130 need remove atom 63132 need remove atom 63143 need remove atom 63145 need remove atom 63223 need remove atom 63225 need remove atom 63233 need remove atom 63235 need remove atom 63238 need remove atom 63240 need remove atom 63251 need remove atom 63253 need remove atom 63331 need remove atom 63333 need remove atom 63341 need remove atom 63343 need remove atom 63346 need remove atom 63348 need remove atom 63359 need remove atom 63361 need remove atom 63439 need remove atom 63441 need remove atom 63449 need remove atom 63451 need remove atom 63454 need remove atom 63456 need remove atom 63467 need remove atom 63469 need remove atom 63547 need remove atom 63549 need remove atom 63557 need remove atom 63559 need remove atom 63562 need remove atom 63564 need remove atom 63575 need remove atom 63577 need remove atom 63655 need remove atom 63657 need remove atom 63665 need remove atom 63667 need remove atom 63670 need remove atom 63672 need remove atom 63683 need remove atom 63685 need remove atom 63763 need remove atom 63765 need remove atom 63773 need remove atom 63775 need remove atom 63778 need remove atom 63780 need remove atom 63791 need remove atom 63793 need remove atom 63871 need remove atom 63873 need remove atom 63881 need remove atom 63883 need remove atom 63886 need remove atom 63888 need remove atom 63899 need remove atom 63901 need remove atom 63979 need remove atom 63981 need remove atom 63989 need remove atom 63991 need remove atom 63994 need remove atom 63996 need remove atom 64007 need remove atom 64009 need remove atom 64087 need remove atom 64089 need remove atom 64097 need remove atom 64099 need remove atom 64102 need remove atom 64104 need remove atom 64115 need remove atom 64117 need remove atom 64195 need remove atom 64197 need remove atom 64205 need remove atom 64207 need remove atom 64210 need remove atom 64212 need remove atom 64223 need remove atom 64225 need remove atom 64303 need remove atom 64305 need remove atom 64313 need remove atom 64315 need remove atom 64318 need remove atom 64320 need remove atom 64331 need remove atom 64333 need remove atom 64411 need remove atom 64413 need remove atom 64421 need remove atom 64423 need remove atom 64426 need remove atom 64428 need remove atom 64439 need remove atom 64441 need remove atom 64519 need remove atom 64521 need remove atom 64529 need remove atom 64531 need remove atom 64534 need remove atom 64536 need remove atom 64547 need remove atom 64549 need remove atom 64627 need remove atom 64629 need remove atom 64637 need remove atom 64639 need remove atom 64642 need remove atom 64644 need remove atom 64655 need remove atom 64657 need remove atom 64735 need remove atom 64737 need remove atom 64745 need remove atom 64747 need remove atom 64750 need remove atom 64752 need remove atom 64763 need remove atom 64765 need remove atom 64843 need remove atom 64845 need remove atom 64853 need remove atom 64855 need remove atom 64858 need remove atom 64860 need remove atom 64871 need remove atom 64873 need remove atom 64951 need remove atom 64953 need remove atom 64961 need remove atom 64963 need remove atom 64966 need remove atom 64968 need remove atom 64979 need remove atom 64981 need remove atom 65059 need remove atom 65061 need remove atom 65069 need remove atom 65071 need remove atom 65074 need remove atom 65076 need remove atom 65087 need remove atom 65089 need remove atom 65167 need remove atom 65169 need remove atom 65177 need remove atom 65179 need remove atom 65182 need remove atom 65184 need remove atom 65195 need remove atom 65197 need remove atom 65275 need remove atom 65277 need remove atom 65285 need remove atom 65287 need remove atom 65290 need remove atom 65292 need remove atom 65303 need remove atom 65305 need remove atom 65383 need remove atom 65385 need remove atom 65393 need remove atom 65395 need remove atom 65398 need remove atom 65400 need remove atom 65411 need remove atom 65413 need remove atom 65491 need remove atom 65493 need remove atom 65501 need remove atom 65503 need remove atom 65506 need remove atom 65508 need remove atom 65519 need remove atom 65521 need remove atom 65599 need remove atom 65601 need remove atom 65609 need remove atom 65611 need remove atom 65614 need remove atom 65616 need remove atom 65627 need remove atom 65629 need remove atom 65707 need remove atom 65709 need remove atom 65717 need remove atom 65719 need remove atom 65722 need remove atom 65724 need remove atom 65735 need remove atom 65737 need remove atom 65815 need remove atom 65817 need remove atom 65825 need remove atom 65827 need remove atom 65830 need remove atom 65832 need remove atom 65843 need remove atom 65845 need remove atom 65923 need remove atom 65925 need remove atom 65933 need remove atom 65935 need remove atom 65938 need remove atom 65940 need remove atom 65951 need remove atom 65953 need remove atom 66031 need remove atom 66033 need remove atom 66041 need remove atom 66043 need remove atom 66046 need remove atom 66048 need remove atom 66059 need remove atom 66061 need remove atom 66139 need remove atom 66141 need remove atom 66149 need remove atom 66151 need remove atom 66154 need remove atom 66156 need remove atom 66167 need remove atom 66169 need remove atom 66247 need remove atom 66249 need remove atom 66257 need remove atom 66259 need remove atom 66262 need remove atom 66264 need remove atom 66275 need remove atom 66277 need remove atom 66355 need remove atom 66357 need remove atom 66365 need remove atom 66367 need remove atom 66370 need remove atom 66372 need remove atom 66383 need remove atom 66385 need remove atom 66463 need remove atom 66465 need remove atom 66473 need remove atom 66475 need remove atom 66478 need remove atom 66480 need remove atom 66491 need remove atom 66493 need remove atom 66571 need remove atom 66573 need remove atom 66581 need remove atom 66583 need remove atom 66586 need remove atom 66588 need remove atom 66599 need remove atom 66601 need remove atom 66679 need remove atom 66681 need remove atom 66689 need remove atom 66691 need remove atom 66694 need remove atom 66696 need remove atom 66707 need remove atom 66709 need remove atom 66797 need remove atom 66799 need remove atom 66802 need remove atom 66804 need remove atom 66905 need remove atom 66907 need remove atom 66910 need remove atom 66912 need remove atom 67013 need remove atom 67015 need remove atom 67018 need remove atom 67020 [I] need removenum=660 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4965759648e-01 1.0966553667e-01 -3.3191754132e-01 dub= -3.6672187348e-01 1.0966800673e-01 3.3811090116e-01 duc= 3.4965858596e-01 -1.1108470972e-01 -3.3191860517e-01 [I] overall tilt ux= -7.1637946996e-01 2.4700582795e-06 6.7002844248e-01 uy= 9.8948547106e-07 -2.2075024639e-01 -1.0638493805e-06 [I] storedr[0]= -2.6394145703e-02 -7.1579282371e-04 -3.9452899750e-02 [I] originally 124740 atoms [I] insert 0 atoms [I] now 124740 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 124740 atoms [I] remove 660 atoms [I] now 124080 atoms [I] NP=124080 n=124080 [I] ASSIGN finalcnfile = dipole_4.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 20:30:12 2023 CPU time spent: 10.587737 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 21:01:51 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 62 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=214272 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.0092592592592593 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.032407407407407 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 9.2592592593e-03 -0.0000000000e+00 -3.2407407407e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=1.859974e+02 pxpb=0.000000e+00 pypb=2.774129e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 87264 need remove atom 87266 need remove atom 87268 need remove atom 87271 need remove atom 87272 need remove atom 87279 need remove atom 87281 need remove atom 87284 need remove atom 87372 need remove atom 87374 need remove atom 87376 need remove atom 87379 need remove atom 87380 need remove atom 87387 need remove atom 87389 need remove atom 87392 need remove atom 87480 need remove atom 87482 need remove atom 87484 need remove atom 87487 need remove atom 87488 need remove atom 87495 need remove atom 87497 need remove atom 87500 need remove atom 87588 need remove atom 87590 need remove atom 87592 need remove atom 87595 need remove atom 87596 need remove atom 87603 need remove atom 87605 need remove atom 87608 need remove atom 87696 need remove atom 87698 need remove atom 87700 need remove atom 87703 need remove atom 87704 need remove atom 87711 need remove atom 87713 need remove atom 87716 need remove atom 87804 need remove atom 87806 need remove atom 87808 need remove atom 87811 need remove atom 87812 need remove atom 87819 need remove atom 87821 need remove atom 87824 need remove atom 87912 need remove atom 87914 need remove atom 87916 need remove atom 87919 need remove atom 87920 need remove atom 87927 need remove atom 87929 need remove atom 87932 need remove atom 88020 need remove atom 88022 need remove atom 88024 need remove atom 88027 need remove atom 88028 need remove atom 88035 need remove atom 88037 need remove atom 88040 need remove atom 88128 need remove atom 88130 need remove atom 88132 need remove atom 88135 need remove atom 88136 need remove atom 88143 need remove atom 88145 need remove atom 88148 need remove atom 88236 need remove atom 88238 need remove atom 88240 need remove atom 88243 need remove atom 88244 need remove atom 88251 need remove atom 88253 need remove atom 88256 need remove atom 88344 need remove atom 88346 need remove atom 88348 need remove atom 88351 need remove atom 88352 need remove atom 88359 need remove atom 88361 need remove atom 88364 need remove atom 88452 need remove atom 88454 need remove atom 88456 need remove atom 88459 need remove atom 88460 need remove atom 88467 need remove atom 88469 need remove atom 88472 need remove atom 88560 need remove atom 88562 need remove atom 88564 need remove atom 88567 need remove atom 88568 need remove atom 88575 need remove atom 88577 need remove atom 88580 need remove atom 88668 need remove atom 88670 need remove atom 88672 need remove atom 88675 need remove atom 88676 need remove atom 88683 need remove atom 88685 need remove atom 88688 need remove atom 88776 need remove atom 88778 need remove atom 88780 need remove atom 88783 need remove atom 88784 need remove atom 88791 need remove atom 88793 need remove atom 88796 need remove atom 88884 need remove atom 88886 need remove atom 88888 need remove atom 88891 need remove atom 88892 need remove atom 88899 need remove atom 88901 need remove atom 88904 need remove atom 88992 need remove atom 88994 need remove atom 88996 need remove atom 88999 need remove atom 89000 need remove atom 89007 need remove atom 89009 need remove atom 89012 need remove atom 89100 need remove atom 89102 need remove atom 89104 need remove atom 89107 need remove atom 89108 need remove atom 89115 need remove atom 89117 need remove atom 89120 need remove atom 89208 need remove atom 89210 need remove atom 89212 need remove atom 89215 need remove atom 89216 need remove atom 89223 need remove atom 89225 need remove atom 89228 need remove atom 89316 need remove atom 89318 need remove atom 89320 need remove atom 89323 need remove atom 89324 need remove atom 89331 need remove atom 89333 need remove atom 89336 need remove atom 89424 need remove atom 89426 need remove atom 89428 need remove atom 89431 need remove atom 89432 need remove atom 89439 need remove atom 89441 need remove atom 89444 need remove atom 89532 need remove atom 89534 need remove atom 89536 need remove atom 89539 need remove atom 89540 need remove atom 89547 need remove atom 89549 need remove atom 89552 need remove atom 89640 need remove atom 89642 need remove atom 89644 need remove atom 89647 need remove atom 89648 need remove atom 89655 need remove atom 89657 need remove atom 89660 need remove atom 89748 need remove atom 89750 need remove atom 89752 need remove atom 89755 need remove atom 89756 need remove atom 89763 need remove atom 89765 need remove atom 89768 need remove atom 89856 need remove atom 89858 need remove atom 89860 need remove atom 89863 need remove atom 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remove atom 90504 need remove atom 90506 need remove atom 90508 need remove atom 90511 need remove atom 90512 need remove atom 90519 need remove atom 90521 need remove atom 90524 need remove atom 90612 need remove atom 90614 need remove atom 90616 need remove atom 90619 need remove atom 90620 need remove atom 90627 need remove atom 90629 need remove atom 90632 need remove atom 90720 need remove atom 90722 need remove atom 90724 need remove atom 90727 need remove atom 90728 need remove atom 90735 need remove atom 90737 need remove atom 90740 need remove atom 90828 need remove atom 90830 need remove atom 90832 need remove atom 90835 need remove atom 90836 need remove atom 90843 need remove atom 90845 need remove atom 90848 need remove atom 90936 need remove atom 90938 need remove atom 90940 need remove atom 90943 need remove atom 90944 need remove atom 90951 need remove atom 90953 need remove atom 90956 need remove atom 91044 need remove atom 91046 need remove atom 91048 need remove atom 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92236 need remove atom 92239 need remove atom 92240 need remove atom 92247 need remove atom 92249 need remove atom 92252 need remove atom 92340 need remove atom 92342 need remove atom 92344 need remove atom 92347 need remove atom 92348 need remove atom 92355 need remove atom 92357 need remove atom 92360 need remove atom 92448 need remove atom 92450 need remove atom 92452 need remove atom 92455 need remove atom 92456 need remove atom 92463 need remove atom 92465 need remove atom 92468 need remove atom 92556 need remove atom 92558 need remove atom 92560 need remove atom 92563 need remove atom 92564 need remove atom 92571 need remove atom 92573 need remove atom 92576 need remove atom 92664 need remove atom 92666 need remove atom 92668 need remove atom 92671 need remove atom 92672 need remove atom 92679 need remove atom 92681 need remove atom 92684 need remove atom 92772 need remove atom 92774 need remove atom 92776 need remove atom 92779 need remove atom 92780 need remove atom 92787 need 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remove atom 96343 need remove atom 96344 need remove atom 96351 need remove atom 96353 need remove atom 96356 need remove atom 96444 need remove atom 96446 need remove atom 96448 need remove atom 96451 need remove atom 96452 need remove atom 96459 need remove atom 96461 need remove atom 96464 need remove atom 96552 need remove atom 96554 need remove atom 96556 need remove atom 96559 need remove atom 96560 need remove atom 96567 need remove atom 96569 need remove atom 96572 need remove atom 96660 need remove atom 96662 need remove atom 96664 need remove atom 96667 need remove atom 96668 need remove atom 96675 need remove atom 96677 need remove atom 96680 need remove atom 96768 need remove atom 96770 need remove atom 96772 need remove atom 96775 need remove atom 96776 need remove atom 96783 need remove atom 96785 need remove atom 96788 need remove atom 96876 need remove atom 96878 need remove atom 96880 need remove atom 96883 need remove atom 96884 need remove atom 96891 need remove atom 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remove atom 97528 need remove atom 97531 need remove atom 97532 need remove atom 97539 need remove atom 97541 need remove atom 97544 need remove atom 97632 need remove atom 97634 need remove atom 97636 need remove atom 97639 need remove atom 97640 need remove atom 97647 need remove atom 97649 need remove atom 97652 need remove atom 97740 need remove atom 97742 need remove atom 97744 need remove atom 97747 need remove atom 97748 need remove atom 97755 need remove atom 97757 need remove atom 97760 need remove atom 97848 need remove atom 97850 need remove atom 97852 need remove atom 97855 need remove atom 97856 need remove atom 97863 need remove atom 97865 need remove atom 97868 need remove atom 97956 need remove atom 97958 need remove atom 97960 need remove atom 97963 need remove atom 97964 need remove atom 97971 need remove atom 97973 need remove atom 97976 need remove atom 98064 need remove atom 98066 need remove atom 98068 need remove atom 98071 need remove atom 98072 need remove atom 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remove atom 98714 need remove atom 98716 need remove atom 98719 need remove atom 98720 need remove atom 98727 need remove atom 98729 need remove atom 98732 need remove atom 98820 need remove atom 98822 need remove atom 98824 need remove atom 98827 need remove atom 98828 need remove atom 98835 need remove atom 98837 need remove atom 98840 need remove atom 98928 need remove atom 98930 need remove atom 98932 need remove atom 98935 need remove atom 98936 need remove atom 98943 need remove atom 98945 need remove atom 98948 need remove atom 99036 need remove atom 99038 need remove atom 99040 need remove atom 99043 need remove atom 99044 need remove atom 99051 need remove atom 99053 need remove atom 99056 need remove atom 99144 need remove atom 99146 need remove atom 99148 need remove atom 99151 need remove atom 99152 need remove atom 99159 need remove atom 99161 need remove atom 99164 need remove atom 99252 need remove atom 99254 need remove atom 99256 need remove atom 99259 need remove atom 99260 need remove atom 99267 need remove atom 99269 need remove atom 99272 need remove atom 99360 need remove atom 99362 need remove atom 99364 need remove atom 99367 need remove atom 99368 need remove atom 99375 need remove atom 99377 need remove atom 99380 need remove atom 99468 need remove atom 99470 need remove atom 99472 need remove atom 99475 need remove atom 99476 need remove atom 99483 need remove atom 99485 need remove atom 99488 need remove atom 99576 need remove atom 99578 need remove atom 99580 need remove atom 99583 need remove atom 99584 need remove atom 99591 need remove atom 99593 need remove atom 99596 need remove atom 99684 need remove atom 99686 need remove atom 99688 need remove atom 99691 need remove atom 99692 need remove atom 99699 need remove atom 99701 need remove atom 99704 need remove atom 99792 need remove atom 99794 need remove atom 99796 need remove atom 99799 need remove atom 99800 need remove atom 99807 need remove atom 99809 need remove atom 99812 need remove atom 99900 need remove atom 99902 need remove atom 99904 need remove atom 99907 need remove atom 99908 need remove atom 99915 need remove atom 99917 need remove atom 99920 need remove atom 100008 need remove atom 100010 need remove atom 100012 need remove atom 100015 need remove atom 100016 need remove atom 100023 need remove atom 100025 need remove atom 100028 need remove atom 100116 need remove atom 100118 need remove atom 100120 need remove atom 100123 need remove atom 100124 need remove atom 100131 need remove atom 100133 need remove atom 100136 need remove atom 100224 need remove atom 100226 need remove atom 100228 need remove atom 100231 need remove atom 100232 need remove atom 100239 need remove atom 100241 need remove atom 100244 need remove atom 100332 need remove atom 100334 need remove atom 100336 need remove atom 100339 need remove atom 100340 need remove atom 100347 need remove atom 100349 need remove atom 100352 need remove atom 100440 need remove atom 100442 need remove atom 100444 need remove atom 100447 need remove atom 100448 need remove atom 100455 need remove atom 100457 need remove atom 100460 need remove atom 100548 need remove atom 100550 need remove atom 100552 need remove atom 100555 need remove atom 100556 need remove atom 100563 need remove atom 100565 need remove atom 100568 [I] need removenum=992 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4844542040e-01 1.1007629836e-01 -3.2991451039e-01 dub= -3.6538050937e-01 1.1007862195e-01 3.3581059357e-01 duc= 3.4844642064e-01 -1.1146553898e-01 -3.2991557089e-01 [I] overall tilt ux= -7.1382592977e-01 2.3235950792e-06 6.6572510397e-01 uy= 1.0002423446e-06 -2.2154183734e-01 -1.0605001303e-06 [I] storedr[0]= -2.3822860327e-02 -7.0315057832e-04 -3.6380182845e-02 [I] originally 214272 atoms [I] insert 0 atoms [I] now 214272 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 214272 atoms [I] remove 992 atoms [I] now 213280 atoms [I] NP=213280 n=213280 [I] ASSIGN finalcnfile = dipole_5.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 21:02:11 2023 CPU time spent: 18.113498 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 21:32:22 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1638794690371 [I] ASSIGN makecnspec = -5 [I] ASSIGN makecnspec(1) = -5 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 9 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 70 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 5 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -5 -1 1 -5 1 1 2 0 5]; basis=[ 0.925926 0 0.12963 0 0 0.962963 0 0.314815 0 1 0.907407 0.5 0.037037 0 2 0.833333 0.5 0.166667 0 3 0.944444 0.5 0.222222 0 4 0.87037 0.5 0.351852 0 5 0.981481 0.5 0.407407 0 6 0.907407 0.5 0.537037 0 7 0.944444 0.5 0.722222 0 8 0.981481 0.5 0.907407 0 9 0.703704 0 0.0185185 0 10 0.814815 0 0.0740741 0 11 0.740741 0 0.203704 0 12 0.851852 0 0.259259 0 13 0.777778 0 0.388889 0 14 0.888889 0 0.444444 0 15 0.814815 0 0.574074 0 16 0.925926 0 0.62963 0 17 0.851852 0 0.759259 0 18 0.962963 0 0.814815 0 19 0.888889 0 0.944444 0 20 0.611111 0.5 0.0555556 0 21 0.722222 0.5 0.111111 0 22 0.648148 0.5 0.240741 0 23 0.759259 0.5 0.296296 0 24 0.685185 0.5 0.425926 0 25 0.796296 0.5 0.481481 0 26 0.722222 0.5 0.611111 0 27 0.833333 0.5 0.666667 0 28 0.759259 0.5 0.796296 0 29 0.87037 0.5 0.851852 0 30 0.796296 0.5 0.981481 0 31 0.518519 0 0.0925926 0 32 0.62963 0 0.148148 0 33 0.555556 0 0.277778 0 34 0.666667 0 0.333333 0 35 0.592593 0 0.462963 0 36 0.703704 0 0.518519 0 37 0.62963 0 0.648148 0 38 0.740741 0 0.703704 0 39 0.666667 0 0.833333 0 40 0.777778 0 0.888889 0 41 0.5 0.5 0 0 42 0.425926 0.5 0.12963 0 43 0.537037 0.5 0.185185 0 44 0.462963 0.5 0.314815 0 45 0.574074 0.5 0.37037 0 46 0.5 0.5 0.5 0 47 0.611111 0.5 0.555556 0 48 0.537037 0.5 0.685185 0 49 0.648148 0.5 0.740741 0 50 0.574074 0.5 0.87037 0 51 0.685185 0.5 0.925926 0 52 0.407407 0 0.037037 0 53 0.333333 0 0.166667 0 54 0.444444 0 0.222222 0 55 0.37037 0 0.351852 0 56 0.481481 0 0.407407 0 57 0.407407 0 0.537037 0 58 0.518519 0 0.592593 0 59 0.444444 0 0.722222 0 60 0.555556 0 0.777778 0 61 0.481481 0 0.907407 0 62 0.592593 0 0.962963 0 63 0.203704 0.5 0.0185185 0 64 0.314815 0.5 0.0740741 0 65 0.240741 0.5 0.203704 0 66 0.351852 0.5 0.259259 0 67 0.277778 0.5 0.388889 0 68 0.388889 0.5 0.444444 0 69 0.314815 0.5 0.574074 0 70 0.425926 0.5 0.62963 0 71 0.351852 0.5 0.759259 0 72 0.462963 0.5 0.814815 0 73 0.388889 0.5 0.944444 0 74 0.111111 0 0.0555556 0 75 0.222222 0 0.111111 0 76 0.148148 0 0.240741 0 77 0.259259 0 0.296296 0 78 0.185185 0 0.425926 0 79 0.296296 0 0.481481 0 80 0.222222 0 0.611111 0 81 0.333333 0 0.666667 0 82 0.259259 0 0.796296 0 83 0.37037 0 0.851852 0 84 0.296296 0 0.981481 0 85 0.0185185 0.5 0.0925926 0 86 0.12963 0.5 0.148148 0 87 0.0555556 0.5 0.277778 0 88 0.166667 0.5 0.333333 0 89 0.0925926 0.5 0.462963 0 90 0.203704 0.5 0.518519 0 91 0.12963 0.5 0.648148 0 92 0.240741 0.5 0.703704 0 93 0.166667 0.5 0.833333 0 94 0.277778 0.5 0.888889 0 95 0 0 0 0 96 0.037037 0 0.185185 0 97 0.0740741 0 0.37037 0 98 0 0 0.5 0 99 0.111111 0 0.555556 0 100 0.037037 0 0.685185 0 101 0.148148 0 0.740741 0 102 0.0740741 0 0.87037 0 103 0.185185 0 0.925926 0 104 0.0185185 0.5 0.592593 0 105 0.0555556 0.5 0.777778 0 106 0.0925926 0.5 0.962963 0 107 ]; [I] makecn: _NP=272160 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.0082304526748971 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.032407407407407 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27789727534142 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 8.2304526749e-03 -0.0000000000e+00 -3.2407407407e-02 b= 1.7221978460e+00 0.0000000000e+00 -2.1311111070e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.7221978459575 by=0 pxpa=2.092470e+02 pxpb=0.000000e+00 pypb=3.132081e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 128779 need remove atom 128789 need remove atom 128791 need remove atom 128794 need remove atom 128796 need remove atom 128805 need remove atom 128807 need remove atom 128810 need remove atom 128887 need remove atom 128897 need remove atom 128899 need remove atom 128902 need remove atom 128904 need remove atom 128913 need remove atom 128915 need remove atom 128918 need remove atom 128995 need remove atom 129005 need remove atom 129007 need remove atom 129010 need remove atom 129012 need remove atom 129021 need remove atom 129023 need remove atom 129026 need remove atom 129103 need remove atom 129113 need remove atom 129115 need remove atom 129118 need remove atom 129120 need remove atom 129129 need remove atom 129131 need remove atom 129134 need remove atom 129211 need remove atom 129221 need remove atom 129223 need remove atom 129226 need remove atom 129228 need remove atom 129237 need remove atom 129239 need remove atom 129242 need remove atom 129319 need remove atom 129329 need remove atom 129331 need remove atom 129334 need remove atom 129336 need remove atom 129345 need remove atom 129347 need remove atom 129350 need remove atom 129427 need remove atom 129437 need remove atom 129439 need remove atom 129442 need remove atom 129444 need remove atom 129453 need remove atom 129455 need remove atom 129458 need remove atom 129535 need remove atom 129545 need remove atom 129547 need remove atom 129550 need remove atom 129552 need remove atom 129561 need remove atom 129563 need remove atom 129566 need remove atom 129643 need remove atom 129653 need remove atom 129655 need remove atom 129658 need remove atom 129660 need remove atom 129669 need remove atom 129671 need remove atom 129674 need remove atom 129751 need remove atom 129761 need remove atom 129763 need remove atom 129766 need remove atom 129768 need remove atom 129777 need remove atom 129779 need remove atom 129782 need remove atom 129859 need remove atom 129869 need remove atom 129871 need remove atom 129874 need remove atom 129876 need remove atom 129885 need remove atom 129887 need remove atom 129890 need remove atom 129967 need remove atom 129977 need remove atom 129979 need remove atom 129982 need remove atom 129984 need remove atom 129993 need remove atom 129995 need remove atom 129998 need remove atom 130075 need remove atom 130085 need remove atom 130087 need remove atom 130090 need remove atom 130092 need remove atom 130101 need remove atom 130103 need remove atom 130106 need remove atom 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remove atom 130735 need remove atom 130738 need remove atom 130740 need remove atom 130749 need remove atom 130751 need remove atom 130754 need remove atom 130831 need remove atom 130841 need remove atom 130843 need remove atom 130846 need remove atom 130848 need remove atom 130857 need remove atom 130859 need remove atom 130862 need remove atom 130939 need remove atom 130949 need remove atom 130951 need remove atom 130954 need remove atom 130956 need remove atom 130965 need remove atom 130967 need remove atom 130970 need remove atom 131047 need remove atom 131057 need remove atom 131059 need remove atom 131062 need remove atom 131064 need remove atom 131073 need remove atom 131075 need remove atom 131078 need remove atom 131155 need remove atom 131165 need remove atom 131167 need remove atom 131170 need remove atom 131172 need remove atom 131181 need remove atom 131183 need remove atom 131186 need remove atom 131263 need remove atom 131273 need remove atom 131275 need remove atom 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remove atom 132991 need remove atom 133001 need remove atom 133003 need remove atom 133006 need remove atom 133008 need remove atom 133017 need remove atom 133019 need remove atom 133022 need remove atom 133099 need remove atom 133109 need remove atom 133111 need remove atom 133114 need remove atom 133116 need remove atom 133125 need remove atom 133127 need remove atom 133130 need remove atom 133207 need remove atom 133217 need remove atom 133219 need remove atom 133222 need remove atom 133224 need remove atom 133233 need remove atom 133235 need remove atom 133238 need remove atom 133315 need remove atom 133325 need remove atom 133327 need remove atom 133330 need remove atom 133332 need remove atom 133341 need remove atom 133343 need remove atom 133346 need remove atom 133423 need remove atom 133433 need remove atom 133435 need remove atom 133438 need remove atom 133440 need remove atom 133449 need remove atom 133451 need remove atom 133454 need remove atom 133531 need remove atom 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remove atom 134086 need remove atom 134088 need remove atom 134097 need remove atom 134099 need remove atom 134102 need remove atom 134179 need remove atom 134189 need remove atom 134191 need remove atom 134194 need remove atom 134196 need remove atom 134205 need remove atom 134207 need remove atom 134210 need remove atom 134287 need remove atom 134297 need remove atom 134299 need remove atom 134302 need remove atom 134304 need remove atom 134313 need remove atom 134315 need remove atom 134318 need remove atom 134395 need remove atom 134405 need remove atom 134407 need remove atom 134410 need remove atom 134412 need remove atom 134421 need remove atom 134423 need remove atom 134426 need remove atom 134503 need remove atom 134513 need remove atom 134515 need remove atom 134518 need remove atom 134520 need remove atom 134529 need remove atom 134531 need remove atom 134534 need remove atom 134611 need remove atom 134621 need remove atom 134623 need remove atom 134626 need remove atom 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remove atom 135179 need remove atom 135182 need remove atom 135259 need remove atom 135269 need remove atom 135271 need remove atom 135274 need remove atom 135276 need remove atom 135285 need remove atom 135287 need remove atom 135290 need remove atom 135367 need remove atom 135377 need remove atom 135379 need remove atom 135382 need remove atom 135384 need remove atom 135393 need remove atom 135395 need remove atom 135398 need remove atom 135475 need remove atom 135485 need remove atom 135487 need remove atom 135490 need remove atom 135492 need remove atom 135501 need remove atom 135503 need remove atom 135506 need remove atom 135583 need remove atom 135593 need remove atom 135595 need remove atom 135598 need remove atom 135600 need remove atom 135609 need remove atom 135611 need remove atom 135614 need remove atom 135691 need remove atom 135701 need remove atom 135703 need remove atom 135706 need remove atom 135708 need remove atom 135717 need remove atom 135719 need remove atom 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remove atom 136349 need remove atom 136351 need remove atom 136354 need remove atom 136356 need remove atom 136365 need remove atom 136367 need remove atom 136370 need remove atom 136447 need remove atom 136457 need remove atom 136459 need remove atom 136462 need remove atom 136464 need remove atom 136473 need remove atom 136475 need remove atom 136478 need remove atom 136555 need remove atom 136565 need remove atom 136567 need remove atom 136570 need remove atom 136572 need remove atom 136581 need remove atom 136583 need remove atom 136586 need remove atom 136663 need remove atom 136673 need remove atom 136675 need remove atom 136678 need remove atom 136680 need remove atom 136689 need remove atom 136691 need remove atom 136694 need remove atom 136771 need remove atom 136781 need remove atom 136783 need remove atom 136786 need remove atom 136788 need remove atom 136797 need remove atom 136799 need remove atom 136802 need remove atom 136879 need remove atom 136889 need remove atom 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remove atom 143050 need remove atom 143052 need remove atom 143061 need remove atom 143063 need remove atom 143066 need remove atom 143143 need remove atom 143153 need remove atom 143155 need remove atom 143158 need remove atom 143160 need remove atom 143169 need remove atom 143171 need remove atom 143174 need remove atom 143251 need remove atom 143261 need remove atom 143263 need remove atom 143266 need remove atom 143268 need remove atom 143277 need remove atom 143279 need remove atom 143282 need remove atom 143359 need remove atom 143369 need remove atom 143371 need remove atom 143374 need remove atom 143376 need remove atom 143385 need remove atom 143387 need remove atom 143390 need remove atom 143467 need remove atom 143477 need remove atom 143479 need remove atom 143482 need remove atom 143484 need remove atom 143493 need remove atom 143495 need remove atom 143498 need remove atom 143575 need remove atom 143585 need remove atom 143587 need remove atom 143590 need remove atom 143592 need remove atom 143601 need remove atom 143603 need remove atom 143606 need remove atom 143683 need remove atom 143693 need remove atom 143695 need remove atom 143698 need remove atom 143700 need remove atom 143709 need remove atom 143711 need remove atom 143714 need remove atom 143791 need remove atom 143801 need remove atom 143803 need remove atom 143806 need remove atom 143808 need remove atom 143817 need remove atom 143819 need remove atom 143822 [I] need removenum=1120 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.4876293642e-01 1.0996931164e-01 -3.3043742060e-01 dub= -3.6573240265e-01 1.0997167397e-01 3.3641122983e-01 duc= 3.4876393389e-01 -1.1136635713e-01 -3.3043848200e-01 [I] overall tilt ux= -7.1449533907e-01 2.3623334627e-06 6.6684865043e-01 uy= 9.9746355320e-07 -2.2133566877e-01 -1.0614047085e-06 [I] storedr[0]= -2.2244444544e-02 -7.0667055152e-04 -3.2300303609e-02 [I] originally 272160 atoms [I] insert 0 atoms [I] now 272160 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 272160 atoms [I] remove 1120 atoms [I] now 271040 atoms [I] NP=271040 n=271040 [I] ASSIGN finalcnfile = dipole_6.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_6.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_6.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 21:32:48 2023 CPU time spent: 23.048420 s {"realtime":11913.59,"usertime":31943.00,"systime":39.44,"memmax":209112,"memavg":0}