improve convergence and clean up:

- use AD to improve convergence
- tighten tolerances
- increase max time step to reduce computational time
- remove heavy tests since the test now runs in less than 3 seconds
- update documentation
- regold

test/tests/val-2a/comparison_val-2a.py

@@ -53,8 +53,8 @@ def numerical_solution_on_experiment_input(experiment_input, tmap_input, tmap_ou
 gs = gridspec.GridSpec(1, 1)
 ax = fig.add_subplot(gs[0])
 
-ax.plot(simulation_time_TMAP4/3600, simulation_recom_flux_right_TMAP4, linestyle='-', label=r"TMAP8", c='tab:brown')
-ax.plot(experiment_time_TMAP4/3600, experiment_flux_TMAP4, linestyle='--', label=r"experiment", c='k')
+ax.plot(simulation_time_TMAP4/3600, simulation_recom_flux_right_TMAP4, linestyle='-', label=r"TMAP8", c='tab:gray')
+ax.scatter(experiment_time_TMAP4/3600, experiment_flux_TMAP4, label=r"experiment", c='k', size=10)
 
 ax.set_xlabel(u'time (hr)')
 ax.set_ylabel(u"Deuterium flux (atom/m$^2$/s)")
@@ -68,7 +68,7 @@ def numerical_solution_on_experiment_input(experiment_input, tmap_input, tmap_ou
 ax.text(1e4/3600.0,40e15, 'RMSPE = %.2f '%RMSPE+'%',fontweight='bold')
 ax.minorticks_on()
 ax.ticklabel_format(axis='y', style='sci', scilimits=(15,15))
-plt.savefig(f'{TMAP4_file_base}.png', bbox_inches='tight')
+plt.savefig(f'{TMAP4_file_base}.png', bbox_inches='tight', dpi=300)
 plt.close(fig)
 
 
@@ -98,5 +98,5 @@ def numerical_solution_on_experiment_input(experiment_input, tmap_input, tmap_ou
 ax.set_xlim(left=0,right=3e-8)
 plt.grid(visible=True, which='major', color='0.65', linestyle='--', alpha=0.3)
 ax.minorticks_on()
-plt.savefig(f'val-2a_comparison_normal_distribution.png', bbox_inches='tight')
+plt.savefig(f'val-2a_comparison_normal_distribution.png', bbox_inches='tight', dpi=300)
 plt.close(fig)