QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters2' [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [I] RUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:04:08 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 4 [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) = 4 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=1872 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.041666666666667 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 4.1666666667e-02 -0.0000000000e+00 -1.6666666667e-01 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=3.798240e+01 pxpb=0.000000e+00 pypb=5.819149e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 581 need remove atom 584 need remove atom 613 need remove atom 617 need remove atom 620 need remove atom 628 need remove atom 649 need remove atom 653 need remove atom 656 need remove atom 664 need remove atom 685 need remove atom 689 need remove atom 692 need remove atom 700 need remove atom 721 need remove atom 725 need remove atom 728 need remove atom 736 need remove atom 757 need remove atom 761 need remove atom 764 need remove atom 772 need remove atom 793 need remove atom 797 need remove atom 800 need remove atom 808 need remove atom 1077 need remove atom 1106 need remove atom 1113 need remove atom 1142 need remove atom 1149 need remove atom 1178 need remove atom 1185 need remove atom 1214 need remove atom 1221 need remove atom 1250 need remove atom 1257 need remove atom 1286 need remove atom 1293 [I] need removenum=39 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2271995944e-01 9.9828371268e-02 -3.5058523813e-01 dub= -3.3856055585e-01 9.9830821829e-02 3.5738503591e-01 duc= 3.2272085958e-01 -1.0116314504e-01 -3.5058635844e-01 [I] overall tilt ux= -6.6128051529e-01 2.4505609372e-06 7.0797027405e-01 uy= 9.0014622078e-07 -2.0099151630e-01 -1.1203107179e-06 [I] storedr[0]= -3.2938039098e-02 -6.4879523035e-04 -5.4348075858e-02 [I] originally 1872 atoms [I] insert 0 atoms [I] now 1872 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1872 atoms [I] remove 39 atoms [I] now 1833 atoms [I] NP=1833 n=1833 [I] ASSIGN finalcnfile = dipole_1.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:04:08 2023 CPU time spent: 0.149211 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:04:24 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 5 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 16 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [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) = 0.033333333333333 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.16666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.3333333333e-02 -0.0000000000e+00 -1.6666666667e-01 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=4.747800e+01 pxpb=0.000000e+00 pypb=7.162030e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1298 need remove atom 1317 need remove atom 1320 need remove atom 1334 need remove atom 1343 need remove atom 1345 need remove atom 1353 need remove atom 1356 need remove atom 1364 need remove atom 1370 need remove atom 1379 need remove atom 1381 need remove atom 1389 need remove atom 1392 need remove atom 1400 need remove atom 1406 need remove atom 1415 need remove atom 1417 need remove atom 1425 need remove atom 1428 need remove atom 1436 need remove atom 1442 need remove atom 1451 need remove atom 1453 need remove atom 1461 need remove atom 1464 need remove atom 1472 need remove atom 1478 need remove atom 1487 need remove atom 1489 need remove atom 1497 need remove atom 1500 need remove atom 1508 need remove atom 1514 need remove atom 1523 need remove atom 1525 need remove atom 1533 need remove atom 1536 need remove atom 1544 need remove atom 1550 need remove atom 1559 need remove atom 1561 need remove atom 1569 need remove atom 1572 need remove atom 1580 need remove atom 1595 need remove atom 1597 need remove atom 1616 [I] need removenum=48 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2147991674e-01 1.0026040380e-01 -3.4822045836e-01 dub= -3.3719383418e-01 1.0026270777e-01 3.5467065031e-01 duc= 3.2148082834e-01 -1.0156415022e-01 -3.4822157504e-01 [I] overall tilt ux= -6.5867375092e-01 2.3039667060e-06 7.0289110867e-01 uy= 9.1159869281e-07 -2.0182455402e-01 -1.1166873585e-06 [I] storedr[0]= -2.8408154823e-02 -6.5247761985e-04 -4.9850601396e-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 48 atoms [I] now 2832 atoms [I] NP=2832 n=2832 [I] ASSIGN finalcnfile = dipole_1.3.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.3.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.3.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:04:24 2023 CPU time spent: 0.241930 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:04:47 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 5 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 16 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=5760 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.033333333333333 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.3333333333e-02 -0.0000000000e+00 -8.3333333333e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=4.747800e+01 pxpb=0.000000e+00 pypb=7.162030e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2594 need remove atom 2613 need remove atom 2616 need remove atom 2630 need remove atom 2649 need remove atom 2652 need remove atom 2666 need remove atom 2675 need remove atom 2677 need remove atom 2685 need remove atom 2688 need remove atom 2696 need remove atom 2702 need remove atom 2711 need remove atom 2713 need remove atom 2721 need remove atom 2724 need remove atom 2732 need remove atom 2738 need remove atom 2747 need remove atom 2749 need remove atom 2757 need remove atom 2760 need remove atom 2768 need remove atom 2774 need remove atom 2783 need remove atom 2785 need remove atom 2793 need remove atom 2796 need remove atom 2804 need remove atom 2810 need remove atom 2819 need remove atom 2821 need remove atom 2829 need remove atom 2832 need remove atom 2840 need remove atom 2846 need remove atom 2855 need remove atom 2857 need remove atom 2865 need remove atom 2868 need remove atom 2876 need remove atom 2882 need remove atom 2891 need remove atom 2893 need remove atom 2901 need remove atom 2904 need remove atom 2912 need remove atom 2918 need remove atom 2927 need remove atom 2929 need remove atom 2937 need remove atom 2940 need remove atom 2948 need remove atom 2954 need remove atom 2963 need remove atom 2965 need remove atom 2973 need remove atom 2976 need remove atom 2984 need remove atom 2990 need remove atom 2999 need remove atom 3001 need remove atom 3009 need remove atom 3012 need remove atom 3020 need remove atom 3026 need remove atom 3035 need remove atom 3037 need remove atom 3045 need remove atom 3048 need remove atom 3056 need remove atom 3062 need remove atom 3071 need remove atom 3073 need remove atom 3081 need remove atom 3084 need remove atom 3092 need remove atom 3098 need remove atom 3107 need remove atom 3109 need remove atom 3117 need remove atom 3120 need remove atom 3128 need remove atom 3134 need remove atom 3143 need remove atom 3145 need remove atom 3153 need remove atom 3156 need remove atom 3164 need remove atom 3179 need remove atom 3181 need remove atom 3200 need remove atom 3215 need remove atom 3217 need remove atom 3236 [I] need removenum=96 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2147991674e-01 1.0026040380e-01 -3.4822045836e-01 dub= -3.3719383418e-01 1.0026270777e-01 3.5467065031e-01 duc= 3.2148082834e-01 -1.0156415022e-01 -3.4822157504e-01 [I] overall tilt ux= -6.5867375092e-01 2.3039667060e-06 7.0289110867e-01 uy= 9.1159869281e-07 -2.0182455402e-01 -1.1166873585e-06 [I] storedr[0]= -2.8408154823e-02 -6.5247761985e-04 -4.9850601396e-02 [I] originally 5760 atoms [I] insert 0 atoms [I] now 5760 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 5760 atoms [I] remove 96 atoms [I] now 5664 atoms [I] NP=5664 n=5664 [I] ASSIGN finalcnfile = dipole_1.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:04:48 2023 CPU time spent: 0.485694 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:05:21 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [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) = 19 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=8208 [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) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.7777777778e-02 -0.0000000000e+00 -8.3333333333e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=5.697360e+01 pxpb=0.000000e+00 pypb=8.504911e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3097 need remove atom 3101 need remove atom 3104 need remove atom 3112 need remove atom 3133 need remove atom 3137 need remove atom 3140 need remove atom 3148 need remove atom 3169 need remove atom 3173 need remove atom 3176 need remove atom 3184 need remove atom 3205 need remove atom 3209 need remove atom 3212 need remove atom 3220 need remove atom 3241 need remove atom 3245 need remove atom 3248 need remove atom 3256 need remove atom 3277 need remove atom 3281 need remove atom 3284 need remove atom 3292 need remove atom 3313 need remove atom 3317 need remove atom 3320 need remove atom 3328 need remove atom 3349 need remove atom 3353 need remove atom 3356 need remove atom 3364 need remove atom 3385 need remove atom 3389 need remove atom 3392 need remove atom 3400 need remove atom 3421 need remove atom 3425 need remove atom 3428 need remove atom 3436 need remove atom 3457 need remove atom 3461 need remove atom 3464 need remove atom 3472 need remove atom 3493 need remove atom 3497 need remove atom 3500 need remove atom 3508 need remove atom 3529 need remove atom 3533 need remove atom 3536 need remove atom 3544 need remove atom 3565 need remove atom 3569 need remove atom 3572 need remove atom 3580 need remove atom 3601 need remove atom 3605 need remove atom 3608 need remove atom 3616 need remove atom 3637 need remove atom 3641 need remove atom 3644 need remove atom 3652 need remove atom 3673 need remove atom 3677 need remove atom 3680 need remove atom 3688 need remove atom 3709 need remove atom 3713 need remove atom 3716 need remove atom 3724 need remove atom 3745 need remove atom 3760 need remove atom 3781 need remove atom 3796 need remove atom 4490 need remove atom 4497 need remove atom 4526 need remove atom 4533 need remove atom 4562 need remove atom 4569 need remove atom 4598 need remove atom 4605 need remove atom 4634 need remove atom 4641 need remove atom 4670 need remove atom 4677 need remove atom 4706 need remove atom 4713 need remove atom 4742 need remove atom 4749 need remove atom 4778 need remove atom 4785 need remove atom 4814 need remove atom 4821 need remove atom 4850 need remove atom 4857 need remove atom 4886 need remove atom 4893 need remove atom 4922 need remove atom 4929 need remove atom 4958 need remove atom 4965 need remove atom 4994 need remove atom 5001 need remove atom 5030 need remove atom 5037 need remove atom 5066 need remove atom 5073 need remove atom 5102 need remove atom 5109 need remove atom 5138 need remove atom 5174 [I] need removenum=114 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2063108374e-01 1.0055199249e-01 -3.4661568903e-01 dub= -3.3625454600e-01 1.0055419346e-01 3.5282765509e-01 duc= 3.2063200291e-01 -1.0183474387e-01 -3.4661680302e-01 [I] overall tilt ux= -6.5688562974e-01 2.2009726606e-06 6.9944334412e-01 uy= 9.1917296041e-07 -2.0238673636e-01 -1.1139900870e-06 [I] storedr[0]= -2.4922088813e-02 -6.4803432614e-04 -4.4619921193e-02 [I] originally 8208 atoms [I] insert 0 atoms [I] now 8208 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 8208 atoms [I] remove 114 atoms [I] now 8094 atoms [I] NP=8094 n=8094 [I] ASSIGN finalcnfile = dipole_1.6.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.6.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.6.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:05:22 2023 CPU time spent: 0.689647 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:06:25 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [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) = 22 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=11088 [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) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.3809523810e-02 -0.0000000000e+00 -8.3333333333e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=6.646920e+01 pxpb=0.000000e+00 pypb=9.847791e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 5186 need remove atom 5195 need remove atom 5197 need remove atom 5205 need remove atom 5208 need remove atom 5216 need remove atom 5222 need remove atom 5231 need remove atom 5233 need remove atom 5241 need remove atom 5244 need remove atom 5252 need remove atom 5258 need remove atom 5267 need remove atom 5269 need remove atom 5277 need remove atom 5280 need remove atom 5288 need remove atom 5294 need remove atom 5303 need remove atom 5305 need remove atom 5313 need remove atom 5316 need remove atom 5324 need remove atom 5330 need remove atom 5339 need remove atom 5341 need remove atom 5349 need remove atom 5352 need remove atom 5360 need remove atom 5366 need remove atom 5375 need remove atom 5377 need remove atom 5385 need remove atom 5388 need remove atom 5396 need remove atom 5402 need remove atom 5411 need remove atom 5413 need remove atom 5421 need remove atom 5424 need remove atom 5432 need remove atom 5438 need remove atom 5447 need remove atom 5449 need remove atom 5457 need remove atom 5460 need remove atom 5468 need remove atom 5474 need remove atom 5483 need remove atom 5485 need remove atom 5493 need remove atom 5496 need remove atom 5504 need remove atom 5510 need remove atom 5519 need remove atom 5521 need remove atom 5529 need remove atom 5532 need remove atom 5540 need remove atom 5546 need remove atom 5555 need remove atom 5557 need remove atom 5565 need remove atom 5568 need remove atom 5576 need remove atom 5582 need remove atom 5591 need remove atom 5593 need remove atom 5601 need remove atom 5604 need remove atom 5612 need remove atom 5618 need remove atom 5627 need remove atom 5629 need remove atom 5637 need remove atom 5640 need remove atom 5648 need remove atom 5654 need remove atom 5663 need remove atom 5665 need remove atom 5673 need remove atom 5676 need remove atom 5684 need remove atom 5690 need remove atom 5699 need remove atom 5701 need remove atom 5709 need remove atom 5712 need remove atom 5720 need remove atom 5726 need remove atom 5735 need remove atom 5737 need remove atom 5745 need remove atom 5748 need remove atom 5756 need remove atom 5762 need remove atom 5771 need remove atom 5773 need remove atom 5781 need remove atom 5784 need remove atom 5792 need remove atom 5798 need remove atom 5807 need remove atom 5809 need remove atom 5817 need remove atom 5820 need remove atom 5828 need remove atom 5834 need remove atom 5843 need remove atom 5845 need remove atom 5853 need remove atom 5856 need remove atom 5864 need remove atom 5870 need remove atom 5879 need remove atom 5881 need remove atom 5889 need remove atom 5892 need remove atom 5900 need remove atom 5906 need remove atom 5915 need remove atom 5917 need remove atom 5925 need remove atom 5928 need remove atom 5936 need remove atom 5942 need remove atom 5951 need remove atom 5953 need remove atom 5961 need remove atom 5964 need remove atom 5972 [I] need removenum=132 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2001359871e-01 1.0076197412e-01 -3.4545530147e-01 dub= -3.3556939593e-01 1.0076409888e-01 3.5149455148e-01 duc= 3.2001452325e-01 -1.0202957601e-01 -3.4545641339e-01 [I] overall tilt ux= -6.5558299463e-01 2.1247612121e-06 6.9694985294e-01 uy= 9.2454707101e-07 -2.0279155013e-01 -1.1119208385e-06 [I] storedr[0]= -2.2326402700e-02 -6.4221592218e-04 -3.9872023098e-02 [I] originally 11088 atoms [I] insert 0 atoms [I] now 11088 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 11088 atoms [I] remove 132 atoms [I] now 10956 atoms [I] NP=10956 n=10956 [I] ASSIGN finalcnfile = dipole_1.9.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.9.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.9.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:06:26 2023 CPU time spent: 0.925830 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:07:12 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [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) = 29 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=18792 [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) = -0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.8518518519e-02 -0.0000000000e+00 -8.3333333333e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=8.546040e+01 pxpb=0.000000e+00 pypb=1.298118e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 8875 need remove atom 8877 need remove atom 8880 need remove atom 8911 need remove atom 8913 need remove atom 8916 need remove atom 8939 need remove atom 8947 need remove atom 8949 need remove atom 8952 need remove atom 8958 need remove atom 8960 need remove atom 8975 need remove atom 8983 need remove atom 8985 need remove atom 8988 need remove atom 8994 need remove atom 8996 need remove atom 9011 need remove atom 9019 need remove atom 9021 need remove atom 9024 need remove atom 9030 need remove atom 9032 need remove atom 9047 need remove atom 9055 need remove atom 9057 need remove atom 9060 need remove atom 9066 need remove atom 9068 need remove atom 9083 need remove atom 9091 need remove atom 9093 need remove atom 9096 need remove atom 9102 need remove atom 9104 need remove atom 9119 need remove atom 9127 need remove atom 9129 need remove atom 9132 need remove atom 9138 need remove atom 9140 need remove atom 9155 need remove atom 9163 need remove atom 9165 need remove atom 9168 need remove atom 9174 need remove atom 9176 need remove atom 9191 need remove atom 9199 need remove atom 9201 need remove atom 9204 need remove atom 9210 need remove atom 9212 need remove atom 9227 need remove atom 9235 need remove atom 9237 need remove atom 9240 need remove atom 9246 need remove atom 9248 need remove atom 9263 need remove atom 9271 need remove atom 9273 need remove atom 9276 need remove atom 9282 need remove atom 9284 need remove atom 9299 need remove atom 9307 need remove atom 9309 need remove atom 9312 need remove atom 9318 need remove atom 9320 need remove atom 9335 need remove atom 9343 need remove atom 9345 need remove atom 9348 need remove atom 9354 need remove atom 9356 need remove atom 9371 need remove atom 9379 need remove atom 9381 need remove atom 9384 need remove atom 9390 need remove atom 9392 need remove atom 9407 need remove atom 9415 need remove atom 9417 need remove atom 9420 need remove atom 9426 need remove atom 9428 need remove atom 9443 need remove atom 9451 need remove atom 9453 need remove atom 9456 need remove atom 9462 need remove atom 9464 need remove atom 9479 need remove atom 9487 need remove atom 9489 need remove atom 9492 need remove atom 9498 need remove atom 9500 need remove atom 9515 need remove atom 9523 need remove atom 9525 need remove atom 9528 need remove atom 9534 need remove atom 9536 need remove atom 9551 need remove atom 9559 need remove atom 9561 need remove atom 9564 need remove atom 9570 need remove atom 9572 need remove atom 9587 need remove atom 9595 need remove atom 9597 need remove atom 9600 need remove atom 9606 need remove atom 9608 need remove atom 9623 need remove atom 9631 need remove atom 9633 need remove atom 9636 need remove atom 9642 need remove atom 9644 need remove atom 9659 need remove atom 9667 need remove atom 9669 need remove atom 9672 need remove atom 9678 need remove atom 9680 need remove atom 9695 need remove atom 9703 need remove atom 9705 need remove atom 9708 need remove atom 9714 need remove atom 9716 need remove atom 9731 need remove atom 9739 need remove atom 9741 need remove atom 9744 need remove atom 9750 need remove atom 9752 need remove atom 9767 need remove atom 9775 need remove atom 9777 need remove atom 9780 need remove atom 9786 need remove atom 9788 need remove atom 9803 need remove atom 9811 need remove atom 9813 need remove atom 9816 need remove atom 9822 need remove atom 9824 need remove atom 9839 need remove atom 9847 need remove atom 9849 need remove atom 9852 need remove atom 9858 need remove atom 9860 need remove atom 9875 need remove atom 9883 need remove atom 9885 need remove atom 9888 need remove atom 9894 need remove atom 9896 need remove atom 9911 need remove atom 9919 need remove atom 9921 need remove atom 9924 need remove atom 9930 need remove atom 9932 [I] need removenum=174 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2203588965e-01 1.0006758731e-01 -3.4927768254e-01 dub= -3.3780741626e-01 1.0006995759e-01 3.5588439338e-01 duc= 3.2203679617e-01 -1.0138519229e-01 -3.4927880090e-01 [I] overall tilt ux= -6.5984330591e-01 2.3702740252e-06 7.0516207593e-01 uy= 9.0652075702e-07 -2.0145277960e-01 -1.1183592600e-06 [I] storedr[0]= -1.9736302666e-02 -6.6523692674e-04 -2.9408611367e-02 [I] originally 18792 atoms [I] insert 0 atoms [I] now 18792 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 18792 atoms [I] remove 174 atoms [I] now 18618 atoms [I] NP=18618 n=18618 [I] ASSIGN finalcnfile = dipole_2.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:07:14 2023 CPU time spent: 1.580643 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:08:04 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [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) = 32 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=34560 [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) = -0.055555555555556 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.6666666667e-02 -0.0000000000e+00 -5.5555555556e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=9.495600e+01 pxpb=0.000000e+00 pypb=1.432406e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 14693 need remove atom 14695 need remove atom 14696 need remove atom 14729 need remove atom 14731 need remove atom 14732 need remove atom 14765 need remove atom 14767 need remove atom 14768 need remove atom 14796 need remove atom 14797 need remove atom 14801 need remove atom 14803 need remove atom 14804 need remove atom 14812 need remove atom 14832 need remove atom 14833 need remove atom 14837 need remove atom 14839 need remove atom 14840 need remove atom 14848 need remove atom 14868 need remove atom 14869 need remove atom 14873 need remove atom 14875 need remove atom 14876 need remove atom 14884 need remove atom 14904 need remove atom 14905 need remove atom 14909 need remove atom 14911 need remove atom 14912 need remove atom 14920 need remove atom 14940 need remove atom 14941 need remove atom 14945 need remove atom 14947 need remove atom 14948 need remove atom 14956 need remove atom 14976 need remove atom 14977 need remove atom 14981 need remove atom 14983 need remove atom 14984 need remove atom 14992 need remove atom 15012 need remove atom 15013 need remove atom 15017 need remove atom 15019 need remove atom 15020 need remove atom 15028 need remove atom 15048 need remove atom 15049 need remove atom 15053 need remove atom 15055 need remove atom 15056 need remove atom 15064 need remove atom 15084 need remove atom 15085 need remove atom 15089 need remove atom 15091 need remove atom 15092 need remove atom 15100 need remove atom 15120 need remove atom 15121 need remove atom 15125 need remove atom 15127 need remove atom 15128 need remove atom 15136 need remove atom 15156 need remove atom 15157 need remove atom 15161 need remove atom 15163 need remove atom 15164 need remove atom 15172 need remove atom 15192 need remove atom 15193 need remove atom 15197 need remove atom 15199 need remove atom 15200 need remove atom 15208 need remove atom 15228 need remove atom 15229 need remove atom 15233 need remove atom 15235 need remove atom 15236 need remove atom 15244 need remove atom 15264 need remove atom 15265 need remove atom 15269 need remove atom 15271 need remove atom 15272 need remove atom 15280 need remove atom 15300 need remove atom 15301 need remove atom 15305 need remove atom 15307 need remove atom 15308 need remove atom 15316 need remove atom 15336 need remove atom 15337 need remove atom 15341 need remove atom 15343 need remove atom 15344 need remove atom 15352 need remove atom 15372 need remove atom 15373 need remove atom 15377 need remove atom 15379 need remove atom 15380 need remove atom 15388 need remove atom 15408 need remove atom 15409 need remove atom 15413 need remove atom 15415 need remove atom 15416 need remove atom 15424 need remove atom 15444 need remove atom 15445 need remove atom 15449 need remove atom 15451 need remove atom 15452 need remove atom 15460 need remove atom 15480 need remove atom 15481 need remove atom 15485 need remove atom 15487 need remove atom 15488 need remove atom 15496 need remove atom 15516 need remove atom 15517 need remove atom 15521 need remove atom 15523 need remove atom 15524 need remove atom 15532 need remove atom 15552 need remove atom 15553 need remove atom 15557 need remove atom 15559 need remove atom 15560 need remove atom 15568 need remove atom 15588 need remove atom 15589 need remove atom 15593 need remove atom 15595 need remove atom 15596 need remove atom 15604 need remove atom 15624 need remove atom 15625 need remove atom 15629 need remove atom 15631 need remove atom 15632 need remove atom 15640 need remove atom 15660 need remove atom 15661 need remove atom 15665 need remove atom 15667 need remove atom 15668 need remove atom 15676 need remove atom 15696 need remove atom 15697 need remove atom 15701 need remove atom 15703 need remove atom 15704 need remove atom 15712 need remove atom 15732 need remove atom 15733 need remove atom 15737 need remove atom 15739 need remove atom 15740 need remove atom 15748 need remove atom 15768 need remove atom 15769 need remove atom 15773 need remove atom 15775 need remove atom 15776 need remove atom 15784 need remove atom 15804 need remove atom 15805 need remove atom 15809 need remove atom 15811 need remove atom 15812 need remove atom 15820 need remove atom 15840 need remove atom 15841 need remove atom 15845 need remove atom 15847 need remove atom 15848 need remove atom 15856 need remove atom 15876 need remove atom 15877 need remove atom 15881 need remove atom 15883 need remove atom 15884 need remove atom 15892 need remove atom 15912 need remove atom 15913 need remove atom 15917 need remove atom 15919 need remove atom 15920 need remove atom 15928 need remove atom 15948 need remove atom 15949 need remove atom 15953 need remove atom 15955 need remove atom 15956 need remove atom 15964 need remove atom 15984 need remove atom 15985 need remove atom 15989 need remove atom 15991 need remove atom 15992 need remove atom 16000 need remove atom 16020 need remove atom 16021 need remove atom 16025 need remove atom 16027 need remove atom 16028 need remove atom 16036 need remove atom 16056 need remove atom 16057 need remove atom 16061 need remove atom 16063 need remove atom 16064 need remove atom 16072 need remove atom 16092 need remove atom 16093 need remove atom 16097 need remove atom 16099 need remove atom 16100 need remove atom 16108 need remove atom 16128 need remove atom 16129 need remove atom 16133 need remove atom 16135 need remove atom 16136 need remove atom 16144 need remove atom 16164 need remove atom 16165 need remove atom 16169 need remove atom 16171 need remove atom 16172 need remove atom 16180 need remove atom 16200 need remove atom 16201 need remove atom 16205 need remove atom 16207 need remove atom 16208 need remove atom 16216 need remove atom 16236 need remove atom 16237 need remove atom 16241 need remove atom 16243 need remove atom 16244 need remove atom 16252 need remove atom 16272 need remove atom 16273 need remove atom 16277 need remove atom 16279 need remove atom 16280 need remove atom 16288 need remove atom 16308 need remove atom 16309 need remove atom 16313 need remove atom 16315 need remove atom 16316 need remove atom 16324 need remove atom 16344 need remove atom 16345 need remove atom 16349 need remove atom 16351 need remove atom 16352 need remove atom 16360 need remove atom 16380 need remove atom 16381 need remove atom 16385 need remove atom 16387 need remove atom 16388 need remove atom 16396 need remove atom 16416 need remove atom 16417 need remove atom 16432 need remove atom 16452 need remove atom 16453 need remove atom 16468 need remove atom 16488 need remove atom 16489 need remove atom 16504 [I] need removenum=288 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2147991674e-01 1.0026040380e-01 -3.4822045836e-01 dub= -3.3719383418e-01 1.0026270777e-01 3.5467065031e-01 duc= 3.2148082834e-01 -1.0156415022e-01 -3.4822157504e-01 [I] overall tilt ux= -6.5867375092e-01 2.3039667070e-06 7.0289110867e-01 uy= 9.1159869281e-07 -2.0182455402e-01 -1.1166873585e-06 [I] storedr[0]= -1.8414194733e-02 -6.5832702820e-04 -2.6959354253e-02 [I] originally 34560 atoms [I] insert 0 atoms [I] now 34560 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 34560 atoms [I] remove 288 atoms [I] now 34272 atoms [I] NP=34272 n=34272 [I] ASSIGN finalcnfile = dipole_3.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:08:07 2023 CPU time spent: 2.919616 s [c013:564724] *** Process received signal *** [c013:564724] Signal: Segmentation fault (11) [c013:564724] Signal code: Address not mapped (1) [c013:564724] Failing at address: 0x30 [c013:564724] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7fdfbe6ab090] [c013:564724] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7fdfba5721c2] [c013:564724] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7fdfbdc36854] [c013:564724] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7fdfbeaa4905] [c013:564724] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7fdfbeaf9d93] [c013:564724] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7fdfbeafa061] [c013:564724] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7fdfba2e9dae] [c013:564724] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7fdfbeabcb10] [c013:564724] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7fdfbf2ea864] [c013:564724] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7fdfbf2e9417] [c013:564724] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7fdfbf091dba] [c013:564724] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7fdfbefa5d0e] [c013:564724] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7fdfbefab300] [c013:564724] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7fdfbefabcd9] [c013:564724] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7fdfbf16bd5b] [c013:564724] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7fdfbf16ca78] [c013:564724] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7fdfbf16383e] [c013:564724] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7fdfbefab138] [c013:564724] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7fdfbefab54e] [c013:564724] [19] lmp(+0x136e)[0x558a9350736e] [c013:564724] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fdfbe68c083] [c013:564724] [21] lmp(+0x13ee)[0x558a935073ee] [c013:564724] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c013 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:08:10 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [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) = 38 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=49248 [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) = -0.055555555555556 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.3888888889e-02 -0.0000000000e+00 -5.5555555556e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=1.139472e+02 pxpb=0.000000e+00 pypb=1.700982e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 21600 need remove atom 21601 need remove atom 21605 need remove atom 21607 need remove atom 21608 need remove atom 21616 need remove atom 21636 need remove atom 21637 need remove atom 21641 need remove atom 21643 need remove atom 21644 need remove atom 21652 need remove atom 21672 need remove atom 21673 need remove atom 21677 need remove atom 21679 need remove atom 21680 need remove atom 21688 need remove atom 21708 need remove atom 21709 need remove atom 21713 need remove atom 21715 need remove atom 21716 need remove atom 21724 need remove atom 21744 need remove atom 21745 need remove atom 21749 need remove atom 21751 need remove atom 21752 need remove atom 21760 need remove atom 21780 need remove atom 21781 need remove atom 21785 need remove atom 21787 need remove atom 21788 need remove atom 21796 need remove atom 21816 need remove atom 21817 need remove atom 21821 need remove atom 21823 need remove atom 21824 need remove atom 21832 need remove atom 21852 need remove atom 21853 need remove atom 21857 need remove atom 21859 need remove atom 21860 need remove atom 21868 need remove atom 21888 need remove atom 21889 need remove atom 21893 need remove atom 21895 need remove atom 21896 need remove atom 21904 need remove atom 21924 need remove atom 21925 need remove atom 21929 need remove atom 21931 need remove atom 21932 need remove atom 21940 need remove atom 21960 need remove atom 21961 need remove atom 21965 need remove atom 21967 need remove atom 21968 need remove atom 21976 need remove atom 21996 need remove atom 21997 need remove atom 22001 need remove atom 22003 need remove atom 22004 need remove atom 22012 need remove atom 22032 need remove atom 22033 need remove atom 22037 need remove atom 22039 need remove atom 22040 need remove atom 22048 need remove atom 22068 need remove atom 22069 need remove atom 22073 need remove atom 22075 need remove atom 22076 need remove atom 22084 need remove atom 22104 need remove atom 22105 need remove atom 22109 need remove atom 22111 need remove atom 22112 need remove atom 22120 need remove atom 22140 need remove atom 22141 need remove atom 22145 need remove atom 22147 need remove atom 22148 need remove atom 22156 need remove atom 22176 need remove atom 22177 need remove atom 22181 need remove atom 22183 need remove atom 22184 need remove atom 22192 need remove atom 22212 need remove atom 22213 need remove atom 22217 need remove atom 22219 need remove atom 22220 need remove atom 22228 need remove atom 22248 need remove atom 22249 need remove atom 22253 need remove atom 22255 need remove atom 22256 need remove atom 22264 need remove atom 22284 need remove atom 22285 need remove atom 22289 need remove atom 22291 need remove atom 22292 need remove atom 22300 need remove atom 22320 need remove atom 22321 need remove atom 22325 need remove atom 22327 need remove atom 22328 need remove atom 22336 need remove atom 22356 need remove atom 22357 need remove atom 22361 need remove atom 22363 need remove atom 22364 need remove atom 22372 need remove atom 22392 need remove atom 22393 need remove atom 22397 need remove atom 22399 need remove atom 22400 need remove atom 22408 need remove atom 22428 need remove atom 22429 need remove atom 22433 need remove atom 22435 need remove atom 22436 need remove atom 22444 need remove atom 22464 need remove atom 22465 need remove atom 22469 need remove atom 22471 need remove atom 22472 need remove atom 22480 need remove atom 22500 need remove atom 22501 need remove atom 22505 need remove atom 22507 need remove atom 22508 need remove atom 22516 need remove atom 22536 need remove atom 22537 need remove atom 22541 need remove atom 22543 need remove atom 22544 need remove atom 22552 need remove atom 22572 need remove atom 22573 need remove atom 22577 need remove atom 22579 need remove atom 22580 need remove atom 22588 need remove atom 22608 need remove atom 22609 need remove atom 22613 need remove atom 22615 need remove atom 22616 need remove atom 22624 need remove atom 22644 need remove atom 22645 need remove atom 22649 need remove atom 22651 need remove atom 22652 need remove atom 22660 need remove atom 22680 need remove atom 22681 need remove atom 22685 need remove atom 22687 need remove atom 22688 need remove atom 22696 need remove atom 22716 need remove atom 22717 need remove atom 22721 need remove atom 22723 need remove atom 22724 need remove atom 22732 need remove atom 22752 need remove atom 22753 need remove atom 22757 need remove atom 22759 need remove atom 22760 need remove atom 22768 need remove atom 22788 need remove atom 22789 need remove atom 22793 need remove atom 22795 need remove atom 22796 need remove atom 22804 need remove atom 22824 need remove atom 22825 need remove atom 22829 need remove atom 22831 need remove atom 22832 need remove atom 22840 need remove atom 22860 need remove atom 22861 need remove atom 22865 need remove atom 22867 need remove atom 22868 need remove atom 22876 need remove atom 22896 need remove atom 22897 need remove atom 22901 need remove atom 22903 need remove atom 22904 need remove atom 22912 need remove atom 22932 need remove atom 22933 need remove atom 22937 need remove atom 22939 need remove atom 22940 need remove atom 22948 need remove atom 22968 need remove atom 22969 need remove atom 22973 need remove atom 22975 need remove atom 22976 need remove atom 22984 need remove atom 23004 need remove atom 23005 need remove atom 23009 need remove atom 23011 need remove atom 23012 need remove atom 23020 need remove atom 23040 need remove atom 23041 need remove atom 23045 need remove atom 23047 need remove atom 23048 need remove atom 23056 need remove atom 23076 need remove atom 23077 need remove atom 23081 need remove atom 23083 need remove atom 23084 need remove atom 23092 need remove atom 23112 need remove atom 23113 need remove atom 23117 need remove atom 23119 need remove atom 23120 need remove atom 23128 need remove atom 23148 need remove atom 23149 need remove atom 23153 need remove atom 23155 need remove atom 23156 need remove atom 23164 need remove atom 23184 need remove atom 23185 need remove atom 23189 need remove atom 23191 need remove atom 23192 need remove atom 23200 need remove atom 23220 need remove atom 23221 need remove atom 23225 need remove atom 23227 need remove atom 23228 need remove atom 23236 need remove atom 23256 need remove atom 23257 need remove atom 23261 need remove atom 23263 need remove atom 23264 need remove atom 23272 need remove atom 23292 need remove atom 23293 need remove atom 23297 need remove atom 23299 need remove atom 23300 need remove atom 23308 need remove atom 23328 need remove atom 23329 need remove atom 23333 need remove atom 23335 need remove atom 23336 need remove atom 23344 need remove atom 23364 need remove atom 23365 need remove atom 23369 need remove atom 23371 need remove atom 23372 need remove atom 23380 need remove atom 23400 need remove atom 23401 need remove atom 23405 need remove atom 23407 need remove atom 23408 need remove atom 23416 need remove atom 23436 need remove atom 23437 need remove atom 23441 need remove atom 23443 need remove atom 23444 need remove atom 23452 need remove atom 23472 need remove atom 23473 need remove atom 23477 need remove atom 23479 need remove atom 23480 need remove atom 23488 need remove atom 23508 need remove atom 23509 need remove atom 23513 need remove atom 23515 need remove atom 23516 need remove atom 23524 need remove atom 23544 need remove atom 23545 need remove atom 23549 need remove atom 23551 need remove atom 23552 need remove atom 23560 need remove atom 23580 need remove atom 23581 need remove atom 23585 need remove atom 23587 need remove atom 23588 need remove atom 23596 need remove atom 23616 need remove atom 23617 need remove atom 23621 need remove atom 23623 need remove atom 23624 need remove atom 23632 [I] need removenum=342 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2063108374e-01 1.0055199249e-01 -3.4661568903e-01 dub= -3.3625454600e-01 1.0055419346e-01 3.5282765509e-01 duc= 3.2063200291e-01 -1.0183474387e-01 -3.4661680302e-01 [I] overall tilt ux= -6.5688562974e-01 2.2009726610e-06 6.9944334412e-01 uy= 9.1917296041e-07 -2.0238673636e-01 -1.1139900870e-06 [I] storedr[0]= -1.6447935610e-02 -6.4730880117e-04 -2.2953721650e-02 [I] originally 49248 atoms [I] insert 0 atoms [I] now 49248 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 49248 atoms [I] remove 342 atoms [I] now 48906 atoms [I] NP=48906 n=48906 [I] ASSIGN finalcnfile = dipole_3.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:08:15 2023 CPU time spent: 4.165377 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:11:20 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 14 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 45 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=68040 [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) = 0.011904761904762 [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) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.1904761905e-02 -0.0000000000e+00 -5.5555555556e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=1.329384e+02 pxpb=0.000000e+00 pypb=2.014321e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 30351 need remove atom 30353 need remove atom 30355 need remove atom 30387 need remove atom 30389 need remove atom 30391 need remove atom 30423 need remove atom 30425 need remove atom 30427 need remove atom 30456 need remove atom 30459 need remove atom 30461 need remove atom 30463 need remove atom 30470 need remove atom 30472 need remove atom 30492 need remove atom 30495 need remove atom 30497 need remove atom 30499 need remove atom 30506 need remove atom 30508 need remove atom 30528 need remove atom 30531 need remove atom 30533 need remove atom 30535 need remove atom 30542 need remove atom 30544 need remove atom 30564 need remove atom 30567 need remove atom 30569 need remove atom 30571 need remove atom 30578 need remove atom 30580 need remove atom 30600 need remove atom 30603 need remove atom 30605 need remove atom 30607 need remove atom 30614 need remove atom 30616 need remove atom 30636 need remove atom 30639 need remove atom 30641 need remove atom 30643 need remove atom 30650 need remove atom 30652 need remove atom 30672 need remove atom 30675 need remove atom 30677 need remove atom 30679 need remove atom 30686 need remove atom 30688 need remove atom 30708 need remove atom 30711 need remove atom 30713 need remove atom 30715 need remove atom 30722 need remove atom 30724 need remove atom 30744 need remove atom 30747 need remove atom 30749 need remove atom 30751 need remove atom 30758 need remove atom 30760 need remove atom 30780 need remove atom 30783 need remove atom 30785 need remove atom 30787 need remove atom 30794 need remove atom 30796 need remove atom 30816 need remove atom 30819 need remove atom 30821 need remove atom 30823 need remove atom 30830 need remove atom 30832 need remove atom 30852 need remove atom 30855 need remove atom 30857 need remove atom 30859 need remove atom 30866 need remove atom 30868 need remove atom 30888 need remove atom 30891 need remove atom 30893 need remove atom 30895 need remove atom 30902 need remove atom 30904 need remove atom 30924 need remove atom 30927 need remove atom 30929 need remove atom 30931 need remove atom 30938 need remove atom 30940 need remove atom 30960 need remove atom 30963 need remove atom 30965 need remove atom 30967 need remove atom 30974 need remove atom 30976 need remove atom 30996 need remove atom 30999 need remove atom 31001 need remove atom 31003 need remove atom 31010 need remove atom 31012 need remove atom 31032 need remove atom 31035 need remove atom 31037 need remove atom 31039 need remove atom 31046 need remove atom 31048 need remove atom 31068 need remove atom 31071 need remove atom 31073 need remove atom 31075 need remove atom 31082 need remove atom 31084 need remove atom 31104 need remove atom 31107 need remove atom 31109 need remove atom 31111 need remove atom 31118 need remove atom 31120 need remove atom 31140 need remove atom 31143 need remove atom 31145 need remove atom 31147 need remove atom 31154 need remove atom 31156 need remove atom 31176 need remove atom 31179 need remove atom 31181 need remove atom 31183 need remove atom 31190 need remove atom 31192 need remove atom 31212 need remove atom 31215 need remove atom 31217 need remove atom 31219 need remove atom 31226 need remove atom 31228 need remove atom 31248 need remove atom 31251 need remove atom 31253 need remove atom 31255 need remove atom 31262 need remove atom 31264 need remove atom 31284 need remove atom 31287 need remove atom 31289 need remove atom 31291 need remove atom 31298 need remove atom 31300 need remove atom 31320 need remove atom 31323 need remove atom 31325 need remove atom 31327 need remove atom 31334 need remove atom 31336 need remove atom 31356 need remove atom 31359 need remove atom 31361 need remove atom 31363 need remove atom 31370 need remove atom 31372 need remove atom 31392 need remove atom 31395 need remove atom 31397 need remove atom 31399 need remove atom 31406 need remove atom 31408 need remove atom 31428 need remove atom 31431 need remove atom 31433 need remove atom 31435 need remove atom 31442 need remove atom 31444 need remove atom 31464 need remove atom 31467 need remove atom 31469 need remove atom 31471 need remove atom 31478 need remove atom 31480 need remove atom 31500 need remove atom 31503 need remove atom 31505 need remove atom 31507 need remove atom 31514 need remove atom 31516 need remove atom 31536 need remove atom 31539 need remove atom 31541 need remove atom 31543 need remove atom 31550 need remove atom 31552 need remove atom 31572 need remove atom 31575 need remove atom 31577 need remove atom 31579 need remove atom 31586 need remove atom 31588 need remove atom 31608 need remove atom 31611 need remove atom 31613 need remove atom 31615 need remove atom 31622 need remove atom 31624 need remove atom 31644 need remove atom 31647 need remove atom 31649 need remove atom 31651 need remove atom 31658 need remove atom 31660 need remove atom 31680 need remove atom 31683 need remove atom 31685 need remove atom 31687 need remove atom 31694 need remove atom 31696 need remove atom 31716 need remove atom 31719 need remove atom 31721 need remove atom 31723 need remove atom 31730 need remove atom 31732 need remove atom 31752 need remove atom 31755 need remove atom 31757 need remove atom 31759 need remove atom 31766 need remove atom 31768 need remove atom 31788 need remove atom 31791 need remove atom 31793 need remove atom 31795 need remove atom 31802 need remove atom 31804 need remove atom 31824 need remove atom 31827 need remove atom 31829 need remove atom 31831 need remove atom 31838 need remove atom 31840 need remove atom 31860 need remove atom 31863 need remove atom 31865 need remove atom 31867 need remove atom 31874 need remove atom 31876 need remove atom 31896 need remove atom 31899 need remove atom 31901 need remove atom 31903 need remove atom 31910 need remove atom 31912 need remove atom 31932 need remove atom 31935 need remove atom 31937 need remove atom 31939 need remove atom 31946 need remove atom 31948 need remove atom 31968 need remove atom 31971 need remove atom 31973 need remove atom 31975 need remove atom 31982 need remove atom 31984 need remove atom 32004 need remove atom 32007 need remove atom 32009 need remove atom 32011 need remove atom 32018 need remove atom 32020 need remove atom 32040 need remove atom 32043 need remove atom 32045 need remove atom 32047 need remove atom 32054 need remove atom 32056 need remove atom 32076 need remove atom 32079 need remove atom 32081 need remove atom 32083 need remove atom 32090 need remove atom 32092 need remove atom 32112 need remove atom 32115 need remove atom 32117 need remove atom 32119 need remove atom 32126 need remove atom 32128 need remove atom 32148 need remove atom 32151 need remove atom 32153 need remove atom 32155 need remove atom 32162 need remove atom 32164 need remove atom 32184 need remove atom 32187 need remove atom 32189 need remove atom 32191 need remove atom 32198 need remove atom 32200 need remove atom 32220 need remove atom 32223 need remove atom 32225 need remove atom 32227 need remove atom 32234 need remove atom 32236 need remove atom 32256 need remove atom 32259 need remove atom 32261 need remove atom 32263 need remove atom 32270 need remove atom 32272 need remove atom 32292 need remove atom 32295 need remove atom 32297 need remove atom 32299 need remove atom 32306 need remove atom 32308 need remove atom 32328 need remove atom 32331 need remove atom 32333 need remove atom 32335 need remove atom 32342 need remove atom 32344 need remove atom 32364 need remove atom 32367 need remove atom 32369 need remove atom 32371 need remove atom 32378 need remove atom 32380 need remove atom 32400 need remove atom 32403 need remove atom 32405 need remove atom 32407 need remove atom 32414 need remove atom 32416 need remove atom 32436 need remove atom 32439 need remove atom 32441 need remove atom 32443 need remove atom 32450 need remove atom 32452 need remove atom 32472 need remove atom 32475 need remove atom 32477 need remove atom 32479 need remove atom 32486 need remove atom 32488 need remove atom 32508 need remove atom 32511 need remove atom 32513 need remove atom 32515 need remove atom 32522 need remove atom 32524 need remove atom 32544 need remove atom 32547 need remove atom 32549 need remove atom 32551 need remove atom 32558 need remove atom 32560 need remove atom 32580 need remove atom 32583 need remove atom 32585 need remove atom 32587 need remove atom 32594 need remove atom 32596 need remove atom 32616 need remove atom 32619 need remove atom 32621 need remove atom 32623 need remove atom 32630 need remove atom 32632 need remove atom 32652 need remove atom 32655 need remove atom 32657 need remove atom 32659 need remove atom 32666 need remove atom 32668 need remove atom 32688 need remove atom 32691 need remove atom 32693 need remove atom 32695 need remove atom 32702 need remove atom 32704 need remove atom 32724 need remove atom 32727 need remove atom 32729 need remove atom 32731 need remove atom 32738 need remove atom 32740 need remove atom 32760 need remove atom 32763 need remove atom 32765 need remove atom 32767 need remove atom 32774 need remove atom 32776 need remove atom 32796 need remove atom 32799 need remove atom 32801 need remove atom 32803 need remove atom 32810 need remove atom 32812 [I] need removenum=405 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2183822634e-01 1.0013630409e-01 -3.4890125108e-01 dub= -3.3758942148e-01 1.0013865089e-01 3.5545227228e-01 duc= 3.2183913468e-01 -1.0144897222e-01 -3.4890236885e-01 [I] overall tilt ux= -6.5942764783e-01 2.3468067045e-06 7.0435352336e-01 uy= 9.0833668492e-07 -2.0158527630e-01 -1.1177735790e-06 [I] storedr[0]= -1.5490303954e-02 -6.6115761044e-04 -1.8537867130e-02 [I] originally 68040 atoms [I] insert 0 atoms [I] now 68040 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 68040 atoms [I] remove 405 atoms [I] now 67635 atoms [I] NP=67635 n=67635 [I] ASSIGN finalcnfile = dipole_4.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:11:27 2023 CPU time spent: 5.741492 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:14:32 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [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) = 48 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=103680 [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) = -0.041666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.1111111111e-02 -0.0000000000e+00 -4.1666666667e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=1.424340e+02 pxpb=0.000000e+00 pypb=2.148609e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 50131 need remove atom 50134 need remove atom 50136 need remove atom 50167 need remove atom 50170 need remove atom 50172 need remove atom 50203 need remove atom 50206 need remove atom 50208 need remove atom 50239 need remove atom 50242 need remove atom 50244 need remove atom 50265 need remove atom 50267 need remove atom 50275 need remove atom 50278 need remove atom 50280 need remove atom 50286 need remove atom 50301 need remove atom 50303 need remove atom 50311 need remove atom 50314 need remove atom 50316 need remove atom 50322 need remove atom 50337 need remove atom 50339 need remove atom 50347 need remove atom 50350 need remove atom 50352 need remove atom 50358 need remove atom 50373 need remove atom 50375 need remove atom 50383 need remove atom 50386 need remove atom 50388 need remove atom 50394 need remove atom 50409 need remove atom 50411 need remove atom 50419 need remove atom 50422 need remove atom 50424 need remove atom 50430 need remove atom 50445 need remove atom 50447 need remove atom 50455 need remove atom 50458 need remove atom 50460 need remove atom 50466 need remove atom 50481 need remove atom 50483 need remove atom 50491 need remove atom 50494 need remove atom 50496 need remove atom 50502 need remove atom 50517 need remove atom 50519 need remove atom 50527 need remove atom 50530 need remove atom 50532 need remove atom 50538 need remove atom 50553 need remove atom 50555 need remove atom 50563 need remove atom 50566 need remove atom 50568 need remove atom 50574 need remove atom 50589 need remove atom 50591 need remove atom 50599 need remove atom 50602 need remove atom 50604 need remove atom 50610 need remove atom 50625 need remove atom 50627 need remove atom 50635 need remove atom 50638 need remove atom 50640 need remove atom 50646 need remove atom 50661 need remove atom 50663 need remove atom 50671 need remove atom 50674 need remove atom 50676 need remove atom 50682 need remove atom 50697 need remove atom 50699 need remove atom 50707 need remove atom 50710 need remove atom 50712 need remove atom 50718 need remove atom 50733 need remove atom 50735 need remove atom 50743 need remove atom 50746 need remove atom 50748 need remove atom 50754 need remove atom 50769 need remove atom 50771 need remove atom 50779 need remove atom 50782 need remove atom 50784 need remove atom 50790 need remove atom 50805 need remove atom 50807 need remove atom 50815 need remove atom 50818 need remove atom 50820 need remove atom 50826 need remove atom 50841 need remove atom 50843 need remove atom 50851 need remove atom 50854 need remove atom 50856 need remove atom 50862 need remove atom 50877 need remove atom 50879 need remove atom 50887 need remove atom 50890 need remove atom 50892 need remove atom 50898 need remove atom 50913 need remove atom 50915 need remove atom 50923 need remove atom 50926 need remove atom 50928 need remove atom 50934 need remove atom 50949 need remove atom 50951 need remove atom 50959 need remove atom 50962 need remove atom 50964 need remove atom 50970 need remove atom 50985 need remove atom 50987 need remove atom 50995 need remove atom 50998 need remove atom 51000 need remove atom 51006 need remove atom 51021 need remove atom 51023 need remove atom 51031 need remove atom 51034 need remove atom 51036 need remove atom 51042 need remove atom 51057 need remove atom 51059 need remove atom 51067 need remove atom 51070 need remove atom 51072 need remove atom 51078 need remove atom 51093 need remove atom 51095 need remove atom 51103 need remove atom 51106 need remove atom 51108 need remove atom 51114 need remove atom 51129 need remove atom 51131 need remove atom 51139 need remove atom 51142 need remove atom 51144 need remove atom 51150 need remove atom 51165 need remove atom 51167 need remove atom 51175 need remove atom 51178 need remove atom 51180 need remove atom 51186 need remove atom 51201 need remove atom 51203 need remove atom 51211 need remove atom 51214 need remove atom 51216 need remove atom 51222 need remove atom 51237 need remove atom 51239 need remove atom 51247 need remove atom 51250 need remove atom 51252 need remove atom 51258 need remove atom 51273 need remove atom 51275 need remove atom 51283 need remove atom 51286 need remove atom 51288 need remove atom 51294 need remove atom 51309 need remove atom 51311 need remove atom 51319 need remove atom 51322 need remove atom 51324 need remove atom 51330 need remove atom 51345 need remove atom 51347 need remove atom 51355 need remove atom 51358 need remove atom 51360 need remove atom 51366 need remove atom 51381 need remove atom 51383 need remove atom 51391 need remove atom 51394 need remove atom 51396 need remove atom 51402 need remove atom 51417 need remove atom 51419 need remove atom 51427 need remove atom 51430 need remove atom 51432 need remove atom 51438 need remove atom 51453 need remove atom 51455 need remove atom 51463 need remove atom 51466 need remove atom 51468 need remove atom 51474 need remove atom 51489 need remove atom 51491 need remove atom 51499 need remove atom 51502 need remove atom 51504 need remove atom 51510 need remove atom 51525 need remove atom 51527 need remove atom 51535 need remove atom 51538 need remove atom 51540 need remove atom 51546 need remove atom 51561 need remove atom 51563 need remove atom 51571 need remove atom 51574 need remove atom 51576 need remove atom 51582 need remove atom 51597 need remove atom 51599 need remove atom 51607 need remove atom 51610 need remove atom 51612 need remove atom 51618 need remove atom 51633 need remove atom 51635 need remove atom 51643 need remove atom 51646 need remove atom 51648 need remove atom 51654 need remove atom 51669 need remove atom 51671 need remove atom 51679 need remove atom 51682 need remove atom 51684 need remove atom 51690 need remove atom 51705 need remove atom 51707 need remove atom 51715 need remove atom 51718 need remove atom 51720 need remove atom 51726 need remove atom 51741 need remove atom 51743 need remove atom 51751 need remove atom 51754 need remove atom 51756 need remove atom 51762 need remove atom 51777 need remove atom 51779 need remove atom 51787 need remove atom 51790 need remove atom 51792 need remove atom 51798 need remove atom 51813 need remove atom 51815 need remove atom 51823 need remove atom 51826 need remove atom 51828 need remove atom 51834 need remove atom 51849 need remove atom 51851 need remove atom 51859 need remove atom 51862 need remove atom 51864 need remove atom 51870 need remove atom 51885 need remove atom 51887 need remove atom 51895 need remove atom 51898 need remove atom 51900 need remove atom 51906 need remove atom 51921 need remove atom 51923 need remove atom 51931 need remove atom 51934 need remove atom 51936 need remove atom 51942 need remove atom 51957 need remove atom 51959 need remove atom 51967 need remove atom 51970 need remove atom 51972 need remove atom 51978 need remove atom 51993 need remove atom 51995 need remove atom 52003 need remove atom 52006 need remove atom 52008 need remove atom 52014 need remove atom 52029 need remove atom 52031 need remove atom 52039 need remove atom 52042 need remove atom 52044 need remove atom 52050 need remove atom 52065 need remove atom 52067 need remove atom 52075 need remove atom 52078 need remove atom 52080 need remove atom 52086 need remove atom 52101 need remove atom 52103 need remove atom 52111 need remove atom 52114 need remove atom 52116 need remove atom 52122 need remove atom 52137 need remove atom 52139 need remove atom 52147 need remove atom 52150 need remove atom 52152 need remove atom 52158 need remove atom 52173 need remove atom 52175 need remove atom 52183 need remove atom 52186 need remove atom 52188 need remove atom 52194 need remove atom 52209 need remove atom 52211 need remove atom 52219 need remove atom 52222 need remove atom 52224 need remove atom 52230 need remove atom 52245 need remove atom 52247 need remove atom 52255 need remove atom 52258 need remove atom 52260 need remove atom 52266 need remove atom 52281 need remove atom 52283 need remove atom 52291 need remove atom 52294 need remove atom 52296 need remove atom 52302 need remove atom 52317 need remove atom 52319 need remove atom 52327 need remove atom 52330 need remove atom 52332 need remove atom 52338 need remove atom 52353 need remove atom 52355 need remove atom 52363 need remove atom 52366 need remove atom 52368 need remove atom 52374 need remove atom 52389 need remove atom 52391 need remove atom 52399 need remove atom 52402 need remove atom 52404 need remove atom 52410 need remove atom 52425 need remove atom 52427 need remove atom 52435 need remove atom 52438 need remove atom 52440 need remove atom 52446 need remove atom 52461 need remove atom 52463 need remove atom 52471 need remove atom 52474 need remove atom 52476 need remove atom 52482 need remove atom 52497 need remove atom 52499 need remove atom 52507 need remove atom 52510 need remove atom 52512 need remove atom 52518 need remove atom 52533 need remove atom 52535 need remove atom 52543 need remove atom 52546 need remove atom 52548 need remove atom 52554 need remove atom 52569 need remove atom 52571 need remove atom 52579 need remove atom 52582 need remove atom 52584 need remove atom 52590 need remove atom 52605 need remove atom 52607 need remove atom 52615 need remove atom 52618 need remove atom 52620 need remove atom 52626 need remove atom 52641 need remove atom 52643 need remove atom 52651 need remove atom 52654 need remove atom 52656 need remove atom 52662 need remove atom 52677 need remove atom 52679 need remove atom 52687 need remove atom 52690 need remove atom 52692 need remove atom 52698 need remove atom 52713 need remove atom 52715 need remove atom 52723 need remove atom 52726 need remove atom 52728 need remove atom 52734 need remove atom 52749 need remove atom 52751 need remove atom 52759 need remove atom 52762 need remove atom 52764 need remove atom 52770 need remove atom 52785 need remove atom 52787 need remove atom 52795 need remove atom 52798 need remove atom 52800 need remove atom 52806 need remove atom 52821 need remove atom 52823 need remove atom 52831 need remove atom 52834 need remove atom 52836 need remove atom 52842 need remove atom 52857 need remove atom 52859 need remove atom 52867 need remove atom 52870 need remove atom 52872 need remove atom 52878 need remove atom 52893 need remove atom 52895 need remove atom 52903 need remove atom 52906 need remove atom 52908 need remove atom 52914 need remove atom 52929 need remove atom 52931 need remove atom 52939 need remove atom 52942 need remove atom 52944 need remove atom 52950 need remove atom 52965 need remove atom 52967 need remove atom 52975 need remove atom 52978 need remove atom 52980 need remove atom 52986 need remove atom 53001 need remove atom 53003 need remove atom 53011 need remove atom 53014 need remove atom 53016 need remove atom 53022 need remove atom 53037 need remove atom 53039 need remove atom 53047 need remove atom 53050 need remove atom 53052 need remove atom 53058 need remove atom 53073 need remove atom 53075 need remove atom 53083 need remove atom 53086 need remove atom 53088 need remove atom 53094 need remove atom 53109 need remove atom 53111 need remove atom 53119 need remove atom 53122 need remove atom 53124 need remove atom 53130 need remove atom 53145 need remove atom 53147 need remove atom 53155 need remove atom 53158 need remove atom 53160 need remove atom 53166 need remove atom 53181 need remove atom 53183 need remove atom 53191 need remove atom 53194 need remove atom 53196 need remove atom 53202 need remove atom 53217 need remove atom 53219 need remove atom 53227 need remove atom 53230 need remove atom 53232 need remove atom 53238 need remove atom 53253 need remove atom 53255 need remove atom 53263 need remove atom 53266 need remove atom 53268 need remove atom 53274 need remove atom 53289 need remove atom 53291 need remove atom 53299 need remove atom 53302 need remove atom 53304 need remove atom 53310 need remove atom 53325 need remove atom 53327 need remove atom 53335 need remove atom 53338 need remove atom 53340 need remove atom 53346 need remove atom 53361 need remove atom 53363 need remove atom 53371 need remove atom 53374 need remove atom 53376 need remove atom 53382 need remove atom 53397 need remove atom 53399 need remove atom 53407 need remove atom 53410 need remove atom 53412 need remove atom 53418 need remove atom 53433 need remove atom 53435 need remove atom 53443 need remove atom 53446 need remove atom 53448 need remove atom 53454 need remove atom 53469 need remove atom 53471 need remove atom 53479 need remove atom 53482 need remove atom 53484 need remove atom 53490 need remove atom 53505 need remove atom 53507 need remove atom 53515 need remove atom 53518 need remove atom 53520 need remove atom 53526 need remove atom 53541 need remove atom 53543 need remove atom 53551 need remove atom 53554 need remove atom 53556 need remove atom 53562 need remove atom 53577 need remove atom 53579 need remove atom 53598 need remove atom 53613 need remove atom 53615 need remove atom 53634 need remove atom 53649 need remove atom 53651 need remove atom 53670 need remove atom 53685 need remove atom 53687 need remove atom 53706 [I] need removenum=576 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2147991674e-01 1.0026040380e-01 -3.4822045836e-01 dub= -3.3719383418e-01 1.0026270777e-01 3.5467065031e-01 duc= 3.2148082834e-01 -1.0156415022e-01 -3.4822157504e-01 [I] overall tilt ux= -6.5867375092e-01 2.3039667069e-06 7.0289110867e-01 uy= 9.1159869176e-07 -2.0182455402e-01 -1.1166873587e-06 [I] storedr[0]= -1.4908257385e-02 -6.5645404880e-04 -1.7389485841e-02 [I] originally 103680 atoms [I] insert 0 atoms [I] now 103680 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 103680 atoms [I] remove 576 atoms [I] now 103104 atoms [I] NP=103104 n=103104 [I] ASSIGN finalcnfile = dipole_4.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Wed May 31 17:14:42 2023 CPU time spent: 8.752700 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed May 31 17:19:39 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = -2 [I] ASSIGN makecnspec(1) = -2 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 17 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 54 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = 4 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ -2 -1 1 -2 1 1 1 0 4]; basis=[ 0.833333 0 0.166667 0 0 0.944444 0 0.388889 0 1 0.5 0.5 0 0 2 0.777778 0.5 0.0555556 0 3 0.611111 0.5 0.222222 0 4 0.888889 0.5 0.277778 0 5 0.722222 0.5 0.444444 0 6 0.833333 0.5 0.666667 0 7 0.944444 0.5 0.888889 0 8 0.277778 0 0.0555556 0 9 0.555556 0 0.111111 0 10 0.388889 0 0.277778 0 11 0.666667 0 0.333333 0 12 0.5 0 0.5 0 13 0.777778 0 0.555556 0 14 0.611111 0 0.722222 0 15 0.888889 0 0.777778 0 16 0.722222 0 0.944444 0 17 0.0555556 0.5 0.111111 0 18 0.333333 0.5 0.166667 0 19 0.166667 0.5 0.333333 0 20 0.444444 0.5 0.388889 0 21 0.277778 0.5 0.555556 0 22 0.555556 0.5 0.611111 0 23 0.388889 0.5 0.777778 0 24 0.666667 0.5 0.833333 0 25 0 0 0 0 26 0.111111 0 0.222222 0 27 0.222222 0 0.444444 0 28 0.0555556 0 0.611111 0 29 0.333333 0 0.666667 0 30 0.166667 0 0.833333 0 31 0.444444 0 0.888889 0 32 0 0.5 0.5 0 33 0.111111 0.5 0.722222 0 34 0.222222 0.5 0.944444 0 35 ]; [I] makecn: _NP=132192 [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) = 0.0098039215686275 [I] ASSIGN mkdipole(3) = -0 [I] ASSIGN mkdipole(4) = -0.041666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 9.8039215686e-03 -0.0000000000e+00 -4.1666666667e-02 b= 1.5825999752e+00 0.0000000000e+00 -2.2381343487e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=1.5825999751687 by=0 pxpa=1.614252e+02 pxpb=0.000000e+00 pypb=2.417185e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 64233 need remove atom 64235 need remove atom 64243 need remove atom 64246 need remove atom 64248 need remove atom 64254 need remove atom 64269 need remove atom 64271 need remove atom 64279 need remove atom 64282 need remove atom 64284 need remove atom 64290 need remove atom 64305 need remove atom 64307 need remove atom 64315 need remove atom 64318 need remove atom 64320 need remove atom 64326 need remove atom 64341 need remove atom 64343 need remove atom 64351 need remove atom 64354 need remove atom 64356 need remove atom 64362 need remove atom 64377 need remove atom 64379 need remove atom 64387 need remove atom 64390 need remove atom 64392 need remove atom 64398 need remove atom 64413 need remove atom 64415 need remove atom 64423 need remove atom 64426 need remove atom 64428 need remove atom 64434 need remove atom 64449 need remove atom 64451 need remove atom 64459 need remove atom 64462 need remove atom 64464 need remove atom 64470 need remove atom 64485 need remove atom 64487 need remove atom 64495 need remove atom 64498 need remove atom 64500 need remove atom 64506 need remove atom 64521 need remove atom 64523 need remove atom 64531 need remove atom 64534 need remove atom 64536 need remove atom 64542 need remove atom 64557 need remove atom 64559 need remove atom 64567 need remove atom 64570 need remove atom 64572 need remove atom 64578 need remove atom 64593 need remove atom 64595 need remove atom 64603 need remove atom 64606 need remove atom 64608 need remove atom 64614 need remove atom 64629 need remove atom 64631 need remove atom 64639 need remove atom 64642 need remove atom 64644 need remove atom 64650 need remove atom 64665 need remove atom 64667 need remove atom 64675 need remove atom 64678 need remove atom 64680 need remove atom 64686 need remove atom 64701 need remove atom 64703 need remove atom 64711 need remove atom 64714 need remove atom 64716 need remove atom 64722 need remove atom 64737 need remove atom 64739 need remove atom 64747 need remove atom 64750 need remove atom 64752 need remove atom 64758 need remove atom 64773 need remove atom 64775 need remove atom 64783 need remove atom 64786 need remove atom 64788 need remove atom 64794 need remove atom 64809 need remove atom 64811 need remove atom 64819 need remove atom 64822 need remove atom 64824 need remove atom 64830 need remove atom 64845 need remove atom 64847 need remove atom 64855 need remove atom 64858 need remove atom 64860 need remove atom 64866 need remove atom 64881 need remove atom 64883 need remove atom 64891 need remove atom 64894 need remove atom 64896 need remove atom 64902 need remove atom 64917 need remove atom 64919 need remove atom 64927 need remove atom 64930 need remove atom 64932 need remove atom 64938 need remove atom 64953 need remove atom 64955 need remove atom 64963 need remove atom 64966 need remove atom 64968 need remove atom 64974 need remove atom 64989 need remove atom 64991 need remove atom 64999 need remove atom 65002 need remove atom 65004 need remove atom 65010 need remove atom 65025 need remove atom 65027 need remove atom 65035 need remove atom 65038 need remove atom 65040 need remove atom 65046 need remove atom 65061 need remove atom 65063 need remove atom 65071 need remove atom 65074 need remove atom 65076 need remove atom 65082 need remove atom 65097 need remove atom 65099 need remove atom 65107 need remove atom 65110 need remove atom 65112 need remove atom 65118 need remove atom 65133 need remove atom 65135 need remove atom 65143 need remove atom 65146 need remove atom 65148 need remove atom 65154 need remove atom 65169 need remove atom 65171 need remove atom 65179 need remove atom 65182 need remove atom 65184 need remove atom 65190 need remove atom 65205 need remove atom 65207 need remove atom 65215 need remove atom 65218 need remove atom 65220 need remove atom 65226 need remove atom 65241 need remove atom 65243 need remove atom 65251 need remove atom 65254 need remove atom 65256 need remove atom 65262 need remove atom 65277 need remove atom 65279 need remove atom 65287 need remove atom 65290 need remove atom 65292 need remove atom 65298 need remove atom 65313 need remove atom 65315 need remove atom 65323 need remove atom 65326 need remove atom 65328 need remove atom 65334 need remove atom 65349 need remove atom 65351 need remove atom 65359 need remove atom 65362 need remove atom 65364 need remove atom 65370 need remove atom 65385 need remove atom 65387 need remove atom 65395 need remove atom 65398 need remove atom 65400 need remove atom 65406 need remove atom 65421 need remove atom 65423 need remove atom 65431 need remove atom 65434 need remove atom 65436 need remove atom 65442 need remove atom 65457 need remove atom 65459 need remove atom 65467 need remove atom 65470 need remove atom 65472 need remove atom 65478 need remove atom 65493 need remove atom 65495 need remove atom 65503 need remove atom 65506 need remove atom 65508 need remove atom 65514 need remove atom 65529 need remove atom 65531 need remove atom 65539 need remove atom 65542 need remove atom 65544 need remove atom 65550 need remove atom 65565 need remove atom 65567 need remove atom 65575 need remove atom 65578 need remove atom 65580 need remove atom 65586 need remove atom 65601 need remove atom 65603 need remove atom 65611 need remove atom 65614 need remove atom 65616 need remove atom 65622 need remove atom 65637 need remove atom 65639 need remove atom 65647 need remove atom 65650 need remove atom 65652 need remove atom 65658 need remove atom 65673 need remove atom 65675 need remove atom 65683 need remove atom 65686 need remove atom 65688 need remove atom 65694 need remove atom 65709 need remove atom 65711 need remove atom 65719 need remove atom 65722 need remove atom 65724 need remove atom 65730 need remove atom 65745 need remove atom 65747 need remove atom 65755 need remove atom 65758 need remove atom 65760 need remove atom 65766 need remove atom 65781 need remove atom 65783 need remove atom 65791 need remove atom 65794 need remove atom 65796 need remove atom 65802 need remove atom 65817 need remove atom 65819 need remove atom 65827 need remove atom 65830 need remove atom 65832 need remove atom 65838 need remove atom 65853 need remove atom 65855 need remove atom 65863 need remove atom 65866 need remove atom 65868 need remove atom 65874 need remove atom 65889 need remove atom 65891 need remove atom 65899 need remove atom 65902 need remove atom 65904 need remove atom 65910 need remove atom 65925 need remove atom 65927 need remove atom 65935 need remove atom 65938 need remove atom 65940 need remove atom 65946 need remove atom 65961 need remove atom 65963 need remove atom 65971 need remove atom 65974 need remove atom 65976 need remove atom 65982 need remove atom 65997 need remove atom 65999 need remove atom 66007 need remove atom 66010 need remove atom 66012 need remove atom 66018 need remove atom 66033 need remove atom 66035 need remove atom 66043 need remove atom 66046 need remove atom 66048 need remove atom 66054 need remove atom 66069 need remove atom 66071 need remove atom 66079 need remove atom 66082 need remove atom 66084 need remove atom 66090 need remove atom 66105 need remove atom 66107 need remove atom 66115 need remove atom 66118 need remove atom 66120 need remove atom 66126 need remove atom 66141 need remove atom 66143 need remove atom 66151 need remove atom 66154 need remove atom 66156 need remove atom 66162 need remove atom 66177 need remove atom 66179 need remove atom 66187 need remove atom 66190 need remove atom 66192 need remove atom 66198 need remove atom 66213 need remove atom 66215 need remove atom 66223 need remove atom 66226 need remove atom 66228 need remove atom 66234 need remove atom 66249 need remove atom 66251 need remove atom 66259 need remove atom 66262 need remove atom 66264 need remove atom 66270 need remove atom 66285 need remove atom 66287 need remove atom 66295 need remove atom 66298 need remove atom 66300 need remove atom 66306 need remove atom 66321 need remove atom 66323 need remove atom 66331 need remove atom 66334 need remove atom 66336 need remove atom 66342 need remove atom 66357 need remove atom 66359 need remove atom 66367 need remove atom 66370 need remove atom 66372 need remove atom 66378 need remove atom 66393 need remove atom 66395 need remove atom 66403 need remove atom 66406 need remove atom 66408 need remove atom 66414 need remove atom 66429 need remove atom 66431 need remove atom 66439 need remove atom 66442 need remove atom 66444 need remove atom 66450 need remove atom 66465 need remove atom 66467 need remove atom 66475 need remove atom 66478 need remove atom 66480 need remove atom 66486 need remove atom 66501 need remove atom 66503 need remove atom 66511 need remove atom 66514 need remove atom 66516 need remove atom 66522 need remove atom 66537 need remove atom 66539 need remove atom 66547 need remove atom 66550 need remove atom 66552 need remove atom 66558 need remove atom 66573 need remove atom 66575 need remove atom 66583 need remove atom 66586 need remove atom 66588 need remove atom 66594 need remove atom 66609 need remove atom 66611 need remove atom 66619 need remove atom 66622 need remove atom 66624 need remove atom 66630 need remove atom 66645 need remove atom 66647 need remove atom 66655 need remove atom 66658 need remove atom 66660 need remove atom 66666 need remove atom 66681 need remove atom 66683 need remove atom 66691 need remove atom 66694 need remove atom 66696 need remove atom 66702 need remove atom 66717 need remove atom 66719 need remove atom 66727 need remove atom 66730 need remove atom 66732 need remove atom 66738 need remove atom 66753 need remove atom 66755 need remove atom 66763 need remove atom 66766 need remove atom 66768 need remove atom 66774 need remove atom 66789 need remove atom 66791 need remove atom 66799 need remove atom 66802 need remove atom 66804 need remove atom 66810 need remove atom 66825 need remove atom 66827 need remove atom 66835 need remove atom 66838 need remove atom 66840 need remove atom 66846 need remove atom 66861 need remove atom 66863 need remove atom 66871 need remove atom 66874 need remove atom 66876 need remove atom 66882 need remove atom 66897 need remove atom 66899 need remove atom 66907 need remove atom 66910 need remove atom 66912 need remove atom 66918 need remove atom 66933 need remove atom 66935 need remove atom 66943 need remove atom 66946 need remove atom 66948 need remove atom 66954 need remove atom 66969 need remove atom 66971 need remove atom 66979 need remove atom 66982 need remove atom 66984 need remove atom 66990 need remove atom 67005 need remove atom 67007 need remove atom 67015 need remove atom 67018 need remove atom 67020 need remove atom 67026 need remove atom 67041 need remove atom 67043 need remove atom 67051 need remove atom 67054 need remove atom 67056 need remove atom 67062 need remove atom 67077 need remove atom 67079 need remove atom 67087 need remove atom 67090 need remove atom 67092 need remove atom 67098 need remove atom 67113 need remove atom 67115 need remove atom 67123 need remove atom 67126 need remove atom 67128 need remove atom 67134 need remove atom 67149 need remove atom 67151 need remove atom 67159 need remove atom 67162 need remove atom 67164 need remove atom 67170 need remove atom 67185 need remove atom 67187 need remove atom 67195 need remove atom 67198 need remove atom 67200 need remove atom 67206 need remove atom 67221 need remove atom 67223 need remove atom 67231 need remove atom 67234 need remove atom 67236 need remove atom 67242 need remove atom 67257 need remove atom 67259 need remove atom 67267 need remove atom 67270 need remove atom 67272 need remove atom 67278 need remove atom 67293 need remove atom 67295 need remove atom 67303 need remove atom 67306 need remove atom 67308 need remove atom 67314 need remove atom 67329 need remove atom 67331 need remove atom 67339 need remove atom 67342 need remove atom 67344 need remove atom 67350 need remove atom 67365 need remove atom 67367 need remove atom 67375 need remove atom 67378 need remove atom 67380 need remove atom 67386 need remove atom 67401 need remove atom 67403 need remove atom 67411 need remove atom 67414 need remove atom 67416 need remove atom 67422 need remove atom 67437 need remove atom 67439 need remove atom 67447 need remove atom 67450 need remove atom 67452 need remove atom 67458 need remove atom 67473 need remove atom 67475 need remove atom 67483 need remove atom 67486 need remove atom 67488 need remove atom 67494 need remove atom 67509 need remove atom 67511 need remove atom 67519 need remove atom 67522 need remove atom 67524 need remove atom 67530 need remove atom 67545 need remove atom 67547 need remove atom 67555 need remove atom 67558 need remove atom 67560 need remove atom 67566 need remove atom 67581 need remove atom 67583 need remove atom 67591 need remove atom 67594 need remove atom 67596 need remove atom 67602 need remove atom 67617 need remove atom 67619 need remove atom 67627 need remove atom 67630 need remove atom 67632 need remove atom 67638 need remove atom 67653 need remove atom 67655 need remove atom 67663 need remove atom 67666 need remove atom 67668 need remove atom 67674 need remove atom 67689 need remove atom 67691 need remove atom 67699 need remove atom 67702 need remove atom 67704 need remove atom 67710 need remove atom 67725 need remove atom 67727 need remove atom 67735 need remove atom 67738 need remove atom 67740 need remove atom 67746 need remove atom 67761 need remove atom 67763 need remove atom 67771 need remove atom 67774 need remove atom 67776 need remove atom 67782 need remove atom 67797 need remove atom 67799 need remove atom 67807 need remove atom 67810 need remove atom 67812 need remove atom 67818 need remove atom 67833 need remove atom 67835 need remove atom 67843 need remove atom 67846 need remove atom 67848 need remove atom 67854 need remove atom 67869 need remove atom 67871 need remove atom 67879 need remove atom 67882 need remove atom 67884 need remove atom 67890 need remove atom 67905 need remove atom 67907 need remove atom 67915 need remove atom 67918 need remove atom 67920 need remove atom 67926 need remove atom 67941 need remove atom 67943 need remove atom 67951 need remove atom 67954 need remove atom 67956 need remove atom 67962 need remove atom 67977 need remove atom 67979 need remove atom 67987 need remove atom 67990 need remove atom 67992 need remove atom 67998 need remove atom 68013 need remove atom 68015 need remove atom 68023 need remove atom 68026 need remove atom 68028 need remove atom 68034 need remove atom 68049 need remove atom 68051 need remove atom 68059 need remove atom 68062 need remove atom 68064 need remove atom 68070 need remove atom 68085 need remove atom 68087 need remove atom 68095 need remove atom 68098 need remove atom 68100 need remove atom 68106 [I] need removenum=648 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 3.2088261733e-01 1.0046593974e-01 -3.4709005923e-01 dub= -3.3653319574e-01 1.0046817145e-01 3.5337252333e-01 duc= 3.2088353428e-01 -1.0175489202e-01 -3.4709117403e-01 [I] overall tilt ux= -6.5741581306e-01 2.2317098947e-06 7.0046258256e-01 uy= 9.1695100291e-07 -2.0222083176e-01 -1.1148073344e-06 [I] storedr[0]= -1.3959986517e-02 -6.4856989361e-04 -1.5417533781e-02 [I] originally 132192 atoms [I] insert 0 atoms [I] now 132192 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 132192 atoms [I] remove 648 atoms [I] now 131544 atoms [I] NP=131544 n=131544 [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 = Wed May 31 17:19:52 2023 CPU time spent: 11.225891 s {"realtime":1283.49,"usertime":3133.86,"systime":40.59,"memmax":152620,"memavg":0}