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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<p><strong>Overview of Drude induced dipoles</strong></p>
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<p>Polarizable atoms acquire an induced electric dipole moment under the
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action of an external electric field, for example the electric field
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created by the surrounding particles. Drude oscillators represent
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these dipoles by two fixed charges: the core (DC) and the Drude
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particle (DP) bound by a harmonic potential. The Drude particle can be
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thought of as the electron cloud whose center can be displaced from
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the position of the the corresponding nucleus.</p>
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<p>The sum of the masses of a core-Drude pair should be the mass of the
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initial (unsplit) atom, <span class="math">\(m_C + m_D = m\)</span>. The sum of their charges
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should be the charge of the initial (unsplit) atom, <span class="math">\(q_C + q_D = q\)</span>.
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A harmonic potential between the core and Drude partners should be
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present, with force constant <span class="math">\(k_D\)</span> and an equilibrium distance of
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zero. The (half-)stiffness of the <a class="reference internal" href="bond_harmonic.html"><span class="doc">harmonic bond</span></a>
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<span class="math">\(K_D = k_D/2\)</span> and the Drude charge <span class="math">\(q_D\)</span> are related to the atom
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polarizability <span class="math">\(\alpha\)</span> by</p>
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<div class="math">
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\[\begin{equation} K_D = \frac 1 2\, \frac {q_D^2} \alpha\end{equation}\]</div>
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<p>Ideally, the mass of the Drude particle should be small, and the
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stiffness of the harmonic bond should be large, so that the Drude
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particle remains close ot the core. The values of Drude mass, Drude
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charge, and force constant can be chosen following different
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strategies, as in the following examples of polarizable force
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fields.</p>
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<ul class="simple">
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<li><a class="reference internal" href="#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a> suggest adopting a global
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half-stiffness, <span class="math">\(K_D\)</span> = 500 kcal/(mol &Aring;<sup>2</sup>) &mdash;
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which corresponds to a force constant <span class="math">\(k_D\)</span> = 4184 kJ/(mol
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&Aring;<sup>2</sup>) &mdash; for all types of core-Drude bond, a
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global mass <span class="math">\(m_D\)</span> = 0.4 g/mol (or u) for all types of Drude
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particle, and to calculate the Drude charges for individual atom types
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from the atom polarizabilities using equation (1). This choice is
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followed in the polarizable CHARMM force field.</li>
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<li><a class="reference internal" href="#schroeder"><span class="std std-ref">Schroeder and Steinhauser</span></a> suggest adopting a global
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charge <span class="math">\(q_D\)</span> = -1.0e and a global mass <span class="math">\(m_D\)</span> = 0.1 g/mol (or u)
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for all Drude particles, and to calculate the force constant for each
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type of core-Drude bond from equation (1). The timesteps used by these
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authors are between 0.5 and 2 fs, with the degrees of freedom of the
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Drude oscillators kept cold at 1 K. In both these force fields
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hydrogen atoms are treated as non-polarizable.</li>
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</ul>
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<p>The motion of of the Drude particles can be calculated by minimizing
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the energy of the induced dipoles at each timestep, by an interative,
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self-consistent procedure. The Drude particles can be massless and
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therefore do not contribute to the kinetic energy. However, the
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relaxed method is computationall slow. An extended-lagrangian method
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can be used to calculate the positions of the Drude particles, but
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this requires them to have mass. It is important in this case to
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decouple the degrees of freedom associated with the Drude oscillators
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from those of the normal atoms. Thermalizing the Drude dipoles at
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temperatures comparable to the rest of the simulation leads to several
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problems (kinetic energy transfer, very short timestep, etc.), which
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can be remediated by the “cold Drude” technique (<a class="reference internal" href="#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a>).</p>
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<p>Two closely related models are used to represent polarization through
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“charges on a spring”: the core-shell model and the Drude
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model. Although the basic idea is the same, the core-shell model is
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normally used for ionic/crystalline materials, whereas the Drude model
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is normally used for molecular systems and fluid states. In ionic
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crystals the symmetry around each ion and the distance between them
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are such that the core-shell model is sufficiently stable. But to be
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applicable to molecular/covalent systems the Drude model includes two
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important features:</p>
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<ol class="arabic simple">
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<li>The possibility to thermostat the additional degrees of freedom</li>
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</ol>
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<blockquote>
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<div>associated with the induced dipoles at very low temperature, in terms
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of the reduced coordinates of the Drude particles with respect to
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their cores. This makes the trajectory close to that of relaxed
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induced dipoles.</div></blockquote>
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<ol class="arabic simple">
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<li>The Drude dipoles on covalently bonded atoms interact too strongly
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due to the short distances, so an atom may capture the Drude particle
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(shell) of a neighbor, or the induced dipoles within the same molecule
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may align too much. To avoid this, damping at short of the
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interactions between the point charges composing the induced dipole
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can be done by <a class="reference internal" href="#thole"><span class="std std-ref">Thole</span></a> functions.</li>
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</ol>
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<hr class="docutils" />
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<p><strong>Preparation of the data file</strong></p>
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<p>The data file is similar to a standard LAMMPS data file for
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<em>atom_style full</em>. The DPs and the <em>harmonic bonds</em> connecting them
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to their DC should appear in the data file as normal atoms and bonds.</p>
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<p>You can use the <em>polarizer</em> tool (Python script distributed with the
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USER-DRUDE package) to convert a non-polarizable data file (here
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<em>data.102494.lmp</em>) to a polarizable data file (<em>data-p.lmp</em>)</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">polarizer</span> <span class="o">-</span><span class="n">q</span> <span class="o">-</span><span class="n">f</span> <span class="n">phenol</span><span class="o">.</span><span class="n">dff</span> <span class="n">data</span><span class="o">.</span><span class="mf">102494.</span><span class="n">lmp</span> <span class="n">data</span><span class="o">-</span><span class="n">p</span><span class="o">.</span><span class="n">lmp</span>
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</pre></div>
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</div>
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<p>This will automatically insert the new atoms and bonds.
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The masses and charges of DCs and DPs are computed
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from <em>phenol.dff</em>, as well as the DC-DP bond constants. The file
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<em>phenol.dff</em> contains the polarizabilities of the atom types
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and the mass of the Drude particles, for instance:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># units: kJ/mol, A, deg</span>
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<span class="c1"># kforce is in the form k/2 r_D^2</span>
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<span class="c1"># type m_D/u q_D/e k_D alpha/A3 thole</span>
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<span class="n">OH</span> <span class="mf">0.4</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">4184.0</span> <span class="mf">0.63</span> <span class="mf">0.67</span>
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<span class="n">CA</span> <span class="mf">0.4</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">4184.0</span> <span class="mf">1.36</span> <span class="mf">2.51</span>
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<span class="n">CAI</span> <span class="mf">0.4</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">4184.0</span> <span class="mf">1.09</span> <span class="mf">2.51</span>
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</pre></div>
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</div>
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<p>The hydrogen atoms are absent from this file, so they will be treated
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as non-polarizable atoms. In the non-polarizable data file
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<em>data.102494.lmp</em>, atom names corresponding to the atom type numbers
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have to be specified as comments at the end of lines of the <em>Masses</em>
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section. You probably need to edit it to add these names. It should
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look like</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Masses</span>
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</pre></div>
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</div>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="mf">12.011</span> <span class="c1"># CAI</span>
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<span class="mi">2</span> <span class="mf">12.011</span> <span class="c1"># CA</span>
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<span class="mi">3</span> <span class="mf">15.999</span> <span class="c1"># OH</span>
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<span class="mi">4</span> <span class="mf">1.008</span> <span class="c1"># HA</span>
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<span class="mi">5</span> <span class="mf">1.008</span> <span class="c1"># HO</span>
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</pre></div>
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</div>
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<hr class="docutils" />
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<p><strong>Basic input file</strong></p>
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<p>The atom style should be set to (or derive from) <em>full</em>, so that you
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can define atomic charges and molecular bonds, angles, dihedrals...</p>
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<p>The <em>polarizer</em> tool also outputs certain lines related to the input
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script (the use of these lines will be explained below). In order for
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LAMMPS to recognize that you are using Drude oscillators, you should
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use the fix <em>drude</em>. The command is</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">DRUDE</span> <span class="nb">all</span> <span class="n">drude</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">N</span> <span class="n">N</span> <span class="n">D</span> <span class="n">D</span> <span class="n">D</span>
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</pre></div>
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</div>
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<p>The N, C, D following the <em>drude</em> keyword have the following meaning:
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There is one tag for each atom type. This tag is C for DCs, D for DPs
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and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O
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atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
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the atom types 6 to 8 are the newly created DPs.</p>
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<p>By recognizing the fix <em>drude</em>, LAMMPS will find and store matching
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DC-DP pairs and will treat DP as equivalent to their DC in the
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<em>special bonds</em> relations. It may be necessary to extend the space
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for storing such special relations. In this case extra space should
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be reserved by using the <em>extra</em> keyword of the <em>special_bonds</em>
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command. With our phenol, there is 1 more special neighbor for which
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space is required. Otherwise LAMMPS crashes and gives the required
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value.</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span> <span class="n">extra</span> <span class="mi">1</span>
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</pre></div>
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</div>
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<p>Let us assume we want to run a simple NVT simulation at 300 K. Note
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that Drude oscillators need to be thermalized at a low temperature in
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order to approximate a self-consistent field (SCF), therefore it is not
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possible to simulate an NVE ensemble with this package. Since dipoles
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are approximated by a charged DC-DP pair, the <em>pair_style</em> must
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include Coulomb interactions, for instance <em>lj/cut/coul/long</em> with
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<em>kspace_style pppm</em>. For example, with a cutoff of 10. and a precision
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1.e-4:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></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">10.0</span>
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<span class="n">kspace_style</span> <span class="n">pppm</span> <span class="mf">1.0e-4</span>
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</pre></div>
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</div>
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<p>As compared to the non-polarizable input file, <em>pair_coeff</em> lines need
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to be added for the DPs. Since the DPs have no Lennard-Jones
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interactions, their <em>epsilon</em> is 0. so the only <em>pair_coeff</em> line
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that needs to be added is</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">6</span><span class="o">*</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="c1"># All-DPs</span>
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</pre></div>
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</div>
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<p>Now for the thermalization, the simplest choice is to use the <a class="reference internal" href="fix_langevin_drude.html"><span class="doc">fix langevin/drude</span></a>.</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">LANG</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="mi">12435</span> <span class="mf">1.</span> <span class="mi">20</span> <span class="mi">13977</span>
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</pre></div>
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</div>
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<p>This applies a Langevin thermostat at temperature 300. to the centers
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of mass of the DC-DP pairs, with relaxation time 100 and with random
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seed 12345. This fix applies also a Langevin thermostat at temperature
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1. to the relative motion of the DPs around their DCs, with relaxation
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time 20 and random seed 13977. Only the DCs and non-polarizable
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atoms need to be in this fix’s group. LAMMPS will thermostate the DPs
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together with their DC. For this, ghost atoms need to know their
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velocities. Thus you need to add the following command:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
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</pre></div>
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</div>
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<p>In order to avoid that the center of mass of the whole system
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drifts due to the random forces of the Langevin thermostat on DCs, you
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can add the <em>zero yes</em> option at the end of the fix line.</p>
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<p>If the fix <em>shake</em> is used to constrain the C-H bonds, it should be
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invoked after the fix <em>langevin/drude</em> for more accuracy.</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">SHAKE</span> <span class="n">ATOMS</span> <span class="n">shake</span> <span class="mf">0.0001</span> <span class="mi">20</span> <span class="mi">0</span> <span class="n">t</span> <span class="mi">4</span> <span class="mi">5</span>
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</pre></div>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The group of the fix <em>shake</em> must not include the DPs. If the
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group <em>ATOMS</em> is defined by non-DPs atom types, you could use</p>
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</div>
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<p>Since the fix <em>langevin/drude</em> does not perform time integration (just
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modification of forces but no position/velocity updates), the fix
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<em>nve</em> should be used in conjunction.</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">NVE</span> <span class="nb">all</span> <span class="n">nve</span>
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</pre></div>
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</div>
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<p>Finally, do not forget to update the atom type elements if you use
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them in a <em>dump_modify ... element ...</em> command, by adding the element
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type of the DPs. Here for instance</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">DUMP</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">10</span> <span class="n">dump</span><span class="o">.</span><span class="n">lammpstrj</span> <span class="nb">id</span> <span class="n">mol</span> <span class="nb">type</span> <span class="n">element</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">ix</span> <span class="n">iy</span> <span class="n">iz</span>
|
|
<span class="n">dump_modify</span> <span class="n">DUMP</span> <span class="n">element</span> <span class="n">C</span> <span class="n">C</span> <span class="n">O</span> <span class="n">H</span> <span class="n">H</span> <span class="n">D</span> <span class="n">D</span> <span class="n">D</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The input file should now be ready for use!</p>
|
|
<p>You will notice that the global temperature <em>thermo_temp</em> computed by
|
|
LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as
|
|
standard atoms in his default compute. If you want to output the
|
|
temperatures of the DC-DP pair centers of mass and of the DPs relative
|
|
to their DCs, you should use the <a class="reference internal" href="compute_temp_drude.html"><span class="doc">compute temp_drude</span></a></p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">TDRUDE</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">drude</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>And then output the correct temperatures of the Drude oscillators
|
|
using <em>thermo_style custom</em> with respectively <em>c_TDRUDE[1]</em> and
|
|
<em>c_TDRUDE[2]</em>. These should be close to 300.0 and 1.0 on average.</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p><strong>Thole screening</strong></p>
|
|
<p>Dipolar interactions represented by point charges on springs may not
|
|
be stable, for example if the atomic polarizability is too high for
|
|
instance, a DP can escape from its DC and be captured by another DC,
|
|
which makes the force and energy diverge and the simulation
|
|
crash. Even without reaching this extreme case, the correlation
|
|
between nearby dipoles on the same molecule may be exagerated. Often,
|
|
special bond relations prevent bonded neighboring atoms to see the
|
|
charge of each other’s DP, so that the problem does not always appear.
|
|
It is possible to use screened dipole dipole interactions by using the
|
|
<a class="reference internal" href="pair_thole.html"><span class="doc">*pair_style thole*</span></a>. This is implemented as a
|
|
correction to the Coulomb pair_styles, which dampens at short distance
|
|
the interactions between the charges representing the induced dipoles.
|
|
It is to be used as <em>hybrid/overlay</em> with any standard <em>coul</em> pair
|
|
style. In our example, we would use</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</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">10.0</span> <span class="n">thole</span> <span class="mf">2.6</span> <span class="mf">10.0</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>This tells LAMMPS that we are using two pair_styles. The first one is
|
|
as above (<em>lj/cut/coul/long 10.0</em>). The second one is a <em>thole</em>
|
|
pair_style with default screening factor 2.6 (<a class="reference internal" href="#noskov"><span class="std std-ref">Noskov</span></a>) and
|
|
cutoff 10.0.</p>
|
|
<p>Since <em>hybrid/overlay</em> does not support mixing rules, the interaction
|
|
coefficients of all the pairs of atom types with i < j should be
|
|
explicitly defined. The output of the <em>polarizer</em> script can be used
|
|
to complete the <em>pair_coeff</em> section of the input file. In our
|
|
example, this will look like:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</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">0.0700</span> <span class="mf">3.550</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</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">0.0700</span> <span class="mf">3.550</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">3</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">0.1091</span> <span class="mf">3.310</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</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">0.0458</span> <span class="mf">2.985</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</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">0.0700</span> <span class="mf">3.550</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</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">0.1091</span> <span class="mf">3.310</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">4</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">0.0458</span> <span class="mf">2.985</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</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">0.1700</span> <span class="mf">3.070</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">4</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">0.0714</span> <span class="mf">2.745</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">4</span> <span class="mi">4</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">0.0300</span> <span class="mf">2.420</span>
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">5</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">0.0000</span> <span class="mf">0.000</span>
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">6</span><span class="o">*</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">0.0000</span> <span class="mf">0.000</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">thole</span> <span class="mf">1.090</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">thole</span> <span class="mf">1.218</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">thole</span> <span class="mf">0.829</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">6</span> <span class="n">thole</span> <span class="mf">1.090</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">7</span> <span class="n">thole</span> <span class="mf">1.218</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">8</span> <span class="n">thole</span> <span class="mf">0.829</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">thole</span> <span class="mf">1.360</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">thole</span> <span class="mf">0.926</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">6</span> <span class="n">thole</span> <span class="mf">1.218</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">7</span> <span class="n">thole</span> <span class="mf">1.360</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">8</span> <span class="n">thole</span> <span class="mf">0.926</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">thole</span> <span class="mf">0.630</span> <span class="mf">0.670</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">6</span> <span class="n">thole</span> <span class="mf">0.829</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">7</span> <span class="n">thole</span> <span class="mf">0.926</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">8</span> <span class="n">thole</span> <span class="mf">0.630</span> <span class="mf">0.670</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">6</span> <span class="mi">6</span> <span class="n">thole</span> <span class="mf">1.090</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">6</span> <span class="mi">7</span> <span class="n">thole</span> <span class="mf">1.218</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">6</span> <span class="mi">8</span> <span class="n">thole</span> <span class="mf">0.829</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">7</span> <span class="mi">7</span> <span class="n">thole</span> <span class="mf">1.360</span> <span class="mf">2.510</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">7</span> <span class="mi">8</span> <span class="n">thole</span> <span class="mf">0.926</span> <span class="mf">1.590</span>
|
|
<span class="n">pair_coeff</span> <span class="mi">8</span> <span class="mi">8</span> <span class="n">thole</span> <span class="mf">0.630</span> <span class="mf">0.670</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>For the <em>thole</em> pair style the coefficients are</p>
|
|
<ol class="arabic simple">
|
|
<li>the atom polarizability in units of cubic length</li>
|
|
<li>the screening factor of the Thole function (optional, default value
|
|
specified by the pair_style command)</li>
|
|
</ol>
|
|
<ul class="simple">
|
|
<li>the cutoff (optional, default value defined by the pair_style command)</li>
|
|
</ul>
|
|
<p>The special neighbors have charge-charge and charge-dipole
|
|
interactions screened by the <em>coul</em> factors of the <em>special_bonds</em>
|
|
command (0.0, 0.0, and 0.5 in the example above). Without using the
|
|
pair_style <em>thole</em>, dipole-dipole interactions are screened by the
|
|
same factor. By using the pair_style <em>thole</em>, dipole-dipole
|
|
interactions are screened by Thole’s function, whatever their special
|
|
relationship (except within each DC-DP pair of course). Consider for
|
|
example 1-2 neighbors: using the pair_style <em>thole</em>, their dipoles
|
|
will see each other (despite the <em>coul</em> factor being 0.) and the
|
|
interactions between these dipoles will be damped by Thole’s function.</p>
|
|
<hr class="docutils" />
|
|
<p><strong>Thermostats and barostats</strong></p>
|
|
<p>Using a Nose-Hoover barostat with the <em>langevin/drude</em> thermostat is
|
|
straightforward using fix <em>nph</em> instead of <em>nve</em>. For example:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">NPH</span> <span class="nb">all</span> <span class="n">nph</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>It is also possible to use a Nose-Hoover instead of a Langevin
|
|
thermostat. This requires to use <a class="reference internal" href="fix_drude_transform.html"><span class="doc">*fix drude/transform*</span></a> just before and after the
|
|
time intergation fixes. The <em>fix drude/transform/direct</em> converts the
|
|
atomic masses, positions, velocities and forces into a reduced
|
|
representation, where the DCs transform into the centers of mass of
|
|
the DC-DP pairs and the DPs transform into their relative position
|
|
with respect to their DC. The <em>fix drude/transform/inverse</em> performs
|
|
the reverse transformation. For a NVT simulation, with the DCs and
|
|
atoms at 300 K and the DPs at 1 K relative to their DC one would use</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
|
|
<span class="n">fix</span> <span class="n">NVT1</span> <span class="n">ATOMS</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span>
|
|
<span class="n">fix</span> <span class="n">NVT2</span> <span class="n">DRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">20</span>
|
|
<span class="n">fix</span> <span class="n">INVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>For our phenol example, the groups would be defined as</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">group</span> <span class="n">ATOMS</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">5</span> <span class="c1"># DCs and non-polarizable atoms</span>
|
|
<span class="n">group</span> <span class="n">CORES</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="c1"># DCs</span>
|
|
<span class="n">group</span> <span class="n">DRUDES</span> <span class="nb">type</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span> <span class="c1"># DPs</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>Note that with the fixes <em>drude/transform</em>, it is not required to
|
|
specify <em>comm_modify vel yes</em> because the fixes do it anyway (several
|
|
times and for the forces also). To avoid the flying ice cube artifact
|
|
<a class="reference internal" href="#lamoureux"><span class="std std-ref">(Lamoureux)</span></a>, where the atoms progressively freeze and the
|
|
center of mass of the whole system drifts faster and faster, the <em>fix
|
|
momentum</em> can be used. For instance:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">MOMENTUM</span> <span class="nb">all</span> <span class="n">momentum</span> <span class="mi">100</span> <span class="n">linear</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>It is a bit more tricky to run a NPT simulation with Nose-Hoover
|
|
barostat and thermostat. First, the volume should be integrated only
|
|
once. So the fix for DCs and atoms should be <em>npt</em> while the fix for
|
|
DPs should be <em>nvt</em> (or vice versa). Second, the <em>fix npt</em> computes a
|
|
global pressure and thus a global temperature whatever the fix group.
|
|
We do want the pressure to correspond to the whole system, but we want
|
|
the temperature to correspond to the fix group only. We must then use
|
|
the <em>fix_modify</em> command for this. In the end, the block of
|
|
instructions for thermostating and barostating will look like</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">TATOMS</span> <span class="n">ATOMS</span> <span class="n">temp</span>
|
|
<span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
|
|
<span class="n">fix</span> <span class="n">NPT</span> <span class="n">ATOMS</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
|
|
<span class="n">fix_modify</span> <span class="n">NPT</span> <span class="n">temp</span> <span class="n">TATOMS</span> <span class="n">press</span> <span class="n">thermo_press</span>
|
|
<span class="n">fix</span> <span class="n">NVT</span> <span class="n">DRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">20</span>
|
|
<span class="n">fix</span> <span class="n">INVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p><strong>Rigid bodies</strong></p>
|
|
<p>You may want to simulate molecules as rigid bodies (but polarizable).
|
|
Common cases are water models such as <a class="reference internal" href="#swm4-ndp"><span class="std std-ref">SWM4-NDP</span></a>, which is a
|
|
kind of polarizable TIP4P water. The rigid bodies and the DPs should
|
|
be integrated separately, even with the Langevin thermostat. Let us
|
|
review the different thermostats and ensemble combinations.</p>
|
|
<p>NVT ensemble using Langevin thermostat:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
|
|
<span class="n">fix</span> <span class="n">LANG</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="mi">12435</span> <span class="mf">1.</span> <span class="mi">20</span> <span class="mi">13977</span>
|
|
<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nve</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span>
|
|
<span class="n">fix</span> <span class="n">NVE</span> <span class="n">DRUDES</span> <span class="n">nve</span>
|
|
</pre></div>
|
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</div>
|
|
<p>NVT ensemble using Nose-Hoover thermostat:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
|
|
<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nvt</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span>
|
|
<span class="n">fix</span> <span class="n">NVT</span> <span class="n">DRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">20</span>
|
|
<span class="n">fix</span> <span class="n">INVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>NPT ensemble with Langevin thermostat:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
|
|
<span class="n">fix</span> <span class="n">LANG</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="mi">12435</span> <span class="mf">1.</span> <span class="mi">20</span> <span class="mi">13977</span>
|
|
<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nph</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
|
|
<span class="n">fix</span> <span class="n">NVE</span> <span class="n">DRUDES</span> <span class="n">nve</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>NPT ensemble using Nose-Hoover thermostat:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">TATOM</span> <span class="n">ATOMS</span> <span class="n">temp</span>
|
|
<span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
|
|
<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
|
|
<span class="n">fix_modify</span> <span class="n">RIGID</span> <span class="n">temp</span> <span class="n">TATOM</span> <span class="n">press</span> <span class="n">thermo_press</span>
|
|
<span class="n">fix</span> <span class="n">NVT</span> <span class="n">DRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">20</span>
|
|
<span class="n">fix</span> <span class="n">INVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p id="lamoureux"><strong>(Lamoureux)</strong> Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)</p>
|
|
<p id="schroeder"><strong>(Schroeder)</strong> Schr&ouml;der and Steinhauser, J Chem Phys, 133,
|
|
154511 (2010).</p>
|
|
<dl class="docutils" id="jiang">
|
|
<dt><strong>(Jiang)</strong> Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,</dt>
|
|
<dd>J Phys Chem Lett, 2, 87-92 (2011).</dd>
|
|
</dl>
|
|
<p id="thole"><strong>(Thole)</strong> Chem Phys, 59, 341 (1981).</p>
|
|
<p id="noskov"><strong>(Noskov)</strong> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).</p>
|
|
<p id="swm4-ndp"><strong>(SWM4-NDP)</strong> Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
|
|
Let, 418, 245-249 (2006)</p>
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|
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