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<title>custodian.cli.converge_kpoints — custodian 2023.5.7 documentation</title>
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<h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python</span>
<span class="sd">"""</span>
<span class="sd">This is a master vasp running script to converging kpoints for a calculation</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.inputs</span> <span class="kn">import</span> <span class="n">VaspInput</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.outputs</span> <span class="kn">import</span> <span class="n">Vasprun</span>
<span class="kn">from</span> <span class="nn">custodian.custodian</span> <span class="kn">import</span> <span class="n">Custodian</span>
<span class="kn">from</span> <span class="nn">custodian.vasp.handlers</span> <span class="kn">import</span> <span class="n">UnconvergedErrorHandler</span><span class="p">,</span> <span class="n">VaspErrorHandler</span>
<span class="kn">from</span> <span class="nn">custodian.vasp.jobs</span> <span class="kn">import</span> <span class="n">VaspJob</span>
<span class="n">FORMAT</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%(asctime)s</span><span class="s2"> </span><span class="si">%(message)s</span><span class="s2">"</span>
<span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="nb">format</span><span class="o">=</span><span class="n">FORMAT</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="n">filename</span><span class="o">=</span><span class="s2">"run.log"</span><span class="p">)</span>
<div class="viewcode-block" id="get_runs"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_kpoints.get_runs">[docs]</a><span class="k">def</span> <span class="nf">get_runs</span><span class="p">(</span><span class="n">vasp_command</span><span class="p">,</span> <span class="n">target</span><span class="o">=</span><span class="mf">1e-3</span><span class="p">,</span> <span class="n">max_steps</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">"linear"</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Generate the runs using a generator until convergence is achieved.</span>
<span class="sd"> """</span>
<span class="n">energy</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">vinput</span> <span class="o">=</span> <span class="n">VaspInput</span><span class="o">.</span><span class="n">from_directory</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
<span class="n">kpoints</span> <span class="o">=</span> <span class="n">vinput</span><span class="p">[</span><span class="s2">"KPOINTS"</span><span class="p">]</span><span class="o">.</span><span class="n">kpts</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_steps</span><span class="p">):</span>
<span class="k">if</span> <span class="n">mode</span> <span class="o">==</span> <span class="s2">"linear"</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="o">*</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kpoints</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="o">+</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kpoints</span><span class="p">]</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">settings</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">backup</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">backup</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Vasprun</span><span class="p">(</span><span class="s2">"vasprun.xml"</span><span class="p">)</span>
<span class="n">e_per_atom</span> <span class="o">=</span> <span class="n">v</span><span class="o">.</span><span class="n">final_energy</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">v</span><span class="o">.</span><span class="n">final_structure</span><span class="p">)</span>
<span class="n">ediff</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">e_per_atom</span> <span class="o">-</span> <span class="n">energy</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ediff</span> <span class="o"><</span> <span class="n">target</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="sa">f</span><span class="s2">"Converged to </span><span class="si">{</span><span class="n">ediff</span><span class="si">}</span><span class="s2"> eV/atom!"</span><span class="p">)</span>
<span class="k">break</span>
<span class="n">energy</span> <span class="o">=</span> <span class="n">e_per_atom</span>
<span class="n">settings</span> <span class="o">=</span> <span class="p">[</span>
<span class="p">{</span><span class="s2">"dict"</span><span class="p">:</span> <span class="s2">"INCAR"</span><span class="p">,</span> <span class="s2">"action"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"_set"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"ISTART"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}}},</span>
<span class="p">{</span><span class="s2">"dict"</span><span class="p">:</span> <span class="s2">"KPOINTS"</span><span class="p">,</span> <span class="s2">"action"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"_set"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"kpoints"</span><span class="p">:</span> <span class="p">[</span><span class="n">m</span><span class="p">]}}},</span>
<span class="p">{</span>
<span class="s2">"filename"</span><span class="p">:</span> <span class="s2">"CONTCAR"</span><span class="p">,</span>
<span class="s2">"action"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"_file_copy"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"dest"</span><span class="p">:</span> <span class="s2">"POSCAR"</span><span class="p">}},</span>
<span class="p">},</span>
<span class="p">]</span>
<span class="k">yield</span> <span class="n">VaspJob</span><span class="p">(</span>
<span class="n">vasp_command</span><span class="p">,</span>
<span class="n">final</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">backup</span><span class="o">=</span><span class="n">backup</span><span class="p">,</span>
<span class="n">suffix</span><span class="o">=</span><span class="sa">f</span><span class="s2">".kpoints.</span><span class="si">{</span><span class="s1">'x'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">m</span><span class="p">))</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
<span class="n">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">,</span>
<span class="p">)</span></div>
<div class="viewcode-block" id="do_run"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_kpoints.do_run">[docs]</a><span class="k">def</span> <span class="nf">do_run</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Perform the run.</span>
<span class="sd"> """</span>
<span class="n">handlers</span> <span class="o">=</span> <span class="p">[</span><span class="n">VaspErrorHandler</span><span class="p">(),</span> <span class="n">UnconvergedErrorHandler</span><span class="p">()]</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">Custodian</span><span class="p">(</span>
<span class="n">handlers</span><span class="p">,</span>
<span class="n">get_runs</span><span class="p">(</span>
<span class="n">vasp_command</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="o">.</span><span class="n">split</span><span class="p">(),</span>
<span class="n">target</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
<span class="n">mode</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">mode</span><span class="p">,</span>
<span class="n">max_steps</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">max_steps</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">max_errors</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
<div class="viewcode-block" id="main"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_kpoints.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
<span class="sd">"""</span>
<span class="sd"> Main method</span>
<span class="sd"> """</span>
<span class="kn">import</span> <span class="nn">argparse</span>
<span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span>
<span class="n">description</span><span class="o">=</span><span class="s2">"""</span>
<span class="s2"> converge_kpoints perform a KPOINTS convergence. What this script will do</span>
<span class="s2"> is to run a particular VASP run with increasing multiples of the initial</span>
<span class="s2"> KPOINT grid until a target convergence in energy per atom is reached.</span>
<span class="s2"> For example, let's say you have vasp input files that has a k-point grid</span>
<span class="s2"> of 1x1x1. This script will perform sequence jobs with k-point grids of</span>
<span class="s2"> 1x1x1, 2x2x2, 3x3x3, 4x4x4, ... until convergence is achieved. The</span>
<span class="s2"> default convergence criteria is 1meV/atom, but this can be set using the</span>
<span class="s2"> --target option.</span>
<span class="s2"> """</span><span class="p">,</span>
<span class="n">epilog</span><span class="o">=</span><span class="s2">"""Author: Shyue Ping Ong"""</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
<span class="s2">"-c"</span><span class="p">,</span>
<span class="s2">"--command"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"command"</span><span class="p">,</span>
<span class="n">nargs</span><span class="o">=</span><span class="s2">"?"</span><span class="p">,</span>
<span class="n">default</span><span class="o">=</span><span class="s2">"pvasp"</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"VASP command. Defaults to pvasp. If you are using mpirun, "</span> <span class="s1">'set this to something like "mpirun pvasp".'</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
<span class="s2">"-i"</span><span class="p">,</span>
<span class="s2">"--increment_mode"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"mode"</span><span class="p">,</span>
<span class="n">nargs</span><span class="o">=</span><span class="s2">"?"</span><span class="p">,</span>
<span class="n">default</span><span class="o">=</span><span class="s2">"linear"</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
<span class="n">choices</span><span class="o">=</span><span class="p">[</span><span class="s2">"linear"</span><span class="p">,</span> <span class="s2">"inc"</span><span class="p">],</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"Mode for increasing kpoints. In linear mode, multiples of "</span>
<span class="s2">"the existing kpoints are done. E.g., 2x4x2 -> 4x8x4 -> 6x12x6. "</span>
<span class="s2">"In inc mode, all KPOINTS are incremented by 1 at each stage, "</span>
<span class="s2">"i.e., 2x4x2 -> 3x5x3 ->4x6x4. Note that the latter mode does "</span>
<span class="s2">"not preserve KPOINTS symmetry, though it is probably less "</span>
<span class="s2">"expensive."</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
<span class="s2">"-m"</span><span class="p">,</span>
<span class="s2">"--max_steps"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"max_steps"</span><span class="p">,</span>
<span class="n">nargs</span><span class="o">=</span><span class="s2">"?"</span><span class="p">,</span>
<span class="n">default</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"The maximum number of KPOINTS increment steps. This puts an "</span>
<span class="s2">"upper bound on the largest KPOINT converge grid attempted."</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
<span class="s2">"-t"</span><span class="p">,</span>
<span class="s2">"--target"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"target"</span><span class="p">,</span>
<span class="n">nargs</span><span class="o">=</span><span class="s2">"?"</span><span class="p">,</span>
<span class="n">default</span><span class="o">=</span><span class="mf">0.001</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"The target converge in energy per atom to achieve "</span>
<span class="s2">"convergence. E.g., 1e-3 means the KPOINTS will be increased "</span>
<span class="s2">"until a converged of 1meV is reached."</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
<span class="n">do_run</span><span class="p">(</span><span class="n">args</span><span class="p">)</span></div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
<span class="n">main</span><span class="p">()</span>
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