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Added a VMD/Ovito tip to tutorial 3 #56

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Merged
merged 4 commits into from
Jan 6, 2025
Merged

Added a VMD/Ovito tip to tutorial 3 #56

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e1dfa84
added a VMD/Ovito tip to tutorial 3
simongravelle Jan 5, 2025
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simongravelle Jan 5, 2025
6fa2b81
Update lammps-tutorials.tex
simongravelle Jan 6, 2025
c54bef6
moved the last Axel comment into a note
simongravelle Jan 6, 2025
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4 changes: 2 additions & 2 deletions files/tutorial3/solution/merge.lmp
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Python script (License CC BY 4.0)
# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
# LAMMPS input file (License CC BY 4.0)
# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
# The DOI will be added upon publication
# Find more on GitHub: https://github.com/lammpstutorials

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35 changes: 35 additions & 0 deletions files/tutorial3/solution/pull-with-tip.lmp
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@@ -0,0 +1,35 @@
# LAMMPS input file (License CC BY 4.0)
# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
# The DOI will be added upon publication
# Find more on GitHub: https://github.com/lammpstutorials

kspace_style pppm 1e-5
read_restart merge.restart

group ends type OAlc
variable xcm equal xcm(ends,x)
variable oxies atom type==label2type(atom,OAlc)
variable end1 atom v_oxies*(x>v_xcm)
variable end2 atom v_oxies*(x<v_xcm)
group topull1 variable end1
group topull2 variable end2

dump mydmp all atom 1000 pull.lammpstrj

timestep 1.0
fix mynvt all nvt temp 300 300 100
fix myrct PEG recenter 0 0 0 shift all

compute rgyr PEG gyration
compute prop PEG property/local dtype
compute dphi PEG dihedral/local phi

thermo_style custom step temp etotal c_rgyr
thermo 250

run 15000

fix myaf1 topull1 addforce 10 0 0
fix myaf2 topull2 addforce -10 0 0

run 15000
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