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sjplimp 2010-09-04 00:17:54 +00:00
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4
doc/Section_commands.html
View File

@ -340,7 +340,7 @@ of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
</TD></TR></TABLE></DIV>
<HR>
@ -398,7 +398,7 @@ potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
</TD></TR></TABLE></DIV>
<HR>

4
doc/Section_commands.txt
View File

@ -470,6 +470,7 @@ These are fix styles contributed by users, which can be used if
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"qeq/reax"_fix_qeq_reax.html,
"smd"_fix_smd.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html :tb(c=6,ea=c)
@ -613,7 +614,8 @@ These are pair styles contributed by users, which can be used if
"cg/cmm/coul/long"_pair_cmm.html,
"eam/cd"_pair_eam.html,
"eff/cut"_pair_eff.html,
"lj/coul"_pair_lj_coul.html :tb(c=4,ea=c)
"lj/coul"_pair_lj_coul.html,
"reax/c"_pair_reax_c.html :tb(c=4,ea=c)
:line

96
doc/pair_reax.html
View File

@ -27,26 +27,38 @@ pair_coeff * * ffield.reax 3 NULL NULL 3
</PRE>
<P><B>Description:</B>
</P>
<P>The pair style computes the ReaxFF potential of van Duin, Goddard and
<P>Style <I>reax</I> 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. There is more than one version of ReaxFF. The version implemented
in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: <A HREF = "#Chenoweth_2008">(Chenoweth et al.,
2008)</A>.
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper:
<A HREF = "#Chenoweth">(Chenoweth)</A>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.
</P>
<P>LAMMPS requires that a file called ffield.reax be provided, containing the
ReaxFF parameters for each atom type, bond type, etc. The format is identical to
the ffield file used by van Duin and co-workers. The filename is also
reuqired as an argument in the pair_coeff command. Any value other than
ffield.reax will be rejected (see below).
<P>The <I>reax</I> style differs from the <A HREF = "pair_reax_c.html">pair_style reax/c</A>
command in the lo-level implementation details. The <I>reax</I> style is a
Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.
</P>
<P>LAMMPS provides several different versions of ffield.reax
in its potentials dir, each called potentials/ffield.reax.label.
These are documented in potentials/README.reax.
The default ffield.reax contains parameterizations for the following
elements: C, H, O, N, S. You can use one of the other files in place of it,
or obtain a file from elsewhere.
<P>LAMMPS requires that a file called ffield.reax be provided, containing
the ReaxFF parameters for each atom type, bond type, etc. The format
is identical to the ffield file used by van Duin and co-workers. The
filename is required as an argument in the pair_coeff command. Any
value other than "ffield.reax" will be rejected (see below).
</P>
<P>LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.
</P>
<P>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <I>pair_style reax/c</I> potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).
</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
@ -55,9 +67,10 @@ 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 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.
atom since the <I>reax</I> pair style performs a charge equilibration (QEq)
calculation. 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
@ -86,25 +99,24 @@ file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it "ffield.reax" and put it
in the directory you run from.
</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
default ffield.reax provided with LAMMPS lists 5 elements: C, H, O, N,
S. Think of these as numbered 1 to 5. When using this file each of
the N indices you specify for the N atom types of LAMMPS atoms must be
an integer from 1 to 5. Atoms with LAMMPS type 1 will be mapped to
whatever element you specify as the first index value, etc. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a ReaxFF potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
<P>In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the <I>ffield</I> file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when a ReaxFF potential is used as part
of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
</P>
<P>In the pair_coeff example above with 3 1 2 2, the LAMMPS simulation
has 4 atoms types and they are set as follows:
<P>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
</P>
<PRE>type 1 = O
type 2 = C
type 3 = H
type 4 = H
<PRE>pair_coeff * * ffield.reax 1 1 4 2
</PRE>
<HR>
@ -129,17 +141,15 @@ 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>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
<P>The ReaxFF potential files provided with LAMMPS in the potentials
directory are 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. This
would be somewhat tricky, so contact the LAMMPS authors if you wish to
do this.
appropriate units if your simulation doesn't use "real" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>
</P>
<P><B>Default:</B> none
</P>
@ -147,7 +157,7 @@ do this.
<A NAME = "Chenoweth_2008"></A>
<P><B>(Chenoweth)</B> Chenoweth, van Duin and Goddard III,
<P><B>(Chenoweth)</B> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
</P>
</HTML>

97
doc/pair_reax.txt
View File

@ -24,26 +24,38 @@ pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
[Description:]
The pair style computes the ReaxFF potential of van Duin, Goddard and
Style {reax} 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. There is more than one version of ReaxFF. The version implemented
in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: "(Chenoweth et al.,
2008)"_#Chenoweth_2008.
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper:
"(Chenoweth)"_#Chenoweth. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.
LAMMPS requires that a file called ffield.reax be provided, containing the
ReaxFF parameters for each atom type, bond type, etc. The format is identical to
the ffield file used by van Duin and co-workers. The filename is also
reuqired as an argument in the pair_coeff command. Any value other than
ffield.reax will be rejected (see below).
The {reax} style differs from the "pair_style reax/c"_pair_reax_c.html
command in the lo-level implementation details. The {reax} style is a
Fortran library, linked to LAMMPS. The {reax/c} style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.
LAMMPS provides several different versions of ffield.reax
in its potentials dir, each called potentials/ffield.reax.label.
These are documented in potentials/README.reax.
The default ffield.reax contains parameterizations for the following
elements: C, H, O, N, S. You can use one of the other files in place of it,
or obtain a file from elsewhere.
LAMMPS requires that a file called ffield.reax be provided, containing
the ReaxFF parameters for each atom type, bond type, etc. The format
is identical to the ffield file used by van Duin and co-workers. The
filename is required as an argument in the pair_coeff command. Any
value other than "ffield.reax" will be rejected (see below).
LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.
The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of {pair_style reax/c} potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).
The {hbcut} and {precision} settings are optional arguments. If
neither is provided, default settings are used: {hbcut} = 10 (which is
@ -52,9 +64,10 @@ 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 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.
atom since the {reax} pair style performs a charge equilibration (QEq)
calculation. 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
@ -83,25 +96,24 @@ file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it "ffield.reax" and put it
in the directory you run from.
In the ReaxFF potential file, near the top, is a section that contains
element names, each with a couple dozen numeric parameters. The
default ffield.reax provided with LAMMPS lists 5 elements: C, H, O, N,
S. Think of these as numbered 1 to 5. When using this file each of
the N indices you specify for the N atom types of LAMMPS atoms must be
an integer from 1 to 5. Atoms with LAMMPS type 1 will be mapped to
whatever element you specify as the first index value, etc. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a ReaxFF potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the {ffield} file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when a ReaxFF potential is used as part
of the {hybrid} pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
In the pair_coeff example above with 3 1 2 2, the LAMMPS simulation
has 4 atoms types and they are set as follows:
As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the {ffield} file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
type 1 = O
type 2 = C
type 3 = H
type 4 = H :pre
pair_coeff * * ffield.reax 1 1 4 2 :pre
:line
@ -126,23 +138,20 @@ 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.
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 files provided with LAMMPS in the potentials
directory are 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. This
would be somewhat tricky, so contact the LAMMPS authors if you wish to
do this.
appropriate units if your simulation doesn't use "real" units.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reax_c.html
[Default:] none
:line
:link(Chenoweth_2008)
[(Chenoweth)] Chenoweth, van Duin and Goddard III,
[(Chenoweth)] Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).