LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Steinhardt-Nelson bond orientational order parameters for icosahedral cluster # W_6_hat is sensitive to icosohedral order variable rcut equal 1.2 # a bit bigger than LJ Rmin variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2) # create a perfect fcc crystallite atom_style atomic boundary s s s lattice fcc 1.0 # neighbors at LJ Rmin Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region box block 0 2 0 2 0 2 create_box 1 box Created orthogonal box = (0 0 0) to (3.1748 3.1748 3.1748) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 63 atoms create_atoms CPU = 0.000341177 secs mass 1 1.0 region centralatom sphere 1 1 1 0.0 side in group centralatom region centralatom 1 atoms in group centralatom region mysphere sphere 1 1 1 ${rcutred} side out region mysphere sphere 1 1 1 0.75 side out delete_atoms region mysphere Deleted 50 atoms, new total = 13 # LJ potential pair_style lj/cut 100.0 pair_coeff * * 1.0 1.0 100.0 # define output for central atom compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL compute qlwlhat all orientorder/atom wl/hat yes cutoff 1.2 nnn NULL compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] variable q6 equal c_avql[2] variable w6hat equal c_avwlhat[2] compute mype all pe/atom compute centralatompe centralatom reduce ave c_mype # gently equilibrate the crystallite velocity all create 0.001 482748 fix 1 all nve neighbor 0.3 bin neigh_modify every 1 check no delay 0 timestep 0.003 thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat thermo 10 run 10 Neighbor list info ... update every 1 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 100.3 ghost atom cutoff = 100.3 binsize = 50.15, bins = 1 1 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) compute orientorder/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 60.87 | 60.87 | 60.87 Mbytes Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat 0 0.001 -3.134107 -3.1327224 -6 0.57452426 -0.013160601 10 0.0021974351 -3.1357656 -3.132723 -5.9995795 0.57450739 -0.013160482 Loop time of 0.210631 on 1 procs for 10 steps with 13 atoms Performance: 12305.887 tau/day, 47.476 timesteps/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.01 Neigh | 0.13335 | 0.13335 | 0.13335 | 0.0 | 63.31 Comm | 1.4782e-05 | 1.4782e-05 | 1.4782e-05 | 0.0 | 0.01 Output | 0.033121 | 0.033121 | 0.033121 | 0.0 | 15.72 Modify | 2.8849e-05 | 2.8849e-05 | 2.8849e-05 | 0.0 | 0.01 Other | | 0.0441 | | | 20.94 Nlocal: 13 ave 13 max 13 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78 ave 78 max 78 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156 ave 156 max 156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156 Ave neighs/atom = 12 Neighbor list builds = 10 Dangerous builds not checked # quench to icosehedral cluster minimize 1.0e-10 1.0e-6 100 1000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat 10 0.0021974351 -3.1357656 -3.132723 -5.9995795 0.57450739 -0.013160482 20 0.0021974351 -3.1449631 -3.1419205 -5.9766502 0.57452794 -0.01317299 30 0.0021974351 -3.377441 -3.3743984 -5.6930377 0.65479437 -0.16922776 40 0.0021974351 -3.4096335 -3.4065909 -5.6325443 0.66328926 -0.16975382 49 0.0021974351 -3.409754 -3.4067114 -5.6323333 0.66332496 -0.16975389 Loop time of 0.0821278 on 1 procs for 39 steps with 13 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3.13576562743 -3.40975395481 -3.40975395503 Force two-norm initial, final = 6.44841 0.000945077 Force max component initial, final = 1.43234 0.000348946 Final line search alpha, max atom move = 1 0.000348946 Iterations, force evaluations = 39 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00020051 | 0.00020051 | 0.00020051 | 0.0 | 0.24 Neigh | 0.024762 | 0.024762 | 0.024762 | 0.0 | 30.15 Comm | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.02 Output | 0.048263 | 0.048263 | 0.048263 | 0.0 | 58.77 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00889 | | | 10.82 Nlocal: 13 ave 13 max 13 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78 ave 78 max 78 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156 ave 156 max 156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156 Ave neighs/atom = 12 Neighbor list builds = 3 Dangerous builds not checked # check Q_l values print " " print "*******************************************************************" ******************************************************************* print " " print "Comparison with reference values of Q_l " Comparison with reference values of Q_l print " [Table I in W. Mickel, S. C. Kapfer," [Table I in W. Mickel, S. C. Kapfer, print " G. E. Schroeder-Turkand, K. Mecke, " G. E. Schroeder-Turkand, K. Mecke, print " J. Chem. Phys. 138, 044501 (2013).]" J. Chem. Phys. 138, 044501 (2013).] print " " variable q4ref equal 0.0 variable q6ref equal 0.663 variable q8ref equal 0.0 variable q10ref equal 0.363 variable q12ref equal 0.585 variable q4 equal c_avql[1] variable q6 equal c_avql[2] variable q8 equal c_avql[3] variable q10 equal c_avql[4] variable q12 equal c_avql[5] print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" q4 = 0.000002 delta = 0.0000 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.663325 delta = 0.0003 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.000003 delta = 0.0000 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.362951 delta = -0.0000 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.585423 delta = 0.0004 # check W_l_hat values print " " print "Comparison with reference values of W_l_hat" Comparison with reference values of W_l_hat print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, print " Phys. Rev. B 28, 784 (1983).]" Phys. Rev. B 28, 784 (1983).] print " " variable w6hatref equal -0.169754 variable w10hatref equal -0.093967 variable w4hat equal c_avwlhat[1] variable w6hat equal c_avwlhat[2] variable w8hat equal c_avwlhat[3] variable w10hat equal c_avwlhat[4] variable w12hat equal c_avwlhat[5] print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = -0.169754 delta = 0.000000 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.093968 delta = -0.000001 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00