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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7546 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-01-12 19:03:12 +00:00
parent e4d07ec55c
commit ec06aed001
43 changed files with 251 additions and 82 deletions
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6
examples/colloid/in.colloid
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@ -33,7 +33,11 @@ fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 &
mtk no pchain 0 tchain 1 mtk no pchain 0 tchain 1
fix 2 all enforce2d fix 2 all enforce2d
dump 1 all atom 200 dump.colloid #dump 1 all atom 1000 dump.colloid
#dump 1 all image 1000 image.*.jpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 1 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol thermo_style custom step temp epair etotal press vol
thermo 1000 thermo 1000

11
examples/comb/in.comb.Cu
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@ -17,9 +17,6 @@ pair_coeff * * ffield.comb Cu
neighbor 0.5 bin neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve fix 1 all nve
timestep 0.00020 timestep 0.00020
@ -27,4 +24,12 @@ thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes thermo_modify norm yes
velocity all create 10.1 2398378 velocity all create 10.1 2398378
thermo 1 thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 1 all image 10 image.*.jpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Cu
run 10 run 10

9
examples/comb/in.comb.HfO2
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@ -24,8 +24,6 @@ neigh_modify every 10 delay 10 check yes
timestep 0.00020 timestep 0.00020
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2 thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes thermo_modify norm yes
@ -40,5 +38,12 @@ fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000 minimize 1.0e-12 1.0e-18 1000 10000
min_modify dmax 0.005 line quadratic min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 1 all image 10 image.*.jpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Hf O
velocity all create 300.1 2398378 velocity all create 300.1 2398378
run 10 run 10

11
examples/comb/in.comb.Si
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@ -17,9 +17,6 @@ pair_coeff * * ffield.comb Si
neighbor 0.5 bin neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve fix 1 all nve
timestep 0.00020 timestep 0.00020
@ -27,4 +24,12 @@ thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes thermo_modify norm yes
velocity all create 10.1 2398378 velocity all create 10.1 2398378
thermo 1 thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 1 all image 10 image.*.jpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Si
run 10 run 10

8
examples/crack/in.crack
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@ -63,5 +63,11 @@ thermo 200
thermo_modify temp new thermo_modify temp new
neigh_modify exclude type 2 3 neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
#dump 1 all atom 500 dump.crack
#dump 1 all image 250 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
run 5000 run 5000

6
examples/dipole/in.dipole
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@ -32,6 +32,10 @@ compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press thermo_style custom step temp epair c_erot etotal press
thermo 500 thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz #dump 1 all custom 500 dump.dipole id type x y z mux muy
#dump 1 all image 250 image.*.jpg mux type &
# zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000 run 10000

8
examples/eim/in.eim
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@ -21,4 +21,10 @@ thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1 fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100 #dump id all atom 100 dump.eim
#dump 1 all image 25 image.*.jpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3 element Na Cl
run 500

14
examples/ellipse/in.ellipse.gayberne
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@ -28,11 +28,6 @@ pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
#pair_style resquared 4.0
#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol thermo_style custom step c_rot epair etotal press vol
@ -42,12 +37,13 @@ timestep 0.002
compute q all property/atom quatw quati quatj quatk compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne & #dump 1 all custom 100 dump.ellipse.gayberne &
id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all custom 100 dump.ellipse.resquared &
# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all image 100 image.*.jpg type type &
# zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
mtk no pchain 0 tchain 1 mtk no pchain 0 tchain 1
fix 2 all enforce2d fix 2 all enforce2d

12
examples/ellipse/in.ellipse.resquared
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@ -23,11 +23,6 @@ compute_modify rot extra ${dof}
velocity all create 2.4 87287 loop geom velocity all create 2.4 87287 loop geom
#pair_style gayberne 1.0 3.0 1.0 4.0
#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
pair_style resquared 4.0 pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0 pair_coeff 1 2 3.0 1 1 1 1 0 0 0
@ -42,11 +37,12 @@ timestep 0.002
compute q all property/atom quatw quati quatj quatk compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne & #dump 1 all custom 100 dump.ellipse.resquared &
# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
dump 1 all custom 100 dump.ellipse.resquared & #dump 1 all image 100 image.*.jpg type type &
id type x y z c_q[1] c_q[2] c_q[3] c_q[4] # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
mtk no pchain 0 tchain 1 mtk no pchain 0 tchain 1

7
examples/flow/in.flow.couette
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@ -65,5 +65,10 @@ timestep 0.003
thermo 500 thermo 500
thermo_modify temp mobile thermo_modify temp mobile
dump 1 all atom 50 dump.flow #dump 1 all atom 500 dump.flow
#dump 1 all image 100 image.*.jpg type type &
# zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000 run 10000

7
examples/flow/in.flow.pois
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@ -65,5 +65,10 @@ timestep 0.003
thermo 500 thermo 500
thermo_modify temp mobile thermo_modify temp mobile
dump 1 all atom 25 dump.flow #dump 1 all atom 500 dump.flow
#dump 1 all image 100 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 10000 run 10000

7
examples/friction/in.friction
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@ -76,5 +76,10 @@ timestep 0.0025
thermo 1000 thermo 1000
thermo_modify temp new thermo_modify temp new
dump 1 all atom 500 dump.friction #dump 1 all atom 500 dump.friction
#dump 1 all image 500 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 20000 run 20000

12
examples/hugoniostat/in.hugoniostat
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@ -82,11 +82,17 @@ variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step variable time equal dt*step
thermo 100 thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)' fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
#dump id all atom 500 dump.hugoniostat
#dump 1 all image 500 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 5
run 10000 run 10000
# Start Run #2 # Start Run #2
@ -122,7 +128,7 @@ variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step variable time equal dt*step
thermo 100 thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)' fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
@ -162,7 +168,7 @@ variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step variable time equal dt*step
thermo 100 thermo 1000
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)' fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'

7
examples/indent/in.indent
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@ -49,7 +49,12 @@ fix 5 all enforce2d
thermo 1000 thermo 1000
thermo_modify temp new thermo_modify temp new
dump 1 all atom 250 dump.indent #dump 1 all atom 250 dump.indent
#dump 1 all image 1000 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 30000 run 30000
# run without indenter # run without indenter

7
examples/indent/in.indent.min
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@ -40,8 +40,11 @@ fix 5 all enforce2d
thermo 10 thermo 10
dump 1 all atom 10 dump.indent #dump 1 all atom 10 dump.indent
dump_modify 1 scale no
#dump 1 all image 25 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
minimize 1.0e-6 1.0e-6 1000 1000 minimize 1.0e-6 1.0e-6 1000 1000

6
examples/meam/in.meam
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@ -17,6 +17,10 @@ fix 1 all nve
thermo 10 thermo 10
timestep 0.001 timestep 0.001
dump 1 all atom 10 dump.meam #dump 1 all atom 50 dump.meam
#dump 1 all image 10 image.*.jpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3 element Si C
run 100 run 100

7
examples/meam/in.meam.shear
View File

@ -62,7 +62,12 @@ unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam #dump 1 all atom 500 dump.meam.shear
#dump 1 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 1 pad 4
thermo 100 thermo 100
thermo_modify temp new2d thermo_modify temp new2d

6
examples/melt/in.melt
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@ -19,7 +19,11 @@ neigh_modify every 20 delay 0 check no
fix 1 all nve fix 1 all nve
dump id all atom 50 dump.melt #dump id all atom 50 dump.melt
#dump 1 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
thermo 50 thermo 50
run 250 run 250

6
examples/micelle/in.micelle
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@ -59,7 +59,11 @@ pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246 pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000 thermo 1000
dump 1 all atom 500 dump.micelle
#dump 1 all atom 2000 dump.micelle
#dump 1 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0 reset_timestep 0
run 60000 run 60000

9
examples/min/in.min
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@ -22,7 +22,11 @@ neigh_modify delay 0 every 1 check yes
fix 1 all nve fix 1 all nve
fix 2 all enforce2d fix 2 all enforce2d
dump 1 all atom 100 dump.min #dump 1 all atom 100 dump.min
#dump 1 all image 50 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
thermo 100 thermo 100
@ -30,6 +34,7 @@ run 1000
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
dump_modify 1 every 25 #dump_modify 1 every 25
thermo 50 thermo 50
minimize 1.0e-6 0.001 1000 10000 minimize 1.0e-6 0.001 1000 10000

8
examples/min/in.min.box
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@ -22,7 +22,11 @@ neigh_modify delay 0 every 1 check yes
fix 1 all nve fix 1 all nve
fix 2 all enforce2d fix 2 all enforce2d
dump 1 all atom 100 dump.min #dump 1 all atom 500 dump.min
#dump 1 all image 500 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
thermo 100 thermo 100
@ -30,9 +34,7 @@ run 1000
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1 velocity all create 0.0 1
dump_modify 1 every 25
thermo 50 thermo 50
minimize 1.0e-6 0.001 1000 10000 minimize 1.0e-6 0.001 1000 10000

6
examples/msst/in.msst
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@ -47,4 +47,10 @@ variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal & thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal &
v_dhug v_dray v_lgr_vel v_lgr_pos f_msst v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
#dump id all atom 50 dump.msst
#dump 1 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100 run 100

4
examples/neb/in.neb.hop1
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@ -53,8 +53,8 @@ fix 3 all enforce2d
thermo 100 thermo 100
dump 1 nebatoms atom 10 dump.neb.$u #dump 1 nebatoms atom 10 dump.neb.$u
dump 2 nonneb atom 10 dump.nonneb.$u #dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance # run NEB for 2000 steps or to force tolerance

4
examples/neb/in.neb.hop2
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@ -55,8 +55,8 @@ fix 3 all enforce2d
thermo 100 thermo 100
dump 1 nebatoms atom 10 dump.neb.$u #dump 1 nebatoms atom 10 dump.neb.$u
dump 2 nonneb atom 10 dump.nonneb.$u #dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance # run NEB for 2000 steps or to force tolerance

5
examples/nemd/in.nemd
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@ -24,7 +24,10 @@ neigh_modify delay 0 every 1
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd id type x y z #dump 1 all custom 5000 dump.nemd id type x y z
#dump 1 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 1 pad 5
thermo 1000 thermo 1000

7
examples/obstacle/in.obstacle
View File

@ -68,7 +68,10 @@ timestep 0.003
thermo 1000 thermo 1000
thermo_modify temp mobile thermo_modify temp mobile
dump 1 all atom 100 dump.obstacle #dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom id type x y z vx vy
#dump 1 all image 500 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000 run 25000

9
examples/peptide/in.peptide
View File

@ -24,10 +24,15 @@ fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
group peptide type <= 12 group peptide type <= 12
dump 1 peptide atom 10 dump.peptide
#dump 1 peptide atom 10 dump.peptide
#dump 1 peptide image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 1 pad 3
compute bnd all property/local btype batom1 batom2 compute bnd all property/local btype batom1 batom2
dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] #dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300 run 300

6
examples/peri/in.peri
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@ -32,6 +32,10 @@ compute 1 all damage/atom
timestep 1.0e-7 timestep 1.0e-7
thermo 100 thermo 100
dump 1 all custom 100 dump.peri id type x y z c_1 #dump 1 all custom 100 dump.peri id type x y z c_1
#dump 1 all image 50 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 1 pad 4
run 1000 run 1000

7
examples/pour/in.pour
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@ -35,7 +35,12 @@ thermo 1000
thermo_modify lost ignore norm no thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour #dump id all atom 1000 dump.pour
#dump 1 all image 1000 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 25000 run 25000
unfix ins unfix ins

7
examples/pour/in.pour.2d
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@ -41,5 +41,10 @@ thermo 1000
thermo_modify lost ignore norm no thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour #dump id all atom 250 dump.pour
#dump 1 all image 500 image.*.jpg type type &
# zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000 run 25000

5
examples/prd/in.prd
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@ -79,8 +79,9 @@ run 100
# only output atoms near vacancy # only output atoms near vacancy
compute coord all coord/atom $r compute coord all coord/atom $r
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4 #dump events all custom 1 dump.prd id type x y z
#dump_modify events thresh c_coord != 4
compute patom all pe/atom compute patom all pe/atom
compute pe all reduce sum c_patom compute pe all reduce sum c_patom

13
examples/reax/in.reax.rdx
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@ -33,12 +33,17 @@ neigh_modify every 10 delay 0 check no
fix 1 all nve fix 1 all nve
thermo 1 thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb &
v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0 timestep 1.0
#dump 1 all atom 10 dump.reax.rdx #dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
dump 1 all custom 1 dump.reax.rdx id type q xs ys zs
#dump 1 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100 run 100

12
examples/reax/in.reax.tatb
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@ -34,12 +34,18 @@ neigh_modify delay 0 every 5 check no
fix 1 all nve fix 1 all nve
thermo 1 thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625 timestep 0.0625
dump 1 all custom 100 dump.reax.tatb id type q x y z #dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 1 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb fix 2 all reax/bonds 25 bonds.reax.tatb

10
examples/reax/in.reaxc.rdx
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@ -33,10 +33,16 @@ fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10 thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0 timestep 1.0
dump 1 all atom 10 dump.reax.rdx #dump 1 all atom 10 dump.reaxc.rdx
#dump 1 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100 run 100

12
examples/reax/in.reaxc.tatb
View File

@ -33,12 +33,18 @@ neigh_modify delay 0 every 5 check no
fix 1 all nve fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 1 thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625 timestep 0.0625
dump 1 all custom 100 dump.reax.tatb id type q x y z #dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 1 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 25 run 25

7
examples/rigid/in.rigid
View File

@ -65,7 +65,12 @@ neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9 neigh_modify exclude group clump9 clump9
thermo 100 thermo 100
dump 1 all atom 50 dump.rigid
#dump 1 all atom 50 dump.rigid
#dump 1 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 5
timestep 0.0001 timestep 0.0001
thermo 50 thermo 50

7
examples/rigid/in.rigid.poems
View File

@ -65,7 +65,12 @@ neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9 neigh_modify exclude group clump9 clump9
thermo 100 thermo 100
dump 1 all atom 50 dump.rigid
#dump 1 all atom 50 dump.rigid.poems
#dump 1 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 5
timestep 0.0001 timestep 0.0001
thermo 50 thermo 50

7
examples/rigid/in.rigid.poems2
View File

@ -65,7 +65,12 @@ neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9 neigh_modify exclude group clump9 clump9
thermo 100 thermo 100
dump 1 all atom 50 dump.rigid
#dump 1 all atom 50 dump.rigid.poems2
#dump 1 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 5
timestep 0.0001 timestep 0.0001
thermo 50 thermo 50

7
examples/shear/in.shear
View File

@ -62,7 +62,12 @@ unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear #dump 1 all atom 100 dump.shear
#dump 1 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 1 pad 4
thermo 100 thermo 100
thermo_modify temp new2d thermo_modify temp new2d

7
examples/shear/in.shear.void
View File

@ -62,7 +62,12 @@ unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear #dump 1 all atom 100 dump.shear.void
#dump 1 all image 100 image.*.jpg type type &
# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 1 pad 4
thermo 100 thermo 100
thermo_modify temp new2d thermo_modify temp new2d

6
examples/srd/in.srd.mixture
View File

@ -95,7 +95,11 @@ thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press &
thermo_modify temp tbig thermo_modify temp tbig
thermo 100 thermo 100
dump 1 all atom 250 dump.srd.mixture
#dump 1 all atom 250 dump.srd.mixture
#dump 1 all image 250 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 4 adiam 1 1 adiam 2 0.2
run 5000 run 5000

6
examples/srd/in.srd.pure
View File

@ -41,6 +41,10 @@ fix 2 all enforce2d
thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6] thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
thermo 100 thermo 100
dump 1 all atom 250 dump.srd.pure
#dump 1 all atom 250 dump.srd.pure
#dump 1 all image 250 image.*.jpg type type zoom 1.6 adiam 0.2
#dump_modify 1 pad 4
run 5000 run 5000

5
examples/tad/in.tad
View File

@ -81,8 +81,9 @@ velocity all zero linear
# only output atoms near vacancy # only output atoms near vacancy
compute coord all coord/atom $r compute coord all coord/atom $r
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4 #dump events all custom 1 dump.prd id type x y z
#dump_modify events thresh c_coord != 4
compute patom all pe/atom compute patom all pe/atom
compute pe all reduce sum c_patom compute pe all reduce sum c_patom