bugfix in graph2rst

Author: tgastine

python/magic/checkpoint.py

@@ -199,7 +199,7 @@ def read(self, filename, endian='l'):
                      np.fromfile(file, dtype=np.float64, count=9)
 
         # Truncation
-        self.n_r_max, self.n_theta_max, self.n_phi_tot, self.minc,\
+        self.n_r_max, self.n_theta_max, self.n_phi_tot, self.minc, \
                       self.nalias, self.n_r_ic_max = \
                       np.fromfile(file, dtype=np.int32, count=6)
         if self.version > 3:
@@ -342,7 +342,7 @@ def write(self, filename):
         file = open(filename, 'wb')
 
         # Header
-        version = np.array([4], np.int32)
+        version = np.array([5], np.int32)
         version.tofile(file)
         time = np.array([self.time], np.float64)
         time.tofile(file)
@@ -369,15 +369,15 @@ def write(self, filename):
                           self.ek, self.stef, self.radratio, self.sigma_ratio],
                          np.float64)
         else:
-            x = np.array([1e5, 1.0,  0.0, 1.0, 5.0, 1.0e-3, self.radratio, 1.0],
+            x = np.array([1e5, 1.0,  0.0, 1.0, 5.0, 1.0e-3, 0., self.radratio, 1.0],
                          np.float64)
         x.tofile(file)
 
         # Truncation
         x = np.array([self.n_r_max, self.n_theta_max,  self.n_phi_tot, self.minc,
                       self.nalias, self.n_r_ic_max], np.int32)
         x.tofile(file)
-        if not hasattr(self,"m_min"):
+        if not hasattr(self, 'm_min'):
             self.m_min = 0
         x = np.array([self.l_max, self.m_min, self.m_max], np.int32)
         x.tofile(file)
@@ -405,7 +405,7 @@ def write(self, filename):
         dumm.tofile(file)
 
         # Logicals
-        if not hasattr(self,"l_phase"):
+        if not hasattr(self, 'l_phase'):
             self.l_phase = False
 
         flags = np.array([self.l_heat, self.l_chem, self.l_phase, self.l_mag, False,
@@ -673,25 +673,48 @@ def graph2rst(self, gr, filename='checkpoint_ave.from_chk'):
             self.fd_ratio = gr.fd_ratio
 
         # Flags
+        self.ek = gr.ek
+        self.radratio = gr.radratio
         if gr.mode in [2, 3, 7, 8, 9, 10] or gr.ra == 0.:
             self.l_heat = False
+            self.ra = 0.
+            self.pr = 0.
         else:
             self.l_heat = True
+            self.ra = gr.ra
+            self.pr = gr.pr
         if not hasattr(gr, 'raxi'):
             self.l_chem = False
+            self.raxi = 0.
+            self.sc = 0.
         else:
             if gr.raxi > 0. or gr.raxi < 0.:
                 self.l_chem = True
             else:
                 self.l_chem = False
+            self.raxi = gr.raxi
+            self.sc = gr.sc
         if gr.mode in [0, 2, 3, 6, 8, 9]:
             self.l_mag = True
+            self.prmag = 0.
         else:
             self.l_mag = False
+            self.prmag = gr.prmag
         if gr.sigma_ratio == 0.:
             self.l_cond_ic = False
+            self.sigma_ratio = 0.
         else:
             self.l_cond_ic = True
+            self.sigma_ratio = gr.sigma
+        if not hasattr(gr, 'stef'):
+            self.l_phase = False
+            self.stef = 0.
+        else:
+            if gr.stef > 0.:
+                self.l_phase = True
+            else:
+                self.l_phase = False
+            self.stef = gr.stef
         self.l_press = False
 
         if self.l_cond_ic:
@@ -747,6 +770,13 @@ def graph2rst(self, gr, filename='checkpoint_ave.from_chk'):
                 p = sh.spat_spec(gr.xi[:, :, i])
                 self.xi[i, :] = p[:]
 
+        # Calculate the phase field
+        if self.l_phase:
+            self.phase = np.zeros_like(self.wpol)
+            for i in range(self.n_r_max):
+                p = sh.spat_spec(gr.phase[:, :, i])
+                self.phase[i, :] = p[:]
+
         # Calculate the magnetic field
         if self.l_mag:
             self.bpol = np.zeros_like(self.wpol)