ecell4-win32.patch

diff --git a/ecell4/bd/functions3d.cpp b/ecell4/bd/functions3d.cpp
index f2a94c7..a1a4692 100644
--- a/ecell4/bd/functions3d.cpp
+++ b/ecell4/bd/functions3d.cpp
@@ -64,11 +64,11 @@ Real Igbd_r_3d(Real r, Real sigma, Real t, Real D)
     const Real sigmasq(sigma * sigma);
 
     const Real sigmacb(sigmasq * sigma);
-    const Real rcb(gsl_pow_3(r));
+    const Real rcb(gsl_pow_int(r, 3));
 
     const Real rsigma(r * sigma);
 
-    const Real rps_sq(gsl_pow_2(r + sigma)), rms_sq(gsl_pow_2(r - sigma));
+    const Real rps_sq(gsl_pow_int(r + sigma, 2)), rms_sq(gsl_pow_int(r - sigma, 2));
 
     const Real term1(-2 * sqrtDt / sqrtPi);
     const Real term2(std::exp(-sigmasq / Dt) * (sigmasq - Dt2));
@@ -98,8 +98,11 @@ Real random_ipv_length_3d(
     const Real ptot(Igbd_3d(sigma, t, D));
 
     Igbd_r_3d_params params = {sigma, t, D, rng.uniform(0, 1) * ptot};
-    gsl_function F = {
-        reinterpret_cast<typeof(F.function)>(&Igbd_r_3d_F), &params};
+	gsl_function F;
+	F.function = reinterpret_cast<double (__cdecl *)(double,void *)>(&Igbd_r_3d_F);
+	F.params = &params;
+	// gsl_function F = {
+	// 	reinterpret_cast<typeof(F.function)>(&Igbd_r_3d_F), &params };
 
     Real low(sigma), high(sigma + 10 * std::sqrt(6 * D * t));
 
diff --git a/ecell4/bd/functions3d.hpp b/ecell4/bd/functions3d.hpp
index 30dbf36..2dabcbd 100644
--- a/ecell4/bd/functions3d.hpp
+++ b/ecell4/bd/functions3d.hpp
@@ -5,12 +5,24 @@
 #include <ecell4/core/Position3.hpp>
 #include <ecell4/core/RandomNumberGenerator.hpp>
 
+#include <boost/math/special_functions/erf.hpp>
+
 namespace ecell4
 {
 
 namespace bd
 {
 
+inline Real erf(const Real& x)
+{
+	return boost::math::erf(x);
+}
+
+inline Real erfc(const Real& x)
+{
+	return boost::math::erfc(x);
+}
+
 /**
  * $\int_0^\infty r^2dr\,g\left(r,\Delta t\right),$
  * where $g\left(r,\Delta t\right)$ is a probability that a pair, which is
diff --git a/ecell4/core/CMakeLists.txt b/ecell4/core/CMakeLists.txt
index 6b9f052..8593313 100644
--- a/ecell4/core/CMakeLists.txt
+++ b/ecell4/core/CMakeLists.txt
@@ -28,8 +28,13 @@ find_package(Boost REQUIRED)
 include_directories(${Boost_INCLUDE_DIRS})
 # set(HAVE_BOOST_REGEX ${Boost_FOUND})
 
+#find_library(GSL_LIBRARIES gsl)
+#find_library(GSL_CBLAS_LIBRARIES gslcblas)
+
+#set(CMAKE_FIND_LIBRARY_PREFIXES "")
+#set(CMAKE_FIND_LIBRARY_SUFFIXES ".lib" ".dll")
 find_library(GSL_LIBRARIES gsl)
-find_library(GSL_CBLAS_LIBRARIES gslcblas)
+find_library(GSL_CBLAS_LIBRARIES cblas)
 
 include(CheckIncludeFileCXX)
 # set(CMAKE_REQUIRED_INCLUDES "/usr/include")
@@ -51,7 +56,9 @@ configure_file(
     ${PROJECT_SOURCE_DIR}/ecell4/core/config.h.in
     ${PROJECT_BINARY_DIR}/ecell4/core/config.h)
 
-add_library(ecell4-core SHARED
+#add_library(ecell4-core SHARED
+#    ${CPP_FILES} ${HPP_FILES} "${PROJECT_BINARY_DIR}/ecell4/core/config.h")
+add_library(ecell4-core
     ${CPP_FILES} ${HPP_FILES} "${PROJECT_BINARY_DIR}/ecell4/core/config.h")
 target_link_libraries(ecell4-core
     ${HDF5_LIBRARIES} ${Boost_LIBRARIES} ${GSL_LIBRARIES} ${GSL_CBLAS_LIBRARIES})
diff --git a/ecell4/core/CompartmentSpace.cpp b/ecell4/core/CompartmentSpace.cpp
index 730f76b..8d94462 100644
--- a/ecell4/core/CompartmentSpace.cpp
+++ b/ecell4/core/CompartmentSpace.cpp
@@ -8,6 +8,11 @@
 namespace ecell4
 {
 
+Real cbrt(const Real& x)
+{
+	return pow(x, 1.0 / 3);
+}
+
 const Real CompartmentSpaceVectorImpl::volume() const
 {
     return volume_;
diff --git a/ecell4/core/CompartmentSpace.hpp b/ecell4/core/CompartmentSpace.hpp
index 20476a9..67c0ae1 100644
--- a/ecell4/core/CompartmentSpace.hpp
+++ b/ecell4/core/CompartmentSpace.hpp
@@ -12,6 +12,8 @@
 namespace ecell4
 {
 
+Real cbrt(const Real& x);
+
 class CompartmentSpace
     : public Space
 {
diff --git a/ecell4/core/DynamicPriorityQueue.hpp b/ecell4/core/DynamicPriorityQueue.hpp
index cb6558f..eb50da2 100644
--- a/ecell4/core/DynamicPriorityQueue.hpp
+++ b/ecell4/core/DynamicPriorityQueue.hpp
@@ -97,8 +97,9 @@ public:
         typename index_map::const_iterator i(index_map_.find(id));
         if (i == index_map_.end())
         {
-            throw std::out_of_range((boost::format("%s: Key not found (%s)") % __PRETTY_FUNCTION__ % boost::lexical_cast<std::string>(id)).str());
-        }
+			throw std::out_of_range((boost::format("%s: Key not found (%s)") % __FUNCTION__ % boost::lexical_cast<std::string>(id)).str());
+			// throw std::out_of_range((boost::format("%s: Key not found (%s)") % __PRETTY_FUNCTION__ % boost::lexical_cast<std::string>(id)).str());
+		}
         return (*i).second;
     }
 
diff --git a/ecell4/core/EventScheduler.hpp b/ecell4/core/EventScheduler.hpp
index 7836e56..f4785c7 100644
--- a/ecell4/core/EventScheduler.hpp
+++ b/ecell4/core/EventScheduler.hpp
@@ -65,10 +65,10 @@ protected:
 
 public:
 
-    typedef typename EventPriorityQueue::size_type size_type;
-    typedef typename EventPriorityQueue::identifier_type identifier_type;
-    typedef typename EventPriorityQueue::value_type value_type;
-    typedef boost::iterator_range<typename EventPriorityQueue::const_iterator>
+    typedef EventPriorityQueue::size_type size_type;
+    typedef EventPriorityQueue::identifier_type identifier_type;
+    typedef EventPriorityQueue::value_type value_type;
+    typedef boost::iterator_range<EventPriorityQueue::const_iterator>
         events_range;
 
 public:
diff --git a/ecell4/core/Journal.cpp b/ecell4/core/Journal.cpp
index 8b3f56e..cc9c898 100644
--- a/ecell4/core/Journal.cpp
+++ b/ecell4/core/Journal.cpp
@@ -38,7 +38,7 @@ void Journal::logv(enum level lv, char const* format, va_list ap)
         return;
 
     char buf[1024];
-    std::vsnprintf(buf, sizeof(buf), format, ap);
+    vsnprintf(buf, sizeof(buf), format, ap);
 
     std::fprintf(stderr, "%s: %-8s ", name_.c_str(), stringize_error_level(lv));
     std::fwrite(buf, sizeof(char), std::strlen(buf), stderr);
diff --git a/ecell4/core/LatticeSpace.cpp b/ecell4/core/LatticeSpace.cpp
index 95eaf4a..e3e8b03 100644
--- a/ecell4/core/LatticeSpace.cpp
+++ b/ecell4/core/LatticeSpace.cpp
@@ -2,9 +2,17 @@
 #include "VacantType.hpp"
 #include "LatticeSpace.hpp"
 
+#include <boost/numeric/interval/detail/msvc_rounding_control.hpp>
+
+
 namespace ecell4
 {
 
+Real rint(const Real& x)
+{
+	return boost::numeric::interval_lib::detail::rint(x);
+}
+
 LatticeSpace::LatticeSpace(const Position3& edge_lengths,
         const Real& voxel_radius, const bool is_periodic) :
     voxel_radius_(voxel_radius), edge_lengths_(edge_lengths), t_(0),
@@ -29,9 +37,9 @@ LatticeSpace::~LatticeSpace()
  */
 void LatticeSpace::set_lattice_properties(const bool is_periodic)
 {
-    HCP_L = voxel_radius_/sqrt(3);
+    HCP_L = voxel_radius_/sqrt(3.0);
     HCP_X = voxel_radius_*sqrt(8.0/3); //Lx
-    HCP_Y = voxel_radius_*sqrt(3); //Ly
+    HCP_Y = voxel_radius_*sqrt(3.0); //Ly
 
     const Real lengthX = edge_lengths_[0];
     const Real lengthY = edge_lengths_[1];
@@ -183,7 +191,7 @@ LatticeSpace::get_voxel(const ParticleID& pid) const
     for (spmap::const_iterator i(spmap_.begin()); i != spmap_.end(); ++i)
     {
         const MolecularType& mt((*i).second);
-        typename MolecularType::container_type::const_iterator j(mt.find(pid));
+        MolecularType::container_type::const_iterator j(mt.find(pid));
         if (j != mt.end())
         {
             const coordinate_type coord(private2coord((*j).first));
@@ -384,7 +392,7 @@ bool LatticeSpace::remove_voxel(const ParticleID& pid)
     for (spmap::iterator i(spmap_.begin()); i != spmap_.end(); ++i)
     {
         MolecularType& mt((*i).second);
-        typename MolecularType::container_type::const_iterator j(mt.find(pid));
+        MolecularType::container_type::const_iterator j(mt.find(pid));
         if (j != mt.end())
         {
             const private_coordinate_type coord((*j).first);
diff --git a/ecell4/core/LatticeSpace.hpp b/ecell4/core/LatticeSpace.hpp
index 3bf1c25..de6a698 100644
--- a/ecell4/core/LatticeSpace.hpp
+++ b/ecell4/core/LatticeSpace.hpp
@@ -17,6 +17,8 @@ namespace ecell4
 class MolecularTypeBase;
 class MolecularType;
 
+Real rint(const Real& x);
+
 class LatticeSpace
     : public Space
 {
diff --git a/ecell4/core/ParticleSpace.cpp b/ecell4/core/ParticleSpace.cpp
index 3f37f48..e052699 100644
--- a/ecell4/core/ParticleSpace.cpp
+++ b/ecell4/core/ParticleSpace.cpp
@@ -102,8 +102,9 @@ std::vector<std::pair<std::pair<ParticleID, Particle>, Real> >
 ParticleSpaceVectorImpl::list_particles_within_radius(
     const Position3& pos, const Real& radius) const
 {
-    const Real rsq(gsl_pow_2(radius));
-    std::vector<std::pair<std::pair<ParticleID, Particle>, Real> > retval;
+	// const Real rsq(gsl_pow_2(radius));
+	const Real rsq(gsl_pow_int(radius, 2));
+	std::vector<std::pair<std::pair<ParticleID, Particle>, Real> > retval;
 
     for (particle_container_type::const_iterator i(particles_.begin());
          i != particles_.end(); ++i)
@@ -122,8 +123,9 @@ std::vector<std::pair<std::pair<ParticleID, Particle>, Real> >
 ParticleSpaceVectorImpl::list_particles_within_radius(
     const Position3& pos, const Real& radius, const ParticleID& ignore) const
 {
-    const Real rsq(gsl_pow_2(radius));
-    std::vector<std::pair<std::pair<ParticleID, Particle>, Real> > retval;
+	// const Real rsq(gsl_pow_2(radius));
+	const Real rsq(gsl_pow_int(radius, 2));
+	std::vector<std::pair<std::pair<ParticleID, Particle>, Real> > retval;
 
     for (particle_container_type::const_iterator i(particles_.begin());
          i != particles_.end(); ++i)
@@ -146,8 +148,9 @@ ParticleSpaceVectorImpl::list_particles_within_radius(
     const Position3& pos, const Real& radius,
     const ParticleID& ignore1, const ParticleID& ignore2) const
 {
-    const Real rsq(gsl_pow_2(radius));
-    std::vector<std::pair<std::pair<ParticleID, Particle>, Real> > retval;
+	const Real rsq(gsl_pow_int(radius, 2));
+	// const Real rsq(gsl_pow_2(radius));
+	std::vector<std::pair<std::pair<ParticleID, Particle>, Real> > retval;
 
     for (particle_container_type::const_iterator i(particles_.begin());
          i != particles_.end(); ++i)
diff --git a/ecell4/core/ParticleSpace.hpp b/ecell4/core/ParticleSpace.hpp
index d63a428..f1c04b5 100644
--- a/ecell4/core/ParticleSpace.hpp
+++ b/ecell4/core/ParticleSpace.hpp
@@ -221,16 +221,19 @@ public:
 
             if (diff > half)
             {
-                retval += gsl_pow_2(diff - edge_length);
-            }
+				retval += gsl_pow_int(diff - edge_length, 2);
+				// retval += gsl_pow_2(diff - edge_length);
+			}
             else if (diff < -half)
             {
-                retval += gsl_pow_2(diff + edge_length);
-            }
+				retval += gsl_pow_int(diff + edge_length, 2);
+				// retval += gsl_pow_2(diff + edge_length);
+			}
             else
             {
-                retval += gsl_pow_2(diff);
-            }
+				retval += gsl_pow_int(diff, 2);
+				// retval += gsl_pow_2(diff);
+			}
         }
         return retval;
     }
diff --git a/ecell4/core/Position3.hpp b/ecell4/core/Position3.hpp
index f722a1d..d99e8ee 100644
--- a/ecell4/core/Position3.hpp
+++ b/ecell4/core/Position3.hpp
@@ -148,7 +148,8 @@ inline Position3 cross_product(const Position3& p1, const Position3& p2)
 
 inline Position3::value_type length_sq(const Position3& r)
 {
-    return gsl_pow_2(r[0]) + gsl_pow_2(r[1]) + gsl_pow_2(r[2]);
+	// return gsl_pow_2(r[0]) + gsl_pow_2(r[1]) + gsl_pow_2(r[2]);
+	return gsl_pow_int(r[0], 2) + gsl_pow_int(r[1], 2) + gsl_pow_int(r[2], 2);
 }
 
 inline Position3::value_type length(const Position3& r)
diff --git a/ecell4/core/UnitSpecies.cpp b/ecell4/core/UnitSpecies.cpp
index 1042a83..0498217 100644
--- a/ecell4/core/UnitSpecies.cpp
+++ b/ecell4/core/UnitSpecies.cpp
@@ -3,11 +3,14 @@
 
 #include "config.h"
 
-#if defined(HAVE_BOOST_REGEX)
-#include <boost/regex.hpp>
-#else
-#include <regex.h>
-#endif /* HAVE_BOOST_REGEX */
+//#if defined(HAVE_BOOST_REGEX)
+//#include <boost/regex.hpp>
+//#else
+//#include <regex.h>
+//#endif /* HAVE_BOOST_REGEX */
+
+#define HAVE_BOOST_REGEX
+#include <regex>
 
 #include "UnitSpecies.hpp"
 
@@ -30,18 +33,20 @@ void UnitSpecies::deserialize(const UnitSpecies::serial_type& serial)
     }
 
 #if defined(HAVE_BOOST_REGEX)
-    boost::regex r1(
+	using namespace std::tr1;
+
+    regex r1(
         "^\\s*(\\w+)\\s*(\\(\\s*([\\w\\s\\^=,]*)\\))?\\s*$");
-    boost::smatch results1;
-    if (boost::regex_match(serial, results1, r1))
+    smatch results1;
+    if (regex_match(serial, results1, r1))
     {
         name_ = std::string(results1.str(1).c_str());
         if (results1.str(3).size() > 0)
         {
-            boost::regex r2(
+            regex r2(
                 "\\s*(\\w+)(\\s*=\\s*(\\w+))?(\\s*\\^\\s*(\\w+))?\\s*");
             // boost::match_results<std::string::const_iterator> results2;
-            boost::smatch results2;
+            smatch results2;
             std::vector<std::string> sites;
             boost::split(
                 sites, static_cast<const std::string>(results1.str(3)),
@@ -50,7 +55,7 @@ void UnitSpecies::deserialize(const UnitSpecies::serial_type& serial)
             for (std::vector<std::string>::const_iterator i(sites.begin());
                 i != sites.end(); ++i)
             {
-                if (boost::regex_match(*i, results2, r2))
+                if (regex_match(*i, results2, r2))
                 {
                     if (results2.str(3).size() > 0)
                     {
diff --git a/ecell4/core/types.hpp b/ecell4/core/types.hpp
index d869ab4..9643cae 100644
--- a/ecell4/core/types.hpp
+++ b/ecell4/core/types.hpp
@@ -2,8 +2,11 @@
 #define __ECELL4_TYPES_HPP
 
 #include <stdint.h>
+
+#define _USE_MATH_DEFINES
 #include <math.h>
 
+
 namespace ecell4
 {
 
diff --git a/ecell4/ode/ODEWorld.hpp b/ecell4/ode/ODEWorld.hpp
index bf3c93d..7203a9e 100644
--- a/ecell4/ode/ODEWorld.hpp
+++ b/ecell4/ode/ODEWorld.hpp
@@ -3,7 +3,8 @@
 
 #include <ecell4/core/Species.hpp>
 #include <ecell4/core/Position3.hpp>
-#include <ecell4/core/Space.hpp>
+// #include <ecell4/core/Space.hpp>
+#include <ecell4/core/CompartmentSpace.hpp>
 #include <ecell4/core/NetworkModel.hpp>
 #include <ecell4/core/CompartmentSpaceHDF5Writer.hpp>
 
diff --git a/python/setup.py b/python/setup.py
index 307cbdf..c7e76c2 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -37,7 +37,7 @@ class run_tests(Command):
         test_runner = unittest.TextTestRunner()
         test_runner.run(suite)
 
-with_cpp_shared_libraries = True
+with_cpp_shared_libraries = False
 if with_cpp_shared_libraries:
     ext_modules = [
         Extension("ecell4.core", sources=["lib/ecell4/core.pyx"],
@@ -57,26 +57,32 @@ if with_cpp_shared_libraries:
         ]
 else:
     dependent_libs = [
-        'gsl', 'gslcblas', 'm', 'hdf5_hl_cpp', 'hdf5_cpp', 'hdf5_hl', 'hdf5']
+        'gsl', 'cblas', 'hdf5_hl_cpp_D', 'hdf5_cpp_D', 'hdf5_hl_D', 'hdf5_D']
+    #     'gsl', 'cblas', 'm', 'hdf5_hl_cpp', 'hdf5_cpp', 'hdf5_hl', 'hdf5']
     core_src = glob.glob("../ecell4/core/*.cpp")
     ext_modules = [
         Extension("ecell4.core", sources=["lib/ecell4/core.pyx"] + core_src,
+            extra_compile_args=["/EHsc", "/w"],
             include_dirs=[".", ".."], libraries=dependent_libs, language="c++"),
         Extension("ecell4.gillespie",
             sources=["lib/ecell4/gillespie.pyx"]
                 + glob.glob("../ecell4/gillespie/*.cpp") + core_src,
+            extra_compile_args=["/EHsc", "/w"],
             libraries=dependent_libs, include_dirs=[".", ".."], language="c++"),
         Extension("ecell4.bd",
             sources=["lib/ecell4/bd.pyx"]
                 + glob.glob("../ecell4/bd/*.cpp") + core_src,
+            extra_compile_args=["/EHsc", "/w"],
             libraries=dependent_libs, include_dirs=[".", ".."], language="c++"),
         Extension("ecell4.ode",
             sources=["lib/ecell4/ode.pyx"]
                 + glob.glob("../ecell4/ode/*.cpp") + core_src,
+            extra_compile_args=["/EHsc", "/w"],
             libraries=dependent_libs, include_dirs=[".", ".."], language="c++"),
         Extension("ecell4.lattice",
             sources=["lib/ecell4/lattice.pyx"]
                 + glob.glob("../ecell4/lattice/*.cpp") + core_src,
+            extra_compile_args=["/EHsc", "/w"],
             libraries=dependent_libs, include_dirs=[".", ".."], language="c++"),
         ]