Modified pair_styles reax and reax/c (ad75964d) · Commits · 郑智淋 / lammps

doc/fix_qeq_reax.html

+2 −2

Original line number	Diff line number	Diff line
		@@ -24,8 +24,8 @@
		</UL>
		<P><B>Examples:</B>
		</P>
		<PRE>fix 1 all qeq 1 0.0 10.0 1.0e-6 reax/c
		fix 1 all qeq 1 0.0 10.0 1.0e-6 param.qeq
		<PRE>fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
		fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
		</PRE>
		<P><B>Description:</B>
		</P>

doc/fix_qeq_reax.txt

+2 −2

Original line number	Diff line number	Diff line
		@@ -21,8 +21,8 @@ params = reax/c or a filename :ul

		[Examples:]

		fix 1 all qeq 1 0.0 10.0 1.0e-6 reax/c
		fix 1 all qeq 1 0.0 10.0 1.0e-6 param.qeq :pre
		fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
		fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre

		[Description:]

doc/pair_reax.html

+40 −36

Original line number	Diff line number	Diff line
		@@ -34,7 +34,7 @@ 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">(Chenoweth)</A>. The version integrated into LAMMPS matches
		<A HREF = "#Chenoweth_2008">(Chenoweth)</A>. The version integrated into LAMMPS matches
		the most up-to-date version of ReaxFF as of summer 2010.
		</P>
		<P>The <I>reax</I> style differs from the <A HREF = "pair_reax_c.html">pair_style reax/c</A>
		@@ -69,6 +69,10 @@ and <I>precision</I> = 1.0e-6 (one part in 10^6).
		If you wish to override any of these defaults, then all settings
		must be specified.
		</P>
		<P>Two examples using <I>pair_style reax</I> are provided in the examples/reax
		sub-directory, along with corresponding examples for
		<A HREF = "pair_reax_c.html">pair_style reax/c</A>.
		</P>
		<P>Use of this pair style requires that a charge be defined for every
		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
		@@ -79,9 +83,39 @@ charges.
		energy contributions, with the exception of the Coulombic and charge
		equilibration contributions which are stored in the thermo variable
		<I>ecoul</I>. The output of these quantities is controlled by the
		<A HREF = "thermo.html">thermo</A> command. See below for how to access
		a more detailed breakdown of ReaxFF energies.
		<A HREF = "thermo.html">thermo</A> command.
		</P>
		<P>This pair style tallies a breakdown of the total ReaxFF potential
		energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
		pair</A> command as a vector of values of length 14.
		The 14 values correspond to the following sub-categories (the variable
		names in italics match those used in the ReaxFF FORTRAN library):
		</P>
		<OL><LI><I>eb</I> = bond energy
		<LI><I>ea</I> = atom energy
		<LI><I>elp</I> = lone-pair energy
		<LI><I>emol</I> = molecule energy (always 0.0)
		<LI><I>ev</I> = valence angle energy
		<LI><I>epen</I> = double-bond valence angle penalty
		<LI><I>ecoa</I> = valence angle conjugation energy
		<LI><I>ehb</I> = hydrogen bond energy
		<LI><I>et</I> = torsion energy
		<LI><I>eco</I> = conjugation energy
		<LI><I>ew</I> = van der Waals energy
		<LI><I>ep</I> = Coulomb energy
		<LI><I>efi</I> = electric field energy (always 0.0)
		<LI><I>eqeq</I> = charge equilibration energy
		</OL>
		<P>To print these quantities to the log file (with descriptive column
		headings) the following commands could be included in an input script:
		</P>
		<PRE>compute reax all pair reax
		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		...
		variable eqeq equal c_reax[14]
		thermo_style custom step temp epair v_eb v_ea ... v_eqeq
		</PRE>
		<P>Only a single pair_coeff command is used with the <I>reax</I> style which
		specifies a ReaxFF potential file with parameters for all needed
		elements. These are mapped to LAMMPS atom types by specifying N
		@@ -138,37 +172,6 @@ script that reads a restart file.
		<A HREF = "run_style.html">run_style respa</A> command. It does not support the
		<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
		</P>
		<P>This pair style tallies a breakdown of the total ReaxFF potential
		energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
		pair</A> command as a vector of values of length 14.
		The 14 values correspond to the following sub-categories (the variable
		names in italics match those used in the ReaxFF FORTRAN library):
		</P>
		<OL><LI><I>eb</I> = bond energy
		<LI><I>ea</I> = atom energy
		<LI><I>elp</I> = lone-pair energy
		<LI><I>emol</I> = molecule energy (always 0.0)
		<LI><I>ev</I> = valence angle energy
		<LI><I>epen</I> = double-bond valence angle penalty
		<LI><I>ecoa</I> = valence angle conjugation energy
		<LI><I>ehb</I> = hydrogen bond energy
		<LI><I>et</I> = torsion energy
		<LI><I>eco</I> = conjugation energy
		<LI><I>ew</I> = van der Waals energy
		<LI><I>ep</I> = Coulomb energy
		<LI><I>efi</I> = electric field energy (always 0.0)
		<LI><I>eqeq</I> = charge equilibration energy
		</OL>
		<P>To print these quantities to the log file (with descriptive column
		headings) the following commands could be included in an input script:
		</P>
		<PRE>compute reax all pair reax
		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		...
		variable eqeq equal c_reax[14]
		thermo_style custom step temp epair v_eb v_ea ... v_eqeq
		</PRE>
		<P><B>Restrictions:</B>
		</P>
		<P>The ReaxFF potential files provided with LAMMPS in the potentials
		@@ -179,7 +182,8 @@ 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>, <A HREF = "pair_reaxc.html">pair_style reax/c</A>
		<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>,
		<A HREF = "fix_reax_bonds.html">fix_reax_bonds</A>
		</P>
		<P><B>Default:</B> none
		</P>
		@@ -187,7 +191,7 @@ appropriate units if your simulation doesn't use "real" units.

		<A NAME = "Chenoweth_2008"></A>

		<P><B>(Chenoweth)</B> Chenoweth, van Duin and Goddard,
		<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
		Journal of Physical Chemistry A, 112, 1040-1053 (2008).
		</P>
		</HTML>

doc/pair_reax.txt

+40 −36

Original line number	Diff line number	Diff line
		@@ -31,7 +31,7 @@ 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)"_#Chenoweth. The version integrated into LAMMPS matches
		"(Chenoweth)"_#Chenoweth_2008. The version integrated into LAMMPS matches
		the most up-to-date version of ReaxFF as of summer 2010.

		The {reax} style differs from the "pair_style reax/c"_pair_reax_c.html
		@@ -66,6 +66,10 @@ and {precision} = 1.0e-6 (one part in 10^6).
		If you wish to override any of these defaults, then all settings
		must be specified.

		Two examples using {pair_style reax} are provided in the examples/reax
		sub-directory, along with corresponding examples for
		"pair_style reax/c"_pair_reax_c.html.

		Use of this pair style requires that a charge be defined for every
		atom since the {reax} pair style performs a charge equilibration (QEq)
		calculation. See the "atom_style"_atom_style.html and
		@@ -76,8 +80,38 @@ 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
		{ecoul}. The output of these quantities is controlled by the
		"thermo"_thermo.html command. See below for how to access
		a more detailed breakdown of ReaxFF energies.
		"thermo"_thermo.html command.

		This pair style tallies a breakdown of the total ReaxFF potential
		energy into sub-categories, which can be accessed via the "compute
		pair"_compute_pair.html command as a vector of values of length 14.
		The 14 values correspond to the following sub-categories (the variable
		names in italics match those used in the ReaxFF FORTRAN library):

		{eb} = bond energy
		{ea} = atom energy
		{elp} = lone-pair energy
		{emol} = molecule energy (always 0.0)
		{ev} = valence angle energy
		{epen} = double-bond valence angle penalty
		{ecoa} = valence angle conjugation energy
		{ehb} = hydrogen bond energy
		{et} = torsion energy
		{eco} = conjugation energy
		{ew} = van der Waals energy
		{ep} = Coulomb energy
		{efi} = electric field energy (always 0.0)
		{eqeq} = charge equilibration energy :ol

		To print these quantities to the log file (with descriptive column
		headings) the following commands could be included in an input script:

		compute reax all pair reax
		variable eb equal c_reax\[1\]
		variable ea equal c_reax\[2\]
		...
		variable eqeq equal c_reax\[14\]
		thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre

		Only a single pair_coeff command is used with the {reax} style which
		specifies a ReaxFF potential file with parameters for all needed
		@@ -135,37 +169,6 @@ This pair style can only be used via the {pair} keyword of the
		"run_style respa"_run_style.html command. It does not support the
		{inner}, {middle}, {outer} keywords.

		This pair style tallies a breakdown of the total ReaxFF potential
		energy into sub-categories, which can be accessed via the "compute
		pair"_compute_pair.html command as a vector of values of length 14.
		The 14 values correspond to the following sub-categories (the variable
		names in italics match those used in the ReaxFF FORTRAN library):

		{eb} = bond energy
		{ea} = atom energy
		{elp} = lone-pair energy
		{emol} = molecule energy (always 0.0)
		{ev} = valence angle energy
		{epen} = double-bond valence angle penalty
		{ecoa} = valence angle conjugation energy
		{ehb} = hydrogen bond energy
		{et} = torsion energy
		{eco} = conjugation energy
		{ew} = van der Waals energy
		{ep} = Coulomb energy
		{efi} = electric field energy (always 0.0)
		{eqeq} = charge equilibration energy :ol

		To print these quantities to the log file (with descriptive column
		headings) the following commands could be included in an input script:

		compute reax all pair reax
		variable eb equal c_reax\[1\]
		variable ea equal c_reax\[2\]
		...
		variable eqeq equal c_reax\[14\]
		thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre

		[Restrictions:]

		The ReaxFF potential files provided with LAMMPS in the potentials
		@@ -176,12 +179,13 @@ appropriate units if your simulation doesn't use "real" units.

		[Related commands:]

		"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html
		"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reax_c.html,
		"fix_reax_bonds"_fix_reax_bonds.html

		[Default:] none

		:line

		:link(Chenoweth_2008)
		[(Chenoweth)] Chenoweth, van Duin and Goddard,
		[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
		Journal of Physical Chemistry A, 112, 1040-1053 (2008).

doc/pair_reax_c.html

+45 −40

Original line number	Diff line number	Diff line
		@@ -40,16 +40,11 @@ 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>The version integrated into LAMMPS matches the most up-to-date version
		of ReaxFF as of summer 2010. The parameter files supplied in the
		potentials directory use parameters from the following publications:
		</P>
		<UL><LI>ffield.CHO: <A HREF = "#Chenoweth">(Chenoweth)</A>
		<LI>ffield.NiCH: <A HREF = "#Mueller">(Mueller)</A>
		<LI>ffield.RDX: <A HREF = "#Zhang">(Zhang)</A>
		<LI>ffield.NaH: <A HREF = "#Ojwang">(Ojwang)</A>
		<LI>ffield.CuOH: ???
		</UL>
		<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
		@@ -62,8 +57,11 @@ settings are used. Or a control file can be specified which contains
		cutoff values for the ReaxFF potential in addition to some performance
		and output controls. Each line in the control specifies the value for
		a control variable. The format of the control file is described
		below. See examples of such files in the examples/USER/reax
		sub-directories.
		below.
		</P>
		<P>Two examples using <I>pair_style reax/c</I> are provided in the examples/reax
		sub-directory, along with corresponding examples for
		<A HREF = "pair_reax.html">pair_style reax</A>.
		</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
		@@ -75,7 +73,7 @@ equilibration (QEq) model for handling the electrostatic interactions.
		Therefore it is highly recommended that the <A HREF = "fix_qeq_reax.html">fix
		qeq/reax</A> command be used with pair style <I>reax/c</I>
		when simulating a ReaxFF model, to equilibrate charge each timestep.
		See the <A HREF = "fix_qeq.html">fix_qeq</A> command for details.
		See the <A HREF = "fix_qeq_reax.html">fix qeq/reax</A> command for details.
		</P>
		<P>However, performing charge equilibration is not a prerequisite for
		performing a ReaxFF simulation. In this case, the static charges you
		@@ -88,7 +86,38 @@ equilibration contributions which are stored in the thermo variable
		<I>ecoul</I>. The output of these quantities is controlled by the
		<A HREF = "thermo.html">thermo</A> command.
		</P>
		<P>Only a single pair_coeff command is used with the <I>reax</I> style which
		<P>This pair style tallies a breakdown of the total ReaxFF potential
		energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
		pair</A> command as a vector of values of length 14.
		The 14 values correspond to the following sub-categories (the variable
		names in italics match those used in the original FORTRAN ReaxFF code):
		</P>
		<OL><LI><I>eb</I> = bond energy
		<LI><I>ea</I> = atom energy
		<LI><I>elp</I> = lone-pair energy
		<LI><I>emol</I> = molecule energy (always 0.0)
		<LI><I>ev</I> = valence angle energy
		<LI><I>epen</I> = double-bond valence angle penalty
		<LI><I>ecoa</I> = valence angle conjugation energy
		<LI><I>ehb</I> = hydrogen bond energy
		<LI><I>et</I> = torsion energy
		<LI><I>eco</I> = conjugation energy
		<LI><I>ew</I> = van der Waals energy
		<LI><I>ep</I> = Coulomb energy
		<LI><I>efi</I> = electric field energy (always 0.0)
		<LI><I>eqeq</I> = charge equilibration energy
		</OL>
		<P>To print these quantities to the log file (with descriptive column
		headings) the following commands could be included in an input script:
		</P>
		<PRE>compute reax all pair reax/c
		variable eb equal c_reax[1]
		variable ea equal c_reax[2]
		...
		variable eqeq equal c_reax[14]
		thermo_style custom step temp epair v_eb v_ea ... v_eqeq
		</PRE>
		<P>Only a single pair_coeff command is used with the <I>reax/c</I> style which
		specifies a ReaxFF potential file with parameters for all needed
		elements. These are mapped to LAMMPS atom types by specifying N
		additional arguments after the filename in the pair_coeff command,
		@@ -220,33 +249,9 @@ appropriate units if your simulation doesn't use "real" units.
		</P>
		<HR>

		<A NAME = "Chenoweth"></A>
		<A NAME = "Chenoweth_2008"></A>

		<P><B>(Chenoweth)</B> Chenoweth, van Duin, and Goddard,
		<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
		Journal of Physical Chemistry A, 112, 1040-1053 (2008).
		</P>
		<A NAME = "Mueller"></A>

		<P><B>(Mueller)</B> Mueller, van Duin, and Goddard,
		submitted for publication in Journal of Physical Chemistry A.
		</P>
		<A NAME = "Zhang"></A>

		<P><B>(Zhang)</B> Zhang, van Duin, Zybin, and Goddard,
		Journal of Physical Chemistry A 113, 10770-10778 (2009).
		</P>
		<P>Zhang, van Duin, Kober, Zybin, and Goddard,
		"HMX/TATB carbon cluster formation",
		accepted for publication in Journal of Physical Chemistry A.
		</P>
		<P>Zhang, van Duin, Zybin, and Goddard,
		"Sensitivity test for RDX, HMX using fast compression",
		submitted for publication to Journal of Physical Chemistry A.
		</P>
		<A NAME = "Ojwang"></A>

		<P><B>(Ojwang)</B> Ojwang, van Santen, Kramer, van Duin, and Goddard,
		"Modeling the sorption dynamics of NaH using a reactive force field",
		Journal of Chemical Physics 128, 164714 (2008).
		</P>
		</HTML>

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