QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters2' [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [I] RUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue May 30 16:30:13 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.7777777778e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=3.313268e+01 pxpb=0.000000e+00 pypb=4.959666e+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= 1.8657986573e-01 5.8450274597e-02 -4.0363796073e-01 dub= -1.9567790630e-01 5.8451568615e-02 4.1093631278e-01 duc= 1.8658039909e-01 -5.9199326158e-02 -4.0363925725e-01 [I] overall tilt ux= -3.8225777202e-01 1.2940178941e-06 8.1457427350e-01 uy= 5.3336484213e-07 -1.1764960076e-01 -1.2965199612e-06 [I] storedr[0]= -1.0599219814e-02 -3.7846515847e-04 -3.2041351333e-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 16:30:13 2023 CPU time spent: 0.134367 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 16:31:59 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.3809523810e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=3.865480e+01 pxpb=0.000000e+00 pypb=5.861423e+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= 1.8718571955e-01 5.8241414511e-02 -4.0593464059e-01 dub= -1.9634751855e-01 5.8242781459e-02 4.1357351375e-01 duc= 1.8718624745e-01 -5.9005502557e-02 -4.0593594087e-01 [I] overall tilt ux= -3.8353323810e-01 1.3669477945e-06 8.1950815434e-01 uy= 5.2790281299e-07 -1.1724691707e-01 -1.3002759153e-06 [I] storedr[0]= -9.8924125711e-03 -3.8531523084e-04 -2.6279269718e-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 16:32:00 2023 CPU time spent: 0.189050 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 16:34:11 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.0833333333e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=4.417691e+01 pxpb=0.000000e+00 pypb=6.763180e+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= 1.8762983207e-01 5.8086442364e-02 -4.0763086448e-01 dub= -1.9683666831e-01 5.8087861564e-02 4.1552032249e-01 duc= 1.8763035585e-01 -5.8861663143e-02 -4.0763216731e-01 [I] overall tilt ux= -3.8446650039e-01 1.4191992989e-06 8.2315118697e-01 uy= 5.2377916890e-07 -1.1694810551e-01 -1.3028314832e-06 [I] storedr[0]= -9.3297275818e-03 -3.9041355564e-04 -2.2046996702e-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 16:34:11 2023 CPU time spent: 0.249926 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 16:35:07 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.8518518519e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=4.969902e+01 pxpb=0.000000e+00 pypb=7.664938e+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= 1.8796932493e-01 5.7966918611e-02 -4.0893485741e-01 dub= -1.9720959815e-01 5.7968377035e-02 4.1701639801e-01 duc= 1.8796984549e-01 -5.8750713148e-02 -4.0893616208e-01 [I] overall tilt ux= -3.8517892308e-01 1.4584237020e-06 8.2595125542e-01 uy= 5.2055882810e-07 -1.1671763176e-01 -1.3046688753e-06 [I] storedr[0]= -8.8735730036e-03 -3.9434738914e-04 -1.8814215083e-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 16:35:07 2023 CPU time spent: 0.309037 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 16:36:04 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.6666666667e-02 -0.0000000000e+00 -1.6666666667e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=5.522114e+01 pxpb=0.000000e+00 pypb=8.115816e+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= 1.8570437335e-01 5.8746833236e-02 -4.0035361463e-01 dub= -1.9470569302e-01 5.8748018696e-02 4.0716275847e-01 duc= 1.8570491427e-01 -5.9474460090e-02 -4.0035490520e-01 [I] overall tilt ux= -3.8041006637e-01 1.1854600646e-06 8.0751637310e-01 uy= 5.4092343763e-07 -1.1822129333e-01 -1.2905649247e-06 [I] storedr[0]= -7.9928145042e-03 -3.6637379242e-04 -1.9471964098e-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 16:36:04 2023 CPU time spent: 0.371802 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 16:37:33 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.6666666667e-02 -0.0000000000e+00 -1.1111111111e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=5.522114e+01 pxpb=0.000000e+00 pypb=8.115816e+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= 1.8570437335e-01 5.8746833236e-02 -4.0035361463e-01 dub= -1.9470569302e-01 5.8748018696e-02 4.0716275847e-01 duc= 1.8570491427e-01 -5.9474460090e-02 -4.0035490520e-01 [I] overall tilt ux= -3.8041006637e-01 1.1854600646e-06 8.0751637310e-01 uy= 5.4092343763e-07 -1.1822129333e-01 -1.2905649246e-06 [I] storedr[0]= -7.9928145042e-03 -3.6637379242e-04 -1.9471964098e-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 16:37:34 2023 CPU time spent: 0.558327 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 16:40:22 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.5151515152e-02 -0.0000000000e+00 -1.1111111111e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=6.074325e+01 pxpb=0.000000e+00 pypb=9.017574e+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= 1.8618593848e-01 5.8584483689e-02 -4.0215518459e-01 dub= -1.9524111967e-01 5.8585729310e-02 4.0923298686e-01 duc= 1.8618647530e-01 -5.9323851009e-02 -4.0215647851e-01 [I] overall tilt ux= -3.8142705815e-01 1.2456215902e-06 8.1138817145e-01 uy= 5.3681480525e-07 -1.1790833470e-01 -1.2939159869e-06 [I] storedr[0]= -7.7738940513e-03 -3.7191045573e-04 -1.6887554233e-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 16:40:22 2023 CPU time spent: 0.672836 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 16:42:40 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.3888888889e-02 -0.0000000000e+00 -1.1111111111e-01 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=6.626536e+01 pxpb=0.000000e+00 pypb=9.919331e+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= 1.8657986573e-01 5.8450274597e-02 -4.0363796073e-01 dub= -1.9567790630e-01 5.8451568615e-02 4.1093631278e-01 duc= 1.8658039909e-01 -5.9199326158e-02 -4.0363925725e-01 [I] overall tilt ux= -3.8225777202e-01 1.2940178934e-06 8.1457427350e-01 uy= 5.3336484213e-07 -1.1764960076e-01 -1.2965199625e-06 [I] storedr[0]= -7.5767919128e-03 -3.7648949297e-04 -1.4793347281e-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 16:42:41 2023 CPU time spent: 0.810955 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 16:46:12 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.1111111111e-02 -0.0000000000e+00 -8.3333333333e-02 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=8.283170e+01 pxpb=0.000000e+00 pypb=1.262460e+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= 1.8742365814e-01 5.8158582145e-02 -4.0684206624e-01 dub= -1.9660976757e-01 5.8159977217e-02 4.1461509395e-01 duc= 1.8742418384e-01 -5.8928623005e-02 -4.0684336791e-01 [I] overall tilt ux= -3.8403342571e-01 1.3950725228e-06 8.2145716020e-01 uy= 5.2570609935e-07 -1.1708720515e-01 -1.3016662663e-06 [I] storedr[0]= -7.0998656056e-03 -3.8643824343e-04 -1.0375037555e-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 16:46:14 2023 CPU time spent: 1.734967 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 16:54:29 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1881937682629 [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) = 0.28113258894964 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 9.2592592593e-03 -0.0000000000e+00 -8.3333333333e-02 b= 9.2035226517e-01 0.0000000000e+00 -2.6031493111e+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=0.92035226516763 by=0 pxpa=9.939804e+01 pxpb=0.000000e+00 pypb=1.487900e+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= 1.8657986573e-01 5.8450274597e-02 -4.0363796073e-01 dub= -1.9567790630e-01 5.8451568615e-02 4.1093631278e-01 duc= 1.8658039909e-01 -5.9199326158e-02 -4.0363925725e-01 [I] overall tilt ux= -3.8225777202e-01 1.2940178939e-06 8.1457427350e-01 uy= 5.3336484260e-07 -1.1764960076e-01 -1.2965199612e-06 [I] storedr[0]= -6.5672464152e-03 -3.7565435678e-04 -8.7311507538e-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 16:54:32 2023 CPU time spent: 2.444083 s /usr/local/lib/python3.8/dist-packages/convergence/zero_rc.py:212: RuntimeWarning: invalid value encountered in scalar divide fdb = (self.fd - self.fb) / (self.d - self.b) {"realtime":2200.25,"usertime":4366.53,"systime":21.19,"memmax":124696,"memavg":0}