added input tutorial 1

Author: simongravelle

tutorial1/solution/improved.md.dat tutorial1/improved.md.dattutorial1/solution/improved.md.dat renamed to tutorial1/improved.md.dat

@@ -8,7 +8,44 @@ units lj
 dimension 3
 atom_style atomic
 boundary p p p
+
 # 2) System definition
+pair_style lj/cut 4.0
+read_data improved.min.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 no longer needed 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
+
 # 3) Settings
+
 # 4) Visualization
+thermo 1000
+thermo_style custom step temp pe ke etotal &
+  press v_n1_in v_n2_in c_sumcoor12
+dump viz all image 1000 myimage-*.ppm type type &
+  shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes size 800 800
+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 10917 zero yes
+timestep 0.005
+run 300000

tutorial1/improved.md.lmp

@@ -8,15 +8,30 @@ 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
+# 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
+
 # 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
+
 # 4) Visualization
 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 system
+write_data improved.min.data
+

tutorial1/solution/improved.min.data tutorial1/improved.min.datatutorial1/solution/improved.min.data renamed to tutorial1/improved.min.data

@@ -5,7 +5,46 @@
 
 # PART A - ENERGY MINIMIZATION
 # 1) Initialization
+units lj
+dimension 3
+atom_style atomic
+boundary p p p
 # 2) System definition
+
+# 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
+
 # 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
+
 # 4) Visualization
+thermo 10
+thermo_style custom step etotal press
+
 # 5) Run
+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 royalblue &
+  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 10917
+timestep 0.005
+run 15000
+