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 30 17:14:06 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 6 [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) = 2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [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) = 0.027777777777778 [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) = 0.27791930643697 [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 -1.6666666667e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=3.283967e+01 pxpb=0.000000e+00 pypb=4.915805e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 870 need remove atom 874 need remove atom 882 need remove atom 886 need remove atom 894 need remove atom 898 need remove atom 906 need remove atom 910 need remove atom 918 need remove atom 922 need remove atom 930 need remove atom 934 need remove atom 942 need remove atom 946 need remove atom 954 need remove atom 958 need remove atom 966 need remove atom 970 need remove atom 978 need remove atom 982 need remove atom 990 need remove atom 1002 [I] need removenum=22 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8473633698e-01 5.8245564965e-02 -4.0006838169e-01 dub= -1.9372517147e-01 5.8246816746e-02 4.0730219064e-01 duc= 1.8473686530e-01 -5.8985626585e-02 -4.0006966675e-01 [I] overall tilt ux= -3.7846150845e-01 1.2517811359e-06 8.0737057234e-01 uy= 5.2831732666e-07 -1.1723119155e-01 -1.2850541662e-06 [I] storedr[0]= -1.0408770071e-02 -3.7390834327e-04 -3.1757993109e-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 22 atoms [I] now 1562 atoms [I] NP=1562 n=1562 [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 30 17:14:07 2023 CPU time spent: 1.015619 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 30 17:14:49 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 7 [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) = 2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [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) = 0.023809523809524 [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) = 0.27791930643697 [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= 2.3809523810e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=3.831295e+01 pxpb=0.000000e+00 pypb=5.809587e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1012 need remove atom 1024 need remove atom 1032 need remove atom 1036 need remove atom 1044 need remove atom 1048 need remove atom 1056 need remove atom 1060 need remove atom 1068 need remove atom 1072 need remove atom 1080 need remove atom 1084 need remove atom 1092 need remove atom 1096 need remove atom 1104 need remove atom 1108 need remove atom 1116 need remove atom 1120 need remove atom 1128 need remove atom 1132 need remove atom 1140 need remove atom 1144 need remove atom 1152 need remove atom 1156 need remove atom 1164 need remove atom 1168 [I] need removenum=26 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8533774216e-01 5.8041023415e-02 -4.0234475083e-01 dub= -1.9439002103e-01 5.8042347409e-02 4.0991606949e-01 duc= 1.8533826510e-01 -5.8795978672e-02 -4.0234603961e-01 [I] overall tilt ux= -3.7972776319e-01 1.3239942825e-06 8.1226082032e-01 uy= 5.2293355096e-07 -1.1683700209e-01 -1.2887768996e-06 [I] storedr[0]= -9.7203164393e-03 -3.8069106042e-04 -2.6046868559e-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 26 atoms [I] now 2158 atoms [I] NP=2158 n=2158 [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 30 17:14:50 2023 CPU time spent: 1.394317 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 30 17:15:42 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 8 [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) = 2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=2880 [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) = 0.020833333333333 [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) = 0.27791930643697 [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= 2.0833333333e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=4.378623e+01 pxpb=0.000000e+00 pypb=6.703370e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1542 need remove atom 1546 need remove atom 1554 need remove atom 1558 need remove atom 1566 need remove atom 1570 need remove atom 1578 need remove atom 1582 need remove atom 1590 need remove atom 1594 need remove atom 1602 need remove atom 1606 need remove atom 1614 need remove atom 1618 need remove atom 1626 need remove atom 1630 need remove atom 1638 need remove atom 1642 need remove atom 1650 need remove atom 1654 need remove atom 1662 need remove atom 1666 need remove atom 1674 need remove atom 1678 need remove atom 1686 need remove atom 1690 need remove atom 1698 need remove atom 1702 need remove atom 1710 need remove atom 1722 [I] need removenum=30 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8577861345e-01 5.7889238353e-02 -4.0402597414e-01 dub= -1.9487572338e-01 5.7890614095e-02 4.1184566160e-01 duc= 1.8577913231e-01 -5.8655221238e-02 -4.0402726544e-01 [I] overall tilt ux= -3.8065433683e-01 1.3757414204e-06 8.1587163573e-01 uy= 5.1886854815e-07 -1.1654445959e-01 -1.2913098708e-06 [I] storedr[0]= -9.1716892369e-03 -3.8574121148e-04 -2.1852023720e-02 [I] originally 2880 atoms [I] insert 0 atoms [I] now 2880 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2880 atoms [I] remove 30 atoms [I] now 2850 atoms [I] NP=2850 n=2850 [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 30 17:15:44 2023 CPU time spent: 1.838072 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 30 17:17:03 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 9 [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) = 2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=3672 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.018518518518519 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.8518518519e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=4.925951e+01 pxpb=0.000000e+00 pypb=7.597153e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1739 need remove atom 1751 need remove atom 1759 need remove atom 1763 need remove atom 1771 need remove atom 1775 need remove atom 1783 need remove atom 1787 need remove atom 1795 need remove atom 1799 need remove atom 1807 need remove atom 1811 need remove atom 1819 need remove atom 1823 need remove atom 1831 need remove atom 1835 need remove atom 1843 need remove atom 1847 need remove atom 1855 need remove atom 1859 need remove atom 1867 need remove atom 1871 need remove atom 1879 need remove atom 1883 need remove atom 1891 need remove atom 1895 need remove atom 1903 need remove atom 1907 need remove atom 1915 need remove atom 1919 need remove atom 1927 need remove atom 1931 need remove atom 1939 need remove atom 1943 [I] need removenum=34 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8611564005e-01 5.7772162972e-02 -4.0531843518e-01 dub= -1.9524604333e-01 5.7773577564e-02 4.1332850654e-01 duc= 1.8611615575e-01 -5.8546639055e-02 -4.0531972831e-01 [I] overall tilt ux= -3.8136168339e-01 1.4145926637e-06 8.1864694172e-01 uy= 5.1569375367e-07 -1.1631880203e-01 -1.2931310159e-06 [I] storedr[0]= -8.7266218536e-03 -3.8963905813e-04 -1.8647831259e-02 [I] originally 3672 atoms [I] insert 0 atoms [I] now 3672 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3672 atoms [I] remove 34 atoms [I] now 3638 atoms [I] NP=3638 n=3638 [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 30 17:17:06 2023 CPU time spent: 2.302289 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 30 17:18:31 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [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) = 18 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [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) = 0.016666666666667 [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) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.6666666667e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=5.473279e+01 pxpb=0.000000e+00 pypb=8.044044e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1849 need remove atom 1853 need remove atom 1861 need remove atom 1865 need remove atom 1873 need remove atom 1877 need remove atom 1885 need remove atom 1889 need remove atom 1897 need remove atom 1901 need remove atom 1909 need remove atom 1913 need remove atom 1921 need remove atom 1925 need remove atom 1933 need remove atom 1937 need remove atom 1945 need remove atom 1949 need remove atom 1957 need remove atom 1961 need remove atom 1969 need remove atom 1973 need remove atom 1981 need remove atom 1985 need remove atom 1993 need remove atom 1997 need remove atom 2005 need remove atom 2009 need remove atom 2017 need remove atom 2021 need remove atom 2029 need remove atom 2033 need remove atom 2041 need remove atom 2045 need remove atom 2053 need remove atom 2057 [I] need removenum=36 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8386732690e-01 5.8535943772e-02 -3.9681308077e-01 dub= -1.9275995958e-01 5.8537088087e-02 4.0356200783e-01 duc= 1.8386786267e-01 -5.9254785957e-02 -3.9681435992e-01 [I] overall tilt ux= -3.7662728649e-01 1.1443149533e-06 8.0037508859e-01 uy= 5.3576645315e-07 -1.1779072973e-01 -1.2791517927e-06 [I] storedr[0]= -7.8565113986e-03 -3.6193001633e-04 -1.9299763459e-02 [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 36 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 = Tue May 30 17:18:34 2023 CPU time spent: 2.710685 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 30 17:19:36 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [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) = 18 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=6480 [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) = 0.016666666666667 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.11111111111111 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.6666666667e-02 -0.0000000000e+00 -1.1111111111e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=5.473279e+01 pxpb=0.000000e+00 pypb=8.044044e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2773 need remove atom 2777 need remove atom 2785 need remove atom 2789 need remove atom 2797 need remove atom 2801 need remove atom 2809 need remove atom 2813 need remove atom 2821 need remove atom 2825 need remove atom 2833 need remove atom 2837 need remove atom 2845 need remove atom 2849 need remove atom 2857 need remove atom 2861 need remove atom 2869 need remove atom 2873 need remove atom 2881 need remove atom 2885 need remove atom 2893 need remove atom 2897 need remove atom 2905 need remove atom 2909 need remove atom 2917 need remove atom 2921 need remove atom 2929 need remove atom 2933 need remove atom 2941 need remove atom 2945 need remove atom 2953 need remove atom 2957 need remove atom 2965 need remove atom 2969 need remove atom 2977 need remove atom 2981 need remove atom 2989 need remove atom 2993 need remove atom 3001 need remove atom 3005 need remove atom 3013 need remove atom 3017 need remove atom 3025 need remove atom 3029 need remove atom 3037 need remove atom 3041 need remove atom 3049 need remove atom 3053 need remove atom 3061 need remove atom 3065 need remove atom 3073 need remove atom 3077 need remove atom 3085 need remove atom 3089 [I] need removenum=54 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8386732690e-01 5.8535943772e-02 -3.9681308077e-01 dub= -1.9275995958e-01 5.8537088087e-02 4.0356200783e-01 duc= 1.8386786267e-01 -5.9254785957e-02 -3.9681435992e-01 [I] overall tilt ux= -3.7662728649e-01 1.1443149533e-06 8.0037508859e-01 uy= 5.3576645315e-07 -1.1779072973e-01 -1.2791517927e-06 [I] storedr[0]= -7.8565113986e-03 -3.6193001633e-04 -1.9299763459e-02 [I] originally 6480 atoms [I] insert 0 atoms [I] now 6480 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 6480 atoms [I] remove 54 atoms [I] now 6426 atoms [I] NP=6426 n=6426 [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 30 17:19:40 2023 CPU time spent: 4.086005 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 30 17:21:02 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [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) = 20 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [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) = 0.015151515151515 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.11111111111111 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.5151515152e-02 -0.0000000000e+00 -1.1111111111e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=6.020607e+01 pxpb=0.000000e+00 pypb=8.937827e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3791 need remove atom 3803 need remove atom 3815 need remove atom 3823 need remove atom 3827 need remove atom 3835 need remove atom 3839 need remove atom 3847 need remove atom 3851 need remove atom 3859 need remove atom 3863 need remove atom 3871 need remove atom 3875 need remove atom 3883 need remove atom 3887 need remove atom 3895 need remove atom 3899 need remove atom 3907 need remove atom 3911 need remove atom 3919 need remove atom 3923 need remove atom 3931 need remove atom 3935 need remove atom 3943 need remove atom 3947 need remove atom 3955 need remove atom 3959 need remove atom 3967 need remove atom 3971 need remove atom 3979 need remove atom 3983 need remove atom 3991 need remove atom 3995 need remove atom 4003 need remove atom 4007 need remove atom 4015 need remove atom 4019 need remove atom 4027 need remove atom 4031 need remove atom 4039 need remove atom 4043 need remove atom 4051 need remove atom 4055 need remove atom 4063 need remove atom 4067 need remove atom 4075 need remove atom 4079 need remove atom 4087 need remove atom 4091 need remove atom 4099 need remove atom 4103 need remove atom 4111 need remove atom 4115 need remove atom 4123 need remove atom 4127 need remove atom 4135 need remove atom 4139 need remove atom 4147 need remove atom 4159 need remove atom 4171 [I] need removenum=60 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8434531867e-01 5.8376984490e-02 -3.9859871852e-01 dub= -1.9329151791e-01 5.8378188358e-02 4.0561392812e-01 duc= 1.8434585038e-01 -5.9107454405e-02 -3.9860000099e-01 [I] overall tilt ux= -3.7763683658e-01 1.2038680394e-06 8.0421264663e-01 uy= 5.3171750261e-07 -1.1748443890e-01 -1.2824732217e-06 [I] storedr[0]= -7.6445227156e-03 -3.6741565272e-04 -1.6738208866e-02 [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 60 atoms [I] now 7860 atoms [I] NP=7860 n=7860 [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 = Tue May 30 17:21:07 2023 CPU time spent: 4.963750 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 30 17:23:35 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [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) = 22 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=9504 [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) = 0.013888888888889 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.11111111111111 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.3888888889e-02 -0.0000000000e+00 -1.1111111111e-01 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=6.567934e+01 pxpb=0.000000e+00 pypb=9.831609e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4177 need remove atom 4181 need remove atom 4189 need remove atom 4193 need remove atom 4201 need remove atom 4205 need remove atom 4213 need remove atom 4217 need remove atom 4225 need remove atom 4229 need remove atom 4237 need remove atom 4241 need remove atom 4249 need remove atom 4253 need remove atom 4261 need remove atom 4265 need remove atom 4273 need remove atom 4277 need remove atom 4285 need remove atom 4289 need remove atom 4297 need remove atom 4301 need remove atom 4309 need remove atom 4313 need remove atom 4321 need remove atom 4325 need remove atom 4333 need remove atom 4337 need remove atom 4345 need remove atom 4349 need remove atom 4357 need remove atom 4361 need remove atom 4369 need remove atom 4373 need remove atom 4381 need remove atom 4385 need remove atom 4393 need remove atom 4397 need remove atom 4405 need remove atom 4409 need remove atom 4417 need remove atom 4421 need remove atom 4429 need remove atom 4433 need remove atom 4441 need remove atom 4445 need remove atom 4453 need remove atom 4457 need remove atom 4465 need remove atom 4469 need remove atom 4477 need remove atom 4481 need remove atom 4489 need remove atom 4493 need remove atom 4501 need remove atom 4505 need remove atom 4513 need remove atom 4517 need remove atom 4525 need remove atom 4529 need remove atom 4537 need remove atom 4541 need remove atom 4549 need remove atom 4553 need remove atom 4561 need remove atom 4565 [I] need removenum=66 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8473633698e-01 5.8245564965e-02 -4.0006838169e-01 dub= -1.9372517147e-01 5.8246816746e-02 4.0730219064e-01 duc= 1.8473686530e-01 -5.8985626585e-02 -4.0006966675e-01 [I] overall tilt ux= -3.7846150845e-01 1.2517811357e-06 8.0737057234e-01 uy= 5.2831732666e-07 -1.1723119155e-01 -1.2850541662e-06 [I] storedr[0]= -7.4532987353e-03 -3.7195295035e-04 -1.4662522068e-02 [I] originally 9504 atoms [I] insert 0 atoms [I] now 9504 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 9504 atoms [I] remove 66 atoms [I] now 9438 atoms [I] NP=9438 n=9438 [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 30 17:23:42 2023 CPU time spent: 6.078514 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 30 17:24:35 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [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) = 28 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=20160 [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) = 0.011111111111111 [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) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.1111111111e-02 -0.0000000000e+00 -8.3333333333e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=8.209918e+01 pxpb=0.000000e+00 pypb=1.251296e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 9755 need remove atom 9767 need remove atom 9779 need remove atom 9791 need remove atom 9799 need remove atom 9803 need remove atom 9811 need remove atom 9815 need remove atom 9823 need remove atom 9827 need remove atom 9835 need remove atom 9839 need remove atom 9847 need remove atom 9851 need remove atom 9859 need remove atom 9863 need remove atom 9871 need remove atom 9875 need remove atom 9883 need remove atom 9887 need remove atom 9895 need remove atom 9899 need remove atom 9907 need remove atom 9911 need remove atom 9919 need remove atom 9923 need remove atom 9931 need remove atom 9935 need remove atom 9943 need remove atom 9947 need remove atom 9955 need remove atom 9959 need remove atom 9967 need remove atom 9971 need remove atom 9979 need remove atom 9983 need remove atom 9991 need remove atom 9995 need remove atom 10003 need remove atom 10007 need remove atom 10015 need remove atom 10019 need remove atom 10027 need remove atom 10031 need remove atom 10039 need remove atom 10043 need remove atom 10051 need remove atom 10055 need remove atom 10063 need remove atom 10067 need remove atom 10075 need remove atom 10079 need remove atom 10087 need remove atom 10091 need remove atom 10099 need remove atom 10103 need remove atom 10111 need remove atom 10115 need remove atom 10123 need remove atom 10127 need remove atom 10135 need remove atom 10139 need remove atom 10147 need remove atom 10151 need remove atom 10159 need remove atom 10163 need remove atom 10171 need remove atom 10175 need remove atom 10183 need remove atom 10187 need remove atom 10195 need remove atom 10199 need remove atom 10207 need remove atom 10211 need remove atom 10219 need remove atom 10223 need remove atom 10231 need remove atom 10235 need remove atom 10243 need remove atom 10247 need remove atom 10255 need remove atom 10259 need remove atom 10267 need remove atom 10271 need remove atom 10279 need remove atom 10283 need remove atom 10291 need remove atom 10295 need remove atom 10303 need remove atom 10307 need remove atom 10315 need remove atom 10319 need remove atom 10327 need remove atom 10331 need remove atom 10339 need remove atom 10343 need remove atom 10351 need remove atom 10355 need remove atom 10363 need remove atom 10367 need remove atom 10375 need remove atom 10379 need remove atom 10387 need remove atom 10391 need remove atom 10399 need remove atom 10403 need remove atom 10411 need remove atom 10415 need remove atom 10423 need remove atom 10435 need remove atom 10447 need remove atom 10459 [I] need removenum=112 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8557394212e-01 5.7959896330e-02 -4.0324415165e-01 dub= -1.9465041840e-01 5.7961248176e-02 4.1094843846e-01 duc= 1.8557446289e-01 -5.8720748130e-02 -4.0324544181e-01 [I] overall tilt ux= -3.8022436052e-01 1.3518465332e-06 8.1419259011e-01 uy= 5.2076812071e-07 -1.1668064446e-01 -1.2901549559e-06 [I] storedr[0]= -6.9895836603e-03 -3.8181253346e-04 -1.0283285737e-02 [I] originally 20160 atoms [I] insert 0 atoms [I] now 20160 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 20160 atoms [I] remove 112 atoms [I] now 20048 atoms [I] NP=20048 n=20048 [I] ASSIGN finalcnfile = dipole_2.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 17:24:50 2023 CPU time spent: 13.228514 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 30 17:25:59 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [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) = 33 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=28512 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.0092592592592593 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 9.2592592593e-03 -0.0000000000e+00 -8.3333333333e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=9.851902e+01 pxpb=0.000000e+00 pypb=1.474741e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 13061 need remove atom 13073 need remove atom 13085 need remove atom 13097 need remove atom 13105 need remove atom 13109 need remove atom 13117 need remove atom 13121 need remove atom 13129 need remove atom 13133 need remove atom 13141 need remove atom 13145 need remove atom 13153 need remove atom 13157 need remove atom 13165 need remove atom 13169 need remove atom 13177 need remove atom 13181 need remove atom 13189 need remove atom 13193 need remove atom 13201 need remove atom 13205 need remove atom 13213 need remove atom 13217 need remove atom 13225 need remove atom 13229 need remove atom 13237 need remove atom 13241 need remove atom 13249 need remove atom 13253 need remove atom 13261 need remove atom 13265 need remove atom 13273 need remove atom 13277 need remove atom 13285 need remove atom 13289 need remove atom 13297 need remove atom 13301 need remove atom 13309 need remove atom 13313 need remove atom 13321 need remove atom 13325 need remove atom 13333 need remove atom 13337 need remove atom 13345 need remove atom 13349 need remove atom 13357 need remove atom 13361 need remove atom 13369 need remove atom 13373 need remove atom 13381 need remove atom 13385 need remove atom 13393 need remove atom 13397 need remove atom 13405 need remove atom 13409 need remove atom 13417 need remove atom 13421 need remove atom 13429 need remove atom 13433 need remove atom 13441 need remove atom 13445 need remove atom 13453 need remove atom 13457 need remove atom 13465 need remove atom 13469 need remove atom 13477 need remove atom 13481 need remove atom 13489 need remove atom 13493 need remove atom 13501 need remove atom 13505 need remove atom 13513 need remove atom 13517 need remove atom 13525 need remove atom 13529 need remove atom 13537 need remove atom 13541 need remove atom 13549 need remove atom 13553 need remove atom 13561 need remove atom 13565 need remove atom 13573 need remove atom 13577 need remove atom 13585 need remove atom 13589 need remove atom 13597 need remove atom 13601 need remove atom 13609 need remove atom 13613 need remove atom 13621 need remove atom 13625 need remove atom 13633 need remove atom 13637 need remove atom 13645 need remove atom 13649 need remove atom 13657 need remove atom 13661 need remove atom 13669 need remove atom 13673 need remove atom 13681 need remove atom 13685 need remove atom 13693 need remove atom 13697 need remove atom 13705 need remove atom 13709 need remove atom 13717 need remove atom 13721 need remove atom 13729 need remove atom 13733 need remove atom 13741 need remove atom 13745 need remove atom 13753 need remove atom 13757 need remove atom 13765 need remove atom 13769 need remove atom 13777 need remove atom 13781 need remove atom 13789 need remove atom 13793 need remove atom 13801 need remove atom 13805 need remove atom 13813 need remove atom 13817 need remove atom 13825 need remove atom 13829 need remove atom 13837 need remove atom 13841 need remove atom 13849 need remove atom 13853 need remove atom 13861 need remove atom 13865 [I] need removenum=132 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8473633698e-01 5.8245564965e-02 -4.0006838169e-01 dub= -1.9372517147e-01 5.8246816746e-02 4.0730219064e-01 duc= 1.8473686530e-01 -5.8985626585e-02 -4.0006966675e-01 [I] overall tilt ux= -3.7846150845e-01 1.2517811355e-06 8.0737057234e-01 uy= 5.2831732630e-07 -1.1723119155e-01 -1.2850541654e-06 [I] storedr[0]= -6.4665874027e-03 -3.7113446082e-04 -8.6539366766e-03 [I] originally 28512 atoms [I] insert 0 atoms [I] now 28512 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 28512 atoms [I] remove 132 atoms [I] now 28380 atoms [I] NP=28380 n=28380 [I] ASSIGN finalcnfile = dipole_3.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 17:26:19 2023 CPU time spent: 18.550828 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 30 17:28:24 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 21 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 39 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=49140 [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) = 0.0079365079365079 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.066666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [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= 7.9365079365e-03 -0.0000000000e+00 -6.6666666667e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=1.149389e+02 pxpb=0.000000e+00 pypb=1.742876e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 24007 need remove atom 24011 need remove atom 24019 need remove atom 24023 need remove atom 24031 need remove atom 24035 need remove atom 24043 need remove atom 24047 need remove atom 24055 need remove atom 24059 need remove atom 24067 need remove atom 24071 need remove atom 24079 need remove atom 24083 need remove atom 24091 need remove atom 24095 need remove atom 24103 need remove atom 24107 need remove atom 24115 need remove atom 24119 need remove atom 24127 need remove atom 24131 need remove atom 24139 need remove atom 24143 need remove atom 24151 need remove atom 24155 need remove atom 24163 need remove atom 24167 need remove atom 24175 need remove atom 24179 need remove atom 24187 need remove atom 24191 need remove atom 24199 need remove atom 24203 need remove atom 24211 need remove atom 24215 need remove atom 24223 need remove atom 24227 need remove atom 24235 need remove atom 24239 need remove atom 24247 need remove atom 24251 need remove atom 24259 need remove atom 24263 need remove atom 24271 need remove atom 24275 need remove atom 24283 need remove atom 24287 need remove atom 24295 need remove atom 24299 need remove atom 24307 need remove atom 24311 need remove atom 24319 need remove atom 24323 need remove atom 24331 need remove atom 24335 need remove atom 24343 need remove atom 24347 need remove atom 24355 need remove atom 24359 need remove atom 24367 need remove atom 24371 need remove atom 24379 need remove atom 24383 need remove atom 24391 need remove atom 24395 need remove atom 24403 need remove atom 24407 need remove atom 24415 need remove atom 24419 need remove atom 24427 need remove atom 24431 need remove atom 24439 need remove atom 24443 need remove atom 24451 need remove atom 24455 need remove atom 24463 need remove atom 24467 need remove atom 24475 need remove atom 24479 need remove atom 24487 need remove atom 24491 need remove atom 24499 need remove atom 24503 need remove atom 24511 need remove atom 24515 need remove atom 24523 need remove atom 24527 need remove atom 24535 need remove atom 24539 need remove atom 24547 need remove atom 24551 need remove atom 24559 need remove atom 24563 need remove atom 24571 need remove atom 24575 need remove atom 24583 need remove atom 24587 need remove atom 24595 need remove atom 24599 need remove atom 24607 need remove atom 24611 need remove atom 24619 need remove atom 24623 need remove atom 24631 need remove atom 24635 need remove atom 24643 need remove atom 24647 need remove atom 24655 need remove atom 24659 need remove atom 24667 need remove atom 24671 need remove atom 24679 need remove atom 24683 need remove atom 24691 need remove atom 24695 need remove atom 24703 need remove atom 24707 need remove atom 24715 need remove atom 24719 need remove atom 24727 need remove atom 24731 need remove atom 24739 need remove atom 24743 need remove atom 24751 need remove atom 24755 need remove atom 24763 need remove atom 24767 need remove atom 24775 need remove atom 24779 need remove atom 24787 need remove atom 24791 need remove atom 24799 need remove atom 24803 need remove atom 24811 need remove atom 24815 need remove atom 24823 need remove atom 24827 need remove atom 24835 need remove atom 24839 need remove atom 24847 need remove atom 24851 need remove atom 24859 need remove atom 24863 need remove atom 24871 need remove atom 24875 need remove atom 24883 need remove atom 24887 need remove atom 24895 need remove atom 24899 need remove atom 24907 need remove atom 24911 need remove atom 24919 need remove atom 24923 need remove atom 24931 need remove atom 24935 need remove atom 24943 need remove atom 24947 need remove atom 24955 need remove atom 24959 need remove atom 24967 need remove atom 24971 need remove atom 24979 need remove atom 24983 need remove atom 24991 need remove atom 24995 need remove atom 25003 need remove atom 25007 need remove atom 25015 need remove atom 25019 need remove atom 25027 need remove atom 25031 need remove atom 25039 need remove atom 25043 need remove atom 25051 need remove atom 25055 need remove atom 25063 need remove atom 25067 need remove atom 25075 need remove atom 25079 need remove atom 25087 need remove atom 25091 need remove atom 25099 need remove atom 25103 need remove atom 25111 need remove atom 25115 need remove atom 25123 need remove atom 25127 need remove atom 25135 need remove atom 25139 need remove atom 25147 need remove atom 25159 need remove atom 25171 need remove atom 25183 need remove atom 25195 [I] need removenum=195 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8533774216e-01 5.8041023415e-02 -4.0234475083e-01 dub= -1.9439002103e-01 5.8042347409e-02 4.0991606949e-01 duc= 1.8533826510e-01 -5.8795978672e-02 -4.0234603961e-01 [I] overall tilt ux= -3.7972776319e-01 1.3239942820e-06 8.1226082032e-01 uy= 5.2293355091e-07 -1.1683700209e-01 -1.2887769015e-06 [I] storedr[0]= -6.2609002151e-03 -3.7831973391e-04 -6.4652945901e-03 [I] originally 49140 atoms [I] insert 0 atoms [I] now 49140 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 49140 atoms [I] remove 195 atoms [I] now 48945 atoms [I] NP=48945 n=48945 [I] ASSIGN finalcnfile = dipole_3.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 17:29:01 2023 CPU time spent: 33.924686 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 30 17:33:07 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 24 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 44 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=63360 [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) = 0.0069444444444444 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.066666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [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= 6.9444444444e-03 -0.0000000000e+00 -6.6666666667e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=1.313587e+02 pxpb=0.000000e+00 pypb=1.966322e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 29705 need remove atom 29717 need remove atom 29729 need remove atom 29741 need remove atom 29753 need remove atom 29761 need remove atom 29765 need remove atom 29773 need remove atom 29777 need remove atom 29785 need remove atom 29789 need remove atom 29797 need remove atom 29801 need remove atom 29809 need remove atom 29813 need remove atom 29821 need remove atom 29825 need remove atom 29833 need remove atom 29837 need remove atom 29845 need remove atom 29849 need remove atom 29857 need remove atom 29861 need remove atom 29869 need remove atom 29873 need remove atom 29881 need remove atom 29885 need remove atom 29893 need remove atom 29897 need remove atom 29905 need remove atom 29909 need remove atom 29917 need remove atom 29921 need remove atom 29929 need remove atom 29933 need remove atom 29941 need remove atom 29945 need remove atom 29953 need remove atom 29957 need remove atom 29965 need remove atom 29969 need remove atom 29977 need remove atom 29981 need remove atom 29989 need remove atom 29993 need remove atom 30001 need remove atom 30005 need remove atom 30013 need remove atom 30017 need remove atom 30025 need remove atom 30029 need remove atom 30037 need remove atom 30041 need remove atom 30049 need remove atom 30053 need remove atom 30061 need remove atom 30065 need remove atom 30073 need remove atom 30077 need remove atom 30085 need remove atom 30089 need remove atom 30097 need remove atom 30101 need remove atom 30109 need remove atom 30113 need remove atom 30121 need remove atom 30125 need remove atom 30133 need remove atom 30137 need remove atom 30145 need remove atom 30149 need remove atom 30157 need remove atom 30161 need remove atom 30169 need remove atom 30173 need remove atom 30181 need remove atom 30185 need remove atom 30193 need remove atom 30197 need remove atom 30205 need remove atom 30209 need remove atom 30217 need remove atom 30221 need remove atom 30229 need remove atom 30233 need remove atom 30241 need remove atom 30245 need remove atom 30253 need remove atom 30257 need remove atom 30265 need remove atom 30269 need remove atom 30277 need remove atom 30281 need remove atom 30289 need remove atom 30293 need remove atom 30301 need remove atom 30305 need remove atom 30313 need remove atom 30317 need remove atom 30325 need remove atom 30329 need remove atom 30337 need remove atom 30341 need remove atom 30349 need remove atom 30353 need remove atom 30361 need remove atom 30365 need remove atom 30373 need remove atom 30377 need remove atom 30385 need remove atom 30389 need remove atom 30397 need remove atom 30401 need remove atom 30409 need remove atom 30413 need remove atom 30421 need remove atom 30425 need remove atom 30433 need remove atom 30437 need remove atom 30445 need remove atom 30449 need remove atom 30457 need remove atom 30461 need remove atom 30469 need remove atom 30473 need remove atom 30481 need remove atom 30485 need remove atom 30493 need remove atom 30497 need remove atom 30505 need remove atom 30509 need remove atom 30517 need remove atom 30521 need remove atom 30529 need remove atom 30533 need remove atom 30541 need remove atom 30545 need remove atom 30553 need remove atom 30557 need remove atom 30565 need remove atom 30569 need remove atom 30577 need remove atom 30581 need remove atom 30589 need remove atom 30593 need remove atom 30601 need remove atom 30605 need remove atom 30613 need remove atom 30617 need remove atom 30625 need remove atom 30629 need remove atom 30637 need remove atom 30641 need remove atom 30649 need remove atom 30653 need remove atom 30661 need remove atom 30665 need remove atom 30673 need remove atom 30677 need remove atom 30685 need remove atom 30689 need remove atom 30697 need remove atom 30701 need remove atom 30709 need remove atom 30713 need remove atom 30721 need remove atom 30725 need remove atom 30733 need remove atom 30737 need remove atom 30745 need remove atom 30749 need remove atom 30757 need remove atom 30761 need remove atom 30769 need remove atom 30773 need remove atom 30781 need remove atom 30785 need remove atom 30793 need remove atom 30797 need remove atom 30805 need remove atom 30809 need remove atom 30817 need remove atom 30821 need remove atom 30829 need remove atom 30833 need remove atom 30841 need remove atom 30845 need remove atom 30853 need remove atom 30857 need remove atom 30865 need remove atom 30869 need remove atom 30877 need remove atom 30881 need remove atom 30889 need remove atom 30893 need remove atom 30901 need remove atom 30905 need remove atom 30913 need remove atom 30917 need remove atom 30925 need remove atom 30929 need remove atom 30937 need remove atom 30941 need remove atom 30949 need remove atom 30953 need remove atom 30961 need remove atom 30965 need remove atom 30973 need remove atom 30977 need remove atom 30985 need remove atom 30989 need remove atom 30997 need remove atom 31001 need remove atom 31009 need remove atom 31013 need remove atom 31021 need remove atom 31033 need remove atom 31045 need remove atom 31057 need remove atom 31069 [I] need removenum=220 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8473633698e-01 5.8245564965e-02 -4.0006838169e-01 dub= -1.9372517147e-01 5.8246816746e-02 4.0730219064e-01 duc= 1.8473686530e-01 -5.8985626585e-02 -4.0006966675e-01 [I] overall tilt ux= -3.7846150845e-01 1.2517811356e-06 8.0737057234e-01 uy= 5.2831732666e-07 -1.1723119155e-01 -1.2850541658e-06 [I] storedr[0]= -5.9733383415e-03 -3.7071030492e-04 -5.6113766763e-03 [I] originally 63360 atoms [I] insert 0 atoms [I] now 63360 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 63360 atoms [I] remove 220 atoms [I] now 63140 atoms [I] NP=63140 n=63140 [I] ASSIGN finalcnfile = dipole_4.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 17:33:51 2023 CPU time spent: 40.579102 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 30 17:40:37 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 26 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 48 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 6 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=89856 [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) = 0.0064102564102564 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.055555555555556 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [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= 6.4102564103e-03 -0.0000000000e+00 -5.5555555556e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=1.423052e+02 pxpb=0.000000e+00 pypb=2.145078e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 42339 need remove atom 42351 need remove atom 42363 need remove atom 42375 need remove atom 42387 need remove atom 42399 need remove atom 42411 need remove atom 42417 need remove atom 42423 need remove atom 42429 need remove atom 42435 need remove atom 42441 need remove atom 42447 need remove atom 42453 need remove atom 42459 need remove atom 42465 need remove atom 42471 need remove atom 42477 need remove atom 42483 need remove atom 42489 need remove atom 42495 need remove atom 42501 need remove atom 42507 need remove atom 42513 need remove atom 42519 need remove atom 42525 need remove atom 42531 need remove atom 42537 need remove atom 42543 need remove atom 42549 need remove atom 42555 need remove atom 42561 need remove atom 42567 need remove atom 42573 need remove atom 42579 need remove atom 42585 need remove atom 42591 need remove atom 42597 need remove atom 42603 need remove atom 42609 need remove atom 42615 need remove atom 42621 need remove atom 42627 need remove atom 42633 need remove atom 42639 need remove atom 42645 need remove atom 42651 need remove atom 42657 need remove atom 42663 need remove atom 42669 need remove atom 42675 need remove atom 42681 need remove atom 42687 need remove atom 42693 need remove atom 42699 need remove atom 42705 need remove atom 42711 need remove atom 42717 need remove atom 42723 need remove atom 42729 need remove atom 42735 need remove atom 42741 need remove atom 42747 need remove atom 42753 need remove atom 42759 need remove atom 42765 need remove atom 42771 need remove atom 42777 need remove atom 42783 need remove atom 42789 need remove atom 42795 need remove atom 42801 need remove atom 42807 need remove atom 42813 need remove atom 42819 need remove atom 42825 need remove atom 42831 need remove atom 42837 need remove atom 42843 need remove atom 42849 need remove atom 42855 need remove atom 42861 need remove atom 42867 need remove atom 42873 need remove atom 42879 need remove atom 42885 need remove atom 42891 need remove atom 42897 need remove atom 42903 need remove atom 42909 need remove atom 42915 need remove atom 42921 need remove atom 42927 need remove atom 42933 need remove atom 42939 need remove atom 42945 need remove atom 42951 need remove atom 42957 need remove atom 42963 need remove atom 42969 need remove atom 42975 need remove atom 42981 need remove atom 42987 need remove atom 42993 need remove atom 42999 need remove atom 43005 need remove atom 43011 need remove atom 43017 need remove atom 43023 need remove atom 43029 need remove atom 43035 need remove atom 43041 need remove atom 43047 need remove atom 43053 need remove atom 43059 need remove atom 43065 need remove atom 43071 need remove atom 43077 need remove atom 43083 need remove atom 43089 need remove atom 43095 need remove atom 43101 need remove atom 43107 need remove atom 43113 need remove atom 43119 need remove atom 43125 need remove atom 43131 need remove atom 43137 need remove atom 43143 need remove atom 43149 need remove atom 43155 need remove atom 43161 need remove atom 43167 need remove atom 43173 need remove atom 43179 need remove atom 43185 need remove atom 43191 need remove atom 43197 need remove atom 43203 need remove atom 43209 need remove atom 43215 need remove atom 43221 need remove atom 43227 need remove atom 43233 need remove atom 43239 need remove atom 43245 need remove atom 43251 need remove atom 43257 need remove atom 43263 need remove atom 43269 need remove atom 43275 need remove atom 43281 need remove atom 43287 need remove atom 43293 need remove atom 43299 need remove atom 43305 need remove atom 43311 need remove atom 43317 need remove atom 43323 need remove atom 43329 need remove atom 43335 need remove atom 43341 need remove atom 43347 need remove atom 43353 need remove atom 43359 need remove atom 43365 need remove atom 43371 need remove atom 43377 need remove atom 43383 need remove atom 43389 need remove atom 43395 need remove atom 43401 need remove atom 43407 need remove atom 43413 need remove atom 43419 need remove atom 43425 need remove atom 43431 need remove atom 43437 need remove atom 43443 need remove atom 43449 need remove atom 43455 need remove atom 43461 need remove atom 43467 need remove atom 43473 need remove atom 43479 need remove atom 43485 need remove atom 43491 need remove atom 43497 need remove atom 43503 need remove atom 43509 need remove atom 43515 need remove atom 43521 need remove atom 43527 need remove atom 43533 need remove atom 43539 need remove atom 43545 need remove atom 43551 need remove atom 43557 need remove atom 43563 need remove atom 43569 need remove atom 43575 need remove atom 43581 need remove atom 43587 need remove atom 43593 need remove atom 43599 need remove atom 43605 need remove atom 43611 need remove atom 43617 need remove atom 43623 need remove atom 43629 need remove atom 43635 need remove atom 43641 need remove atom 43647 need remove atom 43653 need remove atom 43659 need remove atom 43665 need remove atom 43671 need remove atom 43677 need remove atom 43683 need remove atom 43689 need remove atom 43695 need remove atom 43701 need remove atom 43707 need remove atom 43713 need remove atom 43719 need remove atom 43725 need remove atom 43731 need remove atom 43737 need remove atom 43743 need remove atom 43749 need remove atom 43755 need remove atom 43761 need remove atom 43767 need remove atom 43773 need remove atom 43779 need remove atom 43785 need remove atom 43791 need remove atom 43797 need remove atom 43803 need remove atom 43809 need remove atom 43815 need remove atom 43821 need remove atom 43827 need remove atom 43833 need remove atom 43839 need remove atom 43845 need remove atom 43851 need remove atom 43857 need remove atom 43863 need remove atom 43869 need remove atom 43875 need remove atom 43881 need remove atom 43887 need remove atom 43893 need remove atom 43899 need remove atom 43905 need remove atom 43911 need remove atom 43917 need remove atom 43923 need remove atom 43929 need remove atom 43935 need remove atom 43941 need remove atom 43947 need remove atom 43953 need remove atom 43959 need remove atom 43965 need remove atom 43971 need remove atom 43977 need remove atom 43983 need remove atom 43989 need remove atom 43995 need remove atom 44001 need remove atom 44007 need remove atom 44013 need remove atom 44019 need remove atom 44025 need remove atom 44031 need remove atom 44037 need remove atom 44043 need remove atom 44049 need remove atom 44055 need remove atom 44061 need remove atom 44073 need remove atom 44085 need remove atom 44097 need remove atom 44109 need remove atom 44121 need remove atom 44133 [I] need removenum=288 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8506212579e-01 5.8135123652e-02 -4.0129909951e-01 dub= -1.9408565314e-01 5.8136414780e-02 4.0871555146e-01 duc= 1.8506265122e-01 -5.8883232026e-02 -4.0130038662e-01 [I] overall tilt ux= -3.7914777893e-01 1.2911274681e-06 8.1001465097e-01 uy= 5.2542402615e-07 -1.1701835568e-01 -1.2871085424e-06 [I] storedr[0]= -5.8967198546e-03 -3.7462562320e-04 -4.6906869008e-03 [I] originally 89856 atoms [I] insert 0 atoms [I] now 89856 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 89856 atoms [I] remove 288 atoms [I] now 89568 atoms [I] NP=89568 n=89568 [I] ASSIGN finalcnfile = dipole_4.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 17:41:39 2023 CPU time spent: 57.205437 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 30 17:49:14 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 29 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 53 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 7 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=129108 [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) = 0.0057471264367816 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.047619047619048 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [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= 5.7471264368e-03 -0.0000000000e+00 -4.7619047619e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=1.587251e+02 pxpb=0.000000e+00 pypb=2.368524e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 63422 need remove atom 63434 need remove atom 63446 need remove atom 63458 need remove atom 63470 need remove atom 63482 need remove atom 63494 need remove atom 63506 need remove atom 63512 need remove atom 63518 need remove atom 63524 need remove atom 63530 need remove atom 63536 need remove atom 63542 need remove atom 63548 need remove atom 63554 need remove atom 63560 need remove atom 63566 need remove atom 63572 need remove atom 63578 need remove atom 63584 need remove atom 63590 need remove atom 63596 need remove atom 63602 need remove atom 63608 need remove atom 63614 need remove atom 63620 need remove atom 63626 need remove atom 63632 need remove atom 63638 need remove atom 63644 need remove atom 63650 need remove atom 63656 need remove atom 63662 need remove atom 63668 need remove atom 63674 need remove atom 63680 need remove atom 63686 need remove atom 63692 need remove atom 63698 need remove atom 63704 need remove atom 63710 need remove atom 63716 need remove atom 63722 need remove atom 63728 need remove atom 63734 need remove atom 63740 need remove atom 63746 need remove atom 63752 need remove atom 63758 need remove atom 63764 need remove atom 63770 need remove atom 63776 need remove atom 63782 need remove atom 63788 need remove atom 63794 need remove atom 63800 need remove atom 63806 need remove atom 63812 need remove atom 63818 need remove atom 63824 need remove atom 63830 need remove atom 63836 need remove atom 63842 need remove atom 63848 need remove atom 63854 need remove atom 63860 need remove atom 63866 need remove atom 63872 need remove atom 63878 need remove atom 63884 need remove atom 63890 need remove atom 63896 need remove atom 63902 need remove atom 63908 need remove atom 63914 need remove atom 63920 need remove atom 63926 need remove atom 63932 need remove atom 63938 need remove atom 63944 need remove atom 63950 need remove atom 63956 need remove atom 63962 need remove atom 63968 need remove atom 63974 need remove atom 63980 need remove atom 63986 need remove atom 63992 need remove atom 63998 need remove atom 64004 need remove atom 64010 need remove atom 64016 need remove atom 64022 need remove atom 64028 need remove atom 64034 need remove atom 64040 need remove atom 64046 need remove atom 64052 need remove atom 64058 need remove atom 64064 need remove atom 64070 need remove atom 64076 need remove atom 64082 need remove atom 64088 need remove atom 64094 need remove atom 64100 need remove atom 64106 need remove atom 64112 need remove atom 64118 need remove atom 64124 need remove atom 64130 need remove atom 64136 need remove atom 64142 need remove atom 64148 need remove atom 64154 need remove atom 64160 need remove atom 64166 need remove atom 64172 need remove atom 64178 need remove atom 64184 need remove atom 64190 need remove atom 64196 need remove atom 64202 need remove atom 64208 need remove atom 64214 need remove atom 64220 need remove atom 64226 need remove atom 64232 need remove atom 64238 need remove atom 64244 need remove atom 64250 need remove atom 64256 need remove atom 64262 need remove atom 64268 need remove atom 64274 need remove atom 64280 need remove atom 64286 need remove atom 64292 need remove atom 64298 need remove atom 64304 need remove atom 64310 need remove atom 64316 need remove atom 64322 need remove atom 64328 need remove atom 64334 need remove atom 64340 need remove atom 64346 need remove atom 64352 need remove atom 64358 need remove atom 64364 need remove atom 64370 need remove atom 64376 need remove atom 64382 need remove atom 64388 need remove atom 64394 need remove atom 64400 need remove atom 64406 need remove atom 64412 need remove atom 64418 need remove atom 64424 need remove atom 64430 need remove atom 64436 need remove atom 64442 need remove atom 64448 need remove atom 64454 need remove atom 64460 need remove atom 64466 need remove atom 64472 need remove atom 64478 need remove atom 64484 need remove atom 64490 need remove atom 64496 need remove atom 64502 need remove atom 64508 need remove atom 64514 need remove atom 64520 need remove atom 64526 need remove atom 64532 need remove atom 64538 need remove atom 64544 need remove atom 64550 need remove atom 64556 need remove atom 64562 need remove atom 64568 need remove atom 64574 need remove atom 64580 need remove atom 64586 need remove atom 64592 need remove atom 64598 need remove atom 64604 need remove atom 64610 need remove atom 64616 need remove atom 64622 need remove atom 64628 need remove atom 64634 need remove atom 64640 need remove atom 64646 need remove atom 64652 need remove atom 64658 need remove atom 64664 need remove atom 64670 need remove atom 64676 need remove atom 64682 need remove atom 64688 need remove atom 64694 need remove atom 64700 need remove atom 64706 need remove atom 64712 need remove atom 64718 need remove atom 64724 need remove atom 64730 need remove atom 64736 need remove atom 64742 need remove atom 64748 need remove atom 64754 need remove atom 64760 need remove atom 64766 need remove atom 64772 need remove atom 64778 need remove atom 64784 need remove atom 64790 need remove atom 64796 need remove atom 64802 need remove atom 64808 need remove atom 64814 need remove atom 64820 need remove atom 64826 need remove atom 64832 need remove atom 64838 need remove atom 64844 need remove atom 64850 need remove atom 64856 need remove atom 64862 need remove atom 64868 need remove atom 64874 need remove atom 64880 need remove atom 64886 need remove atom 64892 need remove atom 64898 need remove atom 64904 need remove atom 64910 need remove atom 64916 need remove atom 64922 need remove atom 64928 need remove atom 64934 need remove atom 64940 need remove atom 64946 need remove atom 64952 need remove atom 64958 need remove atom 64964 need remove atom 64970 need remove atom 64976 need remove atom 64982 need remove atom 64988 need remove atom 64994 need remove atom 65000 need remove atom 65006 need remove atom 65012 need remove atom 65018 need remove atom 65024 need remove atom 65030 need remove atom 65036 need remove atom 65042 need remove atom 65048 need remove atom 65054 need remove atom 65060 need remove atom 65066 need remove atom 65072 need remove atom 65078 need remove atom 65084 need remove atom 65090 need remove atom 65096 need remove atom 65102 need remove atom 65108 need remove atom 65114 need remove atom 65120 need remove atom 65126 need remove atom 65132 need remove atom 65138 need remove atom 65144 need remove atom 65150 need remove atom 65156 need remove atom 65162 need remove atom 65168 need remove atom 65174 need remove atom 65180 need remove atom 65186 need remove atom 65192 need remove atom 65198 need remove atom 65204 need remove atom 65210 need remove atom 65216 need remove atom 65222 need remove atom 65228 need remove atom 65234 need remove atom 65240 need remove atom 65246 need remove atom 65252 need remove atom 65258 need remove atom 65264 need remove atom 65270 need remove atom 65276 need remove atom 65282 need remove atom 65288 need remove atom 65294 need remove atom 65300 need remove atom 65306 need remove atom 65312 need remove atom 65318 need remove atom 65324 need remove atom 65330 need remove atom 65336 need remove atom 65342 need remove atom 65348 need remove atom 65354 need remove atom 65360 need remove atom 65366 need remove atom 65372 need remove atom 65378 need remove atom 65384 need remove atom 65390 need remove atom 65396 need remove atom 65402 need remove atom 65408 need remove atom 65414 need remove atom 65420 need remove atom 65426 need remove atom 65432 need remove atom 65438 need remove atom 65444 need remove atom 65450 need remove atom 65456 need remove atom 65462 need remove atom 65468 need remove atom 65474 need remove atom 65480 need remove atom 65486 need remove atom 65492 need remove atom 65498 need remove atom 65504 need remove atom 65510 need remove atom 65516 need remove atom 65522 need remove atom 65528 need remove atom 65534 need remove atom 65540 need remove atom 65546 need remove atom 65552 need remove atom 65558 need remove atom 65564 need remove atom 65570 need remove atom 65576 need remove atom 65582 need remove atom 65588 need remove atom 65594 need remove atom 65600 need remove atom 65606 need remove atom 65612 need remove atom 65618 need remove atom 65624 need remove atom 65630 need remove atom 65636 need remove atom 65642 need remove atom 65648 need remove atom 65654 need remove atom 65660 need remove atom 65666 need remove atom 65672 need remove atom 65678 need remove atom 65684 [I] need removenum=371 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8458879120e-01 5.8295300204e-02 -3.9951287090e-01 dub= -1.9356166454e-01 5.8296533993e-02 4.0666411456e-01 duc= 1.8458932081e-01 -5.9031734057e-02 -3.9951415499e-01 [I] overall tilt ux= -3.7815045574e-01 1.2337887171e-06 8.0617698546e-01 uy= 5.2960962918e-07 -1.1732703426e-01 -1.2840948994e-06 [I] storedr[0]= -5.7019836597e-03 -3.6867826184e-04 -4.1213748488e-03 [I] originally 129108 atoms [I] insert 0 atoms [I] now 129108 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 129108 atoms [I] remove 371 atoms [I] now 128737 atoms [I] NP=128737 n=128737 [I] ASSIGN finalcnfile = dipole_5.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.0.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 30 17:50:43 2023 CPU time spent: 82.204163 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 30 17:56:24 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1599989235401 [I] ASSIGN makecnspec = -1 [I] ASSIGN makecnspec(1) = -1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 32 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 59 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 2 [I] ASSIGN makecnspec(11) = 7 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -1 -1 1 -1 1 1 1 0 2]; basis=[ 0.5 0 0 0 0 0.833333 0 0.333333 0 1 0.166667 0.5 0.166667 0 2 0.666667 0.5 0.166667 0 3 0.5 0.5 0.5 0 4 0.833333 0.5 0.833333 0 5 0 0 0 0 6 0.333333 0 0.333333 0 7 0.166667 0 0.666667 0 8 0.666667 0 0.666667 0 9 0 0.5 0.5 0 10 0.333333 0.5 0.833333 0 11 ]; [I] makecn: _NP=158592 [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) = 0.0052083333333333 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.047619047619048 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27791930643697 [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= 5.2083333333e-03 -0.0000000000e+00 -4.7619047619e-02 b= 9.1221311457e-01 0.0000000000e+00 -2.5801283168e+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=0.91221311457241 by=0 pxpa=1.751449e+02 pxpb=0.000000e+00 pypb=2.636659e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 75603 need remove atom 75609 need remove atom 75615 need remove atom 75621 need remove atom 75627 need remove atom 75633 need remove atom 75639 need remove atom 75645 need remove atom 75651 need remove atom 75657 need remove atom 75663 need remove atom 75669 need remove atom 75675 need remove atom 75681 need remove atom 75687 need remove atom 75693 need remove atom 75699 need remove atom 75705 need remove atom 75711 need remove atom 75717 need remove atom 75723 need remove atom 75729 need remove atom 75735 need remove atom 75741 need remove atom 75747 need remove atom 75753 need remove atom 75759 need remove atom 75765 need remove atom 75771 need remove atom 75777 need remove atom 75783 need remove atom 75789 need remove atom 75795 need remove atom 75801 need remove atom 75807 need remove atom 75813 need remove atom 75819 need remove atom 75825 need remove atom 75831 need remove atom 75837 need remove atom 75843 need remove atom 75849 need remove atom 75855 need remove atom 75861 need remove atom 75867 need remove atom 75873 need remove atom 75879 need remove atom 75885 need remove atom 75891 need remove atom 75897 need remove atom 75903 need remove atom 75909 need remove atom 75915 need remove atom 75921 need remove atom 75927 need remove atom 75933 need remove atom 75939 need remove atom 75945 need remove atom 75951 need remove atom 75957 need remove atom 75963 need remove atom 75969 need remove atom 75975 need remove atom 75981 need remove atom 75987 need remove atom 75993 need remove atom 75999 need remove atom 76005 need remove atom 76011 need remove atom 76017 need remove atom 76023 need remove atom 76029 need remove atom 76035 need remove atom 76041 need remove atom 76047 need remove atom 76053 need remove atom 76059 need remove atom 76065 need remove atom 76071 need remove atom 76077 need remove atom 76083 need remove atom 76089 need remove atom 76095 need remove atom 76101 need remove atom 76107 need remove atom 76113 need remove atom 76119 need remove atom 76125 need remove atom 76131 need remove atom 76137 need remove atom 76143 need remove atom 76149 need remove atom 76155 need remove atom 76161 need remove atom 76167 need remove atom 76173 need remove atom 76179 need remove atom 76185 need remove atom 76191 need remove atom 76197 need remove atom 76203 need remove atom 76209 need remove atom 76215 need remove atom 76221 need remove atom 76227 need remove atom 76233 need remove atom 76239 need remove atom 76245 need remove atom 76251 need remove atom 76257 need remove atom 76263 need remove atom 76269 need remove atom 76275 need remove atom 76281 need remove atom 76287 need remove atom 76293 need remove atom 76299 need remove atom 76305 need remove atom 76311 need remove atom 76317 need remove atom 76323 need remove atom 76329 need remove atom 76335 need remove atom 76341 need remove atom 76347 need remove atom 76353 need remove atom 76359 need remove atom 76365 need remove atom 76371 need remove atom 76377 need remove atom 76383 need remove atom 76389 need remove atom 76395 need remove atom 76401 need remove atom 76407 need remove atom 76413 need remove atom 76419 need remove atom 76425 need remove atom 76431 need remove atom 76437 need remove atom 76443 need remove atom 76449 need remove atom 76455 need remove atom 76461 need remove atom 76467 need remove atom 76473 need remove atom 76479 need remove atom 76485 need remove atom 76491 need remove atom 76497 need remove atom 76503 need remove atom 76509 need remove atom 76515 need remove atom 76521 need remove atom 76527 need remove atom 76533 need remove atom 76539 need remove atom 76545 need remove atom 76551 need remove atom 76557 need remove atom 76563 need remove atom 76569 need remove atom 76575 need remove atom 76581 need remove atom 76587 need remove atom 76593 need remove atom 76599 need remove atom 76605 need remove atom 76611 need remove atom 76617 need remove atom 76623 need remove atom 76629 need remove atom 76635 need remove atom 76641 need remove atom 76647 need remove atom 76653 need remove atom 76659 need remove atom 76665 need remove atom 76671 need remove atom 76677 need remove atom 76683 need remove atom 76689 need remove atom 76695 need remove atom 76701 need remove atom 76707 need remove atom 76713 need remove atom 76719 need remove atom 76725 need remove atom 76731 need remove atom 76737 need remove atom 76743 need remove atom 76749 need remove atom 76755 need remove atom 76761 need remove atom 76767 need remove atom 76773 need remove atom 76779 need remove atom 76785 need remove atom 76791 need remove atom 76797 need remove atom 76803 need remove atom 76809 need remove atom 76815 need remove atom 76821 need remove atom 76827 need remove atom 76833 need remove atom 76839 need remove atom 76845 need remove atom 76851 need remove atom 76857 need remove atom 76863 need remove atom 76869 need remove atom 76875 need remove atom 76881 need remove atom 76887 need remove atom 76893 need remove atom 76899 need remove atom 76905 need remove atom 76911 need remove atom 76917 need remove atom 76923 need remove atom 76929 need remove atom 76935 need remove atom 76941 need remove atom 76947 need remove atom 76953 need remove atom 76959 need remove atom 76965 need remove atom 76971 need remove atom 76977 need remove atom 76983 need remove atom 76989 need remove atom 76995 need remove atom 77001 need remove atom 77007 need remove atom 77013 need remove atom 77019 need remove atom 77025 need remove atom 77031 need remove atom 77037 need remove atom 77043 need remove atom 77049 need remove atom 77055 need remove atom 77061 need remove atom 77067 need remove atom 77073 need remove atom 77079 need remove atom 77085 need remove atom 77091 need remove atom 77097 need remove atom 77103 need remove atom 77109 need remove atom 77115 need remove atom 77121 need remove atom 77127 need remove atom 77133 need remove atom 77139 need remove atom 77145 need remove atom 77151 need remove atom 77157 need remove atom 77163 need remove atom 77169 need remove atom 77175 need remove atom 77181 need remove atom 77187 need remove atom 77193 need remove atom 77199 need remove atom 77205 need remove atom 77211 need remove atom 77217 need remove atom 77223 need remove atom 77229 need remove atom 77235 need remove atom 77241 need remove atom 77247 need remove atom 77253 need remove atom 77259 need remove atom 77265 need remove atom 77271 need remove atom 77277 need remove atom 77283 need remove atom 77289 need remove atom 77295 need remove atom 77301 need remove atom 77307 need remove atom 77313 need remove atom 77319 need remove atom 77325 need remove atom 77331 need remove atom 77337 need remove atom 77343 need remove atom 77349 need remove atom 77355 need remove atom 77361 need remove atom 77367 need remove atom 77373 need remove atom 77379 need remove atom 77385 need remove atom 77391 need remove atom 77397 need remove atom 77403 need remove atom 77409 need remove atom 77415 need remove atom 77421 need remove atom 77427 need remove atom 77433 need remove atom 77439 need remove atom 77445 need remove atom 77451 need remove atom 77457 need remove atom 77463 need remove atom 77469 need remove atom 77475 need remove atom 77481 need remove atom 77487 need remove atom 77493 need remove atom 77499 need remove atom 77505 need remove atom 77511 need remove atom 77517 need remove atom 77523 need remove atom 77529 need remove atom 77535 need remove atom 77541 need remove atom 77547 need remove atom 77553 need remove atom 77559 need remove atom 77565 need remove atom 77571 need remove atom 77577 need remove atom 77583 need remove atom 77589 need remove atom 77595 need remove atom 77601 need remove atom 77607 need remove atom 77613 need remove atom 77619 need remove atom 77625 need remove atom 77631 need remove atom 77637 need remove atom 77643 need remove atom 77649 need remove atom 77655 need remove atom 77661 need remove atom 77667 need remove atom 77673 need remove atom 77679 need remove atom 77685 need remove atom 77691 need remove atom 77697 need remove atom 77703 need remove atom 77709 need remove atom 77715 need remove atom 77721 need remove atom 77727 need remove atom 77733 need remove atom 77739 need remove atom 77745 need remove atom 77751 need remove atom 77757 need remove atom 77763 need remove atom 77769 need remove atom 77775 need remove atom 77781 need remove atom 77787 need remove atom 77793 need remove atom 77799 need remove atom 77805 need remove atom 77811 need remove atom 77817 need remove atom 77823 need remove atom 77829 need remove atom 77835 need remove atom 77841 need remove atom 77847 need remove atom 77853 need remove atom 77859 need remove atom 77865 need remove atom 77871 need remove atom 77877 need remove atom 77883 need remove atom 77889 need remove atom 77895 need remove atom 77901 need remove atom 77907 need remove atom 77913 need remove atom 77919 need remove atom 77925 need remove atom 77931 need remove atom 77937 need remove atom 77943 need remove atom 77949 need remove atom 77955 need remove atom 77961 need remove atom 77967 need remove atom 77973 need remove atom 77979 need remove atom 77985 need remove atom 77991 need remove atom 77997 need remove atom 78003 need remove atom 78009 need remove atom 78015 need remove atom 78021 need remove atom 78027 need remove atom 78033 need remove atom 78045 need remove atom 78057 need remove atom 78069 need remove atom 78081 need remove atom 78093 need remove atom 78105 need remove atom 78117 [I] need removenum=413 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 1.8500139018e-01 5.8155777742e-02 -4.0106922908e-01 dub= -1.9401850769e-01 5.8157061574e-02 4.0845159709e-01 duc= 1.8500191615e-01 -5.8902382174e-02 -4.0107051581e-01 [I] overall tilt ux= -3.7901989787e-01 1.2838326533e-06 8.0952082617e-01 uy= 5.2596756753e-07 -1.1705815992e-01 -1.2867322659e-06 [I] storedr[0]= -5.6308140721e-03 -3.7365177853e-04 -3.1598518872e-03 [I] originally 158592 atoms [I] insert 0 atoms [I] now 158592 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 158592 atoms [I] remove 413 atoms [I] now 158179 atoms [I] NP=158179 n=158179 [I] ASSIGN finalcnfile = dipole_5.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue May 30 17:58:13 2023 CPU time spent: 100.272646 s Traceback (most recent call last): File "../../td/DislocationCoreEnergyCubic__TD_452950666597_002/runner", line 2675, in msg = cr.run_length_control( File "/usr/local/lib/python3.8/dist-packages/convergence/timeseries.py", line 1071, in run_length_control msg += 'for variable number {},\n'.format(i + 1) UnboundLocalError: local variable 'msg' referenced before assignment During handling of the above exception, another exception occurred: Traceback (most recent call last): File "../../td/DislocationCoreEnergyCubic__TD_452950666597_002/runner", line 2689, in raise cr.CVGError(msg) convergence.err.CVGError: ERROR(@): local variable 'msg' referenced before assignment Command exited with non-zero status 1 {"realtime":3072.80,"usertime":7089.42,"systime":164.89,"memmax":128284,"memavg":0}