mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8951 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
6984d53442
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08a691bfed
|
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@ -17,7 +17,7 @@
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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>gewald</I> or <I>slab</I> or (nozforce</I> or <I>compute</I> or <I>diff</I>
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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>diff</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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@ -27,6 +27,9 @@
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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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@ -37,7 +40,7 @@
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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>diff</I> value = <I>ik</I> or <I>ad</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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</PRE>
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</UL>
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@ -69,30 +72,60 @@ 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 4 for MSM, which means
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each charge spans 5 or 4 grid cells in each dimension, respectively.
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For the LAMMPS implementation of MSM, the order can range from 4 to 10
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and must be even. For PPPM, the minimum allowed setting is 2 and the
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maximum allowed setting is 7. The larger the value of this parameter,
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the smaller the grid will need to be to achieve the requested accuracy.
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Conversely, the smaller the order value, the larger the grid will be.
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Note that there is an inherent trade-off involved: a small grid will
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lower the cost of FFTs or MSM direct sum, but a larger order parameter
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will increase the cost of interpolating charge/fields to/from the grid.
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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 4 for MSM, which
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means each charge spans 5 or 4 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 PPPM order parameter may be reset by LAMMPS when it sets up the
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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.
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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>.
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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 reduction of order is not currently
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implemented in MSM, so an error (instead of a warning) will be generated.
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LAMMPS to run the problem. Automatic reduction of order is not
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currently implemented in MSM, so an error (instead of a warning) will
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be generated.
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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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@ -148,17 +181,23 @@ This keyword gives you that option.
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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. It performs differentiation in Kspace, but uses 3 FFTs to
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transfer the computed fields back to real space (total of 4 FFTs per
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timestep). The analytic differentiation, or <I>ad</I> approach uses only 1
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FFT to transfer the computed fields back to real space (total of 2
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FFTs per timestep), but requires a somewhat larger PPPM mesh to
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achieve the same accuracy as the <I>ik</I> approach. Analogous approaches
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have been implemented in MSM and can be specified using the same
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keywords. The <I>ad</I> approach is the default for MSM.
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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>IMPORTANT NOTE: Currently, not all <I>pppm</I> styles support the <I>ad</I>
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option. Support for those <I>pppm</I> variants will be added later.
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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. Analogous approaches have been implemented in MSM
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and can be specified using the same keywords. The <I>ad</I> approach is
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the default 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><B>Restrictions:</B> none
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</P>
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@ -169,11 +208,17 @@ option. Support for those <I>pppm</I> variants will be added later.
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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 = 4 (MSM), force = -1.0, gewald = gewald/disp = 0.0,
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slab = 1.0, compute = yes, and diff = ik (PPPM), diff = ad (MSM).
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5 (PPPM), order = 4 (MSM), minorder = 2, overlap = yes, force = -1.0,
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gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, and diff = ik
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(PPPM), diff = ad (MSM).
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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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|
|
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@ -13,7 +13,7 @@ kspace_modify command :h3
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kspace_modify keyword value ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or {diff} :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 {diff} :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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@ -22,6 +22,9 @@ keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or
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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)
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{gewald} value = rinv (1/distance units)
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rinv = G-ewald parameter for Coulombics
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|
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@ -32,7 +35,7 @@ keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or
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2d approximation compared with the volume of the simulation domain
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{nozforce} turns off kspace forces in the z direction
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{compute} value = {yes} or {no}
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{diff} value = {ik} or {ad} :pre
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{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode :pre
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:ule
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[Examples:]
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|
|
@ -63,30 +66,60 @@ 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
|
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extends when it is mapped to the grid in kspace style {pppm} or {msm}.
|
||||
The default for this parameter is 5 for PPPM and 4 for MSM, which means
|
||||
each charge spans 5 or 4 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
|
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maximum allowed setting is 7. The larger the value of this parameter,
|
||||
the smaller the grid will need to be to achieve the requested accuracy.
|
||||
Conversely, the smaller the order value, the larger the grid 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.
|
||||
extends when it is mapped to the grid in kspace style {pppm} or {msm}.
|
||||
The default for this parameter is 5 for PPPM and 4 for MSM, which
|
||||
means each charge spans 5 or 4 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 PPPM order parameter may be reset by LAMMPS when it sets up the
|
||||
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 {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 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 reduction of order is not currently
|
||||
implemented in MSM, so an error (instead of a warning) will be generated.
|
||||
LAMMPS to run the problem. Automatic reduction of order is not
|
||||
currently implemented in MSM, so an error (instead of a warning) will
|
||||
be generated.
|
||||
|
||||
The {force} keyword overrides the relative accuracy parameter set by
|
||||
the "kspace_style"_kspace_style.html command with an absolute
|
||||
|
|
@ -142,17 +175,23 @@ This keyword gives you that option.
|
|||
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. It performs differentiation in Kspace, but uses 3 FFTs to
|
||||
transfer the computed fields back to real space (total of 4 FFTs per
|
||||
timestep). The analytic differentiation, or {ad} approach uses only 1
|
||||
FFT to transfer the computed fields back to real space (total of 2
|
||||
FFTs per timestep), but requires a somewhat larger PPPM mesh to
|
||||
achieve the same accuracy as the {ik} approach. Analogous approaches
|
||||
have been implemented in MSM and can be specified using the same
|
||||
keywords. The {ad} approach is the default for MSM.
|
||||
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.
|
||||
|
||||
IMPORTANT NOTE: Currently, not all {pppm} styles support the {ad}
|
||||
option. Support for those {pppm} variants will be added later.
|
||||
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. Analogous approaches have been implemented in MSM
|
||||
and can be specified using the same keywords. The {ad} approach is
|
||||
the default for MSM.
|
||||
|
||||
IMPORTANT NOTE: Currently, not all PPPM styles support the {ad}
|
||||
option. Support for those PPPM variants will be added later.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
@ -163,10 +202,15 @@ option. Support for those {pppm} variants will be added later.
|
|||
[Default:]
|
||||
|
||||
The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
|
||||
5 (PPPM), order = 4 (MSM), force = -1.0, gewald = gewald/disp = 0.0,
|
||||
slab = 1.0, compute = yes, and diff = ik (PPPM), diff = ad (MSM).
|
||||
5 (PPPM), order = 4 (MSM), minorder = 2, overlap = yes, force = -1.0,
|
||||
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, and diff = ik
|
||||
(PPPM), diff = ad (MSM).
|
||||
|
||||
: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).
|
||||
|
|
|
|||
|
|
@ -153,12 +153,13 @@ manual.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>msm</I> style invokes a multi-level summation method MSM solver
|
||||
<A HREF = "#Hardy">(Hardy)</A> which maps atom charge to a 3d mesh, and uses a
|
||||
multi-level hierarchy of coarser and coarser meshes on which direct
|
||||
coulomb solves are done. This method does not use FFTs and scales
|
||||
as N. It may therefore be faster than the other K-space solvers for
|
||||
relatively large problems when running on large core counts.
|
||||
<P>The <I>msm</I> style invokes a multi-level summation method MSM solver,
|
||||
<A HREF = "#Hardy">(Hardy)</A> or <A HREF = "#Hardy2">(Hardy2)</A>, which maps atom charge to a 3d
|
||||
mesh, and uses a multi-level hierarchy of coarser and coarser meshes
|
||||
on which direct coulomb solves are done. This method does not use
|
||||
FFTs and scales as N. It may therefore be faster than the other
|
||||
K-space solvers for relatively large problems when running on large
|
||||
core counts.
|
||||
</P>
|
||||
<P>MSM is most competitive versus Ewald and PPPM when only relatively
|
||||
low accuracy forces, about 1e-4 relative error or less accurate,
|
||||
|
|
@ -284,8 +285,13 @@ Adam Hilger, NY (1989).
|
|||
</P>
|
||||
<A NAME = "Hardy"></A>
|
||||
|
||||
<P><B>(Hardy)</B> David, Thesis: Multilevel Summation for the Fast Evaluation
|
||||
of Forces for the Simulation of Biomolecules, University of Illinois
|
||||
at Urbana-Champaign, (2006).
|
||||
<P><B>(Hardy)</B> David Hardy thesis: Multilevel Summation for the Fast
|
||||
Evaluation of Forces for the Simulation of Biomolecules, University of
|
||||
Illinois at Urbana-Champaign, (2006).
|
||||
</P>
|
||||
<A NAME = "Hardy2"></A>
|
||||
|
||||
<P><B>(Hardy)</B> Hardy, Stone, Schulten, Parallel Computing 35 (2009)
|
||||
164-177.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -146,12 +146,13 @@ manual.
|
|||
|
||||
:line
|
||||
|
||||
The {msm} style invokes a multi-level summation method MSM solver
|
||||
"(Hardy)"_#Hardy which maps atom charge to a 3d mesh, and uses a
|
||||
multi-level hierarchy of coarser and coarser meshes on which direct
|
||||
coulomb solves are done. This method does not use FFTs and scales
|
||||
as N. It may therefore be faster than the other K-space solvers for
|
||||
relatively large problems when running on large core counts.
|
||||
The {msm} style invokes a multi-level summation method MSM solver,
|
||||
"(Hardy)"_#Hardy or "(Hardy2)"_#Hardy2, which maps atom charge to a 3d
|
||||
mesh, and uses a multi-level hierarchy of coarser and coarser meshes
|
||||
on which direct coulomb solves are done. This method does not use
|
||||
FFTs and scales as N. It may therefore be faster than the other
|
||||
K-space solvers for relatively large problems when running on large
|
||||
core counts.
|
||||
|
||||
MSM is most competitive versus Ewald and PPPM when only relatively
|
||||
low accuracy forces, about 1e-4 relative error or less accurate,
|
||||
|
|
@ -269,6 +270,10 @@ Adam Hilger, NY (1989).
|
|||
[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, in press (2007).
|
||||
|
||||
:link(Hardy)
|
||||
[(Hardy)] David, Thesis: Multilevel Summation for the Fast Evaluation
|
||||
of Forces for the Simulation of Biomolecules, University of Illinois
|
||||
at Urbana-Champaign, (2006).
|
||||
[(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(Hardy2)
|
||||
[(Hardy)] Hardy, Stone, Schulten, Parallel Computing 35 (2009)
|
||||
164-177.
|
||||
|
|
|
|||
Loading…
Reference in New Issue