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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2089 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2008-08-21 13:53:06 +00:00
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49
doc/communicate.html
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@ -19,16 +19,18 @@
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>group</I>
<LI>keyword = <I>group</I> or <I>cutoff</I>
<PRE> <I>group</I> value = group-ID = only communicate atoms in the group
<PRE> <I>group</I> value = group-ID = only communicate atoms in the group
<I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>communicate multi
communicate multi group solvent
communicate multi group solvent
communicate single cutoff 5.0
</PRE>
<P><B>Description:</B>
</P>
@ -57,6 +59,45 @@ specified group) will still migrate to new processors as they move.
The group specified with this option must also be specified via the
<A HREF = "atom_modify.html">atom_modify first</A> command.
</P>
<P>The <I>cutoff</I> option allows you to set a ghost cutoff distance which is
the distance from the borders of a processor's sub-domain at which
ghost atoms are acquired from other processors. By default the ghost
cutoff = the neighbor cutoff = the pairwise force cutoff + the
neighbor skin. See the <A HREF = "neighbor.html">neighbor</A> command for more
information about the skin distance. If the specified Rcut is greater
than the neighbor cutoff, then extra ghost atoms will be acquired. If
it is smaller, the ghost cutoff is set to the neighbor cutoff.
</P>
<P>These are simulation scenarios in which it may be useful to set a
ghost cutoff > neighbor cutoff:
</P>
<UL><LI>a single polymer chain with bond interactions, but no pairwise interactions
<LI>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
<LI>ghost atoms beyond the pairwise cutoff are needed for some computation
</UL>
<P>In the first scenario, a pairwise potential may not be defined. Thus
the pairwise neighbor cutoff will be 0.0. But ghost atoms are still
needed for computing bond, angle, etc interactions between atoms on
different processors. The appropriate ghost cutoff depends on the
<A HREF = "newton.html">newton bond</A> setting. For newton bond <I>off</I>, the
distance needs to be the furthest distance between any two atoms in
the bond, angle, etc. E.g. the distance between 1-4 atoms in a
dihedral. For newton bond <I>on</I>, the distance between the central atom
in the bond, angle, etc and any other atom is sufficient. E.g. the
distance between 2-4 atoms in a dihedral.
</P>
<P>In the second scenario, a pairwise potential is defined, but its
neighbor cutoff is not sufficiently long enough to enable bond, angle,
etc terms to be computed. As in the previous scenario, an appropriate
ghost cutoff should be set.
</P>
<P>In the last scenario, a <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> or
<A HREF = "pair_style.html">pairwise potential</A> needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
@ -65,6 +106,6 @@ The group specified with this option must also be specified via the
</P>
<P><B>Default:</B>
</P>
<P>The default settings are style = single and group = all.
<P>The default settings are style = single, group = all, cutoff = 0.0.
</P>
</HTML>

49
doc/communicate.txt
View File

@ -14,14 +14,16 @@ communicate style keyword value ... :pre
style = {single} or {multi} :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {group} :l
{group} value = group-ID = only communicate atoms in the group :pre
keyword = {group} or {cutoff} :l
{group} value = group-ID = only communicate atoms in the group
{cutoff} value = Rcut (distance units) = communicate atoms from this far away :pre
:ule
[Examples:]
communicate multi
communicate multi group solvent :pre
communicate multi group solvent
communicate single cutoff 5.0 :pre
[Description:]
@ -50,6 +52,45 @@ specified group) will still migrate to new processors as they move.
The group specified with this option must also be specified via the
"atom_modify first"_atom_modify.html command.
The {cutoff} option allows you to set a ghost cutoff distance which is
the distance from the borders of a processor's sub-domain at which
ghost atoms are acquired from other processors. By default the ghost
cutoff = the neighbor cutoff = the pairwise force cutoff + the
neighbor skin. See the "neighbor"_neighbor.html command for more
information about the skin distance. If the specified Rcut is greater
than the neighbor cutoff, then extra ghost atoms will be acquired. If
it is smaller, the ghost cutoff is set to the neighbor cutoff.
These are simulation scenarios in which it may be useful to set a
ghost cutoff > neighbor cutoff:
a single polymer chain with bond interactions, but no pairwise interactions
bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
ghost atoms beyond the pairwise cutoff are needed for some computation :ul
In the first scenario, a pairwise potential may not be defined. Thus
the pairwise neighbor cutoff will be 0.0. But ghost atoms are still
needed for computing bond, angle, etc interactions between atoms on
different processors. The appropriate ghost cutoff depends on the
"newton bond"_newton.html setting. For newton bond {off}, the
distance needs to be the furthest distance between any two atoms in
the bond, angle, etc. E.g. the distance between 1-4 atoms in a
dihedral. For newton bond {on}, the distance between the central atom
in the bond, angle, etc and any other atom is sufficient. E.g. the
distance between 2-4 atoms in a dihedral.
In the second scenario, a pairwise potential is defined, but its
neighbor cutoff is not sufficiently long enough to enable bond, angle,
etc terms to be computed. As in the previous scenario, an appropriate
ghost cutoff should be set.
In the last scenario, a "fix"_fix.html or "compute"_compute.html or
"pairwise potential"_pair_style.html needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.
[Restrictions:] none
[Related commands:]
@ -58,4 +99,4 @@ The group specified with this option must also be specified via the
[Default:]
The default settings are style = single and group = all.
The default settings are style = single, group = all, cutoff = 0.0.

6
doc/delete_atoms.html
View File

@ -71,7 +71,11 @@ would foul up the bond connectivity that has already been assigned.
<P>The <I>overlap</I> styles requires inter-processor communication to acquire
ghost atoms and build a neighbor list. This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc).
fields setup, atom masses set, etc). Since a neighbor list is used to
find overlapping atom pairs, it also means that you must define a
<A HREF = "pair_style.html">pair style</A> with force cutoffs greater than or equal
to the desired overlap cutoff between pairs of relevant atom types,
even though the pair potential will not be evaluated.
</P>
<P>If the <A HREF = "special_bonds.html">special_bonds</A> command is used with a
setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not

6
doc/delete_atoms.txt
View File

@ -66,7 +66,11 @@ would foul up the bond connectivity that has already been assigned.
The {overlap} styles requires inter-processor communication to acquire
ghost atoms and build a neighbor list. This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc).
fields setup, atom masses set, etc). Since a neighbor list is used to
find overlapping atom pairs, it also means that you must define a
"pair style"_pair_style.html with force cutoffs greater than or equal
to the desired overlap cutoff between pairs of relevant atom types,
even though the pair potential will not be evaluated.
If the "special_bonds"_special_bonds.html command is used with a
setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not

5
doc/neigh_modify.html
View File

@ -56,9 +56,10 @@ neigh_modify exclude molecule rigid
</PRE>
<P><B>Description:</B>
</P>
<P>This command sets parameters that affect the pairwise neighbor list.
<P>This command sets parameters that affect the building and use of
pairwise neighbor lists.
</P>
<P>The <I>every</I>, <I>delay</I>, and <I>check</I> options affect how often the list is
<P>The <I>every</I>, <I>delay</I>, and <I>check</I> options affect how often lists are
built as a simulation runs. The <I>delay</I> setting means never build a
new list until at least N steps after the previous build. The <I>every</I>
setting means build the list every M steps (after the delay has

5
doc/neigh_modify.txt
View File

@ -50,9 +50,10 @@ neigh_modify exclude molecule rigid :pre
[Description:]
This command sets parameters that affect the pairwise neighbor list.
This command sets parameters that affect the building and use of
pairwise neighbor lists.
The {every}, {delay}, and {check} options affect how often the list is
The {every}, {delay}, and {check} options affect how often lists are
built as a simulation runs. The {delay} setting means never build a
new list until at least N steps after the previous build. The {every}
setting means build the list every M steps (after the delay has

42
doc/neighbor.html
View File

@ -25,13 +25,22 @@ neighbor 2.0 nsq
</PRE>
<P><B>Description:</B>
</P>
<P>This command sets parameters that affect the building of the pairwise
neighbor list. All atom pairs within a cutoff distance equal to the
<P>This command sets parameters that affect the building of pairwise
neighbor lists. All atom pairs within a cutoff distance equal to the
their force cutoff plus the <I>skin</I> distance are stored in the list.
Typically, the larger the skin distance, the less often neighbor lists
need to be built, but more pairs must be checked for possible force
interactions every timestep. The default value for <I>skin</I> depends on
the choice of units for the simulation (see below).
the choice of units for the simulation; see the default values below.
</P>
<P>Even if pairwise neighbor lists are not used in a simulation (e.g. a
pair potential is not defined), the skin distance may still determine
how often atoms migrate to new processors due to atom motion and
should thus be set appropriately. This is because atoms migrate on
the same timestep that neighbor lists are built. See the various
settings of the <A HREF = "neigh_modify">neigh_modify</A> command which control when
neighbor lists are built, based on atom movement via the "check yes"
option.
</P>
<P>The <I>style</I> value selects what algorithm is used to build the list.
The <I>bin</I> style creates the list by binning which is an operation that
@ -64,24 +73,7 @@ the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See <A HREF = "Section_start.html#2_7">this
section</A> for details.
</P>
<P><B>Restrictions:</B>
</P>
<P>For simulations without pairwise interactions (see "pair_style none"
command), but that include bonded interactions, you still need to set
the neighbor skin distance. Pairwise neighbor lists will not be
formed, but the pair cutoff (0.0 in this case) plus the skin distance
is the range at which atoms are communicated from nearby processors.
This needs to be large enough that atoms in the same bond, angle, etc
as an atom owned by a processor are acquired. What distance is
appropriate depends on the <A HREF = "newton.html">newton bond</A> setting. For
newton bond off, the distance needs to be the furthest distance
between any two atoms in the bond, angle, etc. E.g. the distance
between the 1-4 atoms in a dihedral. For newton bond on, the distance
is between the central atom in the bond, angle, etc and any other
atom. E.g. the distance between the 2-4 atoms in a dihedral.
</P>
<P>The same logic applies to systems that include bonded interactions and
a pairwise cutoff shorter than the distances just described.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
@ -90,7 +82,9 @@ a pairwise cutoff shorter than the distances just described.
</P>
<P><B>Default:</B>
</P>
<PRE>0.3 bin for lj units (0.3 sigma)
2.0 bin for real or metal units (2.0 Angstroms)
</PRE>
0.3 bin for units = lj, skin = 0.3 sigma<BR>
2.0 bin for units = real or metal, skin = 2.0 Angstroms<BR>
0.001 bin for units = si, skin = 0.001 meters = 1.0 mm<BR>
0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm <BR>
</HTML>

40
doc/neighbor.txt
View File

@ -22,13 +22,22 @@ neighbor 2.0 nsq :pre
[Description:]
This command sets parameters that affect the building of the pairwise
neighbor list. All atom pairs within a cutoff distance equal to the
This command sets parameters that affect the building of pairwise
neighbor lists. All atom pairs within a cutoff distance equal to the
their force cutoff plus the {skin} distance are stored in the list.
Typically, the larger the skin distance, the less often neighbor lists
need to be built, but more pairs must be checked for possible force
interactions every timestep. The default value for {skin} depends on
the choice of units for the simulation (see below).
the choice of units for the simulation; see the default values below.
Even if pairwise neighbor lists are not used in a simulation (e.g. a
pair potential is not defined), the skin distance may still determine
how often atoms migrate to new processors due to atom motion and
should thus be set appropriately. This is because atoms migrate on
the same timestep that neighbor lists are built. See the various
settings of the "neigh_modify"_neigh_modify command which control when
neighbor lists are built, based on atom movement via the "check yes"
option.
The {style} value selects what algorithm is used to build the list.
The {bin} style creates the list by binning which is an operation that
@ -61,24 +70,7 @@ the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See "this
section"_Section_start.html#2_7 for details.
[Restrictions:]
For simulations without pairwise interactions (see "pair_style none"
command), but that include bonded interactions, you still need to set
the neighbor skin distance. Pairwise neighbor lists will not be
formed, but the pair cutoff (0.0 in this case) plus the skin distance
is the range at which atoms are communicated from nearby processors.
This needs to be large enough that atoms in the same bond, angle, etc
as an atom owned by a processor are acquired. What distance is
appropriate depends on the "newton bond"_newton.html setting. For
newton bond off, the distance needs to be the furthest distance
between any two atoms in the bond, angle, etc. E.g. the distance
between the 1-4 atoms in a dihedral. For newton bond on, the distance
is between the central atom in the bond, angle, etc and any other
atom. E.g. the distance between the 2-4 atoms in a dihedral.
The same logic applies to systems that include bonded interactions and
a pairwise cutoff shorter than the distances just described.
[Restrictions:] none
[Related commands:]
@ -87,5 +79,7 @@ a pairwise cutoff shorter than the distances just described.
[Default:]
0.3 bin for lj units (0.3 sigma)
2.0 bin for real or metal units (2.0 Angstroms) :pre
0.3 bin for units = lj, skin = 0.3 sigma
2.0 bin for units = real or metal, skin = 2.0 Angstroms
0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm :all(b)

7
doc/timestep.html
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@ -26,8 +26,8 @@ timestep 0.003
</P>
<P>Set the timestep size for subsequent molecular dynamics simulations.
See the <A HREF = "units.html">units</A> command for a discussion of time units.
Note that using the units command also sets the timestep to its
default value in the chosen units.
The default value for the timestep also depends on the choice of units
for the simulation; see the default values below.
</P>
<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, dt is the timestep for
the outer loop (largest) timestep.
@ -43,6 +43,7 @@ the outer loop (largest) timestep.
</P>
timestep = 0.005 tau for units = lj<BR>
timestep = 1.0 fmsec for units = real<BR>
timestep = 0.001 psec for units = metal <BR>
timestep = 0.001 psec for units = metal<BR>
timestep = 1.0e-8 sec (10 nsec) for units = si or cgs <BR>
</HTML>

10
doc/timestep.txt
View File

@ -23,8 +23,8 @@ timestep 0.003 :pre
Set the timestep size for subsequent molecular dynamics simulations.
See the "units"_units.html command for a discussion of time units.
Note that using the units command also sets the timestep to its
default value in the chosen units.
The default value for the timestep also depends on the choice of units
for the simulation; see the default values below.
When the "run style"_run_style.html is {respa}, dt is the timestep for
the outer loop (largest) timestep.
@ -40,7 +40,5 @@ the outer loop (largest) timestep.
timestep = 0.005 tau for units = lj
timestep = 1.0 fmsec for units = real
timestep = 0.001 psec for units = metal :all(b)
timestep = 0.001 psec for units = metal
timestep = 1.0e-8 sec (10 nsec) for units = si or cgs :all(b)