From c5113159b526462f84aaadf16b369d7dd4ea4a85 Mon Sep 17 00:00:00 2001
From: Ikrom Akramov <96234984+ikrom96git@users.noreply.github.com>
Date: Tue, 6 Feb 2024 10:56:25 +0100
Subject: [PATCH] Bug fix (#395)

* readme file changes

* fixed bugs for stability plots and some edits in README file

* some edits

* typo in citation
---
 pySDC/projects/Second_orderSDC/README.rst                | 4 ++--
 .../Second_orderSDC/harmonic_oscillator_params.py        | 2 +-
 .../Second_orderSDC/harmonic_oscillator_run_stability.py | 9 ++++++++-
 .../Second_orderSDC/penningtrap_run_Hamiltonian_error.py | 2 +-
 pySDC/projects/Second_orderSDC/penningtrap_run_error.py  | 2 +-
 .../Second_orderSDC/penningtrap_run_work_precision.py    | 2 +-
 6 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/pySDC/projects/Second_orderSDC/README.rst b/pySDC/projects/Second_orderSDC/README.rst
index 21946f2f92..8f678d0487 100644
--- a/pySDC/projects/Second_orderSDC/README.rst
+++ b/pySDC/projects/Second_orderSDC/README.rst
@@ -14,7 +14,7 @@ If you utilize it, either in whole or in part, for a publication, please provide
        year={2023},
        eprint={2310.08352},
        archivePrefix={arXiv},
-       primaryClass={math.NA}
+       primaryClass={math.NA}}
 
 
 Reproducing Figures from the Publication
@@ -54,4 +54,4 @@ Reproducing Figures from the Publication
 
 Contact
 -------
-This code is written by `Ikrom Akramov`<https://www.mat.tuhh.de/home/iakramov/?homepage_id=iakramov)>_
+This code is written by `Ikrom Akramov <https://www.mat.tuhh.de/home/iakramov/?homepage_id=iakramov)>`_
diff --git a/pySDC/projects/Second_orderSDC/harmonic_oscillator_params.py b/pySDC/projects/Second_orderSDC/harmonic_oscillator_params.py
index daf6f40d15..2a5c41f112 100644
--- a/pySDC/projects/Second_orderSDC/harmonic_oscillator_params.py
+++ b/pySDC/projects/Second_orderSDC/harmonic_oscillator_params.py
@@ -21,7 +21,7 @@ def get_default_harmonic_oscillator_description():
     sweeper_params = {'quad_type': 'GAUSS', 'num_nodes': 3, 'do_coll_update': True, 'picard_mats_sweep': True}
 
     # Initialize step parameters
-    step_params = {'maxiter': 5}
+    step_params = {'maxiter': 50}
 
     # Fill description dictionary for easy step instantiation
     description = {
diff --git a/pySDC/projects/Second_orderSDC/harmonic_oscillator_run_stability.py b/pySDC/projects/Second_orderSDC/harmonic_oscillator_run_stability.py
index a89f740e2f..3f0e7325cd 100644
--- a/pySDC/projects/Second_orderSDC/harmonic_oscillator_run_stability.py
+++ b/pySDC/projects/Second_orderSDC/harmonic_oscillator_run_stability.py
@@ -15,9 +15,16 @@
         Iteration matrix of Picard method: model_stab.run_Kpicard()
 
     """
+    # This code checks if the "data" folder exists or not.
+    exec(open("check_data_folder.py").read())
     # Execute the stability analysis for the damped harmonic oscillator
     description = get_default_harmonic_oscillator_description()
-    model_stab = StabilityImplementation(description, kappa_max=30, mu_max=30, Num_iter=(200, 200))
+    # =============================================================================
+    #    maxiter can be changed here manually. By default, maxiter is 50
+    description['step_params']['maxiter'] = 50
+    # =============================================================================
+
+    model_stab = StabilityImplementation(description, kappa_max=18, mu_max=18, Num_iter=(200, 200))
 
     model_stab.run_SDC_stability()
     model_stab.run_Picard_stability()
diff --git a/pySDC/projects/Second_orderSDC/penningtrap_run_Hamiltonian_error.py b/pySDC/projects/Second_orderSDC/penningtrap_run_Hamiltonian_error.py
index cab9299836..28f9ea01bb 100644
--- a/pySDC/projects/Second_orderSDC/penningtrap_run_Hamiltonian_error.py
+++ b/pySDC/projects/Second_orderSDC/penningtrap_run_Hamiltonian_error.py
@@ -1,4 +1,4 @@
-# It checks whether data folder exicits or not
+# This code checks if the "data" folder exists or not.
 exec(open("check_data_folder.py").read())
 
 import matplotlib.pyplot as plt
diff --git a/pySDC/projects/Second_orderSDC/penningtrap_run_error.py b/pySDC/projects/Second_orderSDC/penningtrap_run_error.py
index 77156b8355..fca61bf9ae 100644
--- a/pySDC/projects/Second_orderSDC/penningtrap_run_error.py
+++ b/pySDC/projects/Second_orderSDC/penningtrap_run_error.py
@@ -15,7 +15,7 @@
     Note:
         Tend: final time value can be given manually by default Tend=2
     """
-    # It checks whether data folder exicits or not
+    # This code checks if the "data" folder exists or not.
     exec(open("check_data_folder.py").read())
     # Get params for the penning trap problem from the function
     controller_params, description = penningtrap_params()
diff --git a/pySDC/projects/Second_orderSDC/penningtrap_run_work_precision.py b/pySDC/projects/Second_orderSDC/penningtrap_run_work_precision.py
index eead34df2c..5bac2f231a 100644
--- a/pySDC/projects/Second_orderSDC/penningtrap_run_work_precision.py
+++ b/pySDC/projects/Second_orderSDC/penningtrap_run_work_precision.py
@@ -1,4 +1,4 @@
-# It checks whether data folder exicits or not
+# This code checks if the "data" folder exists or not.
 exec(open("check_data_folder.py").read())
 
 from pySDC.projects.Second_orderSDC.penningtrap_Simulation import ComputeError