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<h1>Source code for custodian.cli.run_vasp</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 perform various combinations of VASP</span>
<span class="sd">runs.</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.inputs</span> <span class="kn">import</span> <span class="n">Incar</span><span class="p">,</span> <span class="n">Kpoints</span><span class="p">,</span> <span class="n">VaspInput</span>
<span class="kn">from</span> <span class="nn">ruamel</span> <span class="kn">import</span> <span class="n">yaml</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.jobs</span> <span class="kn">import</span> <span class="n">VaspJob</span>
<div class="viewcode-block" id="load_class"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.run_vasp.load_class">[docs]</a><span class="k">def</span> <span class="nf">load_class</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Load the class from mod and name specification.</span>
<span class="sd"> """</span>
<span class="n">toks</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"?"</span><span class="p">)</span>
<span class="n">params</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">toks</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">toks</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">","</span><span class="p">):</span>
<span class="n">ptoks</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"="</span><span class="p">)</span>
<span class="n">params</span><span class="p">[</span><span class="n">ptoks</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">ptoks</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">toks</span><span class="p">)</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Bad handler specification"</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="nb">globals</span><span class="p">(),</span> <span class="nb">locals</span><span class="p">(),</span> <span class="p">[</span><span class="n">toks</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="mi">0</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="n">toks</span><span class="p">[</span><span class="mi">0</span><span class="p">])(</span><span class="o">**</span><span class="n">params</span><span class="p">)</span></div>
<div class="viewcode-block" id="get_jobs"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.run_vasp.get_jobs">[docs]</a><span class="k">def</span> <span class="nf">get_jobs</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Returns a generator of jobs. Allows of "infinite" jobs.</span>
<span class="sd"> """</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="c1"># save initial INCAR for rampU runs</span>
<span class="n">n_ramp_u</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">jobs</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s2">"rampU"</span><span class="p">)</span>
<span class="n">ramps</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="n">n_ramp_u</span><span class="p">:</span>
<span class="n">incar</span> <span class="o">=</span> <span class="n">Incar</span><span class="o">.</span><span class="n">from_file</span><span class="p">(</span><span class="s2">"INCAR"</span><span class="p">)</span>
<span class="n">ldauu</span> <span class="o">=</span> <span class="n">incar</span><span class="p">[</span><span class="s2">"LDAUU"</span><span class="p">]</span>
<span class="n">ldauj</span> <span class="o">=</span> <span class="n">incar</span><span class="p">[</span><span class="s2">"LDAUJ"</span><span class="p">]</span>
<span class="n">njobs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">jobs</span><span class="p">)</span>
<span class="n">post_settings</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># append to this list to have settings applied on next job</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">job</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">jobs</span><span class="p">):</span>
<span class="n">final</span> <span class="o">=</span> <span class="n">i</span> <span class="o">==</span> <span class="n">njobs</span> <span class="o">-</span> <span class="mi">1</span>
<span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">job</span><span class="p">):</span>
<span class="n">suffix</span> <span class="o">=</span> <span class="s2">"."</span> <span class="o">+</span> <span class="n">job</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">suffix</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">".</span><span class="si">{</span><span class="n">job</span><span class="si">}{</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="si">}</span><span class="s2">"</span>
<span class="n">settings</span> <span class="o">=</span> <span class="n">post_settings</span>
<span class="n">post_settings</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">backup</span> <span class="o">=</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span>
<span class="n">copy_magmom</span> <span class="o">=</span> <span class="kc">False</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="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="n">append</span><span class="p">({</span><span class="s2">"file"</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="n">job_type</span> <span class="o">=</span> <span class="n">job</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="n">auto_npar</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">no_auto_npar</span><span class="p">:</span>
<span class="n">auto_npar</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">if</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"static_derived"</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.sets</span> <span class="kn">import</span> <span class="n">MPStaticSet</span>
<span class="n">vis</span> <span class="o">=</span> <span class="n">MPStaticSet</span><span class="o">.</span><span class="n">from_prev_calc</span><span class="p">(</span>
<span class="s2">"."</span><span class="p">,</span>
<span class="n">user_incar_settings</span><span class="o">=</span><span class="p">{</span><span class="s2">"LWAVE"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="s2">"EDIFF"</span><span class="p">:</span> <span class="mf">1e-6</span><span class="p">},</span>
<span class="n">ediff_per_atom</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">settings</span><span class="o">.</span><span class="n">extend</span><span class="p">(</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="nb">dict</span><span class="p">(</span><span class="n">vis</span><span class="o">.</span><span class="n">incar</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="n">vis</span><span class="o">.</span><span class="n">kpoints</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()}},</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"static_dielectric_derived"</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.sets</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">MPStaticDielectricDFPTVaspInputSet</span><span class="p">,</span>
<span class="n">MPStaticSet</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># vis = MPStaticSet.from_prev_calc(</span>
<span class="c1"># ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8,</span>
<span class="c1"># "LEPSILON": True, 'LREAL':False,</span>
<span class="c1"># "LPEAD": True, "ISMEAR": 0,</span>
<span class="c1"># "SIGMA": 0.01},</span>
<span class="c1"># ediff_per_atom=False)</span>
<span class="n">vis</span> <span class="o">=</span> <span class="n">MPStaticDielectricDFPTVaspInputSet</span><span class="p">()</span>
<span class="n">incar</span> <span class="o">=</span> <span class="n">vis</span><span class="o">.</span><span class="n">get_incar</span><span class="p">(</span><span class="n">vinput</span><span class="p">[</span><span class="s2">"POSCAR"</span><span class="p">]</span><span class="o">.</span><span class="n">structure</span><span class="p">)</span>
<span class="n">unset</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"NPAR"</span><span class="p">,</span> <span class="s2">"KPOINT_BSE"</span><span class="p">,</span> <span class="s2">"LAECHG"</span><span class="p">,</span> <span class="s2">"LCHARG"</span><span class="p">,</span> <span class="s2">"LVHAR"</span><span class="p">,</span> <span class="s2">"NSW"</span><span class="p">]:</span>
<span class="n">incar</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">vinput</span><span class="p">[</span><span class="s2">"INCAR"</span><span class="p">]:</span>
<span class="n">unset</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">kpoints</span> <span class="o">=</span> <span class="n">vis</span><span class="o">.</span><span class="n">get_kpoints</span><span class="p">(</span><span class="n">vinput</span><span class="p">[</span><span class="s2">"POSCAR"</span><span class="p">]</span><span class="o">.</span><span class="n">structure</span><span class="p">)</span>
<span class="n">settings</span><span class="o">.</span><span class="n">extend</span><span class="p">(</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="nb">dict</span><span class="p">(</span><span class="n">incar</span><span class="p">),</span> <span class="s2">"_unset"</span><span class="p">:</span> <span class="n">unset</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="n">kpoints</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()}},</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="n">auto_npar</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"static"</span><span class="p">):</span>
<span class="n">m</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="o">*</span> <span class="n">args</span><span class="o">.</span><span class="n">static_kpoint</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</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="n">settings</span><span class="o">.</span><span class="n">extend</span><span class="p">(</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">"NSW"</span><span class="p">:</span> <span class="mi">0</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="p">)</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"nonscf_derived"</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.sets</span> <span class="kn">import</span> <span class="n">MPNonSCFSet</span>
<span class="n">vis</span> <span class="o">=</span> <span class="n">MPNonSCFSet</span><span class="o">.</span><span class="n">from_prev_calc</span><span class="p">(</span><span class="s2">"."</span><span class="p">,</span> <span class="n">copy_chgcar</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">user_incar_settings</span><span class="o">=</span><span class="p">{</span><span class="s2">"LWAVE"</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
<span class="n">settings</span><span class="o">.</span><span class="n">extend</span><span class="p">(</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="nb">dict</span><span class="p">(</span><span class="n">vis</span><span class="o">.</span><span class="n">incar</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="n">vis</span><span class="o">.</span><span class="n">kpoints</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()}},</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"optics_derived"</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp.sets</span> <span class="kn">import</span> <span class="n">MPNonSCFSet</span>
<span class="n">vis</span> <span class="o">=</span> <span class="n">MPNonSCFSet</span><span class="o">.</span><span class="n">from_prev_calc</span><span class="p">(</span>
<span class="s2">"."</span><span class="p">,</span>
<span class="n">optics</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">copy_chgcar</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">nedos</span><span class="o">=</span><span class="mi">2001</span><span class="p">,</span>
<span class="n">mode</span><span class="o">=</span><span class="s2">"uniform"</span><span class="p">,</span>
<span class="n">nbands_factor</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
<span class="n">user_incar_settings</span><span class="o">=</span><span class="p">{</span>
<span class="s2">"LWAVE"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
<span class="s2">"ALGO"</span><span class="p">:</span> <span class="s2">"Exact"</span><span class="p">,</span>
<span class="s2">"SIGMA"</span><span class="p">:</span> <span class="mf">0.01</span><span class="p">,</span>
<span class="s2">"EDIFF"</span><span class="p">:</span> <span class="mf">1e-6</span><span class="p">,</span>
<span class="p">},</span>
<span class="n">ediff_per_atom</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">settings</span><span class="o">.</span><span class="n">extend</span><span class="p">(</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="nb">dict</span><span class="p">(</span><span class="n">vis</span><span class="o">.</span><span class="n">incar</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="n">vis</span><span class="o">.</span><span class="n">kpoints</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()}},</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"rampu"</span><span class="p">):</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">ramps</span> <span class="o">/</span> <span class="p">(</span><span class="n">n_ramp_u</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">settings</span><span class="o">.</span><span class="n">append</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">"LDAUJ"</span><span class="p">:</span> <span class="p">[</span><span class="n">j</span> <span class="o">*</span> <span class="n">f</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">ldauj</span><span class="p">],</span>
<span class="s2">"LDAUU"</span><span class="p">:</span> <span class="p">[</span><span class="n">u</span> <span class="o">*</span> <span class="n">f</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">ldauu</span><span class="p">],</span>
<span class="p">}</span>
<span class="p">},</span>
<span class="p">}</span>
<span class="p">)</span>
<span class="n">copy_magmom</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">ramps</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"quick_relax"</span><span class="p">)</span> <span class="ow">or</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"quickrelax"</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="n">incar</span> <span class="o">=</span> <span class="n">vinput</span><span class="p">[</span><span class="s2">"INCAR"</span><span class="p">]</span>
<span class="n">structure</span> <span class="o">=</span> <span class="n">vinput</span><span class="p">[</span><span class="s2">"POSCAR"</span><span class="p">]</span><span class="o">.</span><span class="n">structure</span>
<span class="k">if</span> <span class="s2">"ISMEAR"</span> <span class="ow">in</span> <span class="n">incar</span><span class="p">:</span>
<span class="n">post_settings</span><span class="o">.</span><span class="n">append</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">"ISMEAR"</span><span class="p">:</span> <span class="n">incar</span><span class="p">[</span><span class="s2">"ISMEAR"</span><span class="p">]}}})</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">post_settings</span><span class="o">.</span><span class="n">append</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">"_unset"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"ISMEAR"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}}})</span>
<span class="n">post_settings</span><span class="o">.</span><span class="n">append</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="n">kpoints</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()}})</span>
<span class="c1"># lattice vectors with length < 9 will get >1 KPOINT</span>
<span class="n">low_kpoints</span> <span class="o">=</span> <span class="n">Kpoints</span><span class="o">.</span><span class="n">gamma_automatic</span><span class="p">([</span><span class="nb">max</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="mi">18</span> <span class="o">/</span> <span class="n">l</span><span class="p">),</span> <span class="mi">1</span><span class="p">)</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">structure</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">abc</span><span class="p">])</span>
<span class="n">settings</span><span class="o">.</span><span class="n">extend</span><span class="p">(</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">"ISMEAR"</span><span class="p">:</span> <span class="mi">0</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="n">low_kpoints</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()}},</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="c1"># let vasp determine encut (will be lower than</span>
<span class="c1"># needed for compatibility with other runs)</span>
<span class="k">if</span> <span class="s2">"ENCUT"</span> <span class="ow">in</span> <span class="n">incar</span><span class="p">:</span>
<span class="n">post_settings</span><span class="o">.</span><span class="n">append</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">"ENCUT"</span><span class="p">:</span> <span class="n">incar</span><span class="p">[</span><span class="s2">"ENCUT"</span><span class="p">]}}})</span>
<span class="n">settings</span><span class="o">.</span><span class="n">append</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">"_unset"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"ENCUT"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}}})</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"relax"</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">elif</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"full_relax"</span><span class="p">):</span>
<span class="k">yield from</span> <span class="n">VaspJob</span><span class="o">.</span><span class="n">full_opt_run</span><span class="p">(</span><span class="n">vasp_command</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Unsupported job type: </span><span class="si">{</span><span class="n">job</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">job_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"full_relax"</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="n">final</span><span class="p">,</span>
<span class="n">suffix</span><span class="o">=</span><span class="n">suffix</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">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">,</span>
<span class="n">copy_magmom</span><span class="o">=</span><span class="n">copy_magmom</span><span class="p">,</span>
<span class="n">auto_npar</span><span class="o">=</span><span class="n">auto_npar</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.run_vasp.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"> Do the run.</span>
<span class="sd"> """</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>
<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">"Handlers used are </span><span class="si">{</span><span class="n">args</span><span class="o">.</span><span class="n">handlers</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
<span class="n">handlers</span> <span class="o">=</span> <span class="p">[</span><span class="n">load_class</span><span class="p">(</span><span class="s2">"custodian.vasp.handlers"</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">args</span><span class="o">.</span><span class="n">handlers</span><span class="p">]</span>
<span class="n">validators</span> <span class="o">=</span> <span class="p">[</span><span class="n">load_class</span><span class="p">(</span><span class="s2">"custodian.vasp.validators"</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">args</span><span class="o">.</span><span class="n">validators</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_jobs</span><span class="p">(</span><span class="n">args</span><span class="p">),</span>
<span class="n">validators</span><span class="p">,</span>
<span class="n">max_errors</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">max_errors</span><span class="p">,</span>
<span class="n">scratch_dir</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">scratch</span><span class="p">,</span>
<span class="n">gzipped_output</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">gzip</span><span class="p">,</span>
<span class="n">checkpoint</span><span class="o">=</span><span class="kc">True</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.run_vasp.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">"run_vasp is a master script to perform various kinds of VASP runs."</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">"--no_auto_npar"</span><span class="p">,</span>
<span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"Set to true to turn off auto_npar. Useful for certain machines "</span>
<span class="s2">"and calculations where you want absolute control."</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">"-z"</span><span class="p">,</span>
<span class="s2">"--gzip"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"gzip"</span><span class="p">,</span>
<span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"Add this option to gzip the final output. Do not gzip if you "</span>
<span class="s2">"are going to perform an additional static run."</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">"-s"</span><span class="p">,</span>
<span class="s2">"--scratch"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"scratch"</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="kc">None</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">"Scratch directory to perform run in. Specify the root scratch "</span>
<span class="s2">"directory as the code will automatically create a temporary "</span>
<span class="s2">"subdirectory to run the job."</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">"-ks"</span><span class="p">,</span>
<span class="s2">"--kpoint-static"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"static_kpoint"</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">1</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 multiplier to use for the KPOINTS of a static run (if "</span>
<span class="s2">"any). For example, setting this to 2 means that if your "</span>
<span class="s2">"original run was done using a k-point grid of 2x3x3, "</span>
<span class="s2">"the static run will be done with a k-point grid of 4x6x6. This "</span>
<span class="s2">"defaults to 1, i.e., static runs are performed with the same "</span>
<span class="s2">"k-point grid as relaxation runs."</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">"-me"</span><span class="p">,</span>
<span class="s2">"--max-errors"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"max_errors"</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">"Maximum number of errors to allow before quitting"</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">"-hd"</span><span class="p">,</span>
<span class="s2">"--handlers"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"handlers"</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="p">[</span>
<span class="s2">"VaspErrorHandler"</span><span class="p">,</span>
<span class="s2">"MeshSymmetryErrorHandler"</span><span class="p">,</span>
<span class="s2">"UnconvergedErrorHandler"</span><span class="p">,</span>
<span class="s2">"NonConvergingErrorHandler"</span><span class="p">,</span>
<span class="s2">"PotimErrorHandler"</span><span class="p">,</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">"The ErrorHandlers to use specified as string class names, "</span>
<span class="s2">"with optional arguments specified as a url-like string. For "</span>
<span class="s2">"example, VaspErrorHandler?output_filename=myfile.out specifies a "</span>
<span class="s2">"VaspErrorHandler with output_name set to myfile.out. Multiple "</span>
<span class="s2">"arguments are joined by a comma. E.g., MyHandler?myfile=a,"</span>
<span class="s2">"data=1. The arguments are deserialized using yaml."</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">"-vd"</span><span class="p">,</span>
<span class="s2">"--validators"</span><span class="p">,</span>
<span class="n">dest</span><span class="o">=</span><span class="s2">"validators"</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="p">[</span><span class="s2">"VasprunXMLValidator"</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">"The Validators to use specified as string class names, "</span>
<span class="s2">"with optional arguments specified as a url-like string. For "</span>
<span class="s2">"example, VaspErrorHandler?output_filename=myfile.out specifies a "</span>
<span class="s2">"VaspErrorHandler with output_name set to myfile.out. Multiple "</span>
<span class="s2">"arguments are joined by a comma. E.g., MyHandler?myfile=a,"</span>
<span class="s2">"data=1. The arguments are deserialized using yaml."</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">"jobs"</span><span class="p">,</span>
<span class="n">metavar</span><span class="o">=</span><span class="s2">"jobs"</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">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="p">[</span><span class="s2">"relax"</span><span class="p">,</span> <span class="s2">"relax"</span><span class="p">],</span>
<span class="n">help</span><span class="o">=</span><span class="s2">"Jobs to execute. Only sequences of relax, "</span>
<span class="s2">"quickrelax, static, rampU, full_relax, static_derived, "</span>
<span class="s2">"nonscf_derived, optics_derived are "</span>
<span class="s1">'supported at the moment. For example, "relax relax static" '</span>
<span class="s2">"will run a double relaxation followed by a static "</span>
<span class="s2">"run. By default, suffixes are given sequential numbering,"</span>
<span class="s2">"but this can be overridden by adding a number to the job"</span>
<span class="s2">"type, e.g. relax5 relax6 relax7"</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>
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