deploy: 5688fd7

_api/cp2kdata.output.html

@@ -446,9 +446,14 @@ <h1>cp2kdata.output module</h1>
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">check_run_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">run_type</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/output.html#Cp2kOutput.check_run_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.output.Cp2kOutput.check_run_type" title="Permalink to this definition">#</a></dt>
 <dd></dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="cp2kdata.output.Cp2kOutput.drop_first_info">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">drop_first_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cp2k_info</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'info'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/output.html#Cp2kOutput.drop_first_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.output.Cp2kOutput.drop_first_info" title="Permalink to this definition">#</a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="cp2kdata.output.Cp2kOutput.drop_last_info">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">drop_last_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cp2k_info</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/output.html#Cp2kOutput.drop_last_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.output.Cp2kOutput.drop_last_info" title="Permalink to this definition">#</a></dt>
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">drop_last_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cp2k_info</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'info'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/output.html#Cp2kOutput.drop_last_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.output.Cp2kOutput.drop_last_info" title="Permalink to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">

_api/cp2kdata.utils.html

@@ -477,13 +477,6 @@ <h1>cp2kdata.utils module</h1>
 <span class="sig-prename descclassname"><span class="pre">cp2kdata.utils.</span></span><span class="sig-name descname"><span class="pre">interpolate_spline</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">old_x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">old_y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/utils.html#interpolate_spline"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.utils.interpolate_spline" title="Permalink to this definition">#</a></dt>
 <dd></dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="cp2kdata.utils.printtbox">
-<span class="sig-prename descclassname"><span class="pre">cp2kdata.utils.</span></span><span class="sig-name descname"><span class="pre">printtbox</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arg</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/utils.html#printtbox"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.utils.printtbox" title="Permalink to this definition">#</a></dt>
-<dd><p>This function is a print decorated with a few characters so that the
-print function present a characteristic string. Useful for postprocess.</p>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="cp2kdata.utils.set_pbc">
 <span class="sig-prename descclassname"><span class="pre">cp2kdata.utils.</span></span><span class="sig-name descname"><span class="pre">set_pbc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cp2kdata/utils.html#set_pbc"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cp2kdata.utils.set_pbc" title="Permalink to this definition">#</a></dt>

_modules/cp2kdata/block_parser/header_info.html

@@ -383,7 +383,9 @@ <h1>Source code for cp2kdata.block_parser.header_info</h1><div class="highlight"
 <span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
 <span class="c1"># use monty.re because it can terminate on match</span>
 <span class="kn">from</span> <span class="nn">monty.re</span> <span class="kn">import</span> <span class="n">regrep</span>
+<span class="kn">from</span> <span class="nn">cp2kdata.log</span> <span class="kn">import</span> <span class="n">get_logger</span>
 
+<span class="n">logger</span> <span class="o">=</span> <span class="n">get_logger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
 
 <div class="viewcode-block" id="Cp2kInfo"><a class="viewcode-back" href="../../../_api/cp2kdata.block_parser.header_info.html#cp2kdata.block_parser.header_info.Cp2kInfo">[docs]</a><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">Cp2kInfo</span><span class="p">:</span>
@@ -424,6 +426,8 @@ <h1>Source code for cp2kdata.block_parser.header_info</h1><div class="highlight"
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;More than one restart information found in </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="k">elif</span> <span class="n">num_match_restart</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
         <span class="n">cp2k_restart</span> <span class="o">=</span> <span class="kc">True</span>
+        <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Found restart information in the output header&quot;</span><span class="p">)</span>
+
     <span class="k">elif</span> <span class="n">num_match_restart</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
         <span class="n">cp2k_restart</span> <span class="o">=</span> <span class="kc">False</span>
 

_modules/cp2kdata/output.html

@@ -480,6 +480,7 @@ <h1>Source code for cp2kdata.output</h1><div class="highlight"><pre>
         <span class="c1"># restart should be true or false</span>
         <span class="k">if</span> <span class="n">restart</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="o">.</span><span class="n">restart</span> <span class="o">=</span> <span class="n">restart</span>
+            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Overwrite restart information with user provided restart = True.&quot;</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">check_run_type</span><span class="p">(</span><span class="n">run_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">global_info</span><span class="o">.</span><span class="n">run_type</span><span class="p">)</span>
 
@@ -782,8 +783,12 @@ <h1>Source code for cp2kdata.output</h1><div class="highlight"><pre>
             <span class="n">format_logger</span><span class="p">(</span><span class="n">info</span><span class="o">=</span><span class="s2">&quot;Forces&quot;</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">atomic_forces_list</span> <span class="o">=</span> <span class="n">parse_atomic_forces_list</span><span class="p">(</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">output_file</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">atomic_forces_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">drop_first_info</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomic_forces_list</span><span class="p">,</span> <span class="n">info</span><span class="o">=</span><span class="s2">&quot;forces&quot;</span><span class="p">)</span>
+
             <span class="bp">self</span><span class="o">.</span><span class="n">atomic_forces_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">drop_last_info</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomic_forces_list</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomic_forces_list</span><span class="p">,</span> <span class="n">info</span><span class="o">=</span><span class="s2">&quot;forces&quot;</span><span class="p">)</span>
 
         <span class="n">stress_file_list</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</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="bp">self</span><span class="o">.</span><span class="n">path_prefix</span><span class="p">,</span> <span class="s2">&quot;*.stress&quot;</span><span class="p">))</span>
@@ -802,8 +807,13 @@ <h1>Source code for cp2kdata.output</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span> <span class="o">=</span> <span class="n">parse_stress_tensor_list</span><span class="p">(</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">output_file</span><span class="p">)</span>
 
-            <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">drop_last_info</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span><span class="p">)</span>
+            <span class="c1"># stress tensor could be None if the output file doesn&#39;t contain stress information</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">drop_first_info</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span><span class="p">,</span> <span class="n">info</span><span class="o">=</span><span class="s2">&quot;stresses&quot;</span><span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">drop_last_info</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stress_tensor_list</span><span class="p">,</span> <span class="n">info</span><span class="o">=</span><span class="s2">&quot;stresses&quot;</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">num_frames</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">energies_list</span><span class="p">)</span>
 
@@ -901,12 +911,22 @@ <h1>Source code for cp2kdata.output</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="Cp2kOutput.get_vib_freq_list"><a class="viewcode-back" href="../../_api/cp2kdata.output.html#cp2kdata.output.Cp2kOutput.get_vib_freq_list">[docs]</a>    <span class="k">def</span> <span class="nf">get_vib_freq_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">vib_freq_list</span></div>
 
+<div class="viewcode-block" id="Cp2kOutput.drop_first_info"><a class="viewcode-back" href="../../_api/cp2kdata.output.html#cp2kdata.output.Cp2kOutput.drop_first_info">[docs]</a>    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">drop_first_info</span><span class="p">(</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">info</span><span class="o">=</span><span class="s2">&quot;info&quot;</span><span class="p">):</span>
+        <span class="c1"># drop first info parsed from output if it restart from preivous MD run</span>
+        <span class="k">if</span> <span class="n">cp2k_info</span><span class="o">.</span><span class="n">restart</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</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;The cp2k output is restarted from previous MD run, drop the first </span><span class="si">{</span><span class="n">info</span><span class="si">}</span><span class="s2">.&quot;</span>
+            <span class="p">)</span>
+            <span class="n">array</span> <span class="o">=</span> <span class="n">array</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+        <span class="k">return</span> <span class="n">array</span></div>
+
 <div class="viewcode-block" id="Cp2kOutput.drop_last_info"><a class="viewcode-back" href="../../_api/cp2kdata.output.html#cp2kdata.output.Cp2kOutput.drop_last_info">[docs]</a>    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">drop_last_info</span><span class="p">(</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="n">array</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">drop_last_info</span><span class="p">(</span><span class="n">cp2k_info</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">info</span><span class="o">=</span><span class="s2">&quot;info&quot;</span><span class="p">):</span>
         <span class="c1"># drop last info parsed from output if it is terminated by request (touch EXIT)</span>
         <span class="k">if</span> <span class="n">cp2k_info</span><span class="o">.</span><span class="n">terminated_by_request</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</span>
             <span class="nb">print</span><span class="p">(</span>
-                <span class="s2">&quot;cp2kdata found the cp2k output is terminated by request, drop the last info.&quot;</span><span class="p">)</span>
+                <span class="sa">f</span><span class="s2">&quot;The cp2k output is terminated by user request, drop the last </span><span class="si">{</span><span class="n">info</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">)</span>
             <span class="n">array</span> <span class="o">=</span> <span class="n">array</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
         <span class="k">return</span> <span class="n">array</span></div>