From a5fef35ebd99ba334052e03f8c2ce02533527f06 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 7 Jun 2016 18:00:49 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15144
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 examples/KAPPA/README  | 25 ++++++++++----
 examples/KAPPA/in.ehex | 76 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 95 insertions(+), 6 deletions(-)
 create mode 100644 examples/KAPPA/in.ehex

diff --git a/examples/KAPPA/README b/examples/KAPPA/README
index ba4938c291..17313b251c 100644
--- a/examples/KAPPA/README
+++ b/examples/KAPPA/README
@@ -1,5 +1,5 @@
-This directory has 4 scripts that compute the thermal conductivity
-(kappa) of a Lennard-Jones fluid using 4 different methods.  See the
+This directory has 5 scripts that compute the thermal conductivity
+(kappa) of a Lennard-Jones fluid using 5 different methods.  See the
 discussion in Section 6.20 of the manual for an overview of the
 methods and pointers to doc pages for the commands which implement
 them.  Citations for the various methods can also be found in the
@@ -13,11 +13,12 @@ These scripts could easily be adapted to work with solids as well.
 
 -------------
 
-These are the 4 methods for computing thermal conductivity.  The first
-3 are non-equilibrium methods; the last is an equilibrium method.
+These are the 5 methods for computing thermal conductivity.  The first
+4 are non-equilibrium methods; the last is an equilibrium method.
 
 in.langevin = thermostat 2 regions at different temperatures via fix langevin
 in.heat = add/subtract energy to 2 regions via fix heat
+in.ehex = add/subtract energy to 2 regions via fix ehex
 in.mp = use fix thermal/conductivity and the Muller-Plathe method
 in.heatflux = use compute heat/flux and the Green-Kubo method
 
@@ -69,7 +70,19 @@ dZ = 18.82
 
 Kappa = 3.39
 
-(3) in.mp 
+(3) in.ehex
+
+dQ = (100*100) / 100 / 18.82^2 / 2
+  100*100 = 100 (time in tau) * 100 (energy delta specified in fix heat)
+  100 = 20,000 steps at 0.005 tau timestep = run time in tau
+  xy box area = 18.82^2
+  divide by 2 since energy flux goes in 2 directions due to periodic z
+TBC: dTemp = 0.783 from log file for average Temp difference between 2 regions
+dZ = 18.82
+
+TBC: Kappa = 3.39
+
+(4) in.mp 
 
 dQ = 15087 / 100 / 18.82^2 / 2
   15087 = cummulative delta energy, tallied by fix thermal/conductivity
@@ -81,7 +94,7 @@ dZ = 18.82
 
 Kappa = 3.45
 
-(4) in.heatflux
+(5) in.heatflux
 
 kappa is computed directly within the script, by performing a time
 integration of the formulas discussed on the compute heat/flux doc
diff --git a/examples/KAPPA/in.ehex b/examples/KAPPA/in.ehex
new file mode 100644
index 0000000000..5620dbbe17
--- /dev/null
+++ b/examples/KAPPA/in.ehex
@@ -0,0 +1,76 @@
+# sample LAMMPS input script for thermal conductivity of liquid LJ
+# use fix ehex to add/subtract energy from 2 regions
+
+# settings
+
+variable	x equal 10
+variable	y equal 10
+variable	z equal 20
+
+variable	rho equal 0.6
+variable        t equal 1.35
+variable	rc equal 2.5
+
+#variable	rho equal 0.85
+#variable        t equal 0.7
+#variable	rc equal 3.0
+
+# setup problem
+
+units		lj
+atom_style	atomic
+
+lattice		fcc ${rho}
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create $t 87287
+
+pair_style	lj/cut ${rc}
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1
+
+# heat layers
+
+region          hot block INF INF INF INF 0 1
+region          cold block  INF INF INF INF 10 11
+compute         Thot all temp/region hot
+compute         Tcold all temp/region cold
+
+# 1st equilibration run
+
+fix             1 all nvt temp $t $t 0.5
+thermo	        100
+run             1000
+
+velocity	all scale $t
+
+unfix		1
+
+# 2nd equilibration run
+
+fix		1 all nve
+fix             hot all ehex 1 100.0 region hot
+fix             cold all ehex 1 -100.0 region cold
+
+thermo_style    custom step temp c_Thot c_Tcold
+thermo	        1000
+run             10000 
+
+# thermal conductivity calculation
+
+compute		ke all ke/atom
+variable	temp atom c_ke/1.5
+
+fix		2 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
+		  file profile.heat units reduced
+
+variable        tdiff equal f_2[11][3]-f_2[1][3]
+fix             ave all ave/time 1 1 1000 v_tdiff ave running start 13000
+thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave
+
+run             20000