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using horton do hirshfeld charge analysis
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<p>In order to do hirshfeld charge analysis, I generate charge density 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 this cube file to do hirshfeld charge analysis (follow this <a href="http://theochem.github.io/horton/tut_part.html#id32">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>First, I need to set up a database for proatoms. I am using cp2k for atom calculation. I need H, O, Na, Cl in my system. So I generate the input files like this.</p>
<p>ppot.inc ( XXX_000_00 XXX stands for element number, GTH-PBE-qX which is the name of the pseudopotential)</p>
<div class="highlight"><pre><span></span><code><span class="mf">001</span><span class="n">_000_00</span> <span class="n">GTH</span><span class="o">-</span><span class="n">PBE</span><span class="o">-</span><span class="n">q0</span>
<span class="mf">008</span><span class="n">_000_00</span> <span class="n">GTH</span><span class="o">-</span><span class="n">PBE</span><span class="o">-</span><span class="n">q6</span>
<span class="mf">011</span><span class="n">_000_00</span> <span class="n">GTH</span><span class="o">-</span><span class="n">PBE</span><span class="o">-</span><span class="n">q9</span>
<span class="mf">017</span><span class="n">_000_00</span> <span class="n">GTH</span><span class="o">-</span><span class="n">PBE</span><span class="o">-</span><span class="n">q7</span>
</code></pre></div>
<p>valence.inc ( NNN_PPP_MM NNN: element number. PPP: atomic population(#electon). MM: spin multiplicity(2S+1) 1s2 2p1: orbital occupations)</p>
<div class="highlight"><pre><span></span><code><span class="mf">001</span><span class="n">_001_02</span> <span class="mf">1</span><span class="n">s1</span>
<span class="mf">001</span><span class="n">_002_01</span> <span class="mf">1</span><span class="n">s2</span>
<span class="mf">008</span><span class="n">_005_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p1</span>
<span class="mf">008</span><span class="n">_006_03</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p2</span>
<span class="mf">008</span><span class="n">_007_04</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p3</span>
<span class="mf">008</span><span class="n">_008_03</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p4</span>
<span class="mf">008</span><span class="n">_009_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p5</span>
<span class="mf">008</span><span class="n">_010_01</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p6</span>
<span class="mf">011</span><span class="n">_005_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p1</span>
<span class="mf">011</span><span class="n">_006_03</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p2</span>
<span class="mf">011</span><span class="n">_007_04</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p3</span>
<span class="mf">011</span><span class="n">_008_03</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p4</span>
<span class="mf">011</span><span class="n">_009_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p5</span>
<span class="mf">011</span><span class="n">_010_01</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p6</span>
<span class="mf">011</span><span class="n">_011_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p6</span> <span class="mf">2</span><span class="n">s1</span>
<span class="mf">011</span><span class="n">_012_01</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p6</span> <span class="mf">2</span><span class="n">s2</span>
<span class="mf">011</span><span class="n">_013_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p6</span> <span class="mf">2</span><span class="n">s2</span> <span class="mf">3</span><span class="n">p1</span>
<span class="mf">017</span><span class="n">_013_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p1</span>
<span class="mf">017</span><span class="n">_014_03</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p2</span>
<span class="mf">017</span><span class="n">_015_04</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p3</span>
<span class="mf">017</span><span class="n">_016_03</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p4</span>
<span class="mf">017</span><span class="n">_017_02</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p5</span>
<span class="mf">017</span><span class="n">_018_01</span> <span class="mf">1</span><span class="n">s2</span> <span class="mf">2</span><span class="n">p6</span>
</code></pre></div>
<p>template.inp</p>
<div class="highlight"><pre><span></span><code><span class="err">&</span>GLOBAL
PROJECT ATOM
PROGRAM_NAME ATOM
<span class="err">&</span>END GLOBAL
<span class="err">&</span>ATOM
ATOMIC_NUMBER <span class="cp">${</span><span class="n">number</span><span class="cp">}</span>
ELECTRON_CONFIGURATION (<span class="cp">${</span><span class="n">mult</span><span class="cp">}</span>) CORE <span class="cp">${</span><span class="n">line</span><span class="p">:</span><span class="n">valence</span><span class="o">.</span><span class="n">inc</span><span class="cp">}</span>
CORE none
MAX_ANGULAR_MOMENTUM 1
<span class="err">&</span>METHOD
METHOD_TYPE UKS
<span class="err">&</span>XC
<span class="err">&</span>XC_FUNCTIONAL PBE
<span class="err">&</span>PBE
PARAMETRIZATION REVPBE
<span class="err">&</span>END PBE
<span class="err">&</span>END XC_FUNCTIONAL
<span class="err">&</span>END XC
<span class="err">&</span>END METHOD
<span class="err">&</span>POTENTIAL
PSEUDO_TYPE GTH
POTENTIAL_FILE_NAME ../../PBE_PSEUDOPOTENTIALS
POTENTIAL_NAME <span class="cp">${</span><span class="n">line</span><span class="p">:</span><span class="n">ppot</span><span class="o">.</span><span class="n">inc</span><span class="cp">}</span>
<span class="err">&</span>END POTENTIAL
<span class="err">&</span>PP_BASIS
BASIS_SET_FILE_NAME ../../BASIS_MOLOPT
BASIS_TYPE CONTRACTED_GTO
BASIS_SET DZVP-MOLOPT-SR-GTH
<span class="err">&</span>END PP_BASIS
<span class="err">&</span>PRINT
<span class="err">&</span>BASIS_SET ON
<span class="err">&</span>END
<span class="err">&</span>ORBITALS ON
<span class="err">&</span>END
<span class="err">&</span>POTENTIAL ON
<span class="err">&</span>END
<span class="err">&</span>END
<span class="err">&</span>END ATOM
</code></pre></div>
<p>After preparing these files. I do</p>
<div class="highlight"><pre><span></span><code>horton-atomdb.py input cp2k 1,8,11,17 template.inp
</code></pre></div>
<p>This will generate several folders and a run_cp2k.sh file. In order to run it on hopper (which supercomputer I use for cp2k) I add several lines in the head of this file.</p>
<table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span class="normal"> 1</span>
<span class="normal"> 2</span>
<span class="normal"> 3</span>
<span class="normal"> 4</span>
<span class="normal"> 5</span>
<span class="normal"> 6</span>
<span class="normal"> 7</span>
<span class="normal"> 8</span>
<span class="normal"> 9</span>
<span class="normal">10</span>
<span class="normal">11</span>
<span class="normal">12</span>
<span class="normal">13</span>
<span class="normal">14</span>
<span class="normal">15</span>
<span class="normal">16</span></pre></div></td><td class="code"><div class="highlight"><pre><span></span><code><span class="ch">#!/bin/bash</span>
<span class="c1">#PBS -N myjob </span>
<span class="c1">###PBS -q regular</span>
<span class="c1">#PBS -q debug</span>
<span class="c1">#PBS -l mppwidth=24</span>
<span class="c1">###PBS -l walltime=96:00:00</span>
<span class="c1">#PBS -l walltime=00:30:00</span>
<span class="c1">#PBS -j oe</span>
<span class="c1">#PBS -V</span>
<span class="c1"># Note: if you want to use an mpi-parallel CP2K binary, uncomment the following</span>
<span class="c1"># line and fill in the right binary and mpirun script:</span>
<span class="nb">cd</span> <span class="nv">$PBS_O_WORKDIR</span>
module load cp2k/2.5.1
<span class="c1">#CP2K_BIN="mpirun -n4 cp2k.popt"</span>
<span class="nv">CP2K_BIN</span><span class="o">=</span><span class="s2">"aprun -n 24 cp2k.popt"</span>
</code></pre></div>
</td></tr></table>
<p>Then I do</p>
<div class="highlight"><pre><span></span><code>qsub run_cp2k.sh
</code></pre></div>
<p>After the calculations are done, I copy the folder back to killdevil and using horton again. This will generate a atom.h5 file for hirshfeld calculation.</p>
<div class="highlight"><pre><span></span><code>horton-atomdb.py convert
</code></pre></div>
<p>Now, I copy atom.h5 file and the cube file from cp2k calculation to another folder. I also modify the cube file based on the 3.4.1 in the <a href="http://theochem.github.io/horton/tut_part.html#id32">manual</a>. The command I use for the real calculation is </p>
<div class="highlight"><pre><span></span><code>horton-cpart.py cube output.h5:group {h,hi,he} atoms.h5
</code></pre></div>
<p>h, hi, he stands for different partitioning schemes.</p>
<p>To make the result readable, there is a tool to convert h5 file to csv file.</p>
<div class="highlight"><pre><span></span><code>horton-hdf2csv.py output.h5 output.csv
</code></pre></div>
<p>The information I got based on hirshfeld analysis are in the file of output.csv.</p>
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