QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters' [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [I] RUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Wed Jun 14 12:08:32 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 6 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 11 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=1584 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.083333333333333 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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= 8.3333333333e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=3.289372e+01 pxpb=0.000000e+00 pypb=4.923895e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 607 need remove atom 609 need remove atom 619 need remove atom 621 need remove atom 631 need remove atom 633 need remove atom 643 need remove atom 645 need remove atom 655 need remove atom 657 need remove atom 667 need remove atom 669 need remove atom 679 need remove atom 681 need remove atom 691 need remove atom 693 need remove atom 703 need remove atom 705 need remove atom 715 need remove atom 717 need remove atom 729 need remove atom 741 need remove atom 864 need remove atom 865 need remove atom 867 need remove atom 868 need remove atom 876 need remove atom 877 need remove atom 879 need remove atom 880 need remove atom 888 need remove atom 889 need remove atom 891 need remove atom 892 need remove atom 900 need remove atom 901 need remove atom 903 need remove atom 904 need remove atom 912 need remove atom 913 need remove atom 915 need remove atom 916 need remove atom 924 need remove atom 925 need remove atom 927 need remove atom 928 need remove atom 936 need remove atom 937 need remove atom 939 need remove atom 940 need remove atom 948 need remove atom 949 need remove atom 951 need remove atom 952 need remove atom 960 need remove atom 961 need remove atom 963 need remove atom 964 need remove atom 972 need remove atom 973 need remove atom 975 need remove atom 976 need remove atom 984 need remove atom 985 need remove atom 996 need remove atom 997 [I] need removenum=66 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5566937139e-01 1.7413981756e-01 0.0000000000e+00 dub= -5.8276170063e-01 1.7414366632e-01 0.0000000000e+00 duc= 5.5567095989e-01 -1.7637035864e-01 0.0000000000e+00 [I] overall tilt ux= -1.1384310720e+00 3.8487625439e-06 0.0000000000e+00 uy= 1.5884974520e-06 -3.5051017619e-01 0.0000000000e+00 [I] storedr[0]= -1.9552326809e-02 -1.1186292818e-03 0.0000000000e+00 [I] originally 1584 atoms [I] insert 0 atoms [I] now 1584 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1584 atoms [I] remove 66 atoms [I] now 1518 atoms [I] NP=1518 n=1518 [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 [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 Jun 14 12:08:33 2023 CPU time spent: 0.988189 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 Jun 14 12:11:00 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 7 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 13 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=2184 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.071428571428571 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 7.1428571429e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=3.837601e+01 pxpb=0.000000e+00 pypb=5.819149e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1013 need remove atom 1014 need remove atom 1019 need remove atom 1025 need remove atom 1026 need remove atom 1031 need remove atom 1034 need remove atom 1037 need remove atom 1038 need remove atom 1040 need remove atom 1042 need remove atom 1043 need remove atom 1046 need remove atom 1049 need remove atom 1050 need remove atom 1052 need remove atom 1054 need remove atom 1055 need remove atom 1058 need remove atom 1061 need remove atom 1062 need remove atom 1064 need remove atom 1066 need remove atom 1067 need remove atom 1070 need remove atom 1073 need remove atom 1074 need remove atom 1076 need remove atom 1078 need remove atom 1079 need remove atom 1082 need remove atom 1085 need remove atom 1086 need remove atom 1088 need remove atom 1090 need remove atom 1091 need remove atom 1094 need remove atom 1097 need remove atom 1098 need remove atom 1100 need remove atom 1102 need remove atom 1103 need remove atom 1106 need remove atom 1109 need remove atom 1110 need remove atom 1112 need remove atom 1114 need remove atom 1115 need remove atom 1118 need remove atom 1121 need remove atom 1122 need remove atom 1124 need remove atom 1126 need remove atom 1127 need remove atom 1130 need remove atom 1133 need remove atom 1134 need remove atom 1136 need remove atom 1138 need remove atom 1139 need remove atom 1142 need remove atom 1145 need remove atom 1146 need remove atom 1148 need remove atom 1150 need remove atom 1151 need remove atom 1154 need remove atom 1157 need remove atom 1158 need remove atom 1160 need remove atom 1162 need remove atom 1163 need remove atom 1166 need remove atom 1169 need remove atom 1170 need remove atom 1172 need remove atom 1174 need remove atom 1175 [I] need removenum=78 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5747398049e-01 1.7351818115e-01 0.0000000000e+00 dub= -5.8475624844e-01 1.7352224711e-01 0.0000000000e+00 duc= 5.5747555272e-01 -1.7579350464e-01 0.0000000000e+00 [I] overall tilt ux= -1.1422302289e+00 4.0659619465e-06 0.0000000000e+00 uy= 1.5722346959e-06 -3.4931168579e-01 0.0000000000e+00 [I] storedr[0]= -1.8921845872e-02 -1.1402244128e-03 0.0000000000e+00 [I] originally 2184 atoms [I] insert 0 atoms [I] now 2184 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2184 atoms [I] remove 78 atoms [I] now 2106 atoms [I] NP=2106 n=2106 [I] ASSIGN finalcnfile = dipole_1.1.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.1.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.1.lammps [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 Jun 14 12:11:01 2023 CPU time spent: 1.355095 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 Jun 14 12:15:10 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 15 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=2880 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.0625 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 6.2500000000e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=4.385830e+01 pxpb=0.000000e+00 pypb=6.714403e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1183 need remove atom 1185 need remove atom 1195 need remove atom 1197 need remove atom 1207 need remove atom 1209 need remove atom 1219 need remove atom 1221 need remove atom 1231 need remove atom 1233 need remove atom 1243 need remove atom 1245 need remove atom 1255 need remove atom 1257 need remove atom 1267 need remove atom 1269 need remove atom 1279 need remove atom 1281 need remove atom 1291 need remove atom 1293 need remove atom 1303 need remove atom 1305 need remove atom 1315 need remove atom 1317 need remove atom 1327 need remove atom 1329 need remove atom 1339 need remove atom 1341 need remove atom 1353 need remove atom 1365 need remove atom 1536 need remove atom 1537 need remove atom 1539 need remove atom 1540 need remove atom 1548 need remove atom 1549 need remove atom 1551 need remove atom 1552 need remove atom 1560 need remove atom 1561 need remove atom 1563 need remove atom 1564 need remove atom 1572 need remove atom 1573 need remove atom 1575 need remove atom 1576 need remove atom 1584 need remove atom 1585 need remove atom 1587 need remove atom 1588 need remove atom 1596 need remove atom 1597 need remove atom 1599 need remove atom 1600 need remove atom 1608 need remove atom 1609 need remove atom 1611 need remove atom 1612 need remove atom 1620 need remove atom 1621 need remove atom 1623 need remove atom 1624 need remove atom 1632 need remove atom 1633 need remove atom 1635 need remove atom 1636 need remove atom 1644 need remove atom 1645 need remove atom 1647 need remove atom 1648 need remove atom 1656 need remove atom 1657 need remove atom 1659 need remove atom 1660 need remove atom 1668 need remove atom 1669 need remove atom 1671 need remove atom 1672 need remove atom 1680 need remove atom 1681 need remove atom 1683 need remove atom 1684 need remove atom 1692 need remove atom 1693 need remove atom 1695 need remove atom 1696 need remove atom 1704 need remove atom 1705 need remove atom 1716 need remove atom 1717 [I] need removenum=90 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5879682692e-01 1.7305693003e-01 0.0000000000e+00 dub= -5.8621326514e-01 1.7306115161e-01 0.0000000000e+00 duc= 5.5879838688e-01 -1.7536540971e-01 0.0000000000e+00 [I] overall tilt ux= -1.1450100921e+00 4.2215786429e-06 0.0000000000e+00 uy= 1.5599567957e-06 -3.4842233974e-01 0.0000000000e+00 [I] storedr[0]= -1.8409333816e-02 -1.1562102153e-03 0.0000000000e+00 [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 90 atoms [I] now 2790 atoms [I] NP=2790 n=2790 [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 [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 Jun 14 12:15:12 2023 CPU time spent: 1.797320 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 Jun 14 12:21:02 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 9 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 17 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=3672 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.055555555555556 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 5.5555555556e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=4.934058e+01 pxpb=0.000000e+00 pypb=7.609656e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1731 need remove atom 1733 need remove atom 1734 need remove atom 1743 need remove atom 1745 need remove atom 1746 need remove atom 1752 need remove atom 1754 need remove atom 1755 need remove atom 1757 need remove atom 1758 need remove atom 1760 need remove atom 1764 need remove atom 1766 need remove atom 1767 need remove atom 1769 need remove atom 1770 need remove atom 1772 need remove atom 1776 need remove atom 1778 need remove atom 1779 need remove atom 1781 need remove atom 1782 need remove atom 1784 need remove atom 1788 need remove atom 1790 need remove atom 1791 need remove atom 1793 need remove atom 1794 need remove atom 1796 need remove atom 1800 need remove atom 1802 need remove atom 1803 need remove atom 1805 need remove atom 1806 need remove atom 1808 need remove atom 1812 need remove atom 1814 need remove atom 1815 need remove atom 1817 need remove atom 1818 need remove atom 1820 need remove atom 1824 need remove atom 1826 need remove atom 1827 need remove atom 1829 need remove atom 1830 need remove atom 1832 need remove atom 1836 need remove atom 1838 need remove atom 1839 need remove atom 1841 need remove atom 1842 need remove atom 1844 need remove atom 1848 need remove atom 1850 need remove atom 1851 need remove atom 1853 need remove atom 1854 need remove atom 1856 need remove atom 1860 need remove atom 1862 need remove atom 1863 need remove atom 1865 need remove atom 1866 need remove atom 1868 need remove atom 1872 need remove atom 1874 need remove atom 1875 need remove atom 1877 need remove atom 1878 need remove atom 1880 need remove atom 1884 need remove atom 1886 need remove atom 1887 need remove atom 1889 need remove atom 1890 need remove atom 1892 need remove atom 1896 need remove atom 1898 need remove atom 1899 need remove atom 1901 need remove atom 1902 need remove atom 1904 need remove atom 1908 need remove atom 1910 need remove atom 1911 need remove atom 1913 need remove atom 1914 need remove atom 1916 need remove atom 1920 need remove atom 1922 need remove atom 1923 need remove atom 1925 need remove atom 1926 need remove atom 1928 need remove atom 1932 need remove atom 1934 need remove atom 1935 need remove atom 1937 need remove atom 1938 need remove atom 1940 [I] need removenum=102 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5980805213e-01 1.7270118402e-01 0.0000000000e+00 dub= -5.8732410399e-01 1.7270552242e-01 0.0000000000e+00 duc= 5.5980960250e-01 -1.7503519866e-01 0.0000000000e+00 [I] overall tilt ux= -1.1471321561e+00 4.3383986524e-06 0.0000000000e+00 uy= 1.5503683820e-06 -3.4773638268e-01 0.0000000000e+00 [I] storedr[0]= -1.7989086829e-02 -1.1685155435e-03 0.0000000000e+00 [I] originally 3672 atoms [I] insert 0 atoms [I] now 3672 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3672 atoms [I] remove 102 atoms [I] now 3570 atoms [I] NP=3570 n=3570 [I] ASSIGN finalcnfile = dipole_1.4.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.4.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.4.lammps [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 Jun 14 12:21:04 2023 CPU time spent: 2.282723 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 Jun 14 12:31:33 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 18 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=4320 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.05 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 5.0000000000e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=5.482287e+01 pxpb=0.000000e+00 pypb=8.057283e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1855 need remove atom 1857 need remove atom 1858 need remove atom 1859 need remove atom 1867 need remove atom 1869 need remove atom 1870 need remove atom 1871 need remove atom 1879 need remove atom 1881 need remove atom 1882 need remove atom 1883 need remove atom 1891 need remove atom 1893 need remove atom 1894 need remove atom 1895 need remove atom 1903 need remove atom 1905 need remove atom 1906 need remove atom 1907 need remove atom 1915 need remove atom 1917 need remove atom 1918 need remove atom 1919 need remove atom 1927 need remove atom 1929 need remove atom 1930 need remove atom 1931 need remove atom 1939 need remove atom 1941 need remove atom 1942 need remove atom 1943 need remove atom 1951 need remove atom 1953 need remove atom 1954 need remove atom 1955 need remove atom 1963 need remove atom 1965 need remove atom 1966 need remove atom 1967 need remove atom 1975 need remove atom 1977 need remove atom 1978 need remove atom 1979 need remove atom 1987 need remove atom 1989 need remove atom 1990 need remove atom 1991 need remove atom 1999 need remove atom 2001 need remove atom 2002 need remove atom 2003 need remove atom 2011 need remove atom 2013 need remove atom 2014 need remove atom 2015 need remove atom 2023 need remove atom 2025 need remove atom 2026 need remove atom 2027 need remove atom 2035 need remove atom 2037 need remove atom 2038 need remove atom 2039 need remove atom 2047 need remove atom 2049 need remove atom 2050 need remove atom 2051 need remove atom 2059 need remove atom 2061 need remove atom 2062 need remove atom 2063 need remove atom 2281 need remove atom 2284 need remove atom 2293 need remove atom 2296 need remove atom 2305 need remove atom 2308 need remove atom 2317 need remove atom 2320 need remove atom 2329 need remove atom 2332 need remove atom 2341 need remove atom 2344 need remove atom 2353 need remove atom 2356 need remove atom 2365 need remove atom 2368 need remove atom 2377 need remove atom 2380 need remove atom 2389 need remove atom 2392 need remove atom 2401 need remove atom 2404 need remove atom 2413 need remove atom 2416 need remove atom 2425 need remove atom 2428 need remove atom 2437 need remove atom 2440 need remove atom 2449 need remove atom 2452 need remove atom 2461 need remove atom 2464 need remove atom 2473 need remove atom 2476 need remove atom 2485 need remove atom 2488 [I] need removenum=108 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5306162038e-01 1.7502246550e-01 0.0000000000e+00 dub= -5.7986582185e-01 1.7502599096e-01 0.0000000000e+00 duc= 5.5306323139e-01 -1.7718919873e-01 0.0000000000e+00 [I] overall tilt ux= -1.1329274422e+00 3.5254605060e-06 0.0000000000e+00 uy= 1.6110023701e-06 -3.5221166423e-01 0.0000000000e+00 [I] storedr[0]= -1.6858586294e-02 -1.0847155655e-03 0.0000000000e+00 [I] originally 4320 atoms [I] insert 0 atoms [I] now 4320 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 4320 atoms [I] remove 108 atoms [I] now 4212 atoms [I] NP=4212 n=4212 [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 [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 Jun 14 12:31:36 2023 CPU time spent: 2.709131 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 Jun 14 12:45:47 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 18 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=6480 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.05 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 5.0000000000e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=5.482287e+01 pxpb=0.000000e+00 pypb=8.057283e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2779 need remove atom 2781 need remove atom 2782 need remove atom 2783 need remove atom 2791 need remove atom 2793 need remove atom 2794 need remove atom 2795 need remove atom 2803 need remove atom 2805 need remove atom 2806 need remove atom 2807 need remove atom 2815 need remove atom 2817 need remove atom 2818 need remove atom 2819 need remove atom 2827 need remove atom 2829 need remove atom 2830 need remove atom 2831 need remove atom 2839 need remove atom 2841 need remove atom 2842 need remove atom 2843 need remove atom 2851 need remove atom 2853 need remove atom 2854 need remove atom 2855 need remove atom 2863 need remove atom 2865 need remove atom 2866 need remove atom 2867 need remove atom 2875 need remove atom 2877 need remove atom 2878 need remove atom 2879 need remove atom 2887 need remove atom 2889 need remove atom 2890 need remove atom 2891 need remove atom 2899 need remove atom 2901 need remove atom 2902 need remove atom 2903 need remove atom 2911 need remove atom 2913 need remove atom 2914 need remove atom 2915 need remove atom 2923 need remove atom 2925 need remove atom 2926 need remove atom 2927 need remove atom 2935 need remove atom 2937 need remove atom 2938 need remove atom 2939 need remove atom 2947 need remove atom 2949 need remove atom 2950 need remove atom 2951 need remove atom 2959 need remove atom 2961 need remove atom 2962 need remove atom 2963 need remove atom 2971 need remove atom 2973 need remove atom 2974 need remove atom 2975 need remove atom 2983 need remove atom 2985 need remove atom 2986 need remove atom 2987 need remove atom 2995 need remove atom 2997 need remove atom 2998 need remove atom 2999 need remove atom 3007 need remove atom 3009 need remove atom 3010 need remove atom 3011 need remove atom 3019 need remove atom 3021 need remove atom 3022 need remove atom 3023 need remove atom 3031 need remove atom 3033 need remove atom 3034 need remove atom 3035 need remove atom 3043 need remove atom 3045 need remove atom 3046 need remove atom 3047 need remove atom 3055 need remove atom 3057 need remove atom 3058 need remove atom 3059 need remove atom 3067 need remove atom 3069 need remove atom 3070 need remove atom 3071 need remove atom 3079 need remove atom 3081 need remove atom 3082 need remove atom 3083 need remove atom 3091 need remove atom 3093 need remove atom 3094 need remove atom 3095 need remove atom 3421 need remove atom 3424 need remove atom 3433 need remove atom 3436 need remove atom 3445 need remove atom 3448 need remove atom 3457 need remove atom 3460 need remove atom 3469 need remove atom 3472 need remove atom 3481 need remove atom 3484 need remove atom 3493 need remove atom 3496 need remove atom 3505 need remove atom 3508 need remove atom 3517 need remove atom 3520 need remove atom 3529 need remove atom 3532 need remove atom 3541 need remove atom 3544 need remove atom 3553 need remove atom 3556 need remove atom 3565 need remove atom 3568 need remove atom 3577 need remove atom 3580 need remove atom 3589 need remove atom 3592 need remove atom 3601 need remove atom 3604 need remove atom 3613 need remove atom 3616 need remove atom 3625 need remove atom 3628 need remove atom 3637 need remove atom 3640 need remove atom 3649 need remove atom 3652 need remove atom 3661 need remove atom 3664 need remove atom 3673 need remove atom 3676 need remove atom 3685 need remove atom 3688 need remove atom 3697 need remove atom 3700 need remove atom 3709 need remove atom 3712 need remove atom 3721 need remove atom 3724 need remove atom 3733 need remove atom 3736 [I] need removenum=162 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5306162038e-01 1.7502246550e-01 0.0000000000e+00 dub= -5.7986582185e-01 1.7502599096e-01 0.0000000000e+00 duc= 5.5306323139e-01 -1.7718919873e-01 0.0000000000e+00 [I] overall tilt ux= -1.1329274422e+00 3.5254605060e-06 0.0000000000e+00 uy= 1.6110023701e-06 -3.5221166423e-01 0.0000000000e+00 [I] storedr[0]= -1.6858586294e-02 -1.0847155655e-03 0.0000000000e+00 [I] originally 6480 atoms [I] insert 0 atoms [I] now 6480 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 6480 atoms [I] remove 162 atoms [I] now 6318 atoms [I] NP=6318 n=6318 [I] ASSIGN finalcnfile = dipole_1.7.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.7.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.7.lammps [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 Jun 14 12:45:51 2023 CPU time spent: 3.983515 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 Jun 14 12:56:39 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 11 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 20 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=7920 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.045454545454545 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 4.5454545455e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=6.030516e+01 pxpb=0.000000e+00 pypb=8.952537e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3783 need remove atom 3785 need remove atom 3786 need remove atom 3795 need remove atom 3797 need remove atom 3798 need remove atom 3807 need remove atom 3809 need remove atom 3810 need remove atom 3816 need remove atom 3818 need remove atom 3819 need remove atom 3821 need remove atom 3822 need remove atom 3824 need remove atom 3828 need remove atom 3830 need remove atom 3831 need remove atom 3833 need remove atom 3834 need remove atom 3836 need remove atom 3840 need remove atom 3842 need remove atom 3843 need remove atom 3845 need remove atom 3846 need remove atom 3848 need remove atom 3852 need remove atom 3854 need remove atom 3855 need remove atom 3857 need remove atom 3858 need remove atom 3860 need remove atom 3864 need remove atom 3866 need remove atom 3867 need remove atom 3869 need remove atom 3870 need remove atom 3872 need remove atom 3876 need remove atom 3878 need remove atom 3879 need remove atom 3881 need remove atom 3882 need remove atom 3884 need remove atom 3888 need remove atom 3890 need remove atom 3891 need remove atom 3893 need remove atom 3894 need remove atom 3896 need remove atom 3900 need remove atom 3902 need remove atom 3903 need remove atom 3905 need remove atom 3906 need remove atom 3908 need remove atom 3912 need remove atom 3914 need remove atom 3915 need remove atom 3917 need remove atom 3918 need remove atom 3920 need remove atom 3924 need remove atom 3926 need remove atom 3927 need remove atom 3929 need remove atom 3930 need remove atom 3932 need remove atom 3936 need remove atom 3938 need remove atom 3939 need remove atom 3941 need remove atom 3942 need remove atom 3944 need remove atom 3948 need remove atom 3950 need remove atom 3951 need remove atom 3953 need remove atom 3954 need remove atom 3956 need remove atom 3960 need remove atom 3962 need remove atom 3963 need remove atom 3965 need remove atom 3966 need remove atom 3968 need remove atom 3972 need remove atom 3974 need remove atom 3975 need remove atom 3977 need remove atom 3978 need remove atom 3980 need remove atom 3984 need remove atom 3986 need remove atom 3987 need remove atom 3989 need remove atom 3990 need remove atom 3992 need remove atom 3996 need remove atom 3998 need remove atom 3999 need remove atom 4001 need remove atom 4002 need remove atom 4004 need remove atom 4008 need remove atom 4010 need remove atom 4011 need remove atom 4013 need remove atom 4014 need remove atom 4016 need remove atom 4020 need remove atom 4022 need remove atom 4023 need remove atom 4025 need remove atom 4026 need remove atom 4028 need remove atom 4032 need remove atom 4034 need remove atom 4035 need remove atom 4037 need remove atom 4038 need remove atom 4040 need remove atom 4044 need remove atom 4046 need remove atom 4047 need remove atom 4049 need remove atom 4050 need remove atom 4052 need remove atom 4056 need remove atom 4058 need remove atom 4059 need remove atom 4061 need remove atom 4062 need remove atom 4064 need remove atom 4068 need remove atom 4070 need remove atom 4071 need remove atom 4073 need remove atom 4074 need remove atom 4076 need remove atom 4080 need remove atom 4082 need remove atom 4083 need remove atom 4085 need remove atom 4086 need remove atom 4088 need remove atom 4092 need remove atom 4094 need remove atom 4095 need remove atom 4097 need remove atom 4098 need remove atom 4100 need remove atom 4104 need remove atom 4106 need remove atom 4107 need remove atom 4109 need remove atom 4110 need remove atom 4112 need remove atom 4116 need remove atom 4118 need remove atom 4119 need remove atom 4121 need remove atom 4122 need remove atom 4124 need remove atom 4128 need remove atom 4130 need remove atom 4131 need remove atom 4133 need remove atom 4134 need remove atom 4136 need remove atom 4140 need remove atom 4142 need remove atom 4148 need remove atom 4152 need remove atom 4154 need remove atom 4160 need remove atom 4164 need remove atom 4166 need remove atom 4172 [I] need removenum=180 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5449601413e-01 1.7453926552e-01 0.0000000000e+00 dub= -5.8146066592e-01 1.7454297015e-01 0.0000000000e+00 duc= 5.5449761290e-01 -1.7674096459e-01 0.0000000000e+00 [I] overall tilt ux= -1.1359566800e+00 3.7046302567e-06 0.0000000000e+00 uy= 1.5987693819e-06 -3.5128023011e-01 0.0000000000e+00 [I] storedr[0]= -1.6699097270e-02 -1.1018743174e-03 0.0000000000e+00 [I] originally 7920 atoms [I] insert 0 atoms [I] now 7920 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7920 atoms [I] remove 180 atoms [I] now 7740 atoms [I] NP=7740 n=7740 [I] ASSIGN finalcnfile = dipole_1.8.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.8.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.8.lammps [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 Jun 14 12:56:45 2023 CPU time spent: 5.195565 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 Jun 14 13:11:41 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 12 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 22 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=9504 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.041666666666667 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=6.578744e+01 pxpb=0.000000e+00 pypb=9.847791e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4183 need remove atom 4185 need remove atom 4186 need remove atom 4187 need remove atom 4195 need remove atom 4197 need remove atom 4198 need remove atom 4199 need remove atom 4207 need remove atom 4209 need remove atom 4210 need remove atom 4211 need remove atom 4219 need remove atom 4221 need remove atom 4222 need remove atom 4223 need remove atom 4231 need remove atom 4233 need remove atom 4234 need remove atom 4235 need remove atom 4243 need remove atom 4245 need remove atom 4246 need remove atom 4247 need remove atom 4255 need remove atom 4257 need remove atom 4258 need remove atom 4259 need remove atom 4267 need remove atom 4269 need remove atom 4270 need remove atom 4271 need remove atom 4279 need remove atom 4281 need remove atom 4282 need remove atom 4283 need remove atom 4291 need remove atom 4293 need remove atom 4294 need remove atom 4295 need remove atom 4303 need remove atom 4305 need remove atom 4306 need remove atom 4307 need remove atom 4315 need remove atom 4317 need remove atom 4318 need remove atom 4319 need remove atom 4327 need remove atom 4329 need remove atom 4330 need remove atom 4331 need remove atom 4339 need remove atom 4341 need remove atom 4342 need remove atom 4343 need remove atom 4351 need remove atom 4353 need remove atom 4354 need remove atom 4355 need remove atom 4363 need remove atom 4365 need remove atom 4366 need remove atom 4367 need remove atom 4375 need remove atom 4377 need remove atom 4378 need remove atom 4379 need remove atom 4387 need remove atom 4389 need remove atom 4390 need remove atom 4391 need remove atom 4399 need remove atom 4401 need remove atom 4402 need remove atom 4403 need remove atom 4411 need remove atom 4413 need remove atom 4414 need remove atom 4415 need remove atom 4423 need remove atom 4425 need remove atom 4426 need remove atom 4427 need remove atom 4435 need remove atom 4437 need remove atom 4438 need remove atom 4439 need remove atom 4447 need remove atom 4449 need remove atom 4450 need remove atom 4451 need remove atom 4459 need remove atom 4461 need remove atom 4462 need remove atom 4463 need remove atom 4471 need remove atom 4473 need remove atom 4474 need remove atom 4475 need remove atom 4483 need remove atom 4485 need remove atom 4486 need remove atom 4487 need remove atom 4495 need remove atom 4497 need remove atom 4498 need remove atom 4499 need remove atom 4507 need remove atom 4509 need remove atom 4510 need remove atom 4511 need remove atom 4519 need remove atom 4521 need remove atom 4522 need remove atom 4523 need remove atom 4531 need remove atom 4533 need remove atom 4534 need remove atom 4535 need remove atom 4543 need remove atom 4545 need remove atom 4546 need remove atom 4547 need remove atom 4555 need remove atom 4557 need remove atom 4558 need remove atom 4559 need remove atom 4567 need remove atom 4569 need remove atom 4570 need remove atom 4571 need remove atom 4969 need remove atom 4972 need remove atom 4981 need remove atom 4984 need remove atom 4993 need remove atom 4996 need remove atom 5005 need remove atom 5008 need remove atom 5017 need remove atom 5020 need remove atom 5029 need remove atom 5032 need remove atom 5041 need remove atom 5044 need remove atom 5053 need remove atom 5056 need remove atom 5065 need remove atom 5068 need remove atom 5077 need remove atom 5080 need remove atom 5089 need remove atom 5092 need remove atom 5101 need remove atom 5104 need remove atom 5113 need remove atom 5116 need remove atom 5125 need remove atom 5128 need remove atom 5137 need remove atom 5140 need remove atom 5149 need remove atom 5152 need remove atom 5161 need remove atom 5164 need remove atom 5173 need remove atom 5176 need remove atom 5185 need remove atom 5188 need remove atom 5197 need remove atom 5200 need remove atom 5209 need remove atom 5212 need remove atom 5221 need remove atom 5224 need remove atom 5233 need remove atom 5236 need remove atom 5245 need remove atom 5248 need remove atom 5257 need remove atom 5260 need remove atom 5269 need remove atom 5272 need remove atom 5281 need remove atom 5284 need remove atom 5293 need remove atom 5296 need remove atom 5305 need remove atom 5308 need remove atom 5317 need remove atom 5320 need remove atom 5329 need remove atom 5332 need remove atom 5341 need remove atom 5344 need remove atom 5353 need remove atom 5356 [I] need removenum=198 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5566937139e-01 1.7413981756e-01 0.0000000000e+00 dub= -5.8276170063e-01 1.7414366632e-01 0.0000000000e+00 duc= 5.5567095989e-01 -1.7637035864e-01 0.0000000000e+00 [I] overall tilt ux= -1.1384310720e+00 3.8487625431e-06 0.0000000000e+00 uy= 1.5884974520e-06 -3.5051017619e-01 0.0000000000e+00 [I] storedr[0]= -1.6548432407e-02 -1.1160226902e-03 0.0000000000e+00 [I] originally 9504 atoms [I] insert 0 atoms [I] now 9504 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 9504 atoms [I] remove 198 atoms [I] now 9306 atoms [I] NP=9306 n=9306 [I] ASSIGN finalcnfile = dipole_2.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.0.lammps [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 Jun 14 13:11:47 2023 CPU time spent: 5.900812 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 Jun 14 13:36:08 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 15 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 28 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=20160 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.033333333333333 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=8.223430e+01 pxpb=0.000000e+00 pypb=1.253355e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 9747 need remove atom 9749 need remove atom 9750 need remove atom 9759 need remove atom 9761 need remove atom 9762 need remove atom 9771 need remove atom 9773 need remove atom 9774 need remove atom 9783 need remove atom 9785 need remove atom 9786 need remove atom 9792 need remove atom 9794 need remove atom 9795 need remove atom 9797 need remove atom 9798 need remove atom 9800 need remove atom 9804 need remove atom 9806 need remove atom 9807 need remove atom 9809 need remove atom 9810 need remove atom 9812 need remove atom 9816 need remove atom 9818 need remove atom 9819 need remove atom 9821 need remove atom 9822 need remove atom 9824 need remove atom 9828 need remove atom 9830 need remove atom 9831 need remove atom 9833 need remove atom 9834 need remove atom 9836 need remove atom 9840 need remove atom 9842 need remove atom 9843 need remove atom 9845 need remove atom 9846 need remove atom 9848 need remove atom 9852 need remove atom 9854 need remove atom 9855 need remove atom 9857 need remove atom 9858 need remove atom 9860 need remove atom 9864 need remove atom 9866 need remove atom 9867 need remove atom 9869 need remove atom 9870 need remove atom 9872 need remove atom 9876 need remove atom 9878 need remove atom 9879 need remove atom 9881 need remove atom 9882 need remove atom 9884 need remove atom 9888 need remove atom 9890 need remove atom 9891 need remove atom 9893 need remove atom 9894 need remove atom 9896 need remove atom 9900 need remove atom 9902 need remove atom 9903 need remove atom 9905 need remove atom 9906 need remove atom 9908 need remove atom 9912 need remove atom 9914 need remove atom 9915 need remove atom 9917 need remove atom 9918 need remove atom 9920 need remove atom 9924 need remove atom 9926 need remove atom 9927 need remove atom 9929 need remove atom 9930 need remove atom 9932 need remove atom 9936 need remove atom 9938 need remove atom 9939 need remove atom 9941 need remove atom 9942 need remove atom 9944 need remove atom 9948 need remove atom 9950 need remove atom 9951 need remove atom 9953 need remove atom 9954 need remove atom 9956 need remove atom 9960 need remove atom 9962 need remove atom 9963 need remove atom 9965 need remove atom 9966 need remove atom 9968 need remove atom 9972 need remove atom 9974 need remove atom 9975 need remove atom 9977 need remove atom 9978 need remove atom 9980 need remove atom 9984 need remove atom 9986 need remove atom 9987 need remove atom 9989 need remove atom 9990 need remove atom 9992 need remove atom 9996 need remove atom 9998 need remove atom 9999 need remove atom 10001 need remove atom 10002 need remove atom 10004 need remove atom 10008 need remove atom 10010 need remove atom 10011 need remove atom 10013 need remove atom 10014 need remove atom 10016 need remove atom 10020 need remove atom 10022 need remove atom 10023 need remove atom 10025 need remove atom 10026 need remove atom 10028 need remove atom 10032 need remove atom 10034 need remove atom 10035 need remove atom 10037 need remove atom 10038 need remove atom 10040 need remove atom 10044 need remove atom 10046 need remove atom 10047 need remove atom 10049 need remove atom 10050 need remove atom 10052 need remove atom 10056 need remove atom 10058 need remove atom 10059 need remove atom 10061 need remove atom 10062 need remove atom 10064 need remove atom 10068 need remove atom 10070 need remove atom 10071 need remove atom 10073 need remove atom 10074 need remove atom 10076 need remove atom 10080 need remove atom 10082 need remove atom 10083 need remove atom 10085 need remove atom 10086 need remove atom 10088 need remove atom 10092 need remove atom 10094 need remove atom 10095 need remove atom 10097 need remove atom 10098 need remove atom 10100 need remove atom 10104 need remove atom 10106 need remove atom 10107 need remove atom 10109 need remove atom 10110 need remove atom 10112 need remove atom 10116 need remove atom 10118 need remove atom 10119 need remove atom 10121 need remove atom 10122 need remove atom 10124 need remove atom 10128 need remove atom 10130 need remove atom 10131 need remove atom 10133 need remove atom 10134 need remove atom 10136 need remove atom 10140 need remove atom 10142 need remove atom 10143 need remove atom 10145 need remove atom 10146 need remove atom 10148 need remove atom 10152 need remove atom 10154 need remove atom 10155 need remove atom 10157 need remove atom 10158 need remove atom 10160 need remove atom 10164 need remove atom 10166 need remove atom 10167 need remove atom 10169 need remove atom 10170 need remove atom 10172 need remove atom 10176 need remove atom 10178 need remove atom 10179 need remove atom 10181 need remove atom 10182 need remove atom 10184 need remove atom 10188 need remove atom 10190 need remove atom 10191 need remove atom 10193 need remove atom 10194 need remove atom 10196 need remove atom 10200 need remove atom 10202 need remove atom 10203 need remove atom 10205 need remove atom 10206 need remove atom 10208 need remove atom 10212 need remove atom 10214 need remove atom 10215 need remove atom 10217 need remove atom 10218 need remove atom 10220 need remove atom 10224 need remove atom 10226 need remove atom 10227 need remove atom 10229 need remove atom 10230 need remove atom 10232 need remove atom 10236 need remove atom 10238 need remove atom 10239 need remove atom 10241 need remove atom 10242 need remove atom 10244 need remove atom 10248 need remove atom 10250 need remove atom 10251 need remove atom 10253 need remove atom 10254 need remove atom 10256 need remove atom 10260 need remove atom 10262 need remove atom 10263 need remove atom 10265 need remove atom 10266 need remove atom 10268 need remove atom 10272 need remove atom 10274 need remove atom 10275 need remove atom 10277 need remove atom 10278 need remove atom 10280 need remove atom 10284 need remove atom 10286 need remove atom 10287 need remove atom 10289 need remove atom 10290 need remove atom 10292 need remove atom 10296 need remove atom 10298 need remove atom 10299 need remove atom 10301 need remove atom 10302 need remove atom 10304 need remove atom 10308 need remove atom 10310 need remove atom 10311 need remove atom 10313 need remove atom 10314 need remove atom 10316 need remove atom 10320 need remove atom 10322 need remove atom 10323 need remove atom 10325 need remove atom 10326 need remove atom 10328 need remove atom 10332 need remove atom 10334 need remove atom 10335 need remove atom 10337 need remove atom 10338 need remove atom 10340 need remove atom 10344 need remove atom 10346 need remove atom 10347 need remove atom 10349 need remove atom 10350 need remove atom 10352 need remove atom 10356 need remove atom 10358 need remove atom 10359 need remove atom 10361 need remove atom 10362 need remove atom 10364 need remove atom 10368 need remove atom 10370 need remove atom 10371 need remove atom 10373 need remove atom 10374 need remove atom 10376 need remove atom 10380 need remove atom 10382 need remove atom 10383 need remove atom 10385 need remove atom 10386 need remove atom 10388 need remove atom 10392 need remove atom 10394 need remove atom 10395 need remove atom 10397 need remove atom 10398 need remove atom 10400 need remove atom 10404 need remove atom 10406 need remove atom 10407 need remove atom 10409 need remove atom 10410 need remove atom 10412 need remove atom 10416 need remove atom 10418 need remove atom 10424 need remove atom 10428 need remove atom 10430 need remove atom 10436 need remove atom 10440 need remove atom 10442 need remove atom 10448 need remove atom 10452 need remove atom 10454 need remove atom 10460 [I] need removenum=336 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5818271090e-01 1.7327164347e-01 0.0000000000e+00 dub= -5.8553740167e-01 1.7327579319e-01 0.0000000000e+00 duc= 5.5818427659e-01 -1.7556469599e-01 0.0000000000e+00 [I] overall tilt ux= -1.1437201126e+00 4.1497235216e-06 0.0000000000e+00 uy= 1.5656941210e-06 -3.4883633945e-01 0.0000000000e+00 [I] storedr[0]= -1.6165139636e-02 -1.1466675229e-03 0.0000000000e+00 [I] originally 20160 atoms [I] insert 0 atoms [I] now 20160 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 20160 atoms [I] remove 336 atoms [I] now 19824 atoms [I] NP=19824 n=19824 [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 [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 Jun 14 13:36:22 2023 CPU time spent: 12.484462 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 Jun 14 13:57:59 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 18 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 33 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=28512 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.027777777777778 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=9.868116e+01 pxpb=0.000000e+00 pypb=1.477169e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 13063 need remove atom 13067 need remove atom 13075 need remove atom 13079 need remove atom 13087 need remove atom 13091 need remove atom 13099 need remove atom 13103 need remove atom 13111 need remove atom 13113 need remove atom 13114 need remove atom 13115 need remove atom 13123 need remove atom 13125 need remove atom 13126 need remove atom 13127 need remove atom 13135 need remove atom 13137 need remove atom 13138 need remove atom 13139 need remove atom 13147 need remove atom 13149 need remove atom 13150 need remove atom 13151 need remove atom 13159 need remove atom 13161 need remove atom 13162 need remove atom 13163 need remove atom 13171 need remove atom 13173 need remove atom 13174 need remove atom 13175 need remove atom 13183 need remove atom 13185 need remove atom 13186 need remove atom 13187 need remove atom 13195 need remove atom 13197 need remove atom 13198 need remove atom 13199 need remove atom 13207 need remove atom 13209 need remove atom 13210 need remove atom 13211 need remove atom 13219 need remove atom 13221 need remove atom 13222 need remove atom 13223 need remove atom 13231 need remove atom 13233 need remove atom 13234 need remove atom 13235 need remove atom 13243 need remove atom 13245 need remove atom 13246 need remove atom 13247 need remove atom 13255 need remove atom 13257 need remove atom 13258 need remove atom 13259 need remove atom 13267 need remove atom 13269 need remove atom 13270 need remove atom 13271 need remove atom 13279 need remove atom 13281 need remove atom 13282 need remove atom 13283 need remove atom 13291 need remove atom 13293 need remove atom 13294 need remove atom 13295 need remove atom 13303 need remove atom 13305 need remove atom 13306 need remove atom 13307 need remove atom 13315 need remove atom 13317 need remove atom 13318 need remove atom 13319 need remove atom 13327 need remove atom 13329 need remove atom 13330 need remove atom 13331 need remove atom 13339 need remove atom 13341 need remove atom 13342 need remove atom 13343 need remove atom 13351 need remove atom 13353 need remove atom 13354 need remove atom 13355 need remove atom 13363 need remove atom 13365 need remove atom 13366 need remove atom 13367 need remove atom 13375 need remove atom 13377 need remove atom 13378 need remove atom 13379 need remove atom 13387 need remove atom 13389 need remove atom 13390 need remove atom 13391 need remove atom 13399 need remove atom 13401 need remove atom 13402 need remove atom 13403 need remove atom 13411 need remove atom 13413 need remove atom 13414 need remove atom 13415 need remove atom 13423 need remove atom 13425 need remove atom 13426 need remove atom 13427 need remove atom 13435 need remove atom 13437 need remove atom 13438 need remove atom 13439 need remove atom 13447 need remove atom 13449 need remove atom 13450 need remove atom 13451 need remove atom 13459 need remove atom 13461 need remove atom 13462 need remove atom 13463 need remove atom 13471 need remove atom 13473 need remove atom 13474 need remove atom 13475 need remove atom 13483 need remove atom 13485 need remove atom 13486 need remove atom 13487 need remove atom 13495 need remove atom 13497 need remove atom 13498 need remove atom 13499 need remove atom 13507 need remove atom 13509 need remove atom 13510 need remove atom 13511 need remove atom 13519 need remove atom 13521 need remove atom 13522 need remove atom 13523 need remove atom 13531 need remove atom 13533 need remove atom 13534 need remove atom 13535 need remove atom 13543 need remove atom 13545 need remove atom 13546 need remove atom 13547 need remove atom 13555 need remove atom 13557 need remove atom 13558 need remove atom 13559 need remove atom 13567 need remove atom 13569 need remove atom 13570 need remove atom 13571 need remove atom 13579 need remove atom 13581 need remove atom 13582 need remove atom 13583 need remove atom 13591 need remove atom 13593 need remove atom 13594 need remove atom 13595 need remove atom 13603 need remove atom 13605 need remove atom 13606 need remove atom 13607 need remove atom 13615 need remove atom 13617 need remove atom 13618 need remove atom 13619 need remove atom 13627 need remove atom 13629 need remove atom 13630 need remove atom 13631 need remove atom 13639 need remove atom 13641 need remove atom 13642 need remove atom 13643 need remove atom 13651 need remove atom 13653 need remove atom 13654 need remove atom 13655 need remove atom 13663 need remove atom 13665 need remove atom 13666 need remove atom 13667 need remove atom 13675 need remove atom 13677 need remove atom 13678 need remove atom 13679 need remove atom 13687 need remove atom 13689 need remove atom 13690 need remove atom 13691 need remove atom 13699 need remove atom 13701 need remove atom 13702 need remove atom 13703 need remove atom 13711 need remove atom 13713 need remove atom 13714 need remove atom 13715 need remove atom 13723 need remove atom 13725 need remove atom 13726 need remove atom 13727 need remove atom 13735 need remove atom 13737 need remove atom 13738 need remove atom 13739 need remove atom 13747 need remove atom 13749 need remove atom 13750 need remove atom 13751 need remove atom 13759 need remove atom 13761 need remove atom 13762 need remove atom 13763 need remove atom 13771 need remove atom 13773 need remove atom 13774 need remove atom 13775 need remove atom 13783 need remove atom 13785 need remove atom 13786 need remove atom 13787 need remove atom 13795 need remove atom 13797 need remove atom 13798 need remove atom 13799 need remove atom 13807 need remove atom 13809 need remove atom 13810 need remove atom 13811 need remove atom 13819 need remove atom 13821 need remove atom 13822 need remove atom 13823 need remove atom 13831 need remove atom 13833 need remove atom 13834 need remove atom 13835 need remove atom 13843 need remove atom 13845 need remove atom 13846 need remove atom 13847 need remove atom 13855 need remove atom 13857 need remove atom 13858 need remove atom 13859 need remove atom 13867 need remove atom 13869 need remove atom 13870 need remove atom 13871 need remove atom 14644 need remove atom 14656 need remove atom 14668 need remove atom 14680 need remove atom 14689 need remove atom 14692 need remove atom 14701 need remove atom 14704 need remove atom 14713 need remove atom 14716 need remove atom 14725 need remove atom 14728 need remove atom 14737 need remove atom 14740 need remove atom 14749 need remove atom 14752 need remove atom 14761 need remove atom 14764 need remove atom 14773 need remove atom 14776 need remove atom 14785 need remove atom 14788 need remove atom 14797 need remove atom 14800 need remove atom 14809 need remove atom 14812 need remove atom 14821 need remove atom 14824 need remove atom 14833 need remove atom 14836 need remove atom 14845 need remove atom 14848 need remove atom 14857 need remove atom 14860 need remove atom 14869 need remove atom 14872 need remove atom 14881 need remove atom 14884 need remove atom 14893 need remove atom 14896 need remove atom 14905 need remove atom 14908 need remove atom 14917 need remove atom 14920 need remove atom 14929 need remove atom 14932 need remove atom 14941 need remove atom 14944 need remove atom 14953 need remove atom 14956 need remove atom 14965 need remove atom 14968 need remove atom 14977 need remove atom 14980 need remove atom 14989 need remove atom 14992 need remove atom 15001 need remove atom 15004 need remove atom 15013 need remove atom 15016 need remove atom 15025 need remove atom 15028 need remove atom 15037 need remove atom 15040 need remove atom 15049 need remove atom 15052 need remove atom 15061 need remove atom 15064 need remove atom 15073 need remove atom 15076 need remove atom 15085 need remove atom 15088 need remove atom 15097 need remove atom 15100 need remove atom 15109 need remove atom 15112 need remove atom 15121 need remove atom 15124 need remove atom 15133 need remove atom 15136 need remove atom 15145 need remove atom 15148 need remove atom 15157 need remove atom 15160 need remove atom 15169 need remove atom 15172 need remove atom 15181 need remove atom 15184 need remove atom 15193 need remove atom 15196 need remove atom 15205 need remove atom 15208 need remove atom 15217 need remove atom 15220 need remove atom 15229 need remove atom 15232 need remove atom 15241 need remove atom 15244 need remove atom 15253 need remove atom 15256 need remove atom 15265 need remove atom 15268 need remove atom 15277 need remove atom 15280 need remove atom 15289 need remove atom 15292 need remove atom 15301 need remove atom 15304 need remove atom 15313 need remove atom 15316 need remove atom 15325 need remove atom 15328 need remove atom 15337 need remove atom 15340 need remove atom 15349 need remove atom 15352 need remove atom 15361 need remove atom 15364 need remove atom 15373 need remove atom 15376 need remove atom 15385 need remove atom 15388 need remove atom 15397 need remove atom 15400 need remove atom 15409 need remove atom 15412 need remove atom 15421 need remove atom 15424 need remove atom 15433 need remove atom 15436 need remove atom 15445 need remove atom 15448 [I] need removenum=396 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5566937139e-01 1.7413981756e-01 0.0000000000e+00 dub= -5.8276170063e-01 1.7414366632e-01 0.0000000000e+00 duc= 5.5567095989e-01 -1.7637035864e-01 0.0000000000e+00 [I] overall tilt ux= -1.1384310720e+00 3.8487625430e-06 0.0000000000e+00 uy= 1.5884974522e-06 -3.5051017619e-01 0.0000000000e+00 [I] storedr[0]= -1.5547326149e-02 -1.1151364289e-03 0.0000000000e+00 [I] originally 28512 atoms [I] insert 0 atoms [I] now 28512 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 28512 atoms [I] remove 396 atoms [I] now 28116 atoms [I] NP=28116 n=28116 [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 [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 Jun 14 13:58:19 2023 CPU time spent: 17.714845 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 Jun 14 14:12:13 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 21 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 39 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=49140 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.023809523809524 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=1.151280e+02 pxpb=0.000000e+00 pypb=1.745745e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 24000 need remove atom 24002 need remove atom 24003 need remove atom 24005 need remove atom 24006 need remove atom 24008 need remove atom 24012 need remove atom 24014 need remove atom 24015 need remove atom 24017 need remove atom 24018 need remove atom 24020 need remove atom 24024 need remove atom 24026 need remove atom 24027 need remove atom 24029 need remove atom 24030 need remove atom 24032 need remove atom 24036 need remove atom 24038 need remove atom 24039 need remove atom 24041 need remove atom 24042 need remove atom 24044 need remove atom 24048 need remove atom 24050 need remove atom 24051 need remove atom 24053 need remove atom 24054 need remove atom 24056 need remove atom 24060 need remove atom 24062 need remove atom 24063 need remove atom 24065 need remove atom 24066 need remove atom 24068 need remove atom 24072 need remove atom 24074 need remove atom 24075 need remove atom 24077 need remove atom 24078 need remove atom 24080 need remove atom 24084 need remove atom 24086 need remove atom 24087 need remove atom 24089 need remove atom 24090 need remove atom 24092 need remove atom 24096 need remove atom 24098 need remove atom 24099 need remove atom 24101 need remove atom 24102 need remove atom 24104 need remove atom 24108 need remove atom 24110 need remove atom 24111 need remove atom 24113 need remove atom 24114 need remove atom 24116 need remove atom 24120 need remove atom 24122 need remove atom 24123 need remove atom 24125 need remove atom 24126 need remove atom 24128 need remove atom 24132 need remove atom 24134 need remove atom 24135 need remove atom 24137 need remove atom 24138 need remove atom 24140 need remove atom 24144 need remove atom 24146 need remove atom 24147 need remove atom 24149 need remove atom 24150 need remove atom 24152 need remove atom 24156 need remove atom 24158 need remove atom 24159 need remove atom 24161 need remove atom 24162 need remove atom 24164 need remove atom 24168 need remove atom 24170 need remove atom 24171 need remove atom 24173 need remove atom 24174 need remove atom 24176 need remove atom 24180 need remove atom 24182 need remove atom 24183 need remove atom 24185 need remove atom 24186 need remove atom 24188 need remove atom 24192 need remove atom 24194 need remove atom 24195 need remove atom 24197 need remove atom 24198 need remove atom 24200 need remove atom 24204 need remove atom 24206 need remove atom 24207 need remove atom 24209 need remove atom 24210 need remove atom 24212 need remove atom 24216 need remove atom 24218 need remove atom 24219 need remove atom 24221 need remove atom 24222 need remove atom 24224 need remove atom 24228 need remove atom 24230 need remove atom 24231 need remove atom 24233 need remove atom 24234 need remove atom 24236 need remove atom 24240 need remove atom 24242 need remove atom 24243 need remove atom 24245 need remove atom 24246 need remove atom 24248 need remove atom 24252 need remove atom 24254 need remove atom 24255 need remove atom 24257 need remove atom 24258 need remove atom 24260 need remove atom 24264 need remove atom 24266 need remove atom 24267 need remove atom 24269 need remove atom 24270 need remove atom 24272 need remove atom 24276 need remove atom 24278 need remove atom 24279 need remove atom 24281 need remove atom 24282 need remove atom 24284 need remove atom 24288 need remove atom 24290 need remove atom 24291 need remove atom 24293 need remove atom 24294 need remove atom 24296 need remove atom 24300 need remove atom 24302 need remove atom 24303 need remove atom 24305 need remove atom 24306 need remove atom 24308 need remove atom 24312 need remove atom 24314 need remove atom 24315 need remove atom 24317 need remove atom 24318 need remove atom 24320 need remove atom 24324 need remove atom 24326 need remove atom 24327 need remove atom 24329 need remove atom 24330 need remove atom 24332 need remove atom 24336 need remove atom 24338 need remove atom 24339 need remove atom 24341 need remove atom 24342 need remove atom 24344 need remove atom 24348 need remove atom 24350 need remove atom 24351 need remove atom 24353 need remove atom 24354 need remove atom 24356 need remove atom 24360 need remove atom 24362 need remove atom 24363 need remove atom 24365 need remove atom 24366 need remove atom 24368 need remove atom 24372 need remove atom 24374 need remove atom 24375 need remove atom 24377 need remove atom 24378 need remove atom 24380 need remove atom 24384 need remove atom 24386 need remove atom 24387 need remove atom 24389 need remove atom 24390 need remove atom 24392 need remove atom 24396 need remove atom 24398 need remove atom 24399 need remove atom 24401 need remove atom 24402 need remove atom 24404 need remove atom 24408 need remove atom 24410 need remove atom 24411 need remove atom 24413 need remove atom 24414 need remove atom 24416 need remove atom 24420 need remove atom 24422 need remove atom 24423 need remove atom 24425 need remove atom 24426 need remove atom 24428 need remove atom 24432 need remove atom 24434 need remove atom 24435 need remove atom 24437 need remove atom 24438 need remove atom 24440 need remove atom 24444 need remove atom 24446 need remove atom 24447 need remove atom 24449 need remove atom 24450 need remove atom 24452 need remove atom 24456 need remove atom 24458 need remove atom 24459 need remove atom 24461 need remove atom 24462 need remove atom 24464 need remove atom 24468 need remove atom 24470 need remove atom 24471 need remove atom 24473 need remove atom 24474 need remove atom 24476 need remove atom 24480 need remove atom 24482 need remove atom 24483 need remove atom 24485 need remove atom 24486 need remove atom 24488 need remove atom 24492 need remove atom 24494 need remove atom 24495 need remove atom 24497 need remove atom 24498 need remove atom 24500 need remove atom 24504 need remove atom 24506 need remove atom 24507 need remove atom 24509 need remove atom 24510 need remove atom 24512 need remove atom 24516 need remove atom 24518 need remove atom 24519 need remove atom 24521 need remove atom 24522 need remove atom 24524 need remove atom 24528 need remove atom 24530 need remove atom 24531 need remove atom 24533 need remove atom 24534 need remove atom 24536 need remove atom 24540 need remove atom 24542 need remove atom 24543 need remove atom 24545 need remove atom 24546 need remove atom 24548 need remove atom 24552 need remove atom 24554 need remove atom 24555 need remove atom 24557 need remove atom 24558 need remove atom 24560 need remove atom 24564 need remove atom 24566 need remove atom 24567 need remove atom 24569 need remove atom 24570 need remove atom 24572 need remove atom 24576 need remove atom 24578 need remove atom 24579 need remove atom 24581 need remove atom 24582 need remove atom 24584 need remove atom 24588 need remove atom 24590 need remove atom 24591 need remove atom 24593 need remove atom 24594 need remove atom 24596 need remove atom 24600 need remove atom 24602 need remove atom 24603 need remove atom 24605 need remove atom 24606 need remove atom 24608 need remove atom 24612 need remove atom 24614 need remove atom 24615 need remove atom 24617 need remove atom 24618 need remove atom 24620 need remove atom 24624 need remove atom 24626 need remove atom 24627 need remove atom 24629 need remove atom 24630 need remove atom 24632 need remove atom 24636 need remove atom 24638 need remove atom 24639 need remove atom 24641 need remove atom 24642 need remove atom 24644 need remove atom 24648 need remove atom 24650 need remove atom 24651 need remove atom 24653 need remove atom 24654 need remove atom 24656 need remove atom 24660 need remove atom 24662 need remove atom 24663 need remove atom 24665 need remove atom 24666 need remove atom 24668 need remove atom 24672 need remove atom 24674 need remove atom 24675 need remove atom 24677 need remove atom 24678 need remove atom 24680 need remove atom 24684 need remove atom 24686 need remove atom 24687 need remove atom 24689 need remove atom 24690 need remove atom 24692 need remove atom 24696 need remove atom 24698 need remove atom 24699 need remove atom 24701 need remove atom 24702 need remove atom 24704 need remove atom 24708 need remove atom 24710 need remove atom 24711 need remove atom 24713 need remove atom 24714 need remove atom 24716 need remove atom 24720 need remove atom 24722 need remove atom 24723 need remove atom 24725 need remove atom 24726 need remove atom 24728 need remove atom 24732 need remove atom 24734 need remove atom 24735 need remove atom 24737 need remove atom 24738 need remove atom 24740 need remove atom 24744 need remove atom 24746 need remove atom 24747 need remove atom 24749 need remove atom 24750 need remove atom 24752 need remove atom 24756 need remove atom 24758 need remove atom 24759 need remove atom 24761 need remove atom 24762 need remove atom 24764 need remove atom 24768 need remove atom 24770 need remove atom 24771 need remove atom 24773 need remove atom 24774 need remove atom 24776 need remove atom 24780 need remove atom 24782 need remove atom 24783 need remove atom 24785 need remove atom 24786 need remove atom 24788 need remove atom 24792 need remove atom 24794 need remove atom 24795 need remove atom 24797 need remove atom 24798 need remove atom 24800 need remove atom 24804 need remove atom 24806 need remove atom 24807 need remove atom 24809 need remove atom 24810 need remove atom 24812 need remove atom 24816 need remove atom 24818 need remove atom 24819 need remove atom 24821 need remove atom 24822 need remove atom 24824 need remove atom 24828 need remove atom 24830 need remove atom 24831 need remove atom 24833 need remove atom 24834 need remove atom 24836 need remove atom 24840 need remove atom 24842 need remove atom 24843 need remove atom 24845 need remove atom 24846 need remove atom 24848 need remove atom 24852 need remove atom 24854 need remove atom 24855 need remove atom 24857 need remove atom 24858 need remove atom 24860 need remove atom 24864 need remove atom 24866 need remove atom 24867 need remove atom 24869 need remove atom 24870 need remove atom 24872 need remove atom 24876 need remove atom 24878 need remove atom 24879 need remove atom 24881 need remove atom 24882 need remove atom 24884 need remove atom 24888 need remove atom 24890 need remove atom 24891 need remove atom 24893 need remove atom 24894 need remove atom 24896 need remove atom 24900 need remove atom 24902 need remove atom 24903 need remove atom 24905 need remove atom 24906 need remove atom 24908 need remove atom 24912 need remove atom 24914 need remove atom 24915 need remove atom 24917 need remove atom 24918 need remove atom 24920 need remove atom 24924 need remove atom 24926 need remove atom 24927 need remove atom 24929 need remove atom 24930 need remove atom 24932 need remove atom 24936 need remove atom 24938 need remove atom 24939 need remove atom 24941 need remove atom 24942 need remove atom 24944 need remove atom 24948 need remove atom 24950 need remove atom 24951 need remove atom 24953 need remove atom 24954 need remove atom 24956 need remove atom 24960 need remove atom 24962 need remove atom 24963 need remove atom 24965 need remove atom 24966 need remove atom 24968 need remove atom 24972 need remove atom 24974 need remove atom 24975 need remove atom 24977 need remove atom 24978 need remove atom 24980 need remove atom 24984 need remove atom 24986 need remove atom 24987 need remove atom 24989 need remove atom 24990 need remove atom 24992 need remove atom 24996 need remove atom 24998 need remove atom 24999 need remove atom 25001 need remove atom 25002 need remove atom 25004 need remove atom 25008 need remove atom 25010 need remove atom 25011 need remove atom 25013 need remove atom 25014 need remove atom 25016 need remove atom 25020 need remove atom 25022 need remove atom 25023 need remove atom 25025 need remove atom 25026 need remove atom 25028 need remove atom 25032 need remove atom 25034 need remove atom 25035 need remove atom 25037 need remove atom 25038 need remove atom 25040 need remove atom 25044 need remove atom 25046 need remove atom 25047 need remove atom 25049 need remove atom 25050 need remove atom 25052 need remove atom 25056 need remove atom 25058 need remove atom 25059 need remove atom 25061 need remove atom 25062 need remove atom 25064 need remove atom 25068 need remove atom 25070 need remove atom 25071 need remove atom 25073 need remove atom 25074 need remove atom 25076 need remove atom 25080 need remove atom 25082 need remove atom 25083 need remove atom 25085 need remove atom 25086 need remove atom 25088 need remove atom 25092 need remove atom 25094 need remove atom 25095 need remove atom 25097 need remove atom 25098 need remove atom 25100 need remove atom 25104 need remove atom 25106 need remove atom 25107 need remove atom 25109 need remove atom 25110 need remove atom 25112 need remove atom 25116 need remove atom 25118 need remove atom 25119 need remove atom 25121 need remove atom 25122 need remove atom 25124 need remove atom 25128 need remove atom 25130 need remove atom 25131 need remove atom 25133 need remove atom 25134 need remove atom 25136 need remove atom 25140 need remove atom 25142 need remove atom 25148 need remove atom 25152 need remove atom 25154 need remove atom 25160 need remove atom 25164 need remove atom 25166 need remove atom 25172 need remove atom 25176 need remove atom 25178 need remove atom 25184 need remove atom 25188 need remove atom 25190 need remove atom 25196 [I] need removenum=585 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5747398049e-01 1.7351818115e-01 0.0000000000e+00 dub= -5.8475624844e-01 1.7352224711e-01 0.0000000000e+00 duc= 5.5747555272e-01 -1.7579350464e-01 0.0000000000e+00 [I] overall tilt ux= -1.1422302289e+00 4.0659619462e-06 0.0000000000e+00 uy= 1.5722346937e-06 -3.4931168579e-01 0.0000000000e+00 [I] storedr[0]= -1.5401197130e-02 -1.1372065081e-03 0.0000000000e+00 [I] originally 49140 atoms [I] insert 0 atoms [I] now 49140 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 49140 atoms [I] remove 585 atoms [I] now 48555 atoms [I] NP=48555 n=48555 [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 [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 Jun 14 14:12:47 2023 CPU time spent: 30.770716 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 Jun 14 14:26:08 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 24 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 44 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=63360 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.020833333333333 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.0833333333e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=1.315749e+02 pxpb=0.000000e+00 pypb=1.969558e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 29707 need remove atom 29711 need remove atom 29719 need remove atom 29723 need remove atom 29731 need remove atom 29735 need remove atom 29743 need remove atom 29747 need remove atom 29755 need remove atom 29759 need remove atom 29767 need remove atom 29769 need remove atom 29770 need remove atom 29771 need remove atom 29779 need remove atom 29781 need remove atom 29782 need remove atom 29783 need remove atom 29791 need remove atom 29793 need remove atom 29794 need remove atom 29795 need remove atom 29803 need remove atom 29805 need remove atom 29806 need remove atom 29807 need remove atom 29815 need remove atom 29817 need remove atom 29818 need remove atom 29819 need remove atom 29827 need remove atom 29829 need remove atom 29830 need remove atom 29831 need remove atom 29839 need remove atom 29841 need remove atom 29842 need remove atom 29843 need remove atom 29851 need remove atom 29853 need remove atom 29854 need remove atom 29855 need remove atom 29863 need remove atom 29865 need remove atom 29866 need remove atom 29867 need remove atom 29875 need remove atom 29877 need remove atom 29878 need remove atom 29879 need remove atom 29887 need remove atom 29889 need remove atom 29890 need remove atom 29891 need remove atom 29899 need remove atom 29901 need remove atom 29902 need remove atom 29903 need remove atom 29911 need remove atom 29913 need remove atom 29914 need remove atom 29915 need remove atom 29923 need remove atom 29925 need remove atom 29926 need remove atom 29927 need remove atom 29935 need remove atom 29937 need remove atom 29938 need remove atom 29939 need remove atom 29947 need remove atom 29949 need remove atom 29950 need remove atom 29951 need remove atom 29959 need remove atom 29961 need remove atom 29962 need remove atom 29963 need remove atom 29971 need remove atom 29973 need remove atom 29974 need remove atom 29975 need remove atom 29983 need remove atom 29985 need remove atom 29986 need remove atom 29987 need remove atom 29995 need remove atom 29997 need remove atom 29998 need remove 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need remove atom 33661 need remove atom 33673 need remove atom 33685 need remove atom 33697 need remove atom 33709 [I] need removenum=660 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5566937139e-01 1.7413981756e-01 0.0000000000e+00 dub= -5.8276170063e-01 1.7414366632e-01 0.0000000000e+00 duc= 5.5567095989e-01 -1.7637035864e-01 0.0000000000e+00 [I] overall tilt ux= -1.1384310720e+00 3.8487625440e-06 0.0000000000e+00 uy= 1.5884974520e-06 -3.5051017619e-01 0.0000000000e+00 [I] storedr[0]= -1.5046807651e-02 -1.1146908787e-03 0.0000000000e+00 [I] originally 63360 atoms [I] insert 0 atoms [I] now 63360 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 63360 atoms [I] remove 660 atoms [I] now 62700 atoms [I] NP=62700 n=62700 [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 [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 Jun 14 14:26:51 2023 CPU time spent: 39.577652 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 Jun 14 14:49:36 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 26 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 48 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 6 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=89856 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.019230769230769 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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= 1.9230769231e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=1.425395e+02 pxpb=0.000000e+00 pypb=2.148609e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 42341 need remove atom 42343 need remove 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atom 43943 need remove atom 43946 need remove atom 43949 need remove atom 43951 need remove atom 43953 need remove atom 43954 need remove atom 43955 need remove atom 43958 need remove atom 43961 need remove atom 43963 need remove atom 43965 need remove atom 43966 need remove atom 43967 need remove atom 43970 need remove atom 43973 need remove atom 43975 need remove atom 43977 need remove atom 43978 need remove atom 43979 need remove atom 43982 need remove atom 43985 need remove atom 43987 need remove atom 43989 need remove atom 43990 need remove atom 43991 need remove atom 43994 need remove atom 43997 need remove atom 43999 need remove atom 44001 need remove atom 44002 need remove atom 44003 need remove atom 44006 need remove atom 44009 need remove atom 44011 need remove atom 44013 need remove atom 44014 need remove atom 44015 need remove atom 44018 need remove atom 44021 need remove atom 44023 need remove atom 44025 need remove atom 44026 need remove atom 44027 need remove atom 44030 need remove atom 44033 need remove atom 44035 need remove atom 44037 need remove atom 44038 need remove atom 44039 need remove atom 44042 need remove atom 44045 need remove atom 44047 need remove atom 44049 need remove atom 44050 need remove atom 44051 need remove atom 44054 need remove atom 44057 need remove atom 44059 need remove atom 44061 need remove atom 44062 need remove atom 44063 need remove atom 44066 need remove atom 44073 need remove atom 44074 need remove atom 44078 need remove atom 44085 need remove atom 44086 need remove atom 44090 need remove atom 44097 need remove atom 44098 need remove atom 44102 need remove atom 44109 need remove atom 44110 need remove atom 44114 need remove atom 44121 need remove atom 44122 need remove atom 44126 need remove atom 44133 need remove atom 44134 [I] need removenum=864 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5664696186e-01 1.7380415805e-01 0.0000000000e+00 dub= -5.8384316256e-01 1.7380812516e-01 0.0000000000e+00 duc= 5.5664854162e-01 -1.7605889459e-01 0.0000000000e+00 [I] overall tilt ux= -1.1404901244e+00 3.9671116676e-06 0.0000000000e+00 uy= 1.5797574276e-06 -3.4986305263e-01 0.0000000000e+00 [I] storedr[0]= -1.5003220423e-02 -1.1266460833e-03 0.0000000000e+00 [I] originally 89856 atoms [I] insert 0 atoms [I] now 89856 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 89856 atoms [I] remove 864 atoms [I] now 88992 atoms [I] NP=88992 n=88992 [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 [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 Jun 14 14:50:37 2023 CPU time spent: 56.661201 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 Jun 14 15:21:44 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 29 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 53 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 7 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=129108 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.017241379310345 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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= 1.7241379310e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=1.589863e+02 pxpb=0.000000e+00 pypb=2.372422e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 63423 need remove atom 63424 need remove atom 63426 need remove atom 63435 need remove atom 63436 need remove atom 63438 need remove atom 63447 need remove atom 63448 need remove atom 63450 need remove atom 63459 need remove atom 63460 need remove atom 63462 need remove atom 63471 need remove atom 63472 need remove atom 63474 need remove atom 63483 need remove atom 63484 need remove atom 63486 need remove atom 63495 need remove atom 63496 need remove atom 63498 need remove atom 63504 need remove atom 63505 need remove atom 63507 need remove atom 63508 need remove atom 63510 need remove atom 63512 need remove atom 63516 need remove atom 63517 need remove atom 63519 need remove atom 63520 need remove atom 63522 need remove atom 63524 need remove atom 63528 need remove atom 63529 need remove atom 63531 need remove atom 63532 need remove atom 63534 need remove atom 63536 need remove atom 63540 need remove atom 63541 need remove atom 63543 need remove atom 63544 need remove atom 63546 need remove atom 63548 need remove atom 63552 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need remove atom 63726 need remove atom 63728 need remove atom 63732 need remove atom 63733 need remove atom 63735 need remove atom 63736 need remove atom 63738 need remove atom 63740 need remove atom 63744 need remove atom 63745 need remove atom 63747 need remove atom 63748 need remove atom 63750 need remove atom 63752 need remove atom 63756 need remove atom 63757 need remove atom 63759 need remove atom 63760 need remove atom 63762 need remove atom 63764 need remove atom 63768 need remove atom 63769 need remove atom 63771 need remove atom 63772 need remove atom 63774 need remove atom 63776 need remove atom 63780 need remove atom 63781 need remove atom 63783 need remove atom 63784 need remove atom 63786 need remove atom 63788 need remove atom 63792 need remove atom 63793 need remove atom 63795 need remove atom 63796 need remove atom 63798 need remove atom 63800 need remove atom 63804 need remove atom 63805 need remove atom 63807 need remove atom 63808 need remove atom 63810 need remove 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atom 64335 need remove atom 64336 need remove atom 64338 need remove atom 64340 need remove atom 64344 need remove atom 64345 need remove atom 64347 need remove atom 64348 need remove atom 64350 need remove atom 64352 need remove atom 64356 need remove atom 64357 need remove atom 64359 need remove atom 64360 need remove atom 64362 need remove atom 64364 need remove atom 64368 need remove atom 64369 need remove atom 64371 need remove atom 64372 need remove atom 64374 need remove atom 64376 need remove atom 64380 need remove atom 64381 need remove atom 64383 need remove atom 64384 need remove atom 64386 need remove atom 64388 need remove atom 64392 need remove atom 64393 need remove atom 64395 need remove atom 64396 need remove atom 64398 need remove atom 64400 need remove atom 64404 need remove atom 64405 need remove atom 64407 need remove atom 64408 need remove atom 64410 need remove atom 64412 need remove atom 64416 need remove atom 64417 need remove atom 64419 need remove atom 64420 need remove atom 64422 need remove atom 64424 need remove atom 64428 need remove atom 64429 need remove atom 64431 need remove atom 64432 need remove atom 64434 need remove atom 64436 need remove atom 64440 need remove atom 64441 need remove atom 64443 need remove atom 64444 need remove atom 64446 need remove atom 64448 need remove atom 64452 need remove atom 64453 need remove atom 64455 need remove atom 64456 need remove atom 64458 need remove atom 64460 need remove atom 64464 need remove atom 64465 need remove atom 64467 need remove atom 64468 need remove atom 64470 need remove atom 64472 need remove atom 64476 need remove atom 64477 need remove atom 64479 need remove atom 64480 need remove atom 64482 need remove atom 64484 need remove atom 64488 need remove atom 64489 need remove atom 64491 need remove atom 64492 need remove atom 64494 need remove atom 64496 need remove atom 64500 need remove atom 64501 need remove atom 64503 need remove atom 64504 need remove atom 64506 need remove atom 64508 need remove atom 64512 need remove atom 64513 need remove atom 64515 need remove atom 64516 need remove atom 64518 need remove atom 64520 need remove atom 64524 need remove atom 64525 need remove atom 64527 need remove atom 64528 need remove atom 64530 need remove atom 64532 need remove atom 64536 need remove atom 64537 need remove atom 64539 need remove atom 64540 need remove atom 64542 need remove atom 64544 need remove atom 64548 need remove atom 64549 need remove atom 64551 need remove atom 64552 need remove atom 64554 need remove atom 64556 need remove atom 64560 need remove atom 64561 need remove atom 64563 need remove atom 64564 need remove atom 64566 need remove atom 64568 need remove atom 64572 need remove atom 64573 need remove atom 64575 need remove atom 64576 need remove atom 64578 need remove atom 64580 need remove atom 64584 need remove atom 64585 need remove atom 64587 need remove atom 64588 need remove atom 64590 need remove atom 64592 need remove atom 64596 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need remove atom 65641 need remove atom 65643 need remove atom 65644 need remove atom 65646 need remove atom 65648 need remove atom 65652 need remove atom 65653 need remove atom 65655 need remove atom 65656 need remove atom 65658 need remove atom 65660 need remove atom 65664 need remove atom 65665 need remove atom 65667 need remove atom 65668 need remove atom 65670 need remove atom 65672 need remove atom 65676 need remove atom 65677 need remove atom 65679 need remove atom 65680 need remove atom 65682 need remove atom 65684 [I] need removenum=1113 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5522662425e-01 1.7429098326e-01 0.0000000000e+00 dub= -5.8227115874e-01 1.7429477790e-01 0.0000000000e+00 duc= 5.5522821665e-01 -1.7651061588e-01 0.0000000000e+00 [I] overall tilt ux= -1.1374977830e+00 3.7946396337e-06 0.0000000000e+00 uy= 1.5924014020e-06 -3.5080159914e-01 0.0000000000e+00 [I] storedr[0]= -1.4755703022e-02 -1.1090243335e-03 0.0000000000e+00 [I] originally 129108 atoms [I] insert 0 atoms [I] now 129108 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 129108 atoms [I] remove 1113 atoms [I] now 127995 atoms [I] NP=127995 n=127995 [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 [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 Jun 14 15:23:13 2023 CPU time spent: 81.866733 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 Jun 14 15:39:43 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.165199816227 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 1 [I] ASSIGN makecnspec(3) = 32 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 59 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -2 [I] ASSIGN makecnspec(11) = 7 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 1 0 -2]; basis=[ 0.166667 0 0.333333 0 0 0 0 0 0 1 0.5 0 0 0 2 0.166667 0.5 0.833333 0 3 0 0.5 0.5 0 4 0.5 0.5 0.5 0 5 0.333333 0.5 0.166667 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.833333 0 0.666667 0 9 0.666667 0 0.333333 0 10 0.666667 0.5 0.833333 0 11 ]; [I] makecn: _NP=158592 [I] ASSIGN finalcnfile = perf.cn [I] EXEC writecn [I] FILEOPEN perf.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE perf.cn [I] ASSIGN mkdipole = 3 [I] ASSIGN mkdipole(1) = 2 [I] ASSIGN mkdipole(2) = 0.015625 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28094955620988 [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= 1.5625000000e-02 0.0000000000e+00 0.0000000000e+00 b= 2.7411434489e+00 0.0000000000e+00 0.0000000000e+00 [I] px= 1.0000000000e+00 0.0000000000e+00 0.0000000000e+00 [I] py= 0.0000000000e+00 1.0000000000e+00 0.0000000000e+00 [I] pz= 0.0000000000e+00 0.0000000000e+00 1.0000000000e+00 [I] bx=2.7411434489064 by=0 pxpa=1.754332e+02 pxpb=0.000000e+00 pypb=2.640998e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 75602 need remove atom 75605 need remove atom 75607 need remove atom 75609 need remove atom 75610 need remove atom 75611 need remove atom 75614 need remove atom 75617 need remove atom 75619 need remove atom 75621 need remove atom 75622 need remove atom 75623 need remove atom 75626 need remove atom 75629 need remove atom 75631 need remove atom 75633 need remove atom 75634 need remove atom 75635 need remove atom 75638 need remove atom 75641 need remove atom 75643 need remove atom 75645 need remove atom 75646 need remove atom 75647 need remove atom 75650 need remove atom 75653 need remove atom 75655 need remove atom 75657 need remove atom 75658 need remove atom 75659 need remove atom 75662 need remove atom 75665 need remove atom 75667 need remove atom 75669 need remove atom 75670 need remove atom 75671 need remove atom 75674 need remove atom 75677 need remove atom 75679 need remove atom 75681 need remove atom 75682 need remove atom 75683 need remove atom 75686 need remove atom 75689 need remove atom 75691 need remove atom 75693 need remove 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need remove atom 78050 need remove atom 78057 need remove atom 78058 need remove atom 78062 need remove atom 78069 need remove atom 78070 need remove atom 78074 need remove atom 78081 need remove atom 78082 need remove atom 78086 need remove atom 78093 need remove atom 78094 need remove atom 78098 need remove atom 78105 need remove atom 78106 need remove atom 78110 need remove atom 78117 need remove atom 78118 [I] need removenum=1239 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5646471519e-01 1.7386692939e-01 0.0000000000e+00 dub= -5.8364172614e-01 1.7387087456e-01 0.0000000000e+00 duc= 5.5646629659e-01 -1.7611714385e-01 0.0000000000e+00 [I] overall tilt ux= -1.1401064413e+00 3.9451706156e-06 0.0000000000e+00 uy= 1.5813993037e-06 -3.4998407324e-01 0.0000000000e+00 [I] storedr[0]= -1.4727034018e-02 -1.1241578762e-03 0.0000000000e+00 [I] originally 158592 atoms [I] insert 0 atoms [I] now 158592 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 158592 atoms [I] remove 1239 atoms [I] now 157353 atoms [I] NP=157353 n=157353 [I] ASSIGN finalcnfile = dipole_5.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.5.lammps [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 Jun 14 15:41:33 2023 CPU time spent: 101.778743 s Traceback (most recent call last): File "../../td/DislocationCoreEnergyCubic__TD_452950666597_002/runner", line 2675, in msg = cr.run_length_control( File "/usr/local/lib/python3.8/dist-packages/convergence/timeseries.py", line 1071, in run_length_control msg += 'for variable number {},\n'.format(i + 1) UnboundLocalError: local variable 'msg' referenced before assignment During handling of the above exception, another exception occurred: Traceback (most recent call last): File "../../td/DislocationCoreEnergyCubic__TD_452950666597_002/runner", line 2689, in raise cr.CVGError(msg) convergence.err.CVGError: ERROR(@): local variable 'msg' referenced before assignment Command exited with non-zero status 1 {"realtime":13980.49,"usertime":31632.04,"systime":320.71,"memmax":126404,"memavg":0}