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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13465 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2015-05-15 16:47:14 +00:00
parent c3fd41010d
commit a32bfebe88
2 changed files with 60 additions and 2 deletions
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31
doc/special_bonds.html
View File

@ -73,6 +73,14 @@ e.g. when using the <A HREF = "pair_hybrid.html">pair_style hybrid</A> command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated.
</P>
<P>IMPORTANT NOTE: Unlike some commands in LAMMPS, you cannot use this
command multiple times in an incremental fashion: e.g. to first set
the LJ settings and then the Coulombic ones. Each time you use this
command it sets all the coefficients to default values and only
overrides the one you specify, so you should set all the options you
need each time you use it. See more details at the bottom of this
page.
</P>
<P>The Coulomb factors are applied to any Coulomb (charge interaction)
term that the potential calculates. The LJ factors are applied to the
remaining terms that the potential calculates, whether they represent
@ -179,6 +187,8 @@ 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
current system has.
</P>
<HR>
<P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system). If new bonds are created (or molecules added
@ -190,15 +200,34 @@ 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>
<HR>
<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
used a 2nd time incrementally, e.g. to add some extra storage
locations via the <I>extra</I> keyword. E.g. these two commands:
</P>
<P>special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0
</P>
<P>are not the same as
</P>
<P>special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
</P>
<P>In the first case you end up with (after the 2nd command):
</P>
<P>LJ: 0.0 0.0 0.0
Coul: coul 0.0 0.0 1.0
</P>
<P>because the LJ settings are reset to their default values
each time the command is issued.
</P>
<P>Likewise
</P>
<PRE>special_bonds amber
special_bonds extra 2
</PRE>
<P>are not the same as this single command:
<P>is not the same as this single command:
</P>
<PRE>special_bonds amber extra 2
</PRE>

31
doc/special_bonds.txt
View File

@ -67,6 +67,14 @@ e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated.
IMPORTANT NOTE: Unlike some commands in LAMMPS, you cannot use this
command multiple times in an incremental fashion: e.g. to first set
the LJ settings and then the Coulombic ones. Each time you use this
command it sets all the coefficients to default values and only
overrides the one you specify, so you should set all the options you
need each time you use it. See more details at the bottom of this
page.
The Coulomb factors are applied to any Coulomb (charge interaction)
term that the potential calculates. The LJ factors are applied to the
remaining terms that the potential calculates, whether they represent
@ -173,6 +181,8 @@ deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which
will have atoms with more special neighbors than any atom in the
current system has.
:line
IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system). If new bonds are created (or molecules added
@ -184,15 +194,34 @@ 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.
:line
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
used a 2nd time incrementally, e.g. to add some extra storage
locations via the {extra} keyword. E.g. these two commands:
special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0
are not the same as
special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
In the first case you end up with (after the 2nd command):
LJ: 0.0 0.0 0.0
Coul: coul 0.0 0.0 1.0
because the LJ settings are reset to their default values
each time the command is issued.
Likewise
special_bonds amber
special_bonds extra 2 :pre
are not the same as this single command:
is not the same as this single command:
special_bonds amber extra 2 :pre