restore derived variables when we read a .h5 file (#294)

also add vorticity to compressible derives

Author: zingale

pyro/compressible/derives.py

@@ -24,6 +24,13 @@ def derive_primitives(myd, varnames):
     gamma = myd.get_aux("gamma")
     p = eos.pres(gamma, dens, e)
 
+    myg = myd.grid
+    vort = myg.scratch_array()
+
+    vort.v()[:, :] = \
+        0.5*(v.ip(1) - v.ip(-1))/myg.dx - \
+        0.5*(u.jp(1) - u.jp(-1))/myg.dy
+
     if isinstance(varnames, str):
         wanted = [varnames]
     else:
@@ -50,6 +57,9 @@ def derive_primitives(myd, varnames):
         elif var == "soundspeed":
             derived_vars.append(np.sqrt(gamma*p/dens))
 
+        elif var == "vorticity":
+            derived_vars.append(vort)
+
     if len(derived_vars) > 1:
         return derived_vars
 

pyro/util/io_pyro.py

@@ -127,6 +127,14 @@ def read(filename):
 
             sim.read_extras(f)
 
+        # check if there are derived variables
+        try:
+            derives = importlib.import_module(f"pyro.{solver_name}.derives")
+            sim.cc_data.add_derived(derives.derive_primitives)
+
+        except ModuleNotFoundError:
+            pass
+
     if solver_name is not None:
         return sim