Added log files and updated README
This commit is contained in:
Aidan Thompson
@ -105,6 +105,7 @@ shear: sideways shear applied to 2d solid, with and without a void
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snap: use of SNAP potential for Ta
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snap: use of SNAP potential for Ta
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srd: stochastic rotation dynamics (SRD) particles as solvent
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srd: stochastic rotation dynamics (SRD) particles as solvent
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snap: NVE dynamics for BCC tantalum crystal using SNAP potential
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snap: NVE dynamics for BCC tantalum crystal using SNAP potential
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steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
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streitz: Streitz-Mintmire potential for Al2O3
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streitz: Streitz-Mintmire potential for Al2O3
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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threebody: regression test input for a variety of manybody potentials
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threebody: regression test input for a variety of manybody potentials
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176
examples/steinhardt/log.13Sept18.bcc.g++.1
Normal file
176
examples/steinhardt/log.13Sept18.bcc.g++.1
Normal file
@ -0,0 +1,176 @@
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LAMMPS (7 Aug 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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# Steinhardt-Nelson bond orientational order parameters for BCC
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variable rcut equal 3.0
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boundary p p p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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# create geometry
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lattice bcc 1.0
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Lattice spacing in x,y,z = 1.25992 1.25992 1.25992
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region box block 0 3 0 3 0 3
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create_box 1 box
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Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 54 atoms
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create_atoms CPU = 0.000282049 secs
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mass 1 1.0
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# LJ potentials
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pair_style lj/cut ${rcut}
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pair_style lj/cut 3
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pair_coeff * * 1.0 1.0 ${rcut}
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pair_coeff * * 1.0 1.0 3
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# 14 neighbors, perfect crystal
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compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes
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compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6]
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compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12]
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thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*]
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run 0
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 3 3 3
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute orientorder/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.746 | 3.746 | 3.746 Mbytes
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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]
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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
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Loop time of 9.53674e-07 on 1 procs for 0 steps with 54 atoms
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209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 9.537e-07 | | |100.00
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Nlocal: 54 ave 54 max 54 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1187 ave 1187 max 1187 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4536 ave 4536 max 4536 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 9072 ave 9072 max 9072 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9072
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Ave neighs/atom = 168
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Neighbor list builds = 0
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Dangerous builds = 0
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# check Q_l values
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print " "
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print "*******************************************************************"
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*******************************************************************
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print " "
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print "Comparison with reference values of Q_l "
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Comparison with reference values of Q_l
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print " [Table I in W. Mickel, S. C. Kapfer,"
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[Table I in W. Mickel, S. C. Kapfer,
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print " G. E. Schroeder-Turkand, K. Mecke, "
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G. E. Schroeder-Turkand, K. Mecke,
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print " J. Chem. Phys. 138, 044501 (2013).]"
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J. Chem. Phys. 138, 044501 (2013).]
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print " "
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variable q2ref equal 0.0
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variable q4ref equal 0.036
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variable q6ref equal 0.511
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variable q8ref equal 0.429
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variable q10ref equal 0.195
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variable q12ref equal 0.405
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variable q2 equal c_avql[1]
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variable q4 equal c_avql[2]
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variable q6 equal c_avql[3]
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variable q8 equal c_avql[4]
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variable q10 equal c_avql[5]
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variable q12 equal c_avql[6]
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print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)"
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q2 = 0.000000 delta = 0.0000
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print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
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q4 = 0.036370 delta = 0.0004
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print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
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q6 = 0.510688 delta = -0.0003
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print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
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q8 = 0.429322 delta = 0.0003
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print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
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q10 = 0.195191 delta = 0.0002
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print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
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q12 = 0.404799 delta = -0.0002
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# check W_l_hat values
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print " "
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print "Comparison with reference values of W_l_hat"
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Comparison with reference values of W_l_hat
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print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
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[Table I in P. Steinhardt, D. Nelson, and M. Ronchetti,
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print " Phys. Rev. B 28, 784 (1983).]"
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Phys. Rev. B 28, 784 (1983).]
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print " "
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variable w4hatref equal 0.159317
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variable w6hatref equal 0.013161
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variable w8hatref equal -0.058455
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variable w10hatref equal -0.090130
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variable w4hat equal c_avwlhat[2]
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variable w6hat equal c_avwlhat[3]
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variable w8hat equal c_avwlhat[4]
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variable w10hat equal c_avwlhat[5]
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print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)"
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w4hat = 0.159317 delta = 0.000000
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print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
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w6hat = 0.013161 delta = -0.000000
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print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
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w8hat = 0.058455 delta = 0.116910
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print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
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w10hat = -0.090130 delta = -0.000000
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print " "
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print "*******************************************************************"
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*******************************************************************
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print " "
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Total wall time: 0:00:00
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176
examples/steinhardt/log.13Sept18.bcc.g++.4
Normal file
176
examples/steinhardt/log.13Sept18.bcc.g++.4
Normal file
@ -0,0 +1,176 @@
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LAMMPS (7 Aug 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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# Steinhardt-Nelson bond orientational order parameters for BCC
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variable rcut equal 3.0
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boundary p p p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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# create geometry
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lattice bcc 1.0
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Lattice spacing in x,y,z = 1.25992 1.25992 1.25992
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region box block 0 3 0 3 0 3
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create_box 1 box
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Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 54 atoms
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create_atoms CPU = 0.000533104 secs
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mass 1 1.0
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# LJ potentials
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pair_style lj/cut ${rcut}
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pair_style lj/cut 3
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pair_coeff * * 1.0 1.0 ${rcut}
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pair_coeff * * 1.0 1.0 3
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# 14 neighbors, perfect crystal
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compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes
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compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6]
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compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12]
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|
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thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*]
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||||||
|
|
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run 0
|
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
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Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
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max neighbors/atom: 2000, page size: 100000
|
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|
master list distance cutoff = 3.3
|
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ghost atom cutoff = 3.3
|
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binsize = 1.65, bins = 3 3 3
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
|
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(2) compute orientorder/atom, occasional
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attributes: full, newton on
|
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
|
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Per MPI rank memory allocation (min/avg/max) = 3.722 | 3.722 | 3.722 Mbytes
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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]
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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
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Loop time of 3.99351e-06 on 4 procs for 0 steps with 54 atoms
|
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|
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87.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
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|
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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
|
||||||
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Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
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Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
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Other | | 3.994e-06 | | |100.00
|
||||||
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|
||||||
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Nlocal: 13.5 ave 15 max 12 min
|
||||||
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Histogram: 2 0 0 0 0 0 0 0 0 2
|
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Nghost: 819.5 ave 821 max 818 min
|
||||||
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Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 1134 ave 1260 max 1008 min
|
||||||
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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
|
||||||
172
examples/steinhardt/log.13Sept18.fcc.g++.1
Normal file
172
examples/steinhardt/log.13Sept18.fcc.g++.1
Normal file
@ -0,0 +1,172 @@
|
|||||||
|
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
|
||||||
172
examples/steinhardt/log.13Sept18.fcc.g++.4
Normal file
172
examples/steinhardt/log.13Sept18.fcc.g++.4
Normal file
@ -0,0 +1,172 @@
|
|||||||
|
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
|
||||||
235
examples/steinhardt/log.13Sept18.icos.g++.1
Normal file
235
examples/steinhardt/log.13Sept18.icos.g++.1
Normal file
@ -0,0 +1,235 @@
|
|||||||
|
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
|
||||||
235
examples/steinhardt/log.13Sept18.icos.g++.4
Normal file
235
examples/steinhardt/log.13Sept18.icos.g++.4
Normal file
@ -0,0 +1,235 @@
|
|||||||
|
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 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 63 atoms
|
||||||
|
create_atoms CPU = 0.000592947 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) = 60.76 | 60.76 | 60.76 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 0.0021821015 -3.1357444 -3.132723 -5.9994885 0.57450756 -0.013160431
|
||||||
|
Loop time of 0.15387 on 4 procs for 10 steps with 13 atoms
|
||||||
|
|
||||||
|
Performance: 16845.410 tau/day, 64.990 timesteps/s
|
||||||
|
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.7752e-06 | 1.7285e-05 | 2.9087e-05 | 0.0 | 0.01
|
||||||
|
Neigh | 0.055218 | 0.065482 | 0.073829 | 2.9 | 42.56
|
||||||
|
Comm | 0.0061202 | 0.018279 | 0.028283 | 6.3 | 11.88
|
||||||
|
Output | 0.020282 | 0.020287 | 0.020298 | 0.0 | 13.18
|
||||||
|
Modify | 2.7895e-05 | 2.8968e-05 | 2.9802e-05 | 0.0 | 0.02
|
||||||
|
Other | | 0.04978 | | | 32.35
|
||||||
|
|
||||||
|
Nlocal: 3.25 ave 4 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||||
|
Nghost: 9.75 ave 11 max 9 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
Neighs: 19.5 ave 35 max 7 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
FullNghs: 39 ave 48 max 24 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||||
|
|
||||||
|
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) = 112.9 | 112.9 | 112.9 Mbytes
|
||||||
|
Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat
|
||||||
|
10 0.0021821015 -3.1357444 -3.132723 -5.9994885 0.57450756 -0.013160431
|
||||||
|
20 0.0021821015 -3.1449613 -3.1419399 -5.9764731 0.57452454 -0.01316152
|
||||||
|
30 0.0021821015 -3.3366586 -3.3336372 -5.7717004 0.63679987 -0.16411081
|
||||||
|
40 0.0021821015 -3.4097262 -3.4067048 -5.6321229 0.66331761 -0.16975374
|
||||||
|
49 0.0021821015 -3.409754 -3.4067326 -5.6323347 0.66332496 -0.16975389
|
||||||
|
Loop time of 0.0932837 on 4 procs for 39 steps with 13 atoms
|
||||||
|
|
||||||
|
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-3.13574438249 -3.40975395519 -3.40975395529
|
||||||
|
Force two-norm initial, final = 6.46606 0.000429142
|
||||||
|
Force max component initial, final = 1.45519 0.000196446
|
||||||
|
Final line search alpha, max atom move = 1 0.000196446
|
||||||
|
Iterations, force evaluations = 39 98
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 5.4121e-05 | 9.0897e-05 | 0.00014281 | 0.0 | 0.10
|
||||||
|
Neigh | 0.019662 | 0.02379 | 0.03176 | 3.0 | 25.50
|
||||||
|
Comm | 0.0072601 | 0.014304 | 0.019575 | 3.8 | 15.33
|
||||||
|
Output | 0.033646 | 0.033654 | 0.03368 | 0.0 | 36.08
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.02144 | | | 22.99
|
||||||
|
|
||||||
|
Nlocal: 3.25 ave 6 max 1 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
Nghost: 9.75 ave 12 max 7 min
|
||||||
|
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||||
|
Neighs: 19.5 ave 49 max 1 min
|
||||||
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||||
|
FullNghs: 39 ave 72 max 12 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 156
|
||||||
|
Ave neighs/atom = 12
|
||||||
|
Neighbor list builds = 5
|
||||||
|
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 = 0.000001 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 = 0.000002 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
|
||||||
Reference in New Issue
Block a user