git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12351 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-08-26 16:44:13 +00:00
parent b74fcc80ac
commit 107a22b9f3
6 changed files with 52 additions and 34 deletions

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@ -155,13 +155,16 @@ data file with no atoms can be used if you wish to add unbonded atoms
via the <A HREF = "create_atoms.html">create atoms</A> command, e.g. for a via the <A HREF = "create_atoms.html">create atoms</A> command, e.g. for a
percolation simulation. percolation simulation.
</P> </P>
<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a <P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
list of 1st, 2nd, and 3rd neighbors of each atom (within the bond list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system) for use in weighting pairwise interactions for topology of the system) for use in weighting pairwise interactions for
bonded atoms. Adding a bond adds a single entry to this list. The bonded atoms. Note that adding a single bond always adds a new 1st
"extra special per atom" parameter must typically be set to allow for neighbor but may also induce *many* new 2nd and 3rd neighbors,
it. There are 3 ways to do this. See the <A HREF = "read_data.html">read_data</A> depending on the molecular topology of your system. The "extra
or <A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for special per atom" parameter must typically be set to allow for the new
maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
There are 3 ways to do this. See the <A HREF = "read_data.html">read_data</A> or
<A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for
details. details.
</P> </P>
<P>IMPORTANT NOTE: Even if you do not use the <I>atype</I>, <I>dtype</I>, or <P>IMPORTANT NOTE: Even if you do not use the <I>atype</I>, <I>dtype</I>, or

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@ -143,13 +143,16 @@ data file with no atoms can be used if you wish to add unbonded atoms
via the "create atoms"_create_atoms.html command, e.g. for a via the "create atoms"_create_atoms.html command, e.g. for a
percolation simulation. percolation simulation.
IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
list of 1st, 2nd, and 3rd neighbors of each atom (within the bond list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system) for use in weighting pairwise interactions for topology of the system) for use in weighting pairwise interactions for
bonded atoms. Adding a bond adds a single entry to this list. The bonded atoms. Note that adding a single bond always adds a new 1st
"extra special per atom" parameter must typically be set to allow for neighbor but may also induce *many* new 2nd and 3rd neighbors,
it. There are 3 ways to do this. See the "read_data"_read_data.html depending on the molecular topology of your system. The "extra
or "create_box"_create_box.html or "special_bonds extra" commands for special per atom" parameter must typically be set to allow for the new
maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
There are 3 ways to do this. See the "read_data"_read_data.html or
"create_box"_create_box.html or "special_bonds extra" commands for
details. details.
IMPORTANT NOTE: Even if you do not use the {atype}, {dtype}, or IMPORTANT NOTE: Even if you do not use the {atype}, {dtype}, or

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@ -13,7 +13,7 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>fix ID group-ID N oneway region-ID direction <PRE>fix ID group-ID oneway N region-ID direction
</PRE> </PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
@ -29,9 +29,9 @@
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>fix ions 10 oneway semi -x <PRE>fix ions oneway 10 semi -x
fix all 1 oneway left -z fix all oneway 1 left -z
fix all 1 oneway right z fix all oneway 1 right z
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>

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@ -10,7 +10,7 @@ fix oneway command :h3
[Syntax:] [Syntax:]
fix ID group-ID N oneway region-ID direction :pre fix ID group-ID oneway N region-ID direction :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l ID, group-ID are documented in "fix"_fix.html command :ulb,l
oneway = style name of this fix command :l oneway = style name of this fix command :l
@ -21,9 +21,9 @@ direction = {x} or {-x} or {y} or {-y} or {z} or {-z} = coordinate and direction
[Examples:] [Examples:]
fix ions 10 oneway semi -x fix ions oneway 10 semi -x
fix all 1 oneway left -z fix all oneway 1 left -z
fix all 1 oneway right z :pre fix all oneway 1 right z :pre
[Description:] [Description:]

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@ -171,18 +171,24 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the <I>dihedral</I> keyword is specified as <I>no</I> which is the of 1.0). If the <I>dihedral</I> keyword is specified as <I>no</I> which is the
default, then the 2,5 interaction will also be weighted by 0.5. default, then the 2,5 interaction will also be weighted by 0.5.
</P> </P>
<P>The <I>extra</I> keyword is used when additional bonds will be created <P>The <I>extra</I> keyword can be used when additional bonds will be created
during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix
bond/create</A> command. It can also be used if bond/create</A> command. It can also be used if
molecules will be added to the system, e.g. via the <A HREF = "fix_deposit.html">fix molecules will be added to the system, e.g. via the <A HREF = "fix_deposit.html">fix
deposit</A>, or <A HREF = "fix_pour.html">fix pour</A> commands, which deposit</A>, or <A HREF = "fix_pour.html">fix pour</A> commands, which
will have atoms with more special neighbors than any atom in the will have atoms with more special neighbors than any atom in the
current system has. A list of 1-2,1-3,1-4 neighbors for each atom is current system has.
calculated and stored by LAMMPS. If new bonds are created (or </P>
molecules added with atoms with more special neighbors), the list <P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
needs to grow. Using the <I>extra</I> keyword leaves empty space in the list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
list for N additional bonds to be added. If you do not do this, you topology of the system). If new bonds are created (or molecules added
may get an error when bonds (or molecules) are added. containing atoms with more special neighbors), the size of this list
needs to grow. Note that adding a single bond always adds a new 1st
neighbor but may also induce *many* new 2nd and 3rd neighbors,
depending on the molecular topology of your syste. Using the <I>extra</I>
keyword leaves empty space in the list for this N additional 1st, 2nd,
or 3rd neighbors to be added. If you do not do this, you may get an
error when bonds (or molecules) are added.
</P> </P>
<P>IMPORTANT NOTE: If you reuse this command in an input script, you <P>IMPORTANT NOTE: If you reuse this command in an input script, you
should set all the options you need each time. This command cannot be should set all the options you need each time. This command cannot be

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@ -165,18 +165,24 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the {dihedral} keyword is specified as {no} which is the of 1.0). If the {dihedral} keyword is specified as {no} which is the
default, then the 2,5 interaction will also be weighted by 0.5. default, then the 2,5 interaction will also be weighted by 0.5.
The {extra} keyword is used when additional bonds will be created The {extra} keyword can be used when additional bonds will be created
during a simulation run, e.g. by the "fix during a simulation run, e.g. by the "fix
bond/create"_fix_bond_create.html command. It can also be used if bond/create"_fix_bond_create.html command. It can also be used if
molecules will be added to the system, e.g. via the "fix molecules will be added to the system, e.g. via the "fix
deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which
will have atoms with more special neighbors than any atom in the will have atoms with more special neighbors than any atom in the
current system has. A list of 1-2,1-3,1-4 neighbors for each atom is current system has.
calculated and stored by LAMMPS. If new bonds are created (or
molecules added with atoms with more special neighbors), the list IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
needs to grow. Using the {extra} keyword leaves empty space in the list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
list for N additional bonds to be added. If you do not do this, you topology of the system). If new bonds are created (or molecules added
may get an error when bonds (or molecules) are added. containing atoms with more special neighbors), the size of this list
needs to grow. Note that adding a single bond always adds a new 1st
neighbor but may also induce *many* new 2nd and 3rd neighbors,
depending on the molecular topology of your syste. Using the {extra}
keyword leaves empty space in the list for this N additional 1st, 2nd,
or 3rd neighbors to be added. If you do not do this, you may get an
error when bonds (or molecules) are added.
IMPORTANT NOTE: If you reuse this command in an input script, you IMPORTANT NOTE: If you reuse this command in an input script, you
should set all the options you need each time. This command cannot be should set all the options you need each time. This command cannot be