Merge pull request #35 from lammpstutorials/improve-tutorial-4

Improve and clean tutorial 4

Author: simongravelle

Makefile

@@ -1,2 +1,15 @@
+# Makefile for building lammps-tutorials.pdf
+all: build
+
+# Target to build the PDF
 build:
-	latexmk -pdf lammps-tutorials.tex
+	latexmk -pdf lammps-tutorials.tex
+
+# Target to clean up generated files
+clean:
+	rm -f lammps-tutorials.pdf \
+	lammps-tutorials.aux \
+	lammps-tutorials.log \
+	lammps-tutorials.out \
+	lammps-tutorials.bbl \
+	lammps-tutorials.blg

figures/NANOSHEAR-density.png

@@ -0,0 +1,40 @@
+# LAMMPS Tutorial manifest file. This file determines what is downloaded when.
+# comments start with a # as the first character.
+# comments and empty lines are ignored
+##############################################################################
+# 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
+water.mol
+
+# 2) solution files
+# only downloaded on request
+solution/groups.inc
+solution/parameters.inc
+solution/create.data
+solution/create.lmp
+solution/create.log
+solution/minimize.data
+solution/minimize.ipynb
+solution/minimize.lmp
+solution/minimize.log
+solution/equilibrate.data
+solution/equilibrate.ipynb
+solution/equilibrate.lmp
+solution/equilibrate.log
+solution/shearing-ions.dat
+solution/shearing.ipynb
+solution/shearing.lmp
+solution/shearing.log
+solution/shearing.png
+solution/shearing-wall.dat
+solution/shearing-water.dat
+solution/water.mol
+
+# 3) support files
+

figures/NANOSHEAR-equilibration.png

@@ -0,0 +1,10 @@
+
+boundary p p f
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
+kspace_style pppm/tip4p 1.0e−5
+kspace_modify slab 3.0
+

figures/NANOSHEAR-minimization.png

@@ -0,0 +1,15 @@
+
+boundary p p f
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
+kspace_style pppm/tip4p 1.0e−5
+kspace_modify slab 3.0
+
+read_data minimize.data
+
+include parameters.inc
+include groups.inc
+

figures/NANOSHEAR-profiles.png

@@ -0,0 +1,14 @@
+
+group H2O type O H
+group Na type Na+
+group Cl type Cl−
+group ions union Na Cl
+group fluid union H2O ions
+
+group wall type WALL
+region rtop block INF INF INF INF 0 INF
+region rbot block INF INF INF INF INF 0
+group top region rtop
+group bot region rbot
+group walltop intersect wall top
+group wallbot intersect wall bot