git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11150 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -21,7 +21,7 @@
|
||||
|
||||
<LI>N = # of atoms or molecules to insert
|
||||
|
||||
<LI>type = atom type to assign to inserted atoms (for atom insertion)
|
||||
<LI>type = atom type to assign to inserted atoms (offset for moleclue insertion)
|
||||
|
||||
<LI>M = insert a single atom or molecule every M steps
|
||||
|
||||
@ -35,6 +35,8 @@
|
||||
region-ID = ID of region to use as insertion volume
|
||||
<I>mol</I> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
|
||||
<I>rigid</I> value = fix-ID
|
||||
fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
|
||||
<I>id</I> value = <I>max</I> or <I>next</I>
|
||||
max = atom ID for new atom(s) is max ID of all current atoms plus one
|
||||
next = atom ID for new atom(s) increments by one for every deposition
|
||||
@ -78,9 +80,11 @@ this doc page, a single inserted atom or molecule is referred to as a
|
||||
"particle".
|
||||
</P>
|
||||
<P>If inserted particles are individual atoms, they are assigned the
|
||||
specified atom type. For molecules the specified type is ignored, and
|
||||
the type of each atom in the inserted molecule is specified in the
|
||||
file read by the <A HREF = "molecule.html">molecule</A> command.
|
||||
specified atom type. If they are molecules, the type of each atom in
|
||||
the inserted molecule is specified in the file read by the
|
||||
<A HREF = "molecule.html">molecule</A> command, and those values are added to the
|
||||
specified atom type. E.g. if <I>type</I> = 2, and the file specifies atom
|
||||
types 1,2,3, then the inserted molecule will have atom types 3,4,5.
|
||||
</P>
|
||||
<P>All atoms in the inserted particle are assigned to two groups: the
|
||||
default group "all" and the group specified in the fix deposit command
|
||||
@ -121,6 +125,11 @@ molecule file. See the <A HREF = "molecule.html">molecule</A> command for detai
|
||||
The only settings required to be in this file are the coordinates and
|
||||
types of atoms in the molecule.
|
||||
</P>
|
||||
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will be
|
||||
treated as rigid bodies, use the <I>rigid</I> keyword, specifying as its
|
||||
value the ID of a separate <A HREF = "fix_rigid_small.html">fix rigid/small</A>
|
||||
command which also appears in your input script.
|
||||
</P>
|
||||
<P>Each timestep a particle is inserted, the coordinates for its atoms
|
||||
are chosen as follows. For insertion of individual atoms, the
|
||||
"position" referred to in the following description is the coordinate
|
||||
|
||||
@ -15,7 +15,7 @@ fix ID group-ID deposit N type M seed keyword values ... :pre
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
deposit = style name of this fix command :l
|
||||
N = # of atoms or molecules to insert :l
|
||||
type = atom type to assign to inserted atoms (for atom insertion) :l
|
||||
type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
|
||||
M = insert a single atom or molecule every M steps :l
|
||||
seed = random # seed (positive integer) :l
|
||||
one or more keyword/value pairs may be appended to args :l
|
||||
@ -24,6 +24,8 @@ keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt
|
||||
region-ID = ID of region to use as insertion volume
|
||||
{mol} value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{rigid} value = fix-ID
|
||||
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
|
||||
{id} value = {max} or {next}
|
||||
max = atom ID for new atom(s) is max ID of all current atoms plus one
|
||||
next = atom ID for new atom(s) increments by one for every deposition
|
||||
@ -66,9 +68,11 @@ this doc page, a single inserted atom or molecule is referred to as a
|
||||
"particle".
|
||||
|
||||
If inserted particles are individual atoms, they are assigned the
|
||||
specified atom type. For molecules the specified type is ignored, and
|
||||
the type of each atom in the inserted molecule is specified in the
|
||||
file read by the "molecule"_molecule.html command.
|
||||
specified atom type. If they are molecules, the type of each atom in
|
||||
the inserted molecule is specified in the file read by the
|
||||
"molecule"_molecule.html command, and those values are added to the
|
||||
specified atom type. E.g. if {type} = 2, and the file specifies atom
|
||||
types 1,2,3, then the inserted molecule will have atom types 3,4,5.
|
||||
|
||||
All atoms in the inserted particle are assigned to two groups: the
|
||||
default group "all" and the group specified in the fix deposit command
|
||||
@ -109,6 +113,11 @@ molecule file. See the "molecule"_molecule.html command for details.
|
||||
The only settings required to be in this file are the coordinates and
|
||||
types of atoms in the molecule.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will be
|
||||
treated as rigid bodies, use the {rigid} keyword, specifying as its
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid_small.html
|
||||
command which also appears in your input script.
|
||||
|
||||
Each timestep a particle is inserted, the coordinates for its atoms
|
||||
are chosen as follows. For insertion of individual atoms, the
|
||||
"position" referred to in the following description is the coordinate
|
||||
|
||||
@ -21,20 +21,16 @@
|
||||
|
||||
<LI>N = # of atoms to insert
|
||||
|
||||
<LI>type = atom type to assign to inserted atoms
|
||||
<LI>type = atom type to assign to inserted atoms (offset for molecule insertion)
|
||||
|
||||
<LI>seed = random # seed (positive integer)
|
||||
|
||||
<LI>one or more keyword/value pairs may be appended to args
|
||||
|
||||
<LI>keyword = <I>region</I> or <I>mol</I> or <I>rigid</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I>
|
||||
<LI>keyword = <I>region</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I> or <I>mol</I> or <I>rigid</I> or <I>shake</I>
|
||||
|
||||
<PRE> <I>region</I> value = region-ID
|
||||
region-ID = ID of region to use as insertion volume
|
||||
<I>mol</I> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
|
||||
<I>rigid</I> value = fix-ID
|
||||
fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
|
||||
<I>diam</I> values = dstyle args
|
||||
dstyle = <I>one</I> or <I>range</I> or <I>poly</I>
|
||||
<I>one</I> args = D
|
||||
@ -58,6 +54,12 @@
|
||||
vz = z velocity (3d) assigned to inserted particles (velocity units)
|
||||
vy = y velocity (2d) assigned to inserted particles (velocity units)
|
||||
</PRE>
|
||||
<I>mol</I> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
|
||||
<I>rigid</I> value = fix-ID
|
||||
fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
|
||||
<I>shake</I> value = fix-ID
|
||||
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
@ -77,9 +79,11 @@ gravity. For the remainder of this doc page, a single inserted atom
|
||||
or molecule is referred to as a "particle".
|
||||
</P>
|
||||
<P>If inserted particles are individual atoms, they are assigned the
|
||||
specified atom type. For molecules the specified type is ignored, and
|
||||
the type of each atom in the inserted molecule is specified in the
|
||||
file read by the <A HREF = "molecule.html">molecule</A> command.
|
||||
specified atom type. If they are molecules, the type of each atom in
|
||||
the inserted molecule is specified in the file read by the
|
||||
<A HREF = "molecule.html">molecule</A> command, and those values are added to the
|
||||
specified atom type. E.g. if <I>type</I> = 2, and the file specifies atom
|
||||
types 1,2,3, then the inserted molecule will have atom types 3,4,5.
|
||||
</P>
|
||||
<P>All atoms in the inserted particle are assigned to two groups: the
|
||||
default group "all" and the group specified in the fix pour command
|
||||
@ -102,10 +106,14 @@ required to be in this file are the coordinates and types of atoms in
|
||||
the molecule.
|
||||
</P>
|
||||
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will be
|
||||
treated as rigid bodies, you can first specify a <A HREF = "fix_rigid.html">fix
|
||||
rigid/small</A> command, and then use the <I>rigid</I> keyword
|
||||
with this command, specifying the ID of the fix rigid/small command as
|
||||
its value.
|
||||
treated as rigid bodies, use the <I>rigid</I> keyword, specifying as its
|
||||
value the ID of a separate <A HREF = "fix_rigid_small.html">fix rigid/small</A>
|
||||
command which also appears in your input script.
|
||||
</P>
|
||||
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
|
||||
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
|
||||
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
|
||||
shake</A> command which also appears in your input script.
|
||||
</P>
|
||||
<P>Each timestep particles are inserted, they are placed randomly inside
|
||||
the insertion volume so as to mimic a stream of poured particles. If
|
||||
|
||||
@ -15,16 +15,12 @@ fix ID group-ID pour N type seed keyword values ... :pre
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
pour = style name of this fix command :l
|
||||
N = # of atoms to insert :l
|
||||
type = atom type to assign to inserted atoms :l
|
||||
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
|
||||
seed = random # seed (positive integer) :l
|
||||
one or more keyword/value pairs may be appended to args :l
|
||||
keyword = {region} or {mol} or {rigid} or {diam} or {dens} or {vol} or {rate} or {vel} :l
|
||||
keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {rigid} or {shake} :l
|
||||
{region} value = region-ID
|
||||
region-ID = ID of region to use as insertion volume
|
||||
{mol} value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{rigid} value = fix-ID
|
||||
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
|
||||
{diam} values = dstyle args
|
||||
dstyle = {one} or {range} or {poly}
|
||||
{one} args = D
|
||||
@ -47,6 +43,12 @@ keyword = {region} or {mol} or {rigid} or {diam} or {dens} or {vol} or {rate} or
|
||||
vylo,vyhi = range of y velocities for inserted particles (velocity units)
|
||||
vz = z velocity (3d) assigned to inserted particles (velocity units)
|
||||
vy = y velocity (2d) assigned to inserted particles (velocity units) :pre
|
||||
{mol} value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{rigid} value = fix-ID
|
||||
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
|
||||
{shake} value = fix-ID
|
||||
fix-ID = ID of "fix shake"_fix_shake.html command
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
@ -66,9 +68,11 @@ gravity. For the remainder of this doc page, a single inserted atom
|
||||
or molecule is referred to as a "particle".
|
||||
|
||||
If inserted particles are individual atoms, they are assigned the
|
||||
specified atom type. For molecules the specified type is ignored, and
|
||||
the type of each atom in the inserted molecule is specified in the
|
||||
file read by the "molecule"_molecule.html command.
|
||||
specified atom type. If they are molecules, the type of each atom in
|
||||
the inserted molecule is specified in the file read by the
|
||||
"molecule"_molecule.html command, and those values are added to the
|
||||
specified atom type. E.g. if {type} = 2, and the file specifies atom
|
||||
types 1,2,3, then the inserted molecule will have atom types 3,4,5.
|
||||
|
||||
All atoms in the inserted particle are assigned to two groups: the
|
||||
default group "all" and the group specified in the fix pour command
|
||||
@ -91,10 +95,14 @@ required to be in this file are the coordinates and types of atoms in
|
||||
the molecule.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will be
|
||||
treated as rigid bodies, you can first specify a "fix
|
||||
rigid/small"_fix_rigid.html command, and then use the {rigid} keyword
|
||||
with this command, specifying the ID of the fix rigid/small command as
|
||||
its value.
|
||||
treated as rigid bodies, use the {rigid} keyword, specifying as its
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid_small.html
|
||||
command which also appears in your input script.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will have
|
||||
their bonds or angles constrained via SHAKE, use the {shake} keyword,
|
||||
specifying as its value the ID of a separate "fix
|
||||
shake"_fix_shake.html command which also appears in your input script.
|
||||
|
||||
Each timestep particles are inserted, they are placed randomly inside
|
||||
the insertion volume so as to mimic a stream of poured particles. If
|
||||
|
||||
@ -153,7 +153,7 @@ the distance.
|
||||
to predict. The best way to decide is to perform a short test run.
|
||||
Both variants should give identical numerical answers for short runs.
|
||||
Long runs should give statistically similar results, but round-off
|
||||
differences will accumulate to produce divergent trajectories.
|
||||
differences may accumulate to produce divergent trajectories.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: You should not update the atoms in rigid bodies via
|
||||
other time-integration fixes (e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix
|
||||
@ -248,10 +248,14 @@ means all types from m to n (inclusive). Note that you can use the
|
||||
particular rigid body has its component flags set multiple times, the
|
||||
settings from the final keyword are used.
|
||||
</P>
|
||||
<P>For computational efficiency, you may wish to turn off pairwise and
|
||||
bond interactions within each rigid body, as they no longer contribute
|
||||
to the motion. The <A HREF = "neigh_modify.html">neigh_modify exclude</A> and
|
||||
<A HREF = "delete_bonds.html">delete_bonds</A> commands are used to do this.
|
||||
<P>IMPORTANT NOTE: For computational efficiency, you may wish to turn off
|
||||
pairwise and bond interactions within each rigid body, as they no
|
||||
longer contribute to the motion. The <A HREF = "neigh_modify.html">neigh_modify
|
||||
exclude</A> and <A HREF = "delete_bonds.html">delete_bonds</A>
|
||||
commands are used to do this. If the rigid bodies have strongly
|
||||
overalapping atoms, you may need to turn off these interactions to
|
||||
avoid numerical problems due to large equal/opposite intra-body forces
|
||||
swamping the contribution of small inter-body forces.
|
||||
</P>
|
||||
<P>For computational efficiency, you should typically define one fix
|
||||
rigid or fix rigid/small command which includes all the desired rigid
|
||||
@ -448,17 +452,17 @@ associated with the fix rigid commands.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>mol</I> keyword can only be used with fix rigid/small. It should
|
||||
be used when other commands, such as <A HREF = "fix_deposit.html">fix deposit</A> or
|
||||
<A HREF = "fix_pour.html">fix pour</A>, which will add rigid bodies on-the-fly
|
||||
during a simulation. You specify a <I>template-ID</I> previously defined
|
||||
using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
|
||||
defines the molecule. You must use the same <I>template-ID</I> that the
|
||||
command adding rigid bodies uses. The coordinates, atom types, atom
|
||||
diameters, center-of-mass, and moments of inertia can be specified in
|
||||
the molecule file. See the <A HREF = "molecule.html">molecule</A> command for
|
||||
details. The only settings required to be in this file are the
|
||||
coordinates and types of atoms in the molecule.
|
||||
<P>The <I>mol</I> keyword can only be used with fix rigid/small. It should be
|
||||
used when other commands, such as <A HREF = "fix_deposit.html">fix deposit</A> or
|
||||
<A HREF = "fix_pour.html">fix pour</A>, add rigid bodies on-the-fly during a
|
||||
simulation. You specify a <I>template-ID</I> previously defined using the
|
||||
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
|
||||
molecule. You must use the same <I>template-ID</I> that the command adding
|
||||
rigid bodies uses. The coordinates, atom types, atom diameters,
|
||||
center-of-mass, and moments of inertia can be specified in the
|
||||
molecule file. See the <A HREF = "molecule.html">molecule</A> command for details.
|
||||
The only settings required to be in this file are the coordinates and
|
||||
types of atoms in the molecule.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
||||
@ -139,7 +139,7 @@ Which of the two variants is faster for a particular problem is hard
|
||||
to predict. The best way to decide is to perform a short test run.
|
||||
Both variants should give identical numerical answers for short runs.
|
||||
Long runs should give statistically similar results, but round-off
|
||||
differences will accumulate to produce divergent trajectories.
|
||||
differences may accumulate to produce divergent trajectories.
|
||||
|
||||
IMPORTANT NOTE: You should not update the atoms in rigid bodies via
|
||||
other time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix
|
||||
@ -234,10 +234,14 @@ means all types from m to n (inclusive). Note that you can use the
|
||||
particular rigid body has its component flags set multiple times, the
|
||||
settings from the final keyword are used.
|
||||
|
||||
For computational efficiency, you may wish to turn off pairwise and
|
||||
bond interactions within each rigid body, as they no longer contribute
|
||||
to the motion. The "neigh_modify exclude"_neigh_modify.html and
|
||||
"delete_bonds"_delete_bonds.html commands are used to do this.
|
||||
IMPORTANT NOTE: For computational efficiency, you may wish to turn off
|
||||
pairwise and bond interactions within each rigid body, as they no
|
||||
longer contribute to the motion. The "neigh_modify
|
||||
exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
|
||||
commands are used to do this. If the rigid bodies have strongly
|
||||
overalapping atoms, you may need to turn off these interactions to
|
||||
avoid numerical problems due to large equal/opposite intra-body forces
|
||||
swamping the contribution of small inter-body forces.
|
||||
|
||||
For computational efficiency, you should typically define one fix
|
||||
rigid or fix rigid/small command which includes all the desired rigid
|
||||
@ -434,17 +438,17 @@ associated with the fix rigid commands.
|
||||
|
||||
:line
|
||||
|
||||
The {mol} keyword can only be used with fix rigid/small. It should
|
||||
be used when other commands, such as "fix deposit"_fix_deposit.html or
|
||||
"fix pour"_fix_pour.html, which will add rigid bodies on-the-fly
|
||||
during a simulation. You specify a {template-ID} previously defined
|
||||
using the "molecule"_molecule.html command, which reads a file that
|
||||
defines the molecule. You must use the same {template-ID} that the
|
||||
command adding rigid bodies uses. The coordinates, atom types, atom
|
||||
diameters, center-of-mass, and moments of inertia can be specified in
|
||||
the molecule file. See the "molecule"_molecule.html command for
|
||||
details. The only settings required to be in this file are the
|
||||
coordinates and types of atoms in the molecule.
|
||||
The {mol} keyword can only be used with fix rigid/small. It should be
|
||||
used when other commands, such as "fix deposit"_fix_deposit.html or
|
||||
"fix pour"_fix_pour.html, add rigid bodies on-the-fly during a
|
||||
simulation. You specify a {template-ID} previously defined using the
|
||||
"molecule"_molecule.html command, which reads a file that defines the
|
||||
molecule. You must use the same {template-ID} that the command adding
|
||||
rigid bodies uses. The coordinates, atom types, atom diameters,
|
||||
center-of-mass, and moments of inertia can be specified in the
|
||||
molecule file. See the "molecule"_molecule.html command for details.
|
||||
The only settings required to be in this file are the coordinates and
|
||||
types of atoms in the molecule.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -15,7 +15,7 @@
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID shake tol iter N keyword values ...
|
||||
<PRE>fix ID group-ID shake tol iter N constraint values ... keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
@ -27,21 +27,29 @@
|
||||
|
||||
<LI>N = print SHAKE statistics every this many timesteps (0 = never)
|
||||
|
||||
<LI>one or more keyword/value pairs are appended
|
||||
<LI>one or more constraint/value pairs are appended
|
||||
|
||||
<LI>keyword = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
|
||||
<LI>constraint = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
|
||||
|
||||
<PRE> <I>b</I> values = one or more bond types
|
||||
<I>a</I> values = one or more angle types
|
||||
<I>t</I> values = one or more atom types
|
||||
<I>m</I> value = one or more mass values
|
||||
</PRE>
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>mol</I>
|
||||
|
||||
<PRE> <I>mol</I> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
|
||||
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
|
||||
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
|
||||
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
@ -71,17 +79,17 @@ also constrained. This means water molecules or CH2 or CH3 groups may
|
||||
be constrained, but not all the C-C backbone bonds of a long polymer
|
||||
chain.
|
||||
</P>
|
||||
<P>The <I>b</I> keyword lists bond types that will be constrained. The <I>t</I>
|
||||
keyword lists atom types. All bonds connected to an atom of the
|
||||
specified type will be constrained. The <I>m</I> keyword lists atom
|
||||
<P>The <I>b</I> constraint lists bond types that will be constrained. The <I>t</I>
|
||||
constraint lists atom types. All bonds connected to an atom of the
|
||||
specified type will be constrained. The <I>m</I> constraint lists atom
|
||||
masses. All bonds connected to atoms of the specified masses will be
|
||||
constrained (within a fudge factor of MASSDELTA specified in
|
||||
fix_shake.cpp). The <I>a</I> keyword lists angle types. If both bonds in
|
||||
the angle are constrained then the angle will also be constrained if
|
||||
its type is in the list.
|
||||
fix_shake.cpp). The <I>a</I> constraint lists angle types. If both bonds
|
||||
in the angle are constrained then the angle will also be constrained
|
||||
if its type is in the list.
|
||||
</P>
|
||||
<P>For all keywords, a particular bond is only constrained if both atoms
|
||||
in the bond are in the group specified with the SHAKE fix.
|
||||
<P>For all constraints, a particular bond is only constrained if both
|
||||
atoms in the bond are in the group specified with the SHAKE fix.
|
||||
</P>
|
||||
<P>The degrees-of-freedom removed by SHAKE bonds and angles are accounted
|
||||
for in temperature and pressure computations. Similarly, the SHAKE
|
||||
@ -101,6 +109,20 @@ which add or change forces (to atoms that fix shake operates on).
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>mol</I> keyword should be used when other commands, such as <A HREF = "fix_deposit.html">fix
|
||||
deposit</A> or <A HREF = "fix_pour.html">fix pour</A>, add molecules
|
||||
on-the-fly during a simulation, and you wish to contrain the new
|
||||
molecules via SHAKE. You specify a <I>template-ID</I> previously defined
|
||||
using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
|
||||
defines the molecule. You must use the same <I>template-ID</I> that the
|
||||
command adding molecules uses. The coordinates, atom types, special
|
||||
bond restrictions, and SHAKE info can be specified in the molecule
|
||||
file. See the <A HREF = "molecule.html">molecule</A> command for details. The only
|
||||
settings required to be in this file (by this command) are the SHAKE
|
||||
info of atoms in the molecule.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
|
||||
corresponding style without the suffix. They have been optimized to
|
||||
run faster, depending on your available hardware, as discussed in
|
||||
|
||||
@ -11,25 +11,30 @@ fix shake/cuda command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID shake tol iter N keyword values ... :pre
|
||||
fix ID group-ID shake tol iter N constraint values ... keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
shake = style name of this fix command :l
|
||||
tol = accuracy tolerance of SHAKE solution :l
|
||||
iter = max # of iterations in each SHAKE solution :l
|
||||
N = print SHAKE statistics every this many timesteps (0 = never) :l
|
||||
one or more keyword/value pairs are appended :l
|
||||
keyword = {b} or {a} or {t} or {m} :l
|
||||
one or more constraint/value pairs are appended :l
|
||||
constraint = {b} or {a} or {t} or {m} :l
|
||||
{b} values = one or more bond types
|
||||
{a} values = one or more angle types
|
||||
{t} values = one or more atom types
|
||||
{m} value = one or more mass values :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {mol} :l
|
||||
{mol} value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
|
||||
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 :pre
|
||||
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
|
||||
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -59,17 +64,17 @@ also constrained. This means water molecules or CH2 or CH3 groups may
|
||||
be constrained, but not all the C-C backbone bonds of a long polymer
|
||||
chain.
|
||||
|
||||
The {b} keyword lists bond types that will be constrained. The {t}
|
||||
keyword lists atom types. All bonds connected to an atom of the
|
||||
specified type will be constrained. The {m} keyword lists atom
|
||||
The {b} constraint lists bond types that will be constrained. The {t}
|
||||
constraint lists atom types. All bonds connected to an atom of the
|
||||
specified type will be constrained. The {m} constraint lists atom
|
||||
masses. All bonds connected to atoms of the specified masses will be
|
||||
constrained (within a fudge factor of MASSDELTA specified in
|
||||
fix_shake.cpp). The {a} keyword lists angle types. If both bonds in
|
||||
the angle are constrained then the angle will also be constrained if
|
||||
its type is in the list.
|
||||
fix_shake.cpp). The {a} constraint lists angle types. If both bonds
|
||||
in the angle are constrained then the angle will also be constrained
|
||||
if its type is in the list.
|
||||
|
||||
For all keywords, a particular bond is only constrained if both atoms
|
||||
in the bond are in the group specified with the SHAKE fix.
|
||||
For all constraints, a particular bond is only constrained if both
|
||||
atoms in the bond are in the group specified with the SHAKE fix.
|
||||
|
||||
The degrees-of-freedom removed by SHAKE bonds and angles are accounted
|
||||
for in temperature and pressure computations. Similarly, the SHAKE
|
||||
@ -89,6 +94,20 @@ which add or change forces (to atoms that fix shake operates on).
|
||||
|
||||
:line
|
||||
|
||||
The {mol} keyword should be used when other commands, such as "fix
|
||||
deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules
|
||||
on-the-fly during a simulation, and you wish to contrain the new
|
||||
molecules via SHAKE. You specify a {template-ID} previously defined
|
||||
using the "molecule"_molecule.html command, which reads a file that
|
||||
defines the molecule. You must use the same {template-ID} that the
|
||||
command adding molecules uses. The coordinates, atom types, special
|
||||
bond restrictions, and SHAKE info can be specified in the molecule
|
||||
file. See the "molecule"_molecule.html command for details. The only
|
||||
settings required to be in this file (by this command) are the SHAKE
|
||||
info of atoms in the molecule.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {cuda} suffix are functionally the same as the
|
||||
corresponding style without the suffix. They have been optimized to
|
||||
run faster, depending on your available hardware, as discussed in
|
||||
|
||||
Reference in New Issue
Block a user