Loading examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -105,6 +105,7 @@ shear: sideways shear applied to 2d solid, with and without a void snap: use of SNAP potential for Ta srd: stochastic rotation dynamics (SRD) particles as solvent snap: NVE dynamics for BCC tantalum crystal using SNAP potential steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom streitz: Streitz-Mintmire potential for Al2O3 tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si threebody: regression test input for a variety of manybody potentials Loading examples/steinhardt/log.13Sept18.bcc.g++.1 0 → 100644 +176 −0 Original line number Diff line number Diff line 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 BCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice bcc 1.0 Lattice spacing in x,y,z = 1.25992 1.25992 1.25992 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 54 atoms create_atoms CPU = 0.000282049 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 14 neighbors, perfect crystal compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.746 | 3.746 | 3.746 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avql[6] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] c_avwlhat[6] 0 0 -7.8104466 -7.8104466 8.6570408e-17 0.036369648 0.51068823 0.42932247 0.19519122 0.40479919 0 0.15931737 0.013160601 0.058454791 -0.090130212 -0.049573639 Loop time of 9.53674e-07 on 1 procs for 0 steps with 54 atoms 209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 54 ave 54 max 54 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1187 ave 1187 max 1187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4536 ave 4536 max 4536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9072 ave 9072 max 9072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9072 Ave neighs/atom = 168 Neighbor list builds = 0 Dangerous builds = 0 # 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 q2ref equal 0.0 variable q4ref equal 0.036 variable q6ref equal 0.511 variable q8ref equal 0.429 variable q10ref equal 0.195 variable q12ref equal 0.405 variable q2 equal c_avql[1] variable q4 equal c_avql[2] variable q6 equal c_avql[3] variable q8 equal c_avql[4] variable q10 equal c_avql[5] variable q12 equal c_avql[6] print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" q2 = 0.000000 delta = 0.0000 print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" q4 = 0.036370 delta = 0.0004 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.510688 delta = -0.0003 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.429322 delta = 0.0003 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.195191 delta = 0.0002 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.404799 delta = -0.0002 # 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 w4hatref equal 0.159317 variable w6hatref equal 0.013161 variable w8hatref equal -0.058455 variable w10hatref equal -0.090130 variable w4hat equal c_avwlhat[2] variable w6hat equal c_avwlhat[3] variable w8hat equal c_avwlhat[4] variable w10hat equal c_avwlhat[5] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = 0.159317 delta = 0.000000 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = 0.013161 delta = -0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.116910 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000000 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00 examples/steinhardt/log.13Sept18.bcc.g++.4 0 → 100644 +176 −0 Original line number Diff line number Diff line 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 BCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice bcc 1.0 Lattice spacing in x,y,z = 1.25992 1.25992 1.25992 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 54 atoms create_atoms CPU = 0.000533104 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 14 neighbors, perfect crystal compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.722 | 3.722 | 3.722 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avql[6] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] c_avwlhat[6] 0 0 -7.8104466 -7.8104466 8.6382997e-17 0.036369648 0.51068823 0.42932247 0.19519122 0.40479919 0 0.15931737 0.013160601 0.058454791 -0.090130212 -0.049573639 Loop time of 3.99351e-06 on 4 procs for 0 steps with 54 atoms 87.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.994e-06 | | |100.00 Nlocal: 13.5 ave 15 max 12 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 819.5 ave 821 max 818 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 1134 ave 1260 max 1008 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 2268 ave 2520 max 2016 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 9072 Ave neighs/atom = 168 Neighbor list builds = 0 Dangerous builds = 0 # 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 q2ref equal 0.0 variable q4ref equal 0.036 variable q6ref equal 0.511 variable q8ref equal 0.429 variable q10ref equal 0.195 variable q12ref equal 0.405 variable q2 equal c_avql[1] variable q4 equal c_avql[2] variable q6 equal c_avql[3] variable q8 equal c_avql[4] variable q10 equal c_avql[5] variable q12 equal c_avql[6] print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" q2 = 0.000000 delta = 0.0000 print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" q4 = 0.036370 delta = 0.0004 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.510688 delta = -0.0003 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.429322 delta = 0.0003 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.195191 delta = 0.0002 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.404799 delta = -0.0002 # 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 w4hatref equal 0.159317 variable w6hatref equal 0.013161 variable w8hatref equal -0.058455 variable w10hatref equal -0.090130 variable w4hat equal c_avwlhat[2] variable w6hat equal c_avwlhat[3] variable w8hat equal c_avwlhat[4] variable w10hat equal c_avwlhat[5] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = 0.159317 delta = 0.000000 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = 0.013161 delta = -0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.116910 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000000 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00 examples/steinhardt/log.13Sept18.fcc.g++.1 0 → 100644 +172 −0 Original line number Diff line number Diff line 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 FCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (4.7622 4.7622 4.7622) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 108 atoms create_atoms CPU = 0.000289917 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 12 neighbors, perfect crystal compute qlwlhat all orientorder/atom wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.767 | 3.767 | 3.767 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] 0 0 -8.1295091 -8.1295091 0.19094065 0.57452426 0.40391456 0.012857043 0.60008302 -0.15931737 -0.013160601 0.058454791 -0.090130212 0.087390889 Loop time of 9.53674e-07 on 1 procs for 0 steps with 108 atoms 209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 108 ave 108 max 108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1580 ave 1580 max 1580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7560 ave 7560 max 7560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15120 ave 15120 max 15120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15120 Ave neighs/atom = 140 Neighbor list builds = 0 Dangerous builds = 0 # 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 0.190 variable q6ref equal 0.575 variable q8ref equal 0.404 variable q10ref equal 0.013 variable q12ref equal 0.600 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 = 0.190941 delta = 0.0009 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.574524 delta = -0.0005 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.403915 delta = -0.0001 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.012857 delta = -0.0001 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.600083 delta = 0.0001 # 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 w4hatref equal -0.159316 variable w6hatref equal -0.013161 variable w8hatref equal 0.058454 variable w10hatref equal -0.090128 variable w4hat equal c_avwlhat[1] variable w6hat equal c_avwlhat[2] variable w8hat equal c_avwlhat[3] variable w10hat equal c_avwlhat[4] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = -0.159317 delta = -0.000001 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = -0.013161 delta = 0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.000001 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000002 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00 examples/steinhardt/log.13Sept18.fcc.g++.4 0 → 100644 +172 −0 Original line number Diff line number Diff line 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 FCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (4.7622 4.7622 4.7622) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 108 atoms create_atoms CPU = 0.000549078 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 12 neighbors, perfect crystal compute qlwlhat all orientorder/atom wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.737 | 3.737 | 3.737 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] 0 0 -8.1295091 -8.1295091 0.19094065 0.57452426 0.40391456 0.012857043 0.60008302 -0.15931737 -0.013160601 0.058454791 -0.090130212 0.087390889 Loop time of 3.09944e-06 on 4 procs for 0 steps with 108 atoms 88.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.099e-06 | | |100.00 Nlocal: 27 ave 27 max 27 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1053 ave 1053 max 1053 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 1890 ave 1890 max 1890 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 3780 ave 3780 max 3780 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15120 Ave neighs/atom = 140 Neighbor list builds = 0 Dangerous builds = 0 # 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 0.190 variable q6ref equal 0.575 variable q8ref equal 0.404 variable q10ref equal 0.013 variable q12ref equal 0.600 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 = 0.190941 delta = 0.0009 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.574524 delta = -0.0005 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.403915 delta = -0.0001 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.012857 delta = -0.0001 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.600083 delta = 0.0001 # 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 w4hatref equal -0.159316 variable w6hatref equal -0.013161 variable w8hatref equal 0.058454 variable w10hatref equal -0.090128 variable w4hat equal c_avwlhat[1] variable w6hat equal c_avwlhat[2] variable w8hat equal c_avwlhat[3] variable w10hat equal c_avwlhat[4] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = -0.159317 delta = -0.000001 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = -0.013161 delta = 0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.000001 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000002 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00 Loading
examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -105,6 +105,7 @@ shear: sideways shear applied to 2d solid, with and without a void snap: use of SNAP potential for Ta srd: stochastic rotation dynamics (SRD) particles as solvent snap: NVE dynamics for BCC tantalum crystal using SNAP potential steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom streitz: Streitz-Mintmire potential for Al2O3 tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si threebody: regression test input for a variety of manybody potentials Loading
examples/steinhardt/log.13Sept18.bcc.g++.1 0 → 100644 +176 −0 Original line number Diff line number Diff line 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 BCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice bcc 1.0 Lattice spacing in x,y,z = 1.25992 1.25992 1.25992 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 54 atoms create_atoms CPU = 0.000282049 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 14 neighbors, perfect crystal compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.746 | 3.746 | 3.746 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avql[6] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] c_avwlhat[6] 0 0 -7.8104466 -7.8104466 8.6570408e-17 0.036369648 0.51068823 0.42932247 0.19519122 0.40479919 0 0.15931737 0.013160601 0.058454791 -0.090130212 -0.049573639 Loop time of 9.53674e-07 on 1 procs for 0 steps with 54 atoms 209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 54 ave 54 max 54 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1187 ave 1187 max 1187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4536 ave 4536 max 4536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9072 ave 9072 max 9072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9072 Ave neighs/atom = 168 Neighbor list builds = 0 Dangerous builds = 0 # 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 q2ref equal 0.0 variable q4ref equal 0.036 variable q6ref equal 0.511 variable q8ref equal 0.429 variable q10ref equal 0.195 variable q12ref equal 0.405 variable q2 equal c_avql[1] variable q4 equal c_avql[2] variable q6 equal c_avql[3] variable q8 equal c_avql[4] variable q10 equal c_avql[5] variable q12 equal c_avql[6] print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" q2 = 0.000000 delta = 0.0000 print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" q4 = 0.036370 delta = 0.0004 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.510688 delta = -0.0003 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.429322 delta = 0.0003 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.195191 delta = 0.0002 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.404799 delta = -0.0002 # 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 w4hatref equal 0.159317 variable w6hatref equal 0.013161 variable w8hatref equal -0.058455 variable w10hatref equal -0.090130 variable w4hat equal c_avwlhat[2] variable w6hat equal c_avwlhat[3] variable w8hat equal c_avwlhat[4] variable w10hat equal c_avwlhat[5] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = 0.159317 delta = 0.000000 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = 0.013161 delta = -0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.116910 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000000 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00
examples/steinhardt/log.13Sept18.bcc.g++.4 0 → 100644 +176 −0 Original line number Diff line number Diff line 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 BCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice bcc 1.0 Lattice spacing in x,y,z = 1.25992 1.25992 1.25992 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 54 atoms create_atoms CPU = 0.000533104 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 14 neighbors, perfect crystal compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.722 | 3.722 | 3.722 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avql[6] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] c_avwlhat[6] 0 0 -7.8104466 -7.8104466 8.6382997e-17 0.036369648 0.51068823 0.42932247 0.19519122 0.40479919 0 0.15931737 0.013160601 0.058454791 -0.090130212 -0.049573639 Loop time of 3.99351e-06 on 4 procs for 0 steps with 54 atoms 87.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.994e-06 | | |100.00 Nlocal: 13.5 ave 15 max 12 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 819.5 ave 821 max 818 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 1134 ave 1260 max 1008 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 2268 ave 2520 max 2016 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 9072 Ave neighs/atom = 168 Neighbor list builds = 0 Dangerous builds = 0 # 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 q2ref equal 0.0 variable q4ref equal 0.036 variable q6ref equal 0.511 variable q8ref equal 0.429 variable q10ref equal 0.195 variable q12ref equal 0.405 variable q2 equal c_avql[1] variable q4 equal c_avql[2] variable q6 equal c_avql[3] variable q8 equal c_avql[4] variable q10 equal c_avql[5] variable q12 equal c_avql[6] print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" q2 = 0.000000 delta = 0.0000 print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" q4 = 0.036370 delta = 0.0004 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.510688 delta = -0.0003 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.429322 delta = 0.0003 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.195191 delta = 0.0002 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.404799 delta = -0.0002 # 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 w4hatref equal 0.159317 variable w6hatref equal 0.013161 variable w8hatref equal -0.058455 variable w10hatref equal -0.090130 variable w4hat equal c_avwlhat[2] variable w6hat equal c_avwlhat[3] variable w8hat equal c_avwlhat[4] variable w10hat equal c_avwlhat[5] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = 0.159317 delta = 0.000000 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = 0.013161 delta = -0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.116910 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000000 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00
examples/steinhardt/log.13Sept18.fcc.g++.1 0 → 100644 +172 −0 Original line number Diff line number Diff line 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 FCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (4.7622 4.7622 4.7622) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 108 atoms create_atoms CPU = 0.000289917 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 12 neighbors, perfect crystal compute qlwlhat all orientorder/atom wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.767 | 3.767 | 3.767 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] 0 0 -8.1295091 -8.1295091 0.19094065 0.57452426 0.40391456 0.012857043 0.60008302 -0.15931737 -0.013160601 0.058454791 -0.090130212 0.087390889 Loop time of 9.53674e-07 on 1 procs for 0 steps with 108 atoms 209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 108 ave 108 max 108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1580 ave 1580 max 1580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7560 ave 7560 max 7560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15120 ave 15120 max 15120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15120 Ave neighs/atom = 140 Neighbor list builds = 0 Dangerous builds = 0 # 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 0.190 variable q6ref equal 0.575 variable q8ref equal 0.404 variable q10ref equal 0.013 variable q12ref equal 0.600 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 = 0.190941 delta = 0.0009 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.574524 delta = -0.0005 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.403915 delta = -0.0001 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.012857 delta = -0.0001 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.600083 delta = 0.0001 # 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 w4hatref equal -0.159316 variable w6hatref equal -0.013161 variable w8hatref equal 0.058454 variable w10hatref equal -0.090128 variable w4hat equal c_avwlhat[1] variable w6hat equal c_avwlhat[2] variable w8hat equal c_avwlhat[3] variable w10hat equal c_avwlhat[4] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = -0.159317 delta = -0.000001 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = -0.013161 delta = 0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.000001 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000002 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00
examples/steinhardt/log.13Sept18.fcc.g++.4 0 → 100644 +172 −0 Original line number Diff line number Diff line 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 FCC variable rcut equal 3.0 boundary p p p atom_style atomic neighbor 0.3 bin neigh_modify delay 5 # create geometry lattice fcc 1.0 Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 region box block 0 3 0 3 0 3 create_box 1 box Created orthogonal box = (0 0 0) to (4.7622 4.7622 4.7622) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 108 atoms create_atoms CPU = 0.000549078 secs mass 1 1.0 # LJ potentials pair_style lj/cut ${rcut} pair_style lj/cut 3 pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 3 # 12 neighbors, perfect crystal compute qlwlhat all orientorder/atom wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 3 3 3 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) = 3.737 | 3.737 | 3.737 Mbytes Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] 0 0 -8.1295091 -8.1295091 0.19094065 0.57452426 0.40391456 0.012857043 0.60008302 -0.15931737 -0.013160601 0.058454791 -0.090130212 0.087390889 Loop time of 3.09944e-06 on 4 procs for 0 steps with 108 atoms 88.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.099e-06 | | |100.00 Nlocal: 27 ave 27 max 27 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1053 ave 1053 max 1053 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 1890 ave 1890 max 1890 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 3780 ave 3780 max 3780 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15120 Ave neighs/atom = 140 Neighbor list builds = 0 Dangerous builds = 0 # 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 0.190 variable q6ref equal 0.575 variable q8ref equal 0.404 variable q10ref equal 0.013 variable q12ref equal 0.600 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 = 0.190941 delta = 0.0009 print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" q6 = 0.574524 delta = -0.0005 print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" q8 = 0.403915 delta = -0.0001 print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" q10 = 0.012857 delta = -0.0001 print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" q12 = 0.600083 delta = 0.0001 # 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 w4hatref equal -0.159316 variable w6hatref equal -0.013161 variable w8hatref equal 0.058454 variable w10hatref equal -0.090128 variable w4hat equal c_avwlhat[1] variable w6hat equal c_avwlhat[2] variable w8hat equal c_avwlhat[3] variable w10hat equal c_avwlhat[4] print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" w4hat = -0.159317 delta = -0.000001 print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" w6hat = -0.013161 delta = 0.000000 print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" w8hat = 0.058455 delta = 0.000001 print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" w10hat = -0.090130 delta = -0.000002 print " " print "*******************************************************************" ******************************************************************* print " " Total wall time: 0:00:00
