From ec06aed001ee138e85825026dd2ef5abe30a40c9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 12 Jan 2012 19:03:12 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7546 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/colloid/in.colloid | 6 +++++- examples/comb/in.comb.Cu | 11 ++++++++--- examples/comb/in.comb.HfO2 | 9 +++++++-- examples/comb/in.comb.Si | 11 ++++++++--- examples/crack/in.crack | 8 +++++++- examples/dipole/in.dipole | 6 +++++- examples/eim/in.eim | 8 +++++++- examples/ellipse/in.ellipse.gayberne | 14 +++++--------- examples/ellipse/in.ellipse.resquared | 12 ++++-------- examples/flow/in.flow.couette | 7 ++++++- examples/flow/in.flow.pois | 7 ++++++- examples/friction/in.friction | 7 ++++++- examples/hugoniostat/in.hugoniostat | 12 +++++++++--- examples/indent/in.indent | 7 ++++++- examples/indent/in.indent.min | 7 +++++-- examples/meam/in.meam | 6 +++++- examples/meam/in.meam.shear | 7 ++++++- examples/melt/in.melt | 6 +++++- examples/micelle/in.micelle | 6 +++++- examples/min/in.min | 9 +++++++-- examples/min/in.min.box | 8 +++++--- examples/msst/in.msst | 6 ++++++ examples/neb/in.neb.hop1 | 4 ++-- examples/neb/in.neb.hop2 | 4 ++-- examples/nemd/in.nemd | 5 ++++- examples/obstacle/in.obstacle | 7 +++++-- examples/peptide/in.peptide | 9 +++++++-- examples/peri/in.peri | 6 +++++- examples/pour/in.pour | 7 ++++++- examples/pour/in.pour.2d | 7 ++++++- examples/prd/in.prd | 5 +++-- examples/reax/in.reax.rdx | 13 +++++++++---- examples/reax/in.reax.tatb | 12 +++++++++--- examples/reax/in.reaxc.rdx | 10 ++++++++-- examples/reax/in.reaxc.tatb | 12 +++++++++--- examples/rigid/in.rigid | 7 ++++++- examples/rigid/in.rigid.poems | 7 ++++++- examples/rigid/in.rigid.poems2 | 7 ++++++- examples/shear/in.shear | 7 ++++++- examples/shear/in.shear.void | 7 ++++++- examples/srd/in.srd.mixture | 6 +++++- examples/srd/in.srd.pure | 6 +++++- examples/tad/in.tad | 5 +++-- 43 files changed, 251 insertions(+), 82 deletions(-) diff --git a/examples/colloid/in.colloid b/examples/colloid/in.colloid index 5265cf1007..fb4d6f3792 100644 --- a/examples/colloid/in.colloid +++ b/examples/colloid/in.colloid @@ -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 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 1000 diff --git a/examples/comb/in.comb.Cu b/examples/comb/in.comb.Cu index 5f72f3781e..6a7ea76dae 100644 --- a/examples/comb/in.comb.Cu +++ b/examples/comb/in.comb.Cu @@ -17,9 +17,6 @@ pair_coeff * * ffield.comb Cu neighbor 0.5 bin 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 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 velocity all create 10.1 2398378 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 diff --git a/examples/comb/in.comb.HfO2 b/examples/comb/in.comb.HfO2 index 9c6e6ae633..fe49d3a254 100644 --- a/examples/comb/in.comb.HfO2 +++ b/examples/comb/in.comb.HfO2 @@ -24,8 +24,6 @@ neigh_modify every 10 delay 10 check yes 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_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 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 run 10 diff --git a/examples/comb/in.comb.Si b/examples/comb/in.comb.Si index 1f140d7ae5..125fb22239 100644 --- a/examples/comb/in.comb.Si +++ b/examples/comb/in.comb.Si @@ -17,9 +17,6 @@ pair_coeff * * ffield.comb Si neighbor 0.5 bin 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 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 velocity all create 10.1 2398378 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 diff --git a/examples/crack/in.crack b/examples/crack/in.crack index a17787a7b4..29bbb37b9f 100644 --- a/examples/crack/in.crack +++ b/examples/crack/in.crack @@ -63,5 +63,11 @@ thermo 200 thermo_modify temp new 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 diff --git a/examples/dipole/in.dipole b/examples/dipole/in.dipole index 5e63206800..1a346c37e9 100644 --- a/examples/dipole/in.dipole +++ b/examples/dipole/in.dipole @@ -32,6 +32,10 @@ compute erot all erotate/sphere thermo_style custom step temp epair c_erot etotal press 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 diff --git a/examples/eim/in.eim b/examples/eim/in.eim index f6230e6073..799ba820f2 100644 --- a/examples/eim/in.eim +++ b/examples/eim/in.eim @@ -21,4 +21,10 @@ thermo 50 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 -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 diff --git a/examples/ellipse/in.ellipse.gayberne b/examples/ellipse/in.ellipse.gayberne index 2c6fe0064a..5143ee7976 100644 --- a/examples/ellipse/in.ellipse.gayberne +++ b/examples/ellipse/in.ellipse.gayberne @@ -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 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 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 -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 & +#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 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 & mtk no pchain 0 tchain 1 fix 2 all enforce2d diff --git a/examples/ellipse/in.ellipse.resquared b/examples/ellipse/in.ellipse.resquared index c9a8fd6b7a..3007114f76 100644 --- a/examples/ellipse/in.ellipse.resquared +++ b/examples/ellipse/in.ellipse.resquared @@ -23,11 +23,6 @@ compute_modify rot extra ${dof} 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_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 @@ -42,11 +37,12 @@ timestep 0.002 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] -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] +#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 & mtk no pchain 0 tchain 1 diff --git a/examples/flow/in.flow.couette b/examples/flow/in.flow.couette index 6eba1c0b31..5f92c15890 100644 --- a/examples/flow/in.flow.couette +++ b/examples/flow/in.flow.couette @@ -65,5 +65,10 @@ timestep 0.003 thermo 500 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 diff --git a/examples/flow/in.flow.pois b/examples/flow/in.flow.pois index 2fa4462c22..e6981bc5be 100644 --- a/examples/flow/in.flow.pois +++ b/examples/flow/in.flow.pois @@ -65,5 +65,10 @@ timestep 0.003 thermo 500 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 diff --git a/examples/friction/in.friction b/examples/friction/in.friction index 938c4f3bc2..3522e065c8 100644 --- a/examples/friction/in.friction +++ b/examples/friction/in.friction @@ -76,5 +76,10 @@ timestep 0.0025 thermo 1000 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 diff --git a/examples/hugoniostat/in.hugoniostat b/examples/hugoniostat/in.hugoniostat index a91111ce8a..ca8d82fb93 100644 --- a/examples/hugoniostat/in.hugoniostat +++ b/examples/hugoniostat/in.hugoniostat @@ -82,11 +82,17 @@ variable pzz equal pzz # axial stress variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress 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 fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)' +#dump id all atom 500 dump.hugoniostat + +#dump 1 all image 500 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 1 pad 5 + run 10000 # Start Run #2 @@ -122,7 +128,7 @@ variable pzz equal pzz # axial stress variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress variable time equal dt*step -thermo 100 +thermo 1000 thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)' @@ -162,7 +168,7 @@ variable pzz equal pzz # axial stress variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress variable time equal dt*step -thermo 100 +thermo 1000 thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)' diff --git a/examples/indent/in.indent b/examples/indent/in.indent index 5eac9aafb7..5e665254ef 100644 --- a/examples/indent/in.indent +++ b/examples/indent/in.indent @@ -49,7 +49,12 @@ fix 5 all enforce2d thermo 1000 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 without indenter diff --git a/examples/indent/in.indent.min b/examples/indent/in.indent.min index a09f3dafc5..1feab005c4 100644 --- a/examples/indent/in.indent.min +++ b/examples/indent/in.indent.min @@ -40,8 +40,11 @@ fix 5 all enforce2d thermo 10 -dump 1 all atom 10 dump.indent -dump_modify 1 scale no +#dump 1 all atom 10 dump.indent + +#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 diff --git a/examples/meam/in.meam b/examples/meam/in.meam index 2c09d33159..7ad2a20ff0 100644 --- a/examples/meam/in.meam +++ b/examples/meam/in.meam @@ -17,6 +17,10 @@ fix 1 all nve thermo 10 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 diff --git a/examples/meam/in.meam.shear b/examples/meam/in.meam.shear index c2aa510a13..8d55227ae8 100644 --- a/examples/meam/in.meam.shear +++ b/examples/meam/in.meam.shear @@ -62,7 +62,12 @@ unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 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_modify temp new2d diff --git a/examples/melt/in.melt b/examples/melt/in.melt index 8367b1f3fe..964f1565bb 100644 --- a/examples/melt/in.melt +++ b/examples/melt/in.melt @@ -19,7 +19,11 @@ neigh_modify every 20 delay 0 check no 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 run 250 diff --git a/examples/micelle/in.micelle b/examples/micelle/in.micelle index 33cda8df93..c1ece0b585 100644 --- a/examples/micelle/in.micelle +++ b/examples/micelle/in.micelle @@ -59,7 +59,11 @@ pair_coeff 2 3 1.0 0.88 1.12246 pair_coeff 2 4 1.0 0.75 1.12246 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 run 60000 diff --git a/examples/min/in.min b/examples/min/in.min index 5001f30ac1..15636e7042 100644 --- a/examples/min/in.min +++ b/examples/min/in.min @@ -22,7 +22,11 @@ neigh_modify delay 0 every 1 check yes fix 1 all nve 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 @@ -30,6 +34,7 @@ run 1000 neigh_modify delay 0 every 1 check yes -dump_modify 1 every 25 +#dump_modify 1 every 25 + thermo 50 minimize 1.0e-6 0.001 1000 10000 diff --git a/examples/min/in.min.box b/examples/min/in.min.box index 509d78d12e..bdf156ab10 100644 --- a/examples/min/in.min.box +++ b/examples/min/in.min.box @@ -22,7 +22,11 @@ neigh_modify delay 0 every 1 check yes fix 1 all nve 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 @@ -30,9 +34,7 @@ run 1000 neigh_modify delay 0 every 1 check yes - velocity all create 0.0 1 -dump_modify 1 every 25 thermo 50 minimize 1.0e-6 0.001 1000 10000 diff --git a/examples/msst/in.msst b/examples/msst/in.msst index 03fc08c6bd..880e990fc5 100644 --- a/examples/msst/in.msst +++ b/examples/msst/in.msst @@ -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 & 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 diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1 index d106d47a1a..9518a997e4 100644 --- a/examples/neb/in.neb.hop1 +++ b/examples/neb/in.neb.hop1 @@ -53,8 +53,8 @@ fix 3 all enforce2d thermo 100 -dump 1 nebatoms atom 10 dump.neb.$u -dump 2 nonneb atom 10 dump.nonneb.$u +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2 index 499d744afd..fd8db22aef 100644 --- a/examples/neb/in.neb.hop2 +++ b/examples/neb/in.neb.hop2 @@ -55,8 +55,8 @@ fix 3 all enforce2d thermo 100 -dump 1 nebatoms atom 10 dump.neb.$u -dump 2 nonneb atom 10 dump.nonneb.$u +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance diff --git a/examples/nemd/in.nemd b/examples/nemd/in.nemd index 4d7291e770..a4aee102b7 100644 --- a/examples/nemd/in.nemd +++ b/examples/nemd/in.nemd @@ -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 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 diff --git a/examples/obstacle/in.obstacle b/examples/obstacle/in.obstacle index 0932c3a701..d6a6cf4602 100644 --- a/examples/obstacle/in.obstacle +++ b/examples/obstacle/in.obstacle @@ -68,7 +68,10 @@ timestep 0.003 thermo 1000 thermo_modify temp mobile -dump 1 all atom 100 dump.obstacle -#dump 1 all custom 100 dump.custom id type x y z vx vy +#dump 1 all atom 100 dump.obstacle + +#dump 1 all image 500 image.*.jpg type type & +# zoom 1.6 adiam 1.5 +#dump_modify 1 pad 5 run 25000 diff --git a/examples/peptide/in.peptide b/examples/peptide/in.peptide index 4093dab30b..4e983bcd0e 100644 --- a/examples/peptide/in.peptide +++ b/examples/peptide/in.peptide @@ -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 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 -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 diff --git a/examples/peri/in.peri b/examples/peri/in.peri index 046cee9417..f382975fc2 100644 --- a/examples/peri/in.peri +++ b/examples/peri/in.peri @@ -32,6 +32,10 @@ compute 1 all damage/atom timestep 1.0e-7 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 diff --git a/examples/pour/in.pour b/examples/pour/in.pour index a0e58db342..9e7871dd74 100644 --- a/examples/pour/in.pour +++ b/examples/pour/in.pour @@ -35,7 +35,12 @@ thermo 1000 thermo_modify lost ignore norm no 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 unfix ins diff --git a/examples/pour/in.pour.2d b/examples/pour/in.pour.2d index ae38792939..3a2f0e3fc5 100644 --- a/examples/pour/in.pour.2d +++ b/examples/pour/in.pour.2d @@ -41,5 +41,10 @@ thermo 1000 thermo_modify lost ignore norm no 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 diff --git a/examples/prd/in.prd b/examples/prd/in.prd index 09a6fd850b..2b8408a783 100644 --- a/examples/prd/in.prd +++ b/examples/prd/in.prd @@ -79,8 +79,9 @@ run 100 # only output atoms near vacancy 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 pe all reduce sum c_patom diff --git a/examples/reax/in.reax.rdx b/examples/reax/in.reax.rdx index ecaf2294e7..e57ee8338d 100644 --- a/examples/reax/in.reax.rdx +++ b/examples/reax/in.reax.rdx @@ -33,12 +33,17 @@ neigh_modify every 10 delay 0 check no fix 1 all nve -thermo 1 -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 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 timestep 1.0 -#dump 1 all atom 10 dump.reax.rdx -dump 1 all custom 1 dump.reax.rdx id type q xs ys zs +#dump 1 all custom 10 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 diff --git a/examples/reax/in.reax.tatb b/examples/reax/in.reax.tatb index e2be3e6b8d..647e586d2c 100644 --- a/examples/reax/in.reax.tatb +++ b/examples/reax/in.reax.tatb @@ -34,12 +34,18 @@ neigh_modify delay 0 every 5 check no fix 1 all nve -thermo 1 -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 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 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 diff --git a/examples/reax/in.reaxc.rdx b/examples/reax/in.reaxc.rdx index 8f5e67c591..a5b911e4df 100644 --- a/examples/reax/in.reaxc.rdx +++ b/examples/reax/in.reaxc.rdx @@ -33,10 +33,16 @@ fix 1 all nve fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c 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 -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 diff --git a/examples/reax/in.reaxc.tatb b/examples/reax/in.reaxc.tatb index 0c959f30fe..03ba5b7ab3 100644 --- a/examples/reax/in.reaxc.tatb +++ b/examples/reax/in.reaxc.tatb @@ -33,12 +33,18 @@ neigh_modify delay 0 every 5 check no fix 1 all nve fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c -thermo 1 -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 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 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 diff --git a/examples/rigid/in.rigid b/examples/rigid/in.rigid index 9bbed9b737..c9de83397f 100644 --- a/examples/rigid/in.rigid +++ b/examples/rigid/in.rigid @@ -65,7 +65,12 @@ neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 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 thermo 50 diff --git a/examples/rigid/in.rigid.poems b/examples/rigid/in.rigid.poems index b05eb8150a..680b8e19dc 100644 --- a/examples/rigid/in.rigid.poems +++ b/examples/rigid/in.rigid.poems @@ -65,7 +65,12 @@ neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 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 thermo 50 diff --git a/examples/rigid/in.rigid.poems2 b/examples/rigid/in.rigid.poems2 index d972225fff..f9a1496adb 100644 --- a/examples/rigid/in.rigid.poems2 +++ b/examples/rigid/in.rigid.poems2 @@ -65,7 +65,12 @@ neigh_modify exclude group clump8 clump8 neigh_modify exclude group clump9 clump9 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 thermo 50 diff --git a/examples/shear/in.shear b/examples/shear/in.shear index 828b867df9..d7d4f9a996 100644 --- a/examples/shear/in.shear +++ b/examples/shear/in.shear @@ -62,7 +62,12 @@ unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 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_modify temp new2d diff --git a/examples/shear/in.shear.void b/examples/shear/in.shear.void index 76f8eaba65..73a25d230e 100644 --- a/examples/shear/in.shear.void +++ b/examples/shear/in.shear.void @@ -62,7 +62,12 @@ unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 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_modify temp new2d diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture index 8bcc48d311..a6c2d2b383 100644 --- a/examples/srd/in.srd.mixture +++ b/examples/srd/in.srd.mixture @@ -95,7 +95,11 @@ thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press & thermo_modify temp tbig 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 diff --git a/examples/srd/in.srd.pure b/examples/srd/in.srd.pure index c9b9e588a1..b89cb54380 100644 --- a/examples/srd/in.srd.pure +++ b/examples/srd/in.srd.pure @@ -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 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 diff --git a/examples/tad/in.tad b/examples/tad/in.tad index 6c270a6ac3..6aaf87622d 100644 --- a/examples/tad/in.tad +++ b/examples/tad/in.tad @@ -81,8 +81,9 @@ velocity all zero linear # only output atoms near vacancy 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 pe all reduce sum c_patom