improve CNT tutorial

docs/inputs/level1/breaking-a-carbon-nanotube/exercises/stress-strain/breakable-bonds/input.lammps

@@ -9,7 +9,7 @@ pair_style airebo 2.5 1 1
 read_data cnt_atom.data
 pair_coeff * * CH.airebo C
 
-change_box all x final -40 40 y final -40 40 z final -60 60
+change_box all x final -60 60 y final -60 60 z final -60 60
 
 group carbon_atoms type 1
 variable carbon_xcm equal -1*xcm(carbon_atoms,x)
@@ -19,7 +19,7 @@ displace_atoms carbon_atoms move ${carbon_xcm} ${carbon_ycm} ${carbon_zcm}
 
 variable zmax equal bound(carbon_atoms,zmax)-0.5
 variable zmin equal bound(carbon_atoms,zmin)+0.5
-region rtop block INF INF INF INF ${zmax} INF
+region 	rtop block INF INF INF INF ${zmax} INF
 region rbot block INF INF INF INF INF ${zmin}
 region rmid block INF INF INF INF ${zmin} ${zmax}
 group carbon_top region rtop
@@ -32,40 +32,41 @@ compute Tmid carbon_mid temp
 fix myber carbon_mid temp/berendsen ${T} ${T} 0.1
 fix_modify myber temp Tmid
 
-fix mysf1 carbon_bot setforce 0 0 0
-fix mysf2 carbon_top setforce 0 0 0
-velocity carbon_bot set 0 0 0
-velocity carbon_top set 0 0 0
+fix mysf1 carbon_top setforce 0 0 NULL
+fix mysf2 carbon_bot setforce 0 0 NULL
+velocity carbon_top set 0 0 NULL
+velocity carbon_bot set 0 0 NULL
+
+dump mydmp all atom 1000 dump.lammpstrj
+
+thermo 100
+thermo_modify temp Tmid
+
+timestep 0.0005
+run 5000
 
 # evaluate strain
 variable L equal xcm(carbon_top,z)-xcm(carbon_bot,z)
 variable strain equal 100*(v_L-${L})/${L} # in %
-fix at1 all ave/time 10 10 100 v_strain file output_cnt_strain.dat
+fix at1 all ave/time 20 100 2000 v_strain file output_cnt_strain1.dat
 
 # evaluate stress
-variable kcal_to_joule equal 4184
-variable Na equal 6.022e23
+variable eV_to_joule equal 1.60218e-19
 variable Atom equal 1e-10
 variable pi equal 3.14159
-variable f_total_kcal equal f_mysf1[1]-f_mysf2[1] # kcal/mol/A
-variable f_total_newton equal v_f_total_kcal*${kcal_to_joule}/${Na}/${Atom}
-variable rad equal 5.2e-10 # radius of the nanotubeub m
+variable f_total_eV equal f_mysf2[3]-f_mysf1[3] # eV/A
+variable f_total_newton equal v_f_total_eV*${eV_to_joule}/${Atom}
+variable rad equal 5.2e-10 # radius of the nanotube m
 variable dC equal 3.4e-10 # effective diameter of the carbon atom
 variable A equal ${pi}*${rad}*${dC} # surface area in m2
-variable s_total equal v_f_total_newton/${A}  # stress in Pascal
+variable stress equal v_f_total_newton/${A}  # stress in Pascal
 
-fix at2 all ave/time 10 10 100 f_mysf1[1] f_mysf2[1] file output_cnt_stress.dat
-
-dump mydmp all atom 1000 dump.lammpstrj
-
-thermo 100
-thermo_modify temp Tmid
-
-timestep 0.0005
-run 5000
+fix at2 all ave/time 20 100 2000 v_stress file output_cnt_stress1.dat
 
-# 0.15 A/ps = 15 m/s
-velocity carbon_top set 0 0 0.15
-velocity carbon_bot set 0 0 -0.15
+fix mysf1 carbon_top setforce 0 0 0
+fix mysf2 carbon_bot setforce 0 0 0
+# 0.05 A/ps per edge -> 10 m/s
+velocity carbon_top set 0 0 0.05
+velocity carbon_bot set 0 0 -0.05
 
-run 150000
+run 400000

docs/inputs/level1/breaking-a-carbon-nanotube/exercises/stress-strain/data_plot/cnt_strain1.dat

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