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using horton do esp charge analysis
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<p>In order to do esp charge analysis, I generate charge density cube file and electric potential cube file from cp2k (with GPW method, GAPW method has a problem generate charge density cube file). I post here the steps I use horton and these cube files to do esp charge analysis (follow this <a href="http://theochem.github.io/horton/tut_espfit.html">link</a> ).</p>
<p>Here is how I use it on killdevil.</p>
<div class="highlight"><pre><span></span><code><span class="n">module</span> <span class="nb">load</span> <span class="n">anaconda</span>
<span class="n">source</span> <span class="n">activate</span> <span class="n">my_root</span>
</code></pre></div>
<p>Here is the input file for cp2k.</p>
<div class="highlight"><pre><span></span><code><span class="nv">@SET</span><span class="w"> </span><span class="n">RTYPE</span><span class="w"> </span><span class="n">MD</span><span class="w"></span>
<span class="nv">@SET</span><span class="w"> </span><span class="n">RESTART</span><span class="w"> </span><span class="k">ON</span><span class="w"></span>
<span class="nv">@SET</span><span class="w"> </span><span class="n">RESTARTFILE</span><span class="w"> </span><span class="n">H2O64NaCl</span><span class="o">-</span><span class="mi">1</span><span class="n">_500</span><span class="p">.</span><span class="n">restart</span><span class="w"></span>
<span class="nv">@SET</span><span class="w"> </span><span class="n">MD_ENS</span><span class="w"> </span><span class="n">NVT</span><span class="w"></span>
<span class="o">&</span><span class="n">FORCE_EVAL</span><span class="w"></span>
<span class="w"> </span><span class="k">METHOD</span><span class="w"> </span><span class="n">QS</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">PROPERTIES</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="n">RESP</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">STRIDE</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">RESP</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">FIT_CHARGE</span><span class="w"></span>
<span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_fit_charge</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">FIT_CHARGE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">PROPERTIES</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">DFT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">DENSITY_FITTING</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">DENSITY_FITTING</span><span class="w"></span>
<span class="w"> </span><span class="n">BASIS_SET_FILE_NAME</span><span class="w"> </span><span class="p">..</span><span class="o">/</span><span class="p">..</span><span class="o">/</span><span class="p">..</span><span class="o">/</span><span class="n">cp2k</span><span class="o">-</span><span class="n">files</span><span class="o">/</span><span class="n">BASIS_MOLOPT</span><span class="w"></span>
<span class="w"> </span><span class="n">POTENTIAL_FILE_NAME</span><span class="w"> </span><span class="p">..</span><span class="o">/</span><span class="p">..</span><span class="o">/</span><span class="p">..</span><span class="o">/</span><span class="n">cp2k</span><span class="o">-</span><span class="n">files</span><span class="o">/</span><span class="n">GTH_POTENTIALS</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">MGRID</span><span class="w"></span>
<span class="w"> </span><span class="n">NGRIDS</span><span class="w"> </span><span class="mi">5</span><span class="w"></span>
<span class="w"> </span><span class="n">CUTOFF</span><span class="w"> </span><span class="mi">280</span><span class="w"></span>
<span class="w"> </span><span class="n">REL_CUTOFF</span><span class="w"> </span><span class="mi">40</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">MGRID</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">SCF</span><span class="w"></span>
<span class="w"> </span><span class="nv">@IF</span><span class="w"> </span><span class="p">(</span><span class="w"> </span><span class="err">${</span><span class="n">RESTART</span><span class="err">}</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="k">OFF</span><span class="w"> </span><span class="p">)</span><span class="w"></span>
<span class="w"> </span><span class="n">SCF_GUESS</span><span class="w"> </span><span class="k">ATOMIC</span><span class="w"></span>
<span class="w"> </span><span class="nv">@ENDIF</span><span class="w"></span>
<span class="w"> </span><span class="nv">@IF</span><span class="w"> </span><span class="p">(</span><span class="w"> </span><span class="err">${</span><span class="n">RESTART</span><span class="err">}</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="k">ON</span><span class="w"> </span><span class="p">)</span><span class="w"></span>
<span class="w"> </span><span class="n">SCF_GUESS</span><span class="w"> </span><span class="n">RESTART</span><span class="w"></span>
<span class="w"> </span><span class="nv">@ENDIF</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">OT</span><span class="w"> </span><span class="k">ON</span><span class="w"></span>
<span class="w"> </span><span class="n">MINIMIZER</span><span class="w"> </span><span class="n">DIIS</span><span class="w"></span>
<span class="w"> </span><span class="n">ENERGY_GAP</span><span class="w"> </span><span class="mf">0.001</span><span class="w"></span>
<span class="w"> </span><span class="n">PRECONDITIONER</span><span class="w"> </span><span class="n">FULL_ALL</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">OT</span><span class="w"></span>
<span class="w"> </span><span class="n">EPS_SCF</span><span class="w"> </span><span class="mf">1.0E-6</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">RESTART</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">SCF</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">QS</span><span class="w"></span>
<span class="w"> </span><span class="n">EXTRAPOLATION</span><span class="w"> </span><span class="n">PS</span><span class="w"></span>
<span class="w"> </span><span class="n">EXTRAPOLATION_ORDER</span><span class="w"> </span><span class="mi">3</span><span class="w"></span>
<span class="w"> </span><span class="k">METHOD</span><span class="w"> </span><span class="n">GPW</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">QS</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">XC</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">XC_FUNCTIONAL</span><span class="w"> </span><span class="n">BLYP</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">XC_FUNCTIONAL</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">XC_GRID</span><span class="w"></span>
<span class="w"> </span><span class="n">XC_SMOOTH_RHO</span><span class="w"> </span><span class="n">NN50</span><span class="w"></span>
<span class="w"> </span><span class="n">XC_DERIV</span><span class="w"> </span><span class="n">NN50_SMOOTH</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="n">vdW_POTENTIAL</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">POTENTIAL_TYPE</span><span class="w"> </span><span class="n">PAIR_POTENTIAL</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">PAIR_POTENTIAL</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">TYPE</span><span class="w"> </span><span class="n">DFTD3</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">PARAMETER_FILE_NAME</span><span class="w"> </span><span class="p">..</span><span class="o">/</span><span class="p">..</span><span class="o">/</span><span class="n">cp2k</span><span class="o">-</span><span class="n">files</span><span class="o">/</span><span class="n">dftd3</span><span class="p">.</span><span class="n">dat</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">REFERENCE_FUNCTIONAL</span><span class="w"> </span><span class="n">revPBE</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">PAIR_POTENTIAL</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">vdW_POTENTIAL</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">XC</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">E_DENSITY_CUBE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">STRIDE</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">E_DENSITY_CUBE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">V_HARTREE_CUBE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">STRIDE</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">V_HARTREE_CUBE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">MULLIKEN</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_mulliken</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">MULLIKEN</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">LOWDIN</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_lowdin</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">LOWDIN</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="n">HIRSCHFELD</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="n">#FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_hirschfeld</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">HIRSCHFELD</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="n">LOCALIZE</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="k">METHOD</span><span class="w"> </span><span class="n">JACOBI</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">#MAX_CRAZY_ANGLE</span><span class="w"> </span><span class="mf">1.0</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MAX_ITER</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">#EPS_LOCALIZATION</span><span class="w"> </span><span class="mf">1E-8</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">#MAX_CRAZY_ANGLE</span><span class="w"> </span><span class="mf">0.05</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">WANNIER_CENTERS</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_wannier_centers</span><span class="p">.</span><span class="n">xyz</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">IONS</span><span class="o">+</span><span class="n">CENTERS</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">WANNIER_CENTERS</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">WANNIER_SPREADS</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">100</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_wannier_spread</span><span class="p">.</span><span class="k">data</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">WANNIER_SPREADS</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">USE_HISTORY</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">LOCALIZE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">DFT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">SUBSYS</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">CELL</span><span class="w"></span>
<span class="w"> </span><span class="n">ABC</span><span class="w"> </span><span class="mf">12.4934</span><span class="w"> </span><span class="mf">12.4934</span><span class="w"> </span><span class="mf">12.4934</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">CELL</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">TOPOLOGY</span><span class="w"></span>
<span class="w"> </span><span class="n">COORD_FILE_NAME</span><span class="w"> </span><span class="n">H2O64NaCl</span><span class="p">.</span><span class="n">xyz</span><span class="w"></span>
<span class="w"> </span><span class="n">COORD_FILE_FORMAT</span><span class="w"> </span><span class="n">xyz</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">TOPOLOGY</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">COLVAR</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">DISTANCE</span><span class="w"></span>
<span class="w"> </span><span class="n">ATOMS</span><span class="w"> </span><span class="mi">193</span><span class="w"> </span><span class="mi">194</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">DISTANCE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">COLVAR</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">KIND</span><span class="w"> </span><span class="n">H</span><span class="w"></span>
<span class="w"> </span><span class="n">BASIS_SET</span><span class="w"> </span><span class="n">DZVP</span><span class="o">-</span><span class="n">MOLOPT</span><span class="o">-</span><span class="n">SR</span><span class="o">-</span><span class="n">GTH</span><span class="o">-</span><span class="n">q1</span><span class="w"></span>
<span class="w"> </span><span class="n">POTENTIAL</span><span class="w"> </span><span class="n">GTH</span><span class="o">-</span><span class="n">BLYP</span><span class="o">-</span><span class="n">q1</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">KIND</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">KIND</span><span class="w"> </span><span class="n">O</span><span class="w"></span>
<span class="w"> </span><span class="n">BASIS_SET</span><span class="w"> </span><span class="n">DZVP</span><span class="o">-</span><span class="n">MOLOPT</span><span class="o">-</span><span class="n">SR</span><span class="o">-</span><span class="n">GTH</span><span class="o">-</span><span class="n">q6</span><span class="w"></span>
<span class="w"> </span><span class="n">POTENTIAL</span><span class="w"> </span><span class="n">GTH</span><span class="o">-</span><span class="n">BLYP</span><span class="o">-</span><span class="n">q6</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">KIND</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">KIND</span><span class="w"> </span><span class="n">Na</span><span class="w"></span>
<span class="w"> </span><span class="n">BASIS_SET</span><span class="w"> </span><span class="n">DZVP</span><span class="o">-</span><span class="n">MOLOPT</span><span class="o">-</span><span class="n">SR</span><span class="o">-</span><span class="n">GTH</span><span class="o">-</span><span class="n">q9</span><span class="w"></span>
<span class="w"> </span><span class="n">POTENTIAL</span><span class="w"> </span><span class="n">GTH</span><span class="o">-</span><span class="n">BLYP</span><span class="o">-</span><span class="n">q9</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">KIND</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">KIND</span><span class="w"> </span><span class="n">Cl</span><span class="w"></span>
<span class="w"> </span><span class="n">BASIS_SET</span><span class="w"> </span><span class="n">DZVP</span><span class="o">-</span><span class="n">MOLOPT</span><span class="o">-</span><span class="n">SR</span><span class="o">-</span><span class="n">GTH</span><span class="o">-</span><span class="n">q7</span><span class="w"></span>
<span class="w"> </span><span class="n">POTENTIAL</span><span class="w"> </span><span class="n">GTH</span><span class="o">-</span><span class="n">BLYP</span><span class="o">-</span><span class="n">q7</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">KIND</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">SUBSYS</span><span class="w"></span>
<span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">FORCE_EVAL</span><span class="w"></span>
<span class="o">&</span><span class="k">GLOBAL</span><span class="w"></span>
<span class="w"> </span><span class="n">PROJECT_NAME</span><span class="w"> </span><span class="n">H2O64NaCl</span><span class="w"></span>
<span class="w"> </span><span class="n">RUN_TYPE</span><span class="w"> </span><span class="n">MD</span><span class="w"></span>
<span class="w"> </span><span class="n">PRINT_LEVEL</span><span class="w"> </span><span class="n">LOW</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">TIMINGS</span><span class="w"></span>
<span class="w"> </span><span class="n">THRESHOLD</span><span class="w"> </span><span class="mf">0.000001</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"></span>
<span class="w"> </span><span class="n">#WALLTIME</span><span class="w"> </span><span class="mi">172500</span><span class="w"></span>
<span class="w"> </span><span class="n">#WALLTIME</span><span class="w"> </span><span class="mi">345000</span><span class="w"></span>
<span class="w"> </span><span class="n">WALLTIME</span><span class="w"> </span><span class="mi">1750</span><span class="w"></span>
<span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">GLOBAL</span><span class="w"></span>
<span class="o">&</span><span class="n">MOTION</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">CONSTRAINT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">COLLECTIVE</span><span class="w"></span>
<span class="w"> </span><span class="n">COLVAR</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="n">INTERMOLECULAR</span><span class="w"></span>
<span class="w"> </span><span class="n">TARGET</span><span class="w"> </span><span class="o">[</span><span class="n">angstrom</span><span class="o">]</span><span class="w"> </span><span class="mf">2.2</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">COLLECTIVE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">LAGRANGE_MULTIPLIERS</span><span class="w"></span>
<span class="w"> </span><span class="n">COMMON_ITERATION_LEVELS</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">CONSTRAINT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">MD</span><span class="w"></span>
<span class="w"> </span><span class="nv">@IF</span><span class="w"> </span><span class="p">(</span><span class="w"> </span><span class="err">${</span><span class="n">MD_ENS</span><span class="err">}</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">NVE</span><span class="w"> </span><span class="p">)</span><span class="w"></span>
<span class="w"> </span><span class="n">ENSEMBLE</span><span class="w"> </span><span class="n">NVE</span><span class="w"></span>
<span class="w"> </span><span class="nv">@ENDIF</span><span class="w"></span>
<span class="w"> </span><span class="nv">@IF</span><span class="w"> </span><span class="p">(</span><span class="w"> </span><span class="err">${</span><span class="n">MD_ENS</span><span class="err">}</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">NVT</span><span class="w"> </span><span class="p">)</span><span class="w"></span>
<span class="w"> </span><span class="n">ENSEMBLE</span><span class="w"> </span><span class="n">NVT</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">THERMOSTAT</span><span class="w"></span>
<span class="w"> </span><span class="n">REGION</span><span class="w"> </span><span class="k">GLOBAL</span><span class="w"></span>
<span class="w"> </span><span class="n">TYPE</span><span class="w"> </span><span class="n">NOSE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="n">NOSE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">NOSE</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">THERMOSTAT</span><span class="w"></span>
<span class="w"> </span><span class="nv">@ENDIF</span><span class="w"></span>
<span class="w"> </span><span class="n">STEPS</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="n">TIMESTEP</span><span class="w"> </span><span class="mf">0.5</span><span class="w"></span>
<span class="w"> </span><span class="n">TEMPERATURE</span><span class="w"> </span><span class="mf">298.0</span><span class="w"></span>
<span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">MD</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="k">PRINT</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">TRAJECTORY</span><span class="w"> </span><span class="n">SILENT</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT</span><span class="p">.</span><span class="n">xyz</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">TRAJECTORY</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">RESTART</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">ADD_LAST</span><span class="w"> </span><span class="nc">NUMERIC</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">RESTART</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">VELOCITIES</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_vel</span><span class="p">.</span><span class="n">xyz</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">VELOCITIES</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="n">FORCES</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="mi">1</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">EACH</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="n">FILENAME</span><span class="w"> </span><span class="o">=</span><span class="n">NaCl_NVT_frc</span><span class="p">.</span><span class="n">xyz</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="w"> </span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">FORCES</span><span class="w"></span>
<span class="w"> </span><span class="err">#</span><span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="k">PRINT</span><span class="w"></span>
<span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">MOTION</span><span class="w"></span>
<span class="o">&</span><span class="n">EXT_RESTART</span><span class="w"> </span><span class="k">ON</span><span class="w"></span>
<span class="w"> </span><span class="n">RESTART_DEFAULT</span><span class="w"> </span><span class="n">F</span><span class="w"></span>
<span class="w"> </span><span class="n">RESTART_FILE_NAME</span><span class="w"> </span><span class="err">${</span><span class="n">RESTARTFILE</span><span class="err">}</span><span class="w"></span>
<span class="w"> </span><span class="n">RESTART_POS</span><span class="w"> </span><span class="n">T</span><span class="w"></span>
<span class="w"> </span><span class="n">RESTART_COUNTERS</span><span class="w"> </span><span class="n">F</span><span class="w"></span>
<span class="w"> </span><span class="nv">@IF</span><span class="w"> </span><span class="p">(</span><span class="w"> </span><span class="err">${</span><span class="n">RTYPE</span><span class="err">}</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">MD</span><span class="w"> </span><span class="p">)</span><span class="w"></span>
<span class="w"> </span><span class="n">RESTART_VEL</span><span class="w"> </span><span class="n">T</span><span class="w"></span>
<span class="w"> </span><span class="nv">@ENDIF</span><span class="w"></span>
<span class="w"> </span><span class="nv">@IF</span><span class="w"> </span><span class="p">(</span><span class="w"> </span><span class="err">${</span><span class="n">MD_ENS</span><span class="err">}</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">NVT</span><span class="w"> </span><span class="p">)</span><span class="w"></span>
<span class="w"> </span><span class="n">RESTART_THERMOSTAT</span><span class="w"> </span><span class="n">T</span><span class="w"></span>
<span class="w"> </span><span class="nv">@ENDIF</span><span class="w"></span>
<span class="o">&</span><span class="k">END</span><span class="w"> </span><span class="n">EXT_RESTART</span><span class="w"></span>
</code></pre></div>
<p>The cube files I have are H2O64NaCl-ELECTRON_DENSITY-1_0.cube and H2O64NaCl-v_hartree-1_0.cube. </p>
<p>This command is used to generate the cost function.</p>
<div class="highlight"><pre><span></span><code>horton-esp-cost.py H2O64NaCl-v_hartree-1_0.cube cost.h5 --wdens=H2O64NaCl-ELECTRON_DENSITY-1_0.cube -s --wnear 8:2.0:2.0 1:2.0:2.0 11:2.0:2.0 17:2.0:2.0 --pbc=111 > esp-cost-out
</code></pre></div>
<p>It took me 6 hours to generate the cost function. After that, charges are fitted to the esp by this command.</p>
<div class="highlight"><pre><span></span><code>horton-esp-fit.py cost.h5 charges.h5
</code></pre></div>
<p>Transfer it to csv file to read.</p>
<div class="highlight"><pre><span></span><code>horton-hdf2csv.py charges.h5 charges.csv
</code></pre></div>
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