Started applying comments from Livecoms Reviewer

files/tutorial1/improved.md.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # 1) Initialization
@@ -10,5 +11,5 @@ atom_style atomic
 boundary p p p
 # 2) System definition
 # 3) Settings
-# 4) Visualization
+# 4) Monitoring
 # 5) Run

files/tutorial1/improved.min.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # 1) Initialization
@@ -15,8 +16,8 @@ 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
+# 4) Monitoring
 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

files/tutorial1/initial.lmp

@@ -1,11 +1,12 @@
-# LAMMPS Input File (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # PART A - ENERGY MINIMIZATION
 # 1) Initialization
 # 2) System definition
 # 3) Settings
-# 4) Visualization
+# 4) Monitoring
 # 5) Run

files/tutorial1/solution/improved.md.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # 1) Initialization
@@ -34,7 +35,7 @@ compute sumcoor12 grp_t1 reduce ave c_coor12
 
 # 3) Settings
 
-# 4) Visualization
+# 4) Monitoring
 thermo 1000
 thermo_style custom step temp pe ke etotal &
   press v_n1_in v_n2_in c_sumcoor12

files/tutorial1/solution/improved.min.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # 1) Initialization
@@ -25,7 +26,7 @@ pair_style lj/cut 4.0
 pair_coeff 1 1 1.0 1.0
 pair_coeff 2 2 0.5 3.0
 
-# 4) Visualization
+# 4) Monitoring
 thermo 10
 thermo_style custom step etotal press
 

files/tutorial1/solution/initial.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # PART A - ENERGY MINIMIZATION
@@ -24,15 +25,15 @@ pair_style lj/cut 4.0
 pair_coeff 1 1 1.0 1.0
 pair_coeff 2 2 0.5 3.0
 
-# 4) Visualization
+# 4) Monitoring
 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
+# 4) Monitoring
 thermo 50
 thermo_style custom step temp etotal pe ke press
 dump viz all image 100 myimage-*.ppm type type &

files/tutorial2/breakable.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 units metal

files/tutorial2/solution/breakable-with-tip.lmp

@@ -1,6 +1,7 @@
-# Python script (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 units metal

files/tutorial2/solution/breakable-yaml-reader.py

@@ -1,3 +1,8 @@
+# Python Script
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
+# Find more on GitHub: https://github.com/lammpstutorials
 import numpy as np
 import re
 import yaml

files/tutorial2/solution/breakable.lmp

@@ -1,6 +1,7 @@
-# Python script (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 units metal

files/tutorial2/solution/unbreakable.lmp

@@ -1,6 +1,7 @@
-# Python script (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 units real

files/tutorial2/unbreakable-yaml-reader.py

@@ -1,6 +1,7 @@
-# Python script (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# Python Script
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 import numpy as np

files/tutorial2/unbreakable.inc

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Include File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 pair_coeff 1 1 0.066 3.4

files/tutorial2/unbreakable.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 units real

files/tutorial3/merge.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 read_restart water.restart

files/tutorial3/parameters.inc

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Include File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 labelmap atom 1 OE 2 C 3 HC 4 H 5 CPos 6 OAlc 7 OW 8 HW

files/tutorial3/peg.mol

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Molecule File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 # PEG molecule

files/tutorial3/pull.lmp

@@ -1,6 +1,7 @@
-# LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
-# The DOI will be added upon publication
+# LAMMPS Input File
+# Licensed under CC BY 4.0
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 kspace_style pppm 1e-5

files/tutorial3/solution/merge.lmp

@@ -1,6 +1,7 @@
-# LAMMPS input file (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 kspace_style pppm 1e-5

files/tutorial3/solution/pull-with-tip.lmp

@@ -1,6 +1,7 @@
-# LAMMPS input file (License CC BY 4.0)
+# LAMMPS Input File
+# Licensed under CC BY 4.0
 # By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
-# The DOI will be added upon publication
+# Please cite doi.org/10.48550/arXiv.2503.14020
 # Find more on GitHub: https://github.com/lammpstutorials
 
 kspace_style pppm 1e-5