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Added FCC, BCC, and ICOS examples

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This commit is contained in:
Aidan Thompson
2019-08-25 23:02:41 -06:00
parent f8e3ea2839
commit fb702fa9d6
4 changed files with 227 additions and 26 deletions
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4
doc/src/compute_orientorder_atom.txt
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@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
{cutoff} value = distance cutoff {cutoff} value = distance cutoff
{nnn} value = number of nearest neighbors {nnn} value = number of nearest neighbors
{degrees} values = nlvalues, l1, l2,... {degrees} values = nlvalues, l1, l2,...
{wl} value = yes or no
{wl/hat} value = yes or no
{components} value = ldegree :pre {components} value = ldegree :pre
:ule :ule
@ -63,7 +65,7 @@ specified distance cutoff are used.
The optional keyword {degrees} defines the list of order parameters to The optional keyword {degrees} defines the list of order parameters to
be computed. The first argument {nlvalues} is the number of order be computed. The first argument {nlvalues} is the number of order
parameters. This is followed by that number of integers giving the parameters. This is followed by that number of non-negative integers giving the
degree of each order parameter. Because {Q}2 and all odd-degree order degree of each order parameter. Because {Q}2 and all odd-degree order
parameters are zero for atoms in cubic crystals (see parameters are zero for atoms in cubic crystals (see
"Steinhardt"_#Steinhardt), the default order parameters are {Q}4, "Steinhardt"_#Steinhardt), the default order parameters are {Q}4,

74
examples/steinhardt/in.bcc
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@ -22,26 +22,70 @@ mass 1 1.0
pair_style lj/cut ${rcut} pair_style lj/cut ${rcut}
pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 ${rcut}
# initial velocities # 14 neighbors, perfect crystal
velocity all create 5.0 482748 compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes
fix 1 all nve 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]
# 8 neighbors, perfect crystal thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*]
compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 8
compute avqn all reduce ave c_qn[*]
thermo_style custom step temp epair etotal c_avqn[*]
run 0 run 0
# 14 neighbors, perfect crystal dynamically melting # check Q_l values
uncompute qn print " "
compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 14 print "*******************************************************************"
print " "
print "Comparison with reference values of Q_l "
print " [Table I in W. Mickel, S. C. Kapfer,"
print " G. E. Schroeder-Turkand, K. Mecke, "
print " J. Chem. Phys. 138, 044501 (2013).]"
print " "
timestep 0.003 variable q2ref equal 0.0
thermo 1 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
run 20 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)"
print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
# check W_l_hat values
print " "
print "Comparison with reference values of W_l_hat"
print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
print " 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)"
print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
print " "
print "*******************************************************************"
print " "

69
examples/steinhardt/in.fcc
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@ -22,18 +22,67 @@ mass 1 1.0
pair_style lj/cut ${rcut} pair_style lj/cut ${rcut}
pair_coeff * * 1.0 1.0 ${rcut} pair_coeff * * 1.0 1.0 ${rcut}
# initial velocities # 12 neighbors, perfect crystal
velocity all create 5.0 482748 compute qlwlhat all orientorder/atom wl/hat yes
fix 1 all nve 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]
# 12 neighbors, perfect crystal dynamically melting thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*]
compute qn all orientorder/atom # degrees 5 4 6 8 10 12 nnn 12 run 0
compute avqn all reduce ave c_qn[*]
timestep 0.003 # check Q_l values
thermo_style custom step temp epair etotal c_avqn[*]
thermo 1
run 20 print " "
print "*******************************************************************"
print " "
print "Comparison with reference values of Q_l "
print " [Table I in W. Mickel, S. C. Kapfer,"
print " G. E. Schroeder-Turkand, K. Mecke, "
print " 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)"
print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
# check W_l_hat values
print " "
print "Comparison with reference values of W_l_hat"
print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
print " 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)"
print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
print " "
print "*******************************************************************"
print " "

106
examples/steinhardt/in.icos Normal file
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@ -0,0 +1,106 @@
# 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
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 box
mass 1 1.0
region centralatom sphere 1 1 1 0.0 side in
group centralatom region centralatom
region mysphere sphere 1 1 1 ${rcutred} side out
delete_atoms region mysphere
# 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 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
# quench to icosehedral cluster
minimize 1.0e-10 1.0e-6 100 1000
# check Q_l values
print " "
print "*******************************************************************"
print " "
print "Comparison with reference values of Q_l "
print " [Table I in W. Mickel, S. C. Kapfer,"
print " G. E. Schroeder-Turkand, K. Mecke, "
print " 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)"
print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
# check W_l_hat values
print " "
print "Comparison with reference values of W_l_hat"
print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
print " 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)"
print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
print " "
print "*******************************************************************"
print " "