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30
doc/kspace_modify.html
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@ -17,7 +17,7 @@
</PRE> </PRE>
<UL><LI>one or more keyword/value pairs may be listed <UL><LI>one or more keyword/value pairs may be listed
<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> <LI>keyword = <I>mesh</I> or <I>order</I> or <I>order/disp</I> or <I>mix/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>fftbench</I> or <I>collective</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>
<PRE> <I>mesh</I> value = x y z <PRE> <I>mesh</I> value = x y z
x,y,z = grid size in each dimension for long-range Coulombics x,y,z = grid size in each dimension for long-range Coulombics
@ -27,6 +27,7 @@
N = extent of Gaussian for PPPM or MSM mapping of charge to grid N = extent of Gaussian for PPPM or MSM mapping of charge to grid
<I>order/disp</I> value = N <I>order/disp</I> value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid N = extent of Gaussian for PPPM mapping of dispersion term to grid
<I>mix/disp</I> value = <I>pair</I> or <I>geom</I> or <I>none</I>
<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 <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
<I>minorder</I> value = M <I>minorder</I> value = M
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
@ -42,10 +43,10 @@
<I>compute</I> value = <I>yes</I> or <I>no</I> <I>compute</I> value = <I>yes</I> or <I>no</I>
<I>cutoff/adjust</I> value = <I>yes</I> or <I>no</I> <I>cutoff/adjust</I> value = <I>yes</I> or <I>no</I>
<I>fftbench</I> value = <I>yes</I> or <I>no</I> <I>fftbench</I> value = <I>yes</I> or <I>no</I>
<I>collective</I> value = <I>yes</I> or <I>no</I>
<I>diff</I> value = <I>ad</I> or <I>ik</I> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode <I>diff</I> value = <I>ad</I> or <I>ik</I> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
<I>kmax/ewald</I> value = kx ky kz <I>kmax/ewald</I> value = kx ky kz
kx,ky,kz = number of Ewald sum kspace vectors in each dimension kx,ky,kz = number of Ewald sum kspace vectors in each dimension
<I>mix/disp</I> value = <I>pair</I> or <I>geom</I> or <I>none</I>
<I>force/disp/real</I> value = accuracy (force units) <I>force/disp/real</I> value = accuracy (force units)
<I>force/disp/kspace</I> value = accuracy (force units) <I>force/disp/kspace</I> value = accuracy (force units)
<I>splittol</I> value = tol <I>splittol</I> value = tol
@ -210,6 +211,14 @@ 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 of a run to give FFT benchmark timings, and will finish a few seconds
faster than it would if this option were on. faster than it would if this option were on.
</P> </P>
<P>The <I>collective</I> keyword applies only to PPPM. It is set to <I>no</I> by
default, except on IBM BlueGene machines. If this option is set to
<I>yes</I>, LAMMPS will use MPI collective operations to remap data for
3d-FFT operations instead of the default point-to-point communication.
This is faster on IBM BlueGene machines, and may also be faster on
other machines if they have an efficient implementation of MPI
collective operations and adequate hardware.
</P>
<P>The <I>diff</I> keyword specifies the differentiation scheme used by the <P>The <I>diff</I> keyword specifies the differentiation scheme used by the
PPPM method to compute forces on particles given electrostatic PPPM method to compute forces on particles given electrostatic
potentials on the PPPM mesh. The <I>ik</I> approach is the default for potentials on the PPPM mesh. The <I>ik</I> approach is the default for
@ -231,16 +240,13 @@ always used for MSM.
<P>IMPORTANT NOTE: Currently, not all PPPM styles support the <I>ad</I> <P>IMPORTANT NOTE: Currently, not all PPPM styles support the <I>ad</I>
option. Support for those PPPM variants will be added later. option. Support for those PPPM variants will be added later.
</P> </P>
<P>The <I>kmax/ewald</I> keyword sets the number of kspace vectors in <P>The <I>kmax/ewald</I> keyword sets the number of kspace vectors in each
each dimension for kspace style <I>ewald</I>. The three values must dimension for kspace style <I>ewald</I>. The three values must be positive
be positive integers, or else (0,0,0), which unsets the option. integers, or else (0,0,0), which unsets the option. When this option
When this option is not is not set, the Ewald sum scheme chooses its own kspace vectors,
set, the Ewald sum scheme chooses its own kspace vectors, consistent with the user-specified accuracy and pairwise cutoff. In
consistent with the any case, if kspace style <I>ewald</I> is invoked, the values used are
user-specified accuracy and pairwise cutoff. In any case, printed to the screen and the log file at the start of the run.
if kspace style <I>ewald</I> is invoked, the values used
are printed to the screen and
the log file at the start of the run.
</P> </P>
<P>With the <I>mix/disp</I> keyword one can select the mixing rule for the <P>With the <I>mix/disp</I> keyword one can select the mixing rule for the
dispersion coefficients. With <I>pair</I>, the dispersion coefficients of dispersion coefficients. With <I>pair</I>, the dispersion coefficients of

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doc/kspace_modify.txt
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@ -13,7 +13,7 @@ kspace_modify command :h3
kspace_modify keyword value ... :pre kspace_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l 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 keyword = {mesh} or {order} or {order/disp} or {mix/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {fftbench} or {collective} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} :l
{mesh} value = x y z {mesh} value = x y z
x,y,z = grid size in each dimension for long-range Coulombics x,y,z = grid size in each dimension for long-range Coulombics
{mesh/disp} value = x y z {mesh/disp} value = x y z
@ -22,6 +22,7 @@ keyword = {mesh} or {order} or {order/disp} or {overlap} or {minorder} or {force
N = extent of Gaussian for PPPM or MSM mapping of charge to grid N = extent of Gaussian for PPPM or MSM mapping of charge to grid
{order/disp} value = N {order/disp} value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid N = extent of Gaussian for PPPM mapping of dispersion term to grid
{mix/disp} value = {pair} or {geom} or {none}
{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
{minorder} value = M {minorder} value = M
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
@ -37,10 +38,10 @@ keyword = {mesh} or {order} or {order/disp} or {overlap} or {minorder} or {force
{compute} value = {yes} or {no} {compute} value = {yes} or {no}
{cutoff/adjust} value = {yes} or {no} {cutoff/adjust} value = {yes} or {no}
{fftbench} value = {yes} or {no} {fftbench} value = {yes} or {no}
{collective} value = {yes} or {no}
{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
{kmax/ewald} value = kx ky kz {kmax/ewald} value = kx ky kz
kx,ky,kz = number of Ewald sum kspace vectors in each dimension 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/real} value = accuracy (force units)
{force/disp/kspace} value = accuracy (force units) {force/disp/kspace} value = accuracy (force units)
{splittol} value = tol {splittol} value = tol
@ -204,6 +205,14 @@ 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 of a run to give FFT benchmark timings, and will finish a few seconds
faster than it would if this option were on. faster than it would if this option were on.
The {collective} keyword applies only to PPPM. It is set to {no} by
default, except on IBM BlueGene machines. If this option is set to
{yes}, LAMMPS will use MPI collective operations to remap data for
3d-FFT operations instead of the default point-to-point communication.
This is faster on IBM BlueGene machines, and may also be faster on
other machines if they have an efficient implementation of MPI
collective operations and adequate hardware.
The {diff} keyword specifies the differentiation scheme used by the The {diff} keyword specifies the differentiation scheme used by the
PPPM method to compute forces on particles given electrostatic PPPM method to compute forces on particles given electrostatic
potentials on the PPPM mesh. The {ik} approach is the default for potentials on the PPPM mesh. The {ik} approach is the default for
@ -225,16 +234,13 @@ always used for MSM.
IMPORTANT NOTE: Currently, not all PPPM styles support the {ad} IMPORTANT NOTE: Currently, not all PPPM styles support the {ad}
option. Support for those PPPM variants will be added later. option. Support for those PPPM variants will be added later.
The {kmax/ewald} keyword sets the number of kspace vectors in The {kmax/ewald} keyword sets the number of kspace vectors in each
each dimension for kspace style {ewald}. The three values must dimension for kspace style {ewald}. The three values must be positive
be positive integers, or else (0,0,0), which unsets the option. integers, or else (0,0,0), which unsets the option. When this option
When this option is not is not set, the Ewald sum scheme chooses its own kspace vectors,
set, the Ewald sum scheme chooses its own kspace vectors, consistent with the user-specified accuracy and pairwise cutoff. In
consistent with the any case, if kspace style {ewald} is invoked, the values used are
user-specified accuracy and pairwise cutoff. In any case, printed to the screen and the log file at the start of the run.
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 With the {mix/disp} keyword one can select the mixing rule for the
dispersion coefficients. With {pair}, the dispersion coefficients of dispersion coefficients. With {pair}, the dispersion coefficients of