Merge pull request #86 from ygeorgi/master

allow crm basis

Author: ygeorgi

src/libmess/crossrate.cc

@@ -1334,6 +1334,8 @@ void CrossRate::MultiArray::run_traj ()
 		  << ", is smaller than the reactive energy: "
 		  << "decrease the reactive energy or change the transition state dividing surface\n";
 
+	IO::log.flush();
+
 	throw Error::Run();
       }
 
@@ -1458,9 +1460,12 @@ int CrossRate::MultiArray::_sample (iterator mit, const std::set<DivSur::face_t
 	//
 	      << " kcal/mol, is lower than the reactive energy, " << reactive_energy() / Phys_const::kcal << "\n";
 
-  if(itemp)
+  if(itemp) {
     //
+    IO::log.flush();
+
     throw Error::Run();
+  }
 
   int isnew = 0;
 
@@ -3150,6 +3155,8 @@ bool CrossRate::MultiArray::_work ()
 	//
 	std::cerr << funame << "reactive transition pair is not properly defined\n";
 
+        IO::log.flush();
+
 	throw Error::Init();
       }
 
@@ -3383,6 +3390,8 @@ CrossRate::MultiArray::MultiArray(const DivSur::MultiSur& ms, Potential::Wrap po
       //
       std::cerr << funame << "too many failures for " << mit - begin() << "-th surface\n";
 
+      IO::log.flush();
+
       throw Error::Run();
     }
 
@@ -3392,6 +3401,8 @@ CrossRate::MultiArray::MultiArray(const DivSur::MultiSur& ms, Potential::Wrap po
 	//
 	std::cerr << funame << mit - begin() << "-th surface, " << sit->first << " facet: " <<"no flux samplings\n";
 
+	IO::log.flush();
+
 	throw Error::Run();
       }//
       //
@@ -3451,6 +3462,8 @@ CrossRate::MultiArray::MultiArray(const DivSur::MultiSur& ms, Potential::Wrap po
 	//
 	std::cerr << mit - begin() << "-th surface,  " << sit->first << " facet: no potential samplings\n";
 
+	IO::log.flush();
+
 	throw Error::Run();
       }
 
@@ -3464,6 +3477,8 @@ CrossRate::MultiArray::MultiArray(const DivSur::MultiSur& ms, Potential::Wrap po
 		//
 		  << " kcal/mol\n";
 
+	IO::log.flush();
+
 	throw Error::Run();
       }
     }

src/libmess/mess.hh

@@ -126,6 +126,8 @@ namespace MasterEquation {
 
   extern double   time_propagation_interval; // time-interval between printouts
 
+  extern int with_crm_basis; 
+
   double temperature            ();
 
   double pressure               ();

src/libmess/mess_2d.hh

@@ -2,6 +2,9 @@
 # define MESS_2D_HH
 
 namespace Mess {
+  //
+  class ReactiveComplex: public Model::ChemGraph {
+  };
 
   extern double energy_reference;
 

src/mess_test.cc src/libmess/mess_test.ccsrc/mess_test.cc renamed to src/libmess/mess_test.cc

@@ -19,10 +19,10 @@
 #include<cmath>
 #include <sys/resource.h>
 
-#include "libmess/mess.hh"
-#include "libmess/key.hh"
-#include "libmess/units.hh"
-#include "libmess/io.hh"
+#include "mess.hh"
+#include "key.hh"
+#include "units.hh"
+#include "io.hh"
 
 
 //auxiliary structures for rate constants storage and output

src/molpro_sampling.cc src/libmess/molpro_sampling.ccsrc/molpro_sampling.cc renamed to src/libmess/molpro_sampling.cc

@@ -13,10 +13,10 @@
         Library General Public License for more details.
 */
 
-#include "libmess/molpro.hh"
-#include "libmess/key.hh"
-#include "libmess/io.hh"
-#include "libmess/system.hh"
+#include "molpro.hh"
+#include "key.hh"
+#include "io.hh"
+#include "system.hh"
 
 #include <cstdlib>
 #include <sys/stat.h>

src/mpi_graph_test.cc src/libmess/mpi_graph_test.ccsrc/mpi_graph_test.cc renamed to src/libmess/mpi_graph_test.cc

@@ -20,10 +20,10 @@
 #include<sstream>
 #include<cmath>
 
-#include "libmess/graph_mpi.hh"
-#include "libmess/key.hh"
-#include "libmess/units.hh"
-#include "libmess/io.hh"
+#include "graph_mpi.hh"
+#include "key.hh"
+#include "units.hh"
+#include "io.hh"
 
 int main (int argc, char* argv [])
 {