forked from lijiext/lammps
173 lines
5.7 KiB
Groff
173 lines
5.7 KiB
Groff
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
|