Update README for tutorial 0

tut0_lj_fluid/README

+# Tutorial 0 -- Lennard-Jones fluids
+
 In this first tutorial, we use LAMMPS to perform molecular dynamics (MD)
 simulations of a Lennard-Jones (LJ) fluid (colloidal particles in a sovlent).
-The particles (atoms) are simulated in a periodic box, and they interact with
-each other via the truncated LJ potential, which is given by
+In the simulation we have two types of particles (atoms) situated in a
+periodic box, and they interact with each other via a truncated and shifted LJ
+potential, which is given by
 
    U_LJ/cut(r) = U_LJ(r)-U_LJ(r_c), if r < r_c
 
@@ -47,32 +50,34 @@ the online LAMMPS documentation:
 
    docs.lammps.org/Manual.html
 
-==============================================================================
+###############################################################################
 
 What to do:
 
-0. Familarise yourself with the truncated LJ potential
+0. Familarise yourself with the LJ potential
 
-   Using your favourite plotting package, plot the truncated LJ potential for
-   different parameter values (epsilon and r_c) and have a think about the
-   following questions:
+   Using your favourite plotting package, plot the truncated and shifted LJ
+   potential for different parameter values (epsilon and r_c) and have a think
+   about the following questions:
    -  At what critical value for r_c does the potential become purely
       repulsive? Note that setting r_c to this value (with epsilon = 1.0)
-      gives a potential also known as the Weeks-Chandler-Anderson (WCA)
+      gives a potential also known as the Weeks-Chandler-Andersen (WCA)
       potential. [Hint: have a look at the provided bash script init.sh if you
       are unsure.]
    -  How does shifting the LJ potential change the value of its global
       minimum? How does this depend on r_c? Is there a way we can ensure that
       the minimum remains the same as that for the non-truncated LJ potential
-      (i.e., that it reaches -epsilon)?
+      (i.e., that the minimum reaches -epsilon)?
 	 
 1. Run the simulation to get a feel of how to use LAMMPS
 
    a. Generate the required input scripts/files
 
+      This is done by running the provided bash script
+
          bash init.sh
 
-      This generates two files that are necessary for running LAMMPS
+      which creates two files that are needed for running LAMMPS:
       -  run.lam file - a 'driver' script that is read by LAMMPS
       -  init.in file - a trajectory file containing the initial configuration
                         of the system (i.e., the atoms' positions, bonds, etc)
@@ -84,13 +89,19 @@ What to do:
 
       You can use the pre-compiled version of LAMMPS available on the school
       linux computers. Alternatively, you can also compile LAMMPS on your
-      own computer. Visit docs.lammps.org/Install.html for more info on how to
-      install LAMMPS. 
+      own computer (visit docs.lammps.org/Install.html for more info on how to
+      install LAMMPS). To start the simulation, we use the command
 
-         lmp -in *.lam
+         lmp -in run.lam
 
-      pos*.lammpstrj files will be generated storing the atoms' positions
-      and velocities. See the 'dump' command in the *.lam script.
+      The simulation generates several files:
+      -  pos*.lammpstrj - these files contain the trajectory of the atoms
+                          (for equilibration and the main simulation)
+      -  log.lammps     - this contains similar info to what has been output
+      	 		  to the screen (e.g., thermodynamic info, computation
+			  time, etc.)
+      See the comments next to the 'dump' command in the run.lam to understand
+      the file format for the trajectory files.
 
    c. Visualise the atoms' trajectories
 
@@ -123,7 +134,7 @@ What to do:
 2. Play around with the simulation parameters
 
    Explore how changing the number (density) of atoms and the interaction
-   strength between different types of atoms changes the overall dynamics of
+   strength between different types of atoms affects the overall dynamics of
    the system. This can be done by editing the parameter values in the init.sh
    script, in particular
 
@@ -143,14 +154,14 @@ What to do:
 
    Simulations are often conducted in 'reduced' units to maintain generality
    of the results and to limit errors introduced from floating-point
-   arithmetic caused by doing computation on variables spanning many different
-   orders of magnitude. This is achieved by rescaling variables/observables by
-   a set of fundamental quantities characteristic to the system. In the case
-   of an LJ fluid, three key properties are the energy, length, and mass of
-   the system, and a natural choice is to rescale these by the thermal energy
-   (k_B*T), the size of a colloidal particle (sigma), and its mass (m). In
-   other words, we have k_B*T = 1.0, sigma = 1.0 and m = 1.0 in
-   reduced/simulation units (also known as LJ units for this particular
+   arithmetic caused by doing computation on variables with values spanning
+   many different orders of magnitude. This is achieved by rescaling variables/
+   observables by a set of fundamental quantities characteristic to the
+   system. In the case of an LJ fluid, three key properties are the energy,
+   length, and mass of the system, and a natural choice is to rescale these by
+   the thermal energy (k_B*T), the size of a colloidal particle (sigma), and
+   its mass (m). In other words, we have k_B*T = 1.0, sigma = 1.0 and m = 1.0
+   in reduced/simulation units (also known as LJ units for this particular
    rescaling in LAMMPS).
    -  Based on these fundamental units, can you construct a natural time
       scale to describe the system? [Hint: take a look at the 'units' command