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 = Mon Jun 12 17:26:00 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 5 [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) = -1 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=1560 [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) = 0.066666666666667 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.083333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 6.6666666667e-02 0.0000000000e+00 8.3333333333e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=3.845699e+01 pxpb=0.000000e+00 pypb=5.772820e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 701 need remove atom 702 need remove atom 713 need remove atom 714 need remove atom 722 need remove atom 725 need remove atom 726 need remove atom 728 need remove atom 734 need remove atom 737 need remove atom 738 need remove atom 740 need remove atom 746 need remove atom 749 need remove atom 750 need remove atom 752 need remove atom 758 need remove atom 761 need remove atom 762 need remove atom 764 need remove atom 770 need remove atom 773 need remove atom 774 need remove atom 776 need remove atom 782 need remove atom 785 need remove atom 786 need remove atom 788 need remove atom 794 need remove atom 797 need remove atom 798 need remove atom 800 need remove atom 806 need remove atom 809 need remove atom 810 need remove atom 812 need remove atom 818 need remove atom 821 need remove atom 822 need remove atom 824 need remove atom 830 need remove atom 833 need remove atom 834 need remove atom 836 need remove atom 842 need remove atom 845 need remove atom 846 need remove atom 848 need remove atom 854 need remove atom 857 need remove atom 858 need remove atom 860 [I] need removenum=52 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1985967362e-01 1.6311592386e-01 1.4072433496e-01 dub= -5.4520478427e-01 1.6311953208e-01 -1.4329152279e-01 duc= 5.1986115569e-01 -1.6520846565e-01 1.4072478672e-01 [I] overall tilt ux= -1.0650644579e+00 3.6082214782e-06 -2.8401585775e-01 uy= 1.4820685457e-06 -3.2832438950e-01 4.5175441041e-07 [I] storedr[0]= -1.2671814292e-02 -1.0444667826e-03 -1.2833680363e-03 [I] originally 1560 atoms [I] insert 0 atoms [I] now 1560 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1560 atoms [I] remove 52 atoms [I] now 1508 atoms [I] NP=1508 n=1508 [I] ASSIGN finalcnfile = dipole_1.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 17:26:01 2023 CPU time spent: 0.959890 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 = Mon Jun 12 17:29:00 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 5 [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) = -1 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=2340 [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) = 0.066666666666667 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.055555555555556 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 6.6666666667e-02 0.0000000000e+00 5.5555555556e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=3.845699e+01 pxpb=0.000000e+00 pypb=5.772820e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1049 need remove atom 1050 need remove atom 1061 need remove atom 1062 need remove atom 1073 need remove atom 1074 need remove atom 1082 need remove atom 1085 need remove atom 1086 need remove atom 1088 need remove atom 1094 need remove atom 1097 need remove atom 1098 need remove atom 1100 need remove atom 1106 need remove atom 1109 need remove atom 1110 need remove atom 1112 need remove atom 1118 need remove atom 1121 need remove atom 1122 need remove atom 1124 need remove atom 1130 need remove atom 1133 need remove atom 1134 need remove atom 1136 need remove atom 1142 need remove atom 1145 need remove atom 1146 need remove atom 1148 need remove atom 1154 need remove atom 1157 need remove atom 1158 need remove atom 1160 need remove atom 1166 need remove atom 1169 need remove atom 1170 need remove atom 1172 need remove atom 1178 need remove atom 1181 need remove atom 1182 need remove atom 1184 need remove atom 1190 need remove atom 1193 need remove atom 1194 need remove atom 1196 need remove atom 1202 need remove atom 1205 need remove atom 1206 need remove atom 1208 need remove atom 1214 need remove atom 1217 need remove atom 1218 need remove atom 1220 need remove atom 1226 need remove atom 1229 need remove atom 1230 need remove atom 1232 need remove atom 1238 need remove atom 1241 need remove atom 1242 need remove atom 1244 need remove atom 1250 need remove atom 1253 need remove atom 1254 need remove atom 1256 need remove atom 1262 need remove atom 1265 need remove atom 1266 need remove atom 1268 need remove atom 1274 need remove atom 1277 need remove atom 1278 need remove atom 1280 need remove atom 1286 need remove atom 1289 need remove atom 1290 need remove atom 1292 [I] need removenum=78 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1985967362e-01 1.6311592386e-01 1.4072433496e-01 dub= -5.4520478427e-01 1.6311953208e-01 -1.4329152279e-01 duc= 5.1986115569e-01 -1.6520846565e-01 1.4072478672e-01 [I] overall tilt ux= -1.0650644579e+00 3.6082214782e-06 -2.8401585775e-01 uy= 1.4820685457e-06 -3.2832438950e-01 4.5175441041e-07 [I] storedr[0]= -1.2671814292e-02 -1.0444667826e-03 -1.2833680363e-03 [I] originally 2340 atoms [I] insert 0 atoms [I] now 2340 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 2340 atoms [I] remove 78 atoms [I] now 2262 atoms [I] NP=2262 n=2262 [I] ASSIGN finalcnfile = dipole_1.2.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.2.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.2.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 17:29:02 2023 CPU time spent: 1.454747 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 = Mon Jun 12 17:32:29 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 6 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 16 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=3456 [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) = 0.055555555555556 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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 5.5555555556e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=4.614839e+01 pxpb=0.000000e+00 pypb=7.105009e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1303 need remove atom 1307 need remove atom 1315 need remove atom 1319 need remove atom 1327 need remove atom 1331 need remove atom 1339 need remove atom 1343 need remove atom 1351 need remove atom 1355 need remove atom 1363 need remove atom 1367 need remove atom 1375 need remove atom 1379 need remove atom 1387 need remove atom 1391 need remove atom 1399 need remove atom 1403 need remove atom 1411 need remove atom 1415 need remove atom 1423 need remove atom 1427 need remove atom 1435 need remove atom 1439 need remove atom 1447 need remove atom 1451 need remove atom 1459 need remove atom 1463 need remove atom 1471 need remove atom 1475 need remove atom 1483 need remove atom 1487 need remove atom 1495 need remove atom 1499 need remove atom 1507 need remove atom 1511 need remove atom 1519 need remove atom 1523 need remove atom 1531 need remove atom 1535 need remove atom 1543 need remove atom 1547 need remove atom 1555 need remove atom 1559 need remove atom 1567 need remove atom 1571 need remove atom 1579 need remove atom 1583 need remove atom 1908 need remove atom 1909 need remove atom 1920 need remove atom 1921 need remove atom 1932 need remove atom 1933 need remove atom 1944 need remove atom 1945 need remove atom 1956 need remove atom 1957 need remove atom 1968 need remove atom 1969 need remove atom 1980 need remove atom 1981 need remove atom 1992 need remove atom 1993 need remove atom 2004 need remove atom 2005 need remove atom 2016 need remove atom 2017 need remove atom 2028 need remove atom 2029 need remove atom 2040 need remove atom 2041 need remove atom 2052 need remove atom 2053 need remove atom 2064 need remove atom 2065 need remove atom 2076 need remove atom 2077 need remove atom 2088 need remove atom 2089 need remove atom 2100 need remove atom 2101 need remove atom 2112 need remove atom 2113 need remove atom 2124 need remove atom 2125 need remove atom 2136 need remove atom 2137 need remove atom 2148 need remove atom 2149 need remove atom 2160 need remove atom 2161 need remove atom 2172 need remove atom 2173 need remove atom 2184 need remove atom 2185 [I] need removenum=96 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.2314283471e-01 1.6198038972e-01 1.4228826211e-01 dub= -5.4882384527e-01 1.6198438555e-01 -1.4508665243e-01 duc= 5.2314428657e-01 -1.6415498169e-01 1.4228871626e-01 [I] overall tilt ux= -1.0719666800e+00 3.9958320295e-06 -2.8737491455e-01 uy= 1.4518654058e-06 -3.2613537141e-01 4.5415076660e-07 [I] storedr[0]= -1.2839779348e-02 -1.0852980723e-03 -1.3989680840e-03 [I] originally 3456 atoms [I] insert 0 atoms [I] now 3456 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3456 atoms [I] remove 96 atoms [I] now 3360 atoms [I] NP=3360 n=3360 [I] ASSIGN finalcnfile = dipole_1.3.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.3.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.3.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 17:32:32 2023 CPU time spent: 2.128660 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 = Mon Jun 12 17:40:01 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 7 [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) = -1 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=4536 [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) = 0.047619047619048 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.055555555555556 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 4.7619047619e-02 0.0000000000e+00 5.5555555556e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=5.383978e+01 pxpb=0.000000e+00 pypb=7.993135e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 2126 need remove atom 2129 need remove atom 2130 need remove atom 2132 need remove atom 2138 need remove atom 2141 need remove atom 2142 need remove atom 2144 need remove atom 2150 need remove atom 2153 need remove atom 2154 need remove atom 2156 need remove atom 2162 need remove atom 2165 need remove atom 2166 need remove atom 2168 need remove atom 2174 need remove atom 2177 need remove atom 2178 need remove atom 2180 need remove atom 2186 need remove atom 2189 need remove atom 2190 need remove atom 2192 need remove atom 2198 need remove atom 2201 need remove atom 2202 need remove atom 2204 need remove atom 2210 need remove atom 2213 need remove atom 2214 need remove atom 2216 need remove atom 2222 need remove atom 2225 need remove atom 2226 need remove atom 2228 need remove atom 2234 need remove atom 2237 need remove atom 2238 need remove atom 2240 need remove atom 2246 need remove atom 2249 need remove atom 2250 need remove atom 2252 need remove atom 2258 need remove atom 2261 need remove atom 2262 need remove atom 2264 need remove atom 2270 need remove atom 2273 need remove atom 2274 need remove atom 2276 need remove atom 2282 need remove atom 2285 need remove atom 2286 need remove atom 2288 need remove atom 2294 need remove atom 2297 need remove atom 2298 need remove atom 2300 need remove atom 2306 need remove atom 2309 need remove atom 2310 need remove atom 2312 need remove atom 2318 need remove atom 2321 need remove atom 2322 need remove atom 2324 need remove atom 2330 need remove atom 2333 need remove atom 2334 need remove atom 2336 need remove atom 2342 need remove atom 2345 need remove atom 2346 need remove atom 2348 need remove atom 2354 need remove atom 2357 need remove atom 2358 need remove atom 2360 need remove atom 2366 need remove atom 2369 need remove atom 2370 need remove atom 2372 need remove atom 2378 need remove atom 2381 need remove atom 2382 need remove atom 2384 need remove atom 2390 need remove atom 2393 need remove atom 2394 need remove atom 2396 need remove atom 2402 need remove atom 2405 need remove atom 2406 need remove atom 2408 need remove atom 2414 need remove atom 2417 need remove atom 2418 need remove atom 2420 need remove atom 2426 need remove atom 2429 need remove atom 2430 need remove atom 2432 need remove atom 2438 need remove atom 2441 need remove atom 2442 need remove atom 2444 [I] need removenum=108 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1839966017e-01 1.6361093396e-01 1.4003721335e-01 dub= -5.4358645002e-01 1.6361436352e-01 -1.4250224082e-01 duc= 5.1840115503e-01 -1.6566757442e-01 1.4003766391e-01 [I] overall tilt ux= -1.0619861102e+00 3.4295530095e-06 -2.8253945417e-01 uy= 1.4948624298e-06 -3.2927850839e-01 4.5055885817e-07 [I] storedr[0]= -1.2592647495e-02 -1.0266054531e-03 -1.2322884555e-03 [I] originally 4536 atoms [I] insert 0 atoms [I] now 4536 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 4536 atoms [I] remove 108 atoms [I] now 4428 atoms [I] NP=4428 n=4428 [I] ASSIGN finalcnfile = dipole_1.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 17:40:04 2023 CPU time spent: 2.812047 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 = Mon Jun 12 17:47:42 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 21 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=8064 [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) = 0.041666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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 4.1666666667e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=6.153118e+01 pxpb=0.000000e+00 pypb=9.325324e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3271 need remove atom 3275 need remove atom 3283 need remove atom 3287 need remove atom 3295 need remove atom 3299 need remove atom 3307 need remove atom 3311 need remove atom 3319 need remove atom 3323 need remove atom 3331 need remove atom 3335 need remove atom 3343 need remove atom 3347 need remove atom 3355 need remove atom 3359 need remove atom 3367 need remove atom 3371 need remove atom 3379 need remove atom 3383 need remove atom 3391 need remove atom 3395 need remove atom 3403 need remove atom 3407 need remove atom 3415 need remove atom 3419 need remove atom 3427 need remove atom 3431 need remove atom 3439 need remove atom 3443 need remove atom 3451 need remove atom 3455 need remove atom 3463 need remove atom 3467 need remove atom 3475 need remove atom 3479 need remove atom 3487 need remove atom 3491 need remove atom 3499 need remove atom 3503 need remove atom 3511 need remove atom 3515 need remove atom 3523 need remove atom 3527 need remove atom 3535 need remove atom 3539 need remove atom 3547 need remove atom 3551 need remove atom 3559 need remove atom 3563 need remove atom 3571 need remove atom 3575 need remove atom 3583 need remove atom 3587 need remove atom 3595 need remove atom 3599 need remove atom 3607 need remove atom 3611 need remove atom 3619 need remove atom 3623 need remove atom 3631 need remove atom 3635 need remove atom 3643 need remove atom 3647 need remove atom 3655 need remove atom 3659 need remove atom 3667 need remove atom 3671 need remove atom 3679 need remove atom 3683 need remove atom 3691 need remove atom 3695 need remove atom 3703 need remove atom 3707 need remove atom 3715 need remove atom 3719 need remove atom 3727 need remove atom 3731 need remove atom 3739 need remove atom 3743 need remove atom 3751 need remove atom 3755 need remove atom 3763 need remove atom 3767 need remove atom 3775 need remove atom 3779 need remove atom 3787 need remove atom 3791 need remove atom 4320 need remove atom 4321 need remove atom 4332 need remove atom 4333 need remove atom 4344 need remove atom 4345 need remove atom 4356 need remove atom 4357 need remove atom 4368 need remove atom 4369 need remove atom 4380 need remove atom 4381 need remove atom 4392 need remove atom 4393 need remove atom 4404 need remove atom 4405 need remove atom 4416 need remove atom 4417 need remove atom 4428 need remove atom 4429 need remove atom 4440 need remove atom 4441 need remove atom 4452 need remove atom 4453 need remove atom 4464 need remove atom 4465 need remove atom 4476 need remove atom 4477 need remove atom 4488 need remove atom 4489 need remove atom 4500 need remove atom 4501 need remove atom 4512 need remove atom 4513 need remove atom 4524 need remove atom 4525 need remove atom 4536 need remove atom 4537 need remove atom 4548 need remove atom 4549 need remove atom 4560 need remove atom 4561 need remove atom 4572 need remove atom 4573 need remove atom 4584 need remove atom 4585 need remove atom 4596 need remove atom 4597 need remove atom 4608 need remove atom 4609 need remove atom 4620 need remove atom 4621 need remove atom 4632 need remove atom 4633 need remove atom 4644 need remove atom 4645 need remove atom 4656 need remove atom 4657 need remove atom 4668 need remove atom 4669 need remove atom 4680 need remove atom 4681 need remove atom 4692 need remove atom 4693 need remove atom 4704 need remove atom 4705 need remove atom 4716 need remove atom 4717 need remove atom 4728 need remove atom 4729 need remove atom 4740 need remove atom 4741 need remove atom 4752 need remove atom 4753 need remove atom 4764 need remove atom 4765 need remove atom 4776 need remove atom 4777 need remove atom 4788 need remove atom 4789 [I] need removenum=168 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.2111075334e-01 1.6268685407e-01 1.4131718350e-01 dub= -5.4658719651e-01 1.6269061238e-01 -1.4397224030e-01 duc= 5.2111222413e-01 -1.6481044543e-01 1.4131763621e-01 [I] overall tilt ux= -1.0676979498e+00 3.7583046598e-06 -2.8528942380e-01 uy= 1.4707928621e-06 -3.2749729950e-01 4.5271625029e-07 [I] storedr[0]= -1.2737486186e-02 -1.0599165259e-03 -1.3273020438e-03 [I] originally 8064 atoms [I] insert 0 atoms [I] now 8064 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 8064 atoms [I] remove 168 atoms [I] now 7896 atoms [I] NP=7896 n=7896 [I] ASSIGN finalcnfile = dipole_1.8.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.8.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.8.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 17:47:47 2023 CPU time spent: 5.028317 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 = Mon Jun 12 18:08:37 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 9 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 23 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=9936 [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) = 0.037037037037037 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.041666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 3.7037037037e-02 0.0000000000e+00 4.1666666667e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=6.922258e+01 pxpb=0.000000e+00 pypb=1.021345e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4706 need remove atom 4709 need remove atom 4710 need remove atom 4712 need remove atom 4718 need remove atom 4721 need remove atom 4722 need remove atom 4724 need remove atom 4730 need remove atom 4733 need remove atom 4734 need remove atom 4736 need remove atom 4742 need remove atom 4745 need remove atom 4746 need remove atom 4748 need remove atom 4754 need remove atom 4757 need remove atom 4758 need remove atom 4760 need remove atom 4766 need remove atom 4769 need remove atom 4770 need remove atom 4772 need remove atom 4778 need remove atom 4781 need remove atom 4782 need remove atom 4784 need remove atom 4790 need remove atom 4793 need remove atom 4794 need remove atom 4796 need remove atom 4802 need remove atom 4805 need remove atom 4806 need remove atom 4808 need remove atom 4814 need remove atom 4817 need remove atom 4818 need remove atom 4820 need remove atom 4826 need remove atom 4829 need remove atom 4830 need remove atom 4832 need remove atom 4838 need remove atom 4841 need remove atom 4842 need remove atom 4844 need remove atom 4850 need remove atom 4853 need remove atom 4854 need remove atom 4856 need remove atom 4862 need remove atom 4865 need remove atom 4866 need remove atom 4868 need remove atom 4874 need remove atom 4877 need remove atom 4878 need remove atom 4880 need remove atom 4886 need remove atom 4889 need remove atom 4890 need remove atom 4892 need remove atom 4898 need remove atom 4901 need remove atom 4902 need remove atom 4904 need remove atom 4910 need remove atom 4913 need remove atom 4914 need remove atom 4916 need remove atom 4922 need remove atom 4925 need remove atom 4926 need remove atom 4928 need remove atom 4934 need remove atom 4937 need remove atom 4938 need remove atom 4940 need remove atom 4946 need remove atom 4949 need remove atom 4950 need remove atom 4952 need remove atom 4958 need remove atom 4961 need remove atom 4962 need remove atom 4964 need remove atom 4970 need remove atom 4973 need remove atom 4974 need remove atom 4976 need remove atom 4982 need remove atom 4985 need remove atom 4986 need remove atom 4988 need remove atom 4994 need remove atom 4997 need remove atom 4998 need remove atom 5000 need remove atom 5006 need remove atom 5009 need remove atom 5010 need remove atom 5012 need remove atom 5018 need remove atom 5021 need remove atom 5022 need remove atom 5024 need remove atom 5030 need remove atom 5033 need remove atom 5034 need remove atom 5036 need remove atom 5042 need remove atom 5045 need remove atom 5046 need remove atom 5048 need remove atom 5054 need remove atom 5057 need remove atom 5058 need remove atom 5060 need remove atom 5066 need remove atom 5069 need remove atom 5070 need remove atom 5072 need remove atom 5078 need remove atom 5081 need remove atom 5082 need remove atom 5084 need remove atom 5090 need remove atom 5093 need remove atom 5094 need remove atom 5096 need remove atom 5102 need remove atom 5105 need remove atom 5106 need remove atom 5108 need remove atom 5114 need remove atom 5117 need remove atom 5118 need remove atom 5120 need remove atom 5126 need remove atom 5129 need remove atom 5130 need remove atom 5132 need remove atom 5138 need remove atom 5141 need remove atom 5142 need remove atom 5144 need remove atom 5150 need remove atom 5153 need remove atom 5154 need remove atom 5156 need remove atom 5162 need remove atom 5165 need remove atom 5166 need remove atom 5168 need remove atom 5174 need remove atom 5177 need remove atom 5178 need remove atom 5180 need remove atom 5186 need remove atom 5189 need remove atom 5190 need remove atom 5192 need remove atom 5198 need remove atom 5201 need remove atom 5202 need remove atom 5204 need remove atom 5210 need remove atom 5213 need remove atom 5214 need remove atom 5216 need remove atom 5222 need remove atom 5225 need remove atom 5226 need remove atom 5228 need remove atom 5234 need remove atom 5240 need remove atom 5246 need remove atom 5252 need remove atom 5258 need remove atom 5264 need remove atom 5270 need remove atom 5276 [I] need removenum=184 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1757427921e-01 1.6388803329e-01 1.3965099067e-01 dub= -5.4266920577e-01 1.6389136022e-01 -1.4205845377e-01 duc= 5.1757578113e-01 -1.6592453575e-01 1.3965144051e-01 [I] overall tilt ux= -1.0602434850e+00 3.3269347784e-06 -2.8170944444e-01 uy= 1.5019208945e-06 -3.2981256904e-01 4.4984909958e-07 [I] storedr[0]= -1.2546712319e-02 -1.0165877632e-03 -1.2035066294e-03 [I] originally 9936 atoms [I] insert 0 atoms [I] now 9936 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 9936 atoms [I] remove 184 atoms [I] now 9752 atoms [I] NP=9752 n=9752 [I] ASSIGN finalcnfile = dipole_2.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 18:08:44 2023 CPU time spent: 6.354022 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 = Mon Jun 12 18:28:08 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 11 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 29 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=19140 [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) = 0.03030303030303 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.033333333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 3.0303030303e-02 0.0000000000e+00 3.3333333333e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=8.460537e+01 pxpb=0.000000e+00 pypb=1.287783e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 9125 need remove atom 9126 need remove atom 9137 need remove atom 9138 need remove atom 9149 need remove atom 9150 need remove atom 9161 need remove atom 9162 need remove atom 9173 need remove atom 9174 need remove atom 9182 need remove atom 9185 need remove atom 9186 need remove atom 9188 need remove atom 9194 need remove atom 9197 need remove atom 9198 need remove atom 9200 need remove atom 9206 need remove atom 9209 need remove atom 9210 need remove atom 9212 need remove atom 9218 need remove atom 9221 need remove atom 9222 need remove atom 9224 need remove atom 9230 need remove atom 9233 need remove atom 9234 need remove atom 9236 need remove atom 9242 need remove atom 9245 need remove atom 9246 need remove atom 9248 need remove atom 9254 need remove atom 9257 need remove atom 9258 need remove atom 9260 need remove atom 9266 need remove atom 9269 need remove atom 9270 need remove atom 9272 need remove atom 9278 need remove atom 9281 need remove atom 9282 need remove atom 9284 need remove atom 9290 need remove atom 9293 need remove atom 9294 need remove atom 9296 need remove atom 9302 need remove atom 9305 need remove atom 9306 need remove atom 9308 need remove atom 9314 need remove atom 9317 need remove atom 9318 need remove atom 9320 need remove atom 9326 need remove atom 9329 need remove atom 9330 need remove atom 9332 need remove atom 9338 need remove atom 9341 need remove atom 9342 need remove atom 9344 need remove atom 9350 need remove atom 9353 need remove atom 9354 need remove atom 9356 need remove atom 9362 need remove atom 9365 need remove atom 9366 need remove atom 9368 need remove atom 9374 need remove atom 9377 need remove atom 9378 need remove atom 9380 need remove atom 9386 need remove atom 9389 need remove atom 9390 need remove atom 9392 need remove atom 9398 need remove atom 9401 need remove atom 9402 need remove atom 9404 need remove atom 9410 need remove atom 9413 need remove atom 9414 need remove atom 9416 need remove atom 9422 need remove atom 9425 need remove atom 9426 need remove atom 9428 need remove atom 9434 need remove atom 9437 need remove atom 9438 need remove atom 9440 need remove atom 9446 need remove atom 9449 need remove atom 9450 need remove atom 9452 need remove atom 9458 need remove atom 9461 need remove atom 9462 need remove atom 9464 need remove atom 9470 need remove atom 9473 need remove atom 9474 need remove atom 9476 need remove atom 9482 need remove atom 9485 need remove atom 9486 need remove atom 9488 need remove atom 9494 need remove atom 9497 need remove atom 9498 need remove atom 9500 need remove atom 9506 need remove atom 9509 need remove atom 9510 need remove atom 9512 need remove atom 9518 need remove atom 9521 need remove atom 9522 need remove atom 9524 need remove atom 9530 need remove atom 9533 need remove atom 9534 need remove atom 9536 need remove atom 9542 need remove atom 9545 need remove atom 9546 need remove atom 9548 need remove atom 9554 need remove atom 9557 need remove atom 9558 need remove atom 9560 need remove atom 9566 need remove atom 9569 need remove atom 9570 need remove atom 9572 need remove atom 9578 need remove atom 9581 need remove atom 9582 need remove atom 9584 need remove atom 9590 need remove atom 9593 need remove atom 9594 need remove atom 9596 need remove atom 9602 need remove atom 9605 need remove atom 9606 need remove atom 9608 need remove atom 9614 need remove atom 9617 need remove atom 9618 need remove atom 9620 need remove atom 9626 need remove atom 9629 need remove atom 9630 need remove atom 9632 need remove atom 9638 need remove atom 9641 need remove atom 9642 need remove atom 9644 need remove atom 9650 need remove atom 9653 need remove atom 9654 need remove atom 9656 need remove atom 9662 need remove atom 9665 need remove atom 9666 need remove atom 9668 need remove atom 9674 need remove atom 9677 need remove atom 9678 need remove atom 9680 need remove atom 9686 need remove atom 9689 need remove atom 9690 need remove atom 9692 need remove atom 9698 need remove atom 9701 need remove atom 9702 need remove atom 9704 need remove atom 9710 need remove atom 9713 need remove atom 9714 need remove atom 9716 need remove atom 9722 need remove atom 9725 need remove atom 9726 need remove atom 9728 need remove atom 9734 need remove atom 9737 need remove atom 9738 need remove atom 9740 need remove atom 9746 need remove atom 9749 need remove atom 9750 need remove atom 9752 need remove atom 9758 need remove atom 9761 need remove atom 9762 need remove atom 9764 need remove atom 9770 need remove atom 9773 need remove atom 9774 need remove atom 9776 need remove atom 9782 need remove atom 9785 need remove atom 9786 need remove atom 9788 need remove atom 9794 need remove atom 9797 need remove atom 9798 need remove atom 9800 need remove atom 9806 need remove atom 9809 need remove atom 9810 need remove atom 9812 need remove atom 9818 need remove atom 9821 need remove atom 9822 need remove atom 9824 need remove atom 9830 need remove atom 9833 need remove atom 9834 need remove atom 9836 need remove atom 9842 need remove atom 9845 need remove atom 9846 need remove atom 9848 need remove atom 9854 need remove atom 9857 need remove atom 9858 need remove atom 9860 need remove atom 9866 need remove atom 9869 need remove atom 9870 need remove atom 9872 need remove atom 9878 need remove atom 9881 need remove atom 9882 need remove atom 9884 need remove atom 9890 need remove atom 9893 need remove atom 9894 need remove atom 9896 need remove atom 9902 need remove atom 9905 need remove atom 9906 need remove atom 9908 need remove atom 9914 need remove atom 9917 need remove atom 9918 need remove atom 9920 need remove atom 9926 need remove atom 9929 need remove atom 9930 need remove atom 9932 need remove atom 9938 need remove atom 9941 need remove atom 9942 need remove atom 9944 need remove atom 9950 need remove atom 9953 need remove atom 9954 need remove atom 9956 need remove atom 9962 need remove atom 9965 need remove atom 9966 need remove atom 9968 need remove atom 9974 need remove atom 9977 need remove atom 9978 need remove atom 9980 need remove atom 9986 need remove atom 9989 need remove atom 9990 need remove atom 9992 need remove atom 9998 need remove atom 10001 need remove atom 10002 need remove atom 10004 need remove atom 10010 need remove atom 10013 need remove atom 10014 need remove atom 10016 [I] need removenum=290 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.2167145185e-01 1.6249309970e-01 1.4158411288e-01 dub= -5.4720543292e-01 1.6249692433e-01 -1.4427864481e-01 duc= 5.2167291750e-01 -1.6463069279e-01 1.4158456601e-01 [I] overall tilt ux= -1.0688768848e+00 3.8246313026e-06 -2.8586275769e-01 uy= 1.4656460009e-06 -3.2712379249e-01 4.5312808378e-07 [I] storedr[0]= -1.2766257710e-02 -1.0668842315e-03 -1.3470394028e-03 [I] originally 19140 atoms [I] insert 0 atoms [I] now 19140 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 19140 atoms [I] remove 290 atoms [I] now 18850 atoms [I] NP=18850 n=18850 [I] ASSIGN finalcnfile = dipole_2.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 18:28:21 2023 CPU time spent: 11.963407 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 = Mon Jun 12 18:37:43 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 13 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 34 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 6 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=31824 [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) = 0.025641025641026 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.027777777777778 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 2.5641025641e-02 0.0000000000e+00 2.7777777778e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=9.998817e+01 pxpb=0.000000e+00 pypb=1.509814e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 15338 need remove atom 15341 need remove atom 15342 need remove atom 15344 need remove atom 15350 need remove atom 15353 need remove atom 15354 need remove atom 15356 need remove atom 15362 need remove atom 15365 need remove atom 15366 need remove atom 15368 need remove atom 15374 need remove atom 15377 need remove atom 15378 need remove atom 15380 need remove atom 15386 need remove atom 15389 need remove atom 15390 need remove atom 15392 need remove atom 15398 need remove atom 15401 need remove atom 15402 need remove atom 15404 need remove atom 15410 need remove atom 15413 need remove atom 15414 need remove atom 15416 need remove atom 15422 need remove atom 15425 need remove atom 15426 need remove atom 15428 need remove atom 15434 need remove atom 15437 need remove atom 15438 need remove atom 15440 need remove atom 15446 need remove atom 15449 need remove atom 15450 need remove atom 15452 need remove atom 15458 need remove atom 15461 need remove atom 15462 need remove atom 15464 need remove atom 15470 need remove atom 15473 need remove atom 15474 need remove atom 15476 need remove atom 15482 need remove atom 15485 need remove atom 15486 need remove atom 15488 need remove atom 15494 need remove atom 15497 need remove atom 15498 need remove atom 15500 need remove atom 15506 need remove atom 15509 need remove atom 15510 need remove atom 15512 need remove atom 15518 need remove atom 15521 need remove atom 15522 need remove atom 15524 need remove atom 15530 need remove atom 15533 need remove atom 15534 need remove atom 15536 need remove atom 15542 need remove atom 15545 need remove atom 15546 need remove atom 15548 need remove atom 15554 need remove atom 15557 need remove atom 15558 need remove atom 15560 need remove atom 15566 need remove atom 15569 need remove atom 15570 need remove atom 15572 need remove atom 15578 need remove atom 15581 need remove atom 15582 need remove atom 15584 need remove atom 15590 need remove atom 15593 need remove atom 15594 need remove atom 15596 need remove atom 15602 need remove atom 15605 need remove atom 15606 need remove atom 15608 need remove atom 15614 need remove atom 15617 need remove atom 15618 need remove atom 15620 need remove atom 15626 need remove atom 15629 need remove atom 15630 need remove atom 15632 need remove atom 15638 need remove atom 15641 need remove atom 15642 need remove atom 15644 need remove atom 15650 need remove atom 15653 need remove atom 15654 need remove atom 15656 need remove atom 15662 need remove atom 15665 need remove atom 15666 need remove atom 15668 need remove atom 15674 need remove atom 15677 need remove atom 15678 need remove atom 15680 need remove atom 15686 need remove atom 15689 need remove atom 15690 need remove atom 15692 need remove atom 15698 need remove atom 15701 need remove atom 15702 need remove atom 15704 need remove atom 15710 need remove atom 15713 need remove atom 15714 need remove atom 15716 need remove atom 15722 need remove atom 15725 need remove atom 15726 need remove atom 15728 need remove atom 15734 need remove atom 15737 need remove atom 15738 need remove atom 15740 need remove atom 15746 need remove atom 15749 need remove atom 15750 need remove atom 15752 need remove atom 15758 need remove atom 15761 need remove atom 15762 need remove atom 15764 need remove atom 15770 need remove atom 15773 need remove atom 15774 need remove atom 15776 need remove atom 15782 need remove atom 15785 need remove atom 15786 need remove atom 15788 need remove atom 15794 need remove atom 15797 need remove atom 15798 need remove atom 15800 need remove atom 15806 need remove atom 15809 need remove atom 15810 need remove atom 15812 need remove atom 15818 need remove atom 15821 need remove atom 15822 need remove atom 15824 need remove atom 15830 need remove atom 15833 need remove atom 15834 need remove atom 15836 need remove atom 15842 need remove atom 15845 need remove atom 15846 need remove atom 15848 need remove atom 15854 need remove atom 15857 need remove atom 15858 need remove atom 15860 need remove atom 15866 need remove atom 15869 need remove atom 15870 need remove atom 15872 need remove atom 15878 need remove atom 15881 need remove atom 15882 need remove atom 15884 need remove atom 15890 need remove atom 15893 need remove atom 15894 need remove atom 15896 need remove atom 15902 need remove atom 15905 need remove atom 15906 need remove atom 15908 need remove atom 15914 need remove atom 15917 need remove atom 15918 need remove atom 15920 need remove atom 15926 need remove atom 15929 need remove atom 15930 need remove atom 15932 need remove atom 15938 need remove atom 15941 need remove atom 15942 need remove atom 15944 need remove atom 15950 need remove atom 15953 need remove atom 15954 need remove atom 15956 need remove atom 15962 need remove atom 15965 need remove atom 15966 need remove atom 15968 need remove atom 15974 need remove atom 15977 need remove atom 15978 need remove atom 15980 need remove atom 15986 need remove atom 15989 need remove atom 15990 need remove atom 15992 need remove atom 15998 need remove atom 16001 need remove atom 16002 need remove atom 16004 need remove atom 16010 need remove atom 16013 need remove atom 16014 need remove atom 16016 need remove atom 16022 need remove atom 16025 need remove atom 16026 need remove atom 16028 need remove atom 16034 need remove atom 16037 need remove atom 16038 need remove atom 16040 need remove atom 16046 need remove atom 16049 need remove atom 16050 need remove atom 16052 need remove atom 16058 need remove atom 16061 need remove atom 16062 need remove atom 16064 need remove atom 16070 need remove atom 16073 need remove atom 16074 need remove atom 16076 need remove atom 16082 need remove atom 16085 need remove atom 16086 need remove atom 16088 need remove atom 16094 need remove atom 16097 need remove atom 16098 need remove atom 16100 need remove atom 16106 need remove atom 16109 need remove atom 16110 need remove atom 16112 need remove atom 16118 need remove atom 16121 need remove atom 16122 need remove atom 16124 need remove atom 16130 need remove atom 16133 need remove atom 16134 need remove atom 16136 need remove atom 16142 need remove atom 16145 need remove atom 16146 need remove atom 16148 need remove atom 16154 need remove atom 16157 need remove atom 16158 need remove atom 16160 need remove atom 16166 need remove atom 16169 need remove atom 16170 need remove atom 16172 need remove atom 16178 need remove atom 16181 need remove atom 16182 need remove atom 16184 need remove atom 16190 need remove atom 16193 need remove atom 16194 need remove atom 16196 need remove atom 16202 need remove atom 16205 need remove atom 16206 need remove atom 16208 need remove atom 16214 need remove atom 16217 need remove atom 16218 need remove atom 16220 need remove atom 16226 need remove atom 16229 need remove atom 16230 need remove atom 16232 need remove atom 16238 need remove atom 16241 need remove atom 16242 need remove atom 16244 need remove atom 16250 need remove atom 16253 need remove atom 16254 need remove atom 16256 need remove atom 16262 need remove atom 16265 need remove atom 16266 need remove atom 16268 need remove atom 16274 need remove atom 16277 need remove atom 16278 need remove atom 16280 need remove atom 16286 need remove atom 16289 need remove atom 16290 need remove atom 16292 need remove atom 16298 need remove atom 16301 need remove atom 16302 need remove atom 16304 need remove atom 16310 need remove atom 16313 need remove atom 16314 need remove atom 16316 need remove atom 16322 need remove atom 16325 need remove atom 16326 need remove atom 16328 need remove atom 16334 need remove atom 16337 need remove atom 16338 need remove atom 16340 need remove atom 16346 need remove atom 16349 need remove atom 16350 need remove atom 16352 need remove atom 16358 need remove atom 16361 need remove atom 16362 need remove atom 16364 need remove atom 16370 need remove atom 16373 need remove atom 16374 need remove atom 16376 need remove atom 16382 need remove atom 16385 need remove atom 16386 need remove atom 16388 need remove atom 16394 need remove atom 16397 need remove atom 16398 need remove atom 16400 need remove atom 16406 need remove atom 16409 need remove atom 16410 need remove atom 16412 need remove atom 16418 need remove atom 16421 need remove atom 16422 need remove atom 16424 need remove atom 16430 need remove atom 16433 need remove atom 16434 need remove atom 16436 need remove atom 16442 need remove atom 16445 need remove atom 16446 need remove atom 16448 need remove atom 16454 need remove atom 16457 need remove atom 16458 need remove atom 16460 need remove atom 16466 need remove atom 16469 need remove atom 16470 need remove atom 16472 need remove atom 16478 need remove atom 16481 need remove atom 16482 need remove atom 16484 need remove atom 16490 need remove atom 16493 need remove atom 16494 need remove atom 16496 need remove atom 16502 need remove atom 16505 need remove atom 16506 need remove atom 16508 need remove atom 16514 need remove atom 16517 need remove atom 16518 need remove atom 16520 need remove atom 16526 need remove atom 16529 need remove atom 16530 need remove atom 16532 need remove atom 16538 need remove atom 16541 need remove atom 16542 need remove atom 16544 need remove atom 16550 need remove atom 16553 need remove atom 16554 need remove atom 16556 [I] need removenum=408 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.2063244414e-01 1.6285142621e-01 1.4109008120e-01 dub= -5.4605915472e-01 1.6285512747e-01 -1.4371150930e-01 duc= 5.2063391928e-01 -1.6496311549e-01 1.4109053356e-01 [I] overall tilt ux= -1.0666915989e+00 3.7012622023e-06 -2.8480159051e-01 uy= 1.4751377705e-06 -3.2781454169e-01 4.5235546484e-07 [I] storedr[0]= -1.2712617719e-02 -1.0539940090e-03 -1.3104878717e-03 [I] originally 31824 atoms [I] insert 0 atoms [I] now 31824 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 31824 atoms [I] remove 408 atoms [I] now 31416 atoms [I] NP=31416 n=31416 [I] ASSIGN finalcnfile = dipole_3.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 18:38:05 2023 CPU time spent: 19.975591 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 = Mon Jun 12 18:47:32 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 15 [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) = -1 [I] ASSIGN makecnspec(11) = 7 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 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) = 0.022222222222222 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.023809523809524 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 2.2222222222e-02 0.0000000000e+00 2.3809523810e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=1.153710e+02 pxpb=0.000000e+00 pypb=1.731846e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 23774 need remove atom 23777 need remove atom 23778 need remove atom 23780 need remove atom 23786 need remove atom 23789 need remove atom 23790 need remove atom 23792 need remove atom 23798 need remove atom 23801 need remove atom 23802 need remove atom 23804 need remove atom 23810 need remove atom 23813 need remove atom 23814 need remove atom 23816 need remove atom 23822 need remove atom 23825 need remove atom 23826 need remove atom 23828 need remove atom 23834 need remove atom 23837 need remove atom 23838 need remove atom 23840 need remove atom 23846 need remove atom 23849 need remove atom 23850 need remove atom 23852 need remove atom 23858 need remove atom 23861 need remove atom 23862 need remove atom 23864 need remove atom 23870 need remove atom 23873 need remove atom 23874 need remove atom 23876 need remove atom 23882 need remove atom 23885 need remove atom 23886 need remove atom 23888 need remove atom 23894 need remove atom 23897 need remove atom 23898 need remove atom 23900 need remove atom 23906 need remove atom 23909 need remove atom 23910 need remove atom 23912 need remove atom 23918 need remove atom 23921 need remove atom 23922 need remove atom 23924 need remove atom 23930 need remove atom 23933 need remove atom 23934 need remove atom 23936 need remove atom 23942 need remove atom 23945 need remove atom 23946 need remove atom 23948 need remove atom 23954 need remove atom 23957 need remove atom 23958 need remove atom 23960 need remove atom 23966 need remove atom 23969 need remove atom 23970 need remove atom 23972 need remove atom 23978 need remove atom 23981 need remove atom 23982 need remove atom 23984 need remove atom 23990 need remove atom 23993 need remove atom 23994 need remove atom 23996 need remove atom 24002 need remove atom 24005 need remove atom 24006 need remove atom 24008 need remove atom 24014 need remove atom 24017 need remove atom 24018 need remove atom 24020 need remove atom 24026 need remove atom 24029 need remove atom 24030 need remove atom 24032 need remove atom 24038 need remove atom 24041 need remove atom 24042 need remove atom 24044 need remove atom 24050 need remove atom 24053 need remove atom 24054 need remove atom 24056 need remove atom 24062 need remove atom 24065 need remove atom 24066 need remove atom 24068 need remove atom 24074 need remove atom 24077 need remove atom 24078 need remove atom 24080 need remove atom 24086 need remove atom 24089 need remove atom 24090 need remove atom 24092 need remove atom 24098 need remove atom 24101 need remove atom 24102 need remove atom 24104 need remove atom 24110 need remove atom 24113 need remove atom 24114 need remove atom 24116 need remove atom 24122 need remove atom 24125 need remove atom 24126 need remove atom 24128 need remove atom 24134 need remove atom 24137 need remove atom 24138 need remove atom 24140 need remove atom 24146 need remove atom 24149 need remove atom 24150 need remove atom 24152 need remove atom 24158 need remove atom 24161 need remove atom 24162 need remove atom 24164 need remove atom 24170 need remove atom 24173 need remove atom 24174 need remove atom 24176 need remove atom 24182 need remove atom 24185 need remove atom 24186 need remove atom 24188 need remove atom 24194 need remove atom 24197 need remove atom 24198 need remove atom 24200 need remove atom 24206 need remove atom 24209 need remove atom 24210 need remove atom 24212 need remove atom 24218 need remove atom 24221 need remove atom 24222 need remove atom 24224 need remove atom 24230 need remove atom 24233 need remove atom 24234 need remove atom 24236 need remove atom 24242 need remove atom 24245 need remove atom 24246 need remove atom 24248 need remove atom 24254 need remove atom 24257 need remove atom 24258 need remove atom 24260 need remove atom 24266 need remove atom 24269 need remove atom 24270 need remove atom 24272 need remove atom 24278 need remove atom 24281 need remove atom 24282 need remove atom 24284 need remove atom 24290 need remove atom 24293 need remove atom 24294 need remove atom 24296 need remove atom 24302 need remove atom 24305 need remove atom 24306 need remove atom 24308 need remove atom 24314 need remove atom 24317 need remove atom 24318 need remove atom 24320 need remove atom 24326 need remove atom 24329 need remove atom 24330 need remove atom 24332 need remove atom 24338 need remove atom 24341 need remove atom 24342 need remove atom 24344 need remove atom 24350 need remove atom 24353 need remove atom 24354 need remove atom 24356 need remove atom 24362 need remove atom 24365 need remove atom 24366 need remove atom 24368 need remove atom 24374 need remove atom 24377 need remove atom 24378 need remove atom 24380 need remove atom 24386 need remove atom 24389 need remove atom 24390 need remove atom 24392 need remove atom 24398 need remove atom 24401 need remove atom 24402 need remove atom 24404 need remove atom 24410 need remove atom 24413 need remove atom 24414 need remove atom 24416 need remove atom 24422 need remove atom 24425 need remove atom 24426 need remove atom 24428 need remove atom 24434 need remove atom 24437 need remove atom 24438 need remove atom 24440 need remove atom 24446 need remove atom 24449 need remove atom 24450 need remove atom 24452 need remove atom 24458 need remove atom 24461 need remove atom 24462 need remove atom 24464 need remove atom 24470 need remove atom 24473 need remove atom 24474 need remove atom 24476 need remove atom 24482 need remove atom 24485 need remove atom 24486 need remove atom 24488 need remove atom 24494 need remove atom 24497 need remove atom 24498 need remove atom 24500 need remove atom 24506 need remove atom 24509 need remove atom 24510 need remove atom 24512 need remove atom 24518 need remove atom 24521 need remove atom 24522 need remove atom 24524 need remove atom 24530 need remove atom 24533 need remove atom 24534 need remove atom 24536 need remove atom 24542 need remove atom 24545 need remove atom 24546 need remove atom 24548 need remove atom 24554 need remove atom 24557 need remove atom 24558 need remove atom 24560 need remove atom 24566 need remove atom 24569 need remove atom 24570 need remove atom 24572 need remove atom 24578 need remove atom 24581 need remove atom 24582 need remove atom 24584 need remove atom 24590 need remove atom 24593 need remove atom 24594 need remove atom 24596 need remove atom 24602 need remove atom 24605 need remove atom 24606 need remove atom 24608 need remove atom 24614 need remove atom 24617 need remove atom 24618 need remove atom 24620 need remove atom 24626 need remove atom 24629 need remove atom 24630 need remove atom 24632 need remove atom 24638 need remove atom 24641 need remove atom 24642 need remove atom 24644 need remove atom 24650 need remove atom 24653 need remove atom 24654 need remove atom 24656 need remove atom 24662 need remove atom 24665 need remove atom 24666 need remove atom 24668 need remove atom 24674 need remove atom 24677 need remove atom 24678 need remove atom 24680 need remove atom 24686 need remove atom 24689 need remove atom 24690 need remove atom 24692 need remove atom 24698 need remove atom 24701 need remove atom 24702 need remove atom 24704 need remove atom 24710 need remove atom 24713 need remove atom 24714 need remove atom 24716 need remove atom 24722 need remove atom 24725 need remove atom 24726 need remove atom 24728 need remove atom 24734 need remove atom 24737 need remove atom 24738 need remove atom 24740 need remove atom 24746 need remove atom 24749 need remove atom 24750 need remove atom 24752 need remove atom 24758 need remove atom 24761 need remove atom 24762 need remove atom 24764 need remove atom 24770 need remove atom 24773 need remove atom 24774 need remove atom 24776 need remove atom 24782 need remove atom 24785 need remove atom 24786 need remove atom 24788 need remove atom 24794 need remove atom 24797 need remove atom 24798 need remove atom 24800 need remove atom 24806 need remove atom 24809 need remove atom 24810 need remove atom 24812 need remove atom 24818 need remove atom 24821 need remove atom 24822 need remove atom 24824 need remove atom 24830 need remove atom 24833 need remove atom 24834 need remove atom 24836 need remove atom 24842 need remove atom 24845 need remove atom 24846 need remove atom 24848 need remove atom 24854 need remove atom 24857 need remove atom 24858 need remove atom 24860 need remove atom 24866 need remove atom 24869 need remove atom 24870 need remove atom 24872 need remove atom 24878 need remove atom 24881 need remove atom 24882 need remove atom 24884 need remove atom 24890 need remove atom 24893 need remove atom 24894 need remove atom 24896 need remove atom 24902 need remove atom 24905 need remove atom 24906 need remove atom 24908 need remove atom 24914 need remove atom 24917 need remove atom 24918 need remove atom 24920 need remove atom 24926 need remove atom 24929 need remove atom 24930 need remove atom 24932 need remove atom 24938 need remove atom 24941 need remove atom 24942 need remove atom 24944 need remove atom 24950 need remove atom 24953 need remove atom 24954 need remove atom 24956 need remove atom 24962 need remove atom 24965 need remove atom 24966 need remove atom 24968 need remove atom 24974 need remove atom 24977 need remove atom 24978 need remove atom 24980 need remove atom 24986 need remove atom 24989 need remove atom 24990 need remove atom 24992 need remove atom 24998 need remove atom 25001 need remove atom 25002 need remove atom 25004 need remove atom 25010 need remove atom 25013 need remove atom 25014 need remove atom 25016 need remove atom 25022 need remove atom 25025 need remove atom 25026 need remove atom 25028 need remove atom 25034 need remove atom 25037 need remove atom 25038 need remove atom 25040 need remove atom 25046 need remove atom 25049 need remove atom 25050 need remove atom 25052 need remove atom 25058 need remove atom 25061 need remove atom 25062 need remove atom 25064 need remove atom 25070 need remove atom 25073 need remove atom 25074 need remove atom 25076 need remove atom 25082 need remove atom 25085 need remove atom 25086 need remove atom 25088 need remove atom 25094 need remove atom 25097 need remove atom 25098 need remove atom 25100 need remove atom 25106 need remove atom 25109 need remove atom 25110 need remove atom 25112 need remove atom 25118 need remove atom 25121 need remove atom 25122 need remove atom 25124 need remove atom 25130 need remove atom 25133 need remove atom 25134 need remove atom 25136 need remove atom 25142 need remove atom 25145 need remove atom 25146 need remove atom 25148 need remove atom 25154 need remove atom 25157 need remove atom 25158 need remove atom 25160 need remove atom 25166 need remove atom 25169 need remove atom 25170 need remove atom 25172 need remove atom 25178 need remove atom 25181 need remove atom 25182 need remove atom 25184 need remove atom 25190 need remove atom 25193 need remove atom 25194 need remove atom 25196 need remove atom 25202 need remove atom 25205 need remove atom 25206 need remove atom 25208 need remove atom 25214 need remove atom 25217 need remove atom 25218 need remove atom 25220 need remove atom 25226 need remove atom 25229 need remove atom 25230 need remove atom 25232 need remove atom 25238 need remove atom 25241 need remove atom 25242 need remove atom 25244 need remove atom 25250 need remove atom 25253 need remove atom 25254 need remove atom 25256 need remove atom 25262 need remove atom 25265 need remove atom 25266 need remove atom 25268 need remove atom 25274 need remove atom 25277 need remove atom 25278 need remove atom 25280 need remove atom 25286 need remove atom 25289 need remove atom 25290 need remove atom 25292 need remove atom 25298 need remove atom 25301 need remove atom 25302 need remove atom 25304 need remove atom 25310 need remove atom 25313 need remove atom 25314 need remove atom 25316 need remove atom 25322 need remove atom 25325 need remove atom 25326 need remove atom 25328 need remove atom 25334 need remove atom 25337 need remove atom 25338 need remove atom 25340 need remove atom 25346 need remove atom 25349 need remove atom 25350 need remove atom 25352 need remove atom 25358 need remove atom 25361 need remove atom 25362 need remove atom 25364 need remove atom 25370 need remove atom 25376 need remove atom 25382 need remove atom 25388 need remove atom 25394 need remove atom 25400 need remove atom 25406 need remove atom 25412 need remove atom 25418 need remove atom 25424 need remove atom 25430 need remove atom 25436 need remove atom 25442 need remove atom 25448 [I] need removenum=546 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1985967362e-01 1.6311592386e-01 1.4072433496e-01 dub= -5.4520478427e-01 1.6311953208e-01 -1.4329152279e-01 duc= 5.1986115569e-01 -1.6520846565e-01 1.4072478672e-01 [I] overall tilt ux= -1.0650644579e+00 3.6082214786e-06 -2.8401585775e-01 uy= 1.4820685467e-06 -3.2832438950e-01 4.5175441071e-07 [I] storedr[0]= -1.2671814292e-02 -1.0444667826e-03 -1.2833680363e-03 [I] originally 49140 atoms [I] insert 0 atoms [I] now 49140 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 49140 atoms [I] remove 546 atoms [I] now 48594 atoms [I] NP=48594 n=48594 [I] ASSIGN finalcnfile = dipole_3.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 18:48:05 2023 CPU time spent: 31.074580 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 = Mon Jun 12 19:03:27 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 17 [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) = -1 [I] ASSIGN makecnspec(11) = 7 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=62832 [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) = 0.019607843137255 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.023809523809524 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 1.9607843137e-02 0.0000000000e+00 2.3809523810e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=1.307538e+02 pxpb=0.000000e+00 pypb=1.953877e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 30495 need remove atom 30496 need remove atom 30507 need remove atom 30508 need remove atom 30519 need remove atom 30520 need remove atom 30531 need remove atom 30532 need remove atom 30543 need remove atom 30544 need remove atom 30555 need remove atom 30556 need remove atom 30567 need remove atom 30568 need remove atom 30578 need remove atom 30579 need remove atom 30580 need remove atom 30584 need remove atom 30590 need remove atom 30591 need remove atom 30592 need remove atom 30596 need remove atom 30602 need remove atom 30603 need remove atom 30604 need remove atom 30608 need remove atom 30614 need remove atom 30615 need remove atom 30616 need remove atom 30620 need remove atom 30626 need remove atom 30627 need remove atom 30628 need remove atom 30632 need remove atom 30638 need remove atom 30639 need remove atom 30640 need remove atom 30644 need remove atom 30650 need remove atom 30651 need remove atom 30652 need remove atom 30656 need remove atom 30662 need remove atom 30663 need remove atom 30664 need remove atom 30668 need remove atom 30674 need remove atom 30675 need remove atom 30676 need remove atom 30680 need remove atom 30686 need remove atom 30687 need remove atom 30688 need remove atom 30692 need remove atom 30698 need remove atom 30699 need remove atom 30700 need remove atom 30704 need remove atom 30710 need remove atom 30711 need remove atom 30712 need remove atom 30716 need remove atom 30722 need remove atom 30723 need remove atom 30724 need remove atom 30728 need remove atom 30734 need remove atom 30735 need remove atom 30736 need remove atom 30740 need remove atom 30746 need remove atom 30747 need remove atom 30748 need remove atom 30752 need remove atom 30758 need remove atom 30759 need remove atom 30760 need remove atom 30764 need remove atom 30770 need remove atom 30771 need remove atom 30772 need remove atom 30776 need remove atom 30782 need remove atom 30783 need remove atom 30784 need remove atom 30788 need remove atom 30794 need remove atom 30795 need remove atom 30796 need remove atom 30800 need remove atom 30806 need remove atom 30807 need remove atom 30808 need remove atom 30812 need remove atom 30818 need remove atom 30819 need remove atom 30820 need remove atom 30824 need remove atom 30830 need remove atom 30831 need remove atom 30832 need remove atom 30836 need remove atom 30842 need remove atom 30843 need remove atom 30844 need remove atom 30848 need remove atom 30854 need remove atom 30855 need remove atom 30856 need remove atom 30860 need remove atom 30866 need remove atom 30867 need remove atom 30868 need remove atom 30872 need remove atom 30878 need remove atom 30879 need remove atom 30880 need remove atom 30884 need remove atom 30890 need remove atom 30891 need remove atom 30892 need remove atom 30896 need remove atom 30902 need remove atom 30903 need remove atom 30904 need remove atom 30908 need remove atom 30914 need remove atom 30915 need remove atom 30916 need remove atom 30920 need remove atom 30926 need remove atom 30927 need remove atom 30928 need remove atom 30932 need remove atom 30938 need remove atom 30939 need remove atom 30940 need remove atom 30944 need remove atom 30950 need remove atom 30951 need remove atom 30952 need remove atom 30956 need remove atom 30962 need remove atom 30963 need remove atom 30964 need remove atom 30968 need remove atom 30974 need remove atom 30975 need remove atom 30976 need remove atom 30980 need remove atom 30986 need remove atom 30987 need remove atom 30988 need remove atom 30992 need remove atom 30998 need remove atom 30999 need remove atom 31000 need remove atom 31004 need remove atom 31010 need remove atom 31011 need remove atom 31012 need remove atom 31016 need remove atom 31022 need remove atom 31023 need remove atom 31024 need remove atom 31028 need remove atom 31034 need remove atom 31035 need remove atom 31036 need remove atom 31040 need remove atom 31046 need remove atom 31047 need remove atom 31048 need remove atom 31052 need remove atom 31058 need remove atom 31059 need remove atom 31060 need remove atom 31064 need remove atom 31070 need remove atom 31071 need remove atom 31072 need remove atom 31076 need remove atom 31082 need remove atom 31083 need remove atom 31084 need remove atom 31088 need remove atom 31094 need remove atom 31095 need remove atom 31096 need remove atom 31100 need remove atom 31106 need remove atom 31107 need remove atom 31108 need remove atom 31112 need remove atom 31118 need remove atom 31119 need remove atom 31120 need remove atom 31124 need remove atom 31130 need remove atom 31131 need remove atom 31132 need remove atom 31136 need remove atom 31142 need remove atom 31143 need remove atom 31144 need remove atom 31148 need remove atom 31154 need remove atom 31155 need remove atom 31156 need remove atom 31160 need remove atom 31166 need remove atom 31167 need remove atom 31168 need remove atom 31172 need remove atom 31178 need remove atom 31179 need remove atom 31180 need remove atom 31184 need remove atom 31190 need remove atom 31191 need remove atom 31192 need remove atom 31196 need remove atom 31202 need remove atom 31203 need remove atom 31204 need remove atom 31208 need remove atom 31214 need remove atom 31215 need remove atom 31216 need remove atom 31220 need remove atom 31226 need remove atom 31227 need remove atom 31228 need remove atom 31232 need remove atom 31238 need remove atom 31239 need remove atom 31240 need remove atom 31244 need remove atom 31250 need remove atom 31251 need remove atom 31252 need remove atom 31256 need remove atom 31262 need remove atom 31263 need remove atom 31264 need remove atom 31268 need remove atom 31274 need remove atom 31275 need remove atom 31276 need remove atom 31280 need remove atom 31286 need remove atom 31287 need remove atom 31288 need remove atom 31292 need remove atom 31298 need remove atom 31299 need remove atom 31300 need remove atom 31304 need remove atom 31310 need remove atom 31311 need remove atom 31312 need remove atom 31316 need remove atom 31322 need remove atom 31323 need remove atom 31324 need remove atom 31328 need remove atom 31334 need remove atom 31335 need remove atom 31336 need remove atom 31340 need remove atom 31346 need remove atom 31347 need remove atom 31348 need remove atom 31352 need remove atom 31358 need remove atom 31359 need remove atom 31360 need remove atom 31364 need remove atom 31370 need remove atom 31371 need remove atom 31372 need remove atom 31376 need remove atom 31382 need remove atom 31383 need remove atom 31384 need remove atom 31388 need remove atom 31394 need remove atom 31395 need remove atom 31396 need remove atom 31400 need remove atom 31406 need remove atom 31407 need remove atom 31408 need remove atom 31412 need remove atom 31418 need remove atom 31419 need remove atom 31420 need remove atom 31424 need remove atom 31430 need remove atom 31431 need remove atom 31432 need remove atom 31436 need remove atom 31442 need remove atom 31443 need remove atom 31444 need remove atom 31448 need remove atom 31454 need remove atom 31455 need remove atom 31456 need remove atom 31460 need remove atom 31466 need remove atom 31467 need remove atom 31468 need remove atom 31472 need remove atom 31478 need remove atom 31479 need remove atom 31480 need remove atom 31484 need remove atom 31490 need remove atom 31491 need remove atom 31492 need remove atom 31496 need remove atom 31502 need remove atom 31503 need remove atom 31504 need remove atom 31508 need remove atom 31514 need remove atom 31515 need remove atom 31516 need remove atom 31520 need remove atom 31526 need remove atom 31527 need remove atom 31528 need remove atom 31532 need remove atom 31538 need remove atom 31539 need remove atom 31540 need remove atom 31544 need remove atom 31550 need remove atom 31551 need remove atom 31552 need remove atom 31556 need remove atom 31562 need remove atom 31563 need remove atom 31564 need remove atom 31568 need remove atom 31574 need remove atom 31575 need remove atom 31576 need remove atom 31580 need remove atom 31586 need remove atom 31587 need remove atom 31588 need remove atom 31592 need remove atom 31598 need remove atom 31599 need remove atom 31600 need remove atom 31604 need remove atom 31610 need remove atom 31611 need remove atom 31612 need remove atom 31616 need remove atom 31622 need remove atom 31623 need remove atom 31624 need remove atom 31628 need remove atom 31634 need remove atom 31635 need remove atom 31636 need remove atom 31640 need remove atom 31646 need remove atom 31647 need remove atom 31648 need remove atom 31652 need remove atom 31658 need remove atom 31659 need remove atom 31660 need remove atom 31664 need remove atom 31670 need remove atom 31671 need remove atom 31672 need remove atom 31676 need remove atom 31682 need remove atom 31683 need remove atom 31684 need remove atom 31688 need remove atom 31694 need remove atom 31695 need remove atom 31696 need remove atom 31700 need remove atom 31706 need remove atom 31707 need remove atom 31708 need remove atom 31712 need remove atom 31718 need remove atom 31719 need remove atom 31720 need remove atom 31724 need remove atom 31730 need remove atom 31731 need remove atom 31732 need remove atom 31736 need remove atom 31742 need remove atom 31743 need remove atom 31744 need remove atom 31748 need remove atom 31754 need remove atom 31755 need remove atom 31756 need remove atom 31760 need remove atom 31766 need remove atom 31767 need remove atom 31768 need remove atom 31772 need remove atom 31778 need remove atom 31779 need remove atom 31780 need remove atom 31784 need remove atom 31790 need remove atom 31791 need remove atom 31792 need remove atom 31796 need remove atom 31802 need remove atom 31803 need remove atom 31804 need remove atom 31808 need remove atom 31814 need remove atom 31815 need remove atom 31816 need remove atom 31820 need remove atom 31826 need remove atom 31827 need remove atom 31828 need remove atom 31832 need remove atom 31838 need remove atom 31839 need remove atom 31840 need remove atom 31844 need remove atom 31850 need remove atom 31851 need remove atom 31852 need remove atom 31856 need remove atom 31862 need remove atom 31863 need remove atom 31864 need remove atom 31868 need remove atom 31874 need remove atom 31875 need remove atom 31876 need remove atom 31880 need remove atom 31886 need remove atom 31887 need remove atom 31888 need remove atom 31892 need remove atom 31898 need remove atom 31899 need remove atom 31900 need remove atom 31904 need remove atom 31910 need remove atom 31911 need remove atom 31912 need remove atom 31916 need remove atom 31922 need remove atom 31923 need remove atom 31924 need remove atom 31928 need remove atom 31934 need remove atom 31935 need remove atom 31936 need remove atom 31940 need remove atom 31946 need remove atom 31947 need remove atom 31948 need remove atom 31952 need remove atom 31958 need remove atom 31959 need remove atom 31960 need remove atom 31964 need remove atom 31970 need remove atom 31971 need remove atom 31972 need remove atom 31976 need remove atom 31982 need remove atom 31983 need remove atom 31984 need remove atom 31988 need remove atom 31994 need remove atom 31995 need remove atom 31996 need remove atom 32000 need remove atom 32006 need remove atom 32007 need remove atom 32008 need remove atom 32012 need remove atom 32018 need remove atom 32019 need remove atom 32020 need remove atom 32024 need remove atom 32030 need remove atom 32031 need remove atom 32032 need remove atom 32036 need remove atom 32042 need remove atom 32043 need remove atom 32044 need remove atom 32048 need remove atom 32054 need remove atom 32055 need remove atom 32056 need remove atom 32060 need remove atom 32066 need remove atom 32067 need remove atom 32068 need remove atom 32072 need remove atom 32078 need remove atom 32079 need remove atom 32080 need remove atom 32084 need remove atom 32090 need remove atom 32091 need remove atom 32092 need remove atom 32096 need remove atom 32102 need remove atom 32103 need remove atom 32104 need remove atom 32108 need remove atom 32114 need remove atom 32115 need remove atom 32116 need remove atom 32120 need remove atom 32126 need remove atom 32127 need remove atom 32128 need remove atom 32132 need remove atom 32138 need remove atom 32139 need remove atom 32140 need remove atom 32144 need remove atom 32150 need remove atom 32151 need remove atom 32152 need remove atom 32156 need remove atom 32162 need remove atom 32163 need remove atom 32164 need remove atom 32168 need remove atom 32174 need remove atom 32175 need remove atom 32176 need remove atom 32180 need remove atom 32186 need remove atom 32187 need remove atom 32188 need remove atom 32192 need remove atom 32198 need remove atom 32199 need remove atom 32200 need remove atom 32204 need remove atom 32210 need remove atom 32211 need remove atom 32212 need remove atom 32216 need remove atom 32222 need remove atom 32223 need remove atom 32224 need remove atom 32228 need remove atom 32234 need remove atom 32235 need remove atom 32236 need remove atom 32240 need remove atom 32246 need remove atom 32247 need remove atom 32248 need remove atom 32252 need remove atom 32258 need remove atom 32259 need remove atom 32260 need remove atom 32264 need remove atom 32270 need remove atom 32271 need remove atom 32272 need remove atom 32276 need remove atom 32282 need remove atom 32283 need remove atom 32284 need remove atom 32288 need remove atom 32294 need remove atom 32295 need remove atom 32296 need remove atom 32300 need remove atom 32306 need remove atom 32307 need remove atom 32308 need remove atom 32312 need remove atom 32318 need remove atom 32319 need remove atom 32320 need remove atom 32324 need remove atom 32330 need remove atom 32331 need remove atom 32332 need remove atom 32336 need remove atom 32342 need remove atom 32348 need remove atom 32354 need remove atom 32360 need remove atom 32366 need remove atom 32372 need remove atom 32378 need remove atom 32384 need remove atom 32390 need remove atom 32396 need remove atom 32402 need remove atom 32408 need remove atom 32414 need remove atom 32420 [I] need removenum=616 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1926244376e-01 1.6331915827e-01 1.4044265087e-01 dub= -5.4454344324e-01 1.6332269385e-01 -1.4296799836e-01 duc= 5.1926393111e-01 -1.6539697107e-01 1.4044310215e-01 [I] overall tilt ux= -1.0638058870e+00 3.5355847608e-06 -2.8341064924e-01 uy= 1.4873495348e-06 -3.2871612933e-01 4.5127473916e-07 [I] storedr[0]= -1.2639756067e-02 -1.0371386080e-03 -1.2624481069e-03 [I] originally 62832 atoms [I] insert 0 atoms [I] now 62832 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 62832 atoms [I] remove 616 atoms [I] now 62216 atoms [I] NP=62216 n=62216 [I] ASSIGN finalcnfile = dipole_4.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 19:04:11 2023 CPU time spent: 39.906034 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 = Mon Jun 12 19:20:11 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 19 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 49 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 8 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=89376 [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) = 0.017543859649123 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.020833333333333 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 1.7543859649e-02 0.0000000000e+00 2.0833333333e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=1.461366e+02 pxpb=0.000000e+00 pypb=2.175909e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 43491 need remove atom 43492 need remove atom 43503 need remove atom 43504 need remove atom 43515 need remove atom 43516 need remove atom 43527 need remove atom 43528 need remove atom 43539 need remove atom 43540 need remove atom 43551 need remove atom 43552 need remove atom 43563 need remove atom 43564 need remove atom 43575 need remove atom 43576 need remove atom 43586 need remove atom 43587 need remove atom 43588 need remove atom 43592 need remove atom 43598 need remove atom 43599 need remove atom 43600 need remove atom 43604 need remove atom 43610 need remove atom 43611 need remove atom 43612 need remove atom 43616 need remove atom 43622 need remove atom 43623 need remove atom 43624 need remove atom 43628 need remove atom 43634 need remove atom 43635 need remove atom 43636 need remove atom 43640 need remove atom 43646 need remove atom 43647 need remove atom 43648 need remove atom 43652 need remove atom 43658 need remove atom 43659 need remove atom 43660 need remove atom 43664 need remove atom 43670 need remove atom 43671 need remove atom 43672 need remove atom 43676 need remove atom 43682 need remove atom 43683 need remove atom 43684 need remove atom 43688 need remove atom 43694 need remove atom 43695 need remove atom 43696 need remove atom 43700 need remove atom 43706 need remove atom 43707 need remove atom 43708 need remove atom 43712 need remove atom 43718 need remove atom 43719 need remove atom 43720 need remove atom 43724 need remove atom 43730 need remove atom 43731 need remove atom 43732 need remove atom 43736 need remove atom 43742 need remove atom 43743 need remove atom 43744 need remove atom 43748 need remove atom 43754 need remove atom 43755 need remove atom 43756 need remove atom 43760 need remove atom 43766 need remove atom 43767 need remove atom 43768 need remove atom 43772 need remove atom 43778 need remove atom 43779 need remove atom 43780 need remove atom 43784 need remove atom 43790 need remove atom 43791 need remove atom 43792 need remove atom 43796 need remove atom 43802 need remove atom 43803 need remove atom 43804 need remove atom 43808 need remove atom 43814 need remove atom 43815 need remove atom 43816 need remove atom 43820 need remove atom 43826 need remove atom 43827 need remove atom 43828 need remove atom 43832 need remove atom 43838 need remove atom 43839 need remove atom 43840 need remove atom 43844 need remove atom 43850 need remove atom 43851 need remove atom 43852 need remove atom 43856 need remove atom 43862 need remove atom 43863 need remove atom 43864 need remove atom 43868 need remove atom 43874 need remove atom 43875 need remove atom 43876 need remove atom 43880 need remove atom 43886 need remove atom 43887 need remove atom 43888 need remove atom 43892 need remove atom 43898 need remove atom 43899 need remove atom 43900 need remove atom 43904 need remove atom 43910 need remove atom 43911 need remove atom 43912 need remove atom 43916 need remove atom 43922 need remove atom 43923 need remove atom 43924 need remove atom 43928 need remove atom 43934 need remove atom 43935 need remove atom 43936 need remove atom 43940 need remove atom 43946 need remove atom 43947 need remove atom 43948 need remove atom 43952 need remove atom 43958 need remove atom 43959 need remove atom 43960 need remove atom 43964 need remove atom 43970 need remove atom 43971 need remove atom 43972 need remove atom 43976 need remove atom 43982 need remove atom 43983 need remove atom 43984 need remove atom 43988 need remove atom 43994 need remove atom 43995 need remove atom 43996 need remove atom 44000 need remove atom 44006 need remove atom 44007 need remove atom 44008 need remove atom 44012 need remove atom 44018 need remove atom 44019 need remove atom 44020 need remove atom 44024 need remove atom 44030 need remove atom 44031 need remove atom 44032 need remove atom 44036 need remove atom 44042 need remove atom 44043 need remove atom 44044 need remove atom 44048 need remove atom 44054 need remove atom 44055 need remove atom 44056 need remove atom 44060 need remove atom 44066 need remove atom 44067 need remove atom 44068 need remove atom 44072 need remove atom 44078 need remove atom 44079 need remove atom 44080 need remove atom 44084 need remove atom 44090 need remove atom 44091 need remove atom 44092 need remove atom 44096 need remove atom 44102 need remove atom 44103 need remove atom 44104 need remove atom 44108 need remove atom 44114 need remove atom 44115 need remove atom 44116 need remove atom 44120 need remove atom 44126 need remove atom 44127 need remove atom 44128 need remove atom 44132 need remove atom 44138 need remove atom 44139 need remove atom 44140 need remove atom 44144 need remove atom 44150 need remove atom 44151 need remove atom 44152 need remove atom 44156 need remove atom 44162 need remove atom 44163 need remove atom 44164 need remove atom 44168 need remove atom 44174 need remove atom 44175 need remove atom 44176 need remove atom 44180 need remove atom 44186 need remove atom 44187 need remove atom 44188 need remove 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minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1878704836e-01 1.6348019462e-01 1.4021903638e-01 dub= -5.4401636946e-01 1.6348367194e-01 -1.4271112905e-01 duc= 5.1878853987e-01 -1.6554632599e-01 1.4021948726e-01 [I] overall tilt ux= -1.0628034178e+00 3.4773196084e-06 -2.8293016543e-01 uy= 1.4915061616e-06 -3.2902652062e-01 4.5088361100e-07 [I] storedr[0]= -1.2613914796e-02 -1.0313270242e-03 -1.2458208925e-03 [I] originally 89376 atoms [I] insert 0 atoms [I] now 89376 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 89376 atoms [I] remove 784 atoms [I] now 88592 atoms [I] NP=88592 n=88592 [I] ASSIGN finalcnfile = dipole_4.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 19:21:12 2023 CPU time spent: 56.303864 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 = Mon Jun 12 19:42:59 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 21 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 55 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 9 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=124740 [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) = 0.015873015873016 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.018518518518519 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 1.5873015873e-02 0.0000000000e+00 1.8518518519e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=1.615193e+02 pxpb=0.000000e+00 pypb=2.442347e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 60914 need remove atom 60915 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need remove atom 63788 need remove atom 63794 need remove atom 63795 need remove atom 63796 need remove atom 63800 need remove atom 63806 need remove atom 63807 need remove atom 63808 need remove atom 63812 need remove atom 63818 need remove atom 63819 need remove atom 63820 need remove atom 63824 need remove atom 63830 need remove atom 63836 need remove atom 63842 need remove atom 63848 need remove atom 63854 need remove atom 63860 need remove atom 63866 need remove atom 63872 need remove atom 63878 need remove atom 63884 need remove atom 63890 need remove atom 63896 need remove atom 63902 need remove atom 63908 need remove atom 63914 need remove atom 63920 need remove atom 63926 need remove atom 63932 [I] need removenum=990 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.2081507819e-01 1.6278866469e-01 1.4117673083e-01 dub= -5.4626084851e-01 1.6279238778e-01 -1.4381099442e-01 duc= 5.2081655167e-01 -1.6490489399e-01 1.4117718332e-01 [I] overall tilt ux= -1.0670759267e+00 3.7230926022e-06 -2.8498772524e-01 uy= 1.4734837137e-06 -3.2769355868e-01 4.5249424704e-07 [I] storedr[0]= -1.2722148418e-02 -1.0562531035e-03 -1.3169055494e-03 [I] originally 124740 atoms [I] insert 0 atoms [I] now 124740 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 124740 atoms [I] remove 990 atoms [I] now 123750 atoms [I] NP=123750 n=123750 [I] ASSIGN finalcnfile = dipole_5.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 19:44:24 2023 CPU time spent: 78.656292 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 = Mon Jun 12 20:04:52 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 23 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 60 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 10 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=165600 [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) = 0.014492753623188 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.016666666666667 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 1.4492753623e-02 0.0000000000e+00 1.6666666667e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=1.769021e+02 pxpb=0.000000e+00 pypb=2.664378e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 81003 need remove atom 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remove atom 84590 need remove atom 84591 need remove atom 84592 need remove atom 84596 need remove atom 84602 need remove atom 84608 need remove atom 84614 need remove atom 84620 need remove atom 84626 need remove atom 84632 need remove atom 84638 need remove atom 84644 need remove atom 84650 need remove atom 84656 need remove atom 84662 need remove atom 84668 need remove atom 84674 need remove atom 84680 need remove atom 84686 need remove atom 84692 need remove atom 84698 need remove atom 84704 need remove atom 84710 need remove atom 84716 [I] need removenum=1200 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.2029759389e-01 1.6296624721e-01 1.4093142279e-01 dub= -5.4568913509e-01 1.6296990829e-01 -1.4352933400e-01 duc= 5.2029907204e-01 -1.6506962727e-01 1.4093187489e-01 [I] overall tilt ux= -1.0659867290e+00 3.6610790828e-06 -2.8446075679e-01 uy= 1.4781544579e-06 -3.2803587447e-01 4.5209775831e-07 [I] storedr[0]= -1.2695031522e-02 -1.0498594902e-03 -1.2987295522e-03 [I] originally 165600 atoms [I] insert 0 atoms [I] now 165600 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 165600 atoms [I] remove 1200 atoms [I] now 164400 atoms [I] NP=164400 n=164400 [I] ASSIGN finalcnfile = dipole_5.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 20:06:48 2023 CPU time spent: 106.164578 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 = Mon Jun 12 20:39:23 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 25 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 65 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 11 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=214500 [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) = 0.013333333333333 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.015151515151515 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 1.3333333333e-02 0.0000000000e+00 1.5151515152e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=1.922849e+02 pxpb=0.000000e+00 pypb=2.886410e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 105075 need remove atom 105076 need remove atom 105087 need remove atom 105088 need remove atom 105099 need remove atom 105100 need remove atom 105111 need remove atom 105112 need remove atom 105123 need remove atom 105124 need remove atom 105135 need remove atom 105136 need remove atom 105147 need remove atom 105148 need remove atom 105159 need remove atom 105160 need remove atom 105171 need remove atom 105172 need remove atom 105183 need remove atom 105184 need remove atom 105195 need remove atom 105196 need remove atom 105206 need remove atom 105207 need remove atom 105208 need remove atom 105212 need remove atom 105218 need remove atom 105219 need remove atom 105220 need remove atom 105224 need remove atom 105230 need remove atom 105231 need remove atom 105232 need remove atom 105236 need remove atom 105242 need remove atom 105243 need remove atom 105244 need remove atom 105248 need remove atom 105254 need remove atom 105255 need remove atom 105256 need remove atom 105260 need remove atom 105266 need 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109372 need remove atom 109376 need remove atom 109382 need remove atom 109383 need remove atom 109384 need remove atom 109388 need remove atom 109394 need remove atom 109395 need remove atom 109396 need remove atom 109400 need remove atom 109406 need remove atom 109407 need remove atom 109408 need remove atom 109412 need remove atom 109418 need remove atom 109419 need remove atom 109420 need remove atom 109424 [I] need removenum=1430 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1985967362e-01 1.6311592386e-01 1.4072433496e-01 dub= -5.4520478427e-01 1.6311953208e-01 -1.4329152279e-01 duc= 5.1986115569e-01 -1.6520846565e-01 1.4072478672e-01 [I] overall tilt ux= -1.0650644579e+00 3.6082214774e-06 -2.8401585775e-01 uy= 1.4820685457e-06 -3.2832438950e-01 4.5175440999e-07 [I] storedr[0]= -1.2671814292e-02 -1.0444667826e-03 -1.2833680363e-03 [I] originally 214500 atoms [I] insert 0 atoms [I] now 214500 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 214500 atoms [I] remove 1430 atoms [I] now 213070 atoms [I] NP=213070 n=213070 [I] ASSIGN finalcnfile = dipole_6.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_6.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_6.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 20:41:50 2023 CPU time spent: 134.669174 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 = Mon Jun 12 21:20:31 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1399998813868 [I] ASSIGN makecnspec = 1 [I] ASSIGN makecnspec(1) = 1 [I] ASSIGN makecnspec(2) = 2 [I] ASSIGN makecnspec(3) = 27 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 70 [I] ASSIGN makecnspec(8) = 1 [I] ASSIGN makecnspec(9) = 1 [I] ASSIGN makecnspec(10) = -1 [I] ASSIGN makecnspec(11) = 12 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 1 -1 1 1 1 1 2 0 -1]; basis=[ 0 0 0.5 0 0 0 0 0 0 1 0.333333 0 0.166667 0 2 0.166667 0.5 0.833333 0 3 0.166667 0.5 0.333333 0 4 0.5 0.5 0.5 0 5 0.5 0.5 0 0 6 0.833333 0.5 0.166667 0 7 0.333333 0 0.666667 0 8 0.666667 0 0.833333 0 9 0.666667 0 0.333333 0 10 0.833333 0.5 0.666667 0 11 ]; [I] makecn: _NP=272160 [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) = 0.012345679012346 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.013888888888889 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.27960454248715 [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= 1.2345679012e-02 0.0000000000e+00 1.3888888889e-02 b= 2.5637991673e+00 0.0000000000e+00 9.0643988839e-01 [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=2.5637991672658 by=0 pxpa=2.076677e+02 pxpb=0.000000e+00 pypb=3.108441e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 133634 need remove atom 133635 need remove atom 133636 need remove atom 133640 need remove atom 133646 need remove atom 133647 need remove atom 133648 need remove atom 133652 need remove atom 133658 need remove atom 133659 need remove atom 133660 need remove atom 133664 need remove atom 133670 need remove atom 133671 need remove atom 133672 need remove atom 133676 need remove atom 133682 need remove atom 133683 need remove atom 133684 need remove atom 133688 need remove atom 133694 need remove atom 133695 need remove atom 133696 need remove atom 133700 need remove atom 133706 need remove atom 133707 need remove atom 133708 need remove atom 133712 need remove atom 133718 need remove atom 133719 need remove atom 133720 need remove atom 133724 need remove atom 133730 need remove atom 133731 need remove atom 133732 need remove atom 133736 need remove atom 133742 need remove atom 133743 need remove atom 133744 need remove atom 133748 need remove atom 133754 need remove atom 133755 need remove atom 133756 need remove atom 133760 need remove atom 133766 need remove atom 133767 need remove atom 133768 need remove atom 133772 need remove atom 133778 need remove atom 133779 need remove atom 133780 need remove atom 133784 need remove atom 133790 need remove atom 133791 need remove atom 133792 need remove atom 133796 need remove atom 133802 need remove atom 133803 need remove atom 133804 need remove atom 133808 need remove atom 133814 need remove atom 133815 need remove atom 133816 need remove atom 133820 need remove atom 133826 need remove atom 133827 need remove atom 133828 need remove atom 133832 need remove atom 133838 need remove atom 133839 need remove atom 133840 need remove atom 133844 need remove atom 133850 need remove atom 133851 need remove atom 133852 need remove atom 133856 need remove atom 133862 need remove atom 133863 need remove atom 133864 need remove atom 133868 need remove atom 133874 need remove atom 133875 need remove atom 133876 need remove atom 133880 need remove atom 133886 need remove atom 133887 need remove atom 133888 need remove atom 133892 need remove atom 133898 need remove atom 133899 need remove atom 133900 need remove atom 133904 need remove atom 133910 need remove atom 133911 need remove atom 133912 need remove atom 133916 need remove atom 133922 need remove atom 133923 need remove atom 133924 need remove atom 133928 need remove atom 133934 need remove atom 133935 need remove atom 133936 need remove atom 133940 need remove atom 133946 need remove atom 133947 need remove atom 133948 need remove atom 133952 need remove atom 133958 need remove atom 133959 need remove atom 133960 need remove atom 133964 need remove atom 133970 need remove atom 133971 need remove atom 133972 need remove atom 133976 need remove atom 133982 need remove atom 133983 need remove atom 133984 need remove atom 133988 need remove atom 133994 need remove atom 133995 need remove atom 133996 need remove atom 134000 need remove atom 134006 need remove atom 134007 need remove atom 134008 need remove atom 134012 need remove atom 134018 need remove atom 134019 need remove atom 134020 need remove atom 134024 need remove atom 134030 need remove atom 134031 need remove atom 134032 need remove atom 134036 need remove atom 134042 need remove atom 134043 need remove atom 134044 need remove atom 134048 need remove atom 134054 need remove atom 134055 need remove atom 134056 need remove atom 134060 need remove atom 134066 need remove atom 134067 need remove atom 134068 need remove atom 134072 need remove atom 134078 need remove atom 134079 need remove atom 134080 need remove atom 134084 need remove atom 134090 need remove atom 134091 need remove atom 134092 need remove atom 134096 need remove atom 134102 need remove atom 134103 need remove atom 134104 need remove atom 134108 need remove atom 134114 need remove atom 134115 need remove atom 134116 need remove atom 134120 need remove atom 134126 need remove atom 134127 need remove atom 134128 need remove atom 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remove atom 134259 need remove atom 134260 need remove atom 134264 need remove atom 134270 need remove atom 134271 need remove atom 134272 need remove atom 134276 need remove atom 134282 need remove atom 134283 need remove atom 134284 need remove atom 134288 need remove atom 134294 need remove atom 134295 need remove atom 134296 need remove atom 134300 need remove atom 134306 need remove atom 134307 need remove atom 134308 need remove atom 134312 need remove atom 134318 need remove atom 134319 need remove atom 134320 need remove atom 134324 need remove atom 134330 need remove atom 134331 need remove atom 134332 need remove atom 134336 need remove atom 134342 need remove atom 134343 need remove atom 134344 need remove atom 134348 need remove atom 134354 need remove atom 134355 need remove atom 134356 need remove atom 134360 need remove atom 134366 need remove atom 134367 need remove atom 134368 need remove atom 134372 need remove atom 134378 need remove atom 134379 need remove atom 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remove atom 134756 need remove atom 134762 need remove atom 134763 need remove atom 134764 need remove atom 134768 need remove atom 134774 need remove atom 134775 need remove atom 134776 need remove atom 134780 need remove atom 134786 need remove atom 134787 need remove atom 134788 need remove atom 134792 need remove atom 134798 need remove atom 134799 need remove atom 134800 need remove atom 134804 need remove atom 134810 need remove atom 134811 need remove atom 134812 need remove atom 134816 need remove atom 134822 need remove atom 134823 need remove atom 134824 need remove atom 134828 need remove atom 134834 need remove atom 134835 need remove atom 134836 need remove atom 134840 need remove atom 134846 need remove atom 134847 need remove atom 134848 need remove atom 134852 need remove atom 134858 need remove atom 134859 need remove atom 134860 need remove atom 134864 need remove atom 134870 need remove atom 134871 need remove atom 134872 need remove atom 134876 need remove atom 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remove atom 135004 need remove atom 135008 need remove atom 135014 need remove atom 135015 need remove atom 135016 need remove atom 135020 need remove atom 135026 need remove atom 135027 need remove atom 135028 need remove atom 135032 need remove atom 135038 need remove atom 135039 need remove atom 135040 need remove atom 135044 need remove atom 135050 need remove atom 135051 need remove atom 135052 need remove atom 135056 need remove atom 135062 need remove atom 135063 need remove atom 135064 need remove atom 135068 need remove atom 135074 need remove atom 135075 need remove atom 135076 need remove atom 135080 need remove atom 135086 need remove atom 135087 need remove atom 135088 need remove atom 135092 need remove atom 135098 need remove atom 135099 need remove atom 135100 need remove atom 135104 need remove atom 135110 need remove atom 135111 need remove atom 135112 need remove atom 135116 need remove atom 135122 need remove atom 135123 need remove atom 135124 need remove atom 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remove atom 135255 need remove atom 135256 need remove atom 135260 need remove atom 135266 need remove atom 135267 need remove atom 135268 need remove atom 135272 need remove atom 135278 need remove atom 135279 need remove atom 135280 need remove atom 135284 need remove atom 135290 need remove atom 135291 need remove atom 135292 need remove atom 135296 need remove atom 135302 need remove atom 135303 need remove atom 135304 need remove atom 135308 need remove atom 135314 need remove atom 135315 need remove atom 135316 need remove atom 135320 need remove atom 135326 need remove atom 135327 need remove atom 135328 need remove atom 135332 need remove atom 135338 need remove atom 135339 need remove atom 135340 need remove atom 135344 need remove atom 135350 need remove atom 135351 need remove atom 135352 need remove atom 135356 need remove atom 135362 need remove atom 135363 need remove atom 135364 need remove atom 135368 need remove atom 135374 need remove atom 135375 need remove atom 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remove atom 135506 need remove atom 135507 need remove atom 135508 need remove atom 135512 need remove atom 135518 need remove atom 135519 need remove atom 135520 need remove atom 135524 need remove atom 135530 need remove atom 135531 need remove atom 135532 need remove atom 135536 need remove atom 135542 need remove atom 135543 need remove atom 135544 need remove atom 135548 need remove atom 135554 need remove atom 135555 need remove atom 135556 need remove atom 135560 need remove atom 135566 need remove atom 135567 need remove atom 135568 need remove atom 135572 need remove atom 135578 need remove atom 135579 need remove atom 135580 need remove atom 135584 need remove atom 135590 need remove atom 135591 need remove atom 135592 need remove atom 135596 need remove atom 135602 need remove atom 135603 need remove atom 135604 need remove atom 135608 need remove atom 135614 need remove atom 135615 need remove atom 135616 need remove atom 135620 need remove atom 135626 need remove atom 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remove atom 136000 need remove atom 136004 need remove atom 136010 need remove atom 136011 need remove atom 136012 need remove atom 136016 need remove atom 136022 need remove atom 136023 need remove atom 136024 need remove atom 136028 need remove atom 136034 need remove atom 136035 need remove atom 136036 need remove atom 136040 need remove atom 136046 need remove atom 136047 need remove atom 136048 need remove atom 136052 need remove atom 136058 need remove atom 136059 need remove atom 136060 need remove atom 136064 need remove atom 136070 need remove atom 136071 need remove atom 136072 need remove atom 136076 need remove atom 136082 need remove atom 136083 need remove atom 136084 need remove atom 136088 need remove atom 136094 need remove atom 136095 need remove atom 136096 need remove atom 136100 need remove atom 136106 need remove atom 136107 need remove atom 136108 need remove atom 136112 need remove atom 136118 need remove atom 136119 need remove atom 136120 need remove atom 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remove atom 136502 need remove atom 136503 need remove atom 136504 need remove atom 136508 need remove atom 136514 need remove atom 136515 need remove atom 136516 need remove atom 136520 need remove atom 136526 need remove atom 136527 need remove atom 136528 need remove atom 136532 need remove atom 136538 need remove atom 136539 need remove atom 136540 need remove atom 136544 need remove atom 136550 need remove atom 136551 need remove atom 136552 need remove atom 136556 need remove atom 136562 need remove atom 136563 need remove atom 136564 need remove atom 136568 need remove atom 136574 need remove atom 136575 need remove atom 136576 need remove atom 136580 need remove atom 136586 need remove atom 136587 need remove atom 136588 need remove atom 136592 need remove atom 136598 need remove atom 136599 need remove atom 136600 need remove atom 136604 need remove atom 136610 need remove atom 136611 need remove atom 136612 need remove atom 136616 need remove atom 136622 need remove atom 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138615 need remove atom 138616 need remove atom 138620 need remove atom 138626 need remove atom 138627 need remove atom 138628 need remove atom 138632 need remove atom 138638 need remove atom 138639 need remove atom 138640 need remove atom 138644 need remove atom 138650 need remove atom 138651 need remove atom 138652 need remove atom 138656 need remove atom 138662 need remove atom 138663 need remove atom 138664 need remove atom 138668 [I] need removenum=1680 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.1948428041e-01 1.6324378876e-01 1.4054718107e-01 dub= -5.4478919941e-01 1.6324735140e-01 -1.4308806172e-01 duc= 5.1948576581e-01 -1.6532706553e-01 1.4054763253e-01 [I] overall tilt ux= -1.0642734798e+00 3.5626385864e-06 -2.8363524280e-01 uy= 1.4853956333e-06 -3.2857085429e-01 4.5145443842e-07 [I] storedr[0]= -1.2651716804e-02 -1.0398570642e-03 -1.2702145979e-03 [I] originally 272160 atoms [I] insert 0 atoms [I] now 272160 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 272160 atoms [I] remove 1680 atoms [I] now 270480 atoms [I] NP=270480 n=270480 [I] ASSIGN finalcnfile = dipole_6.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_6.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_6.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Mon Jun 12 21:23:37 2023 CPU time spent: 171.134491 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":16715.40,"usertime":48185.67,"systime":432.82,"memmax":210364,"memavg":0}