forked from lijiext/lammps
Adding MSM documentation.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8778 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
pscrozi
parent
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@ -46,25 +46,28 @@ kspace_modify slab 3.0
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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 3d FFT grid size for kspace style pppm.
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Each dimension must be factorizable into powers of 2, 3, and 5. When
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this 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>The <I>mesh</I> keyword sets the grid size for kspace style <I>pppm</I> or <I>msm</I>.
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In the case of PPPM, each dimension must be factorizable into powers
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of 2, 3, and 5. In the case of MSM, 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>order</I> keyword determines how many grid spacings an atom's charge
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extends when it is mapped to the FFT grid in kspace style pppm. The
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default for this parameter is 5, which means each charge spans 5 grid
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cells in each dimension. 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 FFT grid will need to be to achieve the requested
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precision. Conversely, the smaller the order value, the larger the
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grid will be. Note that there is an inherent trade-off involved: a
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small grid will lower the cost of FFTs, but a large order parameter
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will increase the cost of intepolating charge/fields to/from the grid.
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And vice versa.
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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, 4 is the only allowable value.
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For PPPM, the minimum allowed setting is 2 and the maximum allowed
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setting is 7. The larger the value of this parameter, the smaller the
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grid will need to be to achieve the requested precision. Conversely,
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the smaller the order value, the larger the grid will be. Note that
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there is an inherent trade-off involved: a small grid will lower the
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cost of FFTs, but a large order parameter will increase the cost of
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interpolating charge/fields to/from the grid. And vice versa.
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</P>
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<P>The order parameter may be reset by LAMMPS when it sets up the PPPM
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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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@ -78,8 +81,8 @@ 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> or the FFT grid size for style
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<I>pppm</I>.
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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 as <I>rinv</I> in reciprocal distance units. Without this
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@ -89,7 +92,8 @@ 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.
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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>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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@ -105,7 +109,8 @@ 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>. An alternative
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slab option can be invoked with the <I>nozforce</I> keyword in lieu of the
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volfactor. This turns off all kspace forces in the z direction.
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volfactor. This turns off all kspace forces in the z direction. The
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<I>slab</I> and <I>nozforce</I> options are not allowed for MSM.
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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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@ -40,25 +40,28 @@ Set parameters used by the kspace solvers defined by the
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"kspace_style"_kspace_style.html command. Not all parameters are
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relevant to all kspace styles.
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The {mesh} keyword sets the 3d FFT grid size for kspace style pppm.
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Each dimension must be factorizable into powers of 2, 3, and 5. When
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this 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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The {mesh} keyword sets the grid size for kspace style {pppm} or {msm}.
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In the case of PPPM, each dimension must be factorizable into powers
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of 2, 3, and 5. In the case of MSM, 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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The {order} keyword determines how many grid spacings an atom's charge
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extends when it is mapped to the FFT grid in kspace style pppm. The
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default for this parameter is 5, which means each charge spans 5 grid
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cells in each dimension. 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 FFT grid will need to be to achieve the requested
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precision. Conversely, the smaller the order value, the larger the
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grid will be. Note that there is an inherent trade-off involved: a
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small grid will lower the cost of FFTs, but a large order parameter
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will increase the cost of intepolating charge/fields to/from the grid.
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And vice versa.
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extends when it is mapped to the grid in kspace style {pppm} or {msm}.
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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, 4 is the only allowable value.
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For PPPM, the minimum allowed setting is 2 and the maximum allowed
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setting is 7. The larger the value of this parameter, the smaller the
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grid will need to be to achieve the requested precision. Conversely,
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the smaller the order value, the larger the grid will be. Note that
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there is an inherent trade-off involved: a small grid will lower the
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cost of FFTs, but a large order parameter will increase the cost of
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interpolating charge/fields to/from the grid. And vice versa.
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The order parameter may be reset by LAMMPS when it sets up the PPPM
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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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@ -72,8 +75,8 @@ 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 {ewald} or the FFT grid size for style
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{pppm}.
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K-space vectors for style {ewald}, the FFT grid size for style
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{pppm}, or the real space grid size for style {msm}.
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The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
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parameter as {rinv} in reciprocal distance units. Without this
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@ -83,7 +86,8 @@ 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.
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LAMMPS will choose the G-ewald parameter automatically. MSM does not
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use the {gewald} parameter.
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The {slab} 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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@ -99,7 +103,8 @@ must prevent particle migration beyond the initial z-bounds, typically
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by providing a wall-style fix. The methodology behind the {slab}
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option is explained in the paper by "(Yeh)"_#Yeh. An alternative
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slab option can be invoked with the {nozforce} keyword in lieu of the
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volfactor. This turns off all kspace forces in the z direction.
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volfactor. This turns off all kspace forces in the z direction. The
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{slab} and {nozforce} options are not allowed for MSM.
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The {compute} keyword allows Kspace computations to be turned off,
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even though a "kspace_style"_kspace_style.html is defined. This is
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@ -40,6 +40,8 @@
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<I>pppm/proxy</I> value = accuracy
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accuracy = desired relative error in forces
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<I>pppm/tip4p/proxy</I> value = accuracy
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accuracy = desired relative error in forces
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<I>msm</I> value = accuracy
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accuracy = desired relative error in forces
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</PRE>
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@ -48,6 +50,7 @@
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</P>
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<PRE>kspace_style pppm 1.0e-4
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kspace_style pppm/cg 1.0e-5 1.0e-6
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kspace style msm 1.0e-4
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kspace_style none
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</PRE>
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<P><B>Description:</B>
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@ -119,6 +122,26 @@ section</A> of the manual.
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</P>
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<HR>
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<P>The <I>msm</I> style invokes a multi-level summation method MSM solver
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<A HREF = "#Hardy">(Hardy)</A> which maps atom charge to a 3d mesh, and uses a
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multi-level hierarchy of coarser and coarser meshes on which direct
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coulomb solves are done. This method does not use FFTs and scales
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as N. It may therefore be faster than the other K-space solvers for
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relatively large problems when running on large core counts.
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</P>
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<P>MSM is most competitive versus Ewald and PPPM when only relatively
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low accuracy forces, about 1% relative error or higher, are needed.
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Note that MSM speed will be poor for large MSM meshes
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(i.e. 64 x 64 x 64 or larger). Also note that use of a larger
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coulomb cutoff (i.e. 15 angstroms instead of 10 angstroms) provides
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better MSM accuracy for both the real space and grid computed forces.
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Beware that the error estimation method for MSM is not very accurate,
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so you should probably set your own mesh size and ensure that you are
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getting adequate force accuracy by doing an energy conservation test
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or comparison versus the Ewald method.
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</P>
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<HR>
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<P>When a kspace style is used, a pair style that includes the
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short-range correction to the pairwise Coulombic or other 1/r^N forces
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must also be selected. For Coulombic interactions, these styles are
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@ -138,7 +161,7 @@ smaller than the reference force.
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</P>
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<P>The accuracy setting is used in conjunction with the pairwise cutoff
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to determine the number of K-space vectors for style <I>ewald</I> or the
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FFT grid size for style <I>pppm</I>.
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FFT grid size for style <I>pppm</I> or <I>msm</I>.
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</P>
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<P>RMS force errors in real space for <I>ewald</I> and <I>pppm</I> are estimated
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using equation 18 of <A HREF = "#Kolafa">(Kolafa)</A>, which is also referenced as
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@ -146,7 +169,9 @@ equation 9 of <A HREF = "#Petersen">(Petersen)</A>. RMS force errors in K-space
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<I>ewald</I> are estimated using equation 11 of <A HREF = "#Petersen">(Petersen)</A>,
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which is similar to equation 32 of <A HREF = "#Kolafa">(Kolafa)</A>. RMS force
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errors in K-space for <I>pppm</I> are estimated using equation 38 of
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<A HREF = "#Deserno">(Deserno)</A>.
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<A HREF = "#Deserno">(Deserno)</A>. RMS force errors for <I>msm</I> are estimated
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following the procedure outlined in chapter 3 of <A HREF = "#Hardy">(Hardy)</A>,
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with equation 3.197 of particular note.
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</P>
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<P>See the <A HREF = "kspace_modify.html">kspace_modify</A> command for additional
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options of the K-space solvers that can be set, including a <I>force</I>
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@ -198,6 +223,14 @@ LAMMPS</A> section for more info.
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<P>When using a long-range pairwise TIP4P potential, you must use kspace
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style <I>pppm/tip4p</I> and vice versa.
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</P>
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<P>The <I>msm</I> style is fairly new, and still lacks some important features
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and optimizations. In particular, the <I>msm</I> style does not include
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long-range virial contributions to the pressure. It should not be used
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for NPT simulations, and the reported total pressures should not be
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trusted. Also the upper MSM levels (above the first level) are not
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parallelized, so this MSM implementation may not yet scale very well
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on large core counts.
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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_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
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@ -240,4 +273,10 @@ Adam Hilger, NY (1989).
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<P><B>(Veld)</B> In 't Veld, Ismail, Grest, J Chem Phys, in press (2007).
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</P>
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<A NAME = "Hardy"></A>
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<P><B>(Hardy)</B> David, Multilevel Summation for the Fast Evaluation of
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Forces for the Simulation of Biomolecules, University of Illinois
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at Urbana-Champaign, (2006).
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</P>
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</HTML>
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@ -36,6 +36,8 @@ style = {none} or {ewald} or {ewald/omp} or {ewald/n} or {pppm} or {pppm/cg} or
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{pppm/proxy} value = accuracy
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accuracy = desired relative error in forces
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{pppm/tip4p/proxy} value = accuracy
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accuracy = desired relative error in forces
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{msm} value = accuracy
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accuracy = desired relative error in forces :pre
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:ule
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@ -43,6 +45,7 @@ style = {none} or {ewald} or {ewald/omp} or {ewald/n} or {pppm} or {pppm/cg} or
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kspace_style pppm 1.0e-4
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kspace_style pppm/cg 1.0e-5 1.0e-6
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kspace style msm 1.0e-4
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kspace_style none :pre
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[Description:]
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@ -114,6 +117,26 @@ section"_Section_start.html#start_2_4 of the manual.
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:line
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The {msm} style invokes a multi-level summation method MSM solver
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"(Hardy)"_#Hardy which maps atom charge to a 3d mesh, and uses a
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multi-level hierarchy of coarser and coarser meshes on which direct
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coulomb solves are done. This method does not use FFTs and scales
|
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as N. It may therefore be faster than the other K-space solvers for
|
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relatively large problems when running on large core counts.
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MSM is most competitive versus Ewald and PPPM when only relatively
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low accuracy forces, about 1% relative error or higher, are needed.
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Note that MSM speed will be poor for large MSM meshes
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(i.e. 64 x 64 x 64 or larger). Also note that use of a larger
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coulomb cutoff (i.e. 15 angstroms instead of 10 angstroms) provides
|
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better MSM accuracy for both the real space and grid computed forces.
|
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Beware that the error estimation method for MSM is not very accurate,
|
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so you should probably set your own mesh size and ensure that you are
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getting adequate force accuracy by doing an energy conservation test
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or comparison versus the Ewald method.
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:line
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When a kspace style is used, a pair style that includes the
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short-range correction to the pairwise Coulombic or other 1/r^N forces
|
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must also be selected. For Coulombic interactions, these styles are
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@ -133,7 +156,7 @@ smaller than the reference force.
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The accuracy setting is used in conjunction with the pairwise cutoff
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to determine the number of K-space vectors for style {ewald} or the
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FFT grid size for style {pppm}.
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FFT grid size for style {pppm} or {msm}.
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RMS force errors in real space for {ewald} and {pppm} are estimated
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using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
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@ -141,7 +164,9 @@ equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
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{ewald} are estimated using equation 11 of "(Petersen)"_#Petersen,
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which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
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errors in K-space for {pppm} are estimated using equation 38 of
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"(Deserno)"_#Deserno.
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"(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
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following the procedure outlined in chapter 3 of "(Hardy)"_#Hardy,
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with equation 3.197 of particular note.
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See the "kspace_modify"_kspace_modify.html command for additional
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options of the K-space solvers that can be set, including a {force}
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@ -193,6 +218,14 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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When using a long-range pairwise TIP4P potential, you must use kspace
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style {pppm/tip4p} and vice versa.
|
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The {msm} style is fairly new, and still lacks some important features
|
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and optimizations. In particular, the {msm} style does not include
|
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long-range virial contributions to the pressure. It should not be used
|
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for NPT simulations, and the reported total pressures should not be
|
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trusted. Also the upper MSM levels (above the first level) are not
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parallelized, so this MSM implementation may not yet scale very well
|
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on large core counts.
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[Related commands:]
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"kspace_modify"_kspace_modify.html, "pair_style
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@ -228,4 +261,7 @@ Adam Hilger, NY (1989).
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:link(Veld)
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[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, in press (2007).
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:link(Hardy)
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[(Hardy)] David, Multilevel Summation for the Fast Evaluation of
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Forces for the Simulation of Biomolecules, University of Illinois
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at Urbana-Champaign, (2006).
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|
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