From 54436b53c265cc10a8b095ca3b75589cb0eddedc Mon Sep 17 00:00:00 2001
From: aasensio <aasensioramos@gmail.com>
Date: Wed, 6 Nov 2019 10:11:52 +0000
Subject: [PATCH] Added vmac to photospheres

---
 README.md                                     |  11 ++++++++-
 docs/io_files/input.rst                       |  15 ++++++++-----
 examples/configurations/conf_single.ini       |   7 ++++--
 examples/example_algorithm.py                 |  10 ++++-----
 examples/example_single_inv.py                |   2 +-
 examples/gen_model.py                         |   2 --
 examples/output.h5                            | Bin 0 -> 74488 bytes
 examples/photospheres/model_photosphere.1d    |   4 ++--
 examples/photospheres/model_photosphere.h5    | Bin 48848 -> 48928 bytes
 .../photospheres/model_photosphere_200.1d     |   4 ++--
 hazel/atmosphere.py                           |   1 +
 hazel/data/FALB.1d                            |   4 ++--
 hazel/data/FALC11.1d                          |   4 ++--
 hazel/data/FALD.1d                            |   4 ++--
 hazel/data/FALE11.1d                          |   4 ++--
 hazel/data/FALF.1d                            |   4 ++--
 hazel/data/FALF11.1d                          |   4 ++--
 hazel/data/FALH.1d                            |   4 ++--
 hazel/data/FALH11.1d                          |   4 ++--
 hazel/data/FALP.1d                            |   4 ++--
 hazel/data/FALP11.1d                          |   4 ++--
 hazel/data/FALR11.1d                          |   4 ++--
 hazel/data/FALS.1d                            |   4 ++--
 hazel/data/FALS11.1d                          |   4 ++--
 hazel/data/cool11.1d                          |   4 ++--
 hazel/data/emaltby11.1d                       |   4 ++--
 hazel/data/grevesse11.1d                      |   4 ++--
 hazel/data/holmu11.1d                         |   4 ++--
 hazel/data/hot11.1d                           |   4 ++--
 hazel/data/hsra.1d                            |   4 ++--
 hazel/data/hsra11.1d                          |   4 ++--
 hazel/data/mackkl11.1d                        |   4 ++--
 hazel/data/mmaltby11.1d                       |   4 ++--
 hazel/data/penumjti11.1d                      |   4 ++--
 hazel/data/solannt11.1d                       |   4 ++--
 hazel/data/solanpl11.1d                       |   4 ++--
 hazel/data/valc11.1d                          |   4 ++--
 hazel/io.py                                   |   7 +++---
 hazel/multiprocess.py                         |   9 ++++++--
 hazel/parametric.py                           |   4 +++-
 hazel/photosphere.py                          |  21 +++++++++++++-----
 hazel/tools.py                                |  14 ++++++++----
 output.h5                                     | Bin 0 -> 27688 bytes
 test/configurations/conf_mpi_invh5.ini        |   3 +++
 test/configurations/conf_mpi_synh5.ini        |   2 ++
 test/configurations/conf_nonmpi_inv1d.ini     |   3 +++
 test/configurations/conf_nonmpi_syn1d.ini     |   4 ++++
 test/configurations/conf_single.ini           |   3 +++
 test/configurations/conf_syn.ini              |   2 ++
 test/configurations/conf_synobs.ini           |   4 ++++
 test/photospheres/model_chromosphere.h5       | Bin 2768 -> 0 bytes
 test/photospheres/model_photosphere.1d        |   4 ++--
 test/photospheres/model_photosphere.h5        | Bin 48848 -> 48928 bytes
 test/photospheres/model_photosphere_200.1d    |   4 ++--
 test/test_file_generators.py                  |   2 +-
 test/test_nonmpi_inv1d.py                     |   2 +-
 test/test_nonmpi_syn1d.py                     |   2 +-
 test/test_programmatic.py                     |   0
 test/test_single_inv.py                       |   4 ++--
 test/test_single_syn.py                       |   2 +-
 60 files changed, 159 insertions(+), 97 deletions(-)
 delete mode 100755 examples/gen_model.py
 create mode 100644 examples/output.h5
 mode change 100755 => 100644 examples/photospheres/model_photosphere.h5
 create mode 100644 output.h5
 delete mode 100755 test/photospheres/model_chromosphere.h5
 mode change 100755 => 100644 test/test_file_generators.py
 mode change 100755 => 100644 test/test_nonmpi_inv1d.py
 mode change 100755 => 100644 test/test_nonmpi_syn1d.py
 mode change 100755 => 100644 test/test_programmatic.py
 mode change 100755 => 100644 test/test_single_inv.py
 mode change 100755 => 100644 test/test_single_syn.py

diff --git a/README.md b/README.md
index 924ef09..5969f34 100755
--- a/README.md
+++ b/README.md
@@ -149,4 +149,13 @@ Install the following packages:
 
 And then compile them typing the following in the ``docs`` directory:
 
-    ./compile
\ No newline at end of file
+    ./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"
\ No newline at end of file
diff --git a/docs/io_files/input.rst b/docs/io_files/input.rst
index 5368309..d5c5217 100755
--- a/docs/io_files/input.rst
+++ b/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
diff --git a/examples/configurations/conf_single.ini b/examples/configurations/conf_single.ini
index 01c3710..f2d55f4 100755
--- a/examples/configurations/conf_single.ini
+++ b/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]]
diff --git a/examples/example_algorithm.py b/examples/example_algorithm.py
index 391766e..0156031 100755
--- a/examples/example_algorithm.py
+++ b/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()
\ No newline at end of file
+pl.show()
diff --git a/examples/example_single_inv.py b/examples/example_single_inv.py
index bfa933e..a636152 100755
--- a/examples/example_single_inv.py
+++ b/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])
diff --git a/examples/gen_model.py b/examples/gen_model.py
deleted file mode 100755
index 242a69f..0000000
--- a/examples/gen_model.py
+++ /dev/null
@@ -1,2 +0,0 @@
-import hazel
-
diff --git a/examples/output.h5 b/examples/output.h5
new file mode 100644
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diff --git a/examples/photospheres/model_photosphere.1d b/examples/photospheres/model_photosphere.1d
index 79100a3..859fe73 100755
--- a/examples/photospheres/model_photosphere.1d
+++ b/examples/photospheres/model_photosphere.1d
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diff --git a/examples/photospheres/model_photosphere.h5 b/examples/photospheres/model_photosphere.h5
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diff --git a/examples/photospheres/model_photosphere_200.1d b/examples/photospheres/model_photosphere_200.1d
index e22fd6d..3aa7462 100755
--- a/examples/photospheres/model_photosphere_200.1d
+++ b/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
diff --git a/hazel/atmosphere.py b/hazel/atmosphere.py
index 63cf8d8..78666c7 100755
--- a/hazel/atmosphere.py
+++ b/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)
diff --git a/hazel/data/FALB.1d b/hazel/data/FALB.1d
index 1eb98f5..a6ebc13 100755
--- a/hazel/data/FALB.1d
+++ b/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
diff --git a/hazel/data/FALC11.1d b/hazel/data/FALC11.1d
index 91677e8..ad8b373 100755
--- a/hazel/data/FALC11.1d
+++ b/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
diff --git a/hazel/data/FALD.1d b/hazel/data/FALD.1d
index 4d107c3..d08615f 100755
--- a/hazel/data/FALD.1d
+++ b/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
diff --git a/hazel/data/FALE11.1d b/hazel/data/FALE11.1d
index d752fd2..ee3a09a 100755
--- a/hazel/data/FALE11.1d
+++ b/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
diff --git a/hazel/data/FALF.1d b/hazel/data/FALF.1d
index 4f3587c..67c5ac5 100755
--- a/hazel/data/FALF.1d
+++ b/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
diff --git a/hazel/data/FALF11.1d b/hazel/data/FALF11.1d
index 70c3045..45fc68e 100755
--- a/hazel/data/FALF11.1d
+++ b/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
diff --git a/hazel/data/FALH.1d b/hazel/data/FALH.1d
index baa0c9a..cd793de 100755
--- a/hazel/data/FALH.1d
+++ b/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
diff --git a/hazel/data/FALH11.1d b/hazel/data/FALH11.1d
index 13b11dd..21b9970 100755
--- a/hazel/data/FALH11.1d
+++ b/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
diff --git a/hazel/data/FALP.1d b/hazel/data/FALP.1d
index 65c4e14..4f29914 100755
--- a/hazel/data/FALP.1d
+++ b/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
diff --git a/hazel/data/FALP11.1d b/hazel/data/FALP11.1d
index 96c71ba..467270e 100755
--- a/hazel/data/FALP11.1d
+++ b/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
diff --git a/hazel/data/FALR11.1d b/hazel/data/FALR11.1d
index 994a8c8..3dd30da 100755
--- a/hazel/data/FALR11.1d
+++ b/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
diff --git a/hazel/data/FALS.1d b/hazel/data/FALS.1d
index 5a91bc2..115e877 100755
--- a/hazel/data/FALS.1d
+++ b/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
diff --git a/hazel/data/FALS11.1d b/hazel/data/FALS11.1d
index 0c3f946..9dae2e2 100755
--- a/hazel/data/FALS11.1d
+++ b/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
diff --git a/hazel/data/cool11.1d b/hazel/data/cool11.1d
index c046a34..52f1ee0 100755
--- a/hazel/data/cool11.1d
+++ b/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
diff --git a/hazel/data/emaltby11.1d b/hazel/data/emaltby11.1d
index ab4b09b..b29a819 100755
--- a/hazel/data/emaltby11.1d
+++ b/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
diff --git a/hazel/data/grevesse11.1d b/hazel/data/grevesse11.1d
index 85954da..dd24892 100755
--- a/hazel/data/grevesse11.1d
+++ b/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
diff --git a/hazel/data/holmu11.1d b/hazel/data/holmu11.1d
index 94820d0..d263b44 100755
--- a/hazel/data/holmu11.1d
+++ b/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
diff --git a/hazel/data/hot11.1d b/hazel/data/hot11.1d
index bf2d26b..1eb1d9b 100755
--- a/hazel/data/hot11.1d
+++ b/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
diff --git a/hazel/data/hsra.1d b/hazel/data/hsra.1d
index 93a6f74..ca48b8c 100755
--- a/hazel/data/hsra.1d
+++ b/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   
diff --git a/hazel/data/hsra11.1d b/hazel/data/hsra11.1d
index 3aae772..ac4f2db 100755
--- a/hazel/data/hsra11.1d
+++ b/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
diff --git a/hazel/data/mackkl11.1d b/hazel/data/mackkl11.1d
index 8104c20..5e5efb6 100755
--- a/hazel/data/mackkl11.1d
+++ b/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
diff --git a/hazel/data/mmaltby11.1d b/hazel/data/mmaltby11.1d
index de6ad33..b0b8fb3 100755
--- a/hazel/data/mmaltby11.1d
+++ b/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
diff --git a/hazel/data/penumjti11.1d b/hazel/data/penumjti11.1d
index 5edf71a..6e3339d 100755
--- a/hazel/data/penumjti11.1d
+++ b/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
diff --git a/hazel/data/solannt11.1d b/hazel/data/solannt11.1d
index 7c4903a..cbf4391 100755
--- a/hazel/data/solannt11.1d
+++ b/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
diff --git a/hazel/data/solanpl11.1d b/hazel/data/solanpl11.1d
index f7d6c2d..382cbd9 100755
--- a/hazel/data/solanpl11.1d
+++ b/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
diff --git a/hazel/data/valc11.1d b/hazel/data/valc11.1d
index e381090..4f3366c 100755
--- a/hazel/data/valc11.1d
+++ b/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
diff --git a/hazel/io.py b/hazel/io.py
index 3a81956..018745a 100755
--- a/hazel/io.py
+++ b/hazel/io.py
@@ -501,12 +501,13 @@ def read(self, pixel=None):
         if (self.extension == '1d'):
             f = open(self.filename, 'r')
             f.readline()
-            ff = float(f.readline())
+            tmp = f.readline().split()
+            ff, vmac = float(tmp[0]), float(tmp[1])
             f.close()
-            return np.loadtxt(self.filename, skiprows=4), ff
+            return np.loadtxt(self.filename, skiprows=4), ff, vmac
 
         if (self.extension == 'h5' or self.extension == 'zarr'):            
-            return self.handler['model'][pixel,...], self.handler['ff'][pixel]
+            return self.handler['model'][pixel,...], self.handler['ff'][pixel], self.handler['vmac'][pixel]
 
     def close(self):
         if (self.extension == '1d'):
diff --git a/hazel/multiprocess.py b/hazel/multiprocess.py
index dbbcbe9..23310d2 100755
--- a/hazel/multiprocess.py
+++ b/hazel/multiprocess.py
@@ -121,8 +121,13 @@ def nonmpi_work(self):
             if all(x == 1 for x in mask):
 
                 for k, v in self.model.atmospheres.items():
-                    args, ff = v.model_handler.read(pixel=i)
-                    v.set_parameters(args, ff)
+                    if (v.type == 'photosphere'):
+                        args, ff, vmac = v.model_handler.read(pixel=i)
+                        v.set_parameters(args, ff, vmac)
+                    else:
+                        args, ff = v.model_handler.read(pixel=i)
+                        v.set_parameters(args, ff)
+                    
                     v.init_reference()
 
                 if (self.model.n_randomization > 1):
diff --git a/hazel/parametric.py b/hazel/parametric.py
index 87ff468..644fdf9 100755
--- a/hazel/parametric.py
+++ b/hazel/parametric.py
@@ -167,7 +167,9 @@ def nodes_to_model(self):
 
     def print_parameters(self, first=False, error=False):
         self.logger.info("     {0}        {1}        {2}        {3}".format('lambda0', 'sigma', 'd', 'a'))        
-        self.logger.info("     {0:8.3f}  {1:8.3f}  {2:8.3f}  {3:8.3f}".format(self.parameters['lambda0'][0], self.parameters['sigma'][0], self.parameters['depth'][0], self.parameters['a'][0]))
+
+        self.logger.info("     {0:8.3f}  {1:8.3f}  {2:8.3f}  {3:8.3f}".format(np.atleast_1d(self.parameters['lambda0'])[0], \
+            np.atleast_1d(self.parameters['sigma'])[0], np.atleast_1d(self.parameters['depth'])[0], np.atleast_1d(self.parameters['a'])[0]))
                 
     def synthesize(self, stokes=None):
         """
diff --git a/hazel/photosphere.py b/hazel/photosphere.py
index 607c67b..483d18d 100755
--- a/hazel/photosphere.py
+++ b/hazel/photosphere.py
@@ -33,6 +33,7 @@ def __init__(self, working_mode, name=''):
         self.parameters['By'] = None
         self.parameters['Bz'] = None
         self.parameters['ff'] = None
+        self.parameters['vmac'] = None
 
         self.nodes_location['T'] = None
         self.nodes_location['vmic'] = None
@@ -41,6 +42,7 @@ def __init__(self, working_mode, name=''):
         self.nodes_location['By'] = None
         self.nodes_location['Bz'] = None
         self.nodes_location['ff'] = None
+        self.nodes_location['vmac'] = None
 
         self.n_nodes['T'] = 0
         self.n_nodes['vmic'] = 0
@@ -49,6 +51,7 @@ def __init__(self, working_mode, name=''):
         self.n_nodes['By'] = 0
         self.n_nodes['Bz'] = 0
         self.n_nodes['ff'] = 0
+        self.n_nodes['vmac'] = 0
 
         self.nodes['T'] = 0
         self.nodes['vmic'] = 0
@@ -57,6 +60,7 @@ def __init__(self, working_mode, name=''):
         self.nodes['By'] = 0
         self.nodes['Bz'] = 0
         self.nodes['ff'] = 0
+        self.nodes['vmac'] = 0
 
         self.ranges['T'] = None
         self.ranges['vmic'] = None
@@ -65,6 +69,7 @@ def __init__(self, working_mode, name=''):
         self.ranges['By'] = None
         self.ranges['Bz'] = None
         self.ranges['ff'] = None
+        self.ranges['vmac'] = None
 
         self.cycles['T'] = None
         self.cycles['vmic'] = None
@@ -73,6 +78,7 @@ def __init__(self, working_mode, name=''):
         self.cycles['By'] = None
         self.cycles['Bz'] = None
         self.cycles['ff'] = None
+        self.cycles['vmac'] = None
 
         self.epsilon['T'] = 0.01
         self.epsilon['vmic'] = 0.01
@@ -81,6 +87,7 @@ def __init__(self, working_mode, name=''):
         self.epsilon['By'] = 0.01
         self.epsilon['Bz'] = 0.01
         self.epsilon['ff'] = 0.01
+        self.epsilon['vmac'] = 0.01
 
         self.regularization['T'] = None
         self.regularization['vmic'] = None
@@ -89,6 +96,7 @@ def __init__(self, working_mode, name=''):
         self.regularization['By'] = None
         self.regularization['Bz'] = None
         self.regularization['ff'] = None
+        self.regularization['vmac'] = None
         
     def list_lines(self):
         """
@@ -211,14 +219,14 @@ def load_reference_model(self, model_file, verbose):
 
         self.model_handler = Generic_SIR_file(model_file)
         self.model_handler.open()
-        out, ff = self.model_handler.read(pixel=0)
+        out, ff, vmac = self.model_handler.read(pixel=0)
         self.model_handler.close()
 
-        self.set_parameters(out, ff)
+        self.set_parameters(out, ff, vmac)
         
         self.init_reference(check_borders=True)
                         
-    def set_parameters(self, model, ff):
+    def set_parameters(self, model, ff, vmac):
         """
         Set the parameters of the current model to those passed as argument
 
@@ -228,6 +236,8 @@ def set_parameters(self, model, ff):
             Array with the model        
         ff : float
             Value of the filling factor
+        vmac : float
+            Value of the macroturbulent velocity
 
         Returns
         -------
@@ -249,6 +259,7 @@ def set_parameters(self, model, ff):
             self.Pe[-1] = 1.11634e-1        
         
         self.parameters['ff'] = ff
+        self.parameters['vmac'] = vmac
 
         # Check that parameters are inside borders by clipping inside the interval with a border of 1e-8
         if (self.working_mode == 'inversion'):
@@ -362,12 +373,12 @@ def synthesize(self, stokes_in, returnRF=False):
         if (returnRF):
             stokes, rf = sir_code.synthRF(self.index, self.n_lambda, self.log_tau, self.parameters['T'], 
                 self.Pe, self.parameters['vmic'], 1e5*self.parameters['v'], self.parameters['Bx'], self.parameters['By'], 
-                self.parameters['Bz'], self.macroturbulence)
+                self.parameters['Bz'], self.parameters['vmac'])
             return self.parameters['ff'] * stokes[1:,:], rf
         else:                        
             stokes, error = sir_code.synth(self.index, self.n_lambda, self.log_tau, self.parameters['T'], 
                 self.Pe, 1e5*self.parameters['vmic'], 1e5*self.parameters['v'], self.parameters['Bx'], self.parameters['By'], 
-                self.parameters['Bz'], self.macroturbulence[0])
+                self.parameters['Bz'], self.parameters['vmac'])
             
             if (error == 1):
                 raise NumericalErrorSIR()
diff --git a/hazel/tools.py b/hazel/tools.py
index 58ddec1..2baa0e5 100755
--- a/hazel/tools.py
+++ b/hazel/tools.py
@@ -121,7 +121,7 @@ def __init__(self, file=None, mode='single'):
 
         self.mode = mode
         
-        self.model = {'model': None, 'ff': None}
+        self.model = {'model': None, 'ff': None, 'vmac': None}
 
     def set_size(self, nz, n_pixel=1):
         """
@@ -148,6 +148,7 @@ def set_size(self, nz, n_pixel=1):
 
         self.model['model'] = np.zeros((n_pixel,nz,8), dtype=np.float64)
         self.model['ff'] = np.zeros((n_pixel,), dtype=np.float64)
+        self.model['vmac'] = np.zeros((n_pixel,), dtype=np.float64)
 
     def set_default(self, n_pixel=1, default='hsra'):
         """
@@ -172,7 +173,8 @@ def set_default(self, n_pixel=1, default='hsra'):
         filename = '/'.join(path[0:-1])+'/data/{0}.1d'.format(default)
         f = open(filename, 'r')
         f.readline()
-        ff = float(f.readline())
+        tmp = f.readline().split()
+        ff, vmac = float(tmp[0]), float(tmp[1])
         f.close()
         model = np.loadtxt(filename, skiprows=4)
 
@@ -180,9 +182,11 @@ def set_default(self, n_pixel=1, default='hsra'):
 
         self.model['model'] = np.zeros((n_pixel,nz,8), dtype=np.float64)
         self.model['ff'] = np.zeros((n_pixel,), dtype=np.float64)
+        self.model['vmac'] = np.zeros((n_pixel,), dtype=np.float64)
 
         self.model['model'][:] = model[None,:,:]
         self.model['ff'][:] = ff
+        self.model['vmac'][:] = vmac
 
     def list_models(self):
         docs = """
@@ -290,8 +294,8 @@ def save(self, file, default=None):
         if (self.mode == 'single'):
             print("Saving photospheric 1D model : {0}.1d".format(file))
             f = open('{0}.1d'.format(file), 'w')
-            f.write('ff\n')
-            f.write('{0}\n'.format(self.model['ff'][0]))
+            f.write('ff  vmac\n')
+            f.write('{0}  {1}\n'.format(self.model['ff'][0], self.model['vmac'][0]))
             f.write('\n')
             f.write('  logtau     T        Pe           vmic        v            Bx           By         Bz\n')            
             
@@ -303,8 +307,10 @@ def save(self, file, default=None):
             f = h5py.File('{0}.h5'.format(file), 'w')
             db_model = f.create_dataset('model', self.model['model'].shape, dtype=np.float64)
             db_ff = f.create_dataset('ff', self.model['ff'].shape, dtype=np.float64)
+            db_vmac = f.create_dataset('vmac', self.model['vmac'].shape, dtype=np.float64)
             db_model[:] = self.model['model']
             db_ff[:] = self.model['ff']
+            db_vmac[:] = self.model['vmac']
             f.close()
 
 
diff --git a/output.h5 b/output.h5
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diff --git a/test/configurations/conf_mpi_invh5.ini b/test/configurations/conf_mpi_invh5.ini
index 8148996..dc3e504 100755
--- a/test/configurations/conf_mpi_invh5.ini
+++ b/test/configurations/conf_mpi_invh5.ini
@@ -34,6 +34,7 @@ Number of cycles = 1
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
         ff     = 0.0, 1.0001
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 2, 3, 5, 5
@@ -43,6 +44,7 @@ Number of cycles = 1
         By     = 0, 1, 1, 1
         Bz     = 0, 1, 1, 1
         ff     = 0, 0, 0, 0
+        vmac   = 0, 0, 0, 0
 
         [[Regularization]]
         T      = None
@@ -51,6 +53,7 @@ Number of cycles = 1
         Bx     = None
         By     = None
         Bz     = None
+        vmac   = None
 
     [[Chromosphere 1]]
     Name = ch1                                              # Name of the atmosphere component
diff --git a/test/configurations/conf_mpi_synh5.ini b/test/configurations/conf_mpi_synh5.ini
index fbb2faf..d631127 100755
--- a/test/configurations/conf_mpi_synh5.ini
+++ b/test/configurations/conf_mpi_synh5.ini
@@ -30,6 +30,7 @@ Output file = output.h5
         Bx     = -1000.0, 1000.0
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 3, 3, 5, 5
@@ -38,4 +39,5 @@ Output file = output.h5
         Bx     = 1, 1, 1, 1
         By     = 1, 1, 1, 1
         Bz     = 1, 1, 1, 1
+        vmac   = 0, 0, 0, 0
 
diff --git a/test/configurations/conf_nonmpi_inv1d.ini b/test/configurations/conf_nonmpi_inv1d.ini
index 7c7a115..6187bfc 100755
--- a/test/configurations/conf_nonmpi_inv1d.ini
+++ b/test/configurations/conf_nonmpi_inv1d.ini
@@ -34,6 +34,7 @@ Number of cycles = 1
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
         ff     = 0.0, 1.00001
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 1, 3, 5, 5
@@ -43,6 +44,7 @@ Number of cycles = 1
         By     = 0, 1, 1, 1
         Bz     = 0, 1, 1, 1
         ff     = 0, 0, 0, 0
+        vmac   = 0, 0, 0, 0
 
         [[Regularization]]
         T      = None
@@ -51,6 +53,7 @@ Number of cycles = 1
         Bx     = None
         By     = None
         Bz     = None
+        vmac   = None
 
     [[Chromosphere 1]]
     Name = ch1                                              # Name of the atmosphere component
diff --git a/test/configurations/conf_nonmpi_syn1d.ini b/test/configurations/conf_nonmpi_syn1d.ini
index 304f0fa..23bfa21 100755
--- a/test/configurations/conf_nonmpi_syn1d.ini
+++ b/test/configurations/conf_nonmpi_syn1d.ini
@@ -33,6 +33,7 @@ Output file = output.h5
         Bx     = -1000.0, 1000.0
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
+        vmac   = 0.0, 5.0
     
         [[[Nodes]]]
         T      = 3, 3, 5, 5
@@ -41,6 +42,7 @@ Output file = output.h5
         Bx     = 1, 1, 1, 1
         By     = 1, 1, 1, 1
         Bz     = 1, 1, 1, 1
+        vmac   = 0, 0, 0, 0
 
     [[Photosphere 2]]
     Name = ph2
@@ -56,6 +58,7 @@ Output file = output.h5
         Bx     = -1000.0, 1000.0
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 3, 3, 5, 5
@@ -64,6 +67,7 @@ Output file = output.h5
         Bx     = 1, 1, 1, 1
         By     = 1, 1, 1, 1
         Bz     = 1, 1, 1, 1
+        vmac   = 0, 0, 0, 0
 
     [[Chromosphere 1]]
     Name = ch1                                              # Name of the atmosphere component
diff --git a/test/configurations/conf_single.ini b/test/configurations/conf_single.ini
index 4efd64d..8e1a35f 100755
--- a/test/configurations/conf_single.ini
+++ b/test/configurations/conf_single.ini
@@ -46,6 +46,7 @@ Number of cycles = 2
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
         ff     = 0.0, 1.0
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 0, 1, 5, 5
@@ -55,6 +56,7 @@ Number of cycles = 2
         By     = 0, 0, 1, 1
         Bz     = 0, 0, 1, 1
         ff     = 0, 0, 0, 0
+        vmac   = 0, 0, 0, 0
 
         [[[Regularization]]]
         T      = 'l2-value', 10.0, 1.0
@@ -64,6 +66,7 @@ Number of cycles = 2
         By     = None
         Bz     = None
         ff     = None
+        vmac   = None
 
 
     [[Chromosphere 1]]
diff --git a/test/configurations/conf_syn.ini b/test/configurations/conf_syn.ini
index 6200cc4..ce80dc3 100755
--- a/test/configurations/conf_syn.ini
+++ b/test/configurations/conf_syn.ini
@@ -38,6 +38,7 @@ Number of cycles = 1
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
         ff     = 0.0, 1.001
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 1, 1, 5, 5
@@ -47,6 +48,7 @@ Number of cycles = 1
         By     = 0, 0, 1, 1
         Bz     = 0, 0, 1, 1
         ff     = 0, 0, 0, 0
+        vmac   = 0, 0, 0, 0
 
 
     [[Chromosphere 1]]
diff --git a/test/configurations/conf_synobs.ini b/test/configurations/conf_synobs.ini
index 62a1f61..ad7d664 100755
--- a/test/configurations/conf_synobs.ini
+++ b/test/configurations/conf_synobs.ini
@@ -41,6 +41,7 @@ Output file = output.h5
         Bx     = -1000.0, 1000.0
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
+        vmac   = 0.0, 5.0
     
         [[[Nodes]]]
         T      = 3, 3, 5, 5
@@ -49,6 +50,7 @@ Output file = output.h5
         Bx     = 1, 1, 1, 1
         By     = 1, 1, 1, 1
         Bz     = 1, 1, 1, 1
+        vmac   = 0, 0, 0, 0
 
     [[Photosphere 2]]
     Name = ph2
@@ -64,6 +66,7 @@ Output file = output.h5
         Bx     = -1000.0, 1000.0
         By     = -1000.0, 1000.0
         Bz     = -1000.0, 1000.0
+        vmac   = 0.0, 5.0
 
         [[[Nodes]]]
         T      = 3, 3, 5, 5
@@ -72,6 +75,7 @@ Output file = output.h5
         Bx     = 1, 1, 1, 1
         By     = 1, 1, 1, 1
         Bz     = 1, 1, 1, 1
+        vmac   = 0, 0, 0, 0
 
     [[Chromosphere 1]]
     Name = ch1                                              # Name of the atmosphere component
diff --git a/test/photospheres/model_chromosphere.h5 b/test/photospheres/model_chromosphere.h5
deleted file mode 100755
index 67448e036cf6ae1257f7587bef39875f96ae6f3b..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/test/photospheres/model_photosphere.1d b/test/photospheres/model_photosphere.1d
index 79100a3..57c6676 100755
--- a/test/photospheres/model_photosphere.1d
+++ b/test/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   
diff --git a/test/photospheres/model_photosphere.h5 b/test/photospheres/model_photosphere.h5
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diff --git a/test/photospheres/model_photosphere_200.1d b/test/photospheres/model_photosphere_200.1d
index e22fd6d..076c93b 100755
--- a/test/photospheres/model_photosphere_200.1d
+++ b/test/photospheres/model_photosphere_200.1d
@@ -1,5 +1,5 @@
-ff
-1.0
+ff  vmac
+1.0  0.0
 
   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
diff --git a/test/test_file_generators.py b/test/test_file_generators.py
old mode 100755
new mode 100644
index 005a496..a9d4780
--- a/test/test_file_generators.py
+++ b/test/test_file_generators.py
@@ -44,4 +44,4 @@ def test_file_generators():
         for f in glob.glob('chromosphere*.*'):
             os.remove(f)
     except:
-        pass
\ No newline at end of file
+        pass
diff --git a/test/test_nonmpi_inv1d.py b/test/test_nonmpi_inv1d.py
old mode 100755
new mode 100644
index a8bf66c..e658aae
--- a/test/test_nonmpi_inv1d.py
+++ b/test/test_nonmpi_inv1d.py
@@ -22,4 +22,4 @@ def test_nonmpi_inv1d():
         try:
             os.remove('output.h5')
         except:
-            pass
\ No newline at end of file
+            pass
diff --git a/test/test_nonmpi_syn1d.py b/test/test_nonmpi_syn1d.py
old mode 100755
new mode 100644
index b43d52b..9d91002
--- a/test/test_nonmpi_syn1d.py
+++ b/test/test_nonmpi_syn1d.py
@@ -20,4 +20,4 @@ def test_nonmpi_syn1d():
         try:
             os.remove('output.h5')
         except:
-            pass
\ No newline at end of file
+            pass
diff --git a/test/test_programmatic.py b/test/test_programmatic.py
old mode 100755
new mode 100644
diff --git a/test/test_single_inv.py b/test/test_single_inv.py
old mode 100755
new mode 100644
index 3710256..44bc062
--- a/test/test_single_inv.py
+++ b/test/test_single_inv.py
@@ -13,7 +13,7 @@ def test_single_inv():
 
     mod.close_output()
 
-    f = h5py.File('output.h5')
+    f = h5py.File('output.h5', 'r')
 
     assert f['spec1']['stokes'].shape == (1,1,2,4,150), "incorrect dimensions in inversion"
 
@@ -22,4 +22,4 @@ def test_single_inv():
     try:
         os.remove('output.h5')
     except:
-        pass
\ No newline at end of file
+        pass
diff --git a/test/test_single_syn.py b/test/test_single_syn.py
old mode 100755
new mode 100644
index 10c1d14..dc655df
--- a/test/test_single_syn.py
+++ b/test/test_single_syn.py
@@ -9,4 +9,4 @@ def test_single_syn():
     mod.write_output()
     mod.close_output()
 
-    assert mod.spectrum['spec1'].stokes.shape == (4,150), "incorrect dimensions in synthesis"    
\ No newline at end of file
+    assert mod.spectrum['spec1'].stokes.shape == (4,150), "incorrect dimensions in synthesis"