fix particle_finite_diff_test

bfps/NavierStokes.py

@@ -579,7 +579,6 @@ class NavierStokes(_fluid_particle_base):
                 self.particle_loop += '{0}->field = fs->rvelocity;\n'.format(interpolator[s])
                 self.particle_loop += 'ps{0}->step();\n'.format(s0 + s)
             self.particle_stat_src += 'ps{0}->write(particle_file, false);\n'.format(s0 + s)
-        self.particle_start += output_vel_acc
         self.particle_stat_src += output_vel_acc
         self.particle_stat_src += '}\n'
         self.particle_species += nspecies
@@ -615,11 +614,6 @@ class NavierStokes(_fluid_particle_base):
             self.statistics['kshell'] = data_file['kspace/kshell'].value
             self.statistics['kM'] = data_file['kspace/kM'].value
             self.statistics['dk'] = data_file['kspace/dk'].value
-            #if self.particle_species > 0:
-            #    self.trajectories = [data_file['particles/' + key + '/state'][
-            #                            iter0//self.parameters['niter_part'] :
-            #                            iter1//self.parameters['niter_part']+1]
-            #                         for key in data_file['particles'].keys()]
             computation_needed = True
             pp_file = h5py.File(self.get_postprocess_file_name(), 'a')
             if 'ii0' in pp_file.keys():

bfps/tools.py

@@ -198,8 +198,12 @@ def particle_finite_diff_test(
 
     .. seealso:: :func:`get_fornberg_coeffs`
     """
-    d = c.get_data_file()
-    group = d['particles/tracers{0}'.format(species)]
+    df = c.get_data_file()
+    if 'particles' in df.keys():
+        group = df['particles/tracers{0}'.format(species)]
+    else:
+        pf = c.get_particle_file()
+        group = pf['tracers{0}'.format(species)]
     acc_on = 'acceleration' in group.keys()
     pos = group['state'].value
     vel = group['velocity'].value
@@ -207,7 +211,7 @@ def particle_finite_diff_test(
         acc = group['acceleration'].value
     n = m
     fc = get_fornberg_coeffs(0, range(-n, n+1))
-    dt = d['parameters/dt'].value*d['parameters/niter_part'].value
+    dt = c.parameters['dt']*c.parameters['niter_part']
 
     num_vel1 = sum(fc[1, n-i]*pos[1+n-i:pos.shape[0]-i-n-1] for i in range(-n, n+1)) / dt
     if acc_on:
@@ -220,7 +224,7 @@ def particle_finite_diff_test(
         pid = np.argmin(SNR(num_acc1, acc[n+1:-n-1]))
     else:
         pid = np.argmin(SNR(num_vel1, vel[n+1:-n-1]))
-    pars = d['parameters']
+    pars = df['parameters']
     to_print = (
             'steps={0}, interp={1}, neighbours={2}, '.format(
                 pars['tracers{0}_integration_steps'.format(species)].value,
@@ -246,7 +250,6 @@ def particle_finite_diff_test(
 
         for n in range(1, m):
             fc = get_fornberg_coeffs(0, range(-n, n+1))
-            dt = d['parameters/dt'].value*d['parameters/niter_part'].value
 
             num_acc1 = sum(fc[1, n-i]*vel[n-i:vel.shape[0]-i-n] for i in range(-n, n+1)) / dt
             num_acc2 = sum(fc[2, n-i]*pos[n-i:pos.shape[0]-i-n] for i in range(-n, n+1)) / dt**2