Changeset 1800 for branches/newmole/source

Timestamp:

02/16/08 10:57:45 (9 months ago)

Author:

rjrw

Message:

Merged from trunk r1779:1799.

Location:

branches/newmole/source

Files:

• cddefines.h (modified) (5 diffs)
• cddrive.cpp (modified) (1 diff)
• cdinit.cpp (modified) (2 diffs)
• container_classes.h (modified) (36 diffs)
• continuum.h (modified) (1 diff)
• cont_createpointers.cpp (modified) (3 diffs)
• cont_gammas.cpp (modified) (4 diffs)
• cont_setintensity.cpp (modified) (3 diffs)
• conv_init_solution.cpp (modified) (1 diff)
• cool_iron.cpp (modified) (1 diff)
• cpu.h (modified) (1 diff)
• date.h (modified) (1 diff)
• headers.txt (modified) (1 diff)
• heat_sum.cpp (modified) (22 diffs)
• helike_cs.cpp (modified) (2 diffs)
• hextra.h (modified) (2 diffs)
• highen.cpp (modified) (8 diffs)
• hydroreccool.cpp (modified) (1 diff)
• ionbal.h (modified) (1 diff)
• iso.h (modified) (17 diffs)
• iso_create.cpp (modified) (18 diffs)
• iso_ionize_recombine.cpp (modified) (1 diff)
• iso_level.cpp (modified) (32 diffs)
• iso_solve.cpp (modified) (2 diffs)
• iter_end_chk.cpp (modified) (7 diffs)
• iter_startend.cpp (modified) (2 diffs)
• mole_drive.cpp (modified) (1 diff)
• nemala2.cpp (modified) (3 diffs)
• neutrn.h (deleted)
• opacity.h (modified) (1 diff)
• opacity_createall.cpp (modified) (6 diffs)
• parse_atom_h2.cpp (modified) (2 diffs)
• parse_atom_iso.cpp (modified) (2 diffs)
• parse_commands.cpp (modified) (2 diffs)
• parse_compile.cpp (modified) (4 diffs)
• parse_constant.cpp (modified) (2 diffs)
• parse_punch.cpp (modified) (1 diff)
• parse_set.cpp (modified) (2 diffs)
• phycon.h (modified) (2 diffs)
• prt_comment.cpp (modified) (1 diff)
• prt_final.cpp (modified) (1 diff)
• radius_increment.cpp (modified) (4 diffs)
• rt_line_all.cpp (modified) (3 diffs)
• secondaries.h (modified) (3 diffs)
• service.cpp (modified) (4 diffs)
• stars.cpp (modified) (34 diffs)
• stars.h (modified) (8 diffs)
• state.cpp (modified) (3 diffs)
• taulines.h (modified) (3 diffs)
• TestMultiArr.cpp (modified) (2 diffs)
• thirdparty.cpp (modified) (1 diff)
• thirdparty.h (modified) (1 diff)
• vs.txt (modified) (1 diff)
• zero.cpp (modified) (4 diffs)

branches/newmole/source/cddefines.h

@@ -445 +445 @@
 };
 
-#define cdEXIT( FAIL ) throw cloudy_exit( DEBUG_ENTRY.name(), __FILE__, __LINE__, FAIL )
+// workarounds for __func__ are defined in cpu.h
+#define cdEXIT( FAIL ) throw cloudy_exit( __func__, __FILE__, __LINE__, FAIL )
 
 // calls like puts( "[Stop in MyRoutine]" ) have been integrated in cdEXIT above
@@ -580 +581 @@
                 return p_line;
         }
+};
+
+class bad_mpi {
+        long p_failMode;
+public:
+        bad_mpi(long failMode) : p_failMode(failMode) {}
+        long failMode() const { return p_failMode; }
 };
 
@@ -599 +607 @@
                                 { \
                                         if( cpu.lgAssertAbort() ) \
-                                                raise( SIGABRT ); \
+                                                abort();          \
                                         else \
                                                 throw bad_assert(__FILE__,__LINE__); \
@@ -609 +617 @@
 #endif
 
+NORETURN inline void OUT_OF_RANGE(const char* str)
+{
+        if( cpu.lgAssertAbort() )
+                abort();
+        else
+                throw out_of_range( str );
+}
+
 /* Windows does not define isnan */
 /* use our version on all platforms since the isnanf
@@ -673 +689 @@
 
 #ifdef DEBUG_FUN
-typedef debugtrace<true> debuginfo;
+#define DEBUG_ENTRY( funcname ) debugtrace<true> DEBUG_ENTRY( funcname )
 #else
-typedef debugtrace<false> debuginfo;
-#endif
-
-#define DEBUG_ENTRY( funcname ) debuginfo DEBUG_ENTRY( funcname )
+#ifdef __GNUC__
+#define DEBUG_ENTRY( funcname ) ((void)0)
+#else
+#define DEBUG_ENTRY( funcname ) debugtrace<false> DEBUG_ENTRY( funcname )
+#endif
+#endif
 
 /* TorF(l) returns a 'T' or 'F' depending on the 'logical' expr 'l' */

branches/newmole/source/cddrive.cpp

@@ -128 +128 @@
                 if( trace.lgTrace )
                         fprintf( ioQQQ, "cdDrive: calling cloudy\n");
-                /* optimize did not occur, only compute one model, call cloudy */
-                lgBAD = cloudy();
+                try {
+
+                        /* optimize did not occur, only compute one model, call cloudy */
+                        lgBAD = cloudy();
+                }
+                catch( bad_mpi &bad_info )
+                {
+                        fprintf( ioQQQ, "An MPI run failed.  The fail mode is %li\n", bad_info.failMode() );
+                        ClosePunchFiles( false );
+                        lgAbort = true;
+                        lgBAD = true;
+                }
         }
 

branches/newmole/source/cdinit.cpp

@@ -82 +82 @@
 #include "mewecoef.h"
 #include "mole.h" 
-#include "neutrn.h"
 #include "nitro.h"
 #include "noexec.h"
@@ -251 +250 @@
                 fprintf(ioQQQ," cdExit called\n");
 
-        /* close any open units */
-        ClosePunchFiles( true );
-
-        /* this routine must be called upon exit or machine will appear to "hang",
-         * but must not be called on MPI machine when used in serial mode,
-         * or it will drop core */
+        /* if doing an MPI run, just throw an exception
+         * so that cddrive can report the problem and continue
+         * computing other grid points */
         if( lgMPI )
         {
-#               ifdef MPI_ENABLED
-                MPI_Finalize();
-#               endif
-        }
-        exit( iexit );
+                throw bad_mpi(-1);
+        }
+        else
+        {
+                /* close any open units */
+                ClosePunchFiles( true );
+                exit( iexit );
+        }
 }
 

branches/newmole/source/container_classes.h

@@ -57 +57 @@
                 {
                         if( t < p_p[1] || t >= p_p[2] )
-                                throw out_of_range( "basic_pntr::p_index_checked()" );
+                                OUT_OF_RANGE( "basic_pntr::p_index_checked()" );
                 }
                 return t;
@@ -627 +627 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "n_pointer::n_pointer()" );
+                        OUT_OF_RANGE( "n_pointer::n_pointer()" );
                 p_p = *((T**)p + i);
                 p_v = &v->d[i];         
@@ -647 +647 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "n_pointer::n_pointer()" );
+                        OUT_OF_RANGE( "n_pointer::n_pointer()" );
                 p_p = p + i*st[d-N];
                 p_v = &v->d[i];
@@ -667 +667 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "n_pointer::n_pointer()" );
+                        OUT_OF_RANGE( "n_pointer::n_pointer()" );
                 p_p = *((T**)p + i);
                 p_v = &v->d[i];
@@ -674 +674 @@
         {
                 if( i >= p_v->n )
-                        throw out_of_range( "n_pointer::operator[]" );
+                        OUT_OF_RANGE( "n_pointer::operator[]" );
                 return *(p_p + i);
         }
@@ -689 +689 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "n_pointer::n_pointer()" );
+                        OUT_OF_RANGE( "n_pointer::n_pointer()" );
                 p_p = p + i*st[d-1];
                 p_v = &v->d[i];
@@ -696 +696 @@
         {
                 if( i >= p_v->n )
-                        throw out_of_range( "n_pointer::operator[]" );
+                        OUT_OF_RANGE( "n_pointer::operator[]" );
                 return *(p_p + i);
         }
@@ -779 +779 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "const_n_pointer::const_n_pointer()" );
+                        OUT_OF_RANGE( "const_n_pointer::const_n_pointer()" );
                 p_p = *((const T**)p + i);
                 p_v = &v->d[i];         
@@ -799 +799 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "const_n_pointer::const_n_pointer()" );
+                        OUT_OF_RANGE( "const_n_pointer::const_n_pointer()" );
                 p_p = p + i*st[d-N];
                 p_v = &v->d[i];
@@ -819 +819 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "const_n_pointer::const_n_pointer()" );
+                        OUT_OF_RANGE( "const_n_pointer::const_n_pointer()" );
                 p_p = *((const T**)p + i);
                 p_v = &v->d[i];
@@ -826 +826 @@
         {
                 if( i >= p_v->n )
-                        throw out_of_range( "const_n_pointer::operator[]" );
+                        OUT_OF_RANGE( "const_n_pointer::operator[]" );
                 return *(p_p + i);
         }
@@ -841 +841 @@
         {
                 if( i >= v->n )
-                        throw out_of_range( "const_n_pointer::const_n_pointer()" );
+                        OUT_OF_RANGE( "const_n_pointer::const_n_pointer()" );
                 p_p = p + i*st[d-1];
                 p_v = &v->d[i];
@@ -848 +848 @@
         {
                 if( i >= p_v->n )
-                        throw out_of_range( "const_n_pointer::operator[]" );
+                        OUT_OF_RANGE( "const_n_pointer::operator[]" );
                 return *(p_p + i);
         }
@@ -1196 +1196 @@
                         multi_arr<T,d,ALLOC,lgBC>* t = const_cast<multi_arr<T,d,ALLOC,lgBC>*>(this);
                         size_type n = p_g.v.getvec( 1, index ).n;
-                        T* s = &(*t)[i1][0];
+                        T* s = ( n > 0 ) ? &(*t)[i1][0] : NULL;
                         if( i2 == npos )
                                 return iterator( s+n, s, s+n );
@@ -1203 +1203 @@
                 }
                 else
-                        throw out_of_range( "multi_arr::p_iterator()" );
+                        OUT_OF_RANGE( "multi_arr::p_iterator()" );
         }
         iterator p_iterator(size_type i1, size_type i2, size_type i3) const
@@ -1226 +1226 @@
                         multi_arr<T,d,ALLOC,lgBC>* t = const_cast<multi_arr<T,d,ALLOC,lgBC>*>(this);
                         size_type n = p_g.v.getvec( 2, index ).n;
-                        T* s = &(*t)[i1][i2][0];
+                        T* s = ( n > 0 ) ? &(*t)[i1][i2][0] : NULL;
                         if( i3 == npos )
                                 return iterator( s+n, s, s+n );
@@ -1233 +1233 @@
                 }
                 else
-                        throw out_of_range( "multi_arr::p_iterator()" );
+                        OUT_OF_RANGE( "multi_arr::p_iterator()" );
         }
         iterator p_iterator(size_type i1, size_type i2, size_type i3, size_type i4) const
@@ -1256 +1256 @@
                         multi_arr<T,d,ALLOC,lgBC>* t = const_cast<multi_arr<T,d,ALLOC,lgBC>*>(this);
                         size_type n = p_g.v.getvec( 3, index ).n;
-                        T* s = &(*t)[i1][i2][i3][0];
+                        T* s = ( n > 0 ) ? &(*t)[i1][i2][i3][0] : NULL;
                         if( i4 == npos )
                                 return iterator( s+n, s, s+n );
@@ -1263 +1263 @@
                 }
                 else
-                        throw out_of_range( "multi_arr::p_iterator()" );
+                        OUT_OF_RANGE( "multi_arr::p_iterator()" );
         }
         iterator p_iterator(size_type i1, size_type i2, size_type i3, size_type i4, size_type i5) const
@@ -1286 +1286 @@
                         multi_arr<T,d,ALLOC,lgBC>* t = const_cast<multi_arr<T,d,ALLOC,lgBC>*>(this);
                         size_type n = p_g.v.getvec( 4, index ).n;
-                        T* s = &(*t)[i1][i2][i3][i4][0];
+                        T* s = ( n > 0 ) ? &(*t)[i1][i2][i3][i4][0] : NULL;
                         if( i5 == npos )
                                 return iterator( s+n, s, s+n );
@@ -1293 +1293 @@
                 }
                 else
-                        throw out_of_range( "multi_arr::p_iterator()" );
+                        OUT_OF_RANGE( "multi_arr::p_iterator()" );
         }
         iterator p_iterator(size_type i1, size_type i2, size_type i3, size_type i4, size_type i5, size_type i6) const
@@ -1316 +1316 @@
                         multi_arr<T,d,ALLOC,lgBC>* t = const_cast<multi_arr<T,d,ALLOC,lgBC>*>(this);
                         size_type n = p_g.v.getvec( 5, index ).n;
-                        T* s = &(*t)[i1][i2][i3][i4][i5][0];
+                        T* s = ( n > 0 ) ? &(*t)[i1][i2][i3][i4][i5][0] : NULL;
                         if( i6 == npos )
                                 return iterator( s+n, s, s+n );
@@ -1323 +1323 @@
                 }
                 else
-                        throw out_of_range( "multi_arr::p_iterator()" );
+                        OUT_OF_RANGE( "multi_arr::p_iterator()" );
         }
 
@@ -1340 +1340 @@
                 size_type index[] = { i1, i2 };
                 if( !p_g.lgInbounds( 2, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2];
         }
@@ -1347 +1347 @@
                 size_type index[] = { i1, i2 };
                 if( !p_g.lgInbounds( 2, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2];
         }
@@ -1354 +1354 @@
                 size_type index[] = { i1, i2, i3 };
                 if( !p_g.lgInbounds( 3, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3];
         }
@@ -1361 +1361 @@
                 size_type index[] = { i1, i2, i3 };
                 if( !p_g.lgInbounds( 3, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3];
         }
@@ -1368 +1368 @@
                 size_type index[] = { i1, i2, i3, i4 };
                 if( !p_g.lgInbounds( 4, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3][i4];
         }
@@ -1375 +1375 @@
                 size_type index[] = { i1, i2, i3, i4 };
                 if( !p_g.lgInbounds( 4, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3][i4];
         }
@@ -1382 +1382 @@
                 size_type index[] = { i1, i2, i3, i4, i5 };
                 if( !p_g.lgInbounds( 5, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3][i4][i5];
         }
@@ -1389 +1389 @@
                 size_type index[] = { i1, i2, i3, i4, i5 };
                 if( !p_g.lgInbounds( 5, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3][i4][i5];
         }
@@ -1396 +1396 @@
                 size_type index[] = { i1, i2, i3, i4, i5, i6 };
                 if( !p_g.lgInbounds( 6, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3][i4][i5][i6];
         }
@@ -1403 +1403 @@
                 size_type index[] = { i1, i2, i3, i4, i5, i6 };
                 if( !p_g.lgInbounds( 6, index ) )
-                        throw out_of_range( "multi_arr::at()" );
+                        OUT_OF_RANGE( "multi_arr::at()" );
                 return (*this)[i1][i2][i3][i4][i5][i6];
         }
@@ -1970 +1970 @@
                 {
                         if( ! p_lgInbounds( i ) )
-                                throw out_of_range( "flex_arr::p_index()" );
+                                OUT_OF_RANGE( "flex_arr::p_index()" );
                 }
                 return *p_pointer(i);
@@ -1988 +1988 @@
         {
                 if( ! p_lgInbounds(i) )
-                        throw out_of_range( "flex_arr::at()" );
+                        OUT_OF_RANGE( "flex_arr::at()" );
                 return (*this)[i];
         }
@@ -1994 +1994 @@
         {
                 if( ! p_lgInbounds(i) )
-                        throw out_of_range( "flex_arr::at()" );
+                        OUT_OF_RANGE( "flex_arr::at()" );
                 return (*this)[i];
         }

branches/newmole/source/continuum.h

@@ -86 +86 @@
           lgCoStarInterpolationCaution;
 
-        /** TotalLumin is total luminosity in incident continuum  */
+        /** TotalLumin is total intensity in incident continuum erg cm-2 s-1 */
         double TotalLumin, 
           totlsv;

branches/newmole/source/cont_createpointers.cpp

@@ -985 +985 @@
         /* first MALLOC LIMELM dimension of space */
         /* >>chng 02 jun 28, malloc this NISO instead of 2.     */
-        iso.ipSym2nu = (long ***)MALLOC(sizeof(long **)*(unsigned)NISO );
-
-        iso.As2nu = (realnum ***)MALLOC(sizeof(realnum **)*(unsigned)NISO );
+        iso.ipSym2nu.reserve( NISO );
 
         /* now loop over the two iso-sequences with two photon continua */
         for( ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
         {
-                iso.ipSym2nu[ipISO] = (long **)MALLOC(sizeof(long *)*(unsigned)LIMELM );
-                iso.As2nu[ipISO] = (realnum **)MALLOC(sizeof(realnum *)*(unsigned)LIMELM );
+                iso.ipSym2nu.reserve( ipISO, LIMELM );
 
                 /* set up two photon emission */
@@ -1001 +998 @@
                         {
                                 double E2nu = Transitions[ipISO][nelem][TwoS][0].EnergyWN * WAVNRYD;
-                                double Aul = Transitions[ipISO][nelem][TwoS][0].Emis->Aul;
-                                double SumShapeFunction = 0., Renorm= 0.;
 
                                 /* pointer to the Lya energy */
@@ -1017 +1012 @@
                                 }
 
-                                iso.ipSym2nu[ipISO][nelem] = (long *)MALLOC(sizeof(long)*(unsigned)iso.ipTwoPhoE[ipISO][nelem] );
-                                iso.As2nu[ipISO][nelem] = (realnum *)MALLOC(sizeof(realnum)*(unsigned)iso.ipTwoPhoE[ipISO][nelem] );
+                                iso.ipSym2nu.reserve( ipISO, nelem, iso.ipTwoPhoE[ipISO][nelem] );
+                        }
+                }
+        }
+
+        iso.ipSym2nu.alloc();
+        iso.As2nu.alloc( iso.ipSym2nu.clone() );
+
+        /* now loop over the two iso-sequences with two photon continua */
+        for( ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
+        {
+                /* set up two photon emission */
+                for( nelem=ipISO; nelem<LIMELM; ++nelem )
+                {
+                        if( dense.lgElmtOn[nelem] )
+                        {
+                                double E2nu = Transitions[ipISO][nelem][TwoS][0].EnergyWN * WAVNRYD;
+                                double Aul = Transitions[ipISO][nelem][TwoS][0].Emis->Aul;
+