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cloudy
cloudy-hotfixes-20080214.patch
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File cloudy-hotfixes-20080214.patch of Package cloudy
diff -ur c07.02.01/source/cont_setintensity.cpp c07.02.01.new/source/cont_setintensity.cpp --- c07.02.01/source/cont_setintensity.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/cont_setintensity.cpp 2008-02-14 12:27:26.000000000 +0100 @@ -199,6 +199,13 @@ /*fprintf(ioQQQ,"DEBUG %4li %e %e %.3e %.3e\n", i , rfield.anu[i] , (amean2/amean) , amean2 , amean );*/ rfield.anu[i] = (float)(amean2/amean); + if( i ) + { + /* prevent roundoff from allowing i cell to lie below i-1 + * * cell when continuum mesh is very fine */ + rfield.anu[i] = MAX2( rfield.anu[i] , rfield.anu[i-1]*(1.f+FLT_EPSILON) ); + ASSERT( rfield.anu[i] > rfield.anu[i-1] ); + } rfield.anu2[i] = (float)(amean3/amean); } diff -ur c07.02.01/source/grid_xspec.cpp c07.02.01.new/source/grid_xspec.cpp --- c07.02.01/source/grid_xspec.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/grid_xspec.cpp 2008-02-14 12:34:06.000000000 +0100 @@ -72,7 +72,7 @@ sprintf( grid.paramNames[i], "%s%ld", "PARAM", i+1 ); /* Method is 0 for linear, 1 for logarithmic, for now all linear. */ - grid.paramMethods[i] = 1; + grid.paramMethods[i] = 0; /* Initial */ grid.paramRange[i][0] = xc[i]+grid.paramIncrements[i]*(grid.numParamValues[i]-1.f)/2.f; /* Delta */ diff -ur c07.02.01/source/iso_create.cpp c07.02.01.new/source/iso_create.cpp --- c07.02.01/source/iso_create.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/iso_create.cpp 2008-02-14 12:31:27.000000000 +0100 @@ -364,7 +364,7 @@ } else { - jj = jj; + jj = j; } hydro.strkar[n][j] = (float)pow(((float)ii*jj),1.2f); hydro.pestrk[n][j] = 0.; diff -ur c07.02.01/source/opacity.h c07.02.01.new/source/opacity.h --- c07.02.01/source/opacity.h 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/opacity.h 2008-02-14 12:40:08.000000000 +0100 @@ -172,7 +172,7 @@ /** another case b option, turn off background opacities, no Pdest */ bool lgCaseB_no_pdest; - /** optical depths to compton and H- */ + /** optical depths to Compton and H- */ float telec, thmin; @@ -203,9 +203,6 @@ * depths have been predicted yet */ bool lgTauOutOn; - /** which opacity to punch out */ - char chOpcTyp[5]; - /** total number of opacity cells used in opacity stack * in OpacityCreateAll used as a counter to remember where * next opacity goes */ @@ -217,7 +214,7 @@ * in OpacityCreateAll */ - /** ipRayScat opacity pointer for rayleigh scattering*/ + /** ipRayScat opacity pointer for Rayleigh scattering*/ long int ipRayScat, /** iopcom compton scatterin, total recoil*/ diff -ur c07.02.01/source/parse_grain.cpp c07.02.01.new/source/parse_grain.cpp --- c07.02.01/source/parse_grain.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/parse_grain.cpp 2008-02-14 12:31:02.000000000 +0100 @@ -364,8 +364,8 @@ /* find out how long chOption is - it was declared as a pointer, then * set equal to a local string */ length = strlen( chOption ); - if( length == 0 ) - TotalInsanity(); + /*if( length == 0 ) + TotalInsanity();*/ /* make sure we have enough room to store the string */ if( length > static_cast<size_t>(FILENAME_PATH_LENGTH_2) ) diff -ur c07.02.01/source/parse_punch.cpp c07.02.01.new/source/parse_punch.cpp --- c07.02.01/source/parse_punch.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/parse_punch.cpp 2008-02-14 12:40:08.000000000 +0100 @@ -239,7 +239,7 @@ { /* DoPunch will call punch_opacity to parse the subcommands * punch total opacity */ - strcpy( opac.chOpcTyp, "TOTL" ); + strcpy( punch.chOpcTyp[punch.npunch], "TOTL" ); sprintf( chHeader, "#nu\tTot opac\tAbs opac\tScat opac\tAlbedo\telem\n" ); } @@ -247,24 +247,25 @@ else if( nMatch("FIGU",chCard) ) { /* do figure for hazy */ - strcpy( opac.chOpcTyp, "FIGU" ); + strcpy( punch.chOpcTyp[punch.npunch], "FIGU" ); sprintf( chHeader, "#nu, H, He, tot opac\n" ); } else if( nMatch("FINE",chCard) ) { - /* punch out the fine opacity array with only lines */ + /* punch the fine opacity array */ rfield.lgPunchOpacityFine = true; - strcpy( opac.chOpcTyp, "FINE" ); + strcpy( punch.chOpcTyp[punch.npunch], "FINE" ); /* check for keyword UNITS on line, then scan wavelength or energy units if present, - * units are copied into punch.chConPunEnr */ + * units are copied into punch.chConPunEnr */ ChkUnits(chCard); sprintf( chHeader, "#nu\topac\n" ); ipFFmt = 5; - /* range option - important since so much data */ + /* range option - important since so much data - usually want to + * only give portion of the continuum */ if( nMatch("RANGE",chCard) ) { /* get lower and upper range, must be in Ryd */ @@ -296,6 +297,7 @@ /* default is to average together ten */ if( lgEOL ) punch.punarg[punch.npunch][2] = 10; + if( punch.punarg[punch.npunch][2] < 1 ) { fprintf(ioQQQ,"The number of fine opacities to skip must be > 0 \nSorry.\n"); @@ -316,7 +318,7 @@ else if( nMatch("BREM",chCard) ) { /* punch bremsstrahlung opacity */ - strcpy( opac.chOpcTyp, "BREM" ); + strcpy( punch.chOpcTyp[punch.npunch], "BREM" ); sprintf( chHeader, "#nu\tbrem opac\n" ); } @@ -327,7 +329,7 @@ strcpy( punch.chPunch[punch.npunch], "OPAC" ); /* punch subshell cross sections */ - strcpy( opac.chOpcTyp, "SHEL" ); + strcpy( punch.chOpcTyp[punch.npunch], "SHEL" ); /* this is element */ ipFFmt = 3; @@ -370,7 +372,7 @@ } /* copy string over */ - strcpy( opac.chOpcTyp, elementnames.chElementNameShort[nelem] ); + strcpy( punch.chOpcTyp[punch.npunch], elementnames.chElementNameShort[nelem] ); } else { @@ -437,7 +439,7 @@ else if( nMatch("OPAC",chCard) ) { /* create table for appendix in AGN */ - strcpy( opac.chOpcTyp, " AGN" ); + strcpy( punch.chOpcTyp[punch.npunch], " AGN" ); strcpy( punch.chPunch[punch.npunch], "OPAC" ); } diff -ur c07.02.01/source/parse_set.cpp c07.02.01.new/source/parse_set.cpp --- c07.02.01/source/parse_set.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/parse_set.cpp 2008-02-14 12:33:46.000000000 +0100 @@ -109,7 +109,7 @@ { if( nMatch( " NEW" , chCard ) ) { - dense.lgAsChoose[nelem][ion] = true; + dense.lgAsChoose[nelem][ion-1] = true; } else if( nMatch( " OLD" , chCard ) ) { diff -ur c07.02.01/source/prt_lines_lv1_li_ne.cpp c07.02.01.new/source/prt_lines_lv1_li_ne.cpp --- c07.02.01/source/prt_lines_lv1_li_ne.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/prt_lines_lv1_li_ne.cpp 2008-02-14 12:28:26.000000000 +0100 @@ -912,6 +912,8 @@ /* recombination and specific pump for OII 4638.86-4696.35 (8 lines) */ rec = GetLineRec(82, 4651 ); + PntForLine(4651.,"O 2",&ipnt); + lindst(rec,4651,"O 2r",ipnt,'i',true ); /* convert UV pump rate to intensity with branching ratio and hnu */ /* recombination part of O II 4651 line */ linadd(rec,4651,"O 2r",'i' ); diff -ur c07.02.01/source/punch.h c07.02.01.new/source/punch.h --- c07.02.01/source/punch.h 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/punch.h 2008-02-14 12:40:08.000000000 +0100 @@ -147,6 +147,9 @@ /**chPunch - what is it we want to punch? set in GetPunch, used in DoPunch */ char chPunch[LIMPUN][5]; + /** which opacity to punch out */ + char chOpcTyp[LIMPUN][5]; + /** this flag tells us whether to punch results of a grid to separate files * for each grid point or all to the same file. Different for different * punch commands */ diff -ur c07.02.01/source/punch_opacity.cpp c07.02.01.new/source/punch_opacity.cpp --- c07.02.01/source/punch_opacity.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/punch_opacity.cpp 2008-02-14 12:40:08.000000000 +0100 @@ -49,7 +49,7 @@ /* punch total opacity in any element, punch opacity command * ioPUN is ioPUN unit number, ipPun is pointer within stack of punches */ - if( strcmp(opac.chOpcTyp,"TOTL") == 0 ) + if( strcmp(punch.chOpcTyp[ipPun],"TOTL") == 0 ) /* total opacity */ { for( j=0; j < rfield.nflux; j++ ) @@ -66,8 +66,8 @@ fprintf( ioPUN, "\n" ); } - else if( strcmp(opac.chOpcTyp,"BREM") == 0 ) - /* brems opacity */ + else if( strcmp(punch.chOpcTyp[ipPun],"BREM") == 0 ) + /* bremsstrahlung opacity */ { for( j=0; j < rfield.nflux; j++ ) { @@ -80,7 +80,7 @@ } /* subshell photo cross sections */ - else if( strcmp(opac.chOpcTyp,"SHEL") == 0 ) + else if( strcmp(punch.chOpcTyp[ipPun],"SHEL") == 0 ) { nelem = (long)punch.punarg[ipPun][0]; ion = (long)punch.punarg[ipPun][1]; @@ -95,7 +95,7 @@ } } - else if( strcmp(opac.chOpcTyp,"FINE") == 0 ) + else if( strcmp(punch.chOpcTyp[ipPun],"FINE") == 0 ) { /* the fine opacity array */ float sum; @@ -119,7 +119,9 @@ { nu_hi = rfield.nfine; } + nskip = (long)punch.punarg[ipPun][2]; + ASSERT( nskip > 0 ); for( i=j; i<nu_hi; i+=nskip ) { @@ -131,12 +133,12 @@ sum /= nskip; if( sum > 0. ) fprintf(ioPUN,"%.5e\t%.3e\n", - AnuUnit( rfield.fine_anu[i+k/2] ), sum ); + AnuUnit( rfield.fine_anu[i+k/2] ), sum ); } } /* figure for hazy */ - else if( strcmp(opac.chOpcTyp,"FIGU") == 0 ) + else if( strcmp(punch.chOpcTyp[ipPun],"FIGU") == 0 ) { nelem = 0; for( i=iso.ipIsoLevNIonCon[ipH_LIKE][ipHYDROGEN][0]-1; i < (iso.ipIsoLevNIonCon[ipHE_LIKE][ipHELIUM][0] - 1); i++ ) @@ -166,7 +168,7 @@ } /* photoionization data table for AGN */ - else if( strcmp(opac.chOpcTyp," AGN") == 0 ) + else if( strcmp(punch.chOpcTyp[ipPun]," AGN") == 0 ) { long int ipop, @@ -234,7 +236,7 @@ } /* hydrogen */ - else if( strcmp(opac.chOpcTyp,"HYDR") == 0 ) + else if( strcmp(punch.chOpcTyp[ipPun],"HYDR") == 0 ) { nelem = ipHYDROGEN; /* zero out the opacity arrays */ @@ -278,7 +280,7 @@ } /* helium */ - else if( strcmp(opac.chOpcTyp,"HELI") == 0 ) + else if( strcmp(punch.chOpcTyp[ipPun],"HELI") == 0 ) { /* atomic helium first, HELI1.opc */ nelem = ipHELIUM; @@ -356,12 +358,12 @@ else { - /* check for hydroge through zinc, nelem is atomic number on the c scale */ + /* check for hydrogen through zinc, nelem is atomic number on the c scale */ nelem = -1; i = 0; while( i < LIMELM ) { - if( strcmp(opac.chOpcTyp,elementnames.chElementNameShort[i]) == 0 ) + if( strcmp(punch.chOpcTyp[ipPun],elementnames.chElementNameShort[i]) == 0 ) { nelem = i; break; @@ -373,7 +375,7 @@ if( nelem < 0 ) { fprintf( ioQQQ, " Unidentified opacity key=%4.4s\n", - opac.chOpcTyp ); + punch.chOpcTyp[ipPun] ); puts( "[Stop in punopac]" ); cdEXIT(EXIT_FAILURE); } diff -ur c07.02.01/source/zero.cpp c07.02.01.new/source/zero.cpp --- c07.02.01/source/zero.cpp 2007-07-09 04:28:29.000000000 +0200 +++ c07.02.01.new/source/zero.cpp 2008-02-14 12:40:08.000000000 +0100 @@ -1011,10 +1011,8 @@ /* another case b option, turn off background opacities, no Pdest */ opac.lgCaseB_no_pdest = false; - strcpy( opac.chOpcTyp, " " ); - /* smallest allowed line and Lya optical depths, reset with - * caseb command */ + * Case B command */ opac.taumin = 1e-20f; opac.tlamin = 1e-20f;
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