git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7259 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
64
doc/angle_sdk.html
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64
doc/angle_sdk.html
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
|
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|
||||
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<HR>
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|
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<H3>angle_style sdk command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>angle_style sdk
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</PRE>
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<PRE>angle_style sdk/omp
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>angle_style sdk
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angle_coeff 1 300.0 107.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>sdk</I> angle style is a combination of the harmonic angle potential,
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</P>
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<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
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</CENTER>
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<P>where theta0 is the equilibrium value of the angle and K a prefactor,
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with the <I>repulsive</I> part of the non-bonded <I>lj/sdk</I> pair style
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between the atoms 1 and 3. This angle potential is intended for
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coarse grained MD simulations with the CMM parametrization using the
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<A HREF = "pair_sdk.html">pair_style lj/sdk</A>. Relative to the pair_style
|
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<I>lj/sdk</I>, however, the energy is shifted by <I>epsilon</I>, to avoid sudden
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jumps. Note that the usual 1/2 factor is included in K.
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</P>
|
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<P>The following coefficients must be defined for each angle type via the
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<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above:
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</P>
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<UL><LI>K (energy/radian^2)
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<LI>theta0 (degrees)
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</UL>
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<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
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internally; hence the units of K are in energy/radian^2.
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The also required <I>lj/sdk</I> parameters will be extracted automatically
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from the pair_style.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This angle style can only be used if LAMMPS was built with the
|
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USER-CG-CMM package. See the <A HREF = "Section_start.html#start_3">Making
|
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LAMMPS</A> section for more info on packages.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_harmonic.html">angle_style
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harmonic</A>, <A HREF = "pair_sdk.html">pair_style lj/sdk</A>,
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<A HREF = "pair_sdk.html">pair_style lj/sdk/coul/long</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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58
doc/angle_sdk.txt
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58
doc/angle_sdk.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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angle_style sdk command :h3
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|
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[Syntax:]
|
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|
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angle_style sdk :pre
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angle_style sdk/omp :pre
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|
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[Examples:]
|
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|
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angle_style sdk
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angle_coeff 1 300.0 107.0 :pre
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[Description:]
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|
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The {sdk} angle style is a combination of the harmonic angle potential,
|
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:c,image(Eqs/angle_harmonic.jpg)
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|
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where theta0 is the equilibrium value of the angle and K a prefactor,
|
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with the {repulsive} part of the non-bonded {lj/sdk} pair style
|
||||
between the atoms 1 and 3. This angle potential is intended for
|
||||
coarse grained MD simulations with the CMM parametrization using the
|
||||
"pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style
|
||||
{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden
|
||||
jumps. Note that the usual 1/2 factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
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"angle_coeff"_angle_coeff.html command as in the example above:
|
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|
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K (energy/radian^2)
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theta0 (degrees) :ul
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|
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Theta0 is specified in degrees, but LAMMPS converts it to radians
|
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internally; hence the units of K are in energy/radian^2.
|
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The also required {lj/sdk} parameters will be extracted automatically
|
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from the pair_style.
|
||||
|
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[Restrictions:]
|
||||
|
||||
This angle style can only be used if LAMMPS was built with the
|
||||
USER-CG-CMM package. See the "Making
|
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
[Related commands:]
|
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|
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"angle_coeff"_angle_coeff.html, "angle_style
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harmonic"_angle_harmonic.html, "pair_style lj/sdk"_pair_sdk.html,
|
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"pair_style lj/sdk/coul/long"_pair_sdk.html
|
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|
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[Default:] none
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118
doc/pair_coul_diel.html
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118
doc/pair_coul_diel.html
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<HTML>
|
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
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|
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|
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<HR>
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<H3>pair_style coul/diel command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style coul/diel cutoff
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</PRE>
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<P>cutoff = global cutoff (distance units)
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</P>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style coul/diel 3.5
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pair_coeff 1 4 78. 1.375 0.112
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>coul/diel</I> computes a Coulomb correction for implict solvent
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ion interactions in which the dielectric perimittivity is distance dependent.
|
||||
The dielectric permittivity epsilon_D(r) connects to limiting regimes:
|
||||
One limit is defined by a small dielectric permittivity (close to vacuum)
|
||||
at or close to contact seperation between the ions. At larger separations
|
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the dielectric permittivity reaches a bulk value used in the regular Coulomb
|
||||
interaction coul/long or coul/cut.
|
||||
The transition is modeled by a hyperbolic function which is incorporated
|
||||
in the Coulomb correction term for small ion separations as follows
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_coul_diel.jpg">
|
||||
</CENTER>
|
||||
<P>where r_me is the inflection point of epsilon_D(r) and sigma_e is a slope
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||||
defining length scale. C is the same Coulomb conversion factor as in the
|
||||
pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb
|
||||
interaction between ions is corrected at small distances r. The lower
|
||||
limit of epsilon_D(r->0)=5.2 due to dielectric saturation <A HREF = "#Stiles">(Stiles)</A>
|
||||
while the Coulomb interaction reaches its bulk limit by setting
|
||||
epsilon_D(r->\infty)=epsilon, the bulk value of the solvent which is 78
|
||||
for water at 298K.
|
||||
</P>
|
||||
<P>Examples of the use of this type of Coulomb interaction include implicit
|
||||
solvent simulations of salt ions
|
||||
<A HREF = "#Lenart">(Lenart)</A> and of ionic surfactants <A HREF = "#Jusufi">(Jusufi)</A>.
|
||||
Note that this potential is only reasonable for implicit solvent simulations
|
||||
and in combiantion with coul/cut or coul/long. It is also usually combined
|
||||
with gauss/cut, see <A HREF = "#Lenart">(Lenart)</A> or <A HREF = "#Jusufi">(Jusufi)</A>.
|
||||
</P>
|
||||
<P>The following coefficients must be defined for each pair of atom
|
||||
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example
|
||||
above, or in the data file or restart files read by the
|
||||
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
|
||||
commands:
|
||||
</P>
|
||||
<UL><LI>epsilon (no units)
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<LI>r_me (distance units)
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<LI>sigma_e (distance units)
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</UL>
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<P>The global cutoff (r_c) specified in the pair_style command is used.
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</P>
|
||||
<HR>
|
||||
|
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
|
||||
</P>
|
||||
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
|
||||
option for the energy of the Gauss-potential portion of the pair
|
||||
interaction.
|
||||
</P>
|
||||
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
|
||||
for this pair style.
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure.
|
||||
</P>
|
||||
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
||||
<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><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This style is part of the "user-gauss" package. It is only enabled
|
||||
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>
|
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<A HREF = "pair_gauss.html">pair_style gauss/cut</A>
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||||
</P>
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||||
<P><B>Default:</B> none
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||||
</P>
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||||
<HR>
|
||||
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||||
<A NAME = "Stiles"></A>
|
||||
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||||
<P><B>(Stiles)</B> Stiles , Hubbard, and Kayser, J Chem Phys, 77,
|
||||
6189 (1982).
|
||||
</P>
|
||||
<A NAME = "Lenart"></A>
|
||||
|
||||
<P><B>(Lenart)</B> Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
|
||||
044509 (2007).
|
||||
</P>
|
||||
<A NAME = "Jusufi"></A>
|
||||
|
||||
<P><B>(Jusufi)</B> Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
|
||||
13783 (2008).
|
||||
</P>
|
||||
</HTML>
|
||||
111
doc/pair_coul_diel.txt
Normal file
111
doc/pair_coul_diel.txt
Normal file
@ -0,0 +1,111 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style coul/diel command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style coul/diel cutoff :pre
|
||||
|
||||
cutoff = global cutoff (distance units)
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style coul/diel 3.5
|
||||
pair_coeff 1 4 78. 1.375 0.112 :pre
|
||||
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {coul/diel} computes a Coulomb correction for implict solvent
|
||||
ion interactions in which the dielectric perimittivity is distance dependent.
|
||||
The dielectric permittivity epsilon_D(r) connects to limiting regimes:
|
||||
One limit is defined by a small dielectric permittivity (close to vacuum)
|
||||
at or close to contact seperation between the ions. At larger separations
|
||||
the dielectric permittivity reaches a bulk value used in the regular Coulomb
|
||||
interaction coul/long or coul/cut.
|
||||
The transition is modeled by a hyperbolic function which is incorporated
|
||||
in the Coulomb correction term for small ion separations as follows
|
||||
|
||||
:c,image(Eqs/pair_coul_diel.jpg)
|
||||
|
||||
where r_me is the inflection point of epsilon_D(r) and sigma_e is a slope
|
||||
defining length scale. C is the same Coulomb conversion factor as in the
|
||||
pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb
|
||||
interaction between ions is corrected at small distances r. The lower
|
||||
limit of epsilon_D(r->0)=5.2 due to dielectric saturation "(Stiles)"_#Stiles
|
||||
while the Coulomb interaction reaches its bulk limit by setting
|
||||
epsilon_D(r->\infty)=epsilon, the bulk value of the solvent which is 78
|
||||
for water at 298K.
|
||||
|
||||
Examples of the use of this type of Coulomb interaction include implicit
|
||||
solvent simulations of salt ions
|
||||
"(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi.
|
||||
Note that this potential is only reasonable for implicit solvent simulations
|
||||
and in combiantion with coul/cut or coul/long. It is also usually combined
|
||||
with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi.
|
||||
|
||||
The following coefficients must be defined for each pair of atom
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the example
|
||||
above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands:
|
||||
|
||||
epsilon (no units)
|
||||
r_me (distance units)
|
||||
sigma_e (distance units) :ul
|
||||
|
||||
The global cutoff (r_c) specified in the pair_style command is used.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
|
||||
|
||||
This pair style supports the "pair_modify"_pair_modify.html shift
|
||||
option for the energy of the Gauss-potential portion of the pair
|
||||
interaction.
|
||||
|
||||
The "pair_modify"_pair_modify.html table option is not relevant
|
||||
for this pair style.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure.
|
||||
|
||||
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.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This style is part of the "user-gauss" package. It is only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_style gauss/cut"_pair_gauss.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Stiles)
|
||||
[(Stiles)] Stiles , Hubbard, and Kayser, J Chem Phys, 77,
|
||||
6189 (1982).
|
||||
|
||||
:link(Lenart)
|
||||
[(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
|
||||
044509 (2007).
|
||||
|
||||
:link(Jusufi)
|
||||
[(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
|
||||
13783 (2008).
|
||||
166
doc/pair_sdk.html
Normal file
166
doc/pair_sdk.html
Normal file
@ -0,0 +1,166 @@
|
||||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>pair_style lj/sdk command
|
||||
</H3>
|
||||
<H3>pair_style lj/sdk/gpu command
|
||||
</H3>
|
||||
<H3>pair_style lj/sdk/omp command
|
||||
</H3>
|
||||
<H3>pair_style lj/sdk/coul/long command
|
||||
</H3>
|
||||
<H3>pair_style lj/sdk/coul/long/gpu command
|
||||
</H3>
|
||||
<H3>pair_style lj/sdk/coul/long/omp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style style args
|
||||
</PRE>
|
||||
<UL><LI>style = <I>lj/sdk</I> or <I>lj/sdk/coul/long</I>
|
||||
<LI>args = list of arguments for a particular style
|
||||
</UL>
|
||||
<PRE> <I>lj/sdk</I> args = cutoff
|
||||
cutoff = global cutoff for Lennard Jones interactions (distance units)
|
||||
<I>lj/sdk/coul/long</I> args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
</PRE>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style lj/sdk 2.5
|
||||
pair_coeff 1 1 lj12_6 1 1.1 2.8
|
||||
</PRE>
|
||||
<PRE>pair_style lj/sdk/coul/long 10.0
|
||||
pair_style lj/sdk/coul/long 10.0 12.0
|
||||
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>The <I>lj/sdk</I> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
|
||||
given by
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_cmm.jpg">
|
||||
</CENTER>
|
||||
<P>as required for the SDK Coarse-grained MD parametrization discussed in
|
||||
<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
|
||||
</P>
|
||||
<P>Style <I>lj/sdk/coul/long</I> computes the adds Coulombic interactions
|
||||
with an additional damping factor applied so it can be used in
|
||||
conjunction with the <A HREF = "kspace_style.html">kspace_style</A> command and
|
||||
its <I>ewald</I> or <I>pppm</I> or <I>pppm/cg</I> option. The Coulombic cutoff
|
||||
specified for this style means that pairwise interactions within
|
||||
this distance are computed directly; interactions outside that
|
||||
distance are computed in reciprocal space.
|
||||
</P>
|
||||
<P>The following coefficients must be defined for each pair of atoms
|
||||
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
|
||||
commands, or by mixing as described below:
|
||||
</P>
|
||||
<UL><LI>cg_type (lj9_6, lj12_4, or lj12_6)
|
||||
<LI>epsilon (energy units)
|
||||
<LI>sigma (distance units)
|
||||
<LI>cutoff1 (distance units)
|
||||
</UL>
|
||||
<P>Note that sigma is defined in the LJ formula as the zero-crossing
|
||||
distance for the potential, not as the energy minimum. The prefactors
|
||||
are chosen so that the potential minimum is at -epsilon.
|
||||
</P>
|
||||
<P>The latter 2 coefficients are optional. If not specified, the global
|
||||
LJ and Coulombic cutoffs specified in the pair_style command are used.
|
||||
If only one cutoff is specified, it is used as the cutoff for both LJ
|
||||
and Coulombic interactions for this type pair. If both coefficients
|
||||
are specified, they are used as the LJ and Coulombic cutoffs for this
|
||||
type pair.
|
||||
</P>
|
||||
<P>For <I>lj/sdk/coul/long</I> only the LJ cutoff can be specified since a
|
||||
Coulombic cutoff cannot be specified for an individual I,J type pair.
|
||||
All type pairs use the same global Coulombic cutoff specified in the
|
||||
pair_style command.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I> or <I>opt</I> suffix are functionally
|
||||
the same as the corresponding style without the suffix. They have been
|
||||
optimized to run faster, depending on your available hardware, as
|
||||
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
|
||||
The accelerated styles take the same arguments and should produce the
|
||||
same results, except for round-off and precision issues.
|
||||
</P>
|
||||
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP, and
|
||||
OPT packages respectively. They are only enabled if LAMMPS was built with
|
||||
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
|
||||
section for more info.
|
||||
</P>
|
||||
<P>You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
|
||||
switch</A> when you invoke LAMMPS, or you can
|
||||
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, and rRESPA info</B>:
|
||||
</P>
|
||||
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of the lj/sdk pair styles <I>cannot</I> be mixed,
|
||||
since different pairs may have different exponents. So all parameters
|
||||
for all pairs have to be specified explicitly through the "pair_coeff"
|
||||
command. Defining then in a data file is also not supported, due to
|
||||
limitations of that file format.
|
||||
</P>
|
||||
<P>All of the lj/sdk pair styles support the
|
||||
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
|
||||
Lennard-Jones portion of the pair interaction.
|
||||
</P>
|
||||
<P>The <I>lj/sdk/coul/long</I> pair styles support the
|
||||
<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
|
||||
the short-range portion of the long-range Coulombic interaction.
|
||||
</P>
|
||||
<P>All of the lj/sdk pair styles write their information to <A HREF = "restart.html">binary
|
||||
restart files</A>, so pair_style and pair_coeff commands do
|
||||
not need to be specified in an input script that reads a restart file.
|
||||
</P>
|
||||
<P>The lj/sdk and lj/cut/coul/long pair styles do not support
|
||||
the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
|
||||
respa</A> command.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>All of the lj/sdk pair styles are part of the USER-CG-CMM package.
|
||||
The <I>lj/sdk/coul/long</I> style also requires the KSPACE package to be
|
||||
built (which is enabled by default). They are 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_coeff.html">pair_coeff</A>, <A HREF = "angle_sdk.html">angle_style sdk</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Shinoda"></A>
|
||||
|
||||
<P><B>(Shinoda)</B> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
|
||||
</P>
|
||||
<A NAME = "DeVane"></A>
|
||||
|
||||
<P><B>(DeVane)</B> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
|
||||
</P>
|
||||
</HTML>
|
||||
154
doc/pair_sdk.txt
Normal file
154
doc/pair_sdk.txt
Normal file
@ -0,0 +1,154 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style lj/sdk command :h3
|
||||
pair_style lj/sdk/gpu command :h3
|
||||
pair_style lj/sdk/omp command :h3
|
||||
pair_style lj/sdk/coul/long command :h3
|
||||
pair_style lj/sdk/coul/long/gpu command :h3
|
||||
pair_style lj/sdk/coul/long/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style args :pre
|
||||
|
||||
style = {lj/sdk} or {lj/sdk/coul/long}
|
||||
args = list of arguments for a particular style :ul
|
||||
{lj/sdk} args = cutoff
|
||||
cutoff = global cutoff for Lennard Jones interactions (distance units)
|
||||
{lj/sdk/coul/long} args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style lj/sdk 2.5
|
||||
pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre
|
||||
|
||||
pair_style lj/sdk/coul/long 10.0
|
||||
pair_style lj/sdk/coul/long 10.0 12.0
|
||||
pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
|
||||
given by
|
||||
|
||||
:c,image(Eqs/pair_cmm.jpg)
|
||||
|
||||
as required for the SDK Coarse-grained MD parametrization discussed in
|
||||
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
|
||||
|
||||
Style {lj/sdk/coul/long} computes the adds Coulombic interactions
|
||||
with an additional damping factor applied so it can be used in
|
||||
conjunction with the "kspace_style"_kspace_style.html command and
|
||||
its {ewald} or {pppm} or {pppm/cg} option. The Coulombic cutoff
|
||||
specified for this style means that pairwise interactions within
|
||||
this distance are computed directly; interactions outside that
|
||||
distance are computed in reciprocal space.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands, or by mixing as described below:
|
||||
|
||||
cg_type (lj9_6, lj12_4, or lj12_6)
|
||||
epsilon (energy units)
|
||||
sigma (distance units)
|
||||
cutoff1 (distance units) :ul
|
||||
|
||||
Note that sigma is defined in the LJ formula as the zero-crossing
|
||||
distance for the potential, not as the energy minimum. The prefactors
|
||||
are chosen so that the potential minimum is at -epsilon.
|
||||
|
||||
The latter 2 coefficients are optional. If not specified, the global
|
||||
LJ and Coulombic cutoffs specified in the pair_style command are used.
|
||||
If only one cutoff is specified, it is used as the cutoff for both LJ
|
||||
and Coulombic interactions for this type pair. If both coefficients
|
||||
are specified, they are used as the LJ and Coulombic cutoffs for this
|
||||
type pair.
|
||||
|
||||
For {lj/sdk/coul/long} only the LJ cutoff can be specified since a
|
||||
Coulombic cutoff cannot be specified for an individual I,J type pair.
|
||||
All type pairs use the same global Coulombic cutoff specified in the
|
||||
pair_style command.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {cuda}, {gpu}, {omp} or {opt} suffix are functionally
|
||||
the same as the corresponding style without the suffix. They have been
|
||||
optimized to run faster, depending on your available hardware, as
|
||||
discussed in "this section"_Section_accelerate.html of the manual.
|
||||
The accelerated styles take the same arguments and should produce the
|
||||
same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP, and
|
||||
OPT packages respectively. They are only enabled if LAMMPS was built with
|
||||
those packages. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "this section"_Section_accelerate.html of the manual for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, and rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of the lj/sdk pair styles {cannot} be mixed,
|
||||
since different pairs may have different exponents. So all parameters
|
||||
for all pairs have to be specified explicitly through the "pair_coeff"
|
||||
command. Defining then in a data file is also not supported, due to
|
||||
limitations of that file format.
|
||||
|
||||
All of the lj/sdk pair styles support the
|
||||
"pair_modify"_pair_modify.html shift option for the energy of the
|
||||
Lennard-Jones portion of the pair interaction.
|
||||
|
||||
The {lj/sdk/coul/long} pair styles support the
|
||||
"pair_modify"_pair_modify.html table option since they can tabulate
|
||||
the short-range portion of the long-range Coulombic interaction.
|
||||
|
||||
All of the lj/sdk pair styles write their information to "binary
|
||||
restart files"_restart.html, so pair_style and pair_coeff commands do
|
||||
not need to be specified in an input script that reads a restart file.
|
||||
|
||||
The lj/sdk and lj/cut/coul/long pair styles do not support
|
||||
the use of the {inner}, {middle}, and {outer} keywords of the "run_style
|
||||
respa"_run_style.html command.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
All of the lj/sdk pair styles are part of the USER-CG-CMM package.
|
||||
The {lj/sdk/coul/long} style also requires the KSPACE package to be
|
||||
built (which is enabled by default). They are 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_coeff"_pair_coeff.html, "angle_style sdk"_angle_sdk.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Shinoda)
|
||||
[(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
|
||||
|
||||
:link(DeVane)
|
||||
[(DeVane)] Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
|
||||
|
||||
Reference in New Issue
Block a user