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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_start.html">2. Getting Started</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_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending 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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<li>kspace_modify command</li>
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<div class="section" id="kspace-modify-command">
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<span id="index-0"></span><h1>kspace_modify command<a class="headerlink" href="#kspace-modify-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>kspace_modify keyword value ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>one or more keyword/value pairs may be listed</li>
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</ul>
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<pre class="literal-block">
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keyword = <em>mesh</em> or <em>order</em> or <em>order/disp</em> or <em>mix/disp</em> or <em>overlap</em> or <em>minorder</em> or <em>force</em> or <em>gewald</em> or <em>gewald/disp</em> or <em>slab</em> or (nozforce* or <em>compute</em> or <em>cutoff/adjust</em> or <em>fftbench</em> or <em>collective</em> or <em>diff</em> or <em>kmax/ewald</em> or <em>force/disp/real</em> or <em>force/disp/kspace</em> or <em>splittol</em> or <em>disp/auto</em>:l
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<em>mesh</em> value = x y z
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x,y,z = grid size in each dimension for long-range Coulombics
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<em>mesh/disp</em> value = x y z
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x,y,z = grid size in each dimension for 1/r^6 dispersion
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<em>order</em> value = N
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N = extent of Gaussian for PPPM or MSM mapping of charge to grid
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<em>order/disp</em> value = N
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N = extent of Gaussian for PPPM mapping of dispersion term to grid
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<em>mix/disp</em> value = <em>pair</em> or <em>geom</em> or <em>none</em>
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<em>overlap</em> = <em>yes</em> or <em>no</em> = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
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<em>minorder</em> value = M
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M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
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<em>force</em> value = accuracy (force units)
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<em>gewald</em> value = rinv (1/distance units)
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rinv = G-ewald parameter for Coulombics
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<em>gewald/disp</em> value = rinv (1/distance units)
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rinv = G-ewald parameter for dispersion
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<em>slab</em> value = volfactor or <em>nozforce</em>
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volfactor = ratio of the total extended volume used in the
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2d approximation compared with the volume of the simulation domain
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<em>nozforce</em> turns off kspace forces in the z direction
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<em>compute</em> value = <em>yes</em> or <em>no</em>
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<em>cutoff/adjust</em> value = <em>yes</em> or <em>no</em>
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<em>pressure/scalar</em> value = <em>yes</em> or <em>no</em>
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<em>fftbench</em> value = <em>yes</em> or <em>no</em>
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<em>collective</em> value = <em>yes</em> or <em>no</em>
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<em>diff</em> value = <em>ad</em> or <em>ik</em> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
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<em>kmax/ewald</em> value = kx ky kz
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kx,ky,kz = number of Ewald sum kspace vectors in each dimension
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<em>force/disp/real</em> value = accuracy (force units)
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<em>force/disp/kspace</em> value = accuracy (force units)
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<em>splittol</em> value = tol
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tol = relative size of two eigenvalues (see discussion below)
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<em>disp/auto</em> value = yes or no
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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>kspace_modify mesh 24 24 30 order 6
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kspace_modify slab 3.0
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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>Set parameters used by the kspace solvers defined by the
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<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Not all parameters are
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relevant to all kspace styles.</p>
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<p>The <em>mesh</em> keyword sets the grid size for kspace style <em>pppm</em> or
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<em>msm</em>. In the case of PPPM, this is the FFT mesh, and each dimension
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must be factorizable into powers of 2, 3, and 5. In the case of MSM,
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this is the finest scale real-space mesh, and each dimension must be
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factorizable into powers of 2. When this option is not set, the PPPM
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or MSM solver chooses its own grid size, consistent with the
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user-specified accuracy and pairwise cutoff. Values for x,y,z of
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0,0,0 unset the option.</p>
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<p>The <em>mesh/disp</em> keyword sets the grid size for kspace style
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<em>pppm/disp</em>. This is the FFT mesh for long-range dispersion and ach
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dimension must be factorizable into powers of 2, 3, and 5. When this
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option is not set, the PPPM solver chooses its own grid size,
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consistent with the user-specified accuracy and pairwise cutoff.
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Values for x,y,z of 0,0,0 unset the option.</p>
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<p>The <em>order</em> keyword determines how many grid spacings an atom’s charge
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extends when it is mapped to the grid in kspace style <em>pppm</em> or <em>msm</em>.
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The default for this parameter is 5 for PPPM and 8 for MSM, which
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means each charge spans 5 or 8 grid cells in each dimension,
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respectively. For the LAMMPS implementation of MSM, the order can
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range from 4 to 10 and must be even. For PPPM, the minimum allowed
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setting is 2 and the maximum allowed setting is 7. The larger the
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value of this parameter, the smaller that LAMMPS will set the grid
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size, to achieve the requested accuracy. Conversely, the smaller the
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order value, the larger the grid size will be. Note that there is an
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inherent trade-off involved: a small grid will lower the cost of FFTs
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or MSM direct sum, but a larger order parameter will increase the cost
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of interpolating charge/fields to/from the grid.</p>
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<p>The <em>order/disp</em> keyword determines how many grid spacings an atom’s
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dispersion term extends when it is mapped to the grid in kspace style
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<em>pppm/disp</em>. It has the same meaning as the <em>order</em> setting for
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Coulombics.</p>
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<p>The <em>overlap</em> keyword can be used in conjunction with the <em>minorder</em>
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keyword with the PPPM styles to adjust the amount of communication
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that occurs when values on the FFT grid are exchangeed between
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processors. This communication is distinct from the communication
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inherent in the parallel FFTs themselves, and is required because
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processors interpolate charge and field values using grid point values
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owned by neighboring processors (i.e. ghost point communication). If
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the <em>overlap</em> keyword is set to <em>yes</em> then this communication is
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allowed to extend beyond nearest-neighbor processors, e.g. when using
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lots of processors on a small problem. If it is set to <em>no</em> then the
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communication will be limited to nearest-neighbor processors and the
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<em>order</em> setting will be reduced if necessary, as explained by the
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<em>minorder</em> keyword discussion. The <em>overlap</em> keyword is always set to
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<em>yes</em> in MSM.</p>
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<p>The <em>minorder</em> keyword allows LAMMPS to reduce the <em>order</em> setting if
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necessary to keep the communication of ghost grid point limited to
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exchanges between nearest-neighbor processors. See the discussion of
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the <em>overlap</em> keyword for details. If the <em>overlap</em> keyword is set to
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<em>yes</em>, which is the default, this is never needed. If it set to <em>no</em>
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and overlap occurs, then LAMMPS will reduce the order setting, one
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step at a time, until the ghost grid overlap only extends to nearest
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neighbor processors. The <em>minorder</em> keyword limits how small the
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<em>order</em> setting can become. The minimum allowed value for PPPM is 2,
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which is the default. If <em>minorder</em> is set to the same value as
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<em>order</em> then no reduction is allowed, and LAMMPS will generate an
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error if the grid communcation is non-nearest-neighbor and <em>overlap</em>
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is set to <em>no</em>. The <em>minorder</em> keyword is not currently supported in
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MSM.</p>
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<p>The PPPM order parameter may be reset by LAMMPS when it sets up the
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FFT grid if the implied grid stencil extends beyond the grid cells
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owned by neighboring processors. Typically this will only occur when
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small problems are run on large numbers of processors. A warning will
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be generated indicating the order parameter is being reduced to allow
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LAMMPS to run the problem. Automatic adjustment of the order parameter
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is not supported in MSM.</p>
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<p>The <em>force</em> keyword overrides the relative accuracy parameter set by
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the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command with an absolute
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accuracy. The accuracy determines the RMS error in per-atom forces
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calculated by the long-range solver and is thus specified in force
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units. A negative value for the accuracy setting means to use the
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relative accuracy parameter. The accuracy setting is used in
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conjunction with the pairwise cutoff to determine the number of
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K-space vectors for style <em>ewald</em>, the FFT grid size for style
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<em>pppm</em>, or the real space grid size for style <em>msm</em>.</p>
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<p>The <em>gewald</em> keyword sets the value of the Ewald or PPPM G-ewald
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parameter for charge as <em>rinv</em> in reciprocal distance units. Without
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this setting, LAMMPS chooses the parameter automatically as a function
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of cutoff, precision, grid spacing, etc. This means it can vary from
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one simulation to the next which may not be desirable for matching a
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KSpace solver to a pre-tabulated pairwise potential. This setting can
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also be useful if Ewald or PPPM fails to choose a good grid spacing
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and G-ewald parameter automatically. If the value is set to 0.0,
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LAMMPS will choose the G-ewald parameter automatically. MSM does not
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use the <em>gewald</em> parameter.</p>
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<p>The <em>gewald/disp</em> keyword sets the value of the Ewald or PPPM G-ewald
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parameter for dispersion as <em>rinv</em> in reciprocal distance units. It
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has the same meaning as the <em>gewald</em> setting for Coulombics.</p>
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<p>The <em>slab</em> keyword allows an Ewald or PPPM solver to be used for a
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systems that are periodic in x,y but non-periodic in z - a
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> setting of “boundary p p f”. This is done by
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treating the system as if it were periodic in z, but inserting empty
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volume between atom slabs and removing dipole inter-slab interactions
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so that slab-slab interactions are effectively turned off. The
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volfactor value sets the ratio of the extended dimension in z divided
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by the actual dimension in z. The recommended value is 3.0. A larger
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value is inefficient; a smaller value introduces unwanted slab-slab
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interactions. The use of fixed boundaries in z means that the user
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must prevent particle migration beyond the initial z-bounds, typically
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by providing a wall-style fix. The methodology behind the <em>slab</em>
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option is explained in the paper by <a class="reference internal" href="#yeh"><span>(Yeh)</span></a>. The <em>slab</em> option
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is also extended to non-neutral systems
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<a class="reference internal" href="#ballenegger"><span>(Ballenegger)</span></a>. An alternative slab option can be
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invoked with the <em>nozforce</em> keyword in lieu of the volfactor. This
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turns off all kspace forces in the z direction. The <em>nozforce</em> option
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is not supported by MSM. For MSM, any combination of periodic,
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non-periodic, or shrink-wrapped boundaries can be set using
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> (the slab approximation in not needed). The
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<em>slab</em> keyword is not currently supported by Ewald or PPPM when using
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a triclinic simulation cell. The slab correction has also been
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extended to point dipole interactions <a class="reference internal" href="#klapp"><span>(Klapp)</span></a> in
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<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> <em>ewald/disp</em>.</p>
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<p>The <em>compute</em> keyword allows Kspace computations to be turned off,
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even though a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> is defined. This is
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not useful for running a real simulation, but can be useful for
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debugging purposes or for computing only partial forces that do not
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include the Kspace contribution. You can also do this by simply not
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defining a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>, but a Kspace-compatible
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<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> requires a kspace style to be defined.
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This keyword gives you that option.</p>
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<p>The <em>cutoff/adjust</em> keyword applies only to MSM. If this option is
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turned on, the Coulombic cutoff will be automatically adjusted at the
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beginning of the run to give the desired estimated error. Other
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cutoffs such as LJ will not be affected. If the grid is not set using
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the <em>mesh</em> command, this command will also attempt to use the optimal
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grid that minimizes cost using an estimate given by
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<a class="reference internal" href="kspace_style.html#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
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experimental, and still may not yield the optimal parameters.</p>
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<p>The <em>pressure/scalar</em> keyword applies only to MSM. If this option is
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turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
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be computed, which can be used, for example, to run an isotropic barostat.
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Computing the full pressure tensor with MSM is expensive, and this option
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provides a faster alternative. The scalar pressure is computed using a
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relationship between the Coulombic energy and pressure <a class="reference internal" href="#hummer"><span>(Hummer)</span></a>
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instead of using the virial equation. This option cannot be used to access
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individual components of the pressure tensor, to compute per-atom virial,
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or with suffix kspace/pair styles of MSM, like OMP or GPU.</p>
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<p>The <em>fftbench</em> keyword applies only to PPPM. It is on by default. If
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this option is turned off, LAMMPS will not take the time at the end
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of a run to give FFT benchmark timings, and will finish a few seconds
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faster than it would if this option were on.</p>
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<p>The <em>collective</em> keyword applies only to PPPM. It is set to <em>no</em> by
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default, except on IBM BlueGene machines. If this option is set to
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<em>yes</em>, LAMMPS will use MPI collective operations to remap data for
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3d-FFT operations instead of the default point-to-point communication.
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This is faster on IBM BlueGene machines, and may also be faster on
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other machines if they have an efficient implementation of MPI
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collective operations and adequate hardware.</p>
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<p>The <em>diff</em> keyword specifies the differentiation scheme used by the
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PPPM method to compute forces on particles given electrostatic
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potentials on the PPPM mesh. The <em>ik</em> approach is the default for
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PPPM and is the original formulation used in <a class="reference internal" href="kspace_style.html#hockney"><span>(Hockney)</span></a>. It
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performs differentiation in Kspace, and uses 3 FFTs to transfer each
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component of the computed fields back to real space for total of 4
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FFTs per timestep.</p>
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<p>The analytic differentiation <em>ad</em> approach uses only 1 FFT to transfer
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information back to real space for a total of 2 FFTs per timestep. It
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then performs analytic differentiation on the single quantity to
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generate the 3 components of the electric field at each grid point.
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This is sometimes referred to as “smoothed” PPPM. This approach
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requires a somewhat larger PPPM mesh to achieve the same accuracy as
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the <em>ik</em> method. Currently, only the <em>ik</em> method (default) can be
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used for a triclinic simulation cell with PPPM. The <em>ad</em> method is
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always used for MSM.</p>
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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">Currently, not all PPPM styles support the <em>ad</em> option. Support
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for those PPPM variants will be added later.</p>
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|
</div>
|
|
<p>The <em>kmax/ewald</em> keyword sets the number of kspace vectors in each
|
|
dimension for kspace style <em>ewald</em>. The three values must be positive
|
|
integers, or else (0,0,0), which unsets the option. When this option
|
|
is not set, the Ewald sum scheme chooses its own kspace vectors,
|
|
consistent with the user-specified accuracy and pairwise cutoff. In
|
|
any case, if kspace style <em>ewald</em> is invoked, the values used are
|
|
printed to the screen and the log file at the start of the run.</p>
|
|
<p>With the <em>mix/disp</em> keyword one can select the mixing rule for the
|
|
dispersion coefficients. With <em>pair</em>, the dispersion coefficients of
|
|
unlike types are computed as indicated with
|
|
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>. With <em>geom</em>, geometric mixing is
|
|
enforced on the dispersion coefficients in the kspace
|
|
coefficients. When using the arithmetic mixing rule, this will
|
|
speed-up the simulations but introduces some error in the force
|
|
computations, as shown in <a class="reference internal" href="#wennberg"><span>(Wennberg)</span></a>. With <em>none</em>, it is
|
|
assumed that no mixing rule is applicable. Splitting of the dispersion
|
|
coefficients will be performed as described in
|
|
<a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
|
|
the <em>splittol</em> keywords. Only the eigenvalues that are larger than tol
|
|
compared to the largest eigenvalues are included. Using this keywords
|
|
the original matrix of dispersion coefficients is approximated. This
|
|
leads to faster computations, but the accuracy in the reciprocal space
|
|
computations of the dispersion part is decreased.</p>
|
|
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
|
|
accuracy for the real and space computations for the dispersion part
|
|
of pppm/disp. As shown in <a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>, optimal
|
|
performance and accuracy in the results is obtained when these values
|
|
are different.</p>
|
|
<p>The <em>disp/auto</em> option controlls whether the pppm/disp is allowed to
|
|
generate PPPM parameters automatically. If set to <em>no</em>, parameters have
|
|
to be specified using the <em>gewald/disp</em>, <em>mesh/disp</em>,
|
|
<em>force/disp/real</em> or <em>force/disp/kspace</em> keywords, or
|
|
the code will stop with an error message. When this option is set to
|
|
<em>yes</em>, the error message will not appear and the simulation will start.
|
|
For a typical application, using the automatic parameter generation will provide
|
|
simulations that are either inaccurate or slow. Using this option is thus not
|
|
recommended. For guidelines on how to obtain good parameters, see the <a class="reference internal" href="Section_howto.html#howto-23"><span>How-To</span></a> discussion.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</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="kspace_style.html"><em>kspace_style</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</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 mesh = mesh/disp = 0 0 0, order = order/disp =
|
|
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
|
|
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
|
|
yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
|
|
(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
|
|
split = 0, tol = 1.0e-6, and disp/auto = no.</p>
|
|
<hr class="docutils" />
|
|
<p id="hockney"><strong>(Hockney)</strong> Hockney and Eastwood, Computer Simulation Using Particles,
|
|
Adam Hilger, NY (1989).</p>
|
|
<p id="yeh"><strong>(Yeh)</strong> Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).</p>
|
|
<p id="ballenegger"><strong>(Ballenegger)</strong> Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
|
|
(2009).</p>
|
|
<p id="klapp"><strong>(Klapp)</strong> Klapp, Schoen, J Chem Phys, 117, 8050 (2002).</p>
|
|
<p id="hardy"><strong>(Hardy)</strong> David Hardy thesis: Multilevel Summation for the Fast
|
|
Evaluation of Forces for the Simulation of Biomolecules, University of
|
|
Illinois at Urbana-Champaign, (2006).</p>
|
|
<p id="hummer"><strong>(Hummer)</strong> Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)</p>
|
|
<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
|
|
Chem Theory Comput, 9, 5412 (2013).</p>
|
|
<p id="wennberg"><strong>(Wennberg)</strong> Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
|
|
9, 3527 (2013).</p>
|
|
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