Added vmac to photospheres

README.md

@@ -149,4 +149,13 @@ Install the following packages:
 
 And then compile them typing the following in the ``docs`` directory:
 
-    ./compile
+    ./compile
+
+## Issues
+
+MacOSX Catalina has some issues with the paths to the include files. Defining the following environment variables might help.
+
+    export CFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+    export CCFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+    export CXXFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+    export CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"

docs/io_files/input.rst

@@ -145,12 +145,13 @@ be perturbed with nodes until a fit is obtained for the observed Stokes paramete
 These are text files which tabulates the depth dependence as a function of the log optical depth at 500 nm
 of the temperature [K], electron pressure [cgs], 
 microturbulent velocity [cm/s], bulk velocity [cm/s], and the cartesian components of the magnetic field,
-Bx, By and Bz [G]. Additionally, the filling factor is given in the header. An example follows:
+Bx, By and Bz [G]. Additionally, the filling factor and the macroscopic velocity in km/s
+is given in the header. An example follows:
 
 ::
 
-    ff
-    1.0
+    ff   vmac
+    1.0  1.0
 
     logtau     T        Pe           vmic        v            Bx           By         Bz
     1.2000   8879.7  2.99831E+03  0.000E+00  0.0000E+00   5.0000E+02    0.0000E+00  0.0000E+00   
@@ -164,9 +165,10 @@ Bx, By and Bz [G]. Additionally, the filling factor is given in the header. An e
 HDF5/zarr 3D files
 ^^^^^^^^^^^^^^^^^^
 
-HDF5/zarr files with model photospheres are defined with two double-precision datasets: ``model`` and ``ff``. The first
+HDF5/zarr files with model photospheres are defined with three double-precision datasets: ``model``, ``ff`` and ``vmac``. The first
 one has size ``(n_pixel,nz,8)``, containing the depth dependence of the 8 variables for all pixels. The second 
-one has size ``(n_pixel,)``, containing the filling factor for each pixel. In the following we show how to
+and the third ones have sizes ``(n_pixel,)``, containing the filling factor and the macroscopic velocity
+for each pixel. In the following we show how to
 create a sample file:
 
 ::
@@ -176,12 +178,15 @@ create a sample file:
     
     model_3d = np.zeros((n_pixel,nz,8), dtype=np.float64)
     ff_3d = np.zeros((n_pixel,), dtype=np.float64)
+    vmac_3d = np.zeros((n_pixel,), dtype=np.float64)
 
     f = h5py.File('photospheres/model_photosphere.h5', 'w')
     db_model = f.create_dataset('model', model_3d.shape, dtype=np.float64)
     db_ff = f.create_dataset('ff', ff_3d.shape, dtype=np.float64)
+    db_vmac = f.create_dataset('vmac', vmac_3d.shape, dtype=np.float64)
     db_model[:] = model_3d
     db_ff[:] = ff_3d
+    db_vmac[:] = vmac_3d
     f.close()
 
 FITS 3D files

examples/configurations/conf_single.ini

@@ -2,7 +2,7 @@
 
 [Working mode]
 Output file = output.h5
-Number of cycles = 2
+Number of cycles = 1
 
 # Topology
 # Always photosphere and then chromosphere
@@ -46,6 +46,7 @@ Number of cycles = 2
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
         ff     = 0.0, 1.001
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 2, 2, 5, 5
@@ -55,15 +56,17 @@ Number of cycles = 2
         By     = 0, 1, 1, 1
         Bz     = 0, 1, 1, 1
         ff     = 0, 0, 0, 0
+        vmac   = 0, 0, 0, 0
 
         [[[Regularization]]]
-        T      = 'l2-value', 10.0, 1.0
+        T      = 'l2-value', 0.0, 5000.0
         vmic   = None
         v      = None
         Bx     = None
         By     = None
         Bz     = None
         ff     = None
+        vmac   = None
 
 
     [[Chromosphere 1]]

examples/example_algorithm.py

@@ -6,7 +6,7 @@
 import gc
 
 # Test a single inversion in non-iterator mode
-mod = hazel.Model('conf_single.ini', working_mode='inversion', verbose=2)
+mod = hazel.Model('configurations/conf_single.ini', working_mode='inversion', verbose=2)
 mod.read_observation()
 mod.open_output()
 mod.invert()
@@ -16,14 +16,14 @@
 
 final = np.loadtxt('photospheres/model_photosphere.1d', skiprows=4)
 start = np.loadtxt('photospheres/model_photosphere_200.1d', skiprows=4)
-f = h5py.File('output.h5')
+f = h5py.File('output.h5', 'r')
 pl.plot(f['ph1']['T'][0,0,:], label='inverted')
 pl.plot(final[:,1], label='target')
 pl.plot(start[:,1], 'x', label='initial')
 f.close()
 pl.legend()
 
-mod = hazel.Model('conf_single.ini', working_mode='inversion', verbose=2)
+mod = hazel.Model('configurations/conf_single.ini', working_mode='inversion', verbose=2)
 mod.read_observation()
 mod.open_output()
 mod.invert_external(minimize, method='Nelder-Mead')
@@ -32,7 +32,7 @@
 
 final = np.loadtxt('photospheres/model_photosphere.1d', skiprows=4)
 start = np.loadtxt('photospheres/model_photosphere_200.1d', skiprows=4)
-f = h5py.File('output.h5')
+f = h5py.File('output.h5', 'r')
 
 pl.figure()
 pl.plot(f['ph1']['T'][0,0,:], label='inverted')
@@ -41,4 +41,4 @@
 f.close()
 pl.legend()
 
-pl.show()
+pl.show()

examples/example_single_inv.py

@@ -15,7 +15,7 @@
 
 final = np.loadtxt('photospheres/model_photosphere.1d', skiprows=4)
 start = np.loadtxt('photospheres/model_photosphere_200.1d', skiprows=4)
-f = h5py.File('output.h5')
+f = h5py.File('output.h5', 'r')
 fig = pl.figure()
 pl.plot(f['ph1']['T'][0,0,0,:])
 pl.plot(final[:,1])

examples/photospheres/model_photosphere.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff   vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
   1.2000   8879.7  2.99831E+03  0.000E+00  0.0000E+00   5.0000E+02    0.0000E+00  0.0000E+00   

examples/photospheres/model_photosphere_200.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0 1.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
 1.2000e+00 8.6797e+03 -2.9983e+03 1.0000e+00 0.0000e+00 5.0000e+02 0.0000e+00 0.0000e+00

hazel/atmosphere.py

@@ -19,6 +19,7 @@ class General_atmosphere(object):
     def __init__(self, atm_type, name):
         self.ff = 1.0
         self.name = name
+        self.type = atm_type
 
         self.logger = logging.getLogger("model")
         self.logger.setLevel(logging.DEBUG)

hazel/data/FALB.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.300    9150.7   3.719000e+03      2.72       0.00       0.00        0.00       0.00

hazel/data/FALC11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    9427.2   5.140000e+03      0.00       0.00       0.00        0.00       0.00

hazel/data/FALD.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.300    9118.0   3.650000e+03      2.73       0.00       0.00        0.00       0.00

hazel/data/FALE11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    9433.3   5.176000e+03      0.00       0.00       0.00        0.00       0.00

hazel/data/FALF.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.300    9032.2   3.367000e+03      2.73       0.00       0.00        0.00       0.00

hazel/data/FALF11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    9443.1   5.236000e+03      0.00       0.00       0.00        0.00       0.00

hazel/data/FALH.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.500    9002.3   3.299000e+03      2.72       0.00       0.00        0.00       0.00

hazel/data/FALH11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    9446.1   5.265000e+03      0.00       0.00       0.00        0.00       0.00

hazel/data/FALP.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.300    8510.2   1.819000e+03      1.83       0.00       0.00        0.00       0.00

hazel/data/FALP11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.100    8692.4   2.308000e+03      0.00       0.00       0.00        0.00       0.00

hazel/data/FALR11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    8763.8   2.949000e+03      0.00       0.00       0.00        0.00       0.00

hazel/data/FALS.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    6628.7   2.439000e+02      1.20       0.00       0.00        0.00       0.00

hazel/data/FALS11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.300    6957.0   4.114000e+02      0.00       0.00       0.00        0.00       0.00

hazel/data/cool11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    6780.3   3.372810e+02      0.60    246200.00       0.00        0.00       0.00

hazel/data/emaltby11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.200    6710.0   2.488480e+02      0.60       0.00       0.00        0.00       0.00

hazel/data/grevesse11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.900   10220.0   1.082510e+04      0.60       0.00       0.00        0.00       0.00

hazel/data/holmu11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.250    8793.9   2.679730e+03      1.00       0.00       0.00        0.00       0.00

hazel/data/hot11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    8004.6   1.551370e+03      0.60    10000.00       0.00        0.00       0.00

hazel/data/hsra.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
   1.2000   8879.7  2.99831E+03  0.000E+00  0.0000E+00   0.0000E+00    0.0000E+00  0.0000E+00   

hazel/data/hsra11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.400    9560.0   6.046790e+03      0.60       0.00       0.00        0.00       0.00

hazel/data/mackkl11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.200    9117.1   3.316670e+03      0.00    100000.00       0.00        0.00       0.00

hazel/data/mmaltby11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.200    6700.0   2.612010e+02      1.00       0.00       0.00        0.00       0.00

hazel/data/penumjti11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.200    8461.0   2.030960e+03      0.60    200000.00       0.00        0.00       0.00

hazel/data/solannt11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.000    8700.0   1.989200e+03      3.00       0.00       0.00        0.00       0.00

hazel/data/solanpl11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.200    9918.0   7.546820e+03      0.60    100000.00       0.00        0.00       0.00

hazel/data/valc11.1d

@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   logtau     T        Pe           vmic        v            Bx           By         Bz
  1.200    8879.7   2.998310e+03      0.00       0.00       0.00        0.00       0.00