Changeset 2266

Timestamp:

2008-07-26T10:13:34Z (15 years ago)

Author:

Gary J. Ferland

Message:

these are a number of small changes which should not affect the calculations in any way

sumlin -> SumLin? - many files have this as the sole change

update comments and remove commented out code in many files

assert_results.cpp - add total insanity block if key not recognized

atom_hyperfine.cpp - define damping constant as very small number - had not been defined before

Location:

trunk/source

Files:

• assert_results.cpp (modified) (3 diffs)
• atmdat.h (modified) (1 diff)
• atom_feii.cpp (modified) (1 diff)
• atom_hyperfine.cpp (modified) (1 diff)
• cddrive.cpp (modified) (6 diffs)
• continuum.txt (modified) (6 diffs)
• conv_base.cpp (modified) (1 diff)
• init_defaults_preparse.cpp (modified) (2 diffs)
• init_sim_postparse.cpp (modified) (1 diff)
• iter_end_chk.cpp (modified) (1 diff)
• lines.h (modified) (1 diff)
• lines_service.cpp (modified) (7 diffs)
• mole_h2_io.cpp (modified) (2 diffs)
• opacity_addtotal.cpp (modified) (1 diff)
• optimize_func.cpp (modified) (3 diffs)
• optimize_phymir.cpp (modified) (1 diff)
• parse_coronal.cpp (modified) (1 diff)
• parse_print.cpp (modified) (2 diffs)
• parse_punch.cpp (modified) (2 diffs)
• path.h (modified) (1 diff)
• pressure_total.cpp (modified) (1 diff)
• prt_comment.cpp (modified) (4 diffs)
• prt_final.cpp (modified) (8 diffs)
• prt_lines.cpp (modified) (1 diff)
• prt_lines_continuum.cpp (modified) (12 diffs)
• prt_lines_hydro.cpp (modified) (2 diffs)
• punch_do.cpp (modified) (4 diffs)
• rt_line_all.cpp (modified) (1 diff)
• rt_line_one_tau_reset.cpp (modified) (1 diff)
• rt_ots.cpp (modified) (1 diff)
• service.cpp (modified) (1 diff)
• zone_startend.cpp (modified) (1 diff)

trunk/source/assert_results.cpp

@@ -544 +544 @@
                         strcpy( chAssertLineLabel[nAsserts] , "+Col");
                 }
+                else
+                {
+                        /*no option found */
+                        fprintf( ioQQQ, 
+                                " I could not identify an iso-sequence on this Case A/B command.\n");
+                        fprintf( ioQQQ, " Sorry.\n" );
+                        cdEXIT(EXIT_FAILURE);
+                }
         }
         else if( nMatch("DEPA",input.chCARDCAPS ) )
@@ -1942 +1950 @@
                         strcat( chElemLabelCaseB , chNumb );
 
-                        int iCase = 1;
+                        /* sets lowest quantum number index */
+                        int iCase;
                         if( strcmp( "Ca A", chAssertLineLabel[i] ) == 0 )
                                 iCase = 0;
@@ -1957 +1966 @@
                         {
                                 fprintf(ioASSERT,"                 Species  nHi nLo  Wl  Computed  Asserted       error\n");
-                                /* limit of 10 is because that is all we printed and saved in prt_lines_hydro */
+                                /* limit of 10 is because that is all we printed and saved in prt_lines_hydro 
+                                 * wavelengths will come out of atmdat.WaveLengthCaseB - first index is
+                                 * nelem on C scale, H is 0, second two are configurations of line on
+                                 * physics scale, so Ha is 3-2 */
                                 for( long int ipLo=1+iCase; ipLo< MIN2(10,nHighestPrinted-1); ++ipLo )
                                 {

trunk/source/atmdat.h

@@ -203 +203 @@
         bool lgCollIonOn;
 
-        /** wavelengths of Hummer & Storey case B lines for H - O */
+        /** wavelengths of Hummer & Storey case B lines for H - O 
+         * first dimension is atomic number of C scale, H is 0
+         * next two are upper and lower configurations on physics 
+         * scale - Lya is 2-1, Lyb is 3-1, Ha is 3-2, etc */
         realnum WaveLengthCaseB[8][25][24];
 

trunk/source/atom_feii.cpp

@@ -1762 +1762 @@
 
         /* get the normalization line */
-        if( LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] > 0. )
-        {
-                renorm = LineSave.ScaleNormLine/LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent];
+        if( LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] > 0. )
+        {
+                renorm = LineSave.ScaleNormLine/LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent];
         }
         else

trunk/source/atom_hyperfine.cpp

@@ -487 +487 @@
                         wavelength = (realnum)help[2];
                         HFLines[j].Emis->Aul = (realnum)Aul;
+                        HFLines[j].Emis->damp = 1e-20f;
                         HFLines[j].Hi->g = (realnum) (2*(spin + .5) + 1);
                         HFLines[j].Lo->g = (realnum) (2*(spin - .5) + 1);

trunk/source/cddrive.cpp

@@ -1377 +1377 @@
 
                                 /* does the normalization line have a positive intensity*/
-                                if( LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] > 0. )
+                                if( LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] > 0. )
                                 {
-                                        *relint = LineSv[ipobs].sumlin[LineSave.lgLineEmergent]/LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent]*
+                                        *relint = LineSv[ipobs].SumLine[LineSave.lgLineEmergent]/LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent]*
                                           LineSave.ScaleNormLine;
                                 }
@@ -1388 +1388 @@
 
                                 /* return log of current line intensity if it is positive */
-                                if( LineSv[ipobs].sumlin[LineSave.lgLineEmergent] > 0. )
+                                if( LineSv[ipobs].SumLine[LineSave.lgLineEmergent] > 0. )
                                 {
-                                        *absint = log10(LineSv[ipobs].sumlin[LineSave.lgLineEmergent]) + radius.Conv2PrtInten;
+                                        *absint = log10(LineSv[ipobs].SumLine[LineSave.lgLineEmergent]) + radius.Conv2PrtInten;
                                 }
                                 else
@@ -1452 +1452 @@
 
         /* does the normalization line have a positive intensity*/
-        if( LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] > 0. )
-        {
-                *relint = LineSv[ipLine].sumlin[LineSave.lgLineEmergent]/LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent]*
+        if( LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] > 0. )
+        {
+                *relint = LineSv[ipLine].SumLine[LineSave.lgLineEmergent]/LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent]*
                   LineSave.ScaleNormLine;
         }
@@ -1463 +1463 @@
 
         /* return log of current line intensity if it is positive */
-        if( LineSv[ipLine].sumlin[LineSave.lgLineEmergent] > 0. )
-        {
-                *absint = log10(LineSv[ipLine].sumlin[LineSave.lgLineEmergent]) + radius.Conv2PrtInten;
+        if( LineSv[ipLine].SumLine[LineSave.lgLineEmergent] > 0. )
+        {
+                *absint = log10(LineSv[ipLine].SumLine[LineSave.lgLineEmergent]) + radius.Conv2PrtInten;
         }
         else
@@ -1541 +1541 @@
 
                                 /* does the normalization line have a positive intensity*/
-                                if( LineSv[LineSave.ipNormWavL].sumlin[1] > 0. )
+                                if( LineSv[LineSave.ipNormWavL].SumLine[1] > 0. )
                                 {
-                                        *relint = LineSv[ipobs].sumlin[1]/LineSv[LineSave.ipNormWavL].sumlin[1]*
+                                        *relint = LineSv[ipobs].SumLine[1]/LineSv[LineSave.ipNormWavL].SumLine[1]*
                                           LineSave.ScaleNormLine;
                                 }
@@ -1552 +1552 @@
 
                                 /* return log of current line intensity if it is positive */
-                                if( LineSv[ipobs].sumlin[1] > 0. )
+                                if( LineSv[ipobs].SumLine[1] > 0. )
                                 {
-                                        *absint = log10(LineSv[ipobs].sumlin[1]) + radius.Conv2PrtInten;
+                                        *absint = log10(LineSv[ipobs].SumLine[1]) + radius.Conv2PrtInten;
                                 }
                                 else

trunk/source/continuum.txt

@@ -8 +8 @@
 SummedCon is added together in RT_OTS_Update (in rtots.c)
 
-rfield.SummedCon[i] = rfield.flux[i] + rfield.SummedDif[i];
+rfield.SummedCon[i] = rfield.flux[0][i] + rfield.SummedDif[i];
 
 rfield.SummedDif[i] = rfield.otscon[i] + rfield.otslin[i] + 
-        rfield.ConInterOut[i]*rfield.lgOutOnly + rfield.outlin[i] +
+        rfield.ConInterOut[i]*rfield.lgOutOnly + rfield.outlin[0][i] +
         rfield.ConOTS_local_OTS_rate[i];
 
@@ -78 +78 @@
 
 incident continua
-rfield.flux_total_incident[j] - the original incident continuum
-rfield.flux - outward attenuated incident continuum
+rfield.flux_total_incident[0][j] - the original incident continuum
+rfield.flux[0] - outward attenuated incident continuum
         incident continuum is initally defined in ContSetIntensity
 
@@ -86 +86 @@
 reflected continua
 inward or reflected part of continuum, only computed in open geometry 
-rfield.ConRefIncid[j] reflected incident continuum
+rfield.ConRefIncid[0][j] reflected incident continuum
 rfield.ConRefDiff[j]) reflected diffuse continua
-rfield.reflin[j] reflected lines 
+rfield.reflin[0][j] reflected lines 
 
 ====================================================================
@@ -102 +102 @@
 
 rfield.ConInterOut - integrated outward beam, interacts
-rfield.ConEmitOut - total outward emission 
+rfield.ConEmitOut[0] - total outward emission 
         calculated from local diffuse emission in radius_increment
 
@@ -112 +112 @@
 
 contains 
-rfield.flux[i] 
+rfield.flux[0][i] 
 rfield.otslin[i] 
 rfield.otscon[i] 
@@ -118 +118 @@
 ====================================================================
 
-rfield.outlin[i] 
+rfield.outlin[0][i] 
 outward lines, included in ionizing radiation
 

trunk/source/conv_base.cpp

@@ -989 +989 @@
         }
 
-        /* check on heating and cooling if vary temp model */
+        /* check on heating and cooling if vary temp model 
+         * >>chng 08 jul 01, over the code's entire history it had tested whether
+         * this is a constant temperature simulation and did not do this test if
+         * the thermal solution was not done.  There are some cases where we do
+         * want to specify the temperature and then find the heating or cooling -
+         * this is done in calculations of cooling curves for instance.  With this
+         * change the heating/cooling are converged even in a constant temperature
+         * sim.  this does make CT sims run more slowly but with greater accuracy
+         * if heating or cooling is reported */
         if( !thermal.lgTemperatureConstant )
         {

trunk/source/init_defaults_preparse.cpp

@@ -2 +2 @@
  * others.  For conditions of distribution and use see copyright notice in license.txt */
 /*InitDefaultsPreparse initialization at start of simulation, called from cloudy
-* before parser, sets initial values of quantities changed by parser */
+* before parser, sets initial values of quantities changed by parser 
+* called for each point in a grid but one time in multi-iteration sims */
 #include "cddefines.h" 
 #include "physconst.h"
@@ -37 +38 @@
  * should only set defaults for variables that change in the parser.
  * It does not initialize variables for the start of a calculation.  That
- * is done by InitSimPostparse */
+ * is done by InitSimPostparse 
+ * called one time in multi iteration sim */
 void InitDefaultsPreparse( void )
 {

trunk/source/init_sim_postparse.cpp

@@ -2 +2 @@
  * others.  For conditions of distribution and use see copyright notice in license.txt */
 /*InitSimPostparse initialization at start of simulation, called from cloudy
-* after parser, will be called one time per sim in grid */
+* after parser, will be called one time per sim in grid 
+* is not called for every iteration */
 #include "cddefines.h" 
 #include "dense.h"

trunk/source/iter_end_chk.cpp

@@ -364 +364 @@
                 {
                         /* the second line is always set to something, default is H beta */
-                        if( LineSv[StopCalc.ipStopLin2[i]].sumlin[LineSave.lgLineEmergent] > 0. )
+                        if( LineSv[StopCalc.ipStopLin2[i]].SumLine[LineSave.lgLineEmergent] > 0. )
                         {
                                 char chString[10];
-                                if( LineSv[StopCalc.ipStopLin1[i]].sumlin[LineSave.lgLineEmergent]/
-                                        LineSv[StopCalc.ipStopLin2[i]].sumlin[LineSave.lgLineEmergent] > StopCalc.stpint[i] )
+                                if( LineSv[StopCalc.ipStopLin1[i]].SumLine[LineSave.lgLineEmergent]/
+                                        LineSv[StopCalc.ipStopLin2[i]].SumLine[LineSave.lgLineEmergent] > StopCalc.stpint[i] )
                                 {
                                         lgDone = true;

trunk/source/lines.h

@@ -113 +113 @@
         char chALab[5];
 
-        /** >>chng 06 mar 09, make intrinsic and emergent one array */
-        /** integrated intensity of the line, [0] is intrinsic, [1] emergent */
-        double sumlin[2];
+        /** integrated intensity of the line, 
+         * [0] is intrinsic, 
+         * [1] emergent 
+         * [2] is intrinsic, 
+         * [3] emergent 
+         */
+        double SumLine[4];
 
         /** the emissivity, per unit vol, for current conditions, */

trunk/source/lines_service.cpp

@@ -470 +470 @@
                 /* not first pass, sum lines only
                  * total emission from vol */
-                LineSv[LineSave.nsum].sumlin[0] += xInten*radius.dVeff;
+                LineSv[LineSave.nsum].SumLine[0] += xInten*radius.dVeff;
                 /* local emissivity in line */
                 LineSv[LineSave.nsum].emslin[0] = xInten;
@@ -481 +481 @@
                          * it would be wrong to predict their transferred intensity */
                         LineSv[LineSave.nsum].emslin[1] = LineSv[LineSave.nsum].emslin[0];
-                        LineSv[LineSave.nsum].sumlin[1] = LineSv[LineSave.nsum].sumlin[0]; 
+                        LineSv[LineSave.nsum].SumLine[1] = LineSv[LineSave.nsum].SumLine[0]; 
                 }
         }
@@ -489 +489 @@
                 /* first call to stuff lines in array, confirm that label is one of
                  * the four correct ones */
-                /* >>chng 04 apr 24, last two had been != so this test never really happened; PvH */
                 ASSERT( (chInfo == 'c') || (chInfo == 'h') || (chInfo == 'i') || (chInfo == 'r' ) );
 
@@ -602 +601 @@
                 LineSv[LineSave.nsum].emslin[0] = xInten;
                 /* integrated intensity or luminosity, the emissivity times the volume */
-                LineSv[LineSave.nsum].sumlin[0] += xInten*radius.dVeff;
+                LineSv[LineSave.nsum].SumLine[0] += xInten*radius.dVeff;
 
                 /* add line to outward beam 
@@ -625 +624 @@
                                 xInten*rt.fracin , xInten*(1.-rt.fracin) , ipnt );
                         LineSv[LineSave.nsum].emslin[1] = saveemis;
-                        LineSv[LineSave.nsum].sumlin[1] += saveemis*radius.dVeff; 
+                        LineSv[LineSave.nsum].SumLine[1] += saveemis*radius.dVeff; 
                 }
         }
@@ -638 +637 @@
                 LineSv[LineSave.nsum].chSumTyp = (char)chInfo;
                 /* number of lines ok, set parameters for first pass */
-                LineSv[LineSave.nsum].sumlin[0] = 0.;
+                LineSv[LineSave.nsum].wavelength = wavelength;
                 LineSv[LineSave.nsum].emslin[0] = 0.;
-                LineSv[LineSave.nsum].wavelength = wavelength;
                 LineSv[LineSave.nsum].emslin[1] = 0.;
-                LineSv[LineSave.nsum].sumlin[1] = 0.;
+                LineSv[LineSave.nsum].SumLine[0] = 0.;
+                LineSv[LineSave.nsum].SumLine[1] = 0.;
                 LineSv[LineSave.nsum].chComment = chComment;
 
@@ -1322 +1321 @@
                 if( LineSv[i].chSumTyp == chInfo )
                 {
-                        totlin_v += LineSv[i].sumlin[0];
+                        totlin_v += LineSv[i].SumLine[0];
                 }
         }

trunk/source/mole_h2_io.cpp

@@ -2120 +2120 @@
                         ASSERT( LineSave.ipNormWavL >= 0 );
                         /* get the normalization line */
-                        if( LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] > SMALLFLOAT )
-                                renorm = LineSave.ScaleNormLine/LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent];
+                        if( LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] > SMALLFLOAT )
+                                renorm = LineSave.ScaleNormLine/LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent];
                         else
                                 renorm = 1.;
@@ -2273 +2273 @@
         ASSERT( LineSave.ipNormWavL >= 0 );
         /* does the normalization line have a positive intensity*/
-        if( LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] > 0. )
+        if( LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] > 0. )
         {
                 *relint = H2_SaveLine[iElecHi][iVibHi][iRotHi][iElecLo][iVibLo][iRotLo]/
-                        LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] * LineSave.ScaleNormLine;
+                        LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] * LineSave.ScaleNormLine;
         }
         else

trunk/source/opacity_addtotal.cpp

@@ -512 +512 @@
                   iso.ConOpacRatio[ipH_LIKE][ipHELIUM][ipH1s] );
         }
+
         {
                 /* following should be set true to print strongest ots contributors */
-                /*@-redef@*/
                 enum {DEBUG_LOC=false};
-                /*@+redef@*/
                 if( DEBUG_LOC && (nzone>=378)/**/ )
                 {

trunk/source/optimize_func.cpp

@@ -144 +144 @@
                 }
 
-                if( (snorm = LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent]) == 0. )
+                if( (snorm = LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent]) == 0. )
                 {
                         fprintf( ioQQQ, "\n\n PROBLEM Normalization line has zero intensity.  What has gone wrong?\n" );
@@ -204 +204 @@
                                 /* and find corresponding model value by straight search */
                                 nfound += 1;
-                                scld = (double)LineSv[ipobs[i]].sumlin[LineSave.lgLineEmergent]/(double)snorm*LineSave.ScaleNormLine;
+                                scld = (double)LineSv[ipobs[i]].SumLine[LineSave.lgLineEmergent]/(double)snorm*LineSave.ScaleNormLine;
                                 chi1 = chi2_func(scld,(double)optimize.xLineInt_Obs[i],(double)optimize.xLineInt_error[i]);
                                 cat = 0;
@@ -300 +300 @@
                 {
                         nfound += 1;
-                        if( LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent] > 0.f )
-                        {
-                                predin = log10(LineSv[LineSave.ipNormWavL].sumlin[LineSave.lgLineEmergent]) + radius.Conv2PrtInten;
+                        if( LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent] > 0.f )
+                        {
+                                predin = log10(LineSv[LineSave.ipNormWavL].SumLine[LineSave.lgLineEmergent]) + radius.Conv2PrtInten;
                                 help = pow(10.,predin-(double)optimize.optint);
                                 chi1 = chi2_func(help,1.,(double)optimize.optier);

trunk/source/optimize_phymir.cpp

@@ -237 +237 @@
 
         if( lgFinish )
-        { 
                 return;
-        }
-        /*       maximum no. of iterations exceeded?  */
+
+        /* maximum no. of iterations exceeded?  */
         if( optimize.nOptimiz >= optimize.nIterOptim )
         {

trunk/source/parse_coronal.cpp

@@ -23 +23 @@
         DEBUG_ENTRY( "ParseCoronal()" );
 
+        /* use coronal command to establish initial conditions in a cooling
+         * time-varying cloud */
         if( nMatch( "INIT" , chCard ) && nMatch( "TIME" , chCard ) )
         {

trunk/source/parse_print.cpp

@@ -264 +264 @@
 
                         prt.lgFntSet = true;
-                        if( a <= 0. )
+                        if( a <= 0. || nMatch(" LOG",chCARD_CAPS) )
                         {
                                 prt.TooFaint = (realnum)pow(10.,a);
@@ -558 +558 @@
         }
 
-        else if( nMatch("EVER",chCARD_CAPS) )
-        {
-                /* print every nth zone */
+        else if( nMatch("ZONE",chCARD_CAPS) || nMatch("EVER",chCARD_CAPS) )
+        {
+                /* print every nth zone - command was originally print every but
+                 * is being changed to print zone */
                 i = 5;
                 num1 = (long int)FFmtRead(chCARD_CAPS,&i,INPUT_LINE_LENGTH,&lgEOL);

trunk/source/parse_punch.cpp

@@ -1586 +1586 @@
         else if( nMatch("LINE",chCard) && !nMatch("XSPE",chCard) && !nMatch("NEAR",chCard))
         {
-                /* punch line emissivity -
+                /* punch line options -
                  * this is not punch xspec lines and not linear option
                  * check for keyword UNITS on line, then scan wavelength or energy units, 
@@ -1608 +1608 @@
                         strcpy( punch.chPunch[punch.npunch], "LINS" );
                         sprintf( chHeader, 
-                                "#Emission line structure:");
+                                "#Emission line emissivity:");
                         /* read in the list of lines to examine */
                         punch_line(punch.ipPnunit[punch.npunch],"READ",false, chTemp);

trunk/source/path.h

@@ -44 +44 @@
  * NB - note that the backslash "\" always needs to be typed twice, as shown below: */
 
-// #define CLOUDY_DATA_PATH "c:\\projects\\cloudy\\data;c:\\users\\gary\\data"
+// #define CLOUDY_DATA_PATH "c:\\projects\\cloudy\\trunk\\data;c:\\users\\gary\\data"
 
 /* The // makes the above line of code a comment

trunk/source/pressure_total.cpp

@@ -959 +959 @@
         pressure.PresTotlCurr = TotalPressure_v;
 
-#       if 0
-        /* this is special case where we are working on first zone, at
-         * illuminated face of the cloud.  Here we want to remember the
-         * initial pressure in case constant pressure is needed */
-        /* >>chng 05 jan 10, chng from nzone==1 to nzone<=1 so pressure not changed
-         * during search phase */
-        /*>>chng 06 jun 20, add test on first iteration, or we are holding
-         * density constant - flag dense.lgDenseInitConstant false if
-         * constant pressure reset is used - default is true, after first iteration
-         * initial density is kept constant, when set false with reset option on
-         * constant pressure density on first iteration is allowed to change to keep
-         * pressure constant */
-        if( nzone <= 1 && (iteration==1 || dense.lgDenseInitConstant) )
-        {
-                double PresTotlInitSave;
-                double PresRamInitSave;
-                /* this is first zone, lock onto pressure */
-                if( conv.nTotalIoniz )
-                {
-                        PresTotlInitSave = pressure.PresTotlInit;
-                        PresRamInitSave = pressure.PresRamInit;
-                }
-                else
-                {
-                        PresTotlInitSave = 0.;
-                        PresRamInitSave = 0.;
-                }
-                pressure.PresTotlInit = pressure.PresTotlCurr;
-                pressure.PresRamInit = pressure.PresRamCurr;
-                if( trace.lgTrace )
-                {
-                        fprintf( ioQQQ, 
-                          "     PresTotCurrent 1st zn reset PresTotlInit to PresTotlCurr=%.3e "
-                          "PresRamInit to PresRamCurr=%.3e old tot=%.3e old ram %.3e hden=%.3e\n", 
-                          pressure.PresTotlInit,
-                          pressure.PresRamInit,
-                          PresTotlInitSave,PresRamInitSave,
-                          dense.gas_phase[ipHYDROGEN] );
-                }
-        }
-#       endif
         return;
 }

trunk/source/prt_comment.cpp

@@ -2986 +2986 @@
 
         /* this is now the linear vol, rel to inner radius */
-        VolComputed = LineSv[i].sumlin[0] /  1e-10;
-
-        /* >>chng 02 apr 22, do not zero this element out, so can be used to get vol */
-        /* set stored number to zero so it does not appear on the emission line list
-        LineSv[i].sumlin[LineSave.lgLineEmergent] = 0.; */
+        VolComputed = LineSv[i].SumLine[0] /  1e-10;
 
         /* spherical or plane parallel case? */
@@ -3154 +3150 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                if( LineSv[i].chSumTyp == chInfo && LineSv[i].sumlin[0]/total > RATIO )
+                if( LineSv[i].chSumTyp == chInfo && LineSv[i].SumLine[0]/total > RATIO )
                 {
                         fprintf( ioQQQ, " %4.4s ", LineSv[i].chALab );
                         prt_wl( ioQQQ, LineSv[i].wavelength );
-                        fprintf( ioQQQ, " %7.3f %c\n", LineSv[i].sumlin[0]/total, chInfo );
+                        fprintf( ioQQQ, " %7.3f %c\n", LineSv[i].SumLine[0]/total, chInfo );
                 }
         }
@@ -3169 +3165 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                if( LineSv[i].chSumTyp == chInfo && LineSv[i].sumlin[0]/total > RATIO )
+                if( LineSv[i].chSumTyp == chInfo && LineSv[i].SumLine[0]/total > RATIO )
                 {
                         fprintf( ioQQQ, " %4.4s ", LineSv[i].chALab );
                         prt_wl( ioQQQ, LineSv[i].wavelength );
-                        fprintf( ioQQQ, " %7.3f %c\n", LineSv[i].sumlin[0]/total, chInfo );
+                        fprintf( ioQQQ, " %7.3f %c\n", LineSv[i].SumLine[0]/total, chInfo );
                 }
         }
@@ -3183 +3179 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                if( LineSv[i].chSumTyp == chInfo && LineSv[i].sumlin[0]/total > RATIO )
+                if( LineSv[i].chSumTyp == chInfo && LineSv[i].SumLine[0]/total > RATIO )
                 {
                         fprintf( ioQQQ, " %4.4s ", LineSv[i].chALab );
                         prt_wl( ioQQQ, LineSv[i].wavelength );
-                        fprintf( ioQQQ, " %7.3f %c\n", LineSv[i].sumlin[0]/total, chInfo );
+                        fprintf( ioQQQ, " %7.3f %c\n", LineSv[i].SumLine[0]/total, chInfo );
                 }
         }

trunk/source/prt_final.cpp

@@ -357 +357 @@
                                         if( fabs(LineSv[i].wavelength-wlh[j] ) <= errorwave )
                                         {
-                                                LineSv[i].sumlin[0] = 0.;
-                                                LineSv[i].sumlin[1] = 0.;
+                                                LineSv[i].SumLine[0] = 0.;
+                                                LineSv[i].SumLine[1] = 0.;
                                                 break;
                                         }
@@ -388 +388 @@
                                         if( fabs(LineSv[i].wavelength-wlhe[j] ) <= errorwave )
                                         {
-                                                LineSv[i].sumlin[0] = 0.;
-                                                LineSv[i].sumlin[1] = 0.;
+                                                LineSv[i].SumLine[0] = 0.;
+                                                LineSv[i].SumLine[1] = 0.;
                                                 break;
                                         }
@@ -706 +706 @@
 
                 /* this is the intensity of the line spectrum will be normalized to */
-                snorm = LineSv[LineSave.ipNormWavL].sumlin[ipEmType];
+                snorm = LineSv[LineSave.ipNormWavL].SumLine[ipEmType];
 
                 /* check that this line has positive intensity */
@@ -723 +723 @@
                          * a realnum - this is not actually a problem since the number will
                          * overflow the format and hence be unreadable */
-                        double scale = LineSv[i].sumlin[ipEmType]/snorm*LineSave.ScaleNormLine;
+                        double scale = LineSv[i].SumLine[ipEmType]/snorm*LineSave.ScaleNormLine;
                         /* this will become a realnum, so limit dynamic range */
                         scale = MIN2(BIGFLOAT , scale );
@@ -731 +731 @@
                         scaled[i] = (realnum)scale;
 
-                        if( LineSv[i].sumlin[ipEmType] > 0. )
-                        {
-                                xLog_line_lumin[i] = log10(LineSv[i].sumlin[ipEmType]) + radius.Conv2PrtInten;
+                        if( LineSv[i].SumLine[ipEmType] > 0. )
+                        {
+                                xLog_line_lumin[i] = log10(LineSv[i].SumLine[ipEmType]) + radius.Conv2PrtInten;
                         }
                         else
@@ -815 +815 @@
                                         if( prt.lgPrtLineLog )
                                         {
-                                                xLog_line_lumin[iprnt] = log10(LineSv[i].sumlin[ipEmType]) + radius.Conv2PrtInten;
+                                                xLog_line_lumin[iprnt] = log10(LineSv[i].SumLine[ipEmType]) + radius.Conv2PrtInten;
                                         }
                                         else
                                         {
-                                                xLog_line_lumin[iprnt] = LineSv[i].sumlin[ipEmType] * pow(10.,radius.Conv2PrtInten);
+                                                xLog_line_lumin[iprnt] = LineSv[i].SumLine[ipEmType] * pow(10.,radius.Conv2PrtInten);
                                         }
                                         sclsav[iprnt] = scaled[i];
@@ -1069 +1069 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                a = (double)LineSv[i].sumlin[LineSave.lgLineEmergent]/(double)thermal.totcol;
+                a = (double)LineSv[i].SumLine[LineSave.lgLineEmergent]/(double)thermal.totcol;
                 if( (a >= 0.05) && LineSv[i].chSumTyp == 'c' )
                 {
@@ -1099 +1099 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                a = (double)LineSv[i].sumlin[LineSave.lgLineEmergent]/(double)thermal.power;
+                a = (double)LineSv[i].SumLine[LineSave.lgLineEmergent]/(double)thermal.power;
                 if( (a >= 0.05) && LineSv[i].chSumTyp == 'h' )
                 {

trunk/source/prt_lines.cpp

@@ -203 +203 @@
          * remember that memory not allocated until ipass >= 0 */
         if( LineSave.ipass > 0 )
-                LineSv[LineSave.nsum].sumlin[LineSave.lgLineEmergent] = 0.;
+                LineSv[LineSave.nsum].SumLine[LineSave.lgLineEmergent] = 0.;
         /* optional sum of certain emission lines, set with "print sum" */
         linadd(sum/radius.dVeff,0,"Stoy",'i' , 

trunk/source/prt_lines_continuum.cpp

@@ -79 +79 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum].sumlin[0] = 0.;
-                LineSv[LineSave.nsum].sumlin[1] = 0.;
+                LineSv[LineSave.nsum].SumLine[0] = 0.;
+                LineSv[LineSave.nsum].SumLine[1] = 0.;
         }
 
@@ -98 +98 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum].sumlin[0] = 0.;
-                LineSv[LineSave.nsum].sumlin[1] = 0.;
+                LineSv[LineSave.nsum].SumLine[0] = 0.;
+                LineSv[LineSave.nsum].SumLine[1] = 0.;
         }
 
@@ -117 +117 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum].sumlin[0] = 0.;
-                LineSv[LineSave.nsum].sumlin[1] = 0.;
+                LineSv[LineSave.nsum].SumLine[0] = 0.;
+                LineSv[LineSave.nsum].SumLine[1] = 0.;
         }
 
@@ -152 +152 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum].sumlin[0] = 0.;
-                LineSv[LineSave.nsum].sumlin[1] = 0.;
+                LineSv[LineSave.nsum].SumLine[0] = 0.;
+                LineSv[LineSave.nsum].SumLine[1] = 0.;
         }
 
@@ -186 +186 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum].sumlin[0] = 0.;
-                LineSv[LineSave.nsum].sumlin[1] = 0.;
+                LineSv[LineSave.nsum].SumLine[0] = 0.;
+                LineSv[LineSave.nsum].SumLine[1] = 0.;
         }
 
@@ -235 +235 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum-1].sumlin[1] = LineSv[LineSave.nsum-1].sumlin[0];
+                LineSv[LineSave.nsum-1].SumLine[1] = LineSv[LineSave.nsum-1].SumLine[0];
         }
 
@@ -244 +244 @@
         if( LineSave.ipass > 0 )
         {
-                LineSv[LineSave.nsum-1].sumlin[1] = LineSv[LineSave.nsum-1].sumlin[0];
+                LineSv[LineSave.nsum-1].SumLine[1] = LineSv[LineSave.nsum-1].SumLine[0];
         }
 
@@ -332 +332 @@
                 if( LineSave.ipass > 0 )
                 {
-                        LineSv[LineSave.nsum].sumlin[0] = 0.;
-                        LineSv[LineSave.nsum].sumlin[1] = 0.;
+                        LineSv[LineSave.nsum].SumLine[0] = 0.;
+                        LineSv[LineSave.nsum].SumLine[1] = 0.;
                 }
 
@@ -465 +465 @@
                 if( LineSave.ipass > 0 )
                 {
-                        LineSv[LineSave.nsum].sumlin[0] = 0.;
-                        LineSv[LineSave.nsum].sumlin[1] = 0.;
+                        LineSv[LineSave.nsum].SumLine[0] = 0.;
+                        LineSv[LineSave.nsum].SumLine[1] = 0.;
                 }
 
@@ -485 +485 @@
                 if( LineSave.ipass > 0 )
                 {
-                        LineSv[LineSave.nsum].sumlin[0] = 0.;
-                        LineSv[LineSave.nsum].sumlin[1] = 0.;
-                }
-
-                /* the nsum-1 -- emslin and nsum -- sumlin is not a bug, look above - they do
+                        LineSv[LineSave.nsum].SumLine[0] = 0.;
+                        LineSv[LineSave.nsum].SumLine[1] = 0.;
+                }
+
+                /* the nsum-1 -- emslin and nsum -- SumLine is not a bug, look above - they do
                  * different things to different saves */
                 Cont_nInu = rfield.flux[ipPredCont[i]]*renorm*radius.r1r0sq +
@@ -519 +519 @@
                 if( LineSave.ipass > 0 )
                 {
-                        LineSv[LineSave.nsum].sumlin[0] = 0.;
-                        LineSv[LineSave.nsum].sumlin[1] = 0.;
+                        LineSv[LineSave.nsum].SumLine[0] = 0.;
+                        LineSv[LineSave.nsum].SumLine[1] = 0.;
                 }
 
@@ -535 +535 @@
                 if( LineSave.ipass > 0 )
                 {
-                        LineSv[LineSave.nsum].sumlin[0] = 0.;
-                        LineSv[LineSave.nsum].sumlin[1] = 0.;
+                        LineSv[LineSave.nsum].SumLine[0] = 0.;
+                        LineSv[LineSave.nsum].SumLine[1] = 0.;
                 }
 

trunk/source/prt_lines_hydro.cpp

@@ -180 +180 @@
                         caseb = rfield.qhtot*4.75e-13;
                 }
-                LineSv[LineSave.nsum].sumlin[LineSave.lgLineEmergent] = 0.;
+                LineSv[LineSave.nsum].SumLine[LineSave.lgLineEmergent] = 0.;
         }
         else
@@ -194 +194 @@
         {
                 caseb = rfield.qhtot*Transitions[ipH_LIKE][ipHYDROGEN][ipH2p][ipH1s].EnergyErg;
-                LineSv[LineSave.nsum].sumlin[LineSave.lgLineEmergent] = 0.;
+                LineSv[LineSave.nsum].SumLine[LineSave.lgLineEmergent] = 0.;
         }
         else

trunk/source/punch_do.cpp

@@ -2163 +2163 @@
                                         {
                                                 if( LineSv[j].wavelength > 0. && 
-                                                        LineSv[j].sumlin[LineSave.lgLineEmergent] > 0. )
+                                                        LineSv[j].SumLine[LineSave.lgLineEmergent] > 0. )
                                                 {
                                                         /* line energy, in units set with units option */
@@ -2175 +2175 @@
                                                         /* intrinsic intensity */
                                                         fprintf( punch.ipPnunit[ipPun], "\t%8.3f", 
-                                                                log10(SDIV(LineSv[j].sumlin[0]) ) + radius.Conv2PrtInten );
+                                                                log10(SDIV(LineSv[j].SumLine[0]) ) + radius.Conv2PrtInten );
                                                         /* emergent line intensity, r recombination  */
                                                         fprintf( punch.ipPnunit[ipPun], "\t%8.3f", 
-                                                                log10(SDIV(LineSv[j].sumlin[1]) ) + radius.Conv2PrtInten );
+                                                                log10(SDIV(LineSv[j].SumLine[1]) ) + radius.Conv2PrtInten );
                                                         /* type of line, i for info, etc */
                                                         fprintf( punch.ipPnunit[ipPun], " \t%c\n", 
@@ -3244 +3244 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                if( LineSv[i].sumlin[LineSave.lgLineEmergent] > 0. )
+                if( LineSv[i].SumLine[LineSave.lgLineEmergent] > 0. )
                 {
                         PunResults1Line(ioPUN,(char*)LineSv[i].chALab,LineSv[i].wavelength,
-                          LineSv[i].sumlin[LineSave.lgLineEmergent], "Line ");
+                          LineSv[i].SumLine[LineSave.lgLineEmergent], "Line ");
                 }
         }
@@ -3695 +3695 @@
         for( i=0; i < LineSave.nsum; i++ )
         {
-                if( LineSv[i].sumlin[LineSave.lgLineEmergent] > 0. )
+                if( LineSv[i].SumLine[LineSave.lgLineEmergent] > 0. )
                 {
                         PunResults1Line(ioPUN,(char*)LineSv[i].chALab,LineSv[i].wavelength,
-                          LineSv[i].sumlin[LineSave.lgLineEmergent],"Line ");
+                          LineSv[i].SumLine[LineSave.lgLineEmergent],"Line ");
                 }
         }

trunk/source/rt_line_all.cpp

@@ -347 +347 @@
                 }
         }
-        /*5986 fprintf(ioQQQ,"DEBUG he rt_all\t%li\t%li\t%.4e\t%.4e\n",
-                iteration, nzone, 
-                                Transitions[1][1][10][5].Emis->TauIn,
-                                Transitions[1][1][10][5].Emis->Pesc);*/
+        /*fprintf(ioQQQ,"DEBUG He Lya dest is %.2e\n",
+                Transitions[ipH_LIKE][ipHELIUM][ipH2p][0].Emis->Pdest );*/
 
         /* is continuum pumping of H Lyman lines included?  yes, but turned off

trunk/source/rt_line_one_tau_reset.cpp

@@ -82 +82 @@
         t->Emis->FracInwd = MIN2(1.f,1.5f-t->Emis->Pesc);
 
-        /* this is destruction probability
-         * >>chng 96 sep 4, was not here, needed to add since now taking
-         * mean of old and new dest prob */
+        /*  destruction probability */
         t->Emis->Pdest = 0.;
         t->Emis->Pelec_esc = 0.;

trunk/source/rt_ots.cpp

@@ -1080 +1080 @@
         if( chFlag == 'l' || chFlag == 'b' )
         {
+                fprintf( ioQQQ, "DEBUG density He %.2e He+2 %.2e O+2 %.2e\n",
+                        dense.gas_phase[ipHELIUM] , dense.xIonDense[ipHELIUM][2],
+                        dense.xIonDense[ipOXYGEN][2] );
                 fprintf( ioQQQ, "     DEBUG OTSLIN array, anu, otslin, opac, OTS*opac Lab nLine limit:%.2e zone:%.2f IonConv?%c\n",
                         weak,fnzone,TorF(conv.lgConvIoniz) );

trunk/source/service.cpp

@@ -151 +151 @@
         DEBUG_ENTRY( "MyAssert()" );
 
-        fprintf(ioQQQ," PROBLEM DISASTER An assert has been thrown, this is bad.\n");
+        fprintf(ioQQQ,"\n\n\n PROBLEM DISASTER\n An assert has been thrown, this is bad.\n");
         fprintf(ioQQQ," It happened in the file %s at line number %i\n", file, line );
         fprintf(ioQQQ," This is iteration %li, nzone %li, fzone %.2f, lgSearch=%c.\n", 

trunk/source/zone_startend.cpp

@@ -205 +205 @@
                                 rfield.flux_isotropic[i];
 
-                        /* actually do the corrections
-                        rfield.flux[i] *= opac.tmn[i]; */
-
                         /* >>chng 03 nov 08, update SummedCon here since flux changed */
                         rfield.SummedCon[i] = rfield.flux[i] + rfield.SummedDif[i];