Merge pull request #49 from lammpstutorials/retest-all-tutorials

- test all tutorials
- fixed the file order in .manifest files
- removed non-ascii parameters

Author: simongravelle

figures/NANOSHEAR-minimization.png

@@ -9,35 +9,41 @@ 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
 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
-stop
+
 # 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 &
+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
+

figures/NANOSHEAR-profiles.png

@@ -27,6 +27,7 @@ solution/breakable.log
 solution/breakable.png
 solution/breakable.dat
 solution/breakable-yaml-reader.py
+solution/breakable-with-tip.lmp
 
 # 3) support files
 unbreakable-yaml-reader.py

figures/PEG-in-vacuum.png

@@ -4,12 +4,12 @@
 ##############################################################################
 # 1) input file templates and data files
 # the first file will be automatically loaded
-peg.mol
-water.mol
-parameters.inc
 water.lmp
 merge.lmp
 pull.lmp
+peg.mol
+water.mol
+parameters.inc
 
 # 2) solution files
 # only downloaded on request

files/tutorial1/solution/initial.lmp

@@ -3,7 +3,7 @@
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
-PEG molecule
+# PEG molecule
 
 59 atoms
 58 bonds

files/tutorial2/.manifest

@@ -3,5 +3,5 @@
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
-kspace_style pull 1e-5
+kspace_style pppm 1e-5
 read_restart merge.restart

files/tutorial3/.manifest

@@ -4,12 +4,12 @@
 ##############################################################################
 # 1) input file templates and data files
 # the first file will be automatically loaded
-groups.inc
-parameters.inc
 create.lmp
 minimize.lmp
 equilibrate.lmp 
 shearing.lmp
+groups.inc
+parameters.inc
 water.mol
 
 # 2) solution files

files/tutorial3/peg.mol

@@ -5,7 +5,7 @@
 
 group H2O type O H
 group Na type Na+
-group Cl type Cl−
+group Cl type Cl-
 group ions union Na Cl
 group fluid union H2O ions