git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12095 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/KAPPA/README

@@ -9,6 +9,8 @@ These scripts are provided for illustration purposes.  No guarantee is
 made that the systems are fully equilibrated or that the runs are long
 enough to generate good statistics and highly accurate results.
 
+These scripts could easily be adapted to work with solids as well.
+
 -------------
 
 These are the 4 methods for computing thermal conductivity.  The first

examples/MC/README

@@ -0,0 +1,33 @@
+This directory has an input script that illustrates how to use LAMMPS
+as an energy-evaluation engine in a Monte Carlo (MC) relaxation loop.
+It is just an illustration of how to do this for a toy 2d problem, but
+the script is fairly sophisticated in its use of variables, looping,
+and an if-the-else statement which applies the Boltzmann factor to
+accept or reject a trial atomic-displacement move.
+
+The script sets up a perfect 2d hex lattice, then perturbs all
+the atom positions to "disorder" the system.  It then
+loops in the following manner:
+
+pick a random atom and displace it to a random new position
+evaluate the change in energy of the system due to
+  the single-atom displacement
+accept or reject the trial move
+if accepted, continue to the next iteration
+if rejected, restore the atom to its original position
+  before continuing to the next iteration
+
+The 6 variables at the top of the input script can be adjusted
+to play with various MC parameters.
+
+When the script is finished, statistics about the MC procedure
+are printed.
+
+Dump file snapshots or images or a movie of the MC relaxation can be
+produced by uncommenting the appropriate dump lines in the script.
+
+At some point, we will add a Python script to the python/examples
+directory that performs the same operation as this script.  It will
+invoke LAMMPS as a library and use Python to implement the MC
+accept/reject logic more cleanly than the LAMMPS input script can do
+it.

examples/MC/in.mc

@@ -0,0 +1,118 @@
+# Monte Carlo relaxation of perturbed 2d hex lattice
+
+# set these parameters
+# make sure neigh skin > 2*deltamove
+
+variable iter loop 3000            # number of Monte Carlo moves
+variable deltaperturb equal 0.2    # max size of initial perturbation per dim
+variable deltamove equal 0.1       # max size of MC move in one dimension
+variable density equal 1.0         # reduced LJ density of atoms on lattice
+variable kT equal 0.05             # effective T in Boltzmann factor
+variable seed equal 582783         # RNG seed
+
+# problem setup
+
+units		lj
+atom_style	atomic
+atom_modify     map array sort 0 0.0
+
+dimension       2
+
+lattice		hex ${density}
+region		box block 0 10 0 5 -0.5 0.5
+
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+pair_modify     shift yes
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+variable        e equal pe
+
+# run 0 to get minimum energy of system
+
+run             0
+variable        emin equal $e
+
+# disorder the system
+# estart = initial energy
+
+variable        x atom x+v_deltaperturb*random(-1.0,1.0,${seed})
+variable        y atom y+v_deltaperturb*random(-1.0,1.0,${seed})
+
+set             group all x v_x
+set             group all y v_y
+
+#dump		1 all atom 25 dump.mc
+
+#dump		2 all image 25 image.*.jpg type type &
+#		zoom 1.6 adiam 1.0
+#dump_modify	2 pad 5
+
+#dump		3 all movie 25 movie.mpg type type &
+#		zoom 1.6 adiam 1.0
+#dump_modify	3 pad 5
+
+variable        elast equal $e
+thermo_style    custom step v_emin v_elast pe
+
+run             0
+
+variable        estart equal $e
+variable        elast equal $e
+
+# loop over Monte Carlo moves
+
+variable        naccept equal 0
+variable        increment equal v_naccept+1
+variable        irandom equal floor(atoms*random(0.0,1.0,${seed})+1)
+variable        rn equal random(0.0,1.0,${seed})
+variable        boltzfactor equal "exp(atoms*(v_elast - v_e) / v_kT)"
+variable        xnew equal x[v_i]+v_deltamove*random(-1.0,1.0,${seed})
+variable        ynew equal y[v_i]+v_deltamove*random(-1.0,1.0,${seed})
+variable        xi equal x[v_i]
+variable        yi equal y[v_i]
+
+label           loop
+
+variable        i equal ${irandom}
+
+variable        x0 equal ${xi}
+variable        y0 equal ${yi}
+
+set             atom $i x ${xnew}
+set             atom $i y ${ynew}
+
+run             1 pre no post no
+
+if              "$e <= ${elast}" then &
+                  "variable elast equal $e" &
+                  "variable naccept equal ${increment}" &
+                elif "${rn} <= ${boltzfactor}" &
+                  "variable elast equal $e" &
+                  "variable naccept equal ${increment}" &
+                else &
+                  "set atom $i x ${x0}" &
+                  "set atom $i y ${y0}"
+
+next            iter
+jump            SELF loop
+
+# final energy and stats
+
+variable       nb equal nbuild
+variable       nbuild equal ${nb}
+
+run             0
+
+print           "MC stats:"
+print           "  starting energy = ${estart}"
+print           "  final energy = $e"
+print           "  minimum energy of perfect lattice = ${emin}"
+print           "  accepted MC moves = ${naccept}"
+print           "  neighbor list rebuilds = ${nbuild}"

examples/README

@@ -132,12 +132,19 @@ The ELASTIC directory has an example script for computing elastic
 constants, using a zero temperature Si example.  See the
 ELASTIC/in.elastic file for more info.
 
-The KAPPA directory has an example scripts for computing the thermal
+The KAPPA directory has example scripts for computing the thermal
 conductivity (kappa) of a LJ liquid using 4 different methods.  See
 the KAPPA/README file for more info.
 
+The MC directory has an example script for using LAMMPS as an
+energy-evaluation engine in a iterative Monte Carlo energy-relaxation
+loop.
+
 The USER directory contains subdirectories of user-provided example
 scripts for ser packages.  See the README files in those directories
 for more info.  See the doc/Section_start.html file for more info
 about installing and building user packages.
 
+The VISCOSITY directory has example scripts for computing the
+viscosity of a LJ liquid using 4 different methods.  See the
+VISCOSITY/README file for more info.