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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2580 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-02-12 20:45:46 +00:00
parent a6e79606be
commit 21ff47f1f4
4 changed files with 82 additions and 46 deletions
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4
doc/compute_pe_atom.html
View File

@ -60,8 +60,8 @@ energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output:
</P>
<PRE>compute peratom all pe/atom
compute p all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_p
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe
</PRE>
<P>IMPORTANT NOTE: The per-atom energy does NOT include contributions due
to long-range Coulombic interactions (via the

4
doc/compute_pe_atom.txt
View File

@ -57,8 +57,8 @@ energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output:
compute peratom all pe/atom
compute p all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_p :pre
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe :pre
IMPORTANT NOTE: The per-atom energy does NOT include contributions due
to long-range Coulombic interactions (via the

60
doc/pair_reax.html
View File

@ -29,14 +29,16 @@ pair_coeff * * ffield.reax C H O N
<P>The pair style computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. Details of the interatomic potential energy calculation are
given in the following publications: <A HREF = "#van_Duin_2001">(van Duin 2001)</A>
and <A HREF = "#van_Duin_2003">(van Duin 2003)</A>.
energy. Details of the ReaxFF and its interatomic potential energy
calculation are given in the following publications: <A HREF = "#van_Duin_2001">(van Duin
2001)</A> and <A HREF = "#van_Duin_2003">(van Duin 2003)</A>.
</P>
<P>ReaxFF parameters for the elements C, H, O, N, S, and Si are provided
in the parameter file ffield.reax in the potentials directory. For
other elements, or for specific chemical systems, other parameter
files may be available elsewhere.
<P>LAMMPS provides a ReaxFF potential file in its potentials dir, namely
potentials/ffield.reax. Its format is identical to that used by van
Duin and co-workers. It contains parameterizations for the following
elements: C, H, O, N, S, and Si. You can use your another file in
place of it, and ReaxFF files with parameterizations for other
elements or for specific chemical systems may be available elsewhere.
</P>
<P>The <I>hbcut</I> and <I>precision</I> settings are optional arguments. If
neither is provided, default settings are used: <I>hbcut</I> = 10 (which is
@ -45,8 +47,9 @@ If you wish to override either of these defaults, then both settings
must be specified.
</P>
<P>Use of this pair style requires that a charge be defined for every
atom. See the <A HREF = "atom_style.html">atom_style</A> and
<A HREF = "read_data.html">read_data</A> commands for details.
atom since the potential performs charge equilibration. See the
<A HREF = "atom_style.html">atom_style</A> and <A HREF = "read_data.html">read_data</A> commands
for details on how to specify charges.
</P>
<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
@ -61,17 +64,34 @@ additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of ReaxFF elements to atom types
<LI>N indices = mapping of ReaxFF elements to atom types
</UL>
<P>The specification of the filename and the mapping of LAMMPS atom types
recognized by the ReaxFF is done differently than for other LAMMPS
potentials, due to the non-portable difficulty of passing character
strings (e.g. filename, element names) between C++ and Fortran.
</P>
<P>The filename has to be "ffield.reax" and it has to exist in the
directory you are running LAMMPS in. This means you cannot prepend a
path to the file in the potentials dir. Rather, you should copy that
file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it "ffield.reax" and put in
your running dir.
</P>
<P>In the ReaxFF potential file, near the top, is a section that contains
element names, each with a couple dozen numeric parameters. The
ffield.reax provided with LAMMPS lists 6 elements: C, H, O, N, S, Si.
Think of these as numbered 1 to 6. Each of the N indices you specify
for the N atom types of LAMMPS atoms must be an integer from 1 to 6.
Atoms with LAMMPS type 1 will be mapped to whatever element you
specify as the first index value, etc.
</P>
<P>As an example, if your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be C, and the 4th to be H, you would use the
following pair_coeff command:
want the 1st two to be C, the 3rd to be N, and the 4th to be H, you
would use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ffield.reax C C C H
<PRE>pair_coeff * * ffield.reax 1 1 4 2
</PRE>
<P>The format of the ReaxFF parameter file is identical to that used by
van Duin and co-workers.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
@ -95,15 +115,13 @@ LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair potential ignores the <A HREF = "newton.html">newton</A>
settings. Internally, the newton setting is "on" for the force
calculation, but "off" for the neighbor list.
</P>
<P>The ffield.reax potential file provided with LAMMPS in the potentials
directory is parameterized for real <A HREF = "units.html">units</A>. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.
appropriate units if your simulation doesn't use "real" units. This
would be somewhat tricky, so contact the LAMMPS authors if you wish to
do this.
</P>
<P><B>Related commands:</B>
</P>

60
doc/pair_reax.txt
View File

@ -26,14 +26,16 @@ pair_coeff * * ffield.reax C H O N :pre
The pair style computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. Details of the interatomic potential energy calculation are
given in the following publications: "(van Duin 2001)"_#van_Duin_2001
and "(van Duin 2003)"_#van_Duin_2003.
energy. Details of the ReaxFF and its interatomic potential energy
calculation are given in the following publications: "(van Duin
2001)"_#van_Duin_2001 and "(van Duin 2003)"_#van_Duin_2003.
ReaxFF parameters for the elements C, H, O, N, S, and Si are provided
in the parameter file ffield.reax in the potentials directory. For
other elements, or for specific chemical systems, other parameter
files may be available elsewhere.
LAMMPS provides a ReaxFF potential file in its potentials dir, namely
potentials/ffield.reax. Its format is identical to that used by van
Duin and co-workers. It contains parameterizations for the following
elements: C, H, O, N, S, and Si. You can use your another file in
place of it, and ReaxFF files with parameterizations for other
elements or for specific chemical systems may be available elsewhere.
The {hbcut} and {precision} settings are optional arguments. If
neither is provided, default settings are used: {hbcut} = 10 (which is
@ -42,8 +44,9 @@ If you wish to override either of these defaults, then both settings
must be specified.
Use of this pair style requires that a charge be defined for every
atom. See the "atom_style"_atom_style.html and
"read_data"_read_data.html commands for details.
atom since the potential performs charge equilibration. See the
"atom_style"_atom_style.html and "read_data"_read_data.html commands
for details on how to specify charges.
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
@ -58,16 +61,33 @@ additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of ReaxFF elements to atom types :ul
N indices = mapping of ReaxFF elements to atom types :ul
The specification of the filename and the mapping of LAMMPS atom types
recognized by the ReaxFF is done differently than for other LAMMPS
potentials, due to the non-portable difficulty of passing character
strings (e.g. filename, element names) between C++ and Fortran.
The filename has to be "ffield.reax" and it has to exist in the
directory you are running LAMMPS in. This means you cannot prepend a
path to the file in the potentials dir. Rather, you should copy that
file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it "ffield.reax" and put in
your running dir.
In the ReaxFF potential file, near the top, is a section that contains
element names, each with a couple dozen numeric parameters. The
ffield.reax provided with LAMMPS lists 6 elements: C, H, O, N, S, Si.
Think of these as numbered 1 to 6. Each of the N indices you specify
for the N atom types of LAMMPS atoms must be an integer from 1 to 6.
Atoms with LAMMPS type 1 will be mapped to whatever element you
specify as the first index value, etc.
As an example, if your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be C, and the 4th to be H, you would use the
following pair_coeff command:
want the 1st two to be C, the 3rd to be N, and the 4th to be H, you
would use the following pair_coeff command:
pair_coeff * * ffield.reax C C C H :pre
The format of the ReaxFF parameter file is identical to that used by
van Duin and co-workers.
pair_coeff * * ffield.reax 1 1 4 2 :pre
:line
@ -92,15 +112,13 @@ LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This pair potential ignores the "newton"_newton.html
settings. Internally, the newton setting is "on" for the force
calculation, but "off" for the neighbor list.
The ffield.reax potential file provided with LAMMPS in the potentials
directory is parameterized for real "units"_units.html. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.
appropriate units if your simulation doesn't use "real" units. This
would be somewhat tricky, so contact the LAMMPS authors if you wish to
do this.
[Related commands:]