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mdcourse · Aug 28, 2024 · 51a9821 · 51a9821
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diff --git a/_sources/chapters/chapter5.rst.txt b/_sources/chapters/chapter5.rst.txt
@@ -42,27 +42,42 @@ All quantities are re-dimensionalized before getting outputed.
 
 .. code-block:: python
 
+    import os
     import logging
-    logging.basicConfig(
-        level=logging.INFO,
-        format='%(message)s'
-    )
-
-    # Create a custom logger
-    logger = logging.getLogger('simulation_logger')
-    logger.setLevel(logging.INFO)
-    # Disable propagation to prevent double logging
-    logger.propagate = False
-
-    console_handler = logging.StreamHandler()  # To log to the terminal
-    file_handler = logging.FileHandler('simulation.log')  # To log to a file
-    formatter = logging.Formatter('%(message)s')
-    console_handler.setFormatter(formatter)
-    file_handler.setFormatter(formatter)
-    logger.addHandler(console_handler)
-    logger.addHandler(file_handler)
+
+    # Function to set up the logger
+    def setup_logger(folder_name):
+        # Create a custom logger
+        logger = logging.getLogger('simulation_logger')
+        logger.setLevel(logging.INFO)
+        logger.propagate = False  # Disable propagation to prevent double logging
+
+        # Clear any existing handlers if this function is called again
+        if logger.hasHandlers():
+            logger.handlers.clear()
+
+        # Create handlers for console and file
+        console_handler = logging.StreamHandler()  # To log to the terminal
+        log_file_path = os.path.join(folder_name, 'simulation.log')
+        file_handler = logging.FileHandler(log_file_path)  # To log to a file
+
+        # Create formatters and add them to the handlers
+        formatter = logging.Formatter('%(message)s')
+        console_handler.setFormatter(formatter)
+        file_handler.setFormatter(formatter)
+
+        # Add handlers to the logger
+        logger.addHandler(console_handler)
+        logger.addHandler(file_handler)
+
+        return logger
 
     def log_simulation_data(code):
+
+        # Setup the logger with the folder name
+        logger = setup_logger(code.data_folder)
+
+        # Logging the simulation data
         if code.thermo_period is not None:
             if code.step % code.thermo_period == 0:
                 if code.step == 0:
@@ -83,9 +98,8 @@ All quantities are re-dimensionalized before getting outputed.
                     logger.info(f"{code.step} {Epot:.2f} {code.MaxF:.2f}")
                 elif code.thermo_outputs == "Epot-press":
                     code.calculate_pressure()
-                    press = code.pressure \
-                        * code.reference_pressure  # Atm
-                    logger.info(f"{code.step} {Epot:.2f} {press:.2f}")    
+                    press = code.pressure * code.reference_pressure  # Atm
+                    logger.info(f"{code.step} {Epot:.2f} {press:.2f}")
 
 .. label:: end_logger_class
 

diff --git a/chapters/chapter5.html b/chapters/chapter5.html
@@ -286,27 +286,42 @@ <h2>Create logger<a class="headerlink" href="#create-logger" title="Link to this
 With the logger, some output are being printed in a file, as well as in the terminal.
 The frequency of printing is set by <em>thermo_period</em>, see <a class="reference internal" href="chapter3.html#chapter3-label"><span class="std std-ref">Initialize the simulation</span></a>.
 All quantities are re-dimensionalized before getting outputed.</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">logging</span>
-<span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span>
-    <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">,</span>
-    <span class="nb">format</span><span class="o">=</span><span class="s1">&#39;</span><span class="si">%(message)s</span><span class="s1">&#39;</span>
-<span class="p">)</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+
+<span class="c1"># Function to set up the logger</span>
+<span class="k">def</span> <span class="nf">setup_logger</span><span class="p">(</span><span class="n">folder_name</span><span class="p">):</span>
+    <span class="c1"># Create a custom logger</span>
+    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s1">&#39;simulation_logger&#39;</span><span class="p">)</span>
+    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+    <span class="n">logger</span><span class="o">.</span><span class="n">propagate</span> <span class="o">=</span> <span class="kc">False</span>  <span class="c1"># Disable propagation to prevent double logging</span>
+
+    <span class="c1"># Clear any existing handlers if this function is called again</span>
+    <span class="k">if</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
+        <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
+
+    <span class="c1"># Create handlers for console and file</span>
+    <span class="n">console_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>  <span class="c1"># To log to the terminal</span>
+    <span class="n">log_file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">folder_name</span><span class="p">,</span> <span class="s1">&#39;simulation.log&#39;</span><span class="p">)</span>
+    <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">log_file_path</span><span class="p">)</span>  <span class="c1"># To log to a file</span>
 
-<span class="c1"># Create a custom logger</span>
-<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s1">&#39;simulation_logger&#39;</span><span class="p">)</span>
-<span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-<span class="c1"># Disable propagation to prevent double logging</span>
-<span class="n">logger</span><span class="o">.</span><span class="n">propagate</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="c1"># Create formatters and add them to the handlers</span>
+    <span class="n">formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%(message)s</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="n">console_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span>
+    <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span>
 
-<span class="n">console_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>  <span class="c1"># To log to the terminal</span>
-<span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="s1">&#39;simulation.log&#39;</span><span class="p">)</span>  <span class="c1"># To log to a file</span>
-<span class="n">formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%(message)s</span><span class="s1">&#39;</span><span class="p">)</span>
-<span class="n">console_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span>
-<span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span>
-<span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">console_handler</span><span class="p">)</span>
-<span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
+    <span class="c1"># Add handlers to the logger</span>
+    <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">console_handler</span><span class="p">)</span>
+    <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">logger</span>
 
 <span class="k">def</span> <span class="nf">log_simulation_data</span><span class="p">(</span><span class="n">code</span><span class="p">):</span>
+
+    <span class="c1"># Setup the logger with the folder name</span>
+    <span class="n">logger</span> <span class="o">=</span> <span class="n">setup_logger</span><span class="p">(</span><span class="n">code</span><span class="o">.</span><span class="n">data_folder</span><span class="p">)</span>
+
+    <span class="c1"># Logging the simulation data</span>
     <span class="k">if</span> <span class="n">code</span><span class="o">.</span><span class="n">thermo_period</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="k">if</span> <span class="n">code</span><span class="o">.</span><span class="n">step</span> <span class="o">%</span> <span class="n">code</span><span class="o">.</span><span class="n">thermo_period</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">if</span> <span class="n">code</span><span class="o">.</span><span class="n">step</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
@@ -327,8 +342,7 @@ <h2>Create logger<a class="headerlink" href="#create-logger" title="Link to this
                 <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">code</span><span class="o">.</span><span class="n">step</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">Epot</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">code</span><span class="o">.</span><span class="n">MaxF</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
             <span class="k">elif</span> <span class="n">code</span><span class="o">.</span><span class="n">thermo_outputs</span> <span class="o">==</span> <span class="s2">&quot;Epot-press&quot;</span><span class="p">:</span>
                 <span class="n">code</span><span class="o">.</span><span class="n">calculate_pressure</span><span class="p">()</span>
-                <span class="n">press</span> <span class="o">=</span> <span class="n">code</span><span class="o">.</span><span class="n">pressure</span> \
-                    <span class="o">*</span> <span class="n">code</span><span class="o">.</span><span class="n">reference_pressure</span>  <span class="c1"># Atm</span>
+                <span class="n">press</span> <span class="o">=</span> <span class="n">code</span><span class="o">.</span><span class="n">pressure</span> <span class="o">*</span> <span class="n">code</span><span class="o">.</span><span class="n">reference_pressure</span>  <span class="c1"># Atm</span>
                 <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">code</span><span class="o">.</span><span class="n">step</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">Epot</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">press</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 </pre></div>
 </div>