Update README and Makefiles

native/HBV/Makefile

@@ -53,4 +53,3 @@ all:
 
 debug:
 	$(CC_SERIAL) -o bin/$(TARGET) $(C_FLAGS_DEBUG) $(HBV_SOURCE)
-

native/HBV/README.md

@@ -1,5 +1,4 @@
 # HBV Rainfall-Runoff Model #
-## Multiobjective Optimization Benchmark ##
 
 Copyright 2011-2012 Josh Kollat, Jon Herman, Patrick Reed and others.
 Intended for use with [MOEAFramework](http://www.moeaframework.org). Licensed under
@@ -14,16 +13,16 @@ Volume 51, January 2013, Pages 438-456, ISSN 0309-1708, 10.1016/j.advwatres.2012
 ([Link to Paper](http://www.sciencedirect.com/science/article/pii/S0309170812000073))
 
 #### Description ####
-The HBV model is a lumped conceptual rainfall–runoff model with three primary routines:
+The HBV model is a lumped conceptual rainfall-runoff model with three primary routines:
 * Snow accumulation and melt, represented by a variant of the degree-day snow model
 * Soil moisture accounting, with a probability distribution to represent the spatial variability of storage elements
 * A response routine, in which the linear outflow from two sub-basins is transformed by a routing parameter. 
 In sum, the model contains 14 real-valued decision variables that require calibration.
 
 In this example, we are calibrating the HBV model for the Williams River, West Virginia,
 United States (USGS Gage 03186500). Calibration was performed using precipitation and
-streamflow data from the MOPEX dataset over the period 1962–1972 with a one-year warmup
-period. Four objective functions are optimized: the Nash–Sutcliffe Efficiency (NSE),
+streamflow data from the MOPEX dataset over the period 1962-1972 with a one-year warmup
+period. Four objective functions are optimized: the Nash-Sutcliffe Efficiency (NSE),
 which measures the model fit primarily during high-flow periods; the Box-Cox transformed
 root mean squared error (TRMSE), which accounts for low-flow periods; the runoff coefficient
 error (ROCE), which accounts for the long-term water balance; and the slope of the flow

native/LakeProblem/README.md

@@ -1,6 +1,4 @@
-### Lake Problem Training (C++)
-
-Copyright (C) 2014-2015 Victoria Ward, Riddhi Singh and Pat Reed. Intended for use with MOEAFramework and Borg. Licensed under the GNU Lesser General Public License.
+# Lake Problem
 
 Contents: 
 * `LakeProblem_4obj_1const_Control.cpp`: C++ source code for the 4 objective formulation
@@ -22,8 +20,36 @@ To compile and run:
 
 * To optimize the lake problem with Borg use the following command
 
+### Usage
+
+```bash
+
+borg.exe -v 100 -o 4 -c 1 -n 10000 -f outputfile.set \
+    -l 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 \
+    -u 0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1 \
+    -e 0.01,0.01,0.0001,0.0001 \
+    -- native/LakeProblem/bin/lake
+```
+
 `./BorgExec.exe -v 100 -o 4 -c 1 -l 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -u 0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1 -e 0.01,0.01,0.0001,0.0001 -n 10000 -f outputfile.set -- ./LakeProblem4obj_control.exe`
 
 Also, note if running these on thecube the executable names will not end in ".exe".  Otherwise, they will remain the same. 
 
+#### Copyright
+
+Copyright 2014-2015 Victoria Ward, Riddhi Singh and Pat Reed.
+
+#### License
+
+The HBV Benchmark Problem is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+The HBV Benchmark Problem is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
 
+You should have received a copy of the GNU Lesser General Public License
+along with the HBV Benchmark Problem.  If not, see <http://www.gnu.org/licenses/>.

native/Radar/README → native/Radar/README.md

@@ -1,3 +1,5 @@
+# Radar Waveform Optimization
+
 This code is adapted from Evan J. Hughes EMO 2007 Many-Objective Radar
 Waveform Software available at http://code.evanhughes.org/.
 
@@ -30,7 +32,7 @@ The arguments to this command are the number of variables, number of
 objectives, number of constraints, the function name to optimize, and
 the port used for communication. 
 
-Troubleshooting:
+#### Troubleshooting
 
 bind: Address already in use
 Unable to establish socket connection

native/WDS/Makefile

@@ -21,4 +21,5 @@ all:
 	$(CC) -o bin/PES -DPES $(SOURCE) $(C_FLAGS)
 	$(CC) -o bin/MOD -DMOD $(SOURCE) $(C_FLAGS)
 	$(CC) -o bin/BIN -DBIN $(SOURCE) $(C_FLAGS)
-	$(CC) -o bin/EXN -DEXN $(SOURCE) $(C_FLAGS)
+	$(CC) -o bin/EXN -DEXN $(SOURCE) $(C_FLAGS)
+

native/WDS/README.md

@@ -1,5 +1,4 @@
 # Water Distribution System #
-## Multiobjective Optimization Benchmark ##
 
 Originally developed by Mr. Qi Wang at the Centre for Water Systems, University
 of Exeter.  This source code is publicly available at