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Commit 8caa0fed authored by Ferland, Gary's avatar Ferland, Gary
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Merge branch 'master' into reactions.2021oct

parents e22b92cb 6ad44c4b
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docs/latex/QuickStart/VeuszCookbook.tex
View file @ 8caa0fed
......@@ -229,6 +229,7 @@ You can also place graphs within a grid widget to get an arrangement of separate
Figure \ref{fig:orion_hii_pdr_pp} shows an example,
taken from the Orion HII region / PDR simulation, of a nested plot.
\begin{figure}
\begin{center}
\includegraphics[clip=on,width=0.8\columnwidth,height=0.8\textheight,keepaspectratio]{orion_hii_pdr_pp}
......@@ -239,4 +240,13 @@ Orion H II region / PDR.}
\label{fig:orion_hii_pdr_pp}
\end{figure}
\subsection{Documenting your work}
The Properties widget includes a Notes field that can be used to keep a history of the
data behind a plot.
This is useful so that you can come back to a project after some time and recover
the history of the work leading up to a result or the location of the helper files that were used
along the way.
%\end{document}
docs/latex/frontis_common.tex
View file @ 8caa0fed
{\small
\noindent
{\em Software:} Copyright \copyright\ 1978-2019 Gary J. Ferland and others. All rights reserved.
{\em Software:} Copyright \copyright\ 1978-2022 Gary J. Ferland and others. All rights reserved.
\vspace{1em}
......@@ -44,7 +44,7 @@ to the following FreeBSD format documentation license:
\vspace{1em}
\noindent
{\em Documentation:} Copyright \copyright\ 1978--2019 Gary J. Ferland and others. All rights reserved.
{\em Documentation:} Copyright \copyright\ 1978--2022 Gary J. Ferland and others. All rights reserved.
\vspace{1em}
......
source/cloudy.cpp
View file @ 8caa0fed
......@@ -127,6 +127,15 @@ bool cloudy()
SetPrintLineCol();
/* Initialize pseudo-continua, if requested */
SpeciesPseudoContCreate();
/* Initialize species bands, if requested
*
* NB NB
* This function requires that the atomic data be read in. */
SpeciesBandsCreate();
/* print header */
PrtHeader();
......
source/continuum.h
View file @ 8caa0fed
......@@ -115,6 +115,15 @@ void SpeciesPseudoContCreate();
/** SpeciesPseudoContAccum - accumulate pseudo-continua */
void SpeciesPseudoContAccum();
/** addUniqueSpeciesBand - add unique combination of species and bands file to list
*
* Note that this command requires that the atomic data be read in.
*
* \param [in] filename name of bands file
* \param [in[ speciesLabel species whose emission to accumulate
*/
void addUniqueSpeciesBand( const string &filename, const string &speciesLabel );
/** SpeciesBandsCreate - initialize requested species bands files */
void SpeciesBandsCreate();
......
source/cool_eval.cpp
View file @ 8caa0fed
......@@ -1293,9 +1293,9 @@ STATIC double CoolH2_GA08 ( double Temp )
{
DEBUG_ENTRY( "CoolH2_GA08()" );
double x_para = h2.para_density / dense.gas_phase[ ipHYDROGEN ];
double x_ortho = h2.ortho_density / dense.gas_phase[ ipHYDROGEN ];
double f_para = h2.para_density / (h2.para_density + h2.ortho_density);
double x_para = safe_div( h2.para_density, double( dense.gas_phase[ ipHYDROGEN ] ) );
double x_ortho = safe_div( h2.ortho_density, double( dense.gas_phase[ ipHYDROGEN ] ) );
double f_para = safe_div( h2.para_density, h2.para_density + h2.ortho_density );
double f_ortho = 1. - f_para;
/* Collisions with atomic H */
......@@ -1354,14 +1354,10 @@ STATIC double CoolH2_GA08 ( double Temp )
}
}
/* NB NB NB
*
* The interpolation below will fail if the high density cooling is 0,
* that is, the total cooling will be 0, even if the low-density cooling
* is not. This may happen if permitted by the function that computes
* LTE cooling, and/or the tabulated data (see definition of
* interpolate_LTE_Cooling() and associated data file). */
return cooling_high / (1. + cooling_high / cooling_low);
// originally cooling_high / (1. + cooling_high / cooling_low)
// See Eq. (39) therein
//
return safe_div( cooling_low * cooling_high, cooling_low + cooling_high );
}
STATIC void CoolHyperfine (void)
......
source/generic_state.cpp
View file @ 8caa0fed
......@@ -35,6 +35,7 @@ double density(const genericState& gs)
else
return 0.;
}
double depart(const genericState& gs)
{
if ( gs.sp != NULL )
......@@ -46,6 +47,7 @@ double depart(const genericState& gs)
else
return 1.0;
}
double energy(const genericState& gs)
{
if ( gs.sp != NULL )
......@@ -57,6 +59,7 @@ double energy(const genericState& gs)
else
return 0.0;
}
double levels(const genericState& gs)
{
if ( gs.sp != NULL && gs.sp->levels != NULL )
......@@ -67,9 +70,17 @@ double levels(const genericState& gs)
return 0.0;
}
bool genericState::isSpecies() const
{
if( sp != NULL && sp != null_molezone )
return true;
else
return false;
}
string genericState::label() const
{
if ( sp != NULL && sp != null_molezone )
if( isSpecies() )
return sp->global()->label;
else if (q.associated())
return q.chLabel();
......@@ -81,7 +92,7 @@ string genericState::label() const
string genericState::database() const
{
if ( sp != NULL && sp != null_molezone && sp->dbase != NULL )
if( isSpecies() && sp->dbase != NULL )
return sp->dbase->database;
else
return "";
......@@ -89,7 +100,7 @@ string genericState::database() const
bool genericState::associated() const
{
if (sp != NULL && sp != null_molezone)
if( isSpecies() )
return true;
else if (q.associated())
return true;
......@@ -342,3 +353,18 @@ vector<genericState> matchGeneric(const string &chLabel, bool lgValidate)
}
return v;
}
genericState getSpeciesGeneric(const string &speciesLabel)
{
DEBUG_ENTRY( "getSpeciesGeneric()" );
vector<genericState> v = matchGeneric( speciesLabel, true );
if( v.size() == 0 || ! v[0].isSpecies() )
{
fprintf( ioQQQ, "PROBLEM: Invalid species '%s' requested.\n",
speciesLabel.c_str() );
cdEXIT( EXIT_FAILURE );
}
return v[0];
}
source/generic_state.h
View file @ 8caa0fed
......@@ -23,6 +23,7 @@ public:
bool associated() const;
string label() const;
string database() const;
bool isSpecies() const;
};
double column(const genericState&);
......@@ -58,4 +59,13 @@ const molezone *getLevelsGeneric(const string &chLabel, bool lgValidate, vector<
*/
vector<genericState> matchGeneric(const string &chLabel, bool lgValidate);
/** getSpeciesGeneric - acquire the species matching the input string
*
* \param [in] speciesLabel input species string
*
* \returns species reference to requested species
*/
genericState getSpeciesGeneric( const string &speciesLabel );
#endif // GENERIC_STATE_H_
source/helike_cs.cpp
View file @ 8caa0fed
......@@ -46,7 +46,7 @@ STATIC double collision_strength_VF01( long ipISO, double velOrEner,
/* These are masses relative to the proton mass of the electron, proton, he+, and alpha particle. */
static const double ColliderCharge[4] = {1.0, 1.0, 1.0, 2.0};
inline double reduced_amu( long nelem, long Collider )
double reduced_amu( long nelem, long Collider )
{
return dense.AtomicWeight[nelem]*colliders.list[Collider].mass_amu/
(dense.AtomicWeight[nelem]+colliders.list[Collider].mass_amu)*ATOMIC_MASS_UNIT;
......@@ -375,7 +375,7 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
realnum cs = -1.f;
/* this may be used for splitting up the collision strength within 2^3P */
realnum factor1 = 1.f;
realnum j_resolve = 1.f;
/* Energy difference in eV */
double deltaE_eV = EnerErg/EN1EV;
......@@ -383,13 +383,13 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
/* lower level is within 2^3P */
if( nLo==2 && lLo==1 && sLo==3 )
{
factor1 *= (2.f*jLo+1.f) / 9.f;
j_resolve *= (2.f*jLo+1.f) / 9.f;
}
/* upper level is within 2^3P */
if( nHi==2 && lHi==1 && sHi==3 )
{
factor1 *= (2.f*jHi+1.f) / 9.f;
j_resolve *= (2.f*jHi+1.f) / 9.f;
}
/* for most of the helium iso sequence, the order of the J levels within 2 3P
......@@ -402,7 +402,7 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
// These are already j-resolved, so return this to unity.
if( nLo==2 && lLo==1 && sLo==3 && nHi==2 && lHi==1 && sHi==3 )
{
factor1 = 1.f;
j_resolve = 1.f;
}
*where = "table";
......@@ -418,9 +418,9 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
*where = "Zhang ";
if( nelem == ipIRON )
*where = "Si+2017";
factor1 = 1.;
j_resolve = 1.;
/* Collisions from gound */
/* Collisions from ground */
if( nLo == 1 )
{
if( lHi==0 && sHi==3 ) // to 2tripS
......@@ -858,11 +858,9 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
{
/* >>refer He CS Vriens, L., & Smeets, A.H.M. 1980, Phys Rev A 22, 940
* statistical weight IS included in the routine */
cs = (realnum)CS_VS80( nHi, gHi, IP_Ryd_Hi, nLo, gLo, IP_Ryd_Lo, Aul, nelem, Collider, phycon.te );
cs = (realnum)CS_VS80( ipHE_LIKE, nHi, IP_Ryd_Hi, nLo, IP_Ryd_Lo, Aul, nelem, Collider, phycon.te );
*where = "Vriens";
lgResolvedData = false;
}
/* only electron impact collisions */
else if (Collider == ipELECTRON)
......@@ -871,84 +869,25 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
{
/* Lebedev and Beigman (1998) Phys. Highly excited atoms and ions p. 225 eq. 8.30
*/
cs = hydro_Lebedev_deexcit(nelem, ipHE_LIKE, nHi, nLo, gLo, IP_Ryd_Lo);
cs = hydro_Lebedev_deexcit(ipHE_LIKE, nelem, nHi, nLo, IP_Ryd_Lo);
*where = "lebed";
lgResolvedData = false;
}
else if(iso_ctrl.lgCS_Fujim[ipHE_LIKE])
{
cs = hydro_Fujimoto_deexcit(gHi, gLo, Aul, IP_Ryd_Hi, IP_Ryd_Lo);
cs = hydro_Fujimoto_deexcit(ipHE_LIKE, nHi, nLo, Aul, IP_Ryd_Hi, IP_Ryd_Lo);
*where = "Fuji ";
lgResolvedData = false;
}
else if( iso_ctrl.lgCS_vrgm[ipHE_LIKE])
{
/* Van regemorter formula for allowed transitions. Van Regemorter, ApJ 136 (1962) 906
* The interval 0.005 < y < infty is interpolated from the results of Table 2
* from Van Regemorter paper and adjusted at high energies to avoid discontinuities.
*/
/* ensure that the transition is allowed */
if ( lHi > 0 && lLo >0 && abs(lHi - lLo) !=1 )
cs =0.;
else
{
double Py = 1.;
double y = deltaE_eV*EVDEGK/phycon.te;
const double valy[11] ={log10(0.005),-2.,log10(0.02),log10(0.04),-1.,log10(0.2),log10(0.4),0.,log10(2.),log10(4.),1.} ;
double a1 = sqrt(3)/2/PI*e1(0.005);
if( nelem == ipHELIUM )
{
if (y <= 0.005)
Py = sqrt(3)/2/PI*e1(y);
else if (y <= 10.)
{
const double val[11]={log10(a1),log10(1.16), log10(0.956),log10(0.758),log10(0.493),log10(0.331),log10(0.209),-1.,log10(0.063),log10(0.040),log10(0.021)};
Py = linint(valy,val,11,log10(y));
Py=exp10(Py);
//Py = 0.128384/sqrt(y)- 0.019719;
}
else
Py = 0.066/sqrt(y);
/*if(nHi==nLo+1)
fprintf(ioQQQ,"vrgm nhi %li, nlo %li, y %g\n",nHi,nLo,y);*/
}
else
{
if (y <= 0.005)
Py = sqrt(3)/2/PI*e1(y);
else if (y <= 10.)
{
const double val[11]={log10(a1),log10(1.16),log10(0.977),log10(0.788),log10(0.554),log10(0.403),log10(0.290),log10(0.214),log10(0.201),log10(0.2),log10(0.2)};
Py = linint(valy,val,11,log10(y));
Py = exp10(Py);
//Py = 0.154023 + 0.1099165/sqrt(y);
}
else
Py = 0.200;
}
double massratio = reduced_amu(nelem,Collider)/ELECTRON_MASS;
cs = 20.6*Aul/pow3(EnerWN)/phycon.sqrte*Py;
double factor = ( COLL_CONST * powpq(massratio, -3, 2) ) / phycon.sqrte / (double)gHi;
/*convert to collision strength*/
cs /= factor;
lgResolvedData = false;
*where = "vrgm ";
}
cs = hydro_vanRegemorter_deexcit( ipHE_LIKE, nelem, nHi, lHi, lLo,
EnerWN, deltaE_eV, Aul,
Collider );
*where = "vrgm ";
lgResolvedData = false;
}
else if( iso_ctrl.nCS_new[ipHE_LIKE] && nelem==ipHELIUM )
{
/* Don't know if stat weights are included in this, but they're probably
......@@ -1010,16 +949,15 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
* repulsion between ions will make these cross sections smaller only to be relevant at even higher energies. */
/* Percival and Richards (1978) have got a Z dependence so their rates are preferred */
cs = CS_ThermAve_PR78( ipH_LIKE, nelem, nHi, nLo,
EnerErg / EN1RYD, phycon.te );
cs = CS_ThermAve_PR78( ipHE_LIKE, nelem, nHi, nLo,
EnerErg / EN1RYD, phycon.te );
*where = "PR78 ";
lgResolvedData = false;
}
}
else
cs =0.;
cs = 0.;
}
else if (sHi != sLo)
{
......@@ -1035,19 +973,53 @@ realnum GetHelikeCollisionStrength( long nelem, long Collider,
TotalInsanity();
/* take factor into account, usually 1, ratio of stat weights if within 2 3P
* and with collisions from collapsed to resolved levels */
cs *= factor1;
/*
* Resolved routines can also provide collapsed data
* Resolve collision strengths for n-changing collisions
* from collapsed to resolved levels
*/
if (!lgResolvedData && nLo <= iso_sp[ipHE_LIKE][nelem].n_HighestResolved_max)
if (!lgResolvedData && nLo <= iso_sp[ipHE_LIKE][nelem].n_HighestResolved_max)
{
cs *= CSresolver(ipHE_LIKE, nHi, lHi, sHi, nLo, lLo, sLo, iso_sp[ipHE_LIKE][nelem].n_HighestResolved_max);
realnum l_resolve =
realnum( CSresolver(ipHE_LIKE, nHi, lHi, sHi, nLo, lLo, sLo,
iso_sp[ipHE_LIKE][nelem].n_HighestResolved_max) );
enum {DEBUG_LOC = false};
if( DEBUG_LOC )
{
if( nelem == ipIRON &&
//(nHi == iso_sp[ipHE_LIKE][nelem].n_HighestResolved_max + 15) &&
// nLo == iso_sp[ipHE_LIKE][nelem].n_HighestResolved_max )
nLo == 1 && nHi == 3 )
// nHi == 3 && sHi == 1 && (nLo == 1 || nLo == 2) )
// sLo == 1 )
{
fprintf( ioQQQ, "nelem: %ld"
" (nHi, lHi, sHi): (%ld, %ld, %ld) ->"
" (nLo, lLo, sLo): (%ld, %ld, %ld)"
"\t nn' CS: %.4e"
"\t l-reslv: %.4e"
"\t j-reslv: %.4e"
"\t lj-reslv: %.4e"
"\t final CS: %.4e"
"\t '%s'\n",
nelem,
nHi, lHi, sHi,
nLo, lLo, sLo,
cs, l_resolve, j_resolve,
l_resolve * j_resolve,
cs * l_resolve * j_resolve,
*where );
}
}
cs *= l_resolve;
}
/* take factor into account, usually 1, ratio of stat weights if within 2 3P
* and with collisions from collapsed to resolved levels */
cs *= j_resolve;
{
/*@-redef@*/
enum {DEBUG_LOC=false};
......@@ -2519,43 +2491,46 @@ STATIC double collision_strength_VF01( long ipISO, double E_Proj_Ryd,
return coll_str;
}
/*resolved to resolved and collapsed to resolved modification */
/***************************************************************
* convert resolved to collapsed:
* rates: q(n->n') = \sum_l' \sum_l (2l+1)(2s+1) q(nl->nl')/ 2n^2
* upsilons: Y(nn') = \sum_l' \sum_l Y(nln'l')
* example: q(n=3->n=2) = 1/18(6q(3p->2s) + 2q(3s->2p) + 10q(3d->2p) + ...
*
* convert collapsed to collapsed to resolved:
* rates: q(nl-n'l') = (2s'+1)(2l'+1)q(n->n')*n2/[\sum\sum(2s+1)(2l+1)(2s'+1)(2l'+1)]
* with the constrains [{|s-s'|=0}]
* upsilons: Y(nln'l') =(2s+1)(2l+1)(2s'+1)(2l'+1)Y(nn')/S
* with the constrains {|s-s'|=0}
*
*where: S=[\sum\sum(2s+1)(2l+1)(2s'+1)(2l'+1)] = (2s+1)^2 n^2n'^2
*
* If i want a collapsed to resolved coefficient:
*
* 1) If the routine returns a collapsed value:
*
* rates: q(n -> n'l') = (2s+1)^2\sum(2l+1)(2l'+1)q(n->n')*n^2/S
* upsilon: Y(nn'l') = (2s+1)^2\sum(2l+1)(2l'+1)Y(nn')/S
*
*
* 2) If it is a resolved value
*
* rates: q(n->n'l') = \sum_l (2l+1)(2s+1)q(nl->n'l')/2n^2
* upsilons: Y(nn'l') = \sum_l Y(nln'l')
*
*/
/* resolved to resolved and collapsed to resolved modification
*
* convert resolved to collapsed:
* rates: q(n->n') = \sum_l' \sum_l (2l+1)(2s+1) q(nl->nl')/ 2n^2
* upsilons: Y(nn') = \sum_l' \sum_l Y(nln'l')
* example: q(n=3->n=2) = 1/18(6q(3p->2s) + 2q(3s->2p) + 10q(3d->2p) + ...
*
* convert collapsed to collapsed to resolved:
* rates: q(nl-n'l') = (2s'+1)(2l'+1)q(n->n')*n2/[\sum\sum(2s+1)(2l+1)(2s'+1)(2l'+1)]
* with the constrains [{|s-s'|=0}]
* upsilons: Y(nln'l') =(2s+1)(2l+1)(2s'+1)(2l'+1)Y(nn')/S
* with the constrains {|s-s'|=0}
*
*where: S=[\sum\sum(2s+1)(2l+1)(2s'+1)(2l'+1)] = (2s+1)^2 n^2n'^2
*
* If i want a collapsed to resolved coefficient:
*
* 1) If the routine returns a collapsed value:
*
* rates: q(n -> n'l') = (2s+1)^2\sum(2l+1)(2l'+1)q(n->n')*n^2/S
* upsilon: Y(nn'l') = (2s+1)^2\sum(2l+1)(2l'+1)Y(nn')/S
*
*
* 2) If it is a resolved value
*
* rates: q(n->n'l') = \sum_l (2l+1)(2s+1)q(nl->n'l')/2n^2
* upsilons: Y(nn'l') = \sum_l Y(nln'l')
*
*/
double CSresolver(long ipISO, long nHi,long lHi,long sHi,long nLo,
long lLo, long sLo, long n_HighestResolved)
{
double factor=1.;
DEBUG_ENTRY( "CSresolver()" );
if (sHi != sLo && nHi <= n_HighestResolved )
return 0.;
double factor=1.;
/* S= \sum\sum (2s+1)(2l+1)(2s'+1)(2l'+1)
* with |s-s'|=0
*/
......@@ -2565,11 +2540,18 @@ double CSresolver(long ipISO, long nHi,long lHi,long sHi,long nLo,
if (ipISO==ipH_LIKE)
{
S *= 4;
ASSERT( sLo == ipDOUBLET );
S *= pow2( ipDOUBLET );
}
else if(ipISO==ipHE_LIKE)
{
S *= 10; //(1*1 + 3*3)
if( nLo == 1 )
{
ASSERT( sLo == ipSINGLET );
S *= pow2( ipSINGLET );
}
else
S *= pow2( ipSINGLET ) + pow2( ipTRIPLET );
}
......@@ -2586,9 +2568,5 @@ double CSresolver(long ipISO, long nHi,long lHi,long sHi,long nLo,
else
TotalInsanity();
return factor;
}
source/helike_cs.h
View file @ 8caa0fed
......@@ -6,6 +6,16 @@
#include "iso.h"
/**reduced_amu - Calculate reduced mass in AMU
*
* \param nelen [in] element index (0 for H)
* \param Collider[in] collision partner
*
* \returns reduced mass
*/
double reduced_amu( long nelem, long Collider );
/**HeCollid evaluate collisional rates
\param nelem
*/
......
source/hextra.h
View file @ 8caa0fed
......@@ -109,7 +109,7 @@ struct t_hextra : public module {
hextra.background_density = 1.99e-9f;*/
/* >>chng 05 apr 16, to get proper ionization rate in ism_set_cr_rate, where
* H is forced to be fully atomic, no molecules, density from 1.99 to 2.15 */
/* >>chng 02 apr 05, update to
/* >>chng 12 apr 05, update to
* >>refer cosmic ray ionization Indriolo, N., Geballe, T., Oka, T., & McCall, B.J. 2007, ApJ, 671, 1736
*/
background_density = 2.15e-9f*7.9f;
......
source/hydro_vs_rates.cpp
View file @ 8caa0fed
......@@ -10,11 +10,33 @@
#include "dense.h"
#include "phycon.h"
#include "iso.h"
#include "helike_cs.h"
#include "hydro_vs_rates.h"
#include "thirdparty.h"
#include "lines_service.h"
#include "integrate.h"
inline double get_iso_statw( const long ipISO, const long n )
{
if( ipISO == ipH_LIKE )
{
return ipDOUBLET * double( pow2(n) );
}
else if( ipISO == ipHE_LIKE )
{
if( n == 1 )
{
return 1.; // ipSINGLET * pow2( 1 );
}
else
{
return (ipSINGLET+ipTRIPLET) * double( pow2(n) );
}
}
else
TotalInsanity();
}
long global_ipISO, global_nelem, global_nHi, global_nLo;
double kTRyd, global_deltaE;
......@@ -52,10 +74,13 @@ namespace {
/* VS80 stands for Vriens and Smeets 1980 */
/* This routine calculates thermally-averaged collision strengths. */
double CS_VS80( long nHi, long gHi, double IP_Ryd_Hi, long nLo, long gLo, double IP_Ryd_Lo, double Aul, long nelem, long Collider, double temp )