pyatomdb 1.2.0__tar.gz → 1.2.2__tar.gz

{pyatomdb-1.2.0/pyatomdb.egg-info → pyatomdb-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyatomdb
-Version: 1.2.0
+Version: 1.2.2
 Summary: AtomDB python library.
 Author-email: Adam Foster <afoster@cfa.harvard.edu>
 Maintainer-email: Adam Foster <afoster@cfa.harvard.edu>
@@ -344,3 +344,11 @@ Made multiple ionization calculation more transparent.
 1.2.0
 April 23rd 2026
 Added in web.py, which is not useful as part of pyatomdb but does generate the online plotting content. This will undergo frequent revision. Other minor changes for making web content with Plotly and Dash.
+
+1.2.1
+August 13th 2026
+Updated solve_ionbal_eigen to work with numpy >=2.5 (issues with matrix data indexing)
+
+1.2.2
+September 15th 2026
+Corrections to eebrems in the  1 < T < 300keV

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/README.rst

@@ -289,3 +289,11 @@ Made multiple ionization calculation more transparent.
 1.2.0
 April 23rd 2026
 Added in web.py, which is not useful as part of pyatomdb but does generate the online plotting content. This will undergo frequent revision. Other minor changes for making web content with Plotly and Dash.
+
+1.2.1
+August 13th 2026
+Updated solve_ionbal_eigen to work with numpy >=2.5 (issues with matrix data indexing)
+
+1.2.2
+September 15th 2026
+Corrections to eebrems in the  1 < T < 300keV

pyatomdb-1.2.2/examples/wrapper_xspec_kappa_example.py

@@ -0,0 +1,48 @@
+# temporarily add the wrappers folder to the path
+import sys
+sys.path.append('../wrappers')
+
+import matplotlib.pyplot as plt
+
+from kappa_xspec import *
+
+# declare a new model
+# inital import creates pykappa, pyvkappa, pyvvkappa, analagous to apec, vapec, vvapec
+
+m = xspec.Model('pykappa')
+
+m.show()
+
+m.pykappa.kT=3.0
+
+m.pykappa.kappa = 2.5
+
+# let's plot a spectrum
+xspec.Plot.device='/xs'
+
+
+#set dummy response
+xspec.AllData.dummyrsp(0.1, 10, 10001,'lin')
+
+xspec.Plot('model')
+
+x1 = xspec.Plot.x(1)
+m1 = xspec.Plot.model(1)
+
+
+m.pykappa.Velocity = 1000.0
+
+
+xspec.Plot('model')
+
+x2 = xspec.Plot.x(1)
+m2 = xspec.Plot.model(1)
+fig = plt.figure()
+fig.show()
+ax = fig.add_subplot(111)
+ax.plot(x1,m1, label='0km/s')
+ax.plot(x2,m2, label='1000km/s')
+ax.legend(loc=0)
+plt.draw()
+
+zzz=input('Press enter')

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/pyatomdb/__init__.py

@@ -10,7 +10,7 @@ from . import apec
 from . import util
 import sys, glob
 
-__version__="1.2.0"
+__version__="1.2.2"
 
 try:
   PATH = os.path.dirname(__file__)

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/pyatomdb/apec.py

@@ -1264,12 +1264,12 @@ def calc_ee_brems(E, T, N):
   Returns
   -------
   array(float)
-    ee_brems in photons cm^s s^-1 keV-1 at each point E.
+    ee_brems in photons cm^3 s^-1 keV-1 at each point E.
     This should be multiplied by the bin width to get flux per bin.
 
   References
   ----------
-  Need to check this!
+  S. Nozawa, K. Takahashi, Y. Kohyama and N. Itoh A&A, 499 3 (2009) 661-667
   """
 #
 #  T is the electron temperature (in keV)
@@ -1279,7 +1279,8 @@ def calc_ee_brems(E, T, N):
 
 # series of data constants
 # Region I, k_BT<=1 keV
-  #print "T=%f"%(T)
+
+  from scipy.special import exp1
 
   aI1 = numpy.array([(3.15847E+0, -2.52430E+0, 4.04877E-1, 6.13466E-1, 6.28867E-1, 3.29441E-1),
              (2.46819E-2, 1.03924E-1, 1.98935E-1, 2.18843E-1, 1.20482E-1, -4.82390E-2),
@@ -1339,7 +1340,7 @@ def calc_ee_brems(E, T, N):
                (0.0000000E+0, -1.6053650E+2, -4.6080700E+1, -2.7617000E+1, -3.4943210E+2),
                (1.9970000E-1, 2.3392500E+1, 8.7301000E+0, 8.8453000E+0, 9.2205900E+1)])
 # column aII_0j-aIII_2j, bIII_0j, bIII_1j; line j=0-8
-  #print "E:",E
+  
   aI = numpy.hstack((aI1,aI2))
 
   inum1 = numpy.arange(11)
@@ -1367,17 +1368,10 @@ def calc_ee_brems(E, T, N):
   tao = T/const.ME_KEV
   # find the length of the input
   Earray, Eisvec =  util.make_vec(E)
-  #if isinstance(E, (collections.Sequence, numpy.ndarray)):
-  #  x = E/T
-  #  (numx,) = x.shape
-  #else:
-  #  Earray = numpy.array([E])
 
   x = Earray/T
   numx=len(Earray)
 
-  #print "x", x
-  #print "numx:", numx
   GI = numpy.zeros((numx,))
   AIIr = numpy.zeros((numx,))
   BIIr = numpy.zeros((numx,))
@@ -1388,8 +1382,8 @@ def calc_ee_brems(E, T, N):
   GpwIII = numpy.zeros((numx,))
   if T<0.05:
     ret = numpy.zeros(len(x), dtype=float)
-  elif 0.05<=T<70.:
-    # hmm
+  elif 0.05<=T<1.:
+
     GI=numpy.zeros(len(x))
     theta = (1/1.35) * ( numpy.log10(tao) + 2.65)
     bigx = (1/2.5) * (numpy.log10(x) + 1.50)
@@ -1398,13 +1392,14 @@ def calc_ee_brems(E, T, N):
          GI += aI[i,j]*(theta**i)*(bigx**j)
     GI *= numpy.sqrt(8/(3*numpy.pi))
     ret = 1.455e-16*N**2*numpy.exp(-x)/(x*numpy.sqrt(tao))*GI
-  elif 70.<=T<300.:
+  elif 1.<=T<300.:
     taoII = tao
+    Ei0[:,] = exp1(x)
     for k in range(numx):
-      def integrand(t):
-        return numpy.exp(-1.0*t)/t
-      [Ei0[k,],error] = scipy.integrate.quad(integrand,x[k,],\
-                                             numpy.inf,args=())
+#      def integrand(t):
+#        return numpy.exp(-1.0*t)/t
+#      [Ei0[k,],error] = scipy.integrate.quad(integrand,x[k,],\
+#                                             numpy.inf,args=())
       AIIr[k,] = numpy.sum(aII*taoII**(aIIj/8.)*x[k,]**(aIIi))
       BIIr[k,] = numpy.sum(bII*taoII**(bIIj/8.)*x[k,]**(bIIi))
       FCCII[k,] = 1.+numpy.sum(cII*taoII**(cIIj/6.)*x[k,]**(cIIi/8.))
@@ -1415,6 +1410,7 @@ def calc_ee_brems(E, T, N):
     ret = 1.455e-16*N**2*numpy.exp(-x)/(x*numpy.sqrt(taoII))*GII
   elif 300.<=T<7000.:
     taoIII = tao
+    Ei0[:,] = exp1(x)
     for k in range(numx):
       GpwIII[k,] = numpy.sum(aIII*taoIII**(aIIj/8.)*x[k,]**(aIIi))-\
                    numpy.exp(x[k,])*(-1.0)*Ei0[k,]*\
@@ -1423,6 +1419,7 @@ def calc_ee_brems(E, T, N):
            (x*numpy.sqrt(taoIII))*GpwIII
   else:
     taoIV = tao
+    Ei0[:,] = exp1(x)
     GIV = 3./(4.*numpy.pi*numpy.sqrt(taoIV))*\
           (28./3.+2.*x+x**2/2.+2.*(8./3.+4.*x/3.+x**2)*\
           (numpy.log(2.*taoIV)-0.57721)-numpy.exp(x) \
@@ -1883,6 +1880,8 @@ def run_apec(fname):
   chdulist.insert(0,PricHDU)
   chdulist.insert(1,seccHDU)
   tmpchdulist = pyfits.HDUList(chdulist)
+  generate_apec_headerblurb(settings, tmplhdulist, tmpchdulist)
+  
   if settings['Ionization']=='CIE':
     tmpchdulist.writeto('%s_coco.fits'%(fileroot), overwrite=True, checksum=True)
   elif settings['Ionization']=='NEI':
@@ -6074,16 +6073,15 @@ def _solve_ionbal_eigen(Z, Te, init_pop=False, tau=False, \
     fspectmp = numpy.matrix(lefteigenvec) * numpy.matrix(work).transpose()
 
     delt = 1.0
-
     worktmp = numpy.zeros(Z)
 
     for itau, ttau in enumerate(tau_vec):
       if Z >1:
         for i in range(Z):
-          worktmp[i] = fspectmp[i]*numpy.exp(dd.data['EIG'][kTindex,i]*delt*ttau)
+          worktmp[i] = numpy.squeeze(fspectmp.item(i)*numpy.exp(dd.data['EIG'][kTindex,i]*delt*ttau))
 
       else:
-        worktmp[0] = fspectmp[0]*numpy.exp(dd.data['EIG'][kTindex]*delt*ttau)
+        worktmp[0] = numpy.squeeze(fspectmp.item(i)*numpy.exp(dd.data['EIG'][kTindex]*delt*ttau))
 
       frac = numpy.zeros(Z+1)
       for i in range(Z):

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/pyatomdb/atomdb.py

@@ -2369,7 +2369,7 @@ def _calc_ionrec_ci(cidat, Te, extrap=False, ionpot=False):
     elif ((cidat['par_type']> const.CI_DERE) &\
           (cidat['par_type']<= const.CI_DERE+20)):
       npts = cidat['par_type']-const.CI_DERE
-      ci[ici] = _calc_ci_dere(Te[ici], ionpot, cidat['Temperature'][:npts], \
+      ci[ici] = _calc_ci_dere(Te[ici], ionpot, cidat['temperature'][:npts], \
                              cidat['ionrec_par'][:npts])
 
 

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/pyatomdb/spectrum.py

@@ -30,15 +30,16 @@ try:
 except ImportError:
   import pyfits
 
-import numpy, os, hashlib, pickle, math, re
+import numpy, os, hashlib, pickle, math#, re
 # other pyatomdb modules
 #import pyatomdb.atomic, pyatomdb.util, pyatomdb.const, atomdb, apec
 from . import atomic, util, const, atomdb, apec
 
-import time, wget, bz2
+import wget, bz2#, time
 import warnings
 from astropy.modeling.models import Voigt1D
-from scipy.interpolate import UnivariateSpline
+import time
+#from scipy.interpolate import UnivariateSpline
 
 
 def __make_spectrum(bins, index, linefile="$ATOMDB/apec_line.fits",\
@@ -1684,7 +1685,7 @@ class _Lorentzian_CDF():
     return ret
 
 
-
+from scipy.special import voigt_profile
 class _Voigt_CDF():
   """
   For fast interpolation, pre-calculate the CDF and interpolate it when
@@ -1715,7 +1716,7 @@ class _Voigt_CDF():
 
 
   def __init__(self, sigma, gamma):
-    from scipy.special import voigt_profile
+    
     self.x = numpy.linspace(-12,12,2400)
     self.broadentype='Voigt'
 
@@ -3004,7 +3005,7 @@ class CIESession():
 
 
 
-  def _adjust_line_lambda(self, change, Z, z1, upper,lower, quantity="Epsilon", method="Replace", trackchanges=False):
+  def _adjust_line_lambda(self, change, Z, z1, upper,lower, quantity="Epsilon", method="Replace", trackchanges=False, z1_drv=0):
     """
     Change the emissivity or wavelength of a line. Integer parameters set to 0 mean "all". Note this all
     happens in memory and does not edit the underlying files.
@@ -3030,6 +3031,8 @@ class CIESession():
       "Divide" : divide existing value by change
       "Add" : add change to existing value
       "Subtract" : subtract change from existing
+    z1_drv : int or array(int)
+      which driving ions to switch the wavelengths for. Default (0) means all.
     Returns
     -------
     None
@@ -3752,7 +3755,7 @@ class CIESession_RS(CIESession):
 
 
 
-  def _adjust_line_lambda(self, change, Z, z1, upper,lower, quantity="Epsilon", method="Replace", trackchanges=False):
+  def _adjust_line_lambda(self, change, Z, z1, upper,lower, quantity="Epsilon", method="Replace", trackchanges=False, z1_drv=0):
     """
     Change the emissivity or wavelength of a line. Integer parameters set to 0 mean "all". Note this all
     happens in memory and does not edit the underlying files.
@@ -3778,6 +3781,9 @@ class CIESession_RS(CIESession):
       "Divide" : divide existing value by change
       "Add" : add change to existing value
       "Subtract" : subtract change from existing
+    z1_drv : int or array(int)
+      which driving ions to switch the wavelengths for. Default (0) means all.
+
     Returns
     -------
     None
@@ -5408,8 +5414,7 @@ class _LineData():
         emax = max(eedges)
         emin = min(eedges)
         # identify all the good lines!
-        igood = numpy.where(((elines >= emin) & (eneg < emax))  |\
-                  ((elines < emin) & (eplu < emin)))[0]
+        igood = numpy.where((eplu > emin) & (eneg < emax))[0]
         spec = numpy.zeros(len(eedges))
 #        t0 = time.time()
         for iline in igood:
@@ -7227,7 +7232,9 @@ class PShockSession(NEISession):
 
   def return_linelist(self,Te, tau_u, specrange, tau_l = 0.0, init_pop='ionizing',specunit='A', \
                                teunit='keV', apply_aeff=False, by_ion_drv = False,\
-                               nearest=False, apply_binwidth=False):
+                               nearest=False, apply_binwidth=False,\
+                               log_interp=True, freeze_ion_pop=False):
+      
     """
     Get the list of line emissivities vs wavelengths
 
@@ -7257,8 +7264,14 @@ class PShockSession(NEISession):
     by_ion_drv : bool
       If true, keep lines which are the same but have different ion_drv separate.
       Otherwise, merge them.
-    nearest :
+    nearest : bool
+      calculate spectrum at nearest temperature in linelist, no
+      interpolation. Ionization fraction calculation still exact.
     apply_binwidth :
+    log_interp : bool
+      Perform linear interpolation on a logT/logEpsilon grid (default), or linear.
+    freeze_ion_pop : bool
+      If True, skip the ion population calculation, use init_pop as the final pop instead.
 
     Returns
     -------
@@ -8328,7 +8341,8 @@ class KappaSession(NEISession):
 
   def return_linelist(self, Te, kappa, specrange, specunit='A', \
                                teunit='keV', apply_aeff=False, \
-                               develop=False):
+                               apply_binwidth=False,\
+                               log_interp=True):
     """
     Get the list of line emissivities vs wavelengths
 
@@ -8348,6 +8362,9 @@ class KappaSession(NEISession):
     apply_aeff : bool
       If true, apply the effective area to the lines in the linelist to
       modify their intensities.
+    apply_binwidth :
+    log_interp : bool
+      Perform linear interpolation on a logT/logEpsilon grid (default), or linear.
 
     Returns
     -------
@@ -9043,7 +9060,7 @@ class _KappaSpectrum(_NEISpectrum):
 
               for i, iikT in enumerate(ikT):
 
-                s[i] += self.spectra[ikT[0]][Z][z1].return_spectrum(self.ebins,\
+                s[i] += self.spectra[iikT][Z][z1].return_spectrum(self.ebins,\
                                   kT,\
                                   ebins_checksum = self.ebins_checksum,\
                                   thermal_broadening = self.thermal_broadening,\
@@ -9337,10 +9354,13 @@ class ir_data():
     self.elements=elements
     ionrec_data = {}
     ir = pyfits.open(irfile)
-    for irdat in ir['KAPPA_IR'].data:
-      Z = irdat['ELEMENT']
+    d = numpy.array(ir['KAPPA_IR'].data)
+    d.dtype.names = [n.lower() for n in d.dtype.names]
 
-      z1 = irdat['ION_INIT']
+    for irdat in d:
+      Z = irdat['element']
+
+      z1 = irdat['ion_init']
       if not Z in ionrec_data.keys():
         ionrec_data[Z] = {}
       if not z1 in ionrec_data[Z].keys():
@@ -9351,15 +9371,15 @@ class ir_data():
         ionrec_data[Z][z1]['DR']=False
 
 #      print(irdat)
-      if ionrec_data[Z][z1][irdat['TR_TYPE']]==False:
-        ionrec_data[Z][z1][irdat['TR_TYPE']]={}
-
-      ionrec_data[Z][z1][irdat['TR_TYPE']][irdat['ION_FINAL']-1]=irdat
+      if ionrec_data[Z][z1][irdat['tr_type'].decode()]==False:
+        ionrec_data[Z][z1][irdat['tr_type'].decode()]={}
+      
+      ionrec_data[Z][z1][irdat['tr_type'].decode()][irdat['ion_final']-1]=numpy.array(irdat)
 
-    for ionpot in ir['IONPOT'].data:
-      ionrec_data[ionpot['ELEMENT']][ionpot['ION']]['IONPOT'] = ionpot['IONPOT']
+    for ionpot in ir['ionpot'].data:
+      ionrec_data[ionpot['element']][ionpot['ion']]['IONPOT'] = ionpot['IONPOT']
 
-      ionrec_data[ionpot['ELEMENT']][ionpot['ION']]['IP_DERE'] = ionpot['IP_DERE']
+      ionrec_data[ionpot['element']][ionpot['ion']]['IP_DERE'] = ionpot['IP_DERE']
 #    print(ionrec_data[12])
 #    zzz=input()
     self.ionrecdata=ionrec_data
@@ -9386,7 +9406,7 @@ class ir_data():
         for dd in self.ionrecdata[Z][z1]['CI'].keys():
           ionpot = self.ionrecdata[Z][z1]['IONPOT']
           d=self.ionrecdata[Z][z1]['CI'][dd]
-          if ((d['PAR_TYPE']>=const.CI_DERE) & (d['PAR_TYPE']<=const.CI_DERE+20)):
+          if ((d['par_type']>=const.CI_DERE) & (d['par_type']<=const.CI_DERE+20)):
             try:
               ionpot = self.ionrecdata[Z][z1]['IP_DERE']
             except:
@@ -9403,8 +9423,9 @@ class ir_data():
           d = self.ionrecdata[Z][z1]['DR'][dd]
           #print('d DR:',d)
           #print(self.ionrecdata[Z][z1]['DR'])
-
-          if d != False:
+          try:
+            d==False
+          except TypeError:
             drrate = atomdb._calc_ionrec_dr(d, Tvec, extrap=True)
             ionrec[d['ion_final']-1, d['ion_init']-1,:]+=drrate
       else:
@@ -9413,9 +9434,10 @@ class ir_data():
       if self.ionrecdata[Z][z1]['RR'] != False:
         for dd in self.ionrecdata[Z][z1]['RR'].keys():
           d = self.ionrecdata[Z][z1]['RR'][dd]
-          #print('d RR:',d)
-
-          if d != False:
+#          print('d RR:',d)
+          try:
+            d == False
+          except TypeError:
             rrrate = atomdb._calc_ionrec_rr(d, Tvec, extrap=True)
             ionrec[d['ion_final']-1, d['ion_init']-1,:]+=rrrate
       else:
@@ -9425,7 +9447,9 @@ class ir_data():
         for dd in self.ionrecdata[Z][z1]['EA'].keys():
           d = self.ionrecdata[Z][z1]['EA'][dd]
           #print('d EA:',d)
-          if d != False:
+          try:
+            d==False
+          except TypeError:
             earate = atomdb._calc_ionrec_ea(d, Tvec, extrap=True)
             ionrec[d['ion_final']-1, d['ion_init']-1,:]+=earate
       else:
@@ -9759,7 +9783,7 @@ def calc_ee_brems_spec(ebins, Te, dens, teunit='keV'):
     electron-electron bremsstrahlung in ph cm^3 s^-1 bin^-1
 
   """
-
+ 
   # convert temperature to keV if required
   kT = util.convert_temp(Te, teunit, 'keV')
 
@@ -9774,6 +9798,109 @@ def calc_ee_brems_spec(ebins, Te, dens, teunit='keV'):
   return ee
 
 
+
+
+def _broaden_lines(linelist, eedges, T,\
+                  thermal_broadening = False, \
+                  velocity_broadening = 0.0, \
+                  broaden_limit = 1e-20,\
+                  broaden_object=False):
+    """
+    return the line emission spectrum at tempterature T
+
+    Parameters
+    ----------
+
+    eedges : array
+      energy bin edges, keV
+    T : float
+      temperature in Kelvin
+    ebins_checksum : string
+      the md5 checksum of eedges
+    thermal_broadening : bool
+      true to apply thermal broadening
+    velocity_broadening : float
+      velocity broadening to apply, km/s. Set <=0 for none (default)
+    broaden_limit : float
+      only broaden lines stronger than this.
+    broaden_object : class
+      Object with routine "broaden" which applies line broadening. Usually a Gaussian.
+
+    Returns
+    -------
+    spectrum : array(float)
+      Emissivity on eedges spectral bins of the lines, in ph cm^3 s^-1 bin^-1
+    """
+    if velocity_broadening is None:
+      velocity_broadening=0.0
+
+    if ((thermal_broadening == False) & \
+        (velocity_broadening == False)):
+    
+      spec,zzz = numpy.histogram(const.HC_IN_KEV_A/linelist['Lambda'], \
+                                 bins=eedges, \
+                                 weights = linelist['Epsilon'])
+    else:
+
+      # ind = strong line indicies
+      # nonind = weak line indicies
+      ind = linelist['Epsilon']>broaden_limit
+      nonind = ~ind
+
+        # calculate the widths of the strong lines
+      llist = linelist[ind]
+
+        # get a raw dictionary of masses in amu
+      masslist = atomic.Z_to_mass(1,raw=True)
+
+      if thermal_broadening==False:
+        T=0.0
+        Tb = 0.0
+      else:
+        Tb = util.convert_temp(T, 'K','keV')*const.ERG_KEV/(masslist[llist['Element']]*1e3*const.AMUKG)
+
+      if velocity_broadening <0:
+        velocity_broadening = 0.0
+        vb=0.0
+      else:
+        vb = (velocity_broadening * 1e5)**2
+
+      wcoeff = numpy.sqrt(Tb+vb) / (const.LIGHTSPEED*1e2)
+
+      elines = const.HC_IN_KEV_A/linelist['Lambda'][ind]
+      width = wcoeff*elines
+
+
+        # Filter out lines more than NSIGMALIMIT sigma outside the range
+      NSIGMALIMIT=4
+      eplu = elines+NSIGMALIMIT*width
+      eneg = elines-NSIGMALIMIT*width
+      emax = max(eedges)
+      emin = min(eedges)
+      # identify all the good lines!
+      igood = numpy.where((eplu > emin) & (eneg < emax))[0]
+      spec = numpy.zeros(len(eedges))
+#        t0 = time.time()
+      for iline in igood:
+
+        spec += broaden_object.broaden(const.HC_IN_KEV_A/llist['Lambda'][iline],\
+                         width[iline],eedges)*llist['Epsilon'][iline]
+
+#        t1 = time.time()
+#        print("Broadeninging %i lines, in %f seconds"%(len(igood), t1-t0))
+      spec = spec[1:]-spec[:-1]
+
+
+        # Then add on the weak lines
+      s,z = numpy.histogram(const.HC_IN_KEV_A/linelist['Lambda'][nonind], \
+                            bins = eedges,\
+                            weights = linelist['Epsilon'][nonind])
+      spec+=s
+      
+    return spec
+
+
+
 #### LEGACY CODE BEYOND THIS POINT
 
 def __get_nei_line_emissivity(Z, z1, up, lo):

{pyatomdb-1.2.0 → pyatomdb-1.2.2/pyatomdb.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyatomdb
-Version: 1.2.0
+Version: 1.2.2
 Summary: AtomDB python library.
 Author-email: Adam Foster <afoster@cfa.harvard.edu>
 Maintainer-email: Adam Foster <afoster@cfa.harvard.edu>
@@ -344,3 +344,11 @@ Made multiple ionization calculation more transparent.
 1.2.0
 April 23rd 2026
 Added in web.py, which is not useful as part of pyatomdb but does generate the online plotting content. This will undergo frequent revision. Other minor changes for making web content with Plotly and Dash.
+
+1.2.1
+August 13th 2026
+Updated solve_ionbal_eigen to work with numpy >=2.5 (issues with matrix data indexing)
+
+1.2.2
+September 15th 2026
+Corrections to eebrems in the  1 < T < 300keV

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/pyatomdb.egg-info/SOURCES.txt

@@ -88,6 +88,7 @@ examples/spectrum_session_examples_7_nei.py
 examples/spectrum_session_examples_8_nei_linelist.py
 examples/spectrum_session_linelist_examples.py
 examples/wrapper_xspec_examples.py
+examples/wrapper_xspec_kappa_example.py
 pyatomdb/__init__.py
 pyatomdb/apec.py
 pyatomdb/atomdb.py
@@ -95,7 +96,6 @@ pyatomdb/atomic.py
 pyatomdb/const.py
 pyatomdb/spectrum.py
 pyatomdb/util.py
-pyatomdb/web.py
 pyatomdb.egg-info/PKG-INFO
 pyatomdb.egg-info/SOURCES.txt
 pyatomdb.egg-info/dependency_links.txt
@@ -107,6 +107,4 @@ wrappers/IonE_apec_xspec.py
 wrappers/apec_xspec.py
 wrappers/bapec_xspec.py
 wrappers/kappa_xspec.py
-wrappers/rsapec_xspec.py
-wrappers/__pycache__/apec_xspec.cpython-312.pyc
-wrappers/__pycache__/rsapec_xspec.cpython-312.pyc
+wrappers/rsapec_xspec.py

{pyatomdb-1.2.0 → pyatomdb-1.2.2}/wrappers/kappa_xspec.py

@@ -24,7 +24,9 @@ kappamodelobject.abund_xspectoatomdb['lodd'] = 'Lodd03'
 
 pykappaInfo = ("kT            \"keV\"   1.0 0.00862 0.00862 86. 86. 0.01",
              "kappa         \"\"      3.0 2.0 2.0 100. 1000. 0.01",
-             "abund         \"\"      1.0 0.0 0.0 10.0 10.0 0.01")
+             "abund         \"\"      1.0 0.0 0.0 10.0 10.0 0.01",
+             "Redshift     \"\"     0.0 0.0 0.0 10.0 10.0 0.01",
+             "Velocity      \"km/s\"      0.0 0.0 0.0 1000.0 2000.0 0.01")
 
 pyvkappaInfo = ("kT            \"keV\"   1.0 0.00862 0.00862 86. 86. 0.01",
               "kappa         \"\"      3.0 2.0 2.0 100. 1000. 0.01",
@@ -42,7 +44,9 @@ pyvkappaInfo = ("kT            \"keV\"   1.0 0.00862 0.00862 86. 86. 0.01",
               "Ar            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
               "Ca            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
               "Fe            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
-              "Ni            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01")
+              "Ni            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
+              "Redshift     \"\"     0.0 0.0 0.0 10.0 10.0 0.01",
+              "Velocity      \"km/s\"      0.0 0.0 0.0 1000.0 2000.0 0.01")
 
 
 pyvvkappaInfo = ("kT            \"keV\"   1.0 0.00862 0.00862 86. 86. 0.01",
@@ -73,7 +77,9 @@ pyvvkappaInfo = ("kT            \"keV\"   1.0 0.00862 0.00862 86. 86. 0.01",
                "Cr            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
                "Mn            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
                "Fe            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
-               "Ni            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01")
+               "Ni            \"\"      1.0 0.0 0.0 10.0 10.0 -0.01",
+               "Redshift     \"\"     0.0 0.0 0.0 10.0 10.0 0.01",
+               "Velocity      \"km/s\"      0.0 0.0 0.0 1000.0 2000.0 0.01")
 
 
 def pykappa(engs, params, flux):
@@ -104,27 +110,35 @@ def pykappa(engs, params, flux):
 
   # This is the call that will return everything. So set everything!
   ebins = numpy.array(engs)
-  kappamodelobject.set_response(ebins, raw=True)
+
   # kappa model has the 14 main elements
+
   elarray = kappamodelobject.elements
   abund = numpy.zeros(len(elarray))
 
+
+  offset = len(params)-3
   
-  if len(params)==4:
+  if len(params)==6:
     # kappa case
     elarray=[2,6,7,8,10,12,13,14,16,18,20,26,28]
     abund = float(params[2])
-  elif len(params)==18:
+  elif len(params)==20:
     # vkappa case
     elarray=[1,2,6,7,8,9,10,12,13,14,16,18,20,26,28]
     abund = numpy.array(params[2:17])
-  elif len(params)==30:
+  elif len(params)==32:
     # vvkappa case
     elarray=[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,\
              20,21,22,23,24,25,26,28]
     abund = numpy.array(params[2:29])
-    
 
+  redshift = float(params[offset])
+  velocity = float(params[offset+1])
+  
+  kappamodelobject.set_response(ebins*(1.0+redshift), raw=True)
+  kappamodelobject.set_broadening(True, velocity_broadening=velocity)
+  
   T = float(params[0])
   k = float(params[1])