QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters' [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 = Tue May 16 11:38:09 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 12 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=1152 [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) = 0.0625 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 6.2500000000e-02 -0.0000000000e+00 -1.6666666667e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=3.581015e+01 pxpb=0.000000e+00 pypb=5.371522e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 614 need remove atom 618 need remove atom 622 need remove atom 626 need remove atom 627 need remove atom 630 need remove atom 631 need remove atom 634 need remove atom 635 need remove atom 638 need remove atom 639 need remove atom 642 need remove atom 643 need remove atom 646 need remove atom 647 need remove atom 650 need remove atom 651 need remove atom 654 need remove atom 655 need remove atom 658 need remove atom 659 need remove atom 662 need remove atom 663 need remove atom 666 need remove atom 667 need remove atom 670 need remove atom 671 need remove atom 674 need remove atom 675 need remove atom 678 need remove atom 679 need remove atom 682 need remove atom 683 need remove atom 687 need remove atom 691 need remove atom 695 [I] need removenum=36 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5399549390e-01 1.4201204938e-01 -2.4561763315e-01 dub= -4.7615003983e-01 1.4201522969e-01 2.5008791040e-01 duc= 4.5399678889e-01 -1.4383981828e-01 -2.4561842175e-01 [I] overall tilt ux= -9.3014553372e-01 3.1803134409e-06 4.9570554355e-01 uy= 1.2949954441e-06 -2.8585186766e-01 -7.8860637745e-07 [I] storedr[0]= -2.2174461097e-02 -9.2132689026e-04 -1.4275146897e-02 [I] originally 1152 atoms [I] insert 0 atoms [I] now 1152 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1152 atoms [I] remove 36 atoms [I] now 1116 atoms [I] NP=1116 n=1116 [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 = Tue May 16 11:38:10 2023 CPU time spent: 0.768071 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 = Tue May 16 11:42:15 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 12 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=1536 [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) = 0.0625 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.125 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 6.2500000000e-02 -0.0000000000e+00 -1.2500000000e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=3.581015e+01 pxpb=0.000000e+00 pypb=5.371522e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 818 need remove atom 822 need remove atom 826 need remove atom 830 need remove atom 834 need remove atom 835 need remove atom 838 need remove atom 839 need remove atom 842 need remove atom 843 need remove atom 846 need remove atom 847 need remove atom 850 need remove atom 851 need remove atom 854 need remove atom 855 need remove atom 858 need remove atom 859 need remove atom 862 need remove atom 863 need remove atom 866 need remove atom 867 need remove atom 870 need remove atom 871 need remove atom 874 need remove atom 875 need remove atom 878 need remove atom 879 need remove atom 882 need remove atom 883 need remove atom 886 need remove atom 887 need remove atom 890 need remove atom 891 need remove atom 894 need remove atom 895 need remove atom 898 need remove atom 899 need remove atom 902 need remove atom 903 need remove atom 906 need remove atom 907 need remove atom 910 need remove atom 911 need remove atom 915 need remove atom 919 need remove atom 923 need remove atom 927 [I] need removenum=48 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5399549390e-01 1.4201204938e-01 -2.4561763315e-01 dub= -4.7615003983e-01 1.4201522969e-01 2.5008791040e-01 duc= 4.5399678889e-01 -1.4383981828e-01 -2.4561842175e-01 [I] overall tilt ux= -9.3014553372e-01 3.1803134409e-06 4.9570554355e-01 uy= 1.2949954441e-06 -2.8585186766e-01 -7.8860637745e-07 [I] storedr[0]= -2.2174461097e-02 -9.2132689026e-04 -1.4275146897e-02 [I] originally 1536 atoms [I] insert 0 atoms [I] now 1536 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1536 atoms [I] remove 48 atoms [I] now 1488 atoms [I] NP=1488 n=1488 [I] ASSIGN finalcnfile = dipole_1.1.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.1.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.1.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 = Tue May 16 11:42:16 2023 CPU time spent: 1.000662 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 = Tue May 16 11:45:30 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 9 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 14 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=2016 [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) = 0.055555555555556 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.125 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 5.5555555556e-02 -0.0000000000e+00 -1.2500000000e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=4.028642e+01 pxpb=0.000000e+00 pypb=6.266776e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 960 need remove atom 961 need remove atom 964 need remove atom 965 need remove atom 968 need remove atom 969 need remove atom 972 need remove atom 973 need remove atom 976 need remove atom 977 need remove atom 980 need remove atom 981 need remove atom 984 need remove atom 985 need remove atom 988 need remove atom 989 need remove atom 992 need remove atom 993 need remove atom 996 need remove atom 997 need remove atom 1000 need remove atom 1001 need remove atom 1004 need remove atom 1005 need remove atom 1008 need remove atom 1009 need remove atom 1012 need remove atom 1013 need remove atom 1016 need remove atom 1017 need remove atom 1020 need remove atom 1021 need remove atom 1024 need remove atom 1025 need remove atom 1028 need remove atom 1029 need remove atom 1032 need remove atom 1033 need remove atom 1036 need remove atom 1037 need remove atom 1040 need remove atom 1041 need remove atom 1044 need remove atom 1045 need remove atom 1048 need remove atom 1049 need remove atom 1052 need remove atom 1053 need remove atom 1056 need remove atom 1057 need remove atom 1060 need remove atom 1061 need remove atom 1064 need remove atom 1065 need remove atom 1068 need remove atom 1069 [I] need removenum=56 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5808870975e-01 1.4057897818e-01 -2.4953284625e-01 dub= -4.8065475421e-01 1.4058263751e-01 2.5458097599e-01 duc= 4.5808996649e-01 -1.4250958799e-01 -2.4953364064e-01 [I] overall tilt ux= -9.3874346397e-01 3.6593279635e-06 5.0411382224e-01 uy= 1.2567415413e-06 -2.8308856617e-01 -7.9439067155e-07 [I] storedr[0]= -2.1766189994e-02 -9.7106098448e-04 -1.1110265500e-02 [I] originally 2016 atoms [I] insert 0 atoms [I] now 2016 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2016 atoms [I] remove 56 atoms [I] now 1960 atoms [I] NP=1960 n=1960 [I] ASSIGN finalcnfile = dipole_1.2.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.2.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.2.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 = Tue May 16 11:45:31 2023 CPU time spent: 1.267767 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 = Tue May 16 11:50:16 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 15 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=2400 [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) = 0.05 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.125 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 5.0000000000e-02 -0.0000000000e+00 -1.2500000000e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=4.476269e+01 pxpb=0.000000e+00 pypb=6.714403e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1266 need remove atom 1267 need remove atom 1270 need remove atom 1271 need remove atom 1274 need remove atom 1275 need remove atom 1278 need remove atom 1279 need remove atom 1282 need remove atom 1283 need remove atom 1286 need remove atom 1287 need remove atom 1290 need remove atom 1291 need remove atom 1294 need remove atom 1295 need remove atom 1298 need remove atom 1299 need remove atom 1302 need remove atom 1303 need remove atom 1306 need remove atom 1307 need remove atom 1310 need remove atom 1311 need remove atom 1314 need remove atom 1315 need remove atom 1318 need remove atom 1319 need remove atom 1322 need remove atom 1323 need remove atom 1326 need remove atom 1327 need remove atom 1330 need remove atom 1331 need remove atom 1334 need remove atom 1335 need remove atom 1338 need remove atom 1339 need remove atom 1342 need remove atom 1343 need remove atom 1346 need remove atom 1347 need remove atom 1350 need remove atom 1351 need remove atom 1354 need remove atom 1355 need remove atom 1358 need remove atom 1359 need remove atom 1362 need remove atom 1363 need remove atom 1366 need remove atom 1367 need remove atom 1370 need remove atom 1371 need remove atom 1374 need remove atom 1375 need remove atom 1379 need remove atom 1383 need remove atom 1387 need remove atom 1391 [I] need removenum=60 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5399549390e-01 1.4201204938e-01 -2.4561763315e-01 dub= -4.7615003983e-01 1.4201522969e-01 2.5008791040e-01 duc= 4.5399678889e-01 -1.4383981828e-01 -2.4561842175e-01 [I] overall tilt ux= -9.3014553372e-01 3.1803134409e-06 4.9570554355e-01 uy= 1.2949954441e-06 -2.8585186766e-01 -7.8860637878e-07 [I] storedr[0]= -1.9956963935e-02 -9.1977529823e-04 -1.1092940414e-02 [I] originally 2400 atoms [I] insert 0 atoms [I] now 2400 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2400 atoms [I] remove 60 atoms [I] now 2340 atoms [I] NP=2340 n=2340 [I] ASSIGN finalcnfile = dipole_1.3.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.3.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.3.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 = Tue May 16 11:50:17 2023 CPU time spent: 1.502606 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 = Tue May 16 11:54:34 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 15 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=3000 [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) = 0.05 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.1 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 5.0000000000e-02 -0.0000000000e+00 -1.0000000000e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=4.476269e+01 pxpb=0.000000e+00 pypb=6.714403e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1582 need remove atom 1583 need remove atom 1586 need remove atom 1587 need remove atom 1590 need remove atom 1591 need remove atom 1594 need remove atom 1595 need remove atom 1598 need remove atom 1599 need remove atom 1602 need remove atom 1603 need remove atom 1606 need remove atom 1607 need remove atom 1610 need remove atom 1611 need remove atom 1614 need remove atom 1615 need remove atom 1618 need remove atom 1619 need remove atom 1622 need remove atom 1623 need remove atom 1626 need remove atom 1627 need remove atom 1630 need remove atom 1631 need remove atom 1634 need remove atom 1635 need remove atom 1638 need remove atom 1639 need remove atom 1642 need remove atom 1643 need remove atom 1646 need remove atom 1647 need remove atom 1650 need remove atom 1651 need remove atom 1654 need remove atom 1655 need remove atom 1658 need remove atom 1659 need remove atom 1662 need remove atom 1663 need remove atom 1666 need remove atom 1667 need remove atom 1670 need remove atom 1671 need remove atom 1674 need remove atom 1675 need remove atom 1678 need remove atom 1679 need remove atom 1682 need remove atom 1683 need remove atom 1686 need remove atom 1687 need remove atom 1690 need remove atom 1691 need remove atom 1694 need remove atom 1695 need remove atom 1698 need remove atom 1699 need remove atom 1702 need remove atom 1703 need remove atom 1706 need remove atom 1707 need remove atom 1710 need remove atom 1711 need remove atom 1714 need remove atom 1715 need remove atom 1718 need remove atom 1719 need remove atom 1723 need remove atom 1727 need remove atom 1731 need remove atom 1735 need remove atom 1739 [I] need removenum=75 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5399549390e-01 1.4201204938e-01 -2.4561763315e-01 dub= -4.7615003983e-01 1.4201522969e-01 2.5008791040e-01 duc= 4.5399678889e-01 -1.4383981828e-01 -2.4561842175e-01 [I] overall tilt ux= -9.3014553372e-01 3.1803134409e-06 4.9570554355e-01 uy= 1.2949954441e-06 -2.8585186766e-01 -7.8860637878e-07 [I] storedr[0]= -1.9956963935e-02 -9.1977529823e-04 -1.1092940414e-02 [I] originally 3000 atoms [I] insert 0 atoms [I] now 3000 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3000 atoms [I] remove 75 atoms [I] now 2925 atoms [I] NP=2925 n=2925 [I] ASSIGN finalcnfile = dipole_1.4.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.4.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.4.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 = Tue May 16 11:54:37 2023 CPU time spent: 1.850863 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 = Tue May 16 12:00:19 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 11 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 16 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=3520 [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) = 0.045454545454545 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.1 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 4.5454545455e-02 -0.0000000000e+00 -1.0000000000e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=4.923896e+01 pxpb=0.000000e+00 pypb=7.162030e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1681 need remove atom 1685 need remove atom 1689 need remove atom 1693 need remove atom 1697 need remove atom 1700 need remove atom 1701 need remove atom 1704 need remove atom 1705 need remove atom 1708 need remove atom 1709 need remove atom 1712 need remove atom 1713 need remove atom 1716 need remove atom 1717 need remove atom 1720 need remove atom 1721 need remove atom 1724 need remove atom 1725 need remove atom 1728 need remove atom 1729 need remove atom 1732 need remove atom 1733 need remove atom 1736 need remove atom 1737 need remove atom 1740 need remove atom 1741 need remove atom 1744 need remove atom 1745 need remove atom 1748 need remove atom 1749 need remove atom 1752 need remove atom 1753 need remove atom 1756 need remove atom 1757 need remove atom 1760 need remove atom 1761 need remove atom 1764 need remove atom 1765 need remove atom 1768 need remove atom 1769 need remove atom 1772 need remove atom 1773 need remove atom 1776 need remove atom 1777 need remove atom 1780 need remove atom 1781 need remove atom 1784 need remove atom 1785 need remove atom 1788 need remove atom 1789 need remove atom 1792 need remove atom 1793 need remove atom 1796 need remove atom 1797 need remove atom 1800 need remove atom 1801 need remove atom 1804 need remove atom 1805 need remove atom 1808 need remove atom 1809 need remove atom 1812 need remove atom 1813 need remove atom 1816 need remove atom 1817 need remove atom 1820 need remove atom 1821 need remove atom 1824 need remove atom 1825 need remove atom 1828 need remove atom 1829 need remove atom 1832 need remove atom 1833 need remove atom 1836 need remove atom 1837 need remove atom 1840 need remove atom 1844 need remove atom 1848 need remove atom 1852 need remove atom 1856 [I] need removenum=80 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5041020480e-01 1.4322158705e-01 -2.4226424134e-01 dub= -4.7216376738e-01 1.4322431943e-01 2.4623447596e-01 duc= 4.5041153039e-01 -1.4496194195e-01 -2.4226502371e-01 [I] overall tilt ux= -9.2257397218e-01 2.7323765952e-06 4.8849871730e-01 uy= 1.3255881018e-06 -2.8818352900e-01 -7.8236870660e-07 [I] storedr[0]= -1.8408763898e-02 -8.7585239909e-04 -1.0965534900e-02 [I] originally 3520 atoms [I] insert 0 atoms [I] now 3520 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3520 atoms [I] remove 80 atoms [I] now 3440 atoms [I] NP=3440 n=3440 [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 = Tue May 16 12:00:21 2023 CPU time spent: 2.185902 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 = Tue May 16 12:07:12 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 12 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 18 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=4320 [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) = 0.041666666666667 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.1 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 4.1666666667e-02 -0.0000000000e+00 -1.0000000000e-01 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=5.371522e+01 pxpb=0.000000e+00 pypb=8.057284e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2262 need remove atom 2263 need remove atom 2266 need remove atom 2267 need remove atom 2270 need remove atom 2271 need remove atom 2274 need remove atom 2275 need remove atom 2278 need remove atom 2279 need remove atom 2282 need remove atom 2283 need remove atom 2286 need remove atom 2287 need remove atom 2290 need remove atom 2291 need remove atom 2294 need remove atom 2295 need remove atom 2298 need remove atom 2299 need remove atom 2302 need remove atom 2303 need remove atom 2306 need remove atom 2307 need remove atom 2310 need remove atom 2311 need remove atom 2314 need remove atom 2315 need remove atom 2318 need remove atom 2319 need remove atom 2322 need remove atom 2323 need remove atom 2326 need remove atom 2327 need remove atom 2330 need remove atom 2331 need remove atom 2334 need remove atom 2335 need remove atom 2338 need remove atom 2339 need remove atom 2342 need remove atom 2343 need remove atom 2346 need remove atom 2347 need remove atom 2350 need remove atom 2351 need remove atom 2354 need remove atom 2355 need remove atom 2358 need remove atom 2359 need remove atom 2362 need remove atom 2363 need remove atom 2366 need remove atom 2367 need remove atom 2370 need remove atom 2371 need remove atom 2374 need remove atom 2375 need remove atom 2378 need remove atom 2379 need remove atom 2382 need remove atom 2383 need remove atom 2386 need remove atom 2387 need remove atom 2390 need remove atom 2391 need remove atom 2394 need remove atom 2395 need remove atom 2398 need remove atom 2399 need remove atom 2402 need remove atom 2403 need remove atom 2406 need remove atom 2407 need remove atom 2410 need remove atom 2411 need remove atom 2414 need remove atom 2415 need remove atom 2418 need remove atom 2419 need remove atom 2422 need remove atom 2423 need remove atom 2426 need remove atom 2427 need remove atom 2430 need remove atom 2431 need remove atom 2434 need remove atom 2435 need remove atom 2438 need remove atom 2439 [I] need removenum=90 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5399549390e-01 1.4201204938e-01 -2.4561763315e-01 dub= -4.7615003983e-01 1.4201522969e-01 2.5008791040e-01 duc= 4.5399678889e-01 -1.4383981828e-01 -2.4561842175e-01 [I] overall tilt ux= -9.3014553372e-01 3.1803134402e-06 4.9570554355e-01 uy= 1.2949954450e-06 -2.8585186766e-01 -7.8860637812e-07 [I] storedr[0]= -1.8477319925e-02 -9.1864083485e-04 -8.9284704873e-03 [I] originally 4320 atoms [I] insert 0 atoms [I] now 4320 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 4320 atoms [I] remove 90 atoms [I] now 4230 atoms [I] NP=4230 n=4230 [I] ASSIGN finalcnfile = dipole_1.6.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.6.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.6.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 = Tue May 16 12:07:15 2023 CPU time spent: 2.697587 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 = Tue May 16 12:18:50 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 13 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 20 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 6 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=6240 [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) = 0.038461538461538 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 3.8461538462e-02 -0.0000000000e+00 -8.3333333333e-02 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=5.819149e+01 pxpb=0.000000e+00 pypb=8.952537e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3001 need remove atom 3005 need remove atom 3009 need remove atom 3013 need remove atom 3017 need remove atom 3021 need remove atom 3024 need remove atom 3025 need remove atom 3028 need remove atom 3029 need remove atom 3032 need remove atom 3033 need remove atom 3036 need remove atom 3037 need remove atom 3040 need remove atom 3041 need remove atom 3044 need remove atom 3045 need remove atom 3048 need remove atom 3049 need remove atom 3052 need remove atom 3053 need remove atom 3056 need remove atom 3057 need remove atom 3060 need remove atom 3061 need remove atom 3064 need remove atom 3065 need remove atom 3068 need remove atom 3069 need remove atom 3072 need remove atom 3073 need remove atom 3076 need remove atom 3077 need remove atom 3080 need remove atom 3081 need remove atom 3084 need remove atom 3085 need remove atom 3088 need remove atom 3089 need remove atom 3092 need remove atom 3093 need remove atom 3096 need remove atom 3097 need remove atom 3100 need remove atom 3101 need remove atom 3104 need remove atom 3105 need remove atom 3108 need remove atom 3109 need remove atom 3112 need remove atom 3113 need remove atom 3116 need remove atom 3117 need remove atom 3120 need remove atom 3121 need remove atom 3124 need remove atom 3125 need remove atom 3128 need remove atom 3129 need remove atom 3132 need remove atom 3133 need remove atom 3136 need remove atom 3137 need remove atom 3140 need remove atom 3141 need remove atom 3144 need remove atom 3145 need remove atom 3148 need remove atom 3149 need remove atom 3152 need remove atom 3153 need remove atom 3156 need remove atom 3157 need remove atom 3160 need remove atom 3161 need remove atom 3164 need remove atom 3165 need remove atom 3168 need remove atom 3169 need remove atom 3172 need remove atom 3173 need remove atom 3176 need remove atom 3177 need remove atom 3180 need remove atom 3181 need remove atom 3184 need remove atom 3185 need remove atom 3188 need remove atom 3189 need remove atom 3192 need remove atom 3193 need remove atom 3196 need remove atom 3197 need remove atom 3200 need remove atom 3201 need remove atom 3204 need remove atom 3205 need remove atom 3208 need remove atom 3209 need remove atom 3212 need remove atom 3213 need remove atom 3216 need remove atom 3217 need remove atom 3220 need remove atom 3221 need remove atom 3224 need remove atom 3225 need remove atom 3228 need remove atom 3229 need remove atom 3232 need remove atom 3233 need remove atom 3236 need remove atom 3237 need remove atom 3240 need remove atom 3244 need remove atom 3248 need remove atom 3252 need remove atom 3256 need remove atom 3260 [I] need removenum=120 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5686142446e-01 1.4101441532e-01 -2.4834892416e-01 dub= -4.7930948591e-01 1.4101793494e-01 2.5322307884e-01 duc= 4.5686269304e-01 -1.4291384396e-01 -2.4834971697e-01 [I] overall tilt ux= -9.3617091036e-01 3.5196227314e-06 5.0157200300e-01 uy= 1.2685816259e-06 -2.8392825928e-01 -7.9281464394e-07 [I] storedr[0]= -1.8374102305e-02 -9.5377278027e-04 -7.3403865709e-03 [I] originally 6240 atoms [I] insert 0 atoms [I] now 6240 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 6240 atoms [I] remove 120 atoms [I] now 6120 atoms [I] NP=6120 n=6120 [I] ASSIGN finalcnfile = dipole_1.7.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.7.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.7.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 = Tue May 16 12:18:56 2023 CPU time spent: 3.856140 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 = Tue May 16 12:25:27 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 14 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 21 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 6 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=7056 [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) = 0.035714285714286 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 3.5714285714e-02 -0.0000000000e+00 -8.3333333333e-02 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=6.266776e+01 pxpb=0.000000e+00 pypb=9.400164e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3650 need remove atom 3654 need remove atom 3658 need remove atom 3662 need remove atom 3666 need remove atom 3670 need remove atom 3674 need remove atom 3675 need remove atom 3678 need remove atom 3679 need remove atom 3682 need remove atom 3683 need remove atom 3686 need remove atom 3687 need remove atom 3690 need remove atom 3691 need remove atom 3694 need remove atom 3695 need remove atom 3698 need remove atom 3699 need remove atom 3702 need remove atom 3703 need remove atom 3706 need remove atom 3707 need remove atom 3710 need remove atom 3711 need remove atom 3714 need remove atom 3715 need remove atom 3718 need remove atom 3719 need remove atom 3722 need remove atom 3723 need remove atom 3726 need remove atom 3727 need remove atom 3730 need remove atom 3731 need remove atom 3734 need remove atom 3735 need remove atom 3738 need remove atom 3739 need remove atom 3742 need remove atom 3743 need remove atom 3746 need remove atom 3747 need remove atom 3750 need remove atom 3751 need remove atom 3754 need remove atom 3755 need remove atom 3758 need remove atom 3759 need remove atom 3762 need remove atom 3763 need remove atom 3766 need remove atom 3767 need remove atom 3770 need remove atom 3771 need remove atom 3774 need remove atom 3775 need remove atom 3778 need remove atom 3779 need remove atom 3782 need remove atom 3783 need remove atom 3786 need remove atom 3787 need remove atom 3790 need remove atom 3791 need remove atom 3794 need remove atom 3795 need remove atom 3798 need remove atom 3799 need remove atom 3802 need remove atom 3803 need remove atom 3806 need remove atom 3807 need remove atom 3810 need remove atom 3811 need remove atom 3814 need remove atom 3815 need remove atom 3818 need remove atom 3819 need remove atom 3822 need remove atom 3823 need remove atom 3826 need remove atom 3827 need remove atom 3830 need remove atom 3831 need remove atom 3834 need remove atom 3835 need remove atom 3838 need remove atom 3839 need remove atom 3842 need remove atom 3843 need remove atom 3846 need remove atom 3847 need remove atom 3850 need remove atom 3851 need remove atom 3854 need remove atom 3855 need remove atom 3858 need remove atom 3859 need remove atom 3862 need remove atom 3863 need remove atom 3866 need remove atom 3867 need remove atom 3870 need remove atom 3871 need remove atom 3874 need remove atom 3875 need remove atom 3878 need remove atom 3879 need remove atom 3882 need remove atom 3883 need remove atom 3886 need remove atom 3887 need remove atom 3890 need remove atom 3891 need remove atom 3894 need remove atom 3895 need remove atom 3898 need remove atom 3899 need remove atom 3902 need remove atom 3903 need remove atom 3906 need remove atom 3907 need remove atom 3910 need remove atom 3911 [I] need removenum=126 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5399549390e-01 1.4201204938e-01 -2.4561763315e-01 dub= -4.7615003983e-01 1.4201522969e-01 2.5008791040e-01 duc= 4.5399678889e-01 -1.4383981828e-01 -2.4561842175e-01 [I] overall tilt ux= -9.3014553372e-01 3.1803134402e-06 4.9570554355e-01 uy= 1.2949954431e-06 -2.8585186766e-01 -7.8860637809e-07 [I] storedr[0]= -1.7420119288e-02 -9.1779237462e-04 -7.3644200289e-03 [I] originally 7056 atoms [I] insert 0 atoms [I] now 7056 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7056 atoms [I] remove 126 atoms [I] now 6930 atoms [I] NP=6930 n=6930 [I] ASSIGN finalcnfile = dipole_1.9.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.9.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.9.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 = Tue May 16 12:25:32 2023 CPU time spent: 4.426719 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 = Tue May 16 12:32:38 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 0 [I] ASSIGN makecnspec(3) = 15 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 22 [I] ASSIGN makecnspec(8) = 0 [I] ASSIGN makecnspec(9) = 0 [I] ASSIGN makecnspec(10) = 1 [I] ASSIGN makecnspec(11) = 6 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 0 -1 1 0 0 0 1]; basis=[ 0.5 0 0.5 0 0 0.5 0.5 0 0 1 0 0.5 0.5 0 2 0 0 0 0 3 ]; [I] makecn: _NP=7920 [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) = 0.033333333333333 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [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= 3.3333333333e-02 -0.0000000000e+00 -8.3333333333e-02 b= 2.2381343487e+00 0.0000000000e+00 -1.5825999752e+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=2.2381343486949 by=0 pxpa=6.714403e+01 pxpb=0.000000e+00 pypb=9.847791e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3840 need remove atom 3841 need remove atom 3844 need remove atom 3845 need remove atom 3848 need remove atom 3849 need remove atom 3852 need remove atom 3853 need remove atom 3856 need remove atom 3857 need remove atom 3860 need remove atom 3861 need remove atom 3864 need remove atom 3865 need remove atom 3868 need remove atom 3869 need remove atom 3872 need remove atom 3873 need remove atom 3876 need remove atom 3877 need remove atom 3880 need remove atom 3881 need remove atom 3884 need remove atom 3885 need remove atom 3888 need remove atom 3889 need remove atom 3892 need remove atom 3893 need remove atom 3896 need remove atom 3897 need remove atom 3900 need remove atom 3901 need remove atom 3904 need remove atom 3905 need remove atom 3908 need remove atom 3909 need remove atom 3912 need remove atom 3913 need remove atom 3916 need remove atom 3917 need remove atom 3920 need remove atom 3921 need remove atom 3924 need remove atom 3925 need remove atom 3928 need remove atom 3929 need remove atom 3932 need remove atom 3933 need remove atom 3936 need remove atom 3937 need remove atom 3940 need remove atom 3941 need remove atom 3944 need remove atom 3945 need remove atom 3948 need remove atom 3949 need remove atom 3952 need remove atom 3953 need remove atom 3956 need remove atom 3957 need remove atom 3960 need remove atom 3961 need remove atom 3964 need remove atom 3965 need remove atom 3968 need remove atom 3969 need remove atom 3972 need remove atom 3973 need remove atom 3976 need remove atom 3977 need remove atom 3980 need remove atom 3981 need remove atom 3984 need remove atom 3985 need remove atom 3988 need remove atom 3989 need remove atom 3992 need remove atom 3993 need remove atom 3996 need remove atom 3997 need remove atom 4000 need remove atom 4001 need remove atom 4004 need remove atom 4005 need remove atom 4008 need remove atom 4009 need remove atom 4012 need remove atom 4013 need remove atom 4016 need remove atom 4017 need remove atom 4020 need remove atom 4021 need remove atom 4024 need remove atom 4025 need remove atom 4028 need remove atom 4029 need remove atom 4032 need remove atom 4033 need remove atom 4036 need remove atom 4037 need remove atom 4040 need remove atom 4041 need remove atom 4044 need remove atom 4045 need remove atom 4048 need remove atom 4049 need remove atom 4052 need remove atom 4053 need remove atom 4056 need remove atom 4057 need remove atom 4060 need remove atom 4061 need remove atom 4064 need remove atom 4065 need remove atom 4068 need remove atom 4069 need remove atom 4072 need remove atom 4073 need remove atom 4076 need remove atom 4077 need remove atom 4080 need remove atom 4081 need remove atom 4084 need remove atom 4085 need remove atom 4088 need remove atom 4089 need remove atom 4092 need remove atom 4093 need remove atom 4096 need remove atom 4097 need remove atom 4100 need remove atom 4101 [I] need removenum=132 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 4.5138820589e-01 1.4289594112e-01 -2.4317216647e-01 dub= -4.7325474132e-01 1.4289879810e-01 2.4727819225e-01 duc= 4.5138952340e-01 -1.4465989775e-01 -2.4317295065e-01 [I] overall tilt ux= -9.2464294721e-01 2.8569719863e-06 4.9045035873e-01 uy= 1.3175140742e-06 -2.8755583888e-01 -7.8417233965e-07 [I] storedr[0]= -1.6565546803e-02 -8.8567909734e-04 -7.3458208767e-03 [I] originally 7920 atoms [I] insert 0 atoms [I] now 7920 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7920 atoms [I] remove 132 atoms [I] now 7788 atoms [I] NP=7788 n=7788 [I] ASSIGN finalcnfile = dipole_2.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.0.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 = Tue May 16 12:32:43 2023 CPU time spent: 4.984905 s /usr/local/lib/python3.8/dist-packages/convergence/zero_rc.py:212: RuntimeWarning: invalid value encountered in scalar divide fdb = (self.fd - self.fb) / (self.d - self.b) {"realtime":3921.69,"usertime":7656.91,"systime":104.29,"memmax":95148,"memavg":0}