forked from lijiext/lammps
Added FCC, BCC, and ICOS examples
This commit is contained in:
Aidan Thompson
parent
f8e3ea2839
commit
fb702fa9d6
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@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
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{cutoff} value = distance cutoff
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{nnn} value = number of nearest neighbors
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{degrees} values = nlvalues, l1, l2,...
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{wl} value = yes or no
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{wl/hat} value = yes or no
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{components} value = ldegree :pre
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:ule
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@ -63,7 +65,7 @@ specified distance cutoff are used.
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The optional keyword {degrees} defines the list of order parameters to
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be computed. The first argument {nlvalues} is the number of order
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parameters. This is followed by that number of integers giving the
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parameters. This is followed by that number of non-negative integers giving the
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degree of each order parameter. Because {Q}2 and all odd-degree order
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parameters are zero for atoms in cubic crystals (see
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"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
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@ -22,26 +22,70 @@ mass 1 1.0
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pair_style lj/cut ${rcut}
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pair_coeff * * 1.0 1.0 ${rcut}
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# initial velocities
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# 14 neighbors, perfect crystal
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velocity all create 5.0 482748
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fix 1 all nve
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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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# 8 neighbors, perfect crystal
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compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 8
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compute avqn all reduce ave c_qn[*]
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thermo_style custom step temp epair etotal c_avqn[*]
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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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# 14 neighbors, perfect crystal dynamically melting
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# check Q_l values
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uncompute qn
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compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 14
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print " "
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print "*******************************************************************"
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print " "
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print "Comparison with reference values of Q_l "
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print " [Table I in W. Mickel, S. C. Kapfer,"
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print " G. E. Schroeder-Turkand, K. Mecke, "
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print " J. Chem. Phys. 138, 044501 (2013).]"
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print " "
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timestep 0.003
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thermo 1
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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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run 20
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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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print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
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print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
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print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
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print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
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print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
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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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print " [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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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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print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
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print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
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print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
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print " "
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print "*******************************************************************"
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print " "
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@ -22,18 +22,67 @@ mass 1 1.0
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pair_style lj/cut ${rcut}
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pair_coeff * * 1.0 1.0 ${rcut}
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# initial velocities
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# 12 neighbors, perfect crystal
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velocity all create 5.0 482748
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fix 1 all nve
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compute qlwlhat all orientorder/atom 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]
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compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10]
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# 12 neighbors, perfect crystal dynamically melting
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thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*]
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compute qn all orientorder/atom # degrees 5 4 6 8 10 12 nnn 12
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compute avqn all reduce ave c_qn[*]
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run 0
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timestep 0.003
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thermo_style custom step temp epair etotal c_avqn[*]
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thermo 1
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# check Q_l values
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run 20
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print " "
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print "*******************************************************************"
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print " "
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print "Comparison with reference values of Q_l "
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print " [Table I in W. Mickel, S. C. Kapfer,"
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print " G. E. Schroeder-Turkand, K. Mecke, "
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print " J. Chem. Phys. 138, 044501 (2013).]"
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print " "
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variable q4ref equal 0.190
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variable q6ref equal 0.575
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variable q8ref equal 0.404
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variable q10ref equal 0.013
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variable q12ref equal 0.600
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variable q4 equal c_avql[1]
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variable q6 equal c_avql[2]
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variable q8 equal c_avql[3]
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variable q10 equal c_avql[4]
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variable q12 equal c_avql[5]
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print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
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print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
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print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
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print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
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print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
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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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print " [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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print " "
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variable w4hatref equal -0.159316
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variable w6hatref equal -0.013161
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variable w8hatref equal 0.058454
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variable w10hatref equal -0.090128
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variable w4hat equal c_avwlhat[1]
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variable w6hat equal c_avwlhat[2]
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variable w8hat equal c_avwlhat[3]
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variable w10hat equal c_avwlhat[4]
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print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)"
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print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
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print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
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print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
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print " "
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print "*******************************************************************"
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print " "
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@ -0,0 +1,106 @@
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# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster
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# W_6_hat is sensitive to icosohedral order
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variable rcut equal 1.2 # a bit bigger than LJ Rmin
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variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2)
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# create a perfect fcc crystallite
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atom_style atomic
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boundary s s s
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lattice fcc 1.0 # neighbors at LJ Rmin
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region box block 0 2 0 2 0 2
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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region centralatom sphere 1 1 1 0.0 side in
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group centralatom region centralatom
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region mysphere sphere 1 1 1 ${rcutred} side out
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delete_atoms region mysphere
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# LJ potential
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pair_style lj/cut 100.0
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pair_coeff * * 1.0 1.0 100.0
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# define output for central atom
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compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL
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compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5]
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compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10]
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variable q6 equal c_avql[2]
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variable w6hat equal c_avwlhat[2]
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compute mype all pe/atom
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compute centralatompe centralatom reduce ave c_mype
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# gently equilibrate the crystallite
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velocity all create 0.001 482748
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fix 1 all nve
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neighbor 0.3 bin
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neigh_modify every 1 check no delay 0
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timestep 0.003
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thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat
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thermo 10
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run 10
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# quench to icosehedral cluster
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minimize 1.0e-10 1.0e-6 100 1000
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# check Q_l values
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print " "
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print "*******************************************************************"
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print " "
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print "Comparison with reference values of Q_l "
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print " [Table I in W. Mickel, S. C. Kapfer,"
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print " G. E. Schroeder-Turkand, K. Mecke, "
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print " J. Chem. Phys. 138, 044501 (2013).]"
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print " "
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variable q4ref equal 0.0
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variable q6ref equal 0.663
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variable q8ref equal 0.0
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variable q10ref equal 0.363
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variable q12ref equal 0.585
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variable q4 equal c_avql[1]
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variable q6 equal c_avql[2]
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variable q8 equal c_avql[3]
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variable q10 equal c_avql[4]
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variable q12 equal c_avql[5]
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print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
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print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
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print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
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print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
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print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
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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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print " [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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print " "
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variable w6hatref equal -0.169754
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variable w10hatref equal -0.093967
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variable w4hat equal c_avwlhat[1]
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variable w6hat equal c_avwlhat[2]
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variable w8hat equal c_avwlhat[3]
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variable w10hat equal c_avwlhat[4]
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variable w12hat equal c_avwlhat[5]
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print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
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print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
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print " "
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print "*******************************************************************"
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print " "
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