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updated documentation for inclusion of airebo/morse

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Axel Kohlmeyer
2016-03-15 17:27:37 -04:00
parent d4f5612904
commit 037e91f77f
1 changed files with 48 additions and 22 deletions
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doc/pair_airebo.txt
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@ -8,6 +8,8 @@
pair_style airebo command :h3
pair_style airebo/omp command :h3
pair_style airebo/morse command :h3
pair_style airebo/morse/omp command :h3
pair_style rebo command :h3
pair_style rebo/omp command :h3
@ -15,10 +17,10 @@ pair_style rebo/omp command :h3
pair_style style cutoff LJ_flag TORSION_flag :pre
style = {airebo} or {rebo}
cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional) :ul
style = {airebo} or {airebo/morse} or {rebo}
cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)
LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)
TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional) :ul
[Examples:]
@ -26,6 +28,9 @@ pair_style airebo 3.0
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C :pre
pair_style airebo/morse 3.0
pair_coeff * * ../potentials/CH.airebo-m H C :pre
pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C :pre
@ -34,12 +39,21 @@ pair_coeff * * ../potentials/CH.airebo H C :pre
The {airebo} pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of "(Stuart)"_#Stuart for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
{rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.
formulation of AIREBO from 2000, not the later formulation.
The {airebo/morse} pair style computes the AIREBO-M potential, which
is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
The Morse potentials are parameterized by high-quality quantum chemistry
(MP2) calculations and do not diverge as quickly as particle density
increases. This allows AIREBO-M to retain accuracy to much higher pressures
than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
and its parameterization are given in "(O'Conner)"_#OConnor.
The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.
The AIREBO potential consists of three terms:
@ -51,7 +65,7 @@ included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
mentioned below. This can be specified directly as pair_style {rebo}
with no additional arguments.
The detailed formulas for this potential are given in
@ -88,12 +102,13 @@ various dihedral angle preferences in hydrocarbon configurations.
:line
Only a single pair_coeff command is used with the {airebo} or {rebo}
style which specifies an AIREBO potential file with parameters for C
and H. Note that the {rebo} style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
Only a single pair_coeff command is used with the {airebo}, {airebo}
or {rebo} style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the {rebo} style in LAMMPS
uses the same AIREBO-formatted potential file. These are mapped to
LAMMPS atom types by specifying N 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 AIREBO elements to atom types :ul
@ -121,6 +136,13 @@ the CH.airebo file to agree with the original "(Stuart)"_#Stuart
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.
Similarly the parameters/coefficients for the AIREBO-M potentials are
listed in the CH.airebo-m file to agree with the "(O'Connor)"_#OConnor
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@ -170,11 +192,12 @@ for more info.
These pair potentials require the "newton"_newton.html setting to be
"on" for pair interactions.
The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal "units"_units.html. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn't use "metal" units.
The CH.airebo and CH.airebo-m potential files provided with LAMMPS
(see the potentials directory) are parameterized for metal "units"_units.html.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
doesn't use "metal" units.
[Related commands:]
@ -191,3 +214,6 @@ the appropriate units if your simulation doesn't use "metal" units.
:link(Brenner)
[(Brenner)] Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).
:link(OConnor)
[(O'Connor)] O'Connor et al., J. Chem. Phys. 142, 024903 (2015).