Merge branch '2.0' into 'trunk'

Conflicts:
	README
	SConstruct
	configure.ac
	doc/sphinx/conf.py

cantera.pc.in

@@ -12,7 +12,7 @@ Name: cantera
 Description: An object-oriented software toolkit for chemical kinetics, thermodynamics, and transport processes.
 URL: http://code.google.com/p/cantera/
 Requires:
-Version: 2.0.0
+Version: 2.0.1
 
 LINK  = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo  -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode -lctlapack -lctblas -lctf2c -lm -lstdc++
 

interfaces/matlab/toolbox/@ThermoPhase/setState_SP.m

@@ -7,9 +7,9 @@ function a = setState_SP(a,sp)
 %    entropy (J/kg/K) and pressure (Pa).
 %
 if sp(1) <= 0.0
-    error('the pressure must be positive');
-end
-if sp(2) <= 0.0
     error('the specific entropy must be positive');
 end
+if sp(2) <= 0.0
+    error('the pressure must be positive');
+end
 thermo_set(a.tp_id,23,sp);

platform/posix/SConscript

@@ -24,7 +24,7 @@ if env['python_package'] == 'full':
 # Cantera.mak include file for Makefile projects
 # cantera.pc for use with pkg-config
 
-pc_libs = []
+pc_libs = list(localenv['cantera_libs'])
 pc_libdirs = []
 pc_incdirs = []
 pc_cflags = []
@@ -47,7 +47,6 @@ else:
     # Add links to the sundials environment
     localenv['mak_sundials_libs'] = ' '.join('-l%s' % s
                                              for s in localenv['sundials_libs'])
-    pc_libs += localenv['sundials_libs']
     if localenv['sundials_libdir']:
         localenv['mak_sundials_libdir'] = '-L' + localenv['sundials_libdir']
         pc_libdirs.append(localenv['sundials_libdir'])
@@ -80,7 +79,6 @@ localenv['mak_have_blas_lapack_dir'] = '1' if localenv['blas_lapack_dir'] else '
 
 if localenv['blas_lapack_dir']:
     localenv['mak_blas_lapack_libs'] = ' '.join('-l%s' % s for s in localenv['blas_lapack_libs'])
-    pc_libs += localenv['blas_lapack_libs']
 elif not env['single_library']:
     localenv['mak_blas_lapack_libs'] = ('-L' + '$inst_libdir' + ' -lctlapack -lctblas')
 else:

platform/posix/cantera.pc.in

@@ -8,5 +8,5 @@ Description: Cantera library
 URL: http://cantera.googlecode.com
 Version: @cantera_version@
 
-Libs: -L${libdir} @pc_libdirs@ -lcantera @pc_libs@
+Libs: -L${libdir} @pc_libdirs@ @pc_libs@
 Cflags: @pc_cflags@ -I${includedir} @pc_incdirs@

site_scons/wxsgen.py

@@ -71,7 +71,7 @@ class WxsGenerator(object):
                                      UpgradeCode='2340BEE1-279D-11E1-A4AA-001FBC085391',
                                      Language='1033',
                                      Codepage='1252',
-                                     Version='2.0.0',
+                                     Version='2.0.1',
                                      Manufacturer='Cantera Developers'))
 
         fields = {'Platform': 'x64'} if self.x64 else {}

src/oneD/StFlow.cpp

@@ -209,6 +209,7 @@ void StFlow::resize(size_t ncomponents, size_t points)
     } else {
         m_multidiff.resize(m_nsp*m_nsp*m_points);
         m_diff.resize(m_nsp*m_points);
+        m_dthermal.resize(m_nsp, m_points, 0.0);
     }
     m_flux.resize(m_nsp,m_points);
     m_wdot.resize(m_nsp,m_points, 0.0);
@@ -988,7 +989,8 @@ void StFlow::updateDiffFluxes(const doublereal* x, size_t j0, size_t j1)
 
     if (m_do_soret) {
         for (m = j0; m < j1; m++) {
-            gradlogT = 2.0*(T(x,m+1) - T(x,m))/(T(x,m+1) + T(x,m));
+            gradlogT = 2.0 * (T(x,m+1) - T(x,m)) /
+                ((T(x,m+1) + T(x,m)) * (z(m+1) - z(m)));
             for (k = 0; k < m_nsp; k++) {
                 m_flux(k,m) -= m_dthermal(k,m)*gradlogT;
             }