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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7453 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-01-06 20:39:16 +00:00
parent 5b62a1cb92
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8
doc/Section_commands.html
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@ -345,10 +345,10 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_nphug.html">nphug</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -457,6 +457,7 @@ of each style or click on the style itself for a full description:
"print"_fix_print.html,
"qeq/comb"_fix_qeq_comb.html,
"reax/bonds"_fix_reax_bonds.html,
"reax/c/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid"_fix_rigid.html,

31
doc/fix_reax_bonds.html
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@ -11,25 +11,29 @@
<H3>fix reax/bonds command
</H3>
<H3>fix reax/c/bonds command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID reax/bonds Nevery filename
<PRE>fix ID group-ID style Nevery filename
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>reax/bonds = style name of this fix command
<LI>style = <I>reax/bonds</I> or <I>reax/c/bonds</I>
<LI>Nevery = output interval in timesteps
<LI>filename = name of output file
</UL>
<P><B>Examples:</B>
</P>
<P>fix 1 all reax/bonds 100 bonds.tatb
</P>
<PRE>fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc
</PRE>
<P><B>Description:</B>
</P>
<P>Write out the bond information computed by the ReaxFF potential
specified by <A HREF = "pair_reax.html">pair_style reax</A>. The bond information
is written to <I>filename</I> on timesteps that are multiples of <I>Nevery</I>,
including timestep 0.
specified by <A HREF = "pair_reax.html">pair_style reax</A> or <A HREF = "pair_reax_c.html">pair_style
reax/c</A>. The bond information is written to
<I>filename</I> on timesteps that are multiples of <I>Nevery</I>, including
timestep 0.
</P>
<P>The format of the output file should be self-explantory.
</P>
@ -47,15 +51,18 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix requires that the <A HREF = "pair_reax.html">pair_style reax</A> be
invoked. This fix is part of the REAX package. It is only enabled if
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#start_3">Making
<P>The fix reax/bonds requires that the <A HREF = "pair_reax.html">pair_style reax</A>
be invoked. This fix is part of the REAX package. It is only enabled
if LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. The fix reax/c/bonds
requires that the <A HREF = "pair_reax_c.html">pair_style reax/c</A> be invoked,
which is part of the USER-REAXC package. It is only enabled if LAMMPS
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_reax.html">pair_style reax</A>
<P><A HREF = "pair_reax.html">pair_style reax</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>
</P>
<P><B>Default:</B>
</P>

26
doc/fix_reax_bonds.txt
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@ -7,26 +7,29 @@
:line
fix reax/bonds command :h3
fix reax/c/bonds command :h3
[Syntax:]
fix ID group-ID reax/bonds Nevery filename :pre
fix ID group-ID style Nevery filename :pre
ID, group-ID are documented in "fix"_fix.html command
reax/bonds = style name of this fix command
style = {reax/bonds} or {reax/c/bonds}
Nevery = output interval in timesteps
filename = name of output file :ul
[Examples:]
fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc :pre
[Description:]
Write out the bond information computed by the ReaxFF potential
specified by "pair_style reax"_pair_reax.html. The bond information
is written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0.
specified by "pair_style reax"_pair_reax.html or "pair_style
reax/c"_pair_reax_c.html. The bond information is written to
{filename} on timesteps that are multiples of {Nevery}, including
timestep 0.
The format of the output file should be self-explantory.
@ -44,15 +47,18 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that the "pair_style reax"_pair_reax.html be
invoked. This fix is part of the REAX package. It is only enabled if
LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the "Making
The fix reax/bonds requires that the "pair_style reax"_pair_reax.html
be invoked. This fix is part of the REAX package. It is only enabled
if LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. The fix reax/c/bonds
requires that the "pair_style reax/c"_pair_reax_c.html be invoked,
which is part of the USER-REAXC package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_style reax"_pair_reax.html
"pair_style reax"_pair_reax.html, "pair_style reax/c"_pair_reax_c.html
[Default:]

26
doc/pair_reax_c.html
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@ -16,10 +16,12 @@
<PRE>pair_style reax/c cfile keyword value
</PRE>
<UL><LI>cfile = NULL or name of a control file
</UL>
<PRE>one keyword value pair may be appended
keyword = <I>checkqeq</I>
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>checkqeq</I> or <I>lgvdw</I>
<I>checkqeq</I> value = <I>yes</I> or <I>no</I> = whether or not to require qeq/reax fix
<I>lgvdw</I> value = <I>yes</I> or <I>no</I> = whether or not to use a low gradient vdW correction
</PRE>
</UL>
@ -27,6 +29,7 @@ keyword = <I>checkqeq</I>
</P>
<PRE>pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_coeff * * ffield.reax 1 2 2 3
</PRE>
<P><B>Description:</B>
@ -89,6 +92,16 @@ assign to each atom will be used for computing the electrostatic
interactions in the system.
See the <A HREF = "fix_qeq_reax.html">fix qeq/reax</A> command for details.
</P>
<P>Using the optional keyword <I>lgvdw</I> with the value <I>yes</I> turns on
the low-gradient correction of the ReaxFF/C for long-range
London Dispersion, as described in the "(Liu)" paper. Force field
file <I>ffield.reax.lg</I> is designed for this correction, and is trained
for several energetic materials (see "Liu"). When using lg-correction,
recommended value for parameter <I>thb</I> is 0.01, which can be set in
the control file. Note: Force field files
are different for the original or lg corrected pair styles, using
wrong ffield file generates an error message.
</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
equilibration contributions which are stored in the thermo variable
@ -260,7 +273,7 @@ appropriate units if your simulation doesn't use "real" units.
</P>
<P><B>Default:</B>
</P>
<P>The keyword default is checkqeq = yes.
<P>The keyword defaults are checkqeq = yes, lgvdw = no.
</P>
<HR>
@ -274,4 +287,9 @@ Journal of Physical Chemistry A, 112, 1040-1053 (2008).
<P><B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
</P>
<A NAME = "Liu"></A>
<P><B>(Liu)</B> L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
of Physical Chemistry A, 115, 11016-11022 (2011).
</P>
</HTML>

27
doc/pair_reax_c.txt
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@ -12,17 +12,18 @@ pair_style reax/c command :h3
pair_style reax/c cfile keyword value :pre
cfile = NULL or name of a control file :ul
one keyword value pair may be appended
keyword = {checkqeq}
{checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix :pre
cfile = NULL or name of a control file :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {checkqeq} or {lgvdw}
{checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix
{lgvdw} value = {yes} or {no} = whether or not to use a low gradient vdW correction :pre
:ule
[Examples:]
pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_coeff * * ffield.reax 1 2 2 3 :pre
[Description:]
@ -85,6 +86,16 @@ assign to each atom will be used for computing the electrostatic
interactions in the system.
See the "fix qeq/reax"_fix_qeq_reax.html command for details.
Using the optional keyword {lgvdw} with the value {yes} turns on
the low-gradient correction of the ReaxFF/C for long-range
London Dispersion, as described in the "(Liu)" paper. Force field
file {ffield.reax.lg} is designed for this correction, and is trained
for several energetic materials (see "Liu"). When using lg-correction,
recommended value for parameter {thb} is 0.01, which can be set in
the control file. Note: Force field files
are different for the original or lg corrected pair styles, using
wrong ffield file generates an error message.
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
@ -256,7 +267,7 @@ appropriate units if your simulation doesn't use "real" units.
[Default:]
The keyword default is checkqeq = yes.
The keyword defaults are checkqeq = yes, lgvdw = no.
:line
@ -267,3 +278,7 @@ Journal of Physical Chemistry A, 112, 1040-1053 (2008).
:link(Aktulga)
[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
:link(Liu)
[(Liu)] L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
of Physical Chemistry A, 115, 11016-11022 (2011).