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<div class="section" id="fix-gcmc-command">
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<span id="index-0"></span><h1>fix gcmc command<a class="headerlink" href="#fix-gcmc-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>gcmc = style name of this fix command</li>
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<li>N = invoke this fix every N steps</li>
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<li>X = average number of GCMC exchanges to attempt every N steps</li>
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<li>M = average number of MC moves to attempt every N steps</li>
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<li>type = atom type for inserted atoms (must be 0 if mol keyword used)</li>
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<li>seed = random # seed (positive integer)</li>
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<li>T = temperature of the ideal gas reservoir (temperature units)</li>
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<li>mu = chemical potential of the ideal gas reservoir (energy units)</li>
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<li>translate = maximum Monte Carlo translation distance (length units)</li>
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<li>zero or more keyword/value pairs may be appended to args</li>
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</ul>
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<pre class="literal-block">
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keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <em>fugacity_coeff</em>, <em>full_energy</em>, <em>charge</em>, <em>group</em>, <em>grouptype</em>, <em>intra_energy</em>, or <em>tfac_insert</em>
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<em>mol</em> value = template-ID
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
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<em>shake</em> value = fix-ID
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fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
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<em>region</em> value = region-ID
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region-ID = ID of region where MC moves are allowed
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<em>maxangle</em> value = maximum molecular rotation angle (degrees)
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<em>pressure</em> value = pressure of the gas reservoir (pressure units)
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<em>fugacity_coeff</em> value = fugacity coefficient of the gas reservoir (unitless)
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<em>full_energy</em> = compute the entire system energy when performing MC moves
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<em>charge</em> value = charge of inserted atoms (charge units)
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<em>group</em> value = group-ID
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group-ID = group-ID for inserted atoms (string)
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<em>grouptype</em> values = type group-ID
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type = atom type (int)
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group-ID = group-ID for inserted atoms (string)
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<em>intra_energy</em> value = intramolecular energy (energy units)
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<em>tfac_insert</em> value = scale up/down temperature of inserted atoms (unitless)
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
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fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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atoms or molecules of the given type with an imaginary ideal gas reservoir at
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the specified T and chemical potential (mu) as discussed in
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<a class="reference internal" href="#frenkel"><span>(Frenkel)</span></a>. If used with the <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> command,
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simulations in the grand canonical ensemble (muVT, constant chemical
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potential, constant volume, and constant temperature) can be
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performed. Specific uses include computing isotherms in microporous
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materials, or computing vapor-liquid coexistence curves.</p>
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<p>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
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or deletions) of gas atoms or molecules of
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the given type between the simulation cell and the imaginary
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reservoir. It also attempts a number of Monte Carlo
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moves (translations and molecule rotations) of gas of the given type
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within the simulation cell or region. The average number of
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attempted GCMC exchanges is X. The average number of attempted MC moves is M.
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M should typically be chosen to be
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approximately equal to the expected number of gas atoms or molecules
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of the given type within the simulation cell or region,
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which will result in roughly one
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MC translation per atom or molecule per MC cycle.</p>
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<p>For MC moves of molecular gasses, rotations and translations are each
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attempted with 50% probability. For MC moves of atomic gasses,
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translations are attempted 100% of the time. For MC exchanges of
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either molecular or atomic gasses, deletions and insertions are each
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attempted with 50% probability.</p>
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<p>All inserted particles are always assigned to two groups: the default group
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“all” and the group specified in the fix gcmc command (which can also
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be “all”). In addition, particles are also added to any groups specified
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by the <em>group</em> and <em>grouptype</em> keywords.
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If inserted particles are individual atoms, they are
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assigned the atom type given by the type argument. If they are molecules,
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the type argument has no effect and must be set to zero. Instead,
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the type of each atom in the inserted molecule is specified
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in the file read by the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command.</p>
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<p>This fix cannot be used to perform MC insertions of gas atoms or
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molecules other than the exchanged type, but MC deletions,
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translations, and rotations can be performed on any atom/molecule in
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the fix group. All atoms in the simulation cell can be moved using
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regular time integration translations, e.g. via
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<code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting in a hybrid GCMC+MD simulation. A
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smaller-than-usual timestep size may be needed when running such a
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hybrid simulation, especially if the inserted molecules are not well
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equilibrated.</p>
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<p>This command may optionally use the <em>region</em> keyword to define an
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exchange and move volume. The specified region must have been
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previously defined with a <a class="reference internal" href="region.html"><em>region</em></a> command. It must be
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defined with side = <em>in</em>. Insertion attempts occur only within the
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specified region. For non-rectangular regions, random trial
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points are generated within the rectangular bounding box until a point is found
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that lies inside the region. If no valid point is generated after 1000 trials,
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no insertion is performed, but it is counted as an attempted insertion.
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Move and deletion attempt candidates are selected
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from gas atoms or molecules within the region. If there are no candidates,
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no move or deletion is performed, but it is counted as an attempt move
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or deletion. If an attempted move places the atom or molecule center-of-mass outside
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the specified region, a new attempted move is generated. This process is repeated
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until the atom or molecule center-of-mass is inside the specified region.</p>
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<p>If used with <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, the temperature of the imaginary
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reservoir, T, should be set to be equivalent to the target temperature
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used in <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>. Otherwise, the imaginary reservoir
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will not be in thermal equilibrium with the simulation cell. Also,
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it is important that the temperature used by fix nvt be dynamic,
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which can be achieved as follows:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute mdtemp mdatoms temp
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compute_modify mdtemp dynamic yes
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fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
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fix_modify mdnvt temp mdtemp
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</pre></div>
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</div>
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<p>Note that neighbor lists are re-built every timestep that this fix is
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invoked, so you should not set N to be too small. However, periodic
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rebuilds are necessary in order to avoid dangerous rebuilds and missed
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interactions. Specifically, avoid performing so many MC translations
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per timestep that atoms can move beyond the neighbor list skin
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distance. See the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command for details.</p>
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<p>When an atom or molecule is to be inserted, its
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coordinates are chosen at a random position within the current
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simulation cell or region, and new atom velocities are randomly chosen from
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the specified temperature distribution given by T. The effective
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temperature for new atom velocities can be increased or decreased
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using the optional keyword <em>tfac_insert</em> (see below). Relative
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coordinates for atoms in a molecule are taken from the template
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molecule provided by the user. The center of mass of the molecule
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is placed at the insertion point. The orientation of the molecule
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is chosen at random by rotating about this point.</p>
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<p>Individual atoms are inserted, unless the <em>mol</em> keyword is used. It
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specifies a <em>template-ID</em> previously defined using the
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<a class="reference internal" href="molecule.html"><em>molecule</em></a> command, which reads a file that defines the
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molecule. The coordinates, atom types, charges, etc, as well as any
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bond/angle/etc and special neighbor information for the molecule can
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be specified in the molecule file. See the <a class="reference internal" href="molecule.html"><em>molecule</em></a>
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command for details. The only settings required to be in this file
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are the coordinates and types of atoms in the molecule.</p>
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<p>When not using the <em>mol</em> keyword, you should ensure you do not delete
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atoms that are bonded to other atoms, or LAMMPS will
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soon generate an error when it tries to find bonded neighbors. LAMMPS will
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warn you if any of the atoms eligible for deletion have a non-zero
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molecule ID, but does not check for this at the time of deletion.</p>
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<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
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their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,
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specifying as its value the ID of a separate <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command which also appears in your input script.</p>
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<p>Optionally, users may specify the maximum rotation angle for
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molecular rotations using the <em>maxangle</em> keyword and specifying
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the angle in degrees. Rotations are performed by generating a random
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point on the unit sphere and a random rotation angle on the
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range [0,maxangle). The molecule is then rotated by that angle about an
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axis passing through the molecule center of mass. The axis is parallel
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to the unit vector defined by the point on the unit sphere.
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The same procedure is used for randomly rotating molecules when they
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are inserted, except that the maximum angle is 360 degrees.</p>
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<p>Note that fix GCMC does not use configurational bias
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MC or any other kind of sampling of intramolecular degrees of freedom.
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Inserted molecules can have different orientations, but they will all
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have the same intramolecular configuration,
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which was specified in the molecule command input.</p>
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<p>For atomic gasses, inserted atoms have the specified atom type, but
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deleted atoms are any atoms that have been inserted or that belong
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to the user-specified fix group. For molecular gasses, exchanged
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molecules use the same atom types as in the template molecule
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supplied by the user. In both cases, exchanged
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atoms/molecules are assigned to two groups: the default group “all”
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and the group specified in the fix gcmc command (which can also be
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“all”).</p>
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<p>The gas reservoir pressure can be specified using the <em>pressure</em>
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keyword, in which case the user-specified chemical potential is
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ignored. For non-ideal gas reservoirs, the user may also specify the
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fugacity coefficient using the <em>fugacity_coeff</em> keyword.</p>
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<p>The <em>full_energy</em> option means that fix GCMC will compute the total
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potential energy of the entire simulated system. The total system
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energy before and after the proposed GCMC move is then used in the
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Metropolis criterion to determine whether or not to accept the
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proposed GCMC move. By default, this option is off, in which case
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only partial energies are computed to determine the difference in
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energy that would be caused by the proposed GCMC move.</p>
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<p>The <em>full_energy</em> option is needed for systems with complicated
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potential energy calculations, including the following:</p>
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<ul class="simple">
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<li>long-range electrostatics (kspace)</li>
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<li>many-body pair styles</li>
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<li>hybrid pair styles</li>
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<li>eam pair styles</li>
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<li>triclinic systems</li>
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<li>need to include potential energy contributions from other fixes</li>
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</ul>
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<p>In these cases, LAMMPS will automatically apply the <em>full_energy</em>
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keyword and issue a warning message.</p>
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<p>When the <em>mol</em> keyword is used, the <em>full_energy</em> option also includes
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the intramolecular energy of inserted and deleted molecules. If this
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is not desired, the <em>intra_energy</em> keyword can be used to define an
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amount of energy that is subtracted from the final energy when a molecule
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is inserted, and added to the initial energy when a molecule is
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deleted. For molecules that have a non-zero intramolecular energy, this
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will ensure roughly the same behavior whether or not the <em>full_energy</em>
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option is used.</p>
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<p>Inserted atoms and molecules are assigned random velocities based on the
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specified temperature T. Because the relative velocity of
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all atoms in the molecule is zero, this may result in inserted molecules
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that are systematically too cold. In addition, the intramolecular potential
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energy of the inserted molecule may cause the kinetic energy
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of the molecule to quickly increase or decrease after insertion.
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The <em>tfac_insert</em> keyword allows the user to counteract these effects
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by changing the temperature used to assign velocities to
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inserted atoms and molecules by a constant factor. For a
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particular application, some experimentation may be required
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to find a value of <em>tfac_insert</em> that results in inserted molecules that
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equilibrate quickly to the correct temperature.</p>
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<p>Some fixes have an associated potential energy. Examples of such fixes
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include: <a class="reference internal" href="fix_efield.html"><em>efield</em></a>, <a class="reference internal" href="fix_gravity.html"><em>gravity</em></a>,
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<a class="reference internal" href="fix_addforce.html"><em>addforce</em></a>, <a class="reference internal" href="fix_langevin.html"><em>langevin</em></a>,
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<a class="reference internal" href="fix_restrain.html"><em>restrain</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen</em></a>,
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<a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>, and <a class="reference internal" href="fix_wall.html"><em>wall fixes</em></a>.
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For that energy to be included in the total potential energy of the
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system (the quantity used when performing GCMC moves),
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you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for
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that fix. The doc pages for individual <a class="reference internal" href="fix.html"><em>fix</em></a> commands
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specify if this should be done.</p>
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<p>Use the <em>charge</em> option to insert atoms with a user-specified point
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charge. Note that doing so will cause the system to become non-neutral.
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LAMMPS issues a warning when using long-range electrostatics (kspace)
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with non-neutral systems. See the
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<a class="reference internal" href="compute_group_group.html"><em>compute_group_group</em></a> documentation for more
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details about simulating non-neutral systems with kspace on.</p>
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<p>Use of this fix typically will cause the number of atoms to fluctuate,
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therefore, you will want to use the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command to insure that the
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current number of atoms is used as a normalizing factor each time
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temperature is computed. Here is the necessary command:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute_modify thermo_temp dynamic yes
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</pre></div>
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</div>
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<p>If LJ units are used, note that a value of 0.18292026 is used by this
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fix as the reduced value for Planck’s constant. This value was
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derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
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epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
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|
mass = 39.948 amu.</p>
|
|
<p>The <em>group</em> keyword assigns all inserted atoms to the <a class="reference internal" href="group.html"><em>group</em></a>
|
|
of the group-ID value. The <em>grouptype</em> keyword assigns all
|
|
inserted atoms of the specified type to the <a class="reference internal" href="group.html"><em>group</em></a>
|
|
of the group-ID value.</p>
|
|
</div>
|
|
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
|
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
|
|
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. This includes information about the random
|
|
number generator seed, the next timestep for MC exchanges, etc. See
|
|
the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to
|
|
re-specify a fix in an input script that reads a restart file, so that
|
|
the operation of the fix continues in an uninterrupted fashion.</p>
|
|
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
|
|
fix.</p>
|
|
<p>This fix computes a global vector of length 8, which can be accessed
|
|
by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector
|
|
values are the following global cumulative quantities:</p>
|
|
<ul class="simple">
|
|
<li>1 = translation attempts</li>
|
|
<li>2 = translation successes</li>
|
|
<li>3 = insertion attempts</li>
|
|
<li>4 = insertion successes</li>
|
|
<li>5 = deletion attempts</li>
|
|
<li>6 = deletion successes</li>
|
|
<li>7 = rotation attempts</li>
|
|
<li>8 = rotation successes</li>
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|
</ul>
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|
<p>The vector values calculated by this fix are “extensive”.</p>
|
|
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
|
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
|
|
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
|
<p>Do not set “neigh_modify once yes” or else this fix will never be
|
|
called. Reneighboring is required.</p>
|
|
<p>Can be run in parallel, but aspects of the GCMC part will not scale
|
|
well in parallel. Only usable for 3D simulations.</p>
|
|
<p>Note that very lengthy simulations involving insertions/deletions of
|
|
billions of gas molecules may run out of atom or molecule IDs and
|
|
trigger an error, so it is better to run multiple shorter-duration
|
|
simulations. Likewise, very large molecules have not been tested
|
|
and may turn out to be problematic.</p>
|
|
<p>Use of multiple fix gcmc commands in the same input script can be
|
|
problematic if using a template molecule. The issue is that the
|
|
user-referenced template molecule in the second fix gcmc command
|
|
may no longer exist since it might have been deleted by the first
|
|
fix gcmc command. An existing template molecule will need to be
|
|
referenced by the user for each subsequent fix gcmc command.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="fix_atom_swap.html"><em>fix atom/swap</em></a>,
|
|
<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
|
|
<a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>,
|
|
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The option defaults are mol = no, maxangle = 10, full_energy = no,
|
|
except for the situations where full_energy is required, as
|
|
listed above.</p>
|
|
<hr class="docutils" />
|
|
<p id="frenkel"><strong>(Frenkel)</strong> Frenkel and Smit, Understanding Molecular Simulation,
|
|
Academic Press, London, 2002.</p>
|
|
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