Loading doc/src/compute_orientorder_atom.txt +3 −1 Original line number Diff line number Diff line Loading @@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} {cutoff} value = distance cutoff {nnn} value = number of nearest neighbors {degrees} values = nlvalues, l1, l2,... {wl} value = yes or no {wl/hat} value = yes or no {components} value = ldegree :pre :ule Loading Loading @@ -63,7 +65,7 @@ specified distance cutoff are used. The optional keyword {degrees} defines the list of order parameters to 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 parameters are zero for atoms in cubic crystals (see "Steinhardt"_#Steinhardt), the default order parameters are {Q}4, Loading examples/steinhardt/in.bcc +62 −18 Original line number Diff line number Diff line Loading @@ -22,26 +22,70 @@ mass 1 1.0 pair_style lj/cut ${rcut} pair_coeff * * 1.0 1.0 ${rcut} # initial velocities # 14 neighbors, perfect crystal velocity all create 5.0 482748 fix 1 all nve compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] # 8 neighbors, perfect crystal 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[*] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 # 14 neighbors, perfect crystal dynamically melting uncompute qn compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 14 timestep 0.003 thermo 1 run 20 # 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 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)" 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 " " examples/steinhardt/in.fcc +59 −10 Original line number Diff line number Diff line Loading @@ -22,18 +22,67 @@ mass 1 1.0 pair_style lj/cut ${rcut} pair_coeff * * 1.0 1.0 ${rcut} # initial velocities # 12 neighbors, perfect crystal velocity all create 5.0 482748 fix 1 all nve 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] # 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 compute avqn all reduce ave c_qn[*] run 0 timestep 0.003 thermo_style custom step temp epair etotal c_avqn[*] thermo 1 # check Q_l values 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 " " examples/steinhardt/in.icos 0 → 100644 +106 −0 Original line number Diff line number Diff line # 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 " " Loading
doc/src/compute_orientorder_atom.txt +3 −1 Original line number Diff line number Diff line Loading @@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} {cutoff} value = distance cutoff {nnn} value = number of nearest neighbors {degrees} values = nlvalues, l1, l2,... {wl} value = yes or no {wl/hat} value = yes or no {components} value = ldegree :pre :ule Loading Loading @@ -63,7 +65,7 @@ specified distance cutoff are used. The optional keyword {degrees} defines the list of order parameters to 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 parameters are zero for atoms in cubic crystals (see "Steinhardt"_#Steinhardt), the default order parameters are {Q}4, Loading
examples/steinhardt/in.bcc +62 −18 Original line number Diff line number Diff line Loading @@ -22,26 +22,70 @@ mass 1 1.0 pair_style lj/cut ${rcut} pair_coeff * * 1.0 1.0 ${rcut} # initial velocities # 14 neighbors, perfect crystal velocity all create 5.0 482748 fix 1 all nve compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] # 8 neighbors, perfect crystal 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[*] thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] run 0 # 14 neighbors, perfect crystal dynamically melting uncompute qn compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 14 timestep 0.003 thermo 1 run 20 # 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 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)" 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 " "
examples/steinhardt/in.fcc +59 −10 Original line number Diff line number Diff line Loading @@ -22,18 +22,67 @@ mass 1 1.0 pair_style lj/cut ${rcut} pair_coeff * * 1.0 1.0 ${rcut} # initial velocities # 12 neighbors, perfect crystal velocity all create 5.0 482748 fix 1 all nve 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] # 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 compute avqn all reduce ave c_qn[*] run 0 timestep 0.003 thermo_style custom step temp epair etotal c_avqn[*] thermo 1 # check Q_l values 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 " "
examples/steinhardt/in.icos 0 → 100644 +106 −0 Original line number Diff line number Diff line # 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 " "
