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simongravellesimongravelle
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removed space in .lmp
1 parent b886126 commit bbf6349

3 files changed

Lines changed: 80 additions & 81 deletions

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‎files/tutorial1/improved.min.lmp‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,18 @@
11
# 1) Initialization
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units lj
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dimension 3
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atom_style atomic
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boundary p p p
2+
units lj
3+
dimension 3
4+
atom_style atomic
5+
boundary p p p
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# 2) System definition
77
# 3) Settings
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mass 1 1.0
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mass 2 10.0
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pair_style lj/cut 4.0
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.5 3.0
8+
mass 1 1.0
9+
mass 2 10.0
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pair_style lj/cut 4.0
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.5 3.0
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# 4) Visualization
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thermo 10
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thermo_style custom step etotal press
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thermo 10
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thermo_style custom step etotal press
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# 5) Run
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minimize 1.0e-6 1.0e-6 1000 10000
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minimize 1.0e-6 1.0e-6 1000 10000
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# 6) Save status

‎files/tutorial2/solution/breakable.lmp‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -37,15 +37,15 @@ fix mysf2 cnt_top setforce 0 0 0
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velocity cnt_bot set 0 0 0
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velocity cnt_top set 0 0 0
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40-
variable L equal xcm(cnt_top,x)−xcm(cnt_bot,x)
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variable F equal f_mysf1[1]−f_mysf2[1]
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variable Lcnt equal xcm(cnt_top,x)-xcm(cnt_bot,x)
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variable Fcnt equal f_mysf1[1]-f_mysf2[1]
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dump mydmp all image 500 dump.*.ppm type type adiam 1.5 box no 0.01 view 0 90 zoom 1.8 shiny 0.1 fsaa yes
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dump_modify mydmp pad 5 backcolor white acolor 1 pink
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dump viz all image 500 myimage.*.ppm type type adiam 1.5 box no 0.01 view 0 90 zoom 1.8 shiny 0.1 fsaa yes
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dump_modify viz pad 5 backcolor white acolor 1 pink
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4646
compute Tmid cnt_mid temp
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thermo 100
48-
thermo_style custom step temp etotal v_L v_F
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thermo_style custom step temp etotal v_Lcnt v_Fcnt
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thermo_modify temp Tmid line yaml
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timestep 0.0005

‎files/tutorial2/solution/unbreakable.lmp‎

Lines changed: 63 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -1,64 +1,63 @@
1-
units real
2-
atom_style molecular
3-
boundary f f f
4-
5-
pair_style lj/cut 14.0
6-
bond_style harmonic
7-
angle_style harmonic
8-
dihedral_style opls
9-
improper_style harmonic
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special_bonds lj 0.0 0.0 0.5
11-
12-
read_data unbreakable.data
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include parameters.inc
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group carbon_atoms type 1
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variable xmax equal bound(carbon_atoms,xmax)-0.5
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variable xmin equal bound(carbon_atoms,xmin)+0.5
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region rtop block ${xmax} INF INF INF INF INF
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region rbot block INF ${xmin} INF INF INF INF
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region rmid block ${xmin} ${xmax} INF INF INF INF
21-
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group cnt_top region rtop
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group cnt_bot region rbot
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group cnt_mid region rmid
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set group cnt_top mol 1
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set group cnt_bot mol 2
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set group cnt_mid mol 3
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variable xmax_del equal ${xmax}-2
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variable xmin_del equal ${xmin}+2
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region rdel block ${xmin_del} ${xmax_del} INF INF INF INF
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group rdel region rdel
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delete_atoms random fraction 0.02 no rdel NULL 2793 bond yes
34-
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reset_atoms id sort yes
36-
velocity cnt_mid create 300 48455 mom yes rot yes
37-
38-
fix mynve1 cnt_top nve
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fix mynve2 cnt_bot nve
40-
fix mynvt cnt_mid nvt temp 300 300 100.0
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fix mysf1 cnt_top setforce 0 0 0
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fix mysf2 cnt_bot setforce 0 0 0
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velocity cnt_top set 0 0 0
44-
velocity cnt_bot set 0 0 0
45-
46-
variable Lcnt equal xcm(cnt_top,x)-xcm(cnt_bot,x)
47-
variable Fcnt equal f_mysf1[1]-f_mysf2[1]
48-
49-
variable colors string "pink white white"
50-
dump mydmp all image 500 dump.*.ppm mol type adiam 1.5 box no 0.01 view 0 90 zoom 1.8 shiny 0.1 fsaa yes
51-
dump_modify mydmp pad 5 amap 0 10 sa 1 3 ${colors} backcolor white
52-
53-
compute Tmid cnt_mid temp
54-
thermo 100
55-
thermo_style custom step temp etotal v_Lcnt v_Fcnt
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thermo_modify temp Tmid line yaml
57-
58-
timestep 1.0
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run 5000
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velocity cnt_top set 0.0005 0 0
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velocity cnt_bot set -0.0005 0 0
63-
64-
run 10000
1+
units real
2+
atom_style molecular
3+
boundary f f f
4+
5+
pair_style lj/cut 14.0
6+
bond_style harmonic
7+
angle_style harmonic
8+
dihedral_style opls
9+
improper_style harmonic
10+
special_bonds lj 0.0 0.0 0.5
11+
12+
read_data unbreakable.data
13+
include parameters.inc
14+
15+
group carbon_atoms type 1
16+
variable xmax equal bound(carbon_atoms,xmax)-0.5
17+
variable xmin equal bound(carbon_atoms,xmin)+0.5
18+
region rtop block ${xmax} INF INF INF INF INF
19+
region rbot block INF ${xmin} INF INF INF INF
20+
region rmid block ${xmin} ${xmax} INF INF INF INF
21+
22+
group cnt_top region rtop
23+
group cnt_bot region rbot
24+
group cnt_mid region rmid
25+
set group cnt_top mol 1
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set group cnt_bot mol 2
27+
set group cnt_mid mol 3
28+
29+
variable xmax_del equal ${xmax}-2
30+
variable xmin_del equal ${xmin}+2
31+
region rdel block ${xmin_del} ${xmax_del} INF INF INF INF
32+
group rdel region rdel
33+
delete_atoms random fraction 0.02 no rdel NULL 2793 bond yes
34+
35+
reset_atoms id sort yes
36+
velocity cnt_mid create 300 48455 mom yes rot yes
37+
38+
fix mynve1 cnt_top nve
39+
fix mynve2 cnt_bot nve
40+
fix mynvt cnt_mid nvt temp 300 300 100
41+
fix mysf1 cnt_top setforce 0 0 0
42+
fix mysf2 cnt_bot setforce 0 0 0
43+
velocity cnt_top set 0 0 0
44+
velocity cnt_bot set 0 0 0
45+
46+
variable Lcnt equal xcm(cnt_top,x)-xcm(cnt_bot,x)
47+
variable Fcnt equal f_mysf1[1]-f_mysf2[1]
48+
49+
dump viz all image 500 myimage-*.ppm element type size 1000 400 zoom 6 shiny 0.3 fsaa yes bond atom 0.8 view 0 90 box no 0.0 axes no 0.0 0.0
50+
dump_modify viz pad 9 backcolor white adiam 1 0.85 bdiam 1 1.0
51+
52+
compute Tmid cnt_mid temp
53+
thermo 100
54+
thermo_style custom step temp etotal v_Lcnt v_Fcnt
55+
thermo_modify temp Tmid line yaml
56+
57+
timestep 1.0
58+
run 5000
59+
60+
velocity cnt_top set 0.0005 0 0
61+
velocity cnt_bot set -0.0005 0 0
62+
63+
run 10000

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