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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>kspace_modify command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>kspace_modify keyword value ...
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</PRE>
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<UL><LI>one or more keyword/value pairs may be listed
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<LI>keyword = <I>mesh</I> or <I>order</I> or <I>order/disp</I> or <I>overlap</I> or <I>minorder</I> or <I>force</I> or <I>gewald</I> or <I>gewald/disp</I> or <I>slab</I> or (nozforce</I> or <I>compute</I> or <I>cutoff/adjust</I> or <I>diff</I> or <I>kmax/ewald</I> or <I>force/disp/real</I> or <I>force/disp/kspace</I> or <I>splittol</I>
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<PRE> <I>mesh</I> value = x y z
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x,y,z = grid size in each dimension for long-range Coulombics
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<I>mesh/disp</I> 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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<I>order</I> value = N
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N = extent of Gaussian for PPPM or MSM mapping of charge to grid
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<I>order/disp</I> value = N
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N = extent of Gaussian for PPPM mapping of dispersion term to grid
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<I>overlap</I> = <I>yes</I> or <I>no</I> = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
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<I>minorder</I> value = M
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M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
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<I>force</I> value = accuracy (force units)
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<I>gewald</I> value = rinv (1/distance units)
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rinv = G-ewald parameter for Coulombics
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<I>gewald/disp</I> value = rinv (1/distance units)
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rinv = G-ewald parameter for dispersion
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<I>slab</I> value = volfactor or <I>nozforce</I>
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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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<I>nozforce</I> turns off kspace forces in the z direction
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<I>compute</I> value = <I>yes</I> or <I>no</I>
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<I>cutoff/adjust</I> value = <I>yes</I> or <I>no</I>
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<I>fftbench</I> value = <I>yes</I> or <I>no</I>
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<I>diff</I> value = <I>ad</I> or <I>ik</I> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
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<I>kmax/ewald</I> value = kx ky kz
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kx,ky,kz = number of Ewald sum kspace vectors in each dimension
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<I>mix/disp</I> value = <I>pair</I> or <I>geom</I> or <I>none</I>
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<I>force/disp/real</I> value = accuracy (force units)
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<I>force/disp/kspace</I> value = accuracy (force units)
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<I>splittol</I> value = tol
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tol = relative size of two eigenvalues (see discussion below)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>kspace_modify mesh 24 24 30 order 6
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kspace_modify slab 3.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Set parameters used by the kspace solvers defined by the
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<A HREF = "kspace_style.html">kspace_style</A> command. Not all parameters are
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relevant to all kspace styles.
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</P>
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<P>The <I>mesh</I> keyword sets the grid size for kspace style <I>pppm</I> or
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<I>msm</I>. 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.
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</P>
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<P>The <I>mesh/disp</I> keyword sets the grid size for kspace style
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<I>pppm/disp</I>. 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.
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</P>
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<P>The <I>order</I> 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 <I>pppm</I> or <I>msm</I>.
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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.
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</P>
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<P>The <I>order/disp</I> 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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<I>pppm/disp</I>. It has the same meaning as the <I>order</I> setting for
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Coulombics.
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</P>
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<P>The <I>overlap</I> keyword can be used in conjunction with the <I>minorder</I>
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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 <I>overlap</I> keyword is set to <I>yes</I> 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 <I>no</I> then the
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communication will be limited to nearest-neighbor processors and the
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<I>order</I> setting will be reduced if necessary, as explained by the
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<I>minorder</I> keyword discussion. The <I>overlap</I> keyword is always set to
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<I>yes</I> in MSM.
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</P>
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<P>The <I>minorder</I> keyword allows LAMMPS to reduce the <I>order</I> 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 <I>overlap</I> keyword for details. If the <I>overlap</I> keyword is set to
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<I>yes</I>, which is the default, this is never needed. If it set to <I>no</I>
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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 <I>minorder</I> keyword limits how small the
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<I>order</I> setting can become. The minimum allowed value for PPPM is 2,
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which is the default. If <I>minorder</I> is set to the same value as
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<I>order</I> then no reduction is allowed, and LAMMPS will generate an
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error if the grid communcation is non-nearest-neighbor and <I>overlap</I>
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is set to <I>no</I>. The <I>minorder</I> keyword is not currently supported in
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MSM.
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</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.
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</P>
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<P>The <I>force</I> keyword overrides the relative accuracy parameter set by
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the <A HREF = "kspace_style.html">kspace_style</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 <I>ewald</I>, the FFT grid size for style
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<I>pppm</I>, or the real space grid size for style <I>msm</I>.
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</P>
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<P>The <I>gewald</I> keyword sets the value of the Ewald or PPPM G-ewald
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parameter for charge as <I>rinv</I> 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 <I>gewald</I> parameter.
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</P>
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<P>The <I>gewald/disp</I> keyword sets the value of the Ewald or PPPM G-ewald
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parameter for dispersion as <I>rinv</I> in reciprocal distance units. It
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has the same meaning as the <I>gewald</I> setting for Coulombics.
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</P>
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<P>The <I>slab</I> 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 HREF = "boundary.html">boundary</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 <I>slab</I>
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option is explained in the paper by <A HREF = "#Yeh">(Yeh)</A>. The <I>slab</I> option
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is also extended to non-neutral systems
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<A HREF = "#Ballenegger">(Ballenegger)</A>. An alternative slab option can be
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invoked with the <I>nozforce</I> keyword in lieu of the volfactor. This
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turns off all kspace forces in the z direction. The <I>nozforce</I> 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 HREF = "boundary.html">boundary</A> (the slab approximation in not needed). The
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<I>slab</I> keyword is not currently supported by Ewald or PPPM when using
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a triclinic simulation cell.
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</P>
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<P>The <I>compute</I> keyword allows Kspace computations to be turned off,
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even though a <A HREF = "kspace_style.html">kspace_style</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 HREF = "kspace_style.html">kspace_style</A>, but a Kspace-compatible
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<A HREF = "pair_style.html">pair_style</A> requires a kspace style to be defined.
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This keyword gives you that option.
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</P>
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<P>The <I>cutoff/adjust</I> 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 <I>mesh</I> 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 HREF = "#Hardy">(Hardy)</A>. Note that this cost estimate is not exact, somewhat
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experimental, and still may not yield the optimal parameters.
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</P>
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<P>The <I>fftbench</I> 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.
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</P>
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<P>The <I>diff</I> 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 <I>ik</I> approach is the default for
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PPPM and is the original formulation used in <A HREF = "#Hockney">(Hockney)</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.
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</P>
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<P>The analytic differentiation <I>ad</I> 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 <I>ik</I> method. Currently, only the <I>ik</I> method (default) can be
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used for a triclinic simulation cell with PPPM. The <I>ad</I> method is
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always used for MSM.
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</P>
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<P>IMPORTANT NOTE: Currently, not all PPPM styles support the <I>ad</I>
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option. Support for those PPPM variants will be added later.
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</P>
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<P>The <I>kmax/ewald</I> keyword sets the number of kspace vectors in
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each dimension for kspace style <I>ewald</I>. The three values must
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be positive integers, or else (0,0,0), which unsets the option.
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When this option is not
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set, the Ewald sum scheme chooses its own kspace vectors,
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consistent with the
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user-specified accuracy and pairwise cutoff. In any case,
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if kspace style <I>ewald</I> is invoked, the values used
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are printed to the screen and
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the log file at the start of the run.
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</P>
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<P>With the <I>mix/disp<I> keyword one can select the mixing rule for the
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dispersion coefficients. With <I>pair</I>, the dispersion coefficients of
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unlike types are computed as indicated with
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<A HREF = "pair_modify.html">pair_modify</A>. With <I>geom</I>, geometric mixing is
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enforced on the dispersion coefficients in the kspace
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coefficients. When using the arithmetic mixing rule, this will
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speed-up the simulations but introduces some error in the force
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computations, as shown in <A HREF = "#Wennberg">(Wennberg)</A>. With <I>none</I>, it is
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assumed that no mixing rule is applicable. Splitting of the dispersion
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coefficients will be performed as described in
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<A HREF = "#Isele-Holder">(Isele-Holder)</A>. This splitting can be influenced with
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the <I>splittol</I> keywords. Only the eigenvalues that are larger than tol
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compared to the largest eigenvalues are included. Using this keywords
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the original matrix of dispersion coefficients is approximated. This
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leads to faster computations, but the accuracy in the reciprocal space
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computations of the dispersion part is decreased.
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</P>
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<P>The <I>force/disp/real</I> and <I>force/disp/kspace</I> keywords set the force
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accuracy for the real and space computations for the dispersion part
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of pppm/disp. as shown in <A HREF = "#Isele-Holder">(Isele-Holder)</A>, optimal
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performance and accuracy in the results is obtained when these values
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are different.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "boundary.html">boundary</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
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5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
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gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
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yes (MSM), fftbench = yes (PPPM), diff = ik (PPPM), mix/disp = pair,
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force/disp/real = -1.0, force/disp/kspace = -1.0, split = 0, and tol = 1.0e-6.
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</P>
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<HR>
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<A NAME = "Hockney"></A>
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<P><B>(Hockney)</B> Hockney and Eastwood, Computer Simulation Using Particles,
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Adam Hilger, NY (1989).
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</P>
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<A NAME = "Yeh"></A>
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<P><B>(Yeh)</B> Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
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</P>
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<A NAME = "Ballenegger"></A>
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<P><B>(Ballenegger)</B> Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
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(2009).
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</P>
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<A NAME = "Hardy"></A>
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<P><B>(Hardy)</B> David Hardy thesis: Multilevel Summation for the Fast
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Evaluation of Forces for the Simulation of Biomolecules, University of
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Illinois at Urbana-Champaign, (2006).
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</P>
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<A NAME = "Isele-Holder"></A>
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<P><B>(Isele-Holder)</B> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
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Chem Theory Comput, 9, 5412 (2013).
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</P>
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<A NAME = "Wennberg"></A>
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<P><B>(Wennberg)</B> Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
|
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9, 3527 (2013).
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</P>
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</HTML>
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|
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@ -1,298 +1,304 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
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:link(lws,http://lammps.sandia.gov)
|
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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kspace_modify command :h3
|
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[Syntax:]
|
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|
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kspace_modify keyword value ... :pre
|
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|
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one or more keyword/value pairs may be listed :ulb,l
|
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keyword = {mesh} or {order} or {order/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} :l
|
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{mesh} value = x y z
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x,y,z = grid size in each dimension for long-range Coulombics
|
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{mesh/disp} 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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{order} value = N
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N = extent of Gaussian for PPPM or MSM mapping of charge to grid
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{order/disp} value = N
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N = extent of Gaussian for PPPM mapping of dispersion term to grid
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{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
|
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{minorder} value = M
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M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
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{force} value = accuracy (force units)
|
||||
{gewald} value = rinv (1/distance units)
|
||||
rinv = G-ewald parameter for Coulombics
|
||||
{gewald/disp} value = rinv (1/distance units)
|
||||
rinv = G-ewald parameter for dispersion
|
||||
{slab} value = volfactor or {nozforce}
|
||||
volfactor = ratio of the total extended volume used in the
|
||||
2d approximation compared with the volume of the simulation domain
|
||||
{nozforce} turns off kspace forces in the z direction
|
||||
{compute} value = {yes} or {no}
|
||||
{cutoff/adjust} value = {yes} or {no}
|
||||
{fftbench} value = {yes} or {no}
|
||||
{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
|
||||
{kmax/ewald} value = kx ky kz
|
||||
kx,ky,kz = number of Ewald sum kspace vectors in each dimension
|
||||
{mix/disp} value = {pair} or {geom} or {none}
|
||||
{force/disp/real} value = accuracy (force units)
|
||||
{force/disp/kspace} value = accuracy (force units)
|
||||
{splittol} value = tol
|
||||
tol = relative size of two eigenvalues (see discussion below) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
kspace_modify mesh 24 24 30 order 6
|
||||
kspace_modify slab 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Set parameters used by the kspace solvers defined by the
|
||||
"kspace_style"_kspace_style.html command. Not all parameters are
|
||||
relevant to all kspace styles.
|
||||
|
||||
The {mesh} keyword sets the grid size for kspace style {pppm} or
|
||||
{msm}. In the case of PPPM, this is the FFT mesh, and each dimension
|
||||
must be factorizable into powers of 2, 3, and 5. In the case of MSM,
|
||||
this is the finest scale real-space mesh, and each dimension must be
|
||||
factorizable into powers of 2. When this option is not set, the PPPM
|
||||
or MSM solver chooses its own grid size, consistent with the
|
||||
user-specified accuracy and pairwise cutoff. Values for x,y,z of
|
||||
0,0,0 unset the option.
|
||||
|
||||
The {mesh/disp} keyword sets the grid size for kspace style
|
||||
{pppm/disp}. This is the FFT mesh for long-range dispersion and ach
|
||||
dimension must be factorizable into powers of 2, 3, and 5. When this
|
||||
option is not set, the PPPM solver chooses its own grid size,
|
||||
consistent with the user-specified accuracy and pairwise cutoff.
|
||||
Values for x,y,z of 0,0,0 unset the option.
|
||||
|
||||
The {order} keyword determines how many grid spacings an atom's charge
|
||||
extends when it is mapped to the grid in kspace style {pppm} or {msm}.
|
||||
The default for this parameter is 5 for PPPM and 8 for MSM, which
|
||||
means each charge spans 5 or 8 grid cells in each dimension,
|
||||
respectively. For the LAMMPS implementation of MSM, the order can
|
||||
range from 4 to 10 and must be even. For PPPM, the minimum allowed
|
||||
setting is 2 and the maximum allowed setting is 7. The larger the
|
||||
value of this parameter, the smaller that LAMMPS will set the grid
|
||||
size, to achieve the requested accuracy. Conversely, the smaller the
|
||||
order value, the larger the grid size will be. Note that there is an
|
||||
inherent trade-off involved: a small grid will lower the cost of FFTs
|
||||
or MSM direct sum, but a larger order parameter will increase the cost
|
||||
of interpolating charge/fields to/from the grid.
|
||||
|
||||
The {order/disp} keyword determines how many grid spacings an atom's
|
||||
dispersion term extends when it is mapped to the grid in kspace style
|
||||
{pppm/disp}. It has the same meaning as the {order} setting for
|
||||
Coulombics.
|
||||
|
||||
The {overlap} keyword can be used in conjunction with the {minorder}
|
||||
keyword with the PPPM styles to adjust the amount of communication
|
||||
that occurs when values on the FFT grid are exchangeed between
|
||||
processors. This communication is distinct from the communication
|
||||
inherent in the parallel FFTs themselves, and is required because
|
||||
processors interpolate charge and field values using grid point values
|
||||
owned by neighboring processors (i.e. ghost point communication). If
|
||||
the {overlap} keyword is set to {yes} then this communication is
|
||||
allowed to extend beyond nearest-neighbor processors, e.g. when using
|
||||
lots of processors on a small problem. If it is set to {no} then the
|
||||
communication will be limited to nearest-neighbor processors and the
|
||||
{order} setting will be reduced if necessary, as explained by the
|
||||
{minorder} keyword discussion. The {overlap} keyword is always set to
|
||||
{yes} in MSM.
|
||||
|
||||
The {minorder} keyword allows LAMMPS to reduce the {order} setting if
|
||||
necessary to keep the communication of ghost grid point limited to
|
||||
exchanges between nearest-neighbor processors. See the discussion of
|
||||
the {overlap} keyword for details. If the {overlap} keyword is set to
|
||||
{yes}, which is the default, this is never needed. If it set to {no}
|
||||
and overlap occurs, then LAMMPS will reduce the order setting, one
|
||||
step at a time, until the ghost grid overlap only extends to nearest
|
||||
neighbor processors. The {minorder} keyword limits how small the
|
||||
{order} setting can become. The minimum allowed value for PPPM is 2,
|
||||
which is the default. If {minorder} is set to the same value as
|
||||
{order} then no reduction is allowed, and LAMMPS will generate an
|
||||
error if the grid communcation is non-nearest-neighbor and {overlap}
|
||||
is set to {no}. The {minorder} keyword is not currently supported in
|
||||
MSM.
|
||||
|
||||
The PPPM order parameter may be reset by LAMMPS when it sets up the
|
||||
FFT grid if the implied grid stencil extends beyond the grid cells
|
||||
owned by neighboring processors. Typically this will only occur when
|
||||
small problems are run on large numbers of processors. A warning will
|
||||
be generated indicating the order parameter is being reduced to allow
|
||||
LAMMPS to run the problem. Automatic adjustment of the order parameter
|
||||
is not supported in MSM.
|
||||
|
||||
The {force} keyword overrides the relative accuracy parameter set by
|
||||
the "kspace_style"_kspace_style.html command with an absolute
|
||||
accuracy. The accuracy determines the RMS error in per-atom forces
|
||||
calculated by the long-range solver and is thus specified in force
|
||||
units. A negative value for the accuracy setting means to use the
|
||||
relative accuracy parameter. The accuracy setting is used in
|
||||
conjunction with the pairwise cutoff to determine the number of
|
||||
K-space vectors for style {ewald}, the FFT grid size for style
|
||||
{pppm}, or the real space grid size for style {msm}.
|
||||
|
||||
The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
|
||||
parameter for charge as {rinv} in reciprocal distance units. Without
|
||||
this setting, LAMMPS chooses the parameter automatically as a function
|
||||
of cutoff, precision, grid spacing, etc. This means it can vary from
|
||||
one simulation to the next which may not be desirable for matching a
|
||||
KSpace solver to a pre-tabulated pairwise potential. This setting can
|
||||
also be useful if Ewald or PPPM fails to choose a good grid spacing
|
||||
and G-ewald parameter automatically. If the value is set to 0.0,
|
||||
LAMMPS will choose the G-ewald parameter automatically. MSM does not
|
||||
use the {gewald} parameter.
|
||||
|
||||
The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
|
||||
parameter for dispersion as {rinv} in reciprocal distance units. It
|
||||
has the same meaning as the {gewald} setting for Coulombics.
|
||||
|
||||
The {slab} keyword allows an Ewald or PPPM solver to be used for a
|
||||
systems that are periodic in x,y but non-periodic in z - a
|
||||
"boundary"_boundary.html setting of "boundary p p f". This is done by
|
||||
treating the system as if it were periodic in z, but inserting empty
|
||||
volume between atom slabs and removing dipole inter-slab interactions
|
||||
so that slab-slab interactions are effectively turned off. The
|
||||
volfactor value sets the ratio of the extended dimension in z divided
|
||||
by the actual dimension in z. The recommended value is 3.0. A larger
|
||||
value is inefficient; a smaller value introduces unwanted slab-slab
|
||||
interactions. The use of fixed boundaries in z means that the user
|
||||
must prevent particle migration beyond the initial z-bounds, typically
|
||||
by providing a wall-style fix. The methodology behind the {slab}
|
||||
option is explained in the paper by "(Yeh)"_#Yeh. The {slab} option
|
||||
is also extended to non-neutral systems
|
||||
"(Ballenegger)"_#Ballenegger. An alternative slab option can be
|
||||
invoked with the {nozforce} keyword in lieu of the volfactor. This
|
||||
turns off all kspace forces in the z direction. The {nozforce} option
|
||||
is not supported by MSM. For MSM, any combination of periodic,
|
||||
non-periodic, or shrink-wrapped boundaries can be set using
|
||||
"boundary"_boundary.html (the slab approximation in not needed). The
|
||||
{slab} keyword is not currently supported by Ewald or PPPM when using
|
||||
a triclinic simulation cell.
|
||||
|
||||
The {compute} keyword allows Kspace computations to be turned off,
|
||||
even though a "kspace_style"_kspace_style.html is defined. This is
|
||||
not useful for running a real simulation, but can be useful for
|
||||
debugging purposes or for computing only partial forces that do not
|
||||
include the Kspace contribution. You can also do this by simply not
|
||||
defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
|
||||
"pair_style"_pair_style.html requires a kspace style to be defined.
|
||||
This keyword gives you that option.
|
||||
|
||||
The {cutoff/adjust} keyword applies only to MSM. If this option is
|
||||
turned on, the Coulombic cutoff will be automatically adjusted at the
|
||||
beginning of the run to give the desired estimated error. Other
|
||||
cutoffs such as LJ will not be affected. If the grid is not set using
|
||||
the {mesh} command, this command will also attempt to use the optimal
|
||||
grid that minimizes cost using an estimate given by
|
||||
"(Hardy)"_#Hardy. Note that this cost estimate is not exact, somewhat
|
||||
experimental, and still may not yield the optimal parameters.
|
||||
|
||||
The {fftbench} keyword applies only to PPPM. It is on by default. If
|
||||
this option is turned off, LAMMPS will not take the time at the end
|
||||
of a run to give FFT benchmark timings, and will finish a few seconds
|
||||
faster than it would if this option were on.
|
||||
|
||||
The {diff} keyword specifies the differentiation scheme used by the
|
||||
PPPM method to compute forces on particles given electrostatic
|
||||
potentials on the PPPM mesh. The {ik} approach is the default for
|
||||
PPPM and is the original formulation used in "(Hockney)"_#Hockney. It
|
||||
performs differentiation in Kspace, and uses 3 FFTs to transfer each
|
||||
component of the computed fields back to real space for total of 4
|
||||
FFTs per timestep.
|
||||
|
||||
The analytic differentiation {ad} approach uses only 1 FFT to transfer
|
||||
information back to real space for a total of 2 FFTs per timestep. It
|
||||
then performs analytic differentiation on the single quantity to
|
||||
generate the 3 components of the electric field at each grid point.
|
||||
This is sometimes referred to as "smoothed" PPPM. This approach
|
||||
requires a somewhat larger PPPM mesh to achieve the same accuracy as
|
||||
the {ik} method. Currently, only the {ik} method (default) can be
|
||||
used for a triclinic simulation cell with PPPM. The {ad} method is
|
||||
always used for MSM.
|
||||
|
||||
IMPORTANT NOTE: Currently, not all PPPM styles support the {ad}
|
||||
option. Support for those PPPM variants will be added later.
|
||||
|
||||
The {kmax/ewald} keyword sets the number of kspace vectors in
|
||||
each dimension for kspace style {ewald}. 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 {ewald} is invoked, the values used
|
||||
are printed to the screen and
|
||||
the log file at the start of the run.
|
||||
|
||||
With the {mix/disp{ keyword one can select the mixing rule for the
|
||||
dispersion coefficients. With {pair}, the dispersion coefficients of
|
||||
unlike types are computed as indicated with
|
||||
"pair_modify"_pair_modify.html. With {geom}, 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 "(Wennberg)"_#Wennberg. With {none}, it is
|
||||
assumed that no mixing rule is applicable. Splitting of the dispersion
|
||||
coefficients will be performed as described in
|
||||
"(Isele-Holder)"_#Isele-Holder. This splitting can be influenced with
|
||||
the {splittol} 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.
|
||||
|
||||
The {force/disp/real} and {force/disp/kspace} keywords set the force
|
||||
accuracy for the real and space computations for the dispersion part
|
||||
of pppm/disp. as shown in "(Isele-Holder)"_#Isele-Holder, optimal
|
||||
performance and accuracy in the results is obtained when these values
|
||||
are different.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"kspace_style"_kspace_style.html, "boundary"_boundary.html
|
||||
|
||||
[Default:]
|
||||
|
||||
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), fftbench = yes (PPPM), diff = ik (PPPM), mix/disp = pair,
|
||||
force/disp/real = -1.0, force/disp/kspace = -1.0, split = 0, and tol = 1.0e-6.
|
||||
|
||||
:line
|
||||
|
||||
:link(Hockney)
|
||||
[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
|
||||
Adam Hilger, NY (1989).
|
||||
|
||||
:link(Yeh)
|
||||
[(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
|
||||
|
||||
:link(Ballenegger)
|
||||
[(Ballenegger)] Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
|
||||
(2009).
|
||||
|
||||
:link(Hardy)
|
||||
[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
|
||||
Evaluation of Forces for the Simulation of Biomolecules, University of
|
||||
Illinois at Urbana-Champaign, (2006).
|
||||
|
||||
:link(Isele-Holder)
|
||||
[(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
|
||||
Chem Theory Comput, 9, 5412 (2013).
|
||||
|
||||
:link(Wennberg)
|
||||
[(Wennberg)] Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
|
||||
9, 3527 (2013).
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
kspace_modify command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
kspace_modify keyword value ... :pre
|
||||
|
||||
one or more keyword/value pairs may be listed :ulb,l
|
||||
keyword = {mesh} or {order} or {order/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} :l
|
||||
{mesh} value = x y z
|
||||
x,y,z = grid size in each dimension for long-range Coulombics
|
||||
{mesh/disp} value = x y z
|
||||
x,y,z = grid size in each dimension for 1/r^6 dispersion
|
||||
{order} value = N
|
||||
N = extent of Gaussian for PPPM or MSM mapping of charge to grid
|
||||
{order/disp} value = N
|
||||
N = extent of Gaussian for PPPM mapping of dispersion term to grid
|
||||
{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
|
||||
{minorder} value = M
|
||||
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
|
||||
{force} value = accuracy (force units)
|
||||
{gewald} value = rinv (1/distance units)
|
||||
rinv = G-ewald parameter for Coulombics
|
||||
{gewald/disp} value = rinv (1/distance units)
|
||||
rinv = G-ewald parameter for dispersion
|
||||
{slab} value = volfactor or {nozforce}
|
||||
volfactor = ratio of the total extended volume used in the
|
||||
2d approximation compared with the volume of the simulation domain
|
||||
{nozforce} turns off kspace forces in the z direction
|
||||
{compute} value = {yes} or {no}
|
||||
{cutoff/adjust} value = {yes} or {no}
|
||||
{fftbench} value = {yes} or {no}
|
||||
{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
|
||||
{kmax/ewald} value = kx ky kz
|
||||
kx,ky,kz = number of Ewald sum kspace vectors in each dimension
|
||||
{mix/disp} value = {pair} or {geom} or {none}
|
||||
{force/disp/real} value = accuracy (force units)
|
||||
{force/disp/kspace} value = accuracy (force units)
|
||||
{splittol} value = tol
|
||||
tol = relative size of two eigenvalues (see discussion below) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
kspace_modify mesh 24 24 30 order 6
|
||||
kspace_modify slab 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Set parameters used by the kspace solvers defined by the
|
||||
"kspace_style"_kspace_style.html command. Not all parameters are
|
||||
relevant to all kspace styles.
|
||||
|
||||
The {mesh} keyword sets the grid size for kspace style {pppm} or
|
||||
{msm}. In the case of PPPM, this is the FFT mesh, and each dimension
|
||||
must be factorizable into powers of 2, 3, and 5. In the case of MSM,
|
||||
this is the finest scale real-space mesh, and each dimension must be
|
||||
factorizable into powers of 2. When this option is not set, the PPPM
|
||||
or MSM solver chooses its own grid size, consistent with the
|
||||
user-specified accuracy and pairwise cutoff. Values for x,y,z of
|
||||
0,0,0 unset the option.
|
||||
|
||||
The {mesh/disp} keyword sets the grid size for kspace style
|
||||
{pppm/disp}. This is the FFT mesh for long-range dispersion and ach
|
||||
dimension must be factorizable into powers of 2, 3, and 5. When this
|
||||
option is not set, the PPPM solver chooses its own grid size,
|
||||
consistent with the user-specified accuracy and pairwise cutoff.
|
||||
Values for x,y,z of 0,0,0 unset the option.
|
||||
|
||||
The {order} keyword determines how many grid spacings an atom's charge
|
||||
extends when it is mapped to the grid in kspace style {pppm} or {msm}.
|
||||
The default for this parameter is 5 for PPPM and 8 for MSM, which
|
||||
means each charge spans 5 or 8 grid cells in each dimension,
|
||||
respectively. For the LAMMPS implementation of MSM, the order can
|
||||
range from 4 to 10 and must be even. For PPPM, the minimum allowed
|
||||
setting is 2 and the maximum allowed setting is 7. The larger the
|
||||
value of this parameter, the smaller that LAMMPS will set the grid
|
||||
size, to achieve the requested accuracy. Conversely, the smaller the
|
||||
order value, the larger the grid size will be. Note that there is an
|
||||
inherent trade-off involved: a small grid will lower the cost of FFTs
|
||||
or MSM direct sum, but a larger order parameter will increase the cost
|
||||
of interpolating charge/fields to/from the grid.
|
||||
|
||||
The {order/disp} keyword determines how many grid spacings an atom's
|
||||
dispersion term extends when it is mapped to the grid in kspace style
|
||||
{pppm/disp}. It has the same meaning as the {order} setting for
|
||||
Coulombics.
|
||||
|
||||
The {overlap} keyword can be used in conjunction with the {minorder}
|
||||
keyword with the PPPM styles to adjust the amount of communication
|
||||
that occurs when values on the FFT grid are exchangeed between
|
||||
processors. This communication is distinct from the communication
|
||||
inherent in the parallel FFTs themselves, and is required because
|
||||
processors interpolate charge and field values using grid point values
|
||||
owned by neighboring processors (i.e. ghost point communication). If
|
||||
the {overlap} keyword is set to {yes} then this communication is
|
||||
allowed to extend beyond nearest-neighbor processors, e.g. when using
|
||||
lots of processors on a small problem. If it is set to {no} then the
|
||||
communication will be limited to nearest-neighbor processors and the
|
||||
{order} setting will be reduced if necessary, as explained by the
|
||||
{minorder} keyword discussion. The {overlap} keyword is always set to
|
||||
{yes} in MSM.
|
||||
|
||||
The {minorder} keyword allows LAMMPS to reduce the {order} setting if
|
||||
necessary to keep the communication of ghost grid point limited to
|
||||
exchanges between nearest-neighbor processors. See the discussion of
|
||||
the {overlap} keyword for details. If the {overlap} keyword is set to
|
||||
{yes}, which is the default, this is never needed. If it set to {no}
|
||||
and overlap occurs, then LAMMPS will reduce the order setting, one
|
||||
step at a time, until the ghost grid overlap only extends to nearest
|
||||
neighbor processors. The {minorder} keyword limits how small the
|
||||
{order} setting can become. The minimum allowed value for PPPM is 2,
|
||||
which is the default. If {minorder} is set to the same value as
|
||||
{order} then no reduction is allowed, and LAMMPS will generate an
|
||||
error if the grid communcation is non-nearest-neighbor and {overlap}
|
||||
is set to {no}. The {minorder} keyword is not currently supported in
|
||||
MSM.
|
||||
|
||||
The PPPM order parameter may be reset by LAMMPS when it sets up the
|
||||
FFT grid if the implied grid stencil extends beyond the grid cells
|
||||
owned by neighboring processors. Typically this will only occur when
|
||||
small problems are run on large numbers of processors. A warning will
|
||||
be generated indicating the order parameter is being reduced to allow
|
||||
LAMMPS to run the problem. Automatic adjustment of the order parameter
|
||||
is not supported in MSM.
|
||||
|
||||
The {force} keyword overrides the relative accuracy parameter set by
|
||||
the "kspace_style"_kspace_style.html command with an absolute
|
||||
accuracy. The accuracy determines the RMS error in per-atom forces
|
||||
calculated by the long-range solver and is thus specified in force
|
||||
units. A negative value for the accuracy setting means to use the
|
||||
relative accuracy parameter. The accuracy setting is used in
|
||||
conjunction with the pairwise cutoff to determine the number of
|
||||
K-space vectors for style {ewald}, the FFT grid size for style
|
||||
{pppm}, or the real space grid size for style {msm}.
|
||||
|
||||
The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
|
||||
parameter for charge as {rinv} in reciprocal distance units. Without
|
||||
this setting, LAMMPS chooses the parameter automatically as a function
|
||||
of cutoff, precision, grid spacing, etc. This means it can vary from
|
||||
one simulation to the next which may not be desirable for matching a
|
||||
KSpace solver to a pre-tabulated pairwise potential. This setting can
|
||||
also be useful if Ewald or PPPM fails to choose a good grid spacing
|
||||
and G-ewald parameter automatically. If the value is set to 0.0,
|
||||
LAMMPS will choose the G-ewald parameter automatically. MSM does not
|
||||
use the {gewald} parameter.
|
||||
|
||||
The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
|
||||
parameter for dispersion as {rinv} in reciprocal distance units. It
|
||||
has the same meaning as the {gewald} setting for Coulombics.
|
||||
|
||||
The {slab} keyword allows an Ewald or PPPM solver to be used for a
|
||||
systems that are periodic in x,y but non-periodic in z - a
|
||||
"boundary"_boundary.html setting of "boundary p p f". This is done by
|
||||
treating the system as if it were periodic in z, but inserting empty
|
||||
volume between atom slabs and removing dipole inter-slab interactions
|
||||
so that slab-slab interactions are effectively turned off. The
|
||||
volfactor value sets the ratio of the extended dimension in z divided
|
||||
by the actual dimension in z. The recommended value is 3.0. A larger
|
||||
value is inefficient; a smaller value introduces unwanted slab-slab
|
||||
interactions. The use of fixed boundaries in z means that the user
|
||||
must prevent particle migration beyond the initial z-bounds, typically
|
||||
by providing a wall-style fix. The methodology behind the {slab}
|
||||
option is explained in the paper by "(Yeh)"_#Yeh. The {slab} option
|
||||
is also extended to non-neutral systems
|
||||
"(Ballenegger)"_#Ballenegger. An alternative slab option can be
|
||||
invoked with the {nozforce} keyword in lieu of the volfactor. This
|
||||
turns off all kspace forces in the z direction. The {nozforce} option
|
||||
is not supported by MSM. For MSM, any combination of periodic,
|
||||
non-periodic, or shrink-wrapped boundaries can be set using
|
||||
"boundary"_boundary.html (the slab approximation in not needed). The
|
||||
{slab} keyword is not currently supported by Ewald or PPPM when using
|
||||
a triclinic simulation cell. The slab correction has also been
|
||||
extended to point dipole interactions "(Klapp)"_#Klapp in
|
||||
"kspace_style"_kspace_style.html {ewald/disp}.
|
||||
|
||||
The {compute} keyword allows Kspace computations to be turned off,
|
||||
even though a "kspace_style"_kspace_style.html is defined. This is
|
||||
not useful for running a real simulation, but can be useful for
|
||||
debugging purposes or for computing only partial forces that do not
|
||||
include the Kspace contribution. You can also do this by simply not
|
||||
defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
|
||||
"pair_style"_pair_style.html requires a kspace style to be defined.
|
||||
This keyword gives you that option.
|
||||
|
||||
The {cutoff/adjust} keyword applies only to MSM. If this option is
|
||||
turned on, the Coulombic cutoff will be automatically adjusted at the
|
||||
beginning of the run to give the desired estimated error. Other
|
||||
cutoffs such as LJ will not be affected. If the grid is not set using
|
||||
the {mesh} command, this command will also attempt to use the optimal
|
||||
grid that minimizes cost using an estimate given by
|
||||
"(Hardy)"_#Hardy. Note that this cost estimate is not exact, somewhat
|
||||
experimental, and still may not yield the optimal parameters.
|
||||
|
||||
The {fftbench} keyword applies only to PPPM. It is on by default. If
|
||||
this option is turned off, LAMMPS will not take the time at the end
|
||||
of a run to give FFT benchmark timings, and will finish a few seconds
|
||||
faster than it would if this option were on.
|
||||
|
||||
The {diff} keyword specifies the differentiation scheme used by the
|
||||
PPPM method to compute forces on particles given electrostatic
|
||||
potentials on the PPPM mesh. The {ik} approach is the default for
|
||||
PPPM and is the original formulation used in "(Hockney)"_#Hockney. It
|
||||
performs differentiation in Kspace, and uses 3 FFTs to transfer each
|
||||
component of the computed fields back to real space for total of 4
|
||||
FFTs per timestep.
|
||||
|
||||
The analytic differentiation {ad} approach uses only 1 FFT to transfer
|
||||
information back to real space for a total of 2 FFTs per timestep. It
|
||||
then performs analytic differentiation on the single quantity to
|
||||
generate the 3 components of the electric field at each grid point.
|
||||
This is sometimes referred to as "smoothed" PPPM. This approach
|
||||
requires a somewhat larger PPPM mesh to achieve the same accuracy as
|
||||
the {ik} method. Currently, only the {ik} method (default) can be
|
||||
used for a triclinic simulation cell with PPPM. The {ad} method is
|
||||
always used for MSM.
|
||||
|
||||
IMPORTANT NOTE: Currently, not all PPPM styles support the {ad}
|
||||
option. Support for those PPPM variants will be added later.
|
||||
|
||||
The {kmax/ewald} keyword sets the number of kspace vectors in
|
||||
each dimension for kspace style {ewald}. 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 {ewald} is invoked, the values used
|
||||
are printed to the screen and
|
||||
the log file at the start of the run.
|
||||
|
||||
With the {mix/disp} keyword one can select the mixing rule for the
|
||||
dispersion coefficients. With {pair}, the dispersion coefficients of
|
||||
unlike types are computed as indicated with
|
||||
"pair_modify"_pair_modify.html. With {geom}, 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 "(Wennberg)"_#Wennberg. With {none}, it is
|
||||
assumed that no mixing rule is applicable. Splitting of the dispersion
|
||||
coefficients will be performed as described in
|
||||
"(Isele-Holder)"_#Isele-Holder. This splitting can be influenced with
|
||||
the {splittol} 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.
|
||||
|
||||
The {force/disp/real} and {force/disp/kspace} keywords set the force
|
||||
accuracy for the real and space computations for the dispersion part
|
||||
of pppm/disp. as shown in "(Isele-Holder)"_#Isele-Holder, optimal
|
||||
performance and accuracy in the results is obtained when these values
|
||||
are different.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"kspace_style"_kspace_style.html, "boundary"_boundary.html
|
||||
|
||||
[Default:]
|
||||
|
||||
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), fftbench = yes (PPPM), diff = ik (PPPM), mix/disp = pair,
|
||||
force/disp/real = -1.0, force/disp/kspace = -1.0, split = 0, and tol =
|
||||
1.0e-6.
|
||||
|
||||
:line
|
||||
|
||||
:link(Hockney)
|
||||
[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
|
||||
Adam Hilger, NY (1989).
|
||||
|
||||
:link(Yeh)
|
||||
[(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
|
||||
|
||||
:link(Ballenegger)
|
||||
[(Ballenegger)] Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
|
||||
(2009).
|
||||
|
||||
:link(Klapp)
|
||||
[(Klapp)] Klapp, Schoen, J Chem Phys, 117, 8050 (2002).
|
||||
|
||||
:link(Hardy)
|
||||
[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
|
||||
Evaluation of Forces for the Simulation of Biomolecules, University of
|
||||
Illinois at Urbana-Champaign, (2006).
|
||||
|
||||
:link(Isele-Holder)
|
||||
[(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
|
||||
Chem Theory Comput, 9, 5412 (2013).
|
||||
|
||||
:link(Wennberg)
|
||||
[(Wennberg)] Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
|
||||
9, 3527 (2013).
|
||||
|
|
|
|||
Loading…
Reference in New Issue