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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11773 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-04-11 14:13:43 +00:00
parent e579757de1
commit 58336dca9a
2 changed files with 24 additions and 28 deletions
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26
doc/fix_bond_create.html
View File

@ -117,22 +117,20 @@ structures that store this information must have space for it. When
LAMMPS is initialized from a data file, the list of bonds is scanned
and the maximum number of bonds per atom is tallied. If some atom
will acquire more bonds than this limit as this fix operates, then the
"extra bonds per atom" parameter in the data file header must be set
to allow for it. See the <A HREF = "read_data.html">read_data</A> command for more
details. Note that if this parameter needs to be set, it means a data
file must be used to initialize the system, even if it initially has
no bonds. A 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 percolation simulation.
"extra bonds per atom" parameter must be set to allow for it. See the
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command for
more details. Note that a 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 percolation simulation.
</P>
<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology
of the system) for use in weighting pairwise interactions for bonded
atoms. Adding a bond adds a single entry to this list. The "extra"
keyword of the <A HREF = "special_bonds.html">special_bonds</A> command should be
used to leave space for new bonds if the maximum number of entries for
any atom will be exceeded as this fix operates. See the
<A HREF = "special_bonds.html">special_bonds</A> command for details.
list of 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system) for use in weighting pairwise interactions for
bonded atoms. Adding a bond adds a single entry to this list. The
"extra special per atom" parameter must typically be set to allow for
it. 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.
</P>
<P>Note that even if your simulation starts with no bonds, you must
define a <A HREF = "bond_style.html">bond_style</A> and use the

26
doc/fix_bond_create.txt
View File

@ -105,22 +105,20 @@ structures that store this information must have space for it. When
LAMMPS is initialized from a data file, the list of bonds is scanned
and the maximum number of bonds per atom is tallied. If some atom
will acquire more bonds than this limit as this fix operates, then the
"extra bonds per atom" parameter in the data file header must be set
to allow for it. See the "read_data"_read_data.html command for more
details. Note that if this parameter needs to be set, it means a data
file must be used to initialize the system, even if it initially has
no bonds. A 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 percolation simulation.
"extra bonds per atom" parameter must be set to allow for it. See the
"read_data"_read_data.html or "create_box"_create_box.html command for
more details. Note that a 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 percolation simulation.
IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology
of the system) for use in weighting pairwise interactions for bonded
atoms. Adding a bond adds a single entry to this list. The "extra"
keyword of the "special_bonds"_special_bonds.html command should be
used to leave space for new bonds if the maximum number of entries for
any atom will be exceeded as this fix operates. See the
"special_bonds"_special_bonds.html command for details.
list of 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system) for use in weighting pairwise interactions for
bonded atoms. Adding a bond adds a single entry to this list. The
"extra special per atom" parameter must typically be set to allow for
it. 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.
Note that even if your simulation starts with no bonds, you must
define a "bond_style"_bond_style.html and use the