Merge pull request #31 from lammpstutorials/improve-tutorial-2

Homogenize and clean tutorial 2

Author: simongravelle

.gitignore

@@ -31,7 +31,4 @@ _region_.*
 *.rej
 
 # LAMMPS output files
-dump.*.jpg
-dump.*.ppm
-dump.*.ppm
 myimage-*.ppm

figures/CNT-breakable-stress-energy.png

@@ -1,18 +1,18 @@
 # 1) Initialization
-units           lj
-dimension       3
-atom_style      atomic
-boundary        p p p
+units lj
+dimension 3
+atom_style atomic
+boundary p p p
 # 2) System definition
 # 3) Settings
-mass            1    1.0
-mass            2    10.0
-pair_style      lj/cut 4.0
-pair_coeff      1    1    1.0 1.0
-pair_coeff      2    2    0.5 3.0
+mass 1 1.0
+mass 2 10.0
+pair_style lj/cut 4.0
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.5 3.0
 # 4) Visualization
-thermo          10
-thermo_style    custom step etotal press
+thermo 10
+thermo_style custom step etotal press
 # 5) Run
-minimize        1.0e-6 1.0e-6 1000 10000
+minimize 1.0e-6 1.0e-6 1000 10000
 # 6) Save status

figures/CNT-lenght-unbreakable.png

@@ -1,41 +1,41 @@
 # 1) Initialization
-units           lj
-dimension       3
-atom_style      atomic
-boundary        p p p
+units lj
+dimension 3
+atom_style atomic
+boundary p p p
 # 2) System definition
-pair_style      lj/cut 4.0
-read_data       min_coords.data
-region          cyl_in cylinder z 0 0 10 INF INF side in
-region          cyl_out cylinder z 0 0 10 INF INF side out
-group           grp_t1 type 1
-group           grp_t2 type 2
-group           grp_in region cyl_in
-group           grp_out region cyl_out
-group           grp_t1_in intersect grp_t1 grp_in
-group           grp_t2_out intersect grp_t2 grp_out
-delete_atoms    group grp_t1_in
-delete_atoms    group grp_t2_out
+pair_style lj/cut 4.0
+read_data min_coords.data
+region cyl_in cylinder z 0 0 10 INF INF side in
+region cyl_out cylinder z 0 0 10 INF INF side out
+group grp_t1 type 1
+group grp_t2 type 2
+group grp_in region cyl_in
+group grp_out region cyl_out
+group grp_t1_in intersect grp_t1 grp_in
+group grp_t2_out intersect grp_t2 grp_out
+delete_atoms group grp_t1_in
+delete_atoms group grp_t2_out
 # delete unnecessary groups
-group           grp_in delete
-group           grp_out delete
-group           grp_t1_in delete
-group           grp_t2_out delete
-variable        n1_in equal count(grp_t1,cyl_in)
-variable        n2_in equal count(grp_t2,cyl_in)
-compute         coor12   grp_t1   coord/atom cutoff 2.0 group grp_t2
-compute         sumcoor12 grp_t1   reduce ave c_coor12
+group grp_in delete
+group grp_out delete
+group grp_t1_in delete
+group grp_t2_out delete
+variable n1_in equal count(grp_t1,cyl_in)
+variable n2_in equal count(grp_t2,cyl_in)
+compute coor12 grp_t1 coord/atom cutoff 2.0 group grp_t2
+compute sumcoor12 grp_t1 reduce ave c_coor12
 # 3) Settings
 # 4) Visualization
-thermo          1000
-thermo_style    custom step temp pe ke etotal press v_n1_in v_n2_in c_sumcoor12
+thermo 1000
+thermo_style custom step temp pe ke etotal press v_n1_in v_n2_in c_sumcoor12
 
-dump            mydmp    all      image 100 dump.md.*.ppm type type shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes
-dump_modify     mydmp adiam 1 1 adiam 2 3 acolor 1 turquoise acolor 2 royalblue backcolor white
+dump viz all image 100 myimage.md.*.ppm type type shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes
+dump_modify viz adiam 1 1 adiam 2 3 acolor 1 turquoise acolor 2 royalblue backcolor white
 
 # 5) Run
-velocity        all create 1.0 49284 mom yes dist gaussian
-fix             mynve    all      nve
-fix             mylgv    all      langevin 1.0 1.0 0.1 1530917 zero yes
-timestep        0.005
-run             300000
+velocity all create 1.0 49284 mom yes dist gaussian
+fix mynve all nve
+fix mylgv all langevin 1.0 1.0 0.1 1530917 zero yes
+timestep 0.005
+run 300000

figures/CNT-unbreakable-length-energy.png

@@ -1,27 +1,27 @@
 # 1) Initialization
-units           lj
-dimension       3
-atom_style      atomic
-boundary        p p p
+units lj
+dimension 3
+atom_style atomic
+boundary p p p
 # 2) System definition
-region          simbox block -20 20 -20 20 -20 20
-create_box      2 simbox
+region simbox block -20 20 -20 20 -20 20
+create_box 2 simbox
 # for creating atoms
-region          cyl_in cylinder z 0 0 10 INF INF side in
-region          cyl_out cylinder z 0 0 10 INF INF side out
-create_atoms    1 random 1000 34134 cyl_out
-create_atoms    2 random 150 12756 cyl_in
+region cyl_in cylinder z 0 0 10 INF INF side in
+region cyl_out cylinder z 0 0 10 INF INF side out
+create_atoms 1 random 1000 34134 cyl_out
+create_atoms 2 random 150 12756 cyl_in
 # 3) Settings
-mass            1    1.0
-mass            2    10.0
-pair_style      lj/cut 4.0
-pair_coeff      1    1    1.0 1.0
-pair_coeff      2    2    0.5 3.0
+mass 1 1.0
+mass 2 10.0
+pair_style lj/cut 4.0
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.5 3.0
 # 4) Visualization
-thermo          10
-thermo_style    custom step etotal press
+thermo 10
+thermo_style custom step etotal press
 # 5) Run
-minimize        1.0e-6 1.0e-6 1000 10000
+minimize 1.0e-6 1.0e-6 1000 10000
 # 6) Save status
-write_data      min_coords.data
+write_data min_coords.data
 

figures/CNT-unbreakable-stress-strain.png

@@ -1,35 +1,35 @@
 # PART A - ENERGY MINIMIZATION
 # 1) Initialization
-units           lj
-dimension       3
-atom_style      atomic
-boundary        p p p
+units lj
+dimension 3
+atom_style atomic
+boundary p p p
 # 2) System definition
-region          simbox block −20 20 −20 20 −20 20
-create_box      2 simbox
-create_atoms    1 random 1500 34134 simbox overlap 0.3
-create_atoms    2 random 100 12756 simbox overlap 0.3
+region simbox block -20 20 -20 20 -20 20
+create_box 2 simbox
+create_atoms 1 random 1500 34134 simbox overlap 0.3
+create_atoms 2 random 100 12756 simbox overlap 0.3
 # 3) Settings
-mass            1    1.0
-mass            2    5.0
-pair_style      lj/cut 4.0
-pair_coeff      1    1    1.0 1.0
-pair_coeff      2    2    0.5 3.0
+mass 1 1.0
+mass 2 5.0
+pair_style lj/cut 4.0
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.5 3.0
 # 4) Visualization
-thermo          10
-thermo_style    custom step etotal press
+thermo 10
+thermo_style custom step etotal press
 # 5) Run
-minimize        1.0e−6 1.0e−6 1000 10000
+minimize 1.0e-6 1.0e-6 1000 10000
 
 # PART B - MOLECULAR DYNAMICS
 # 4) Visualization
-thermo          50
-thermo_style    custom step temp etotal pe ke press
-dump            viz      all      image 100 myimage−*.ppm type type size 800 800 zoom 1.452 shiny 0.7 fsaa yes &
-                                  view 80 10 box yes 0.025 axes no 0.0 0.0 center s 0.483725 0.510373 0.510373
-dump_modify     viz pad 9 boxcolor darkblue backcolor white adiam 1 1.6 adiam 2 4.8
+thermo 50
+thermo_style custom step temp etotal pe ke press
+dump viz all image 100 myimage-*.ppm type type size 800 800 zoom 1.452 shiny 0.7 fsaa yes &
+ view 80 10 box yes 0.025 axes no 0.0 0.0 center s 0.483725 0.510373 0.510373
+dump_modify viz pad 9 boxcolor darkblue backcolor white adiam 1 1.6 adiam 2 4.8
 # 5) Run
-fix             mynve    all      nve
-fix             mylgv    all      langevin 1.0 1.0 0.1 1530917
-timestep        0.005
-run             10000
+fix mynve all nve
+fix mylgv all langevin 1.0 1.0 0.1 1530917
+timestep 0.005
+run 10000