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doc/PDF/kspace.pdf Executable file
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doc/compute_group_group.html
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@ -13,31 +13,73 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID group/group group2-ID
<PRE>compute ID group-ID group/group group2-ID keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>group/group = style name of this compute command
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>group/group = style name of this compute command
<LI>group2-ID = group ID of second (or same) group
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>pair</I> or <I>kspace</I>
<PRE> <I>pair</I> value = <I>yes</I> or <I>no</I>
<I>kspace</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 lower group/group upper
compute 1 lower group/group upper kspace yes
compute mine fluid group/group wall
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the total energy and force
interaction between two groups of atoms: the compute group and the
specified group2. The two groups can be the same. The interaction
energy is defined as the pairwise energy between all pairs of atoms
where one atom in the pair is in the first group and the other is in
the second group. Likewise, the interaction force calculated by this
compute is the force on the compute group atoms due to pairwise
specified group2. The two groups can be the same.
</P>
<P>If the <I>pair</I> keyword is set to <I>yes</I>, which is the default, then the
the interaction energy will include a pair component which is defined
as the pairwise energy between all pairs of atoms where one atom in
the pair is in the first group and the other is in the second group.
Likewise, the interaction force calculated by this compute will
include the force on the compute group atoms due to pairwise
interactions with atoms in the specified group2.
</P>
<P>The energy and force are calculated by looping over a neighbor list of
pairwise interactions. Thus it can be inefficient to compute this
quantity too frequently.
<P>If the <I>kspace</I> keyword is set to <I>yes</I>, which is not the default, and
if a <A HREF = "kspace_style.html">kspace_style</A> is defined, then the the
interaction energy will include a Kspace component which is the
long-range Coulombic energy between all the atoms in the first group
and all the atoms in the 2nd group. group. Likewise, the interaction
force calculated by this compute will include the force on the compute
group atoms due to long-range Coulombic interactions with atoms in the
specified group2.
</P>
<P>This compute does not calculate any bond or angle or dihedral or
improper interactions between atoms in the two groups.
</P>
<HR>
<P>The pairwise contributions to the group-group interactions are
calculated by looping over a neighbor list. The Kspace contribution
to the group-group interactions require essentially the same amount of
work (FFTs, Ewald summation) as computing long-range forces for the
entire system. Thus it can be costly to invoke this compute too
frequently.
</P>
<P>If you desire a breakdown of the interactions into a pairwise and
Kspace component, simply invoke the compute twice with the appropriate
yes/no settings for the <I>pair</I> and <I>kspace</I> keywords. This is no more
costly than using a single compute with both keywords set to <I>yes</I>.
The individual contributions can be summed in a
<A HREF = "variable.html">variable</A> if desired.
</P>
<P>Thie <A HREF = "PDF/kspace.pdf">document</A> describes how the long-range
group-group calculations are performed.
</P>
<P><B>Output info:</B>
</P>
@ -54,20 +96,20 @@ The vector values will be in force <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Only pairwise interactions, as defined by the
<A HREF = "pair_style.html">pair_style</A> command, are included in this
calculation. Bond (angle, dihedral, etc) interactions between atoms
in the two groups are not included. Long-range interactions due to a
<A HREF = "kspace_style.html">kspace_style</A> command are also not included. Not
all pair potentials can be evaluated in a pairwise mode as required by
this compute. For example, 3-body potentials, such as
<A HREF = "pair_tersoff.html">Tersoff</A> and <A HREF = "pair_sw.html">Stillinger-Weber</A> cannot
be used. <A HREF = "pair_eam.html">EAM</A> potentials for metals only include the
pair potential portion of the EAM interaction, not the embedding
term.
<P>Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as <A HREF = "pair_tersoff.html">Tersoff</A> and
<A HREF = "pair_sw.html">Stillinger-Weber</A> cannot be used. <A HREF = "pair_eam.html">EAM</A>
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term.
</P>
<P>Not all Kspace styles support calculation of group/group interactions.
The <I>ewald</I> and <I>pppm</I> styles do.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The option defaults are pair = yes and kspace = no.
</P>
</HTML>

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doc/compute_group_group.txt
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@ -10,31 +10,68 @@ compute group/group command :h3
[Syntax:]
compute ID group-ID group/group group2-ID :pre
compute ID group-ID group/group group2-ID keyword value ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
group/group = style name of this compute command :l
group2-ID = group ID of second (or same) group :l
zero or more keyword/value pairs may be appended :l
keyword = {pair} or {kspace} :l
{pair} value = {yes} or {no}
{kspace} value = {yes} or {no} :pre
:ule
ID, group-ID are documented in "compute"_compute.html command
group/group = style name of this compute command
group2-ID = group ID of second (or same) group :ul
[Examples:]
compute 1 lower group/group upper
compute 1 lower group/group upper kspace yes
compute mine fluid group/group wall :pre
[Description:]
Define a computation that calculates the total energy and force
interaction between two groups of atoms: the compute group and the
specified group2. The two groups can be the same. The interaction
energy is defined as the pairwise energy between all pairs of atoms
where one atom in the pair is in the first group and the other is in
the second group. Likewise, the interaction force calculated by this
compute is the force on the compute group atoms due to pairwise
specified group2. The two groups can be the same.
If the {pair} keyword is set to {yes}, which is the default, then the
the interaction energy will include a pair component which is defined
as the pairwise energy between all pairs of atoms where one atom in
the pair is in the first group and the other is in the second group.
Likewise, the interaction force calculated by this compute will
include the force on the compute group atoms due to pairwise
interactions with atoms in the specified group2.
The energy and force are calculated by looping over a neighbor list of
pairwise interactions. Thus it can be inefficient to compute this
quantity too frequently.
If the {kspace} keyword is set to {yes}, which is not the default, and
if a "kspace_style"_kspace_style.html is defined, then the the
interaction energy will include a Kspace component which is the
long-range Coulombic energy between all the atoms in the first group
and all the atoms in the 2nd group. group. Likewise, the interaction
force calculated by this compute will include the force on the compute
group atoms due to long-range Coulombic interactions with atoms in the
specified group2.
This compute does not calculate any bond or angle or dihedral or
improper interactions between atoms in the two groups.
:line
The pairwise contributions to the group-group interactions are
calculated by looping over a neighbor list. The Kspace contribution
to the group-group interactions require essentially the same amount of
work (FFTs, Ewald summation) as computing long-range forces for the
entire system. Thus it can be costly to invoke this compute too
frequently.
If you desire a breakdown of the interactions into a pairwise and
Kspace component, simply invoke the compute twice with the appropriate
yes/no settings for the {pair} and {kspace} keywords. This is no more
costly than using a single compute with both keywords set to {yes}.
The individual contributions can be summed in a
"variable"_variable.html if desired.
Thie "document"_PDF/kspace.pdf describes how the long-range
group-group calculations are performed.
[Output info:]
@ -51,18 +88,18 @@ The vector values will be in force "units"_units.html.
[Restrictions:]
Only pairwise interactions, as defined by the
"pair_style"_pair_style.html command, are included in this
calculation. Bond (angle, dihedral, etc) interactions between atoms
in the two groups are not included. Long-range interactions due to a
"kspace_style"_kspace_style.html command are also not included. Not
all pair potentials can be evaluated in a pairwise mode as required by
this compute. For example, 3-body potentials, such as
"Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot
be used. "EAM"_pair_eam.html potentials for metals only include the
pair potential portion of the EAM interaction, not the embedding
term.
Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as "Tersoff"_pair_tersoff.html and
"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term.
Not all Kspace styles support calculation of group/group interactions.
The {ewald} and {pppm} styles do.
[Related commands:] none
[Default:] none
[Default:]
The option defaults are pair = yes and kspace = no.

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doc/compute_pe.html
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@ -41,11 +41,12 @@ potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed,
then only those components are summed to compute the potential energy.
</P>
<P>The KSpace contribution requires 1 extra FFT each timestep the
<P>The Kspace contribution requires 1 extra FFT each timestep the
per-atom energy is calculated, if using the PPPM solver via the
<A HREF = "kspace_style.html">kspace_style pppm</A> command. Thus it can increase
the cost of the PPPM calculation if it is needed on a large fraction
of the simulation timesteps.
of the simulation timesteps. Thie <A HREF = "PDF/kspace.pdf">document</A> describes
how the long-range per-atom energy calculation is performed.
</P>
<P>Various fixes can contribute to the total potential energy of the
system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for

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doc/compute_pe.txt
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@ -37,11 +37,12 @@ potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed,
then only those components are summed to compute the potential energy.
The KSpace contribution requires 1 extra FFT each timestep the
The Kspace contribution requires 1 extra FFT each timestep the
per-atom energy is calculated, if using the PPPM solver via the
"kspace_style pppm"_kspace_style.html command. Thus it can increase
the cost of the PPPM calculation if it is needed on a large fraction
of the simulation timesteps.
of the simulation timesteps. Thie "document"_PDF/kspace.pdf describes
how the long-range per-atom energy calculation is performed.
Various fixes can contribute to the total potential energy of the
system. See the doc pages for "individual fixes"_fix.html for