From 1b0b5c1d96632608c05635cff8079b688b2ae61e Mon Sep 17 00:00:00 2001
From: dmayerich <dmayerich@gmail.com>
Date: Sat, 24 Aug 2013 14:47:50 -0500
Subject: [PATCH] first commit

---
 CMakeLists.txt       |   64 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 FindCUDASDK.cmake    |  142 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 FindFFTW.cmake       |   25 +++++++++++++++++++++++++
 FindRTS.cmake        |   14 ++++++++++++++
 README.md            |   19 +++++++++++++++++++
 Win32/libfftw3-3.dll | Bin 0 -> 2365756 bytes
 Win32/ricalc.exe     | Bin 0 -> 228864 bytes
 etaPolyethylene.txt  |  768 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 etaTeflon.txt        |  768 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 etaToluene.txt       | 1602 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 main.cpp             |   83 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 11 files changed, 3485 insertions(+), 0 deletions(-)
 create mode 100644 CMakeLists.txt
 create mode 100644 FindCUDASDK.cmake
 create mode 100644 FindFFTW.cmake
 create mode 100644 FindRTS.cmake
 create mode 100644 README.md
 create mode 100644 Win32/libfftw3-3.dll
 create mode 100644 Win32/ricalc.exe
 create mode 100644 etaPolyethylene.txt
 create mode 100644 etaTeflon.txt
 create mode 100644 etaToluene.txt
 create mode 100644 main.cpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..07f1673
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,64 @@
+#Specify the version being used aswell as the language
+cmake_minimum_required(VERSION 2.8)
+#Name your project here
+project(ricalc)
+
+#set the module directory
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
+
+#find BOOST
+set(Boost_USE_STATIC_LIBS        ON)
+set(Boost_USE_MULTITHREADED      ON)
+set(Boost_USE_STATIC_RUNTIME    OFF)
+find_package( Boost 1.54.0 COMPONENTS program_options )
+
+#set up CUDA
+find_package(CUDA)
+if(CUDA_FOUND)
+    link_libraries(${CUDA_cufft_LIBRARY})
+    add_definitions(-DCUDA_AVAILABLE)
+endif(CUDA_FOUND)
+
+#set up the FFTW package (fast Fourier transform)
+find_package(FFTW)
+if(FFTW_FOUND)
+    include_directories(${FFTW_INCLUDE_DIR})
+    link_libraries(${FFTW_LIBRARY})
+    add_definitions(-DFFTW_AVAILABLE)
+endif(FFTW_FOUND)
+
+#ask the user for the RTS location
+set(RTS_ROOT_PATH $ENV{RTS_ROOT_PATH})
+find_package(RTS REQUIRED)
+
+#set the include directories
+include_directories(
+	${CMAKE_CURRENT_BINARY_DIR}
+	${RTS_INCLUDE_DIR}
+    ${Boost_INCLUDE_DIR}
+)
+
+#enable warnings
+if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
+	add_definitions(-Wall -lfftw3 -lm)
+endif()
+
+#Assign source files to the appropriate variables
+file(GLOB SRC_CPP "*.cpp")
+file(GLOB SRC_H "*.h")
+file(GLOB SRC_CU "*.cu")
+
+#copy example material files
+configure_file(etaPolyethylene.txt ${CMAKE_CURRENT_BINARY_DIR}/etaPolyethylene.txt COPYONLY)
+configure_file(etaTeflon.txt ${CMAKE_CURRENT_BINARY_DIR}/etaTeflon.txt COPYONLY)
+configure_file(etaToluene.txt ${CMAKE_CURRENT_BINARY_DIR}/etaToluene.txt COPYONLY)
+
+
+#create an executable
+cuda_add_executable(ricalc ${SRC_CPP} ${SRC_H} ${SRC_CU})
+
+#set the link libraries
+target_link_libraries(ricalc ${Boost_LIBRARIES})
+
+
+
diff --git a/FindCUDASDK.cmake b/FindCUDASDK.cmake
new file mode 100644
index 0000000..f3bee90
--- /dev/null
+++ b/FindCUDASDK.cmake
@@ -0,0 +1,142 @@
+#
+# The script defines the following variables:
+#
+##############################################################################
+#  Note: Removed everything related to CUDA_SDK_ROOT_DIR and only left this as 
+#        a possible environment variable to set the SDK directory. 
+#        Include file will be: CUDA_CUT_INCLUDE_DIR
+#        Cutil library:        CUDA_CUT_LIBRARY
+##############################################################################
+# 
+#
+#  CUDA_SDK_ROOT_DIR     -- Path to the CUDA SDK.  Use this to find files in the
+#                           SDK.  This script will not directly support finding
+#                           specific libraries or headers, as that isn't
+#                           supported by NVIDIA.  If you want to change
+#                           libraries when the path changes see the
+#                           FindCUDA.cmake script for an example of how to clear
+#                           these variables.  There are also examples of how to
+#                           use the CUDA_SDK_ROOT_DIR to locate headers or
+#                           libraries, if you so choose (at your own risk).
+#
+#  This code is licensed under the MIT License.  See the FindCUDASDK.cmake script
+#  for the text of the license.
+
+# The MIT License
+#
+# License for the specific language governing rights and limitations under
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+
+# FindCUDASDK.cmake
+
+# # Check to see if the CUDA_SDK_ROOT_DIR has changed,
+# # if it has then clear the cache variable, so that it will be detected again.
+# if(NOT "${CUDA_SDK_ROOT_DIR}" STREQUAL "${CUDA_SDK_ROOT_DIR_INTERNAL}")
+#   # No specific variables to catch.  Use this kind of code before calling
+#   # find_package(CUDA) to clean up any variables that may depend on this path.
+# 
+#   #   unset(MY_SPECIAL_CUDA_SDK_INCLUDE_DIR CACHE)
+#   #   unset(MY_SPECIAL_CUDA_SDK_LIBRARY CACHE)
+# endif()
+# 
+# ########################
+# # Look for the SDK stuff
+# find_path(CUDA_SDK_ROOT_DIR cutil.h
+#   PATH_SUFFIXES  "common/inc" "C/common/inc"
+#   "$ENV{NVSDKCUDA_ROOT}"
+#   "[HKEY_LOCAL_MACHINE\\SOFTWARE\\NVIDIA Corporation\\Installed Products\\NVIDIA SDK 10\\Compute;InstallDir]"
+#   "/Developer/GPU\ Computing/C"
+#   )
+# 
+# # fallback method for determining CUDA_SDK_ROOT_DIR in case the previous one failed!
+# if (NOT CUDA_SDK_ROOT_DIR)
+#   find_path(CUDA_SDK_ROOT_DIR C/common/inc/cutil.h
+#   "$ENV{NVSDKCUDA_ROOT}"
+#   "[HKEY_LOCAL_MACHINE\\SOFTWARE\\NVIDIA Corporation\\Installed Products\\NVIDIA SDK 10\\Compute;InstallDir]"
+#   "/Developer/GPU\ Computing/C"
+#   )
+# endif()
+
+# Keep the CUDA_SDK_ROOT_DIR first in order to be able to override the
+# environment variables.
+set(CUDA_SDK_SEARCH_PATH
+  "${CUDA_SDK_ROOT_DIR}"
+  "${CUDA_TOOLKIT_ROOT_DIR}/local/NVSDK0.2"
+  "${CUDA_TOOLKIT_ROOT_DIR}/NVSDK0.2"
+  "${CUDA_TOOLKIT_ROOT_DIR}/NV_SDK"
+  "${CUDA_TOOLKIT_ROOT_DIR}/NV_CUDA_SDK"
+  "$ENV{HOME}/NVIDIA_CUDA_SDK"
+  "$ENV{HOME}/NVIDIA_CUDA_SDK_MACOSX"
+  "$ENV{HOME}/NVIDIA_GPU_Computing_SDK" 
+  "/Developer/CUDA"
+  )
+
+# Find include file from the CUDA_SDK_SEARCH_PATH
+
+find_path(CUDA_CUT_INCLUDE_DIR
+  cutil.h
+  PATHS ${CUDA_SDK_SEARCH_PATH}
+  PATH_SUFFIXES "common/inc" "C/common/inc"
+  DOC "Location of cutil.h"
+  NO_DEFAULT_PATH
+  )
+# Now search system paths
+find_path(CUDA_CUT_INCLUDE_DIR cutil.h DOC "Location of cutil.h")
+
+# mark_as_advanced(CUDA_CUT_INCLUDE_DIR)
+
+
+# Example of how to find a library in the CUDA_SDK_ROOT_DIR
+
+# cutil library is called cutil64 for 64 bit builds on windows.  We don't want
+# to get these confused, so we are setting the name based on the word size of
+# the build.
+
+# New library might be called cutil_x86_64 !
+
+if(CMAKE_SIZEOF_VOID_P EQUAL 8)
+  set(cuda_cutil_name cutil64)
+else(CMAKE_SIZEOF_VOID_P EQUAL 8)
+  set(cuda_cutil_name cutil32)
+endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+
+find_library(CUDA_CUT_LIBRARY
+  NAMES ${cuda_cutil_name} cutil cutil_x86_64 cutil_i386
+  PATHS ${CUDA_SDK_SEARCH_PATH}
+  # The new version of the sdk shows up in common/lib, but the old one is in lib
+  # The very newest installation Path of the SDK is in subdirectory 'C'. Please add this Path to the possible suffixes.
+  PATH_SUFFIXES "C/lib" "common/lib" "lib" "C/common/lib" "common/lib"
+  DOC "Location of cutil library"
+  NO_DEFAULT_PATH
+  )
+# # Now search system paths
+# find_library(CUDA_CUT_LIBRARY NAMES cutil ${cuda_cutil_name} DOC "Location of cutil library")
+mark_as_advanced(CUDA_CUT_LIBRARY)
+set(CUDA_CUT_LIBRARIES ${CUDA_CUT_LIBRARY})
+
+#############################
+# Check for required components
+if(CUDA_CUT_INCLUDE_DIR)
+  set(CUDASDK_FOUND TRUE)
+endif(CUDA_CUT_INCLUDE_DIR)
+
+# set(CUDA_SDK_ROOT_DIR_INTERNAL "${CUDA_SDK_ROOT_DIR}" CACHE INTERNAL
+#   "This is the value of the last time CUDA_SDK_ROOT_DIR was set successfully." FORCE)
diff --git a/FindFFTW.cmake b/FindFFTW.cmake
new file mode 100644
index 0000000..5a9ac50
--- /dev/null
+++ b/FindFFTW.cmake
@@ -0,0 +1,25 @@
+# - Find the native FFTW includes and library
+#
+# This module defines
+#
+#  FFTW_INCLUDE_DIR, where to find fftw3.h, etc.
+#  FFTW_LIBRARY, the libraries to link against to use FFTW.
+#
+#  FFTW_FOUND
+#
+# Was borrowed from http://houdini-ocean-toolkit.googlecode.com
+#
+
+find_path(FFTW_INCLUDE_DIR fftw3.h
+          PATHS ${CMAKE_SOURCE_DIR}/../3rdparty/include;
+                ${CMAKE_SOURCE_DIR}/3rdparty/include)
+
+find_library(FFTW_LIBRARY fftw3
+             PATHS ${CMAKE_SOURCE_DIR}/../3rdparty/lib;
+                   ${CMAKE_SOURCE_DIR}/3rdparty/lib)
+
+if (FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
+   set(FFTW_FOUND TRUE)
+else (FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
+   set(FFTW_FOUND FALSE)
+endif (FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
diff --git a/FindRTS.cmake b/FindRTS.cmake
new file mode 100644
index 0000000..fbfcc44
--- /dev/null
+++ b/FindRTS.cmake
@@ -0,0 +1,14 @@
+# Tries to find the RTS include directory
+
+  FIND_PATH( RTS_INCLUDE_DIR NAMES rts_glShaderProgram.h
+    PATHS
+	${CMAKE_CURRENT_SOURCE_DIR}/rts
+	${RTS_ROOT_PATH}
+)
+ 
+IF (RTS_FOUND)    
+  #The following deprecated settings are for backwards compatibility with CMake1.4
+  SET (RTS_INCLUDE_PATH ${RTS_INCLUDE_DIR})
+ENDIF(RTS_FOUND)
+
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(RTS REQUIRED_VARS TRUE RTS_INCLUDE_DIR)
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..6d66e7a
--- /dev/null
+++ b/README.md
@@ -0,0 +1,19 @@
+Computes the dispersion of a material given material properties. For example, given an absorbance spectrum, this software can estimate the complex refractive index and Chi values.
+
+A Windows 32 executable is provided in the Win32 directory.  All of the necessary runtime libraries are included.  Start by running 'ricalc -h' for command-line options.
+
+This software is designed to be used with CMake, so we recommend using it to build the application.
+
+This software requires the following libraries for compiling:
+
+FFTW - Fast Fourier Transform library -- http://www.fftw.org
+    or
+CUDA - NVidia's GPU programming toolkit -- https://developer.nvidia.com/
+
+RTS - Real-Time Scraps C++ library (my codebase) -- https://github.com/dmayerich/RTS
+
+
+
+
+
+
diff --git a/Win32/libfftw3-3.dll b/Win32/libfftw3-3.dll
new file mode 100644
index 0000000..a8f033a
Binary files /dev/null and b/Win32/libfftw3-3.dll differ
diff --git a/Win32/ricalc.exe b/Win32/ricalc.exe
new file mode 100644
index 0000000..190942f
Binary files /dev/null and b/Win32/ricalc.exe differ
diff --git a/etaPolyethylene.txt b/etaPolyethylene.txt
new file mode 100644
index 0000000..d8a5dad
--- /dev/null
+++ b/etaPolyethylene.txt
@@ -0,0 +1,768 @@
+#nu	n	k
+898.666	1.54119	0.00042801
+902.523	1.54118	0.00038246
+906.38	1.541	0.00040294
+910.237	1.54094	0.00039488
+914.094	1.54085	0.00037618
+917.95	1.54084	0.0003536
+921.807	1.54082	0.0003278
+925.664	1.54081	0.0003156
+929.521	1.54084	0.00028804
+933.378	1.54084	0.00032099
+937.235	1.54084	0.00031952
+941.092	1.54084	0.00033633
+944.949	1.54087	0.00036991
+948.806	1.54083	0.00040887
+952.663	1.54078	0.00044517
+956.52	1.54076	0.00043966
+960.377	1.54073	0.00044863
+964.234	1.54068	0.00044314
+968.091	1.54065	0.00045241
+971.948	1.54062	0.00043188
+975.804	1.54052	0.00039329
+979.661	1.54055	0.00034324
+983.518	1.54054	0.00027772
+987.375	1.54053	0.00024005
+991.232	1.54061	0.00018819
+995.089	1.54062	0.00017644
+998.946	1.54068	0.0001743
+1002.8	1.5407	0.0001892
+1006.66	1.54073	0.00022698
+1010.52	1.54072	0.00025522
+1014.37	1.54074	0.00027914
+1018.23	1.54071	0.00028447
+1022.09	1.54068	0.00030539
+1025.94	1.54067	0.00030134
+1029.8	1.54064	0.00030709
+1033.66	1.54061	0.00030649
+1037.52	1.54057	0.00027764
+1041.37	1.54054	0.00024089
+1045.23	1.54051	0.00017639
+1049.09	1.54056	0.00013155
+1052.94	1.54056	7.972e-005
+1056.8	1.54061	4.678e-005
+1060.66	1.54065	2.414e-005
+1064.51	1.54066	6.56e-006
+1068.37	1.54075	4.52e-006
+1072.23	1.54077	1.86e-006
+1076.08	1.54081	3.15e-005
+1079.94	1.54086	5.205e-005
+1083.8	1.54083	9.191e-005
+1087.66	1.54083	0.00012551
+1091.51	1.54082	0.00013487
+1095.37	1.54082	0.0001366
+1099.23	1.54081	0.00012324
+1103.08	1.54082	0.00011624
+1106.94	1.5408	9.228e-005
+1110.8	1.54081	7.841e-005
+1114.65	1.54084	5.534e-005
+1118.51	1.54084	3.409e-005
+1122.37	1.54087	1.855e-005
+1126.22	1.54091	0
+1130.08	1.54097	7.19e-006
+1133.94	1.54103	1.989e-005
+1137.8	1.54105	5.403e-005
+1141.65	1.54112	8.195e-005
+1145.51	1.54112	0.00012699
+1149.37	1.54114	0.0001768
+1153.22	1.54114	0.00021147
+1157.08	1.54112	0.00025829
+1160.94	1.54113	0.00029061
+1164.79	1.54108	0.00032397
+1168.65	1.54108	0.00034385
+1172.51	1.54107	0.00036836
+1176.36	1.54104	0.0003735
+1180.22	1.54101	0.00035023
+1184.08	1.54101	0.00033782
+1187.94	1.541	0.00032161
+1191.79	1.54104	0.00032158
+1195.65	1.54104	0.00031863
+1199.51	1.54107	0.00033038
+1203.36	1.54108	0.00035069
+1207.22	1.54107	0.00037485
+1211.08	1.54113	0.00041366
+1214.93	1.54108	0.00045119
+1218.79	1.54104	0.0004902
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+1226.51	1.54101	0.00053244
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+1249.65	1.54085	0.00045921
+1253.5	1.54083	0.00043153
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+1288.22	1.54091	0.00040998
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+1322.93	1.54083	0.00022097
+1326.79	1.54089	0.00019314
+1330.64	1.54091	0.00016466
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+1338.36	1.541	0.00019304
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+1357.64	1.54113	0.00026467
+1361.5	1.54111	0.00032192
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+1446.35	1.54205	0.00063101
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+1454.06	1.54272	0.00099416
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+1473.35	1.53961	0.00253731
+1477.21	1.53925	0.00128331
+1481.06	1.53969	0.0006213
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+1508.06	1.54061	0.00064828
+1511.92	1.5406	0.00055856
+1515.78	1.54067	0.00052929
+1519.63	1.54066	0.00059563
+1523.49	1.54066	0.0005584
+1527.35	1.54065	0.00048296
+1531.2	1.54072	0.00043625
+1535.06	1.54079	0.00046385
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diff --git a/etaTeflon.txt b/etaTeflon.txt
new file mode 100644
index 0000000..1e41957
--- /dev/null
+++ b/etaTeflon.txt
@@ -0,0 +1,768 @@
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diff --git a/etaToluene.txt b/etaToluene.txt
new file mode 100644
index 0000000..2b04adc
--- /dev/null
+++ b/etaToluene.txt
@@ -0,0 +1,1602 @@
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diff --git a/main.cpp b/main.cpp
new file mode 100644
index 0000000..6df71dc
--- /dev/null
+++ b/main.cpp
@@ -0,0 +1,83 @@
+#include <iostream>
+#include <vector>
+#include <complex>
+#include <fstream>
+#include <stdio.h>
+#include <string.h>
+using namespace std;
+
+//fftw fourier transform library
+#ifdef FFTW_AVAILABLE
+#include <fftw3.h>
+#endif
+
+#include "rts/material.h"
+//#include "options.h"
+
+#include <boost/program_options.hpp>
+namespace po = boost::program_options;
+
+
+typedef double ptype;
+typedef complex<ptype> pcomplex;
+
+rts::material<ptype> M;
+
+#define PI  3.14159
+
+int main(int argc, char* argv[])
+{
+	po::options_description desc("Allowed options");
+	desc.add_options()
+		("help,h", "Display this help message.")
+		("input-file,i", po::value<string>(), "Input file containing material information.")
+		("input-format,f", po::value<string>()->default_value("wavenumber,n,k"), "Format string identifying the order of material properties in the input file. Options include: microns, wavenumber, n (real RI), k (imaginary RI), A (absorbance), Xp (real Chi), Xpp (imaginary Chi).\n\nThe default [microns,n,k] will load a material file with columns representing the wavelength in microns, followed by the real and imaginary parts of the refractive index.")
+		("output-file,o", po::value<string>()->default_value("out.txt"), "Output file containing the processed material information.")
+		("output-format,t", po::value<string>()->default_value("wavenumber,n,k"), "Format string for the output file (similar to --input-format).")		
+		("scaling,s", po::value<ptype>()->default_value(1.0), "Scaling value for the absorbance parameter. This value gives the thickness (in microns) of the measured material.")
+		("n0,n", po::value<ptype>()->default_value(1.48), "Average effective refractive index. This is required when computing the real refractive index from the absorption.")
+		("padding,p", po::value<int>()->default_value(2), "Padding factor used to remove edge artifacts in the Kramers-Kronig computation for computing the real RI from absorption. The default value of p=2 is sufficient in most cases.")
+		("resolution,r", po::value<int>(), "Resolution of the spectrum. The default value is based on the number of spectral samples provided in the input file.");
+
+	po::positional_options_description pos;
+	pos.add("input-file", 1);
+	pos.add("output-file", 1);
+
+	po::variables_map vm;
+	po::store(po::command_line_parser(argc, argv).options(desc).positional(pos).run(), vm);
+	po::notify(vm);
+
+	if(vm.count("help"))
+	{
+		cout<<desc<<endl;
+		return 1;
+	}
+	
+	//if the input file is given, load it, otherwise exit
+	if(vm.count("input-file"))
+	{
+		M.fromFile(vm["input-file"].as<string>(),
+				   vm["input-format"].as<string>(),
+				   vm["scaling"].as<ptype>());
+	}
+	else
+	{
+		cout<<"No input file was provided."<<endl;
+		exit(1);
+	}
+
+	//the default sample rate of the spectrum is given by the number of samples in the input file
+	int R = M.nSamples();
+	if(vm.count("resolution"))
+		R = vm["resolution"].as<int>();
+
+	//compute the real refractive index
+	rts::material<ptype> N = M.computeN(vm["n0"].as<ptype>(), 
+										R,
+										vm["padding"].as<int>());
+
+	//output the file using the standard format
+	N.save(vm["output-file"].as<string>(), vm["output-format"].as<string>());
+
+	return 0;
+}
--
libgit2 0.21.4