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 = Wed May 24 15:29:40 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 11 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=1320 [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) = 0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28113258894964 [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 1.6666666667e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=3.188194e+01 pxpb=0.000000e+00 pypb=4.959666e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 697 need remove atom 699 need remove atom 701 need remove atom 703 need remove atom 705 need remove atom 707 need remove atom 709 need remove atom 711 need remove atom 713 need remove atom 715 need remove atom 717 need remove atom 719 need remove atom 721 need remove atom 723 need remove atom 725 need remove atom 727 need remove atom 729 need remove atom 731 need remove atom 733 need remove atom 735 need remove atom 737 need remove atom 739 need remove atom 741 need remove atom 743 need remove atom 745 need remove atom 747 need remove atom 749 need remove atom 751 need remove atom 753 need remove atom 755 need remove atom 757 need remove atom 761 need remove atom 765 [I] need removenum=33 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2625409032e-01 1.0015968206e-01 3.5546411952e-01 dub= -3.4232395690e-01 1.0016228549e-01 -3.6265625524e-01 duc= 3.2625498536e-01 -1.0153458967e-01 3.5546525113e-01 [I] overall tilt ux= -6.6857804722e-01 2.6034279456e-06 -7.1812037476e-01 uy= 8.9504071143e-07 -2.0169427173e-01 1.1316091988e-06 [I] storedr[0]= -1.3257086386e-02 6.4663592406e-02 1.5586364191e-02 [I] originally 1320 atoms [I] insert 0 atoms [I] now 1320 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1320 atoms [I] remove 33 atoms [I] now 1287 atoms [I] NP=1287 n=1287 [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 24 15:29:41 2023 CPU time spent: 0.841611 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 24 15:34:32 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 11 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 12 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=1584 [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) = 0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28113258894964 [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 1.6666666667e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=3.507013e+01 pxpb=0.000000e+00 pypb=5.410544e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 756 need remove atom 760 need remove atom 764 need remove atom 768 need remove atom 770 need remove atom 772 need remove atom 774 need remove atom 776 need remove atom 778 need remove atom 780 need remove atom 782 need remove atom 784 need remove atom 786 need remove atom 788 need remove atom 790 need remove atom 792 need remove atom 794 need remove atom 796 need remove atom 798 need remove atom 800 need remove atom 802 need remove atom 804 need remove atom 806 need remove atom 808 need remove atom 810 need remove atom 812 need remove atom 814 need remove atom 816 need remove atom 818 need remove atom 820 need remove atom 822 need remove atom 824 need remove atom 826 need remove atom 830 need remove atom 834 need remove atom 838 [I] need removenum=36 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2559850946e-01 1.0039242673e-01 3.5419820682e-01 dub= -3.4160566677e-01 1.0039495578e-01 -3.6120441552e-01 duc= 3.2559941085e-01 -1.0175065977e-01 3.5419933677e-01 [I] overall tilt ux= -6.6720417624e-01 2.5290526151e-06 -7.1540262234e-01 uy= 9.0138450809e-07 -2.0214308650e-01 1.1299449325e-06 [I] storedr[0]= -1.2859503504e-02 5.8716933598e-02 1.4059657362e-02 [I] originally 1584 atoms [I] insert 0 atoms [I] now 1584 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1584 atoms [I] remove 36 atoms [I] now 1548 atoms [I] NP=1548 n=1548 [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 = Wed May 24 15:34:33 2023 CPU time spent: 0.999102 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 24 15:40:54 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 12 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 13 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=1872 [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) = 0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28113258894964 [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 1.6666666667e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=3.825833e+01 pxpb=0.000000e+00 pypb=5.861423e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 975 need remove atom 979 need remove atom 983 need remove atom 985 need remove atom 987 need remove atom 989 need remove atom 991 need remove atom 993 need remove atom 995 need remove atom 997 need remove atom 999 need remove atom 1001 need remove atom 1003 need remove atom 1005 need remove atom 1007 need remove atom 1009 need remove atom 1011 need remove atom 1013 need remove atom 1015 need remove atom 1017 need remove atom 1019 need remove atom 1021 need remove atom 1023 need remove atom 1025 need remove atom 1027 need remove atom 1029 need remove atom 1031 need remove atom 1033 need remove atom 1035 need remove atom 1037 need remove atom 1039 need remove atom 1041 need remove atom 1043 need remove atom 1045 need remove atom 1047 need remove atom 1049 need remove atom 1051 need remove atom 1053 need remove atom 1055 [I] need removenum=39 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2504358268e-01 1.0058790567e-01 3.5313208928e-01 dub= -3.4099618736e-01 1.0059037068e-01 -3.5998128467e-01 duc= 3.2504448934e-01 -1.0193211769e-01 3.5313321773e-01 [I] overall tilt ux= -6.6603977004e-01 2.4650123559e-06 -7.1311337396e-01 uy= 9.0665538188e-07 -2.0252002336e-01 1.1284492948e-06 [I] storedr[0]= -1.2500251751e-02 5.3752325059e-02 1.2781580281e-02 [I] originally 1872 atoms [I] insert 0 atoms [I] now 1872 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1872 atoms [I] remove 39 atoms [I] now 1833 atoms [I] NP=1833 n=1833 [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 = Wed May 24 15:40:56 2023 CPU time spent: 1.164941 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 24 15:45:48 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 13 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 14 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=2184 [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) = 0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28113258894964 [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 1.6666666667e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=4.144652e+01 pxpb=0.000000e+00 pypb=6.312302e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1056 need remove atom 1058 need remove atom 1060 need remove atom 1062 need remove atom 1064 need remove atom 1066 need remove atom 1068 need remove atom 1070 need remove atom 1072 need remove atom 1074 need remove atom 1076 need remove atom 1078 need remove atom 1080 need remove atom 1082 need remove atom 1084 need remove atom 1086 need remove atom 1088 need remove atom 1090 need remove atom 1092 need remove atom 1094 need remove atom 1096 need remove atom 1098 need remove atom 1100 need remove atom 1102 need remove atom 1104 need remove atom 1106 need remove atom 1108 need remove atom 1110 need remove atom 1112 need remove atom 1114 need remove atom 1116 need remove atom 1118 need remove atom 1120 need remove atom 1122 need remove atom 1124 need remove atom 1126 need remove atom 1128 need remove atom 1130 need remove atom 1132 need remove atom 1134 need remove atom 1136 need remove atom 1138 [I] need removenum=42 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2456779684e-01 1.0075438158e-01 3.5222193839e-01 dub= -3.4047257034e-01 1.0075679092e-01 -3.5893679139e-01 duc= 3.2456870794e-01 -1.0208663997e-01 3.5222306549e-01 [I] overall tilt ux= -6.6504036718e-01 2.4093352686e-06 -7.1115872978e-01 uy= 9.1110211753e-07 -2.0284102155e-01 1.1271048103e-06 [I] storedr[0]= -1.2177873947e-02 4.9546996350e-02 1.1693890793e-02 [I] originally 2184 atoms [I] insert 0 atoms [I] now 2184 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2184 atoms [I] remove 42 atoms [I] now 2142 atoms [I] NP=2142 n=2142 [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 = Wed May 24 15:45:50 2023 CPU time spent: 1.451262 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 24 15:53:15 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 14 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 15 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=2520 [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) = 0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28113258894964 [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 1.6666666667e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=4.463471e+01 pxpb=0.000000e+00 pypb=6.763180e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1309 need remove atom 1311 need remove atom 1313 need remove atom 1315 need remove atom 1317 need remove atom 1319 need remove atom 1321 need remove atom 1323 need remove atom 1325 need remove atom 1327 need remove atom 1329 need remove atom 1331 need remove atom 1333 need remove atom 1335 need remove atom 1337 need remove atom 1339 need remove atom 1341 need remove atom 1343 need remove atom 1345 need remove atom 1347 need remove atom 1349 need remove atom 1351 need remove atom 1353 need remove atom 1355 need remove atom 1357 need remove atom 1359 need remove atom 1361 need remove atom 1363 need remove atom 1365 need remove atom 1367 need remove atom 1369 need remove atom 1371 need remove atom 1373 need remove atom 1375 need remove atom 1377 need remove atom 1379 need remove atom 1381 need remove atom 1383 need remove atom 1385 need remove atom 1387 need remove atom 1389 need remove atom 1391 need remove atom 1393 need remove atom 1397 need remove atom 1401 [I] need removenum=45 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2415535827e-01 1.0089784809e-01 3.5143586879e-01 dub= -3.4001788816e-01 1.0090020860e-01 -3.5803448035e-01 duc= 3.2415627317e-01 -1.0221979472e-01 3.5143699468e-01 [I] overall tilt ux= -6.6417324643e-01 2.3605096865e-06 -7.0947034913e-01 uy= 9.1490257292e-07 -2.0311764282e-01 1.1258937224e-06 [I] storedr[0]= -1.1889126243e-02 4.5940397073e-02 1.0755675523e-02 [I] originally 2520 atoms [I] insert 0 atoms [I] now 2520 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2520 atoms [I] remove 45 atoms [I] now 2475 atoms [I] NP=2475 n=2475 [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 = Wed May 24 15:53:17 2023 CPU time spent: 1.620106 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 24 15:57:31 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 15 [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) = 0 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=3840 [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) = 0.125 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28113258894964 [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 1.2500000000e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=4.782291e+01 pxpb=0.000000e+00 pypb=7.214059e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1856 need remove atom 1860 need remove atom 1864 need remove atom 1868 need remove atom 1872 need remove atom 1874 need remove atom 1876 need remove atom 1878 need remove atom 1880 need remove atom 1882 need remove atom 1884 need remove atom 1886 need remove atom 1888 need remove atom 1890 need remove atom 1892 need remove atom 1894 need remove atom 1896 need remove atom 1898 need remove atom 1900 need remove atom 1902 need remove atom 1904 need remove atom 1906 need remove atom 1908 need remove atom 1910 need remove atom 1912 need remove atom 1914 need remove atom 1916 need remove atom 1918 need remove atom 1920 need remove atom 1922 need remove atom 1924 need remove atom 1926 need remove atom 1928 need remove atom 1930 need remove atom 1932 need remove atom 1934 need remove atom 1936 need remove atom 1938 need remove atom 1940 need remove atom 1942 need remove atom 1944 need remove atom 1946 need remove atom 1948 need remove atom 1950 need remove atom 1952 need remove atom 1954 need remove atom 1956 need remove atom 1958 need remove atom 1960 need remove atom 1962 need remove atom 1964 need remove atom 1966 need remove atom 1968 need remove atom 1970 need remove atom 1972 need remove atom 1974 need remove atom 1976 need remove atom 1978 need remove atom 1980 need remove atom 1982 need remove atom 1986 need remove atom 1990 need remove atom 1994 need remove atom 1998 [I] need removenum=64 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2379441149e-01 1.0102275710e-01 3.5075013040e-01 dub= -3.3961938341e-01 1.0102507446e-01 -3.5724718023e-01 duc= 3.2379532967e-01 -1.0233571757e-01 3.5075125520e-01 [I] overall tilt ux= -6.6341379490e-01 2.3173609887e-06 -7.0799731063e-01 uy= 9.1818715592e-07 -2.0335847467e-01 1.1247996134e-06 [I] storedr[0]= -1.1630302738e-02 4.2813999870e-02 9.9372424336e-03 [I] originally 3840 atoms [I] insert 0 atoms [I] now 3840 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3840 atoms [I] remove 64 atoms [I] now 3776 atoms [I] NP=3776 n=3776 [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 24 15:57:34 2023 CPU time spent: 2.599628 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 24 16:05:19 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 16 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 17 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=4352 [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) = 0.03125 [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) = 0.28113258894964 [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= 3.1250000000e-02 0.0000000000e+00 1.2500000000e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=5.101110e+01 pxpb=0.000000e+00 pypb=7.664938e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2243 need remove atom 2247 need remove atom 2251 need remove atom 2255 need remove atom 2257 need remove atom 2259 need remove atom 2261 need remove atom 2263 need remove atom 2265 need remove atom 2267 need remove atom 2269 need remove atom 2271 need remove atom 2273 need remove atom 2275 need remove atom 2277 need remove atom 2279 need remove atom 2281 need remove atom 2283 need remove atom 2285 need remove atom 2287 need remove atom 2289 need remove atom 2291 need remove atom 2293 need remove atom 2295 need remove atom 2297 need remove atom 2299 need remove atom 2301 need remove atom 2303 need remove atom 2305 need remove atom 2307 need remove atom 2309 need remove atom 2311 need remove atom 2313 need remove atom 2315 need remove atom 2317 need remove atom 2319 need remove atom 2321 need remove atom 2323 need remove atom 2325 need remove atom 2327 need remove atom 2329 need remove atom 2331 need remove atom 2333 need remove atom 2335 need remove atom 2337 need remove atom 2339 need remove atom 2341 need remove atom 2343 need remove atom 2345 need remove atom 2347 need remove atom 2349 need remove atom 2351 need remove atom 2353 need remove atom 2355 need remove atom 2357 need remove atom 2359 need remove atom 2361 need remove atom 2363 need remove atom 2365 need remove atom 2367 need remove atom 2369 need remove atom 2371 need remove atom 2373 need remove atom 2375 need remove atom 2377 need remove atom 2379 need remove atom 2381 need remove atom 2383 [I] need removenum=68 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2347588434e-01 1.0113248370e-01 3.5014666986e-01 dub= -3.3926726052e-01 1.0113476266e-01 -3.5655422620e-01 duc= 3.2347680539e-01 -1.0243754358e-01 3.5014779367e-01 [I] overall tilt ux= -6.6274314486e-01 2.2789645963e-06 -7.0670089607e-01 uy= 9.2105358912e-07 -2.0357002728e-01 1.1238079095e-06 [I] storedr[0]= -1.1397799957e-02 4.0078459905e-02 9.2164538762e-03 [I] originally 4352 atoms [I] insert 0 atoms [I] now 4352 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 4352 atoms [I] remove 68 atoms [I] now 4284 atoms [I] NP=4284 n=4284 [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 = Wed May 24 16:05:22 2023 CPU time spent: 2.748895 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 24 16:13:20 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 17 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 18 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=4896 [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) = 0.029411764705882 [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) = 0.28113258894964 [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= 2.9411764706e-02 0.0000000000e+00 1.2500000000e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=5.419929e+01 pxpb=0.000000e+00 pypb=8.115816e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2384 need remove atom 2386 need remove atom 2388 need remove atom 2390 need remove atom 2392 need remove atom 2394 need remove atom 2396 need remove atom 2398 need remove atom 2400 need remove atom 2402 need remove atom 2404 need remove atom 2406 need remove atom 2408 need remove atom 2410 need remove atom 2412 need remove atom 2414 need remove atom 2416 need remove atom 2418 need remove atom 2420 need remove atom 2422 need remove atom 2424 need remove atom 2426 need remove atom 2428 need remove atom 2430 need remove atom 2432 need remove atom 2434 need remove atom 2436 need remove atom 2438 need remove atom 2440 need remove atom 2442 need remove atom 2444 need remove atom 2446 need remove atom 2448 need remove atom 2450 need remove atom 2452 need remove atom 2454 need remove atom 2456 need remove atom 2458 need remove atom 2460 need remove atom 2462 need remove atom 2464 need remove atom 2466 need remove atom 2468 need remove atom 2470 need remove atom 2472 need remove atom 2474 need remove atom 2476 need remove atom 2478 need remove atom 2480 need remove atom 2482 need remove atom 2484 need remove atom 2486 need remove atom 2488 need remove atom 2490 need remove atom 2492 need remove atom 2494 need remove atom 2496 need remove atom 2498 need remove atom 2500 need remove atom 2502 need remove atom 2504 need remove atom 2506 need remove atom 2508 need remove atom 2510 need remove atom 2512 need remove atom 2514 need remove atom 2516 need remove atom 2518 need remove atom 2520 need remove atom 2522 need remove atom 2524 need remove atom 2526 [I] need removenum=72 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2319271679e-01 1.0122963264e-01 3.4961151940e-01 dub= -3.3895387420e-01 1.0123187722e-01 -3.5593962291e-01 duc= 3.2319364037e-01 -1.0252769212e-01 3.4961264231e-01 [I] overall tilt ux= -6.6214659099e-01 2.2445839133e-06 -7.0555114232e-01 uy= 9.2357649173e-07 -2.0375732476e-01 1.1229059295e-06 [I] storedr[0]= -1.1188336668e-02 3.7665193555e-02 8.5764263120e-03 [I] originally 4896 atoms [I] insert 0 atoms [I] now 4896 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 4896 atoms [I] remove 72 atoms [I] now 4824 atoms [I] NP=4824 n=4824 [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 = Wed May 24 16:13:24 2023 CPU time spent: 3.086458 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 24 16:22:46 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 18 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 19 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=5472 [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) = 0.027777777777778 [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) = 0.28113258894964 [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= 2.7777777778e-02 0.0000000000e+00 1.2500000000e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=5.738749e+01 pxpb=0.000000e+00 pypb=8.566695e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2817 need remove atom 2819 need remove atom 2821 need remove atom 2823 need remove atom 2825 need remove atom 2827 need remove atom 2829 need remove atom 2831 need remove atom 2833 need remove atom 2835 need remove atom 2837 need remove atom 2839 need remove atom 2841 need remove atom 2843 need remove atom 2845 need remove atom 2847 need remove atom 2849 need remove atom 2851 need remove atom 2853 need remove atom 2855 need remove atom 2857 need remove atom 2859 need remove atom 2861 need remove atom 2863 need remove atom 2865 need remove atom 2867 need remove atom 2869 need remove atom 2871 need remove atom 2873 need remove atom 2875 need remove atom 2877 need remove atom 2879 need remove atom 2881 need remove atom 2883 need remove atom 2885 need remove atom 2887 need remove atom 2889 need remove atom 2891 need remove atom 2893 need remove atom 2895 need remove atom 2897 need remove atom 2899 need remove atom 2901 need remove atom 2903 need remove atom 2905 need remove atom 2907 need remove atom 2909 need remove atom 2911 need remove atom 2913 need remove atom 2915 need remove atom 2917 need remove atom 2919 need remove atom 2921 need remove atom 2923 need remove atom 2925 need remove atom 2927 need remove atom 2929 need remove atom 2931 need remove atom 2933 need remove atom 2935 need remove atom 2937 need remove atom 2939 need remove atom 2941 need remove atom 2943 need remove atom 2945 need remove atom 2947 need remove atom 2949 need remove atom 2951 need remove atom 2953 need remove atom 2955 need remove atom 2957 need remove atom 2959 need remove atom 2961 need remove atom 2965 need remove atom 2969 need remove atom 2973 [I] need removenum=76 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2293933260e-01 1.0131624595e-01 3.4913370311e-01 dub= -3.3867317055e-01 1.0131845958e-01 -3.5539079644e-01 duc= 3.2294025841e-01 -1.0260805976e-01 3.4913482519e-01 [I] overall tilt ux= -6.6161250314e-01 2.2136255136e-06 -7.0452449954e-01 uy= 9.2581381150e-07 -2.0392430572e-01 1.1220827459e-06 [I] storedr[0]= -1.0999017400e-02 3.5520703648e-02 8.0040327056e-03 [I] originally 5472 atoms [I] insert 0 atoms [I] now 5472 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 5472 atoms [I] remove 76 atoms [I] now 5396 atoms [I] NP=5396 n=5396 [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 24 16:22:49 2023 CPU time spent: 3.438830 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 24 16:31:47 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [I] ASSIGN makecnspec = 0 [I] ASSIGN makecnspec(1) = 0 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 19 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 20 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 0 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 0 -1 1 0 1 1 1 0 0]; basis=[ 0.5 0.5 0 0 0 0 0 0 0 1 0.5 0 0.5 0 2 0 0.5 0.5 0 3 ]; [I] makecn: _NP=7600 [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) = 0.026315789473684 [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) = 0.28113258894964 [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= 2.6315789474e-02 0.0000000000e+00 1.0000000000e-01 b= 1.5940968841e+00 0.0000000000e+00 2.2543934333e+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=1.5940968841314 by=0 pxpa=6.057568e+01 pxpb=0.000000e+00 pypb=9.017574e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3700 need remove atom 3704 need remove atom 3708 need remove atom 3712 need remove atom 3716 need remove atom 3720 need remove atom 3722 need remove atom 3724 need remove atom 3726 need remove atom 3728 need remove atom 3730 need remove atom 3732 need remove atom 3734 need remove atom 3736 need remove atom 3738 need remove atom 3740 need remove atom 3742 need remove atom 3744 need remove atom 3746 need remove atom 3748 need remove atom 3750 need remove atom 3752 need remove atom 3754 need remove atom 3756 need remove atom 3758 need remove atom 3760 need remove atom 3762 need remove atom 3764 need remove atom 3766 need remove atom 3768 need remove atom 3770 need remove atom 3772 need remove atom 3774 need remove atom 3776 need remove atom 3778 need remove atom 3780 need remove atom 3782 need remove atom 3784 need remove atom 3786 need remove atom 3788 need remove atom 3790 need remove atom 3792 need remove atom 3794 need remove atom 3796 need remove atom 3798 need remove atom 3800 need remove atom 3802 need remove atom 3804 need remove atom 3806 need remove atom 3808 need remove atom 3810 need remove atom 3812 need remove atom 3814 need remove atom 3816 need remove atom 3818 need remove atom 3820 need remove atom 3822 need remove atom 3824 need remove atom 3826 need remove atom 3828 need remove atom 3830 need remove atom 3832 need remove atom 3834 need remove atom 3836 need remove atom 3838 need remove atom 3840 need remove atom 3842 need remove atom 3844 need remove atom 3846 need remove atom 3848 need remove atom 3850 need remove atom 3852 need remove atom 3854 need remove atom 3856 need remove atom 3858 need remove atom 3860 need remove atom 3862 need remove atom 3864 need remove atom 3866 need remove atom 3868 need remove atom 3870 need remove atom 3872 need remove atom 3874 need remove atom 3876 need remove atom 3878 need remove atom 3880 need remove atom 3882 need remove atom 3884 need remove atom 3886 need remove atom 3888 need remove atom 3890 need remove atom 3892 need remove atom 3894 need remove atom 3896 need remove atom 3898 need remove atom 3902 need remove atom 3906 need remove atom 3910 need remove atom 3914 need remove atom 3918 [I] need removenum=100 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2271126909e-01 1.0139394693e-01 3.4870447669e-01 dub= -3.3842029383e-01 1.0139613254e-01 -3.5489772613e-01 duc= 3.2271219690e-01 -1.0268015403e-01 3.4870559802e-01 [I] overall tilt ux= -6.6113156292e-01 2.1856063686e-06 -7.0360220282e-01 uy= 9.2781120975e-07 -2.0407410096e-01 1.1213289627e-06 [I] storedr[0]= -1.0827327052e-02 3.3602663221e-02 7.4888960120e-03 [I] originally 7600 atoms [I] insert 0 atoms [I] now 7600 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7600 atoms [I] remove 100 atoms [I] now 7500 atoms [I] NP=7500 n=7500 [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 = Wed May 24 16:31:53 2023 CPU time spent: 4.882718 s {"realtime":4603.66,"usertime":9121.66,"systime":51.54,"memmax":82852,"memavg":0}