Changeset 1830 for branches/newmole/source

Timestamp:

03/08/08 12:55:20 (9 months ago)

Author:

rjrw

Message:

Merged from trunk r1803:1829

Location:

branches/newmole/source

Files:

• atmdat.h (modified) (2 diffs)
• atmdat_adfa.cpp (modified) (9 diffs)
• atmdat_chianti.cpp (modified) (2 diffs)
• atmdat_lamda.cpp (modified) (2 diffs)
• atmdat_readin.cpp (modified) (14 diffs)
• atom_fe2ovr.cpp (modified) (1 diff)
• atom_feii.cpp (modified) (14 diffs)
• atom_hyperfine.cpp (modified) (3 diffs)
• atom_level2.cpp (modified) (1 diff)
• atom_level3.cpp (modified) (3 diffs)
• atom_seq_beryllium.cpp (modified) (1 diff)
• atom_seq_boron.cpp (modified) (1 diff)
• cddefines.h (modified) (2 diffs)
• cddrive.h (modified) (1 diff)
• cdgetlinelist.cpp (modified) (3 diffs)
• container_classes.h (modified) (35 diffs)
• cont_createmesh.cpp (modified) (2 diffs)
• cont_createpointers.cpp (modified) (6 diffs)
• cont_ffun.cpp (modified) (1 diff)
• cont_setintensity.cpp (modified) (3 diffs)
• conv_base.cpp (modified) (1 diff)
• cool_eval.cpp (modified) (1 diff)
• cool_iron.cpp (modified) (2 diffs)
• cpu.cpp (modified) (3 diffs)
• cpu.h (modified) (4 diffs)
• dynamics.h (modified) (1 diff)
• grains.cpp (modified) (28 diffs)
• grains_mie.cpp (modified) (6 diffs)
• grains_qheat.cpp (modified) (1 diff)
• grainvar.h (modified) (2 diffs)
• h2_priv.h (modified) (1 diff)
• hcmap.cpp (modified) (2 diffs)
• he.h (modified) (1 diff)
• heat_sum.cpp (modified) (8 diffs)
• helike_cs.cpp (modified) (8 diffs)
• helike_einsta.cpp (modified) (3 diffs)
• highen.cpp (modified) (2 diffs)
• hydrogenic.h (modified) (1 diff)
• hydrot2low.cpp (modified) (8 diffs)
• ionbal.h (modified) (1 diff)
• ion_helium.cpp (modified) (1 diff)
• ion_recomb_Badnell.cpp (modified) (6 diffs)
• iso.h (modified) (1 diff)
• iso_cool.cpp (modified) (8 diffs)
• iso_create.cpp (modified) (5 diffs)
• iso_ionize_recombine.cpp (modified) (7 diffs)
• iso_level.cpp (modified) (6 diffs)
• iso_radiative_recomb.cpp (modified) (3 diffs)
• iso_solve.cpp (modified) (2 diffs)
• lines_service.cpp (modified) (2 diffs)
• mole_h2.cpp (modified) (1 diff)
• mole_h2_coll.cpp (modified) (9 diffs)
• mole_h2_io.cpp (modified) (10 diffs)
• mole_reactions.cpp (modified) (1 diff)
• nemala.cpp (modified) (3 diffs)
• opacity_add1element.cpp (modified) (4 diffs)
• opacity_add1subshell.cpp (modified) (4 diffs)
• opacity_addtotal.cpp (modified) (11 diffs)
• optimize_do.cpp (modified) (1 diff)
• optimize_phymir.cpp (modified) (7 diffs)
• parse_init.cpp (modified) (3 diffs)
• parse_optimize.cpp (modified) (1 diff)
• parse_print.cpp (modified) (1 diff)
• parse_punch.cpp (modified) (2 diffs)
• parse_state.cpp (modified) (2 diffs)
• parse_table.cpp (modified) (2 diffs)
• path.h (modified) (3 diffs)
• pressure_total.cpp (modified) (2 diffs)
• prt_linepres.cpp (modified) (4 diffs)
• prt_lines_helium.cpp (modified) (14 diffs)
• prt_lines_hydro.cpp (modified) (2 diffs)
• punch_opacity.cpp (modified) (4 diffs)
• radius_increment.cpp (modified) (1 diff)
• rt.h (modified) (1 diff)
• rt_continuum_shield_fcn.cpp (modified) (7 diffs)
• rt_diffuse.cpp (modified) (1 diff)
• rt_line_one.cpp (modified) (2 diffs)
• rt_ots.cpp (modified) (4 diffs)
• rt_tau_inc.cpp (modified) (1 diff)
• sanity_check.cpp (modified) (2 diffs)
• service.cpp (modified) (3 diffs)
• stars.cpp (modified) (58 diffs)
• state.cpp (modified) (3 diffs)
• sys_icc/Makefile.conf (modified) (1 diff)
• temp_change.cpp (modified) (3 diffs)

branches/newmole/source/atmdat.h

@@ -140 +140 @@
         /** [0] is Atom^+1 + H0 => Atom^0 + H^+
          * [n] is Atom^+n+1 + H0 => Atom^+n + H^+ */
-        double HCharExcIonOf[LIMELM][LIMELM+1], 
-          HCharExcRecTo[LIMELM][LIMELM+1], 
+        double HCharExcIonOf[LIMELM][LIMELM+1], //(cm3 s-1)
+          HCharExcRecTo[LIMELM][LIMELM+1],              //(cm3 s-1)
           HCharHeatMax, 
           HCharCoolMax, 
@@ -167 +167 @@
          *that go into the ionization balance
          *Ion[ion] is ionization, Rec[ion] is recombination
-         *units cm-3 s-1
+         *units cm3 s-1
          */
         double HeCharExcIonOf[LIMELM][LIMELM], 

branches/newmole/source/atmdat_adfa.cpp

@@ -10 +10 @@
 t_ADfA::t_ADfA()
 {
-        const long VERSION_MAGIC = 20061204L;
-        const static char chFile[] = "phfit.dat";
-        char chString[FILENAME_PATH_LENGTH_2];
-        double help[9];
-
         DEBUG_ENTRY( "t_ADfA()" );
 
@@ -20 +15 @@
         version = PHFIT_UNDEF;
 
-        strcpy( chString, cpu.DataPath()  );
-        strcat( chString, chFile );
-
-        FILE *io;
-        /* this is the first attempt at opening a data file in this core load
-         * if the path is bad this is where we will fail */
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        double help[9];
+        const long VERSION_MAGIC = 20061204L;
+
+        const static char chFile[] = "phfit.dat";
+
+        FILE *io = open_data( chFile, "r" );
 
         bool lgErr = false;
@@ -75 +65 @@
         const static char chFile2[] = "hpfit.dat";
 
-        strcpy( chString,cpu.DataPath());
-        strcat( chString, chFile2 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile2, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );
@@ -107 +89 @@
         const static char chFile3[] = "rec_lines.dat";
 
-        strcpy( chString, cpu.DataPath() );
-        strcat( chString, chFile3 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile3, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );
@@ -148 +122 @@
         const static char chFile4[] = "rad_rec.dat";
 
-        strcpy( chString,  cpu.DataPath()  );
-        strcat( chString, chFile4 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile4, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );
@@ -201 +167 @@
         const static char chFile5[] = "h_rad_rec.dat";
 
-        strcpy( chString, cpu.DataPath()  );
-        strcat( chString, chFile5 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile5, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );
@@ -233 +191 @@
         const static char chFile6[] = "h_phot_cs.dat";
 
-        strcpy( chString, cpu.DataPath()  );
-        strcat( chString, chFile6 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile6, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );
@@ -263 +213 @@
         const static char chFile7[] = "coll_ion.dat";
 
-        strcpy( chString, cpu.DataPath());
-        strcat( chString, chFile7 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile7, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );
@@ -296 +238 @@
         const static char chFile8[] = "h_coll_str.dat";
 
-        strcpy( chString, cpu.DataPath());
-        strcat( chString, chFile8 );
-
-        if( (io = fopen(chString,"r")) == NULL )
-        {
-                fprintf( ioQQQ, " Could not open %s for reading\n", chString );
-                path_not_set();
-                cdEXIT(EXIT_FAILURE);
-        }
+        io = open_data( chFile8, "r" );
 
         lgErr = lgErr || ( fscanf( io, "%ld", &i ) != 1 );

branches/newmole/source/atmdat_chianti.cpp

@@ -31 +31 @@
 
         char chLine[FILENAME_PATH_LENGTH_2] ,
-                chFilename[FILENAME_PATH_LENGTH_2],
                 chEnFilename[FILENAME_PATH_LENGTH_2],
                 chTraFilename[FILENAME_PATH_LENGTH_2],
@@ -54 +53 @@
         /*For the CHIANTI DATABASE*/
         /*First Opening the energy levels file*/
-        strcpy( chFilename , Species[intNS].chptrSpName );                      
-        strcat( chFilename , ".elvlc");
-        uncaps( chFilename );
-        strcpy( chEnFilename , cpu.DataPath() );
-        strcat( chEnFilename , chFilename );
-        if(DEBUGSTATE)
-                printf("The data file is %s \n",chFilename);
+        strcpy( chEnFilename , Species[intNS].chptrSpName );                    
+        strcat( chEnFilename , ".elvlc");
+        uncaps( chEnFilename );
+        if(DEBUGSTATE)
+                printf("The data file is %s \n",chEnFilename);
 
         /*Open the files*/
         if( trace.lgTrace )
-                fprintf( ioQQQ," moldat_readin opening %s:",chFilename);
-
-        if( ( atmolLevDATA = fopen( chEnFilename , "r" ) ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename );
-                fprintf( ioQQQ, " even tried path\n" );
-
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename);
-                fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                fprintf( ioQQQ, " final path is ==%s==\n",chEnFilename );
-
-                /* make announcement that path probably not set */
-                path_not_set();
-
-                cdEXIT(EXIT_FAILURE);
-        }
-
-        if( read_whole_line( chLine , (int)sizeof(chLine) , atmolLevDATA ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not read first line of %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
-        /*Rewind the file*/
-        if( fseek( atmolLevDATA , 0 , SEEK_SET ) != 0 )
-        {
-                fprintf( ioQQQ, " moldat_readin could not rewind %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
+                fprintf( ioQQQ," moldat_readin opening %s:",chEnFilename);
+
+        atmolLevDATA = open_data( chEnFilename, "r" );
+
         /*Second:Opening the transition probabilities file*/
-        strcpy( chFilename , Species[intNS].chptrSpName );                      
-        strcat( chFilename , ".wgfa");
-        uncaps( chFilename );
-        strcpy( chTraFilename , cpu.DataPath() );
-        strcat( chTraFilename , chFilename );
-        if(DEBUGSTATE)
-                printf("The data file is %s \n",chFilename);
+        strcpy( chTraFilename , Species[intNS].chptrSpName );                   
+        strcat( chTraFilename , ".wgfa");
+        uncaps( chTraFilename );
+        if(DEBUGSTATE)
+                printf("The data file is %s \n",chTraFilename);
 
         /*Open the files*/
         if( trace.lgTrace )
-                fprintf( ioQQQ," moldat_readin opening %s:",chFilename);
-
-        if( ( atmolTraDATA = fopen( chTraFilename , "r" ) ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename );
-                fprintf( ioQQQ, " even tried path\n" );
-
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename);
-                fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                fprintf( ioQQQ, " final path is ==%s==\n",chTraFilename );
-
-                /* make announcement that path probably not set */
-                path_not_set();
-
-                cdEXIT(EXIT_FAILURE);
-        }
-
-        if( read_whole_line( chLine , (int)sizeof(chLine) , atmolTraDATA ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not read first line of %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
-        /*Rewind the file*/
-        if( fseek( atmolTraDATA , 0 , SEEK_SET ) != 0 )
-        {
-                fprintf( ioQQQ, " moldat_readin could not rewind %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
+                fprintf( ioQQQ," moldat_readin opening %s:",chTraFilename);
+
+        atmolTraDATA = open_data( chTraFilename, "r" );
+
         /*Third: Opening the electron collision data*/
-        strcpy( chFilename , Species[intNS].chptrSpName );                      
-        strcat( chFilename , ".splups");
-        uncaps( chFilename );
-        strcpy( chEleColFilename , cpu.DataPath() );
-        strcat( chEleColFilename , chFilename );
-        if(DEBUGSTATE)
-                printf("The data file is %s \n",chFilename);
+        strcpy( chEleColFilename , Species[intNS].chptrSpName );                        
+        strcat( chEleColFilename , ".splups");
+        uncaps( chEleColFilename );
+        if(DEBUGSTATE)
+                printf("The data file is %s \n",chEleColFilename);
         /*Open the files*/
         if( trace.lgTrace )
-                fprintf( ioQQQ," moldat_readin opening %s:",chFilename);
-        if( ( atmolEleColDATA = fopen( chEleColFilename , "r" ) ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename );
-                fprintf( ioQQQ, " even tried path\n" );
-
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename);
-                fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                fprintf( ioQQQ, " final path is ==%s==\n",chEleColFilename );
-
-                /* make announcement that path probably not set */
-                path_not_set();
-
-                cdEXIT(EXIT_FAILURE);
-        }
-
-        if( read_whole_line( chLine , (int)sizeof(chLine) , atmolEleColDATA ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not read first line of %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
-        /*Rewind the electron collision data file*/
-        if( fseek(atmolEleColDATA , 0 , SEEK_SET ) != 0 )
-        {
-                fprintf( ioQQQ, " moldat_readin could not rewind %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
+                fprintf( ioQQQ," moldat_readin opening %s:",chEleColFilename);
+
+        atmolEleColDATA = open_data( chEleColFilename, "r" );
+
         /*Fourth: Opening the proton collision data*/
-        strcpy( chFilename , Species[intNS].chptrSpName );                      
-        strcat( chFilename , ".psplups");
-        uncaps( chFilename );
-        strcpy( chProColFilename , cpu.DataPath() );
-        strcat( chProColFilename , chFilename );
-        if(DEBUGSTATE)
-                printf("The data file is %s \n",chFilename);
+        strcpy( chProColFilename , Species[intNS].chptrSpName );                        
+        strcat( chProColFilename , ".psplups");
+        uncaps( chProColFilename );
+        if(DEBUGSTATE)
+                printf("The data file is %s \n",chProColFilename);
         /*Open the files*/
         if( trace.lgTrace )
-                fprintf( ioQQQ," moldat_readin opening %s:",chFilename);
+                fprintf( ioQQQ," moldat_readin opening %s:",chProColFilename);
 
         nMolLevs = 0;

branches/newmole/source/atmdat_lamda.cpp

@@ -26 +26 @@
 
         char chLine[FILENAME_PATH_LENGTH_2] ,
-                chFilename[FILENAME_PATH_LENGTH_2],
                 chEFilename[FILENAME_PATH_LENGTH_2],
                 *chColltemp,*chCollName;
@@ -35 +34 @@
         if(DEBUGSTATE)
                 printf("The name of the %li species is %s \n",intNS+1,Species[intNS].chptrSpName);
-        strcpy( chFilename , Species[intNS].chptrSpName );                      
-        strcat( chFilename , ".dat");
-        uncaps( chFilename );
-        strcpy( chEFilename , cpu.DataPath() );
-        strcat( chEFilename , chFilename );
+        strcpy( chEFilename , Species[intNS].chptrSpName );                     
+        strcat( chEFilename , ".dat");
+        uncaps( chEFilename );
 
         /*Open the files*/
         if( trace.lgTrace )
-                fprintf( ioQQQ," moldat_readin opening %s:",chFilename);
-
-        if( ( atmolLevDATA = fopen( chEFilename , "r" ) ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename );
-                fprintf( ioQQQ, " even tried path\n" );
-
-                fprintf( ioQQQ, " moldat_readin could not open %s \n",chFilename);
-                fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                fprintf( ioQQQ, " final path is ==%s==\n",chEFilename );
-
-                /* make announcement that path probably not set */
-                path_not_set();
-
-                cdEXIT(EXIT_FAILURE);
-        }
-
-        if( read_whole_line( chLine , (int)sizeof(chLine) , atmolLevDATA ) == NULL )
-        {
-                fprintf( ioQQQ, " moldat_readin could not read first line of %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
-        /*Rewind the file*/
-        if( fseek( atmolLevDATA , 0 , SEEK_SET ) != 0 )
-        {
-                fprintf( ioQQQ, " moldat_readin could not rewind %s.\n",chFilename);
-                cdEXIT(EXIT_FAILURE);
-        }
+                fprintf( ioQQQ," moldat_readin opening %s:",chEFilename);
+
+        atmolLevDATA = open_data( chEFilename, "r" );
 
         nMolLevs = 0;

branches/newmole/source/atmdat_readin.cpp

@@ -338 +338 @@
          *************************************************************/
 
-        strcpy( chFilename , cpu.DataPath() );
-        strcat( chFilename , "level1.dat" );
-
         if( trace.lgTrace )
                 fprintf( ioQQQ," atmdat_readin opening level1.dat:");
 
-        if( ( ioDATA = fopen( chFilename , "r" ) ) == NULL )
-        {
-                fprintf( ioQQQ, " atmdat_readin could not open level1.dat\n" );
-                fprintf( ioQQQ, " even tried path\n" );
-
-                fprintf( ioQQQ, " atmdat_readin could not open level1.dat\n");
-                fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                fprintf( ioQQQ, " final path is ==%s==\n",chFilename );
-
-
-                /* make announcement that path probably not set */
-                path_not_set();
-
-                cdEXIT(EXIT_FAILURE);
-        }
+        ioDATA = open_data( "level1.dat", "r" );
 
         /* first line is a version number and does not count */
@@ -596 +579 @@
                 }
 
-                strcpy( chFilename , cpu.DataPath() );
-                strcat( chFilename , "level2.dat" );
-
                 if( trace.lgTrace )
                         fprintf( ioQQQ," atmdat_readin opening level2.dat:");
 
-                if( ( ioDATA = fopen( chFilename , "r" ) ) == NULL )
-                {
-                        fprintf( ioQQQ, " atmdat_readin could not open level2.dat\n" );
-                        fprintf( ioQQQ, " atmdat_readin could not open level2.dat, even tried path.\n");
-                        fprintf( ioQQQ, " path is *%s*\n",cpu.DataPath() );
-                        fprintf( ioQQQ, " final path is *%s*\n",chFilename );
-                        cdEXIT(EXIT_FAILURE);
-                }
+                ioDATA = open_data( "level2.dat", "r" );
 
                 /* get magic number off first line */
@@ -712 +685 @@
         if( ionbal.lgInnerShell_Gu06 )
         {
-                strcpy( chFilename , cpu.DataPath() );
-                strcat( chFilename , "UTA_Gu06.dat" );
                 if( trace.lgTrace )
                         fprintf( ioQQQ," atmdat_readin opening UTA_Gu06.dat:");
 
-                if( ( ioGU06 = fopen( chFilename , "r" ) ) == NULL )
-                {
-                        fprintf( ioQQQ, " atmdat_readin could not open UTA_Gu06.dat\n" );
-                        fprintf( ioQQQ, " even tried path\n" );
-
-                        fprintf( ioQQQ, " atmdat_readin could not open UTA_Gu06.dat\n");
-                        fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                        fprintf( ioQQQ, " final path is ==%s==\n",chFilename );
-                        cdEXIT(EXIT_FAILURE);
-                }
+                ioGU06 = open_data( "UTA_Gu06.dat", "r" );
 
                 /* count how many non-comment lines there are in Gu06 file */
@@ -784 +746 @@
                  * >>refer      Fe      inner shell UTA Behar, E., & Netzer, H., 2002, ApJ, 570, 165-170 */
 
-                strcpy( chFilename , cpu.DataPath() );
-                strcat( chFilename , "UTA_Behar.dat" );
                 if( trace.lgTrace )
                         fprintf( ioQQQ," atmdat_readin opening UTA_Behar.dat:");
 
-                if( ( ioBEHAR = fopen( chFilename , "r" ) ) == NULL )
-                {
-                        fprintf( ioQQQ, " atmdat_readin could not open UTA_Behar.dat\n" );
-                        fprintf( ioQQQ, " even tried path\n" );
-
-                        fprintf( ioQQQ, " atmdat_readin could not open UTA_Behar.dat\n");
-                        fprintf( ioQQQ, " path is ==%s==\n",cpu.DataPath() );
-                        fprintf( ioQQQ, " final path is ==%s==\n",chFilename );
-
-
-                        cdEXIT(EXIT_FAILURE);
-                }
+                ioBEHAR = open_data( "UTA_Behar.dat", "r" );
 
                 /* count number