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molecular-dynamics-simulations-by-gromacs-lammps-cpmd-cp2k-cpx-qbox-from-scratch.html
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<p>Example of setting up first principle molecular dynamics (FPMD) simulation from scratch. </p>
<hr>
<p>In FPMD simulations for liquids, usually, a classical MD simulation is needed to equilibrate the system. I gave examples of using gromacs and lammps as classical MD simulator and cpmd, cp2k, cp.x, qbox as FPMD simulator. The system of 55 water at room temperature is used as the example. </p>
<p>From scratch means I generate the initial structure from the water molecular structure. </p>
<p>In this post, 3 steps are listed. <br>
1. generating initial structure <br>
2. equilibrate the system by classical MD ( 2.1 gromacs code, 2.2 lammps code ) <br>
3. running a short FPMD simulation ( 3.1 cpmd code 3.2 cp2k code 3.3 cp.x code 3.4 qbox code )</p>
<hr>
<p>softwares used:
<a href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a>
<a href="http://www.ime.unicamp.br/~martinez/packmol/home.shtml">packmol</a>
<a href="http://www.gromacs.org/">gromacs</a>
<a href="http://lammps.sandia.gov/">lammps</a>
<a href="http://www.cpmd.org/">cpmd</a>
<a href="https://www.cp2k.org/">cp2k</a>
<a href="http://www.quantum-espresso.org/">cp.x quantum-espresso</a>
<a href="http://eslab.ucdavis.edu/software/qbox/">qbox</a></p>
<hr>
<h3>0 download the files</h3>
<p>All the files needed are included here. </p>
<p><a href="./codes/AIMD_setup.tar.gz">AIMD_setup.tar.gz</a></p>
<hr>
<h3>1.1 generate initial structure for gromacs</h3>
<p>Note: in gromacs, genbox command can be used to generate a water box. Here I use packmol to generate the input structure and convert it to gro file as input.</p>
<p>The water structure is as follow (water.xyz):</p>
<div class="highlight"><pre><span></span><code><span class="mf">3</span>
<span class="n">OW</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">HW1</span> <span class="o">-</span><span class="mf">0.81649</span> <span class="mf">0.57736</span> <span class="mf">0.0</span>
<span class="n">HW2</span> <span class="mf">0.81649</span> <span class="mf">0.57736</span> <span class="mf">0.0</span>
</code></pre></div>
<p>a packmol input (water55_packmol.in) script is used here to generate the structure of the total system.</p>
<div class="highlight"><pre><span></span><code><span class="nv">tolerance</span> <span class="mi">2</span>.<span class="mi">0</span>
<span class="nv">filetype</span> <span class="nv">xyz</span>
<span class="nv">output</span> <span class="nv">water55</span>.<span class="nv">xyz</span>
<span class="nv">structure</span> <span class="nv">water</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">55</span>
<span class="nv">inside</span> <span class="nv">box</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">10</span>.<span class="mi">8172</span> <span class="mi">10</span>.<span class="mi">8172</span> <span class="mi">10</span>.<span class="mi">8172</span>
<span class="k">end</span> <span class="nv">structure</span>
</code></pre></div>
<p>And also I have a python script for the convertion from xyz to gro file (convert_xyz_to_gro.py), the class mdsystem.py can be download here.</p>
<div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">mdsystem</span> <span class="kn">import</span> <span class="o">*</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">file</span><span class="p">(</span><span class="s2">"water55.xyz"</span><span class="p">)</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">mdsystem</span><span class="p">(</span><span class="n">cell</span> <span class="o">=</span> <span class="p">[</span><span class="mf">11.8172</span><span class="p">,</span> <span class="mf">11.8172</span><span class="p">,</span> <span class="mf">11.8172</span><span class="p">])</span>
<span class="n">s</span><span class="o">.</span><span class="n">xyzinput</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">generate_bonds</span><span class="p">(</span><span class="n">cutoff</span> <span class="o">=</span> <span class="mf">1.2</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">molecular_detection</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">moleculars</span><span class="p">)):</span>
<span class="n">s</span><span class="o">.</span><span class="n">molecular_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"SOL"</span><span class="p">)</span>
<span class="nb">print</span> <span class="n">s</span><span class="o">.</span><span class="n">grooutput</span><span class="p">()</span>
<span class="n">python</span> <span class="n">convert_xyz_to_gro</span><span class="o">.</span><span class="n">py</span> <span class="o">></span> <span class="n">water55</span><span class="o">.</span><span class="n">gro</span>
</code></pre></div>
<p>I use this structure for the input of classical molecular dynamics simulation in gromacs.</p>
<hr>
<h3>1.2 generate initial structure for lammps</h3>
<p>The water structure is as follow (water.xyz):</p>
<div class="highlight"><pre><span></span><code><span class="mf">3</span>
<span class="n">O</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="o">-</span><span class="mf">0.81649</span> <span class="mf">0.57736</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="mf">0.81649</span> <span class="mf">0.57736</span> <span class="mf">0.0</span>
</code></pre></div>
<p>a packmol input (water55_packmol.in) script is used here to generate the structure of the total system.</p>
<div class="highlight"><pre><span></span><code><span class="nv">tolerance</span> <span class="mi">2</span>.<span class="mi">0</span>
<span class="nv">filetype</span> <span class="nv">xyz</span>
<span class="nv">output</span> <span class="nv">water55</span>.<span class="nv">xyz</span>
<span class="nv">structure</span> <span class="nv">water</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">55</span>
<span class="nv">inside</span> <span class="nv">box</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">10</span>.<span class="mi">8172</span> <span class="mi">10</span>.<span class="mi">8172</span> <span class="mi">10</span>.<span class="mi">8172</span>
<span class="k">end</span> <span class="nv">structure</span>
</code></pre></div>
<p>And also I have a vmd script for the generation of psf and pdb and lammps data file.</p>
<div class="highlight"><pre><span></span><code><span class="x">mol new water55.xyz</span>
<span class="x">pbc set </span><span class="cp">{</span> <span class="m">11.8172</span> <span class="m">11.8172</span> <span class="m">11.8172</span> <span class="cp">}</span><span class="x"></span>
<span class="x">topo clearbonds</span>
<span class="x">for </span><span class="cp">{</span><span class="nf">set</span> <span class="na">i</span> <span class="m">0</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span><span class="nv">$i</span> <span class="o"><</span> <span class="m">55</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span><span class="nf">incr</span> <span class="na">i</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">1</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">2</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">1</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">2</span><span class="o">]</span>
<span class="cp">}</span><span class="x"></span>
<span class="x">animate write psf water55.psf</span>
<span class="x">animate write pdb water55.pdb</span>
<span class="x">topo writelammpsdata water55.data</span>
</code></pre></div>
<p>I use this structure for the input of classical molecular dynamics simulation in lammps.</p>
<hr>
<h3>2.1 gromacs code</h3>
<p>for gromacs simulation, there is separate forcefield file and topology file ( spcfw.itp and water55.top ).</p>
<p>two mdp input files needed ( min.mdp nvt.mdp ), the first one is used to minimize the structure, the second one is used for the simulation. Here is the command I use for the simulation.</p>
<div class="highlight"><pre><span></span><code>gmx grompp -f min.mdp -c water55.gro -p water55.top -o min.tpr
gmx mdrun -s min.tpr -c em.gro
gmx grompp -f nvt.mdp -c em.gro -p water55.top -o nvt.tpr
gmx mdrun -s nvt.tpr
</code></pre></div>
<p>In the example, I run 100ps for equlibrating the system. In real simulation, longer is usually needed.</p>
<p>I also like to convert the trajectory so that the atom in the same molecule are not separate in the edge of the box.</p>
<div class="highlight"><pre><span></span><code>gmx trjconv -s nvt.tpr -f traj_comp.xtc -o traj_comp_whole.xtc -pbc whole <<< "0"
</code></pre></div>
<p>Then, the script ( take_last_snapshot.vmd ) can be used to take the last snapshot of the simulation as the initial structure for FPMD.</p>
<div class="highlight"><pre><span></span><code><span class="nv">mol</span> <span class="nv">new</span> <span class="nv">water55</span>.<span class="nv">psf</span>
<span class="nv">mol</span> <span class="nv">addfile</span> <span class="nv">traj_comp_whole</span>.<span class="nv">xtc</span> <span class="nv">waitfor</span> <span class="nv">all</span>
<span class="nv">pbc</span> <span class="nv">wrap</span> <span class="o">-</span><span class="nv">all</span> <span class="o">-</span><span class="nv">compound</span> <span class="nv">residue</span>
<span class="nv">set</span> <span class="nv">nframes</span> [<span class="nv">molinfo</span> <span class="nv">top</span> <span class="nv">get</span> <span class="nv">numframes</span>]
<span class="nv">set</span> <span class="nv">nframes</span> [<span class="nv">expr</span> $<span class="nv">nframes</span> <span class="o">-</span> <span class="mi">1</span>]
<span class="nv">animate</span> <span class="nv">write</span> <span class="nv">xyz</span> <span class="nv">eq</span>.<span class="nv">xyz</span> <span class="nv">beg</span> $<span class="nv">nframes</span>
<span class="k">exit</span>
</code></pre></div>
<hr>
<h3>2.2 lammps code</h3>
<p>Here we use the generated initial structure to run molecular dynamics with lammps. SPC/Fw force field is used.<br>
Here is the ( in.spcf ) lammps input script</p>
<div class="highlight"><pre><span></span><code><span class="n">units</span> <span class="n">real</span>
<span class="n">dimension</span> <span class="mi">3</span>
<span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">p</span>
<span class="n">atom_style</span> <span class="n">full</span>
<span class="n">read_data</span> <span class="n">water55</span><span class="o">.</span><span class="n">data</span>
<span class="c1">## alternate way to set charges - besides manually in data file ###</span>
<span class="n">group</span> <span class="n">ox</span> <span class="n">type</span> <span class="mi">2</span>
<span class="n">group</span> <span class="n">hy</span> <span class="n">type</span> <span class="mi">1</span>
<span class="n">set</span> <span class="n">group</span> <span class="n">ox</span> <span class="n">charge</span> <span class="o">-</span><span class="mf">0.8200</span>
<span class="n">set</span> <span class="n">group</span> <span class="n">hy</span> <span class="n">charge</span> <span class="mf">0.4100</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">5.9086</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">0.1553537</span> <span class="mf">3.166</span>
<span class="n">bond_style</span> <span class="n">harmonic</span>
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">529.581</span> <span class="mf">1.0120</span>
<span class="n">angle_style</span> <span class="n">harmonic</span>
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">37.95</span> <span class="mf">113.24</span>
<span class="n">kspace_style</span> <span class="n">ewald</span> <span class="mf">1.0e-5</span>
<span class="n">velocity</span> <span class="n">all</span> <span class="n">create</span> <span class="mf">298.0</span> <span class="mi">12345689</span> <span class="n">dist</span> <span class="n">uniform</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">all</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">298.0</span> <span class="mf">298.0</span> <span class="mf">100.0</span>
<span class="n">neighbor</span> <span class="mf">2.0</span> <span class="n">bin</span>
<span class="n">neigh_modify</span> <span class="n">delay</span> <span class="mi">0</span> <span class="n">every</span> <span class="mi">10</span> <span class="n">check</span> <span class="n">yes</span>
<span class="n">thermo</span> <span class="mi">200</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">time</span> <span class="n">temp</span>
<span class="n">thermo_modify</span> <span class="n">norm</span> <span class="n">no</span> <span class="n">flush</span> <span class="n">yes</span>
<span class="n">minimize</span> <span class="mf">1.0e-8</span> <span class="mf">1.0e-8</span> <span class="mi">10000</span> <span class="mi">10000</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="n">all</span> <span class="n">dcd</span> <span class="mi">2000</span> <span class="n">result</span><span class="o">.</span><span class="n">dcd</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">unwrap</span> <span class="n">yes</span>
<span class="c1">#run variables</span>
<span class="n">timestep</span> <span class="mf">0.5</span>
<span class="n">run</span> <span class="mi">200000</span> <span class="c1"># 100ps, longer needed ( 2000000 10ns )</span>
</code></pre></div>
<p>after the simulation, the ( result.dcd ) together with the ( water55.psf )</p>
<div class="highlight"><pre><span></span><code><span class="nv">mol</span> <span class="nv">new</span> <span class="nv">water55</span>.<span class="nv">psf</span>
<span class="nv">mol</span> <span class="nv">addfile</span> <span class="nb">result</span>.<span class="nv">dcd</span> <span class="nv">waitfor</span> <span class="nv">all</span>
<span class="nv">pbc</span> <span class="nv">wrap</span> <span class="o">-</span><span class="nv">all</span> <span class="o">-</span><span class="nv">compound</span> <span class="nv">residue</span>
<span class="nv">set</span> <span class="nv">nframes</span> [<span class="nv">molinfo</span> <span class="nv">top</span> <span class="nv">get</span> <span class="nv">numframes</span>]
<span class="nv">set</span> <span class="nv">nframes</span> [<span class="nv">expr</span> $<span class="nv">nframes</span> <span class="o">-</span> <span class="mi">1</span>]
<span class="nv">animate</span> <span class="nv">write</span> <span class="nv">xyz</span> <span class="nv">eq</span>.<span class="nv">xyz</span> <span class="nv">beg</span> $<span class="nv">nframes</span>
<span class="k">exit</span>
</code></pre></div>
<hr>
<p>After the equilibrium run. I got the equilibrium structure (eq.xyz) from gromacs or lammps run. Now, I will use this structure as starting point for FPMD simulations.</p>
<hr>
<h3>3.1 cpmd code</h3>
<p>I recommend a tutorial about cpmd code ( <a href="http://www.ipcms.unistra.fr/wp-content/uploads/2016/03/cpmd.pdf">cpmd.pdf</a> ).</p>
<p>First, the equilibrium structure need to be transformed to CPMD format. Here is the script ( cpmd_initial_structures.py ).</p>
<div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">sys</span> <span class="kn">import</span> <span class="n">argv</span>
<span class="kn">from</span> <span class="nn">mdsystem</span> <span class="kn">import</span> <span class="o">*</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">file</span><span class="p">(</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">mdsystem</span><span class="p">([],[],[])</span>
<span class="n">s</span><span class="o">.</span><span class="n">xyzinput</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
<span class="n">atom_number</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">atom_xyz</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">s</span><span class="p">:</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">species</span> <span class="ow">in</span> <span class="n">atom_number</span><span class="p">:</span>
<span class="n">atom_number</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">species</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">atom_xyz</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">species</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">coordinates</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atom_number</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">species</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">atom_xyz</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">species</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">coordinates</span><span class="p">]</span>
<span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">"coord"</span> <span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"&ATOMS</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"ISOTOPES</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"16.01</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"1.008</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"*O_MT_PBE.psp KLEINMAN-BYLANDER</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">" LMAX=P LOC=P</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="nb">str</span><span class="p">(</span><span class="n">atom_number</span><span class="p">[</span><span class="s2">"O"</span><span class="p">])</span><span class="o">+</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">coord</span> <span class="ow">in</span> <span class="n">atom_xyz</span><span class="p">[</span><span class="s2">"O"</span><span class="p">]:</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span> <span class="n">coord</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">coord</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">coord</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="p">))</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"*H_MT_PBE.psp KLEINMAN-BYLANDER</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">" LMAX=S LOC=S</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="nb">str</span><span class="p">(</span><span class="n">atom_number</span><span class="p">[</span><span class="s2">"H"</span><span class="p">])</span><span class="o">+</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">coord</span> <span class="ow">in</span> <span class="n">atom_xyz</span><span class="p">[</span><span class="s2">"H"</span><span class="p">]:</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span> <span class="n">coord</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">coord</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">coord</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="p">))</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"&END</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</code></pre></div>
<p>I am using cpmd simulation in cpmd code, so wavefucntion need to be optimized, first. Append the coord file at the end of the input file.</p>
<div class="highlight"><pre><span></span><code><span class="o">&</span><span class="n">INFO</span>
<span class="n">wf</span> <span class="n">opt</span> <span class="n">for</span> <span class="n">pure</span> <span class="mi">55</span> <span class="n">water</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">CPMD</span>
<span class="n">OPTIMIZE</span> <span class="n">WAVEFUNCTION</span>
<span class="n">CONVERGENCE</span> <span class="n">ORBITALS</span>
<span class="mf">1.0</span><span class="n">d</span><span class="o">-</span><span class="mi">7</span>
<span class="n">ODIIS</span> <span class="n">NO_RESET</span><span class="o">=</span><span class="mi">50</span>
<span class="mi">5</span>
<span class="n">MAXSTEP</span>
<span class="mi">1000</span>
<span class="n">MEMORY</span> <span class="n">BIG</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">SYSTEM</span>
<span class="n">SYMMETRY</span>
<span class="mi">1</span>
<span class="n">ANGSTROM</span>
<span class="n">CELL</span>
<span class="mf">11.8172</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">CUTOFF</span>
<span class="mf">80.0</span>
<span class="n">TESR</span>
<span class="mi">4</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">DFT</span>
<span class="n">NEWCODE</span>
<span class="n">FUNCTIONAL</span> <span class="n">PBE</span>
<span class="o">&</span><span class="kr">END</span>
</code></pre></div>
<p>after the wavefunction optimization, a RESTART.1 file should be there. And we generate a LATEST file for the restart.</p>
<div class="highlight"><pre><span></span><code><span class="o">&</span><span class="n">INFO</span>
<span class="n">equilibrium</span> <span class="n">steps</span> <span class="n">md</span> <span class="n">at</span> <span class="n">T</span><span class="o">=</span><span class="mi">300</span><span class="n">K</span> <span class="n">to</span> <span class="n">get</span> <span class="n">thermo</span> <span class="n">info</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">CPMD</span>
<span class="n">MOLECULAR</span> <span class="n">DYNAMICS</span>
<span class="n">RESTART</span> <span class="n">WAVEFUNCTIONS</span> <span class="n">COORDINATES</span> <span class="n">LATEST</span>
<span class="n">RESTFILE</span>
<span class="mi">3</span>
<span class="n">TRAJECTORY</span> <span class="n">SAMPLE</span> <span class="n">XYZ</span>
<span class="mi">10</span>
<span class="n">TEMPERATURE</span>
<span class="mi">300</span>
<span class="n">NOSE</span> <span class="n">IONS</span>
<span class="mi">300</span> <span class="mf">3000.0</span>
<span class="n">NOSE</span> <span class="n">ELECTRONS</span>
<span class="mf">0.03</span> <span class="mf">9000.0</span>
<span class="n">MAXSTEP</span>
<span class="mi">100</span>
<span class="n">TIMESTEP</span>
<span class="mf">4.0</span>
<span class="n">EMASS</span>
<span class="mf">400.0</span>
<span class="n">MEMORY</span> <span class="n">BIG</span>
<span class="n">RHOOUT</span> <span class="n">SAMPLE</span><span class="o">=</span><span class="mi">100</span>
<span class="n">SUBTRACT</span> <span class="n">COMVEL</span> <span class="n">ROTVEL</span>
<span class="mi">1</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">SYSTEM</span>
<span class="n">SYMMETRY</span>
<span class="mi">1</span>
<span class="n">ANGSTROM</span>
<span class="n">CELL</span>
<span class="mf">11.8172</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">CUTOFF</span>
<span class="mf">80.0</span>
<span class="n">TESR</span>
<span class="mi">4</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">DFT</span>
<span class="n">NEWCODE</span>
<span class="n">FUNCTIONAL</span> <span class="n">PBE</span>
<span class="o">&</span><span class="kr">END</span>
</code></pre></div>
<hr>
<h3>3.2 cp2k code</h3>
<p>In cp2k, BOMD is running. </p>
<p>copy the eq.xyz file to the cp2k folder and write this input file for FPMD. (water55.inp) </p>
<div class="highlight"><pre><span></span><code><span class="o">&</span><span class="n">FORCE_EVAL</span>
<span class="n">METHOD</span> <span class="n">Quickstep</span>
<span class="o">&</span><span class="n">DFT</span>
<span class="n">BASIS_SET_FILE_NAME</span> <span class="n">BASIS_MOLOPT</span>
<span class="n">POTENTIAL_FILE_NAME</span> <span class="n">GTH_POTENTIALS</span>
<span class="o">&</span><span class="n">MGRID</span>
<span class="n">CUTOFF</span> <span class="mi">200</span>
<span class="n">REL_CUTOFF</span> <span class="mi">50</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">MGRID</span>
<span class="o">&</span><span class="n">QS</span>
<span class="n">EPS_DEFAULT</span> <span class="mf">1.0E-12</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">QS</span>
<span class="o">&</span><span class="n">SCF</span>
<span class="n">SCF_GUESS</span> <span class="n">ATOMIC</span>
<span class="n">EPS_SCF</span> <span class="mf">1.0E-6</span>
<span class="n">MAX_SCF</span> <span class="mi">30</span>
<span class="o">&</span><span class="n">OT</span>
<span class="n">MINIMIZER</span> <span class="n">DIIS</span>
<span class="n">PRECONDITIONER</span> <span class="n">FULL_ALL</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">OUTER_SCF</span>
<span class="n">EPS_SCF</span> <span class="mf">1.0E-6</span>
<span class="n">MAX_SCF</span> <span class="mi">20</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="n">PRINT</span>
<span class="o">&</span><span class="n">RESTART</span>
<span class="n">BACKUP_COPIES</span> <span class="mi">0</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="kr">END</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">SCF</span>
<span class="o">&</span><span class="n">XC</span>
<span class="o">&</span><span class="n">XC_FUNCTIONAL</span> <span class="n">PBE</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">XC_FUNCTIONAL</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">XC</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">DFT</span>
<span class="o">&</span><span class="n">SUBSYS</span>
<span class="o">&</span><span class="n">CELL</span>
<span class="n">ABC</span> <span class="mf">11.8172</span> <span class="mf">11.8172</span> <span class="mf">11.8172</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">CELL</span>
<span class="o">&</span><span class="n">TOPOLOGY</span>
<span class="n">COORD_FILE_NAME</span> <span class="p">.</span><span class="o">/</span><span class="n">eq</span><span class="p">.</span><span class="n">xyz</span>
<span class="n">COORD_FILE_FORMAT</span> <span class="n">xyz</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">TOPOLOGY</span>
<span class="o">&</span><span class="n">KIND</span> <span class="n">H</span>
<span class="n">BASIS_SET</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="n">POTENTIAL</span> <span class="n">GTH</span><span class="o">-</span><span class="n">PBE</span><span class="o">-</span><span class="n">q1</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">KIND</span>
<span class="o">&</span><span class="n">KIND</span> <span class="n">O</span>
<span class="n">BASIS_SET</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="n">POTENTIAL</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="o">&</span><span class="kr">END</span> <span class="n">KIND</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">SUBSYS</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">FORCE_EVAL</span>
<span class="o">&</span><span class="n">MOTION</span>
<span class="o">&</span><span class="n">MD</span>
<span class="n">ENSEMBLE</span> <span class="n">NVE</span>
<span class="n">STEPS</span> <span class="mi">100</span>
<span class="n">TIMESTEP</span> <span class="mf">0.5</span>
<span class="n">TEMPERATURE</span> <span class="mf">300.0</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">MD</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">MOTION</span>
<span class="o">&</span><span class="n">GLOBAL</span>
<span class="n">PROJECT</span> <span class="n">H2O</span><span class="o">-</span><span class="mi">55</span><span class="o">-</span><span class="n">PBE</span>
<span class="n">RUN_TYPE</span> <span class="n">MD</span>
<span class="n">PRINT_LEVEL</span> <span class="n">MEDIUM</span>
<span class="o">&</span><span class="kr">END</span> <span class="n">GLOBAL</span>
</code></pre></div>
<hr>
<h3>3.3 cp.x code</h3>
<p>The script here.</p>
<div class="highlight"><pre><span></span><code>cd <span class="nv">$PWD</span>
Name=cp-H2O
fricei=( 1.0 1.0 0.5 0.1 0.0 0.0 0.0 )
fricpi=( 0.9 1.0 0.3 0.05 0.0 0.0 0.0 )
runi=( 100 100 200 200 1500 1500 35000 )
orthoi=( Gram-Schmidt ortho ortho ortho ortho ortho ortho )
modei=( from_scratch reset_counters restart restart reset_counters restart restart)
wfr=( 51 51 51 51 51 71 72 )
wfw=( 51 51 51 51 71 72 73 )
ions=( none none none none verlet verlet verlet)
tempi=( 50 50 50 50 300 350 375 )
electrons=( damp damp damp damp verlet verlet verlet )
typeset -i j=1
while (( j == 1 ));do
if [[ -d "H2O_<span class="cp">${</span><span class="n">wfw</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="cp">}</span>.save" ]]; then
wfr[6]=<span class="cp">${</span><span class="n">wfw</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="cp">}</span>
wfw[6]=$((<span class="cp">${</span><span class="n">wfw</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="cp">}</span>+1))
else
j=0
fi
done
echo "in"
for i in 0 1 2 3 4 ;
do
rm -f in.00
cat <span class="nt"><< EOF</span> <span class="nt">> in.00</span>
<span class="err">&CONTROL</span>
<span class="na">outdir =</span> <span class="s">'</span><span class="nv">$PWD</span><span class="s">'</span>
<span class="na">pseudo_dir =</span> <span class="s">'./'</span>
<span class="na">title =</span> <span class="s">'H2O'</span><span class="err">,</span>
<span class="na">prefix =</span> <span class="s">'H2O'</span><span class="err">,</span>
<span class="na">calculation =</span> <span class="s">'cp'</span><span class="err">,</span>
<span class="na">restart_mode =</span> <span class="s">'</span><span class="cp">${</span><span class="n">modei</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">'</span><span class="err">,</span>
<span class="na">ndr =</span> <span class="cp">${</span><span class="n">wfr</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">,</span>
<span class="na">ndw =</span> <span class="cp">${</span><span class="n">wfw</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">,</span>
<span class="na">nstep =</span> <span class="cp">${</span><span class="n">runi</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">,</span>
<span class="na">iprint =</span> <span class="s">20,</span>
<span class="na">isave =</span> <span class="s">1000,</span>
<span class="na">tstress =</span> <span class="s">.true.,</span>
<span class="na">tprnfor =</span> <span class="s">.true.,</span>
<span class="na">dt =</span> <span class="s">3.d0,</span>
<span class="err">!</span> <span class="na">etot_conv_thr =</span> <span class="s">1.D-8</span>
<span class="err">!</span> <span class="na">forc_conv_thr =</span> <span class="s">1.D-3</span>
<span class="err">/</span>
<span class="err">&SYSTEM</span>
<span class="na">ibrav =</span> <span class="s">1,</span>
<span class="err">celldm(1)</span> <span class="err">=</span> <span class="err">CELL_X_YY,</span>
<span class="err">celldm(2)</span> <span class="err">=</span> <span class="err">1.00,</span>
<span class="err">celldm(3)</span> <span class="err">=</span> <span class="err">1.00,</span>
<span class="err">celldm(4)</span> <span class="err">=</span> <span class="err">0.0,</span>
<span class="err">celldm(5)</span> <span class="err">=</span> <span class="err">0.0,</span>
<span class="err">celldm(6)</span> <span class="err">=</span> <span class="err">0.0,</span>
<span class="na">nat =</span> <span class="s">NATOMS_YY,</span>
<span class="na">ntyp =</span> <span class="s">2,</span>
<span class="na">nspin =</span> <span class="s">1,</span>
<span class="na">ecutwfc =</span> <span class="s">25.0,</span>
<span class="na">ecutrho =</span> <span class="s">200.0,</span>
<span class="na">nr1b=</span> <span class="s">20,</span> <span class="na">nr2b =</span> <span class="s">20,</span> <span class="na">nr3b =</span> <span class="s">20,</span>
<span class="err">!</span> <span class="err">starting_magnetization(1)=0.1,</span>
<span class="err">!</span> <span class="na">occupations=</span><span class="s">'from_input'</span><span class="err">,</span>
<span class="err">/</span>
<span class="err">&ELECTRONS</span>
<span class="na">emass =</span> <span class="s">340.d0,</span>
<span class="na">emass_cutoff =</span> <span class="s">2.0d0,</span>
<span class="na">orthogonalization =</span> <span class="s">'</span><span class="cp">${</span><span class="n">orthoi</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">'</span><span class="err">,</span>
<span class="na">ortho_eps =</span> <span class="s">5.d-8,</span>
<span class="na">ortho_max =</span> <span class="s">200,</span>
<span class="na">electron_dynamics =</span> <span class="s">'</span><span class="cp">${</span><span class="n">electrons</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">'</span><span class="err">,</span>
<span class="na">electron_damping =</span> <span class="cp">${</span><span class="n">fricei</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">,</span>
<span class="err">/</span>
<span class="err">&IONS</span>
<span class="na">ion_dynamics =</span> <span class="s">'</span><span class="cp">${</span><span class="n">ions</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">'</span><span class="err">,</span>
<span class="na">ion_damping =</span> <span class="cp">${</span><span class="n">fricpi</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">,</span>
<span class="na">tempw =</span> <span class="cp">${</span><span class="n">tempi</span><span class="p">[</span><span class="err">$</span><span class="n">i</span><span class="p">]</span><span class="cp">}</span><span class="s">,</span>
<span class="err">!</span> <span class="na">ion_temperature =</span> <span class="s">'rescaling'</span><span class="err">,</span>
<span class="na">ion_temperature =</span> <span class="s">'nose'</span><span class="err">,</span>
<span class="na">fnosep =</span> <span class="s">10.0</span> <span class="err">30.0</span> <span class="err">60.0</span> <span class="err">100.0,</span>
<span class="na">nhpcl =</span> <span class="s">4,</span>
<span class="na">nhptyp =</span> <span class="s">2,</span>
<span class="err">/</span>
<span class="err">ATOMIC_SPECIES</span>
<span class="err">H</span> <span class="err">1.008</span> <span class="err">H.pbe-van_ak.UPF</span>
<span class="err">O</span> <span class="err">15.999</span> <span class="err">O.pbe-van_ak.UPF</span>
<span class="err">ATOMIC_POSITIONS</span> <span class="err">(</span> <span class="err">angstrom</span> <span class="err">)</span>
<span class="err">COORD_YY</span>
<span class="err">EOF</span>
<span class="err">echo</span> <span class="err">'Strat</span> <span class="err">turn</span> <span class="err">of'</span> <span class="nv">$i</span>
<span class="err">mpirun</span> <span class="err">~/software/qe/qe-6.0/bin/cp.x</span> <span class="nt">< in.00</span> <span class="nt">>></span> <span class="nv">$Name.out</span>
done
echo 'ALL DONE'
</code></pre></div>
<p>The coord generate script.</p>
<div class="highlight"><pre><span></span><code>head -n 167 eq.xyz | tail -n 165 > coord
sed 's/CELL_X_YY/22.331269952/' water_template.j > water_tmp.j
sed 's/NATOMS_YY/165/' water_tmp.j > water_tmp2.j
sed "/COORD_YY/ r coord" water_tmp2.j > water_tmp3.j
sed "s/COORD_YY/ /" water_tmp3.j > water.j
rm water_tmp.j water_tmp2.j water_tmp3.j
</code></pre></div>
<hr>
<h3>3.4 qbox code</h3>
<p>For qbox code, also a convertor script is needed. The units used in qbox is atomic units. I list the script here.</p>
<div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">mdsystem</span> <span class="kn">import</span> <span class="o">*</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">file</span><span class="p">(</span><span class="s2">"eq.xyz"</span><span class="p">)</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">mdsystem</span><span class="p">(</span><span class="n">cell</span> <span class="o">=</span> <span class="p">[</span><span class="mf">11.8172</span><span class="p">,</span> <span class="mf">11.8172</span><span class="p">,</span> <span class="mf">11.8172</span><span class="p">])</span>
<span class="n">s</span><span class="o">.</span><span class="n">xyzinput</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">generate_bonds</span><span class="p">(</span><span class="n">cutoff</span> <span class="o">=</span> <span class="mf">1.2</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">molecular_detection</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">moleculars</span><span class="p">)):</span>
<span class="n">s</span><span class="o">.</span><span class="n">molecular_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"SOL"</span><span class="p">)</span>
<span class="n">AtoBohr</span> <span class="o">=</span> <span class="mf">1.8897259886</span>
<span class="nb">print</span> <span class="s2">"set cell "</span> <span class="p">,</span> <span class="n">s</span><span class="o">.</span><span class="n">cell</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="n">AtoBohr</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="mi">0</span><span class="p">,</span> <span class="n">s</span><span class="o">.</span><span class="n">cell</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">AtoBohr</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="mi">0</span><span class="p">,</span> <span class="n">s</span><span class="o">.</span><span class="n">cell</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">*</span> <span class="n">AtoBohr</span>
<span class="nb">print</span> <span class="s2">"species oxygen O_HSCV_PBE-1.0.xml"</span>
<span class="nb">print</span> <span class="s2">"species hydrogen H_HSCV_PBE-1.0.xml"</span>
<span class="n">nO</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">nH</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">s</span><span class="p">:</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">species</span> <span class="o">==</span> <span class="s2">"O"</span><span class="p">:</span>
<span class="n">nO</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">xyz</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">*</span> <span class="n">AtoBohr</span>
<span class="nb">print</span> <span class="s2">"atom "</span><span class="p">,</span> <span class="s2">"O</span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span><span class="n">nO</span><span class="p">,</span> <span class="s2">"oxygen"</span><span class="p">,</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">species</span> <span class="o">==</span> <span class="s2">"H"</span><span class="p">:</span>
<span class="n">nH</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">xyz</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">*</span> <span class="n">AtoBohr</span>
<span class="nb">print</span> <span class="s2">"atom "</span><span class="p">,</span> <span class="s2">"H</span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span><span class="n">nH</span><span class="p">,</span> <span class="s2">"hydrogen"</span><span class="p">,</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</code></pre></div>
<p>with pseudopotentials files and sample.xsd, species.xsd (taken from xml folder in qbox package) in the same folder. <br>
We then append these commands at the end of the structure information.</p>
<div class="highlight"><pre><span></span><code>set ecut 70
set wf_dyn PSDA
set ecutprec 5
randomize_wf
run 0 100
set atoms_dyn MD
set dt 40
run 100 10
</code></pre></div>
<p>Run the calculation like this.</p>
<div class="highlight"><pre><span></span><code>mpirun /nas02/home/y/i/yiy/bin/qb < test.i > test.out
</code></pre></div>
<hr>
<p>After the simulation, I got trajs like this. </p>
<p><img alt="Alt Text" src="./images/water55_aimd.gif"></p>
<hr>
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