QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-bwaters2' [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [I] RUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 18:13:47 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 2 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 12 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=1632 [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) = 0.073529411764706 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.029411764705882 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 7.3529411765e-02 0.0000000000e+00 2.9411764706e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=3.691226e+01 pxpb=0.000000e+00 pypb=5.371522e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 250 need remove atom 265 need remove atom 271 need remove atom 318 need remove atom 326 need remove atom 333 need remove atom 337 need remove atom 338 need remove atom 339 need remove atom 386 need remove atom 394 need remove atom 401 need remove atom 405 need remove atom 406 need remove atom 407 need remove atom 454 need remove atom 462 need remove atom 469 need remove atom 473 need remove atom 474 need remove atom 475 need remove atom 522 need remove atom 530 need remove atom 537 need remove atom 541 need remove atom 542 need remove atom 543 need remove atom 590 need remove atom 598 need remove atom 605 need remove atom 609 need remove atom 610 need remove atom 611 need remove atom 666 need remove atom 677 need remove atom 678 need remove atom 1023 need remove atom 1035 need remove atom 1088 need remove atom 1089 need remove atom 1091 need remove atom 1103 need remove atom 1156 need remove atom 1157 need remove atom 1159 need remove atom 1171 need remove atom 1224 need remove atom 1225 need remove atom 1227 need remove atom 1239 need remove atom 1292 need remove atom 1293 need remove atom 1295 need remove atom 1307 need remove atom 1360 need remove atom 1361 need remove atom 1363 need remove atom 1375 need remove atom 1428 need remove atom 1429 [I] need removenum=60 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.4626850959e-01 1.7365984380e-01 5.8769914068e-02 dub= -5.7265627593e-01 1.7366316574e-01 -5.9734664553e-02 duc= 5.4627011656e-01 -1.7577191885e-01 5.8770103845e-02 [I] overall tilt ux= -1.1189247855e+00 3.3219444423e-06 -1.1850457862e-01 uy= 1.6069740661e-06 -3.4943176265e-01 1.8977706468e-07 [I] storedr[0]= -1.6143857211e-02 -1.0570443264e-03 5.4680405520e-04 [I] originally 1632 atoms [I] insert 0 atoms [I] now 1632 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1632 atoms [I] remove 60 atoms [I] now 1572 atoms [I] NP=1572 n=1572 [I] ASSIGN finalcnfile = dipole_1.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 18:13:48 2023 CPU time spent: 0.153235 s [c021:06448] *** Process received signal *** [c021:06448] Signal: Segmentation fault (11) [c021:06448] Signal code: Address not mapped (1) [c021:06448] Failing at address: 0x30 [c021:06448] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7f19cf79c090] [c021:06448] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7f19cc00b1c2] [c021:06448] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7f19ced27854] [c021:06448] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7f19cfb95905] [c021:06448] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7f19cfbead93] [c021:06448] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7f19cfbeb061] [c021:06448] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7f19c73d7dae] [c021:06448] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7f19cfbadb10] [c021:06448] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7f19d03db864] [c021:06448] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7f19d03da417] [c021:06448] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7f19d0182dba] [c021:06448] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7f19d0096d0e] [c021:06448] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7f19d009c300] [c021:06448] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7f19d009ccd9] [c021:06448] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7f19d025cd5b] [c021:06448] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7f19d025da78] [c021:06448] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7f19d025483e] [c021:06448] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7f19d009c138] [c021:06448] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7f19d009c54e] [c021:06448] [19] lmp(+0x136e)[0x5649c5f1f36e] [c021:06448] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f19cf77d083] [c021:06448] [21] lmp(+0x13ee)[0x5649c5f1f3ee] [c021:06448] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c021 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 18:14:04 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 2 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 12 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=1632 [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) = 0.073529411764706 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.029411764705882 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 7.3529411765e-02 0.0000000000e+00 2.9411764706e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=3.691226e+01 pxpb=0.000000e+00 pypb=5.371522e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 250 need remove atom 265 need remove atom 271 need remove atom 318 need remove atom 326 need remove atom 333 need remove atom 337 need remove atom 338 need remove atom 339 need remove atom 386 need remove atom 394 need remove atom 401 need remove atom 405 need remove atom 406 need remove atom 407 need remove atom 454 need remove atom 462 need remove atom 469 need remove atom 473 need remove atom 474 need remove atom 475 need remove atom 522 need remove atom 530 need remove atom 537 need remove atom 541 need remove atom 542 need remove atom 543 need remove atom 590 need remove atom 598 need remove atom 605 need remove atom 609 need remove atom 610 need remove atom 611 need remove atom 666 need remove atom 677 need remove atom 678 need remove atom 1023 need remove atom 1035 need remove atom 1088 need remove atom 1089 need remove atom 1091 need remove atom 1103 need remove atom 1156 need remove atom 1157 need remove atom 1159 need remove atom 1171 need remove atom 1224 need remove atom 1225 need remove atom 1227 need remove atom 1239 need remove atom 1292 need remove atom 1293 need remove atom 1295 need remove atom 1307 need remove atom 1360 need remove atom 1361 need remove atom 1363 need remove atom 1375 need remove atom 1428 need remove atom 1429 [I] need removenum=60 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.4626850959e-01 1.7365984380e-01 5.8769914068e-02 dub= -5.7265627593e-01 1.7366316574e-01 -5.9734664553e-02 duc= 5.4627011656e-01 -1.7577191885e-01 5.8770103845e-02 [I] overall tilt ux= -1.1189247855e+00 3.3219444423e-06 -1.1850457862e-01 uy= 1.6069740661e-06 -3.4943176265e-01 1.8977706468e-07 [I] storedr[0]= -1.6143857211e-02 -1.0570443264e-03 5.4680405520e-04 [I] originally 1632 atoms [I] insert 0 atoms [I] now 1632 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 1632 atoms [I] remove 60 atoms [I] now 1572 atoms [I] NP=1572 n=1572 [I] ASSIGN finalcnfile = dipole_1.1.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.1.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.1.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 18:14:05 2023 CPU time spent: 0.149650 s [c021:13091] *** Process received signal *** [c021:13091] Signal: Segmentation fault (11) [c021:13091] Signal code: Address not mapped (1) [c021:13091] Failing at address: 0x30 [c021:13091] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7ffb81134090] [c021:13091] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7ffb7cffc1c2] [c021:13091] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7ffb806bf854] [c021:13091] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7ffb8152d905] [c021:13091] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7ffb81582d93] [c021:13091] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7ffb81583061] [c021:13091] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7ffb7cd73dae] [c021:13091] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7ffb81545b10] [c021:13091] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7ffb81d73864] [c021:13091] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7ffb81d72417] [c021:13091] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7ffb81b1adba] [c021:13091] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7ffb81a2ed0e] [c021:13091] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7ffb81a34300] [c021:13091] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7ffb81a34cd9] [c021:13091] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7ffb81bf4d5b] [c021:13091] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7ffb81bf5a78] [c021:13091] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7ffb81bec83e] [c021:13091] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7ffb81a34138] [c021:13091] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7ffb81a3454e] [c021:13091] [19] lmp(+0x136e)[0x55b446daa36e] [c021:13091] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7ffb81115083] [c021:13091] [21] lmp(+0x13ee)[0x55b446daa3ee] [c021:13091] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c021 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 18:14:19 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 19 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=3876 [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) = 0.049019607843137 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.029411764705882 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 4.9019607843e-02 0.0000000000e+00 2.9411764706e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=5.536839e+01 pxpb=0.000000e+00 pypb=8.504911e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1645 need remove atom 1652 need remove atom 1654 need remove atom 1655 need remove atom 1662 need remove atom 1663 need remove atom 1670 need remove atom 1671 need remove atom 1679 need remove atom 1681 need remove atom 1713 need remove atom 1720 need remove atom 1722 need remove atom 1723 need remove atom 1730 need remove atom 1731 need remove atom 1738 need remove atom 1739 need remove atom 1747 need remove atom 1749 need remove atom 1781 need remove atom 1788 need remove atom 1790 need remove atom 1791 need remove atom 1798 need remove atom 1799 need remove atom 1806 need remove atom 1807 need remove atom 1815 need remove atom 1817 need remove atom 1849 need remove atom 1856 need remove atom 1858 need remove atom 1859 need remove atom 1866 need remove atom 1867 need remove atom 1874 need remove atom 1875 need remove atom 1883 need remove atom 1885 need remove atom 1917 need remove atom 1924 need remove atom 1926 need remove atom 1927 need remove atom 1934 need remove atom 1935 need remove atom 1942 need remove atom 1943 need remove atom 1951 need remove atom 1953 need remove atom 1985 need remove atom 1992 need remove atom 1994 need remove atom 1995 need remove atom 2002 need remove atom 2003 need remove atom 2010 need remove atom 2011 need remove atom 2019 need remove atom 2021 need remove atom 2053 need remove atom 2060 need remove atom 2062 need remove atom 2063 need remove atom 2070 need remove atom 2071 need remove atom 2078 need remove atom 2079 need remove atom 2087 need remove atom 2089 need remove atom 2121 need remove atom 2128 need remove atom 2130 need remove atom 2131 need remove atom 2138 need remove atom 2139 need remove atom 2146 need remove atom 2147 need remove atom 2155 need remove atom 2157 need remove atom 2189 need remove atom 2196 need remove atom 2198 need remove atom 2199 need remove atom 2206 need remove atom 2207 need remove atom 2214 need remove atom 2215 need remove atom 2223 need remove atom 2225 need remove atom 2257 need remove atom 2274 need remove atom 2275 need remove atom 2291 need remove atom 2293 [I] need removenum=95 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5381395369e-01 1.7107979624e-01 6.0192749819e-02 dub= -5.8101539229e-01 1.7108403994e-01 -6.1368909892e-02 duc= 5.5381549408e-01 -1.7337783753e-01 6.0192942047e-02 [I] overall tilt ux= -1.1348293460e+00 4.2437065219e-06 -1.2156165971e-01 uy= 1.5403943056e-06 -3.4445763377e-01 1.9222863558e-07 [I] storedr[0]= -1.5807573571e-02 -1.1488707301e-03 2.5442853394e-05 [I] originally 3876 atoms [I] insert 0 atoms [I] now 3876 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3876 atoms [I] remove 95 atoms [I] now 3781 atoms [I] NP=3781 n=3781 [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 = Tue Sep 19 18:14:19 2023 CPU time spent: 0.350871 s [c021:23242] *** Process received signal *** [c021:23242] Signal: Segmentation fault (11) [c021:23242] Signal code: Address not mapped (1) [c021:23242] Failing at address: 0x30 [c021:23242] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7fefcb5cf090] [c021:23242] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7fefc34971c2] [c021:23242] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7fefcab5a854] [c021:23242] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7fefcb9c8905] [c021:23242] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7fefcba1dd93] [c021:23242] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7fefcba1e061] [c021:23242] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7fefc320edae] [c021:23242] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7fefcb9e0b10] [c021:23242] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7fefcc20e864] [c021:23242] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7fefcc20d417] [c021:23242] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7fefcbfb5dba] [c021:23242] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7fefcbec9d0e] [c021:23242] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7fefcbecf300] [c021:23242] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7fefcbecfcd9] [c021:23242] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7fefcc08fd5b] [c021:23242] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7fefcc090a78] [c021:23242] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7fefcc08783e] [c021:23242] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7fefcbecf138] [c021:23242] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7fefcbecf54e] [c021:23242] [19] lmp(+0x136e)[0x558fa765236e] [c021:23242] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fefcb5b0083] [c021:23242] [21] lmp(+0x13ee)[0x558fa76523ee] [c021:23242] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c021 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 18:14:37 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 19 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 1 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=3876 [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) = 0.049019607843137 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.029411764705882 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 4.9019607843e-02 0.0000000000e+00 2.9411764706e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=5.536839e+01 pxpb=0.000000e+00 pypb=8.504911e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 1645 need remove atom 1652 need remove atom 1654 need remove atom 1655 need remove atom 1662 need remove atom 1663 need remove atom 1670 need remove atom 1671 need remove atom 1679 need remove atom 1681 need remove atom 1713 need remove atom 1720 need remove atom 1722 need remove atom 1723 need remove atom 1730 need remove atom 1731 need remove atom 1738 need remove atom 1739 need remove atom 1747 need remove atom 1749 need remove atom 1781 need remove atom 1788 need remove atom 1790 need remove atom 1791 need remove atom 1798 need remove atom 1799 need remove atom 1806 need remove atom 1807 need remove atom 1815 need remove atom 1817 need remove atom 1849 need remove atom 1856 need remove atom 1858 need remove atom 1859 need remove atom 1866 need remove atom 1867 need remove atom 1874 need remove atom 1875 need remove atom 1883 need remove atom 1885 need remove atom 1917 need remove atom 1924 need remove atom 1926 need remove atom 1927 need remove atom 1934 need remove atom 1935 need remove atom 1942 need remove atom 1943 need remove atom 1951 need remove atom 1953 need remove atom 1985 need remove atom 1992 need remove atom 1994 need remove atom 1995 need remove atom 2002 need remove atom 2003 need remove atom 2010 need remove atom 2011 need remove atom 2019 need remove atom 2021 need remove atom 2053 need remove atom 2060 need remove atom 2062 need remove atom 2063 need remove atom 2070 need remove atom 2071 need remove atom 2078 need remove atom 2079 need remove atom 2087 need remove atom 2089 need remove atom 2121 need remove atom 2128 need remove atom 2130 need remove atom 2131 need remove atom 2138 need remove atom 2139 need remove atom 2146 need remove atom 2147 need remove atom 2155 need remove atom 2157 need remove atom 2189 need remove atom 2196 need remove atom 2198 need remove atom 2199 need remove atom 2206 need remove atom 2207 need remove atom 2214 need remove atom 2215 need remove atom 2223 need remove atom 2225 need remove atom 2257 need remove atom 2274 need remove atom 2275 need remove atom 2291 need remove atom 2293 [I] need removenum=95 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5381395369e-01 1.7107979624e-01 6.0192749819e-02 dub= -5.8101539229e-01 1.7108403994e-01 -6.1368909892e-02 duc= 5.5381549408e-01 -1.7337783753e-01 6.0192942047e-02 [I] overall tilt ux= -1.1348293460e+00 4.2437065219e-06 -1.2156165971e-01 uy= 1.5403943056e-06 -3.4445763377e-01 1.9222863558e-07 [I] storedr[0]= -1.5807573571e-02 -1.1488707301e-03 2.5442853394e-05 [I] originally 3876 atoms [I] insert 0 atoms [I] now 3876 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 3876 atoms [I] remove 95 atoms [I] now 3781 atoms [I] NP=3781 n=3781 [I] ASSIGN finalcnfile = dipole_1.3.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.3.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.3.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 18:14:38 2023 CPU time spent: 0.349651 s [c021:31466] *** Process received signal *** [c021:31466] Signal: Segmentation fault (11) [c021:31466] Signal code: Address not mapped (1) [c021:31466] Failing at address: 0x30 [c021:31466] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7f4967a0c090] [c021:31466] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7f495f8d41c2] [c021:31466] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7f4966f97854] [c021:31466] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7f4967e05905] [c021:31466] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7f4967e5ad93] [c021:31466] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7f4967e5b061] [c021:31466] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7f495f64bdae] [c021:31466] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7f4967e1db10] [c021:31466] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7f496864b864] [c021:31466] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7f496864a417] [c021:31466] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7f49683f2dba] [c021:31466] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7f4968306d0e] [c021:31466] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7f496830c300] [c021:31466] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7f496830ccd9] [c021:31466] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7f49684ccd5b] [c021:31466] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7f49684cda78] [c021:31466] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7f49684c483e] [c021:31466] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7f496830c138] [c021:31466] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7f496830c54e] [c021:31466] [19] lmp(+0x136e)[0x56086cb6836e] [c021:31466] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f49679ed083] [c021:31466] [21] lmp(+0x13ee)[0x56086cb683ee] [c021:31466] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c021 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 18:14:53 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 3 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 19 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=7752 [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) = 0.049019607843137 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.014705882352941 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 4.9019607843e-02 0.0000000000e+00 1.4705882353e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=5.536839e+01 pxpb=0.000000e+00 pypb=8.504911e+01 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 3277 need remove atom 3284 need remove atom 3286 need remove atom 3287 need remove atom 3294 need remove atom 3295 need remove atom 3302 need remove atom 3303 need remove atom 3311 need remove atom 3313 need remove atom 3345 need remove atom 3352 need remove atom 3354 need remove atom 3355 need remove atom 3362 need remove atom 3363 need remove atom 3370 need remove atom 3371 need remove atom 3379 need remove atom 3381 need remove atom 3413 need remove atom 3420 need remove atom 3422 need remove atom 3423 need remove atom 3430 need remove atom 3431 need remove atom 3438 need remove atom 3439 need remove atom 3447 need remove atom 3449 need remove atom 3481 need remove atom 3488 need remove atom 3490 need remove atom 3491 need remove atom 3498 need remove atom 3499 need remove atom 3506 need remove atom 3507 need remove atom 3515 need remove atom 3517 need remove atom 3549 need remove atom 3556 need remove atom 3558 need remove atom 3559 need remove atom 3566 need remove atom 3567 need remove atom 3574 need remove atom 3575 need remove atom 3583 need remove atom 3585 need remove atom 3617 need remove atom 3624 need remove atom 3626 need remove atom 3627 need remove atom 3634 need remove atom 3635 need remove atom 3642 need remove atom 3643 need remove atom 3651 need remove atom 3653 need remove atom 3685 need remove atom 3692 need remove atom 3694 need remove atom 3695 need remove atom 3702 need remove atom 3703 need remove atom 3710 need remove atom 3711 need remove atom 3719 need remove atom 3721 need remove atom 3753 need remove atom 3760 need remove atom 3762 need remove atom 3763 need remove atom 3770 need remove atom 3771 need remove atom 3778 need remove atom 3779 need remove atom 3787 need remove atom 3789 need remove atom 3821 need remove atom 3828 need remove atom 3830 need remove atom 3831 need remove atom 3838 need remove atom 3839 need remove atom 3846 need remove atom 3847 need remove atom 3855 need remove atom 3857 need remove atom 3889 need remove atom 3896 need remove atom 3898 need remove atom 3899 need remove atom 3906 need remove atom 3907 need remove atom 3914 need remove atom 3915 need remove atom 3923 need remove atom 3925 need remove atom 3957 need remove atom 3964 need remove atom 3966 need remove atom 3967 need remove atom 3974 need remove atom 3975 need remove atom 3982 need remove atom 3983 need remove atom 3991 need remove atom 3993 need remove atom 4025 need remove atom 4032 need remove atom 4034 need remove atom 4035 need remove atom 4042 need remove atom 4043 need remove atom 4050 need remove atom 4051 need remove atom 4059 need remove atom 4061 need remove atom 4093 need remove atom 4100 need remove atom 4102 need remove atom 4103 need remove atom 4110 need remove atom 4111 need remove atom 4118 need remove atom 4119 need remove atom 4127 need remove atom 4129 need remove atom 4161 need remove atom 4168 need remove atom 4170 need remove atom 4171 need remove atom 4178 need remove atom 4179 need remove atom 4186 need remove atom 4187 need remove atom 4195 need remove atom 4197 need remove atom 4229 need remove atom 4236 need remove atom 4238 need remove atom 4239 need remove atom 4246 need remove atom 4247 need remove atom 4254 need remove atom 4255 need remove atom 4263 need remove atom 4265 need remove atom 4297 need remove atom 4304 need remove atom 4306 need remove atom 4307 need remove atom 4314 need remove atom 4315 need remove atom 4322 need remove atom 4323 need remove atom 4331 need remove atom 4333 need remove atom 4365 need remove atom 4372 need remove atom 4374 need remove atom 4375 need remove atom 4382 need remove atom 4383 need remove atom 4390 need remove atom 4391 need remove atom 4399 need remove atom 4401 need remove atom 4433 need remove atom 4440 need remove atom 4442 need remove atom 4443 need remove atom 4450 need remove atom 4451 need remove atom 4458 need remove atom 4459 need remove atom 4467 need remove atom 4469 need remove atom 4501 need remove atom 4518 need remove atom 4519 need remove atom 4535 need remove atom 4537 need remove atom 4569 need remove atom 4586 need remove atom 4587 need remove atom 4603 need remove atom 4605 [I] need removenum=190 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5381395369e-01 1.7107979624e-01 6.0192749819e-02 dub= -5.8101539229e-01 1.7108403994e-01 -6.1368909892e-02 duc= 5.5381549408e-01 -1.7337783753e-01 6.0192942047e-02 [I] overall tilt ux= -1.1348293460e+00 4.2437065219e-06 -1.2156165971e-01 uy= 1.5403943056e-06 -3.4445763377e-01 1.9222863558e-07 [I] storedr[0]= -1.5807573571e-02 -1.1488707301e-03 2.5442853394e-05 [I] originally 7752 atoms [I] insert 0 atoms [I] now 7752 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 7752 atoms [I] remove 190 atoms [I] now 7562 atoms [I] NP=7562 n=7562 [I] ASSIGN finalcnfile = dipole_1.4.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.4.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.4.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 18:14:54 2023 CPU time spent: 0.647041 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 19:11:46 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 4 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 25 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=13600 [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) = 0.036764705882353 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.014705882352941 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.6764705882e-02 0.0000000000e+00 1.4705882353e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=7.382451e+01 pxpb=0.000000e+00 pypb=1.119067e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4262 need remove atom 4277 need remove atom 4283 need remove atom 4330 need remove atom 4345 need remove atom 4351 need remove atom 4398 need remove atom 4406 need remove atom 4413 need remove atom 4417 need remove atom 4418 need remove atom 4419 need remove atom 4466 need remove atom 4474 need remove atom 4481 need remove atom 4485 need remove atom 4486 need remove atom 4487 need remove atom 4534 need remove atom 4542 need remove atom 4549 need remove atom 4553 need remove atom 4554 need remove atom 4555 need remove atom 4602 need remove atom 4610 need remove atom 4617 need remove atom 4621 need remove atom 4622 need remove atom 4623 need remove atom 4670 need remove atom 4678 need remove atom 4685 need remove atom 4689 need remove atom 4690 need remove atom 4691 need remove atom 4738 need remove atom 4746 need remove atom 4753 need remove atom 4757 need remove atom 4758 need remove atom 4759 need remove atom 4806 need remove atom 4814 need remove atom 4821 need remove atom 4825 need remove atom 4826 need remove atom 4827 need remove atom 4874 need remove atom 4882 need remove atom 4889 need remove atom 4893 need remove atom 4894 need remove atom 4895 need remove atom 4942 need remove atom 4950 need remove atom 4957 need remove atom 4961 need remove atom 4962 need remove atom 4963 need remove atom 5010 need remove atom 5018 need remove atom 5025 need remove atom 5029 need remove atom 5030 need remove atom 5031 need remove atom 5078 need remove atom 5086 need remove atom 5093 need remove atom 5097 need remove atom 5098 need remove atom 5099 need remove atom 5146 need remove atom 5154 need remove atom 5161 need remove atom 5165 need remove atom 5166 need remove atom 5167 need remove atom 5214 need remove atom 5222 need remove atom 5229 need remove atom 5233 need remove atom 5234 need remove atom 5235 need remove atom 5282 need remove atom 5290 need remove atom 5297 need remove atom 5301 need remove atom 5302 need remove atom 5303 need remove atom 5350 need remove atom 5358 need remove atom 5365 need remove atom 5369 need remove atom 5370 need remove atom 5371 need remove atom 5418 need remove atom 5426 need remove atom 5433 need remove atom 5437 need remove atom 5438 need remove atom 5439 need remove atom 5486 need remove atom 5494 need remove atom 5501 need remove atom 5505 need remove atom 5506 need remove atom 5507 need remove atom 5554 need remove atom 5562 need remove atom 5569 need remove atom 5573 need remove atom 5574 need remove atom 5575 need remove atom 5622 need remove atom 5630 need remove atom 5637 need remove atom 5641 need remove atom 5642 need remove atom 5643 need remove atom 5690 need remove atom 5698 need remove atom 5705 need remove atom 5709 need remove atom 5710 need remove atom 5711 need remove atom 5758 need remove atom 5766 need remove atom 5773 need remove atom 5777 need remove atom 5778 need remove atom 5779 need remove atom 5826 need remove atom 5834 need remove atom 5841 need remove atom 5845 need remove atom 5846 need remove atom 5847 need remove atom 5894 need remove atom 5902 need remove atom 5909 need remove atom 5913 need remove atom 5914 need remove atom 5915 need remove atom 5962 need remove atom 5970 need remove atom 5977 need remove atom 5981 need remove atom 5982 need remove atom 5983 need remove atom 7619 need remove atom 7631 need remove atom 7687 need remove atom 7699 need remove atom 7752 need remove atom 7753 need remove atom 7755 need remove atom 7767 need remove atom 7820 need remove atom 7821 need remove atom 7823 need remove atom 7835 need remove atom 7888 need remove atom 7889 need remove atom 7891 need remove atom 7903 need remove atom 7956 need remove atom 7957 need remove atom 7959 need remove atom 7971 need remove atom 8024 need remove atom 8025 need remove atom 8027 need remove atom 8039 need remove atom 8092 need remove atom 8093 need remove atom 8095 need remove atom 8107 need remove atom 8160 need remove atom 8161 need remove atom 8163 need remove atom 8175 need remove atom 8228 need remove atom 8229 need remove atom 8231 need remove atom 8243 need remove atom 8296 need remove atom 8297 need remove atom 8299 need remove atom 8311 need remove atom 8364 need remove atom 8365 need remove atom 8367 need remove atom 8379 need remove atom 8432 need remove atom 8433 need remove atom 8435 need remove atom 8447 need remove atom 8500 need remove atom 8501 need remove atom 8503 need remove atom 8515 need remove atom 8568 need remove atom 8569 need remove atom 8571 need remove atom 8583 need remove atom 8636 need remove atom 8637 need remove atom 8639 need remove atom 8651 need remove atom 8704 need remove atom 8705 need remove atom 8707 need remove atom 8719 need remove atom 8772 need remove atom 8773 need remove atom 8775 need remove atom 8787 need remove atom 8840 need remove atom 8841 need remove atom 8843 need remove atom 8855 need remove atom 8908 need remove atom 8909 need remove atom 8911 need remove atom 8923 need remove atom 8976 need remove atom 8977 need remove atom 8979 need remove atom 8991 need remove atom 9044 need remove atom 9045 need remove atom 9047 need remove atom 9059 need remove atom 9112 need remove atom 9113 need remove atom 9115 need remove atom 9127 need remove atom 9180 need remove atom 9181 need remove atom 9183 need remove atom 9195 need remove atom 9248 need remove atom 9249 need remove atom 9251 need remove atom 9263 need remove atom 9316 need remove atom 9317 need remove atom 9319 need remove atom 9331 [I] need removenum=250 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5200419369e-01 1.7171283244e-01 5.9846764259e-02 dub= -5.7902306978e-01 1.7171686387e-01 -6.0971837639e-02 duc= 5.5200575096e-01 -1.7396544181e-01 5.9846955972e-02 [I] overall tilt ux= -1.1310272635e+00 4.0314253253e-06 -1.2081860190e-01 uy= 1.5572697394e-06 -3.4567827426e-01 1.9171335081e-07 [I] storedr[0]= -1.5125585314e-02 -1.1257401098e-03 -8.8807108760e-05 [I] originally 13600 atoms [I] insert 0 atoms [I] now 13600 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 13600 atoms [I] remove 250 atoms [I] now 13350 atoms [I] NP=13350 n=13350 [I] ASSIGN finalcnfile = dipole_1.8.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.8.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.8.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 19:11:47 2023 CPU time spent: 1.126046 s [c021:60435] *** Process received signal *** [c021:60435] Signal: Segmentation fault (11) [c021:60435] Signal code: Address not mapped (1) [c021:60435] Failing at address: 0x30 [c021:60435] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7fa5bb8d9090] [c021:60435] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7fa5b80a31c2] [c021:60435] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7fa5bae64854] [c021:60435] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7fa5bbcd2905] [c021:60435] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7fa5bbd27d93] [c021:60435] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7fa5bbd28061] [c021:60435] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7fa5b3518dae] [c021:60435] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7fa5bbceab10] [c021:60435] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7fa5bc518864] [c021:60435] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7fa5bc517417] [c021:60435] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7fa5bc2bfdba] [c021:60435] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7fa5bc1d3d0e] [c021:60435] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7fa5bc1d9300] [c021:60435] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7fa5bc1d9cd9] [c021:60435] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7fa5bc399d5b] [c021:60435] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7fa5bc39aa78] [c021:60435] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7fa5bc39183e] [c021:60435] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7fa5bc1d9138] [c021:60435] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7fa5bc1d954e] [c021:60435] [19] lmp(+0x136e)[0x557bf783636e] [c021:60435] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fa5bb8ba083] [c021:60435] [21] lmp(+0x13ee)[0x557bf78363ee] [c021:60435] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c021 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 19:12:09 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 4 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 25 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=13600 [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) = 0.036764705882353 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.014705882352941 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.6764705882e-02 0.0000000000e+00 1.4705882353e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=7.382451e+01 pxpb=0.000000e+00 pypb=1.119067e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4262 need remove atom 4277 need remove atom 4283 need remove atom 4330 need remove atom 4345 need remove atom 4351 need remove atom 4398 need remove atom 4406 need remove atom 4413 need remove atom 4417 need remove atom 4418 need remove atom 4419 need remove atom 4466 need remove atom 4474 need remove atom 4481 need remove atom 4485 need remove atom 4486 need remove atom 4487 need remove atom 4534 need remove atom 4542 need remove atom 4549 need remove atom 4553 need remove atom 4554 need remove atom 4555 need remove atom 4602 need remove atom 4610 need remove atom 4617 need remove atom 4621 need remove atom 4622 need remove atom 4623 need remove atom 4670 need remove atom 4678 need remove atom 4685 need remove atom 4689 need remove atom 4690 need remove atom 4691 need remove atom 4738 need remove atom 4746 need remove atom 4753 need remove atom 4757 need remove atom 4758 need remove atom 4759 need remove atom 4806 need remove atom 4814 need remove atom 4821 need remove atom 4825 need remove atom 4826 need remove atom 4827 need remove atom 4874 need remove atom 4882 need remove atom 4889 need remove atom 4893 need remove atom 4894 need remove atom 4895 need remove atom 4942 need remove atom 4950 need remove atom 4957 need remove atom 4961 need remove atom 4962 need remove atom 4963 need remove atom 5010 need remove atom 5018 need remove atom 5025 need remove atom 5029 need remove atom 5030 need remove atom 5031 need remove atom 5078 need remove atom 5086 need remove atom 5093 need remove atom 5097 need remove atom 5098 need remove atom 5099 need remove atom 5146 need remove atom 5154 need remove atom 5161 need remove atom 5165 need remove atom 5166 need remove atom 5167 need remove atom 5214 need remove atom 5222 need remove atom 5229 need remove atom 5233 need remove atom 5234 need remove atom 5235 need remove atom 5282 need remove atom 5290 need remove atom 5297 need remove atom 5301 need remove atom 5302 need remove atom 5303 need remove atom 5350 need remove atom 5358 need remove atom 5365 need remove atom 5369 need remove atom 5370 need remove atom 5371 need remove atom 5418 need remove atom 5426 need remove atom 5433 need remove atom 5437 need remove atom 5438 need remove atom 5439 need remove atom 5486 need remove atom 5494 need remove atom 5501 need remove atom 5505 need remove atom 5506 need remove atom 5507 need remove atom 5554 need remove atom 5562 need remove atom 5569 need remove atom 5573 need remove atom 5574 need remove atom 5575 need remove atom 5622 need remove atom 5630 need remove atom 5637 need remove atom 5641 need remove atom 5642 need remove atom 5643 need remove atom 5690 need remove atom 5698 need remove atom 5705 need remove atom 5709 need remove atom 5710 need remove atom 5711 need remove atom 5758 need remove atom 5766 need remove atom 5773 need remove atom 5777 need remove atom 5778 need remove atom 5779 need remove atom 5826 need remove atom 5834 need remove atom 5841 need remove atom 5845 need remove atom 5846 need remove atom 5847 need remove atom 5894 need remove atom 5902 need remove atom 5909 need remove atom 5913 need remove atom 5914 need remove atom 5915 need remove atom 5962 need remove atom 5970 need remove atom 5977 need remove atom 5981 need remove atom 5982 need remove atom 5983 need remove atom 7619 need remove atom 7631 need remove atom 7687 need remove atom 7699 need remove atom 7752 need remove atom 7753 need remove atom 7755 need remove atom 7767 need remove atom 7820 need remove atom 7821 need remove atom 7823 need remove atom 7835 need remove atom 7888 need remove atom 7889 need remove atom 7891 need remove atom 7903 need remove atom 7956 need remove atom 7957 need remove atom 7959 need remove atom 7971 need remove atom 8024 need remove atom 8025 need remove atom 8027 need remove atom 8039 need remove atom 8092 need remove atom 8093 need remove atom 8095 need remove atom 8107 need remove atom 8160 need remove atom 8161 need remove atom 8163 need remove atom 8175 need remove atom 8228 need remove atom 8229 need remove atom 8231 need remove atom 8243 need remove atom 8296 need remove atom 8297 need remove atom 8299 need remove atom 8311 need remove atom 8364 need remove atom 8365 need remove atom 8367 need remove atom 8379 need remove atom 8432 need remove atom 8433 need remove atom 8435 need remove atom 8447 need remove atom 8500 need remove atom 8501 need remove atom 8503 need remove atom 8515 need remove atom 8568 need remove atom 8569 need remove atom 8571 need remove atom 8583 need remove atom 8636 need remove atom 8637 need remove atom 8639 need remove atom 8651 need remove atom 8704 need remove atom 8705 need remove atom 8707 need remove atom 8719 need remove atom 8772 need remove atom 8773 need remove atom 8775 need remove atom 8787 need remove atom 8840 need remove atom 8841 need remove atom 8843 need remove atom 8855 need remove atom 8908 need remove atom 8909 need remove atom 8911 need remove atom 8923 need remove atom 8976 need remove atom 8977 need remove atom 8979 need remove atom 8991 need remove atom 9044 need remove atom 9045 need remove atom 9047 need remove atom 9059 need remove atom 9112 need remove atom 9113 need remove atom 9115 need remove atom 9127 need remove atom 9180 need remove atom 9181 need remove atom 9183 need remove atom 9195 need remove atom 9248 need remove atom 9249 need remove atom 9251 need remove atom 9263 need remove atom 9316 need remove atom 9317 need remove atom 9319 need remove atom 9331 [I] need removenum=250 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5200419369e-01 1.7171283244e-01 5.9846764259e-02 dub= -5.7902306978e-01 1.7171686387e-01 -6.0971837639e-02 duc= 5.5200575096e-01 -1.7396544181e-01 5.9846955972e-02 [I] overall tilt ux= -1.1310272635e+00 4.0314253253e-06 -1.2081860190e-01 uy= 1.5572697394e-06 -3.4567827426e-01 1.9171335081e-07 [I] storedr[0]= -1.5125585314e-02 -1.1257401098e-03 -8.8807108760e-05 [I] originally 13600 atoms [I] insert 0 atoms [I] now 13600 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 13600 atoms [I] remove 250 atoms [I] now 13350 atoms [I] NP=13350 n=13350 [I] ASSIGN finalcnfile = dipole_1.9.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_1.9.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_1.9.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 19:12:10 2023 CPU time spent: 1.132074 s [c021:60675] *** Process received signal *** [c021:60675] Signal: Segmentation fault (11) [c021:60675] Signal code: Address not mapped (1) [c021:60675] Failing at address: 0x30 [c021:60675] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x7fc87f6cf090] [c021:60675] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_ofi.so(ompi_mtl_ofi_progress_no_inline+0x1a2)[0x7fc8775971c2] [c021:60675] [ 2] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x34)[0x7fc87ec5a854] [c021:60675] [ 3] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x135)[0x7fc87fac8905] [c021:60675] [ 4] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_generic+0x503)[0x7fc87fb1dd93] [c021:60675] [ 5] /lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_bcast_intra_pipeline+0xd1)[0x7fc87fb1e061] [c021:60675] [ 6] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_dec_fixed+0x12e)[0x7fc87730edae] [c021:60675] [ 7] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Bcast+0x120)[0x7fc87fae0b10] [c021:60675] [ 8] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS9read_fileEPc+0x1014)[0x7fc88030e864] [c021:60675] [ 9] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS9PairEAMFS5coeffEiPPc+0x2d7)[0x7fc88030d417] [c021:60675] [10] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS17PairHybridOverlay5coeffEiPPc+0x38a)[0x7fc8800b5dba] [c021:60675] [11] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input10pair_coeffEv+0xde)[0x7fc87ffc9d0e] [c021:60675] [12] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xe00)[0x7fc87ffcf300] [c021:60675] [13] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input3oneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa9)[0x7fc87ffcfcd9] [c021:60675] [14] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions8do_setupEiPPc+0xf8b)[0x7fc88018fd5b] [c021:60675] [15] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS15KimInteractions7commandEiPPc+0x38)[0x7fc880190a78] [c021:60675] [16] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS10KimCommand7commandEiPPc+0x3ee)[0x7fc88018783e] [c021:60675] [17] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc38)[0x7fc87ffcf138] [c021:60675] [18] /usr/local/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x17e)[0x7fc87ffcf54e] [c021:60675] [19] lmp(+0x136e)[0x563e65e9a36e] [c021:60675] [20] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fc87f6b0083] [c021:60675] [21] lmp(+0x13ee)[0x563e65e9a3ee] [c021:60675] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node c021 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 19:12:33 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 4 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 25 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=13600 [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) = 0.036764705882353 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.014705882352941 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 3.6764705882e-02 0.0000000000e+00 1.4705882353e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=7.382451e+01 pxpb=0.000000e+00 pypb=1.119067e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 4262 need remove atom 4277 need remove atom 4283 need remove atom 4330 need remove atom 4345 need remove atom 4351 need remove atom 4398 need remove atom 4406 need remove atom 4413 need remove atom 4417 need remove atom 4418 need remove atom 4419 need remove atom 4466 need remove atom 4474 need remove atom 4481 need remove atom 4485 need remove atom 4486 need remove atom 4487 need remove atom 4534 need remove atom 4542 need remove atom 4549 need remove atom 4553 need remove atom 4554 need remove atom 4555 need remove atom 4602 need remove atom 4610 need remove atom 4617 need remove atom 4621 need remove atom 4622 need remove atom 4623 need remove atom 4670 need remove atom 4678 need remove atom 4685 need remove atom 4689 need remove atom 4690 need remove atom 4691 need remove atom 4738 need remove atom 4746 need remove atom 4753 need remove atom 4757 need remove atom 4758 need remove atom 4759 need remove atom 4806 need remove atom 4814 need remove atom 4821 need remove atom 4825 need remove atom 4826 need remove atom 4827 need remove atom 4874 need remove atom 4882 need remove atom 4889 need remove atom 4893 need remove atom 4894 need remove atom 4895 need remove atom 4942 need remove atom 4950 need remove atom 4957 need remove atom 4961 need remove atom 4962 need remove atom 4963 need remove atom 5010 need remove atom 5018 need remove atom 5025 need remove atom 5029 need remove atom 5030 need remove atom 5031 need remove atom 5078 need remove atom 5086 need remove atom 5093 need remove atom 5097 need remove atom 5098 need remove atom 5099 need remove atom 5146 need remove atom 5154 need remove atom 5161 need remove atom 5165 need remove atom 5166 need remove atom 5167 need remove atom 5214 need remove atom 5222 need remove atom 5229 need remove atom 5233 need remove atom 5234 need remove atom 5235 need remove atom 5282 need remove atom 5290 need remove atom 5297 need remove atom 5301 need remove atom 5302 need remove atom 5303 need remove atom 5350 need remove atom 5358 need remove atom 5365 need remove atom 5369 need remove atom 5370 need remove atom 5371 need remove atom 5418 need remove atom 5426 need remove atom 5433 need remove atom 5437 need remove atom 5438 need remove atom 5439 need remove atom 5486 need remove atom 5494 need remove atom 5501 need remove atom 5505 need remove atom 5506 need remove atom 5507 need remove atom 5554 need remove atom 5562 need remove atom 5569 need remove atom 5573 need remove atom 5574 need remove atom 5575 need remove atom 5622 need remove atom 5630 need remove atom 5637 need remove atom 5641 need remove atom 5642 need remove atom 5643 need remove atom 5690 need remove atom 5698 need remove atom 5705 need remove atom 5709 need remove atom 5710 need remove atom 5711 need remove atom 5758 need remove atom 5766 need remove atom 5773 need remove atom 5777 need remove atom 5778 need remove atom 5779 need remove atom 5826 need remove atom 5834 need remove atom 5841 need remove atom 5845 need remove atom 5846 need remove atom 5847 need remove atom 5894 need remove atom 5902 need remove atom 5909 need remove atom 5913 need remove atom 5914 need remove atom 5915 need remove atom 5962 need remove atom 5970 need remove atom 5977 need remove atom 5981 need remove atom 5982 need remove atom 5983 need remove atom 7619 need remove atom 7631 need remove atom 7687 need remove atom 7699 need remove atom 7752 need remove atom 7753 need remove atom 7755 need remove atom 7767 need remove atom 7820 need remove atom 7821 need remove atom 7823 need remove atom 7835 need remove atom 7888 need remove atom 7889 need remove atom 7891 need remove atom 7903 need remove atom 7956 need remove atom 7957 need remove atom 7959 need remove atom 7971 need remove atom 8024 need remove atom 8025 need remove atom 8027 need remove atom 8039 need remove atom 8092 need remove atom 8093 need remove atom 8095 need remove atom 8107 need remove atom 8160 need remove atom 8161 need remove atom 8163 need remove atom 8175 need remove atom 8228 need remove atom 8229 need remove atom 8231 need remove atom 8243 need remove atom 8296 need remove atom 8297 need remove atom 8299 need remove atom 8311 need remove atom 8364 need remove atom 8365 need remove atom 8367 need remove atom 8379 need remove atom 8432 need remove atom 8433 need remove atom 8435 need remove atom 8447 need remove atom 8500 need remove atom 8501 need remove atom 8503 need remove atom 8515 need remove atom 8568 need remove atom 8569 need remove atom 8571 need remove atom 8583 need remove atom 8636 need remove atom 8637 need remove atom 8639 need remove atom 8651 need remove atom 8704 need remove atom 8705 need remove atom 8707 need remove atom 8719 need remove atom 8772 need remove atom 8773 need remove atom 8775 need remove atom 8787 need remove atom 8840 need remove atom 8841 need remove atom 8843 need remove atom 8855 need remove atom 8908 need remove atom 8909 need remove atom 8911 need remove atom 8923 need remove atom 8976 need remove atom 8977 need remove atom 8979 need remove atom 8991 need remove atom 9044 need remove atom 9045 need remove atom 9047 need remove atom 9059 need remove atom 9112 need remove atom 9113 need remove atom 9115 need remove atom 9127 need remove atom 9180 need remove atom 9181 need remove atom 9183 need remove atom 9195 need remove atom 9248 need remove atom 9249 need remove atom 9251 need remove atom 9263 need remove atom 9316 need remove atom 9317 need remove atom 9319 need remove atom 9331 [I] need removenum=250 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5200419369e-01 1.7171283244e-01 5.9846764259e-02 dub= -5.7902306978e-01 1.7171686387e-01 -6.0971837639e-02 duc= 5.5200575096e-01 -1.7396544181e-01 5.9846955972e-02 [I] overall tilt ux= -1.1310272635e+00 4.0314253253e-06 -1.2081860190e-01 uy= 1.5572697394e-06 -3.4567827426e-01 1.9171335081e-07 [I] storedr[0]= -1.5125585314e-02 -1.1257401098e-03 -8.8807108760e-05 [I] originally 13600 atoms [I] insert 0 atoms [I] now 13600 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 13600 atoms [I] remove 250 atoms [I] now 13350 atoms [I] NP=13350 n=13350 [I] ASSIGN finalcnfile = dipole_2.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 19:12:34 2023 CPU time spent: 1.132125 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 20:31:46 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 5 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 31 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 2 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=21080 [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) = 0.029411764705882 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.014705882352941 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.9411764706e-02 0.0000000000e+00 1.4705882353e-02 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=9.228064e+01 pxpb=0.000000e+00 pypb=1.387643e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 9533 need remove atom 9540 need remove atom 9541 need remove atom 9543 need remove atom 9548 need remove atom 9550 need remove atom 9551 need remove atom 9558 need remove atom 9559 need remove atom 9567 need remove atom 9601 need remove atom 9608 need remove atom 9609 need remove atom 9611 need remove atom 9616 need remove atom 9618 need remove atom 9619 need remove atom 9626 need remove atom 9627 need remove atom 9635 need remove atom 9669 need remove atom 9676 need remove atom 9677 need remove atom 9679 need remove atom 9684 need remove atom 9686 need remove atom 9687 need remove atom 9694 need remove atom 9695 need remove atom 9703 need remove atom 9737 need remove atom 9744 need remove atom 9745 need remove atom 9747 need remove atom 9752 need remove atom 9754 need remove atom 9755 need remove atom 9762 need remove atom 9763 need remove atom 9771 need remove atom 9805 need remove atom 9812 need remove atom 9813 need remove atom 9815 need remove atom 9820 need remove atom 9822 need remove atom 9823 need remove atom 9830 need remove atom 9831 need remove atom 9839 need remove atom 9873 need remove atom 9880 need remove atom 9881 need remove atom 9883 need remove atom 9888 need remove atom 9890 need remove atom 9891 need remove atom 9898 need remove atom 9899 need remove atom 9907 need remove atom 9941 need remove atom 9948 need remove atom 9949 need remove atom 9951 need remove atom 9956 need remove atom 9958 need remove atom 9959 need remove atom 9966 need remove atom 9967 need remove atom 9975 need remove atom 10009 need remove atom 10016 need remove atom 10017 need remove atom 10019 need remove atom 10024 need remove atom 10026 need remove atom 10027 need remove atom 10034 need remove atom 10035 need remove atom 10043 need remove atom 10077 need remove atom 10084 need remove atom 10085 need remove atom 10087 need remove atom 10092 need remove atom 10094 need remove atom 10095 need remove atom 10102 need remove atom 10103 need remove atom 10111 need remove atom 10145 need remove atom 10152 need remove atom 10153 need remove atom 10155 need remove atom 10160 need remove atom 10162 need remove atom 10163 need remove atom 10170 need remove atom 10171 need remove atom 10179 need remove atom 10213 need remove atom 10220 need remove atom 10221 need remove atom 10223 need remove atom 10228 need remove atom 10230 need remove atom 10231 need remove atom 10238 need remove atom 10239 need remove atom 10247 need remove atom 10281 need remove atom 10288 need remove atom 10289 need remove atom 10291 need remove atom 10296 need remove atom 10298 need remove atom 10299 need remove atom 10306 need remove atom 10307 need remove atom 10315 need remove atom 10349 need remove atom 10356 need remove atom 10357 need remove atom 10359 need remove atom 10364 need remove atom 10366 need remove atom 10367 need remove atom 10374 need remove atom 10375 need remove atom 10383 need remove atom 10417 need remove atom 10424 need remove atom 10425 need remove atom 10427 need remove atom 10432 need remove atom 10434 need remove atom 10435 need remove atom 10442 need remove atom 10443 need remove atom 10451 need remove atom 10485 need remove atom 10492 need remove atom 10493 need remove atom 10495 need remove atom 10500 need remove atom 10502 need remove atom 10503 need remove atom 10510 need remove atom 10511 need remove atom 10519 need remove atom 10553 need remove atom 10560 need remove atom 10561 need remove atom 10563 need remove atom 10568 need remove atom 10570 need remove atom 10571 need remove atom 10578 need remove atom 10579 need remove atom 10587 need remove atom 10621 need remove atom 10628 need remove atom 10629 need remove atom 10631 need remove atom 10636 need remove atom 10638 need remove atom 10639 need remove atom 10646 need remove atom 10647 need remove atom 10655 need remove atom 10689 need remove atom 10696 need remove atom 10697 need remove atom 10699 need remove atom 10704 need remove atom 10706 need remove atom 10707 need remove atom 10714 need remove atom 10715 need remove atom 10723 need remove atom 10757 need remove atom 10764 need remove atom 10765 need remove atom 10767 need remove atom 10772 need remove atom 10774 need remove atom 10775 need remove atom 10782 need remove atom 10783 need remove atom 10791 need remove atom 10825 need remove atom 10832 need remove atom 10833 need remove atom 10835 need remove atom 10840 need remove atom 10842 need remove atom 10843 need remove atom 10850 need remove atom 10851 need remove atom 10859 need remove atom 10893 need remove atom 10900 need remove atom 10901 need remove atom 10903 need remove atom 10908 need remove atom 10910 need remove atom 10911 need remove atom 10918 need remove atom 10919 need remove atom 10927 need remove atom 10961 need remove atom 10968 need remove atom 10969 need remove atom 10971 need remove atom 10976 need remove atom 10978 need remove atom 10979 need remove atom 10986 need remove atom 10987 need remove atom 10995 need remove atom 11029 need remove atom 11036 need remove atom 11037 need remove atom 11039 need remove atom 11044 need remove atom 11046 need remove atom 11047 need remove atom 11054 need remove atom 11055 need remove atom 11063 need remove atom 11097 need remove atom 11104 need remove atom 11105 need remove atom 11107 need remove atom 11112 need remove atom 11114 need remove atom 11115 need remove atom 11122 need remove atom 11123 need remove atom 11131 need remove atom 11165 need remove atom 11172 need remove atom 11173 need remove atom 11175 need remove atom 11180 need remove atom 11182 need remove atom 11183 need remove atom 11190 need remove atom 11191 need remove atom 11199 need remove atom 11233 need remove atom 11240 need remove atom 11241 need remove atom 11243 need remove atom 11248 need remove atom 11250 need remove atom 11251 need remove atom 11258 need remove atom 11259 need remove atom 11267 need remove atom 11301 need remove atom 11308 need remove atom 11309 need remove atom 11311 need remove atom 11316 need remove atom 11318 need remove atom 11319 need remove atom 11326 need remove atom 11327 need remove atom 11335 need remove atom 11369 need remove atom 11376 need remove atom 11377 need remove atom 11379 need remove atom 11384 need remove atom 11386 need remove atom 11387 need remove atom 11394 need remove atom 11395 need remove atom 11403 need remove atom 11437 need remove atom 11444 need remove atom 11445 need remove atom 11447 need remove atom 11452 need remove atom 11454 need remove atom 11455 need remove atom 11462 need remove atom 11463 need remove atom 11471 need remove atom 11505 need remove atom 11512 need remove atom 11513 need remove atom 11515 need remove atom 11520 need remove atom 11522 need remove atom 11523 need remove atom 11530 need remove atom 11531 need remove atom 11539 need remove atom 11573 need remove atom 11588 need remove atom 11590 need remove atom 11591 need remove atom 11607 need remove atom 11641 need remove atom 11656 need remove atom 11658 need remove atom 11659 need remove atom 11675 [I] need removenum=310 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5089453786e-01 1.7209657944e-01 5.9636122905e-02 dub= -5.7779744699e-01 1.7210047782e-01 -6.0729985554e-02 duc= 5.5089610520e-01 -1.7432159299e-01 5.9636314279e-02 [I] overall tilt ux= -1.1286919848e+00 3.8983857582e-06 -1.2036610846e-01 uy= 1.5673348553e-06 -3.4641817243e-01 1.9137393967e-07 [I] storedr[0]= -1.4723971491e-02 -1.1117008413e-03 -1.6129990753e-04 [I] originally 21080 atoms [I] insert 0 atoms [I] now 21080 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 21080 atoms [I] remove 310 atoms [I] now 20770 atoms [I] NP=20770 n=20770 [I] ASSIGN finalcnfile = dipole_2.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_2.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_2.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 20:31:48 2023 CPU time spent: 1.755272 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 21:27:13 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 6 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 37 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=45288 [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) = 0.024509803921569 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0098039215686275 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.4509803922e-02 0.0000000000e+00 9.8039215686e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=1.107368e+02 pxpb=0.000000e+00 pypb=1.656219e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 16978 need remove atom 16991 need remove atom 16993 need remove atom 16999 need remove atom 17046 need remove atom 17059 need remove atom 17061 need remove atom 17067 need remove atom 17114 need remove atom 17127 need remove atom 17129 need remove atom 17135 need remove atom 17182 need remove atom 17190 need remove atom 17191 need remove atom 17195 need remove atom 17197 need remove atom 17201 need remove atom 17202 need remove atom 17203 need remove atom 17250 need remove atom 17258 need remove atom 17259 need remove atom 17263 need remove atom 17265 need remove atom 17269 need remove atom 17270 need remove atom 17271 need remove atom 17318 need remove atom 17326 need remove atom 17327 need remove atom 17331 need remove atom 17333 need remove atom 17337 need remove atom 17338 need remove atom 17339 need remove atom 17386 need remove atom 17394 need remove atom 17395 need remove atom 17399 need remove atom 17401 need remove atom 17405 need remove atom 17406 need remove atom 17407 need remove atom 17454 need remove atom 17462 need remove atom 17463 need remove atom 17467 need remove atom 17469 need remove atom 17473 need remove atom 17474 need remove atom 17475 need remove atom 17522 need remove atom 17530 need remove atom 17531 need remove atom 17535 need remove atom 17537 need remove atom 17541 need remove atom 17542 need remove atom 17543 need remove atom 17590 need remove atom 17598 need remove atom 17599 need remove atom 17603 need remove atom 17605 need remove atom 17609 need remove atom 17610 need remove atom 17611 need remove atom 17658 need remove atom 17666 need remove atom 17667 need remove atom 17671 need remove atom 17673 need remove atom 17677 need remove atom 17678 need remove atom 17679 need remove atom 17726 need remove atom 17734 need remove atom 17735 need remove atom 17739 need remove atom 17741 need remove atom 17745 need remove atom 17746 need remove atom 17747 need remove atom 17794 need remove atom 17802 need remove atom 17803 need remove atom 17807 need remove atom 17809 need remove atom 17813 need remove atom 17814 need remove atom 17815 need remove atom 17862 need remove atom 17870 need remove atom 17871 need remove atom 17875 need remove atom 17877 need remove atom 17881 need remove atom 17882 need remove atom 17883 need remove atom 17930 need remove atom 17938 need remove atom 17939 need remove atom 17943 need remove atom 17945 need remove atom 17949 need remove atom 17950 need remove atom 17951 need remove atom 17998 need remove atom 18006 need remove atom 18007 need remove atom 18011 need remove atom 18013 need remove atom 18017 need remove atom 18018 need remove atom 18019 need remove atom 18066 need remove atom 18074 need remove atom 18075 need remove atom 18079 need remove atom 18081 need remove atom 18085 need remove atom 18086 need remove atom 18087 need remove atom 18134 need remove atom 18142 need remove atom 18143 need remove atom 18147 need remove atom 18149 need remove atom 18153 need remove atom 18154 need remove atom 18155 need remove atom 18202 need remove atom 18210 need remove atom 18211 need remove atom 18215 need remove atom 18217 need remove atom 18221 need remove atom 18222 need remove atom 18223 need remove atom 18270 need remove atom 18278 need remove atom 18279 need remove atom 18283 need remove atom 18285 need remove atom 18289 need remove atom 18290 need remove atom 18291 need remove atom 18338 need remove atom 18346 need remove atom 18347 need remove atom 18351 need remove atom 18353 need remove atom 18357 need remove atom 18358 need remove atom 18359 need remove atom 18406 need remove atom 18414 need remove atom 18415 need remove atom 18419 need remove atom 18421 need remove atom 18425 need remove atom 18426 need remove atom 18427 need remove atom 18474 need remove atom 18482 need remove atom 18483 need remove atom 18487 need remove atom 18489 need remove atom 18493 need remove atom 18494 need remove atom 18495 need remove atom 18542 need remove atom 18550 need remove atom 18551 need remove atom 18555 need remove atom 18557 need remove atom 18561 need remove atom 18562 need remove atom 18563 need remove atom 18610 need remove atom 18618 need remove atom 18619 need remove atom 18623 need remove atom 18625 need remove atom 18629 need remove atom 18630 need remove atom 18631 need remove atom 18678 need remove atom 18686 need remove atom 18687 need remove atom 18691 need remove atom 18693 need remove atom 18697 need remove atom 18698 need remove atom 18699 need remove atom 18746 need remove atom 18754 need remove atom 18755 need remove atom 18759 need remove atom 18761 need remove atom 18765 need remove atom 18766 need remove atom 18767 need remove atom 18814 need remove atom 18822 need remove atom 18823 need remove atom 18827 need remove atom 18829 need remove atom 18833 need remove atom 18834 need remove atom 18835 need remove atom 18882 need remove atom 18890 need remove atom 18891 need remove atom 18895 need remove atom 18897 need remove atom 18901 need remove atom 18902 need remove atom 18903 need remove atom 18950 need remove atom 18958 need remove atom 18959 need remove atom 18963 need remove atom 18965 need remove atom 18969 need remove atom 18970 need remove atom 18971 need remove atom 19018 need remove atom 19026 need remove atom 19027 need remove atom 19031 need remove atom 19033 need remove atom 19037 need remove atom 19038 need remove atom 19039 need remove atom 19086 need remove atom 19094 need remove atom 19095 need remove atom 19099 need remove atom 19101 need remove atom 19105 need remove atom 19106 need remove atom 19107 need remove atom 19154 need remove atom 19162 need remove atom 19163 need remove atom 19167 need remove atom 19169 need remove atom 19173 need remove atom 19174 need remove atom 19175 need remove atom 19222 need remove atom 19230 need remove atom 19231 need remove atom 19235 need remove atom 19237 need remove atom 19241 need remove atom 19242 need remove atom 19243 need remove atom 19290 need remove atom 19298 need remove atom 19299 need remove atom 19303 need remove atom 19305 need remove atom 19309 need remove atom 19310 need remove atom 19311 need remove atom 19358 need remove atom 19366 need remove atom 19367 need remove atom 19371 need remove atom 19373 need remove atom 19377 need remove atom 19378 need remove atom 19379 need remove atom 19426 need remove atom 19434 need remove atom 19435 need remove atom 19439 need remove atom 19441 need remove atom 19445 need remove atom 19446 need remove atom 19447 need remove atom 19494 need remove atom 19502 need remove atom 19503 need remove atom 19507 need remove atom 19509 need remove atom 19513 need remove atom 19514 need remove atom 19515 need remove atom 19562 need remove atom 19570 need remove atom 19571 need remove atom 19575 need remove atom 19577 need remove atom 19581 need remove atom 19582 need remove atom 19583 need remove atom 19630 need remove atom 19638 need remove atom 19639 need remove atom 19643 need remove atom 19645 need remove atom 19649 need remove atom 19650 need remove atom 19651 need remove atom 19698 need remove atom 19706 need remove atom 19707 need remove atom 19711 need remove atom 19713 need remove atom 19717 need remove atom 19718 need remove atom 19719 need remove atom 19766 need remove atom 19774 need remove atom 19775 need remove atom 19779 need remove atom 19781 need remove atom 19785 need remove atom 19786 need remove atom 19787 need remove atom 19834 need remove atom 19842 need remove atom 19843 need remove atom 19847 need remove atom 19849 need remove atom 19853 need remove atom 19854 need remove atom 19855 need remove atom 19902 need remove atom 19910 need remove atom 19911 need remove atom 19915 need remove atom 19917 need remove atom 19921 need remove atom 19922 need remove atom 19923 need remove atom 19970 need remove atom 19978 need remove atom 19979 need remove atom 19983 need remove atom 19985 need remove atom 19989 need remove atom 19990 need remove atom 19991 need remove atom 20038 need remove atom 20046 need remove atom 20047 need remove atom 20051 need remove atom 20053 need remove atom 20057 need remove atom 20058 need remove atom 20059 need remove atom 20106 need remove atom 20114 need remove atom 20115 need remove atom 20119 need remove atom 20121 need remove atom 20125 need remove atom 20126 need remove atom 20127 need remove atom 20174 need remove atom 20182 need remove atom 20183 need remove atom 20187 need remove atom 20189 need remove atom 20193 need remove atom 20194 need remove atom 20195 need remove atom 20242 need remove atom 20250 need remove atom 20251 need remove atom 20255 need remove atom 20257 need remove atom 20261 need remove atom 20262 need remove atom 20263 need remove atom 20310 need remove atom 20318 need remove atom 20319 need remove atom 20323 need remove atom 20325 need remove atom 20329 need remove atom 20330 need remove atom 20331 need remove atom 20378 need remove atom 20386 need remove atom 20387 need remove atom 20391 need remove atom 20393 need remove atom 20397 need remove atom 20398 need remove atom 20399 need remove atom 20446 need remove atom 20454 need remove atom 20455 need remove atom 20459 need remove atom 20461 need remove atom 20465 need remove atom 20466 need remove atom 20467 need remove atom 20514 need remove atom 20522 need remove atom 20523 need remove atom 20527 need remove atom 20529 need remove atom 20533 need remove atom 20534 need remove atom 20535 need remove atom 20582 need remove atom 20590 need remove atom 20591 need remove atom 20595 need remove atom 20597 need remove atom 20601 need remove atom 20602 need remove atom 20603 need remove atom 20650 need remove atom 20658 need remove atom 20659 need remove atom 20663 need remove atom 20665 need remove atom 20669 need remove atom 20670 need remove atom 20671 need remove atom 20718 need remove atom 20726 need remove atom 20727 need remove atom 20731 need remove atom 20733 need remove atom 20737 need remove atom 20738 need remove atom 20739 need remove atom 20786 need remove atom 20794 need remove atom 20795 need remove atom 20799 need remove atom 20801 need remove atom 20805 need remove atom 20806 need remove atom 20807 need remove atom 24483 need remove atom 24551 need remove atom 24619 need remove atom 24685 need remove atom 24687 need remove atom 24753 need remove atom 24755 need remove atom 24821 need remove atom 24823 need remove atom 24889 need remove atom 24891 need remove atom 24957 need remove atom 24959 need remove atom 25025 need remove atom 25027 need remove atom 25093 need remove atom 25095 need remove atom 25161 need remove atom 25163 need remove atom 25229 need remove atom 25231 need remove atom 25297 need remove atom 25299 need remove atom 25365 need remove atom 25367 need remove atom 25433 need remove atom 25435 need remove atom 25501 need remove atom 25503 need remove atom 25569 need remove atom 25571 need remove atom 25637 need remove atom 25639 need remove atom 25705 need remove atom 25707 need remove atom 25773 need remove atom 25775 need remove atom 25841 need remove atom 25843 need remove atom 25909 need remove atom 25911 need remove atom 25977 need remove atom 25979 need remove atom 26045 need remove atom 26047 need remove atom 26113 need remove atom 26115 need remove atom 26181 need remove atom 26183 need remove atom 26249 need remove atom 26251 need remove atom 26317 need remove atom 26319 need remove atom 26385 need remove atom 26387 need remove atom 26453 need remove atom 26455 need remove atom 26521 need remove atom 26523 need remove atom 26589 need remove atom 26591 need remove atom 26657 need remove atom 26659 need remove atom 26725 need remove atom 26727 need remove atom 26793 need remove atom 26795 need remove atom 26861 need remove atom 26863 need remove atom 26929 need remove atom 26931 need remove atom 26997 need remove atom 26999 need remove atom 27065 need remove atom 27067 need remove atom 27133 need remove atom 27135 need remove atom 27201 need remove atom 27203 need remove atom 27269 need remove atom 27271 need remove atom 27337 need remove atom 27339 need remove atom 27405 need remove atom 27407 need remove atom 27473 need remove atom 27475 need remove atom 27541 need remove atom 27543 need remove atom 27609 need remove atom 27611 need remove atom 27677 need remove atom 27679 need remove atom 27745 need remove atom 27747 need remove atom 27813 need remove atom 27815 need remove atom 27881 need remove atom 27883 need remove atom 27949 need remove atom 27951 need remove atom 28017 need remove atom 28019 need remove atom 28085 need remove atom 28087 need remove atom 28153 need remove atom 28155 need remove atom 28221 need remove atom 28223 need remove atom 28289 need remove atom 28291 [I] need removenum=555 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5014460869e-01 1.7235401671e-01 5.9494403453e-02 dub= -5.7696744405e-01 1.7235782399e-01 -6.0567223908e-02 duc= 5.5014618271e-01 -1.7456049185e-01 5.9494594587e-02 [I] overall tilt ux= -1.1271120527e+00 3.8072807595e-06 -1.2006162736e-01 uy= 1.5740153233e-06 -3.4691450855e-01 1.9113472395e-07 [I] storedr[0]= -1.4459891009e-02 -1.1022753079e-03 -2.1131101991e-04 [I] originally 45288 atoms [I] insert 0 atoms [I] now 45288 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 45288 atoms [I] remove 555 atoms [I] now 44733 atoms [I] NP=44733 n=44733 [I] ASSIGN finalcnfile = dipole_3.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 21:27:17 2023 CPU time spent: 3.810078 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 22:16:51 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 7 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 43 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 3 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=61404 [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) = 0.021008403361345 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0098039215686275 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 2.1008403361e-02 0.0000000000e+00 9.8039215686e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=1.291929e+02 pxpb=0.000000e+00 pypb=1.924796e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 28573 need remove atom 28580 need remove atom 28581 need remove atom 28583 need remove atom 28588 need remove atom 28590 need remove atom 28591 need remove atom 28598 need remove atom 28599 need remove atom 28607 need remove atom 28641 need remove atom 28648 need remove atom 28649 need remove atom 28651 need remove atom 28656 need remove atom 28658 need remove atom 28659 need remove atom 28666 need remove atom 28667 need remove atom 28675 need remove atom 28709 need remove atom 28716 need remove atom 28717 need remove atom 28719 need remove atom 28724 need remove atom 28726 need remove atom 28727 need remove atom 28734 need remove atom 28735 need remove atom 28743 need remove atom 28777 need remove atom 28784 need remove atom 28785 need remove atom 28787 need remove atom 28792 need remove atom 28794 need remove atom 28795 need remove atom 28802 need remove atom 28803 need remove atom 28811 need remove atom 28845 need remove atom 28852 need remove atom 28853 need remove atom 28855 need remove atom 28860 need remove atom 28862 need remove atom 28863 need remove atom 28870 need remove atom 28871 need remove atom 28879 need remove atom 28913 need remove atom 28920 need remove atom 28921 need remove atom 28923 need remove atom 28928 need remove atom 28930 need remove atom 28931 need remove atom 28938 need remove atom 28939 need remove atom 28947 need remove atom 28981 need remove atom 28988 need remove atom 28989 need remove atom 28991 need remove atom 28996 need remove atom 28998 need remove atom 28999 need remove atom 29006 need remove atom 29007 need remove atom 29015 need remove atom 29049 need remove atom 29056 need remove atom 29057 need remove atom 29059 need remove atom 29064 need remove atom 29066 need remove atom 29067 need remove atom 29074 need remove atom 29075 need remove atom 29083 need remove atom 29117 need remove atom 29124 need remove atom 29125 need remove atom 29127 need remove atom 29132 need remove atom 29134 need remove atom 29135 need remove atom 29142 need remove atom 29143 need remove atom 29151 need remove atom 29185 need remove atom 29192 need remove atom 29193 need remove atom 29195 need remove atom 29200 need remove atom 29202 need remove atom 29203 need remove atom 29210 need remove atom 29211 need remove atom 29219 need remove atom 29253 need remove atom 29260 need remove atom 29261 need remove atom 29263 need remove atom 29268 need remove atom 29270 need remove atom 29271 need remove atom 29278 need remove atom 29279 need remove atom 29287 need remove atom 29321 need remove atom 29328 need remove atom 29329 need remove atom 29331 need remove atom 29336 need remove atom 29338 need remove atom 29339 need remove atom 29346 need remove atom 29347 need remove atom 29355 need remove atom 29389 need remove atom 29396 need remove atom 29397 need remove atom 29399 need remove atom 29404 need remove atom 29406 need remove atom 29407 need remove atom 29414 need remove atom 29415 need remove atom 29423 need remove atom 29457 need remove atom 29464 need remove atom 29465 need remove atom 29467 need remove atom 29472 need remove atom 29474 need remove atom 29475 need remove atom 29482 need remove atom 29483 need remove atom 29491 need remove atom 29525 need remove atom 29532 need remove atom 29533 need remove atom 29535 need remove atom 29540 need remove atom 29542 need remove atom 29543 need remove atom 29550 need remove atom 29551 need remove atom 29559 need remove atom 29593 need remove atom 29600 need remove atom 29601 need remove atom 29603 need remove atom 29608 need remove atom 29610 need remove atom 29611 need remove atom 29618 need remove atom 29619 need remove atom 29627 need remove atom 29661 need remove atom 29668 need remove atom 29669 need remove atom 29671 need remove atom 29676 need remove atom 29678 need remove atom 29679 need remove atom 29686 need remove atom 29687 need remove atom 29695 need remove atom 29729 need remove atom 29736 need remove atom 29737 need remove atom 29739 need remove atom 29744 need remove atom 29746 need remove atom 29747 need remove atom 29754 need remove atom 29755 need remove atom 29763 need remove atom 29797 need remove atom 29804 need remove atom 29805 need remove atom 29807 need remove atom 29812 need remove atom 29814 need remove atom 29815 need remove atom 29822 need remove atom 29823 need remove atom 29831 need remove atom 29865 need remove atom 29872 need remove atom 29873 need remove atom 29875 need remove atom 29880 need remove atom 29882 need remove atom 29883 need remove atom 29890 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need remove atom 32875 need remove atom 32891 need remove atom 32925 need remove atom 32940 need remove atom 32942 need remove atom 32943 need remove atom 32959 need remove atom 32993 need remove atom 33008 need remove atom 33010 need remove atom 33011 need remove atom 33027 [I] need removenum=645 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.4960389125e-01 1.7253867679e-01 5.9392535781e-02 dub= -5.7636815124e-01 1.7254241780e-01 -6.0450210288e-02 duc= 5.4960547002e-01 -1.7473184078e-01 5.9392726739e-02 [I] overall tilt ux= -1.1259720425e+00 3.7410090724e-06 -1.1984274607e-01 uy= 1.5787710912e-06 -3.4727051757e-01 1.9095740809e-07 [I] storedr[0]= -1.4273220149e-02 -1.0955107960e-03 -2.4786995559e-04 [I] originally 61404 atoms [I] insert 0 atoms [I] now 61404 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 61404 atoms [I] remove 645 atoms [I] now 60759 atoms [I] NP=60759 n=60759 [I] ASSIGN finalcnfile = dipole_3.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_3.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_3.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 22:16:57 2023 CPU time spent: 5.171237 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 22:46:11 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 8 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 49 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=106624 [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) = 0.018382352941176 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0073529411764706 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.8382352941e-02 0.0000000000e+00 7.3529411765e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=1.476490e+02 pxpb=0.000000e+00 pypb=2.193372e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 43294 need remove atom 43307 need remove atom 43308 need remove atom 43309 need remove atom 43315 need remove atom 43362 need remove atom 43375 need remove atom 43376 need remove atom 43377 need remove atom 43383 need remove atom 43430 need remove atom 43443 need remove atom 43444 need remove atom 43445 need remove atom 43451 need remove atom 43498 need remove atom 43511 need remove atom 43512 need remove atom 43513 need remove atom 43519 need remove atom 43566 need remove atom 43574 need remove atom 43575 need remove atom 43579 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minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.4919555900e-01 1.7267759222e-01 5.9315782702e-02 dub= -5.7591512251e-01 1.7268128286e-01 -6.0362034155e-02 duc= 5.4919714133e-01 -1.7486073480e-01 5.9315973522e-02 [I] overall tilt ux= -1.1251106815e+00 3.6906450467e-06 -1.1967781686e-01 uy= 1.5823285774e-06 -3.4753832702e-01 1.9082085276e-07 [I] storedr[0]= -1.4134352190e-02 -1.0904200594e-03 -2.7575157329e-04 [I] originally 106624 atoms [I] insert 0 atoms [I] now 106624 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 106624 atoms [I] remove 980 atoms [I] now 105644 atoms [I] NP=105644 n=105644 [I] ASSIGN finalcnfile = dipole_4.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_4.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_4.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 22:46:21 2023 CPU time spent: 9.024387 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 23:31:20 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 9 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 56 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 4 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=137088 [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) = 0.016339869281046 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0073529411764706 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.6339869281e-02 0.0000000000e+00 7.3529411765e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=1.661052e+02 pxpb=0.000000e+00 pypb=2.506710e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 64756 need remove atom 64757 need remove atom 64772 need remove atom 64774 need remove atom 64775 need remove atom 64824 need remove atom 64825 need remove atom 64840 need remove atom 64842 need remove atom 64843 need remove atom 64892 need remove atom 64893 need remove atom 64908 need remove atom 64910 need remove atom 64911 need remove atom 64960 need remove atom 64961 need remove atom 64976 need remove atom 64978 need remove atom 64979 need remove atom 65021 need remove atom 65028 need remove atom 65029 need remove atom 65036 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need remove atom 67409 need remove atom 67416 need remove atom 67417 need remove atom 67419 need remove atom 67424 need remove atom 67426 need remove atom 67427 need remove atom 67435 need remove atom 67469 need remove atom 67476 need remove atom 67477 need remove atom 67484 need remove atom 67485 need remove atom 67487 need remove atom 67492 need remove atom 67494 need remove atom 67495 need remove atom 67503 need remove atom 67537 need remove atom 67544 need remove atom 67545 need remove atom 67552 need remove atom 67553 need remove atom 67555 need remove atom 67560 need remove atom 67562 need remove atom 67563 need remove atom 67571 need remove atom 67605 need remove atom 67612 need remove atom 67613 need remove atom 67620 need remove atom 67621 need remove atom 67623 need remove atom 67628 need remove atom 67630 need remove atom 67631 need remove atom 67639 need remove atom 67673 need remove atom 67680 need remove atom 67681 need remove atom 67688 need remove atom 67689 need remove atom 67691 need remove atom 67696 need remove atom 67698 need remove atom 67699 need remove atom 67707 need remove atom 67741 need remove atom 67748 need remove atom 67749 need remove atom 67756 need remove atom 67757 need remove atom 67759 need remove atom 67764 need remove atom 67766 need remove atom 67767 need remove atom 67775 need remove atom 67809 need remove atom 67816 need remove atom 67817 need remove atom 67824 need remove atom 67825 need remove atom 67827 need remove atom 67832 need remove atom 67834 need remove atom 67835 need remove atom 67843 need remove atom 67877 need remove atom 67884 need remove atom 67885 need remove atom 67892 need remove atom 67893 need remove atom 67895 need remove atom 67900 need remove atom 67902 need remove atom 67903 need remove atom 67911 need remove atom 67945 need remove atom 67952 need remove atom 67953 need remove atom 67960 need remove atom 67961 need remove atom 67963 need remove atom 67968 need remove atom 67970 need remove atom 67971 need remove atom 67979 need remove atom 68013 need remove atom 68020 need remove atom 68021 need remove atom 68028 need remove atom 68029 need remove atom 68031 need remove atom 68036 need remove atom 68038 need remove atom 68039 need remove atom 68047 need remove atom 68081 need remove atom 68088 need remove atom 68089 need remove atom 68096 need remove atom 68097 need remove atom 68099 need remove atom 68104 need remove atom 68106 need remove atom 68107 need remove atom 68115 need remove atom 68149 need remove atom 68156 need remove atom 68157 need remove atom 68164 need remove atom 68165 need remove atom 68167 need remove atom 68172 need remove atom 68174 need remove atom 68175 need remove atom 68183 need remove atom 68217 need remove atom 68224 need remove atom 68225 need remove atom 68232 need remove atom 68233 need remove atom 68235 need remove atom 68240 need remove atom 68242 need remove atom 68243 need remove atom 68251 need remove atom 68285 need remove atom 68292 need remove atom 68293 need remove atom 68300 need remove atom 68301 need remove atom 68303 need remove atom 68308 need remove atom 68310 need remove atom 68311 need remove atom 68319 need remove atom 68353 need remove atom 68360 need remove atom 68361 need remove atom 68368 need remove atom 68369 need remove atom 68371 need remove atom 68376 need remove atom 68378 need remove atom 68379 need remove atom 68387 need remove atom 68421 need remove atom 68428 need remove atom 68429 need remove atom 68436 need remove atom 68437 need remove atom 68439 need remove atom 68444 need remove atom 68446 need remove atom 68447 need remove atom 68455 need remove atom 68489 need remove atom 68496 need remove atom 68497 need remove atom 68504 need remove atom 68505 need remove atom 68507 need remove atom 68512 need remove atom 68514 need remove atom 68515 need remove atom 68523 need remove atom 68557 need remove atom 68564 need remove atom 68565 need remove atom 68572 need remove atom 68573 need remove atom 68575 need remove atom 68580 need remove atom 68582 need remove atom 68583 need remove atom 68591 need remove atom 68625 need remove atom 68632 need remove atom 68633 need remove atom 68640 need remove atom 68641 need remove atom 68643 need remove atom 68648 need remove atom 68650 need remove atom 68651 need remove atom 68659 need remove atom 68693 need remove atom 68700 need remove atom 68701 need remove atom 68708 need remove atom 68709 need remove atom 68711 need remove atom 68716 need remove atom 68718 need remove atom 68719 need remove atom 68727 need remove atom 68761 need remove atom 68768 need remove atom 68769 need remove atom 68776 need remove atom 68777 need remove atom 68779 need remove atom 68784 need remove atom 68786 need remove atom 68787 need remove atom 68795 need remove atom 68829 need remove atom 68836 need remove atom 68837 need remove atom 68844 need remove atom 68845 need remove atom 68847 need remove atom 68852 need remove atom 68854 need remove atom 68855 need remove atom 68863 need remove atom 68897 need remove atom 68904 need remove atom 68905 need remove atom 68912 need remove atom 68913 need remove atom 68915 need remove atom 68920 need remove atom 68922 need remove atom 68923 need remove atom 68931 need remove atom 68965 need remove atom 68972 need remove atom 68973 need remove atom 68980 need remove atom 68981 need remove atom 68983 need remove atom 68988 need remove atom 68990 need remove atom 68991 need remove atom 68999 need remove atom 69033 need remove atom 69040 need remove atom 69041 need remove atom 69048 need remove atom 69049 need remove atom 69051 need remove atom 69056 need remove atom 69058 need remove atom 69059 need remove atom 69067 need remove atom 69101 need remove atom 69108 need remove atom 69109 need remove atom 69116 need remove atom 69117 need remove atom 69119 need remove atom 69124 need remove atom 69126 need remove atom 69127 need remove atom 69135 need remove atom 69169 need remove atom 69176 need remove atom 69177 need remove atom 69184 need remove atom 69185 need remove atom 69187 need remove atom 69192 need remove atom 69194 need remove atom 69195 need remove atom 69203 need remove atom 69237 need remove atom 69244 need remove atom 69245 need remove atom 69252 need remove atom 69253 need remove atom 69255 need remove atom 69260 need remove atom 69262 need remove atom 69263 need remove atom 69271 need remove atom 69305 need remove atom 69312 need remove atom 69313 need remove atom 69320 need remove atom 69321 need remove atom 69323 need remove atom 69328 need remove atom 69330 need remove atom 69331 need remove atom 69339 need remove atom 69373 need remove atom 69380 need remove atom 69381 need remove atom 69388 need remove atom 69389 need remove atom 69391 need remove atom 69396 need remove atom 69398 need remove atom 69399 need remove atom 69407 need remove atom 69441 need remove atom 69448 need remove atom 69449 need remove atom 69456 need remove atom 69457 need remove atom 69459 need remove atom 69464 need remove atom 69466 need remove atom 69467 need remove atom 69475 need remove atom 69509 need remove atom 69516 need remove atom 69517 need remove atom 69524 need remove atom 69525 need remove atom 69527 need remove atom 69532 need remove atom 69534 need remove atom 69535 need remove atom 69543 need remove atom 69577 need remove atom 69584 need remove atom 69585 need remove atom 69592 need remove atom 69593 need remove atom 69595 need remove atom 69600 need remove atom 69602 need remove atom 69603 need remove atom 69611 need remove atom 69645 need remove atom 69652 need remove atom 69653 need remove atom 69660 need remove atom 69661 need remove atom 69663 need remove atom 69668 need remove atom 69670 need remove atom 69671 need remove atom 69679 need remove atom 69713 need remove atom 69720 need remove atom 69721 need remove atom 69728 need remove atom 69729 need remove atom 69731 need remove atom 69736 need remove atom 69738 need remove atom 69739 need remove atom 69747 need remove atom 69781 need remove atom 69788 need remove atom 69789 need remove atom 69796 need remove atom 69797 need remove atom 69799 need remove atom 69804 need remove atom 69806 need remove atom 69807 need remove atom 69815 need remove atom 69849 need remove atom 69856 need remove atom 69857 need remove atom 69864 need remove atom 69865 need remove atom 69867 need remove atom 69872 need remove atom 69874 need remove atom 69875 need remove atom 69883 need remove atom 69917 need remove atom 69924 need remove atom 69925 need remove atom 69932 need remove atom 69933 need remove atom 69935 need remove atom 69940 need remove atom 69942 need remove atom 69943 need remove atom 69951 need remove atom 69985 need remove atom 69992 need remove atom 69993 need remove atom 70000 need remove atom 70001 need remove atom 70003 need remove atom 70008 need remove atom 70010 need remove atom 70011 need remove atom 70019 need remove atom 70053 need remove atom 70060 need remove atom 70061 need remove atom 70068 need remove atom 70069 need remove atom 70071 need remove atom 70076 need remove atom 70078 need remove atom 70079 need remove atom 70087 need remove atom 70121 need remove atom 70128 need remove atom 70129 need remove atom 70136 need remove atom 70137 need remove atom 70139 need remove atom 70144 need remove atom 70146 need remove atom 70147 need remove atom 70155 need remove atom 70189 need remove atom 70196 need remove atom 70197 need remove atom 70204 need remove atom 70205 need remove atom 70207 need remove atom 70212 need remove atom 70214 need remove atom 70215 need remove atom 70223 need remove atom 70257 need remove atom 70264 need remove atom 70265 need remove atom 70272 need remove atom 70273 need remove atom 70275 need remove atom 70280 need remove atom 70282 need remove atom 70283 need remove atom 70291 need remove atom 70325 need remove atom 70332 need remove atom 70333 need remove atom 70340 need remove atom 70341 need remove atom 70343 need remove atom 70348 need remove atom 70350 need remove atom 70351 need remove atom 70359 need remove atom 70393 need remove atom 70400 need remove atom 70401 need remove atom 70408 need remove atom 70409 need remove atom 70411 need remove atom 70416 need remove atom 70418 need remove atom 70419 need remove atom 70427 need remove atom 70461 need remove atom 70468 need remove atom 70469 need remove atom 70476 need remove atom 70477 need remove atom 70479 need remove atom 70484 need remove atom 70486 need remove atom 70487 need remove atom 70495 need remove atom 70529 need remove atom 70536 need remove atom 70537 need remove atom 70544 need remove atom 70545 need remove atom 70547 need remove atom 70552 need remove atom 70554 need remove atom 70555 need remove atom 70563 need remove atom 70597 need remove atom 70604 need remove atom 70605 need remove atom 70612 need remove atom 70613 need remove atom 70615 need remove atom 70620 need remove atom 70622 need remove atom 70623 need remove atom 70631 need remove atom 70665 need remove atom 70672 need remove atom 70673 need remove atom 70680 need remove atom 70681 need remove atom 70683 need remove atom 70688 need remove atom 70690 need remove atom 70691 need remove atom 70699 need remove atom 70733 need remove atom 70740 need remove atom 70741 need remove atom 70748 need remove atom 70749 need remove atom 70751 need remove atom 70756 need remove atom 70758 need remove atom 70759 need remove atom 70767 need remove atom 70801 need remove atom 70808 need remove atom 70809 need remove atom 70816 need remove atom 70817 need remove atom 70819 need remove atom 70824 need remove atom 70826 need remove atom 70827 need remove atom 70835 need remove atom 70869 need remove atom 70876 need remove atom 70877 need remove atom 70884 need remove atom 70885 need remove atom 70887 need remove atom 70892 need remove atom 70894 need remove atom 70895 need remove atom 70903 need remove atom 70937 need remove atom 70944 need remove atom 70945 need remove atom 70952 need remove atom 70953 need remove atom 70955 need remove atom 70960 need remove atom 70962 need remove atom 70963 need remove atom 70971 need remove atom 71005 need remove atom 71012 need remove atom 71013 need remove atom 71020 need remove atom 71021 need remove atom 71023 need remove atom 71028 need remove atom 71030 need remove atom 71031 need remove atom 71039 need remove atom 71073 need remove atom 71080 need remove atom 71081 need remove atom 71088 need remove atom 71089 need remove atom 71091 need remove atom 71096 need remove atom 71098 need remove atom 71099 need remove atom 71107 need remove atom 71141 need remove atom 71148 need remove atom 71149 need remove atom 71156 need remove atom 71157 need remove atom 71159 need remove atom 71164 need remove atom 71166 need remove atom 71167 need remove atom 71175 need remove atom 71209 need remove atom 71216 need remove atom 71217 need remove atom 71224 need remove atom 71225 need remove atom 71227 need remove atom 71232 need remove atom 71234 need remove atom 71235 need remove atom 71243 need remove atom 71277 need remove atom 71284 need remove atom 71285 need remove atom 71292 need remove atom 71293 need remove atom 71295 need remove atom 71300 need remove atom 71302 need remove atom 71303 need remove atom 71311 need remove atom 71345 need remove atom 71352 need remove atom 71353 need remove atom 71360 need remove atom 71361 need remove atom 71363 need remove atom 71368 need remove atom 71370 need remove atom 71371 need remove atom 71379 need remove atom 71413 need remove atom 71420 need remove atom 71421 need remove atom 71428 need remove atom 71429 need remove atom 71431 need remove atom 71436 need remove atom 71438 need remove atom 71439 need remove atom 71447 need remove atom 71481 need remove atom 71488 need remove atom 71489 need remove atom 71496 need remove atom 71497 need remove atom 71499 need remove atom 71504 need remove atom 71506 need remove atom 71507 need remove atom 71515 need remove atom 71549 need remove atom 71556 need remove atom 71557 need remove atom 71564 need remove atom 71565 need remove atom 71567 need remove atom 71572 need remove atom 71574 need remove atom 71575 need remove atom 71583 need remove atom 71617 need remove atom 71624 need remove atom 71625 need remove atom 71632 need remove atom 71633 need remove atom 71635 need remove atom 71640 need remove atom 71642 need remove atom 71643 need remove atom 71651 need remove atom 71685 need remove atom 71692 need remove atom 71693 need remove atom 71700 need remove atom 71701 need remove atom 71703 need remove atom 71708 need remove atom 71710 need remove atom 71711 need remove atom 71719 need remove atom 71753 need remove atom 71760 need remove atom 71761 need remove atom 71768 need remove atom 71769 need remove atom 71771 need remove atom 71776 need remove atom 71778 need remove atom 71779 need remove atom 71787 need remove atom 71821 need remove atom 71828 need remove atom 71829 need remove atom 71836 need remove atom 71837 need remove atom 71839 need remove atom 71844 need remove atom 71846 need remove atom 71847 need remove atom 71855 need remove atom 71889 need remove atom 71896 need remove atom 71897 need remove atom 71904 need remove atom 71905 need remove atom 71907 need remove atom 71912 need remove atom 71914 need remove atom 71915 need remove atom 71923 need remove atom 71957 need remove atom 71964 need remove atom 71965 need remove atom 71972 need remove atom 71973 need remove atom 71975 need remove atom 71980 need remove atom 71982 need remove atom 71983 need remove atom 71991 need remove atom 72025 need remove atom 72032 need remove atom 72033 need remove atom 72040 need remove atom 72041 need remove atom 72043 need remove atom 72048 need remove atom 72050 need remove atom 72051 need remove atom 72059 need remove atom 72093 need remove atom 72100 need remove atom 72101 need remove atom 72108 need remove atom 72109 need remove atom 72111 need remove atom 72116 need remove atom 72118 need remove atom 72119 need remove atom 72127 need remove atom 72161 need remove atom 72168 need remove atom 72169 need remove atom 72176 need remove atom 72177 need remove atom 72179 need remove atom 72184 need remove atom 72186 need remove atom 72187 need remove atom 72195 need remove atom 72229 need remove atom 72236 need remove atom 72237 need remove atom 72244 need remove atom 72245 need remove atom 72247 need remove atom 72252 need remove atom 72254 need remove atom 72255 need remove atom 72263 need remove atom 72297 need remove atom 72304 need remove atom 72305 need remove atom 72312 need remove atom 72313 need remove atom 72315 need remove atom 72320 need remove atom 72322 need remove atom 72323 need remove atom 72331 need remove atom 72365 need remove atom 72380 need remove atom 72381 need remove atom 72383 need remove atom 72399 need remove atom 72433 need remove atom 72448 need remove atom 72449 need remove atom 72451 need remove atom 72467 need remove atom 72501 need remove atom 72516 need remove atom 72517 need remove atom 72519 need remove atom 72535 need remove atom 72569 need remove atom 72584 need remove atom 72585 need remove atom 72587 need remove atom 72603 [I] need removenum=1120 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5138995751e-01 1.7192566602e-01 5.9730026796e-02 dub= -5.7834501514e-01 1.7192962407e-01 -6.0837812949e-02 duc= 5.5139152038e-01 -1.7416297570e-01 5.9730218324e-02 [I] overall tilt ux= -1.1297349727e+00 3.9580468236e-06 -1.2056783975e-01 uy= 1.5628677027e-06 -3.4608864172e-01 1.9152763933e-07 [I] storedr[0]= -1.4189223152e-02 -1.1173181831e-03 -3.4111666549e-04 [I] originally 137088 atoms [I] insert 0 atoms [I] now 137088 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 137088 atoms [I] remove 1120 atoms [I] now 135968 atoms [I] NP=135968 n=135968 [I] ASSIGN finalcnfile = dipole_5.0.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.0.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.0.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 23:31:33 2023 CPU time spent: 11.608886 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 23:38:31 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 10 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 62 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=210800 [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) = 0.014705882352941 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0058823529411765 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.4705882353e-02 0.0000000000e+00 5.8823529412e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=1.845613e+02 pxpb=0.000000e+00 pypb=2.775287e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 89806 need remove atom 89814 need remove atom 89815 need remove atom 89819 need remove atom 89820 need remove atom 89821 need remove atom 89823 need remove atom 89825 need remove atom 89826 need remove atom 89827 need remove atom 89874 need remove atom 89882 need remove atom 89883 need remove atom 89887 need remove atom 89888 need remove atom 89889 need remove atom 89891 need remove atom 89893 need remove atom 89894 need remove atom 89895 need remove atom 89942 need remove atom 89950 need remove atom 89951 need remove atom 89955 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atom 99687 need remove atom 99734 need remove atom 99742 need remove atom 99743 need remove atom 99747 need remove atom 99748 need remove atom 99749 need remove atom 99751 need remove atom 99753 need remove atom 99754 need remove atom 99755 need remove atom 99802 need remove atom 99810 need remove atom 99811 need remove atom 99815 need remove atom 99816 need remove atom 99817 need remove atom 99819 need remove atom 99821 need remove atom 99822 need remove atom 99823 need remove atom 99870 need remove atom 99878 need remove atom 99879 need remove atom 99883 need remove atom 99884 need remove atom 99885 need remove atom 99887 need remove atom 99889 need remove atom 99890 need remove atom 99891 need remove atom 99938 need remove atom 99946 need remove atom 99947 need remove atom 99951 need remove atom 99952 need remove atom 99953 need remove atom 99955 need remove atom 99957 need remove atom 99958 need remove atom 99959 need remove atom 100006 need remove atom 100014 need remove atom 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remove atom 100292 need remove atom 100293 need remove atom 100295 need remove atom 100297 need remove atom 100298 need remove atom 100299 [I] need removenum=1550 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5089453786e-01 1.7209657944e-01 5.9636122905e-02 dub= -5.7779744699e-01 1.7210047782e-01 -6.0729985554e-02 duc= 5.5089610520e-01 -1.7432159299e-01 5.9636314279e-02 [I] overall tilt ux= -1.1286919848e+00 3.8983857579e-06 -1.2036610846e-01 uy= 1.5673348578e-06 -3.4641817243e-01 1.9137393956e-07 [I] storedr[0]= -1.4087317002e-02 -1.1111308485e-03 -3.5395902820e-04 [I] originally 210800 atoms [I] insert 0 atoms [I] now 210800 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 210800 atoms [I] remove 1550 atoms [I] now 209250 atoms [I] NP=209250 n=209250 [I] ASSIGN finalcnfile = dipole_5.5.lammps [I] EXEC writeLAMMPS [I] FILEOPEN dipole_5.5.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE dipole_5.5.lammps [W] *********************************************** [W] * H is reoriented to upper triangular matrix! * [W] *********************************************** [I] writevelocity=0 [I] ASSIGN color00 = red [I] ASSIGN color01 = blue [I] ASSIGN color02 = green [I] ASSIGN color03 = magenta [I] ASSIGN color04 = cyan [I] ASSIGN color05 = purple [I] ASSIGN color06 = gray80 [I] ASSIGN color07 = white [I] ASSIGN atomradius = 0.67 [I] ASSIGN bondradius = 0.3 [I] ASSIGN bondlength = 0 [I] ASSIGN atomcolor = cyan [I] ASSIGN highlightcolor = purple [I] ASSIGN bondcolor = red [I] ASSIGN backgroundcolor = gray [I] ASSIGN fixatomcolor = yellow [I] ASSIGN plotfreq = 10 [I] ASSIGN rotateangles = 0 [I] ASSIGN rotateangles(1) = 0 [I] ASSIGN rotateangles(2) = 0 [I] ASSIGN rotateangles(3) = 1.2 [I] ASSIGN win_width = 500 [I] ASSIGN win_height = 500 [I] EXEC openwin [I] EXEC reversergb [I] EXEC alloccolors [W] No window to allocate color for! [I] EXEC rotate [W] No window to rotate for! [I] EXEC saverot [W] No window to rotate for! [I] ASSIGN NIC = 100 [I] ASSIGN NNM = 100 [I] ASSIGN plot_color_axis = 2 [I] EXEC refreshnnlist [I] ASSIGN NCS = 8 [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] ASSIGN finalcnfile = topol.cn [I] EXEC writecn [I] FILEOPEN topol.cn Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE topol.cn [I] ASSIGN plot_color_windows = 2 [I] ASSIGN plot_color_windows(1) = 0.2 [I] ASSIGN plot_color_windows(2) = 4 [I] ASSIGN plot_color_windows(3) = 0 [I] ASSIGN plot_color_windows(4) = 4 [I] ASSIGN plot_color_windows(5) = 20 [I] ASSIGN plot_color_windows(6) = 7 [I] EXEC plot [I] ASSIGN conj_ftol = 1e-07 [I] ASSIGN conj_fevalmax = 3000 [I] ASSIGN conj_fixbox = 1 [I] ASSIGN conj_dfpred = 0.0001 [I] ASSIGN stressmul = 0 [I] EXEC relax [I] Relax [I] Empty potential [I] relax: 1st potential call finished. [I] ############################################################ [I] iteration neval energy (eV) |gradient|^2 (eV^2) [I] ############################################################ 0 1 0.00000000000000e+00 0.00000000000000e+00 conj_f = 0 [I] ASSIGN finalcnfile = relaxed_b01_70_b02_50.lammps [I] EXEC calcentralsymmetry [I] ASSIGN writeall = 1 [I] EXEC writecn [I] FILEOPEN relaxed_b01_70_b02_50.lammps Configuration File for Atom Positions, Format: sx1 sy1 sz1; ... ; sxn syn szn; H(3x3) [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] EXEC writeLAMMPS [I] FILEOPEN relaxed_b01_70_b02_50.lammps data file MD++ -> LAMMPS dump file LAMMPS --> MD++ [I] WRITEFILE relaxed_b01_70_b02_50.lammps [I] writevelocity=0 [I] End Time = Tue Sep 19 23:38:51 2023 CPU time spent: 17.817980 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 23:45:20 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 11 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 68 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=254320 [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) = 0.013368983957219 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0058823529411765 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.3368983957e-02 0.0000000000e+00 5.8823529412e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=2.030174e+02 pxpb=0.000000e+00 pypb=3.043863e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 121400 need remove atom 121401 need remove atom 121416 need remove atom 121417 need remove atom 121419 need remove atom 121468 need remove atom 121469 need remove atom 121484 need remove atom 121485 need remove atom 121487 need remove atom 121536 need remove atom 121537 need remove atom 121552 need remove atom 121553 need remove atom 121555 need remove atom 121604 need remove atom 121605 need remove atom 121620 need remove atom 121621 need remove atom 121623 need remove atom 121672 need remove atom 121673 need remove atom 121688 need remove atom 121689 need remove atom 121691 need remove atom 121731 need remove atom 121733 need remove atom 121740 need remove atom 121741 need remove atom 121748 need remove atom 121749 need remove atom 121756 need remove atom 121757 need remove atom 121759 need remove atom 121767 need remove atom 121799 need remove atom 121801 need remove atom 121808 need remove atom 121809 need remove atom 121816 need remove atom 121817 need remove atom 121824 need remove atom 121825 need remove atom 121827 need remove atom 121835 need remove atom 121867 need remove atom 121869 need remove atom 121876 need remove atom 121877 need remove atom 121884 need remove atom 121885 need remove atom 121892 need remove atom 121893 need remove atom 121895 need remove atom 121903 need remove atom 121935 need remove atom 121937 need remove atom 121944 need remove atom 121945 need remove atom 121952 need remove atom 121953 need remove atom 121960 need remove atom 121961 need remove atom 121963 need remove atom 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remove atom 122277 need remove atom 122284 need remove atom 122285 need remove atom 122292 need remove atom 122293 need remove atom 122300 need remove atom 122301 need remove atom 122303 need remove atom 122311 need remove atom 122343 need remove atom 122345 need remove atom 122352 need remove atom 122353 need remove atom 122360 need remove atom 122361 need remove atom 122368 need remove atom 122369 need remove atom 122371 need remove atom 122379 need remove atom 122411 need remove atom 122413 need remove atom 122420 need remove atom 122421 need remove atom 122428 need remove atom 122429 need remove atom 122436 need remove atom 122437 need remove atom 122439 need remove atom 122447 need remove atom 122479 need remove atom 122481 need remove atom 122488 need remove atom 122489 need remove atom 122496 need remove atom 122497 need remove atom 122504 need remove atom 122505 need remove atom 122507 need remove atom 122515 need remove atom 122547 need remove atom 122549 need remove atom 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remove atom 123389 need remove atom 123391 need remove atom 123399 need remove atom 123431 need remove atom 123433 need remove atom 123440 need remove atom 123441 need remove atom 123448 need remove atom 123449 need remove atom 123456 need remove atom 123457 need remove atom 123459 need remove atom 123467 need remove atom 123499 need remove atom 123501 need remove atom 123508 need remove atom 123509 need remove atom 123516 need remove atom 123517 need remove atom 123524 need remove atom 123525 need remove atom 123527 need remove atom 123535 need remove atom 123567 need remove atom 123569 need remove atom 123576 need remove atom 123577 need remove atom 123584 need remove atom 123585 need remove atom 123592 need remove atom 123593 need remove atom 123595 need remove atom 123603 need remove atom 123635 need remove atom 123637 need remove atom 123644 need remove atom 123645 need remove atom 123652 need remove atom 123653 need remove atom 123660 need remove atom 123661 need remove atom 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remove atom 123975 need remove atom 123977 need remove atom 123984 need remove atom 123985 need remove atom 123992 need remove atom 123993 need remove atom 124000 need remove atom 124001 need remove atom 124003 need remove atom 124011 need remove atom 124043 need remove atom 124045 need remove atom 124052 need remove atom 124053 need remove atom 124060 need remove atom 124061 need remove atom 124068 need remove atom 124069 need remove atom 124071 need remove atom 124079 need remove atom 124111 need remove atom 124113 need remove atom 124120 need remove atom 124121 need remove atom 124128 need remove atom 124129 need remove atom 124136 need remove atom 124137 need remove atom 124139 need remove atom 124147 need remove atom 124179 need remove atom 124181 need remove atom 124188 need remove atom 124189 need remove atom 124196 need remove atom 124197 need remove atom 124204 need remove atom 124205 need remove atom 124207 need remove atom 124215 need remove atom 124247 need remove atom 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remove atom 124529 need remove atom 124536 need remove atom 124537 need remove atom 124544 need remove atom 124545 need remove atom 124547 need remove atom 124555 need remove atom 124587 need remove atom 124589 need remove atom 124596 need remove atom 124597 need remove atom 124604 need remove atom 124605 need remove atom 124612 need remove atom 124613 need remove atom 124615 need remove atom 124623 need remove atom 124655 need remove atom 124657 need remove atom 124664 need remove atom 124665 need remove atom 124672 need remove atom 124673 need remove atom 124680 need remove atom 124681 need remove atom 124683 need remove atom 124691 need remove atom 124723 need remove atom 124725 need remove atom 124732 need remove atom 124733 need remove atom 124740 need remove atom 124741 need remove atom 124748 need remove atom 124749 need remove atom 124751 need remove atom 124759 need remove atom 124791 need remove atom 124793 need remove atom 124800 need remove atom 124801 need remove atom 124808 need remove atom 124809 need remove atom 124816 need remove atom 124817 need remove atom 124819 need remove atom 124827 need remove atom 124859 need remove atom 124861 need remove atom 124868 need remove atom 124869 need remove atom 124876 need remove atom 124877 need remove atom 124884 need remove atom 124885 need remove atom 124887 need remove atom 124895 need remove atom 124927 need remove atom 124929 need remove atom 124936 need remove atom 124937 need remove atom 124944 need remove atom 124945 need remove atom 124952 need remove atom 124953 need remove atom 124955 need remove atom 124963 need remove atom 124995 need remove atom 124997 need remove atom 125004 need remove atom 125005 need remove atom 125012 need remove atom 125013 need remove atom 125020 need remove atom 125021 need remove atom 125023 need remove atom 125031 need remove atom 125063 need remove atom 125065 need remove atom 125072 need remove atom 125073 need remove atom 125080 need remove atom 125081 need 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remove atom 133037 need remove atom 133055 need remove atom 133087 need remove atom 133089 need remove atom 133104 need remove atom 133105 need remove atom 133123 need remove atom 133155 need remove atom 133157 need remove atom 133172 need remove atom 133173 need remove atom 133191 need remove atom 133223 need remove atom 133225 need remove atom 133240 need remove atom 133241 need remove atom 133259 [I] need removenum=1700 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5048650307e-01 1.7223684180e-01 5.9558950371e-02 dub= -5.7734601299e-01 1.7224069073e-01 -6.0641358859e-02 duc= 5.5048807405e-01 -1.7445175752e-01 5.9559141616e-02 [I] overall tilt ux= -1.1278325161e+00 3.8489333041e-06 -1.2020030923e-01 uy= 1.5709818753e-06 -3.4668859932e-01 1.9124475602e-07 [I] storedr[0]= -1.4004248091e-02 -1.1060507807e-03 -3.6467104306e-04 [I] originally 254320 atoms [I] insert 0 atoms [I] now 254320 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 254320 atoms [I] remove 1700 atoms [I] now 252620 atoms [I] NP=252620 n=252620 [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 = Tue Sep 19 23:45:45 2023 CPU time spent: 21.572614 s [I] MDFrame::initvars() [I] MDFrame::initparser() [I] EXEC setnolog [I] EXEC setoverwrite [I] ASSIGN dirname = output/lammps/in/dipole_ref [W] directory output/lammps/in/dipole_ref already exists [I] RERUN dirname = output/lammps/in/dipole_ref [I] Begin Time = Tue Sep 19 23:54:02 2023 [I] ASSIGN latticestructure = body-centered-cubic [I] ASSIGN latticeconst = 3.1651999503374 [I] ASSIGN makecnspec = 3 [I] ASSIGN makecnspec(1) = 3 [I] ASSIGN makecnspec(2) = 4 [I] ASSIGN makecnspec(3) = 12 [I] ASSIGN makecnspec(4) = -1 [I] ASSIGN makecnspec(5) = 1 [I] ASSIGN makecnspec(6) = 0 [I] ASSIGN makecnspec(7) = 74 [I] ASSIGN makecnspec(8) = 2 [I] ASSIGN makecnspec(9) = 2 [I] ASSIGN makecnspec(10) = -3 [I] ASSIGN makecnspec(11) = 5 [I] EXEC makecn [I] makecrystal [I] my_unitcell h=[ 3 -1 2 3 1 2 4 0 -3]; basis=[ 0.0294118 0 0.205882 0 0 0 0 0 0 1 0.147059 0 0.0294118 0 2 2.77556e-17 0.5 0.5 0 3 0.117647 0.5 0.323529 0 4 0.0882353 0.5 0.117647 0 5 0.235294 0.5 0.147059 0 6 0.0882353 0 0.617647 0 7 0.0588235 0 0.411765 0 8 0.205882 0 0.441176 0 9 0.176471 0 0.235294 0 10 0.323529 0 0.264706 0 11 0.294118 0 0.0588235 0 12 0.441176 0 0.0882353 0 13 0.0588235 0.5 0.911765 0 14 0.0294118 0.5 0.705882 0 15 0.176471 0.5 0.735294 0 16 0.147059 0.5 0.529412 0 17 0.294118 0.5 0.558824 0 18 0.264706 0.5 0.352941 0 19 0.411765 0.5 0.382353 0 20 0.382353 0.5 0.176471 0 21 0.529412 0.5 0.205882 0 22 0.5 0.5 -5.55112e-17 0 23 0.647059 0.5 0.0294118 0 24 0.117647 0 0.823529 0 25 0.264706 0 0.852941 0 26 0.235294 0 0.647059 0 27 0.382353 0 0.676471 0 28 0.352941 0 0.470588 0 29 0.5 0 0.5 0 30 0.470588 0 0.294118 0 31 0.617647 0 0.323529 0 32 0.588235 0 0.117647 0 33 0.735294 0 0.147059 0 34 0.205882 0.5 0.941176 0 35 0.352941 0.5 0.970588 0 36 0.323529 0.5 0.764706 0 37 0.470588 0.5 0.794118 0 38 0.441176 0.5 0.588235 0 39 0.588235 0.5 0.617647 0 40 0.558824 0.5 0.411765 0 41 0.705882 0.5 0.441176 0 42 0.676471 0.5 0.235294 0 43 0.823529 0.5 0.264706 0 44 0.794118 0.5 0.0588235 0 45 0.941176 0.5 0.0882353 0 46 0.411765 0 0.882353 0 47 0.558824 0 0.911765 0 48 0.529412 0 0.705882 0 49 0.676471 0 0.735294 0 50 0.647059 0 0.529412 0 51 0.794118 0 0.558824 0 52 0.764706 0 0.352941 0 53 0.911765 0 0.382353 0 54 0.882353 0 0.176471 0 55 0.617647 0.5 0.823529 0 56 0.764706 0.5 0.852941 0 57 0.735294 0.5 0.647059 0 58 0.882353 0.5 0.676471 0 59 0.852941 0.5 0.470588 0 60 0.970588 0.5 0.294118 0 61 0.705882 0 0.941176 0 62 0.852941 0 0.970588 0 63 0.823529 0 0.764706 0 64 0.970588 0 0.794118 0 65 0.941176 0 0.588235 0 66 0.911765 0.5 0.882353 0 67 ]; [I] makecn: _NP=301920 [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) = 0.012254901960784 [I] ASSIGN mkdipole(3) = 0 [I] ASSIGN mkdipole(4) = 0.0058823529411765 [I] ASSIGN mkdipole(5) = -0.01 [I] ASSIGN mkdipole(6) = -0.2499 [I] ASSIGN mkdipole(7) = 0.251 [I] ASSIGN mkdipole(8) = 0.28133098335885 [I] ASSIGN mkdipole(9) = -10 [I] ASSIGN mkdipole(10) = 10 [I] ASSIGN mkdipole(11) = -10 [I] ASSIGN mkdipole(12) = 10 [I] ASSIGN mkdipole(13) = 1 [I] EXEC makedipole [I] sb= 1.2254901961e-02 0.0000000000e+00 5.8823529412e-03 b= 2.7141365659e+00 0.0000000000e+00 3.8383687416e-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=2.71413656588 by=0 pxpa=2.214735e+02 pxpb=0.000000e+00 pypb=3.312439e+02 pypa=0.000000e+00 [I] allocate storedr [I] Need to remove atoms need remove atom 132304 need remove atom 132306 need remove atom 132314 need remove atom 132315 need remove atom 132319 need remove atom 132320 need remove atom 132323 need remove atom 132324 need remove atom 132326 need remove atom 132327 need remove atom 132372 need remove atom 132374 need remove atom 132382 need remove atom 132383 need remove atom 132387 need remove atom 132388 need remove atom 132391 need remove atom 132392 need remove atom 132394 need remove atom 132395 need remove atom 132440 need remove atom 132442 need remove atom 132450 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remove atom 144839 [I] need removenum=1850 minx = -10 maxx = 10 miny = -10 maxy = 10 [I] dua= 5.5014460869e-01 1.7235401671e-01 5.9494403453e-02 dub= -5.7696744405e-01 1.7235782399e-01 -6.0567223908e-02 duc= 5.5014618271e-01 -1.7456049185e-01 5.9494594587e-02 [I] overall tilt ux= -1.1271120527e+00 3.8072807593e-06 -1.2006162736e-01 uy= 1.5740153233e-06 -3.4691450855e-01 1.9113472395e-07 [I] storedr[0]= -1.3935250527e-02 -1.1018052262e-03 -3.7373964356e-04 [I] originally 301920 atoms [I] insert 0 atoms [I] now 301920 atoms [I] shiftbox to accommodate plastic strain makedipole: store=0 [I] free storedr [I] originally 301920 atoms [I] remove 1850 atoms [I] now 300070 atoms [I] NP=300070 n=300070 [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 = Tue Sep 19 23:54:31 2023 CPU time spent: 25.611222 s {"realtime":21141.73,"usertime":14482.45,"systime":73.22,"memmax":230392,"memavg":0}