forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7257 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
70a85bddfd
commit
750c4b07bb
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@ -211,28 +211,38 @@ have questions.
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<H4>USER-CG-CMM package
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</H4>
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<P>This package implements 4 commands which can be used in a LAMMPS input
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<P>This package implements 3 commands which can be used in a LAMMPS input
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script:
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</P>
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<UL><LI>pair_style cg/cmm
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<LI>pair_style cg/cmm/coul/cut
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<LI>pair_style cg/cmm/coul/long
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<LI>angle_style cg/cmm
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<UL><LI>pair_style lj/sdk
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<LI>pair_style lj/sdk/coul/long
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<LI>angle_style sdk
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</UL>
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<P>These styles allow coarse grained MD simulations with the
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parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
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(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
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lipids and charged amino acids (to be published soon).
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(SDK), with extensions to simulate ionic liquids, electrolytes,
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lipids and charged amino acids.
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</P>
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<P>See the doc pages for these commands for details.
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</P>
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<P>There are example scripts for using this package in
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examples/USER/cg-cmm.
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</P>
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<P>This is the second generation implementation reducing the the clutter
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of the previous version. For many systems with long range
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electrostatics, it will be faster to use pair_style hybrid/overlay
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with lj/sdk and coul/long instead of the combined lj/sdk/coul/long
|
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style, since the number of charged atom types is usually small. To
|
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exploit this property, the use of the kspace_style pppm/cg is
|
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recommended over regular pppm. For all new styles, input file backward
|
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compatibility is provided. The old implementation is still available
|
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through appending the /old suffix. These will be discontinued and
|
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removed after the new implementation has been fully validated.
|
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</P>
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<P>The current version of this package should be considered beta
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quality. The CG potentials work correctly and well, but there will be
|
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optimizations, cleanups and additional tools to aid in setting up and
|
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analyzing simulations with this package added in the next months.
|
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quality. The CG potentials work correctly for "normal" situations, but
|
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have not been testing with all kinds of potential parameters and
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simuation systems.
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</P>
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<P>The person who created this package is Axel Kohlmeyer at Temple U
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(akohlmey at gmail.com). Contact him directly if you have questions.
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|
|
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@ -199,28 +199,38 @@ have questions.
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USER-CG-CMM package :h4
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This package implements 4 commands which can be used in a LAMMPS input
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This package implements 3 commands which can be used in a LAMMPS input
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script:
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|
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pair_style cg/cmm
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pair_style cg/cmm/coul/cut
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pair_style cg/cmm/coul/long
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angle_style cg/cmm :ul
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pair_style lj/sdk
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pair_style lj/sdk/coul/long
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angle_style sdk :ul
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|
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These styles allow coarse grained MD simulations with the
|
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parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
|
||||
(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
|
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lipids and charged amino acids (to be published soon).
|
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(SDK), with extensions to simulate ionic liquids, electrolytes,
|
||||
lipids and charged amino acids.
|
||||
|
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See the doc pages for these commands for details.
|
||||
|
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There are example scripts for using this package in
|
||||
examples/USER/cg-cmm.
|
||||
|
||||
This is the second generation implementation reducing the the clutter
|
||||
of the previous version. For many systems with long range
|
||||
electrostatics, it will be faster to use pair_style hybrid/overlay
|
||||
with lj/sdk and coul/long instead of the combined lj/sdk/coul/long
|
||||
style, since the number of charged atom types is usually small. To
|
||||
exploit this property, the use of the kspace_style pppm/cg is
|
||||
recommended over regular pppm. For all new styles, input file backward
|
||||
compatibility is provided. The old implementation is still available
|
||||
through appending the /old suffix. These will be discontinued and
|
||||
removed after the new implementation has been fully validated.
|
||||
|
||||
The current version of this package should be considered beta
|
||||
quality. The CG potentials work correctly and well, but there will be
|
||||
optimizations, cleanups and additional tools to aid in setting up and
|
||||
analyzing simulations with this package added in the next months.
|
||||
quality. The CG potentials work correctly for "normal" situations, but
|
||||
have not been testing with all kinds of potential parameters and
|
||||
simuation systems.
|
||||
|
||||
The person who created this package is Axel Kohlmeyer at Temple U
|
||||
(akohlmey at gmail.com). Contact him directly if you have questions.
|
||||
|
|
|
|||
|
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@ -13,9 +13,14 @@
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</H3>
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<H3>pair_style gauss/omp command
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</H3>
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<H3>pair_style gauss/cut command
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</H3>
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<H3>pair_style gauss/cut/omp 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 gauss cutoff
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pair_style gauss/cut cutoff
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</PRE>
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<UL><LI>cutoff = global cutoff for Gauss interactions (distance units)
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</UL>
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@ -25,6 +30,9 @@
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pair_coeff * * 1.0 0.9
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pair_coeff 1 4 1.0 0.9 10.0
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</PRE>
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<PRE>pair_style gauss/cut 3.5
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pair_coeff 1 4 0.2805 1.45 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>gauss</I> computes a tethering potential of the form
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@ -47,12 +55,38 @@ commands:
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<P>The last coefficient is optional. If not specified, the global cutoff
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is used.
|
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</P>
|
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<P>Style <I>gauss/cut</I> computes a generalized Gaussian interaction potential
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between pairs of particles:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_gauss_cut.jpg">
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</CENTER>
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<P>where H determines together with the standard deviation sigma_h the
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peak height of the Gaussian function, and r_mh the peak position.
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Examples of the use of the Gaussian potentials include implicit
|
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solvent simulations of salt ions <A HREF = "#Lenart">(Lenart)</A> and of surfactants
|
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<A HREF = "#Jusufi">(Jusufi)</A>. In these instances the Gaussian potential mimics
|
||||
the hydration barrier between a pair of particles. The hydration
|
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barrier is located at r_mh and has a width of sigma_h. The prefactor
|
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determines the hight of the potential barrier.
|
||||
</P>
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<P>The following coefficients must be defined for each pair of atom types
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via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example above,
|
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or in the data file or restart files read by the
|
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands:
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</P>
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<UL><LI>H (energy * distance units)
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<LI>r_mh (distance units)
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<LI>sigma_h (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>
|
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<HR>
|
||||
|
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<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.
|
||||
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>
|
||||
|
|
@ -73,13 +107,17 @@ instructions on how to use the accelerated styles effectively.
|
|||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>This pair style does not support mixing. Thus, coefficients for all
|
||||
<P>These pair style do not support mixing. Thus, coefficients for all
|
||||
I,J pairs must be specified explicitly.
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
<P>The <I>gauss</I> style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
shift option. There is no effect due to the Gaussian well beyond the
|
||||
cutoff; hence reasonable cutoffs need to be specified.
|
||||
</P>
|
||||
<P>The <I>gauss/cut</I> 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 and tail options are not
|
||||
relevant for this pair style.
|
||||
</P>
|
||||
|
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@ -95,7 +133,7 @@ to be specified in an input script that reads a restart file.
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<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 an "occupancy" count of how many Gaussian-well
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<P>Thes <I>gauss</I> pair style tallies an "occupancy" count of how many Gaussian-well
|
||||
sites have an atom within the distance at which the force is a maximum
|
||||
= sqrt(0.5/b). This quantity can be accessed via the <A HREF = "compute_pair.html">compute
|
||||
pair</A> command as a vector of values of length 1.
|
||||
|
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@ -109,11 +147,16 @@ thermo_style custom step temp epair v_occ
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</PRE>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B> none
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>gauss/cut</I> style is part of the "user-misc" package. It is only enabled
|
||||
if LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of 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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<P><A HREF = "pair_coeff.html">pair_coeff</A>,
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<A HREF = "pair_coul_diel.html">pair_style coul/diel</A>
|
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</P>
|
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<P><B>Default:</B> none
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</P>
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|
|
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|
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@ -8,10 +8,13 @@
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|||
|
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pair_style gauss command :h3
|
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pair_style gauss/omp command :h3
|
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pair_style gauss/cut command :h3
|
||||
pair_style gauss/cut/omp command :h3
|
||||
|
||||
[Syntax:]
|
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|
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pair_style gauss cutoff :pre
|
||||
pair_style gauss cutoff
|
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pair_style gauss/cut cutoff :pre
|
||||
|
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cutoff = global cutoff for Gauss interactions (distance units) :ul
|
||||
|
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|
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@ -21,6 +24,10 @@ pair_style gauss 12.0
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|||
pair_coeff * * 1.0 0.9
|
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pair_coeff 1 4 1.0 0.9 10.0 :pre
|
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|
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pair_style gauss/cut 3.5
|
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pair_coeff 1 4 0.2805 1.45 0.112 :pre
|
||||
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {gauss} computes a tethering potential of the form
|
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|
|
@ -43,12 +50,38 @@ cutoff (distance units) :ul
|
|||
The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.
|
||||
|
||||
Style {gauss/cut} computes a generalized Gaussian interaction potential
|
||||
between pairs of particles:
|
||||
|
||||
:c,image(Eqs/pair_gauss_cut.jpg)
|
||||
|
||||
where H determines together with the standard deviation sigma_h the
|
||||
peak height of the Gaussian function, and r_mh the peak position.
|
||||
Examples of the use of the Gaussian potentials include implicit
|
||||
solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
|
||||
"(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics
|
||||
the hydration barrier between a pair of particles. The hydration
|
||||
barrier is located at r_mh and has a width of sigma_h. The prefactor
|
||||
determines the hight of the potential barrier.
|
||||
|
||||
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:
|
||||
|
||||
H (energy * distance units)
|
||||
r_mh (distance units)
|
||||
sigma_h (distance units) :ul
|
||||
|
||||
The global cutoff (r_c) specified in the pair_style command is used.
|
||||
|
||||
: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.
|
||||
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.
|
||||
|
||||
|
|
@ -69,13 +102,17 @@ instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support mixing. Thus, coefficients for all
|
||||
These pair style do not support mixing. Thus, coefficients for all
|
||||
I,J pairs must be specified explicitly.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
The {gauss} style does not support the "pair_modify"_pair_modify.html
|
||||
shift option. There is no effect due to the Gaussian well beyond the
|
||||
cutoff; hence reasonable cutoffs need to be specified.
|
||||
|
||||
The {gauss/cut} 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 and tail options are not
|
||||
relevant for this pair style.
|
||||
|
||||
|
|
@ -91,7 +128,7 @@ 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 an "occupancy" count of how many Gaussian-well
|
||||
Thes {gauss} pair style tallies an "occupancy" count of how many Gaussian-well
|
||||
sites have an atom within the distance at which the force is a maximum
|
||||
= sqrt(0.5/b). This quantity can be accessed via the "compute
|
||||
pair"_compute_pair.html command as a vector of values of length 1.
|
||||
|
|
@ -105,10 +142,15 @@ thermo_style custom step temp epair v_occ :pre
|
|||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
The {gauss/cut} style is part of the "user-misc" package. It is only enabled
|
||||
if LAMMPS is build with that package. See the "Making of LAMMPS"_Section_start.html#3
|
||||
section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_style coul/diel"_pair_coul_diel.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -11,20 +11,29 @@
|
|||
|
||||
<H3>pair_style tersoff command
|
||||
</H3>
|
||||
<H3>pair_style tersoff/table command
|
||||
</H3>
|
||||
<H3>pair_style tersoff/cuda
|
||||
</H3>
|
||||
<H3>pair_style tersoff/omp
|
||||
</H3>
|
||||
<H3>pair_style tersoff/table/omp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style tersoff
|
||||
</PRE>
|
||||
<PRE>pair_style tersoff/cuda
|
||||
</PRE>
|
||||
<PRE>pair_style tersoff/omp
|
||||
<PRE>pair_style style
|
||||
</PRE>
|
||||
<P>style = <I>tersoff</I> or <I>tersoff/table</I> or <I>tersoff/cuda</I> or <I>tersoff/omp</I> or <I>tersoff/table/omp</I>
|
||||
</P>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si
|
||||
pair_coeff * * SiC.tersoff Si C Si
|
||||
</PRE>
|
||||
<PRE>pair_style tersoff/table
|
||||
pair_coeff * * SiCGe.tersoff Si(D)
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>The <I>tersoff</I> style computes a 3-body Tersoff potential
|
||||
|
|
@ -36,6 +45,12 @@ pair_coeff * * SiC.tersoff Si C Si
|
|||
The summations in the formula are over all neighbors J and K of atom I
|
||||
within a cutoff distance = R + D.
|
||||
</P>
|
||||
<P>The <I>tersoff/table</I> style uses tabulated forms for the two-body,
|
||||
environment and angular functions. Linear interpolation is performed
|
||||
between adjacent table entries. The table length is chosen to be
|
||||
accurate within 10^-6 with respect to the <I>tersoff</I> style energy.
|
||||
The <I>tersoff/table</I> should give better performance in terms of speed.
|
||||
</P>
|
||||
<P>Only a single pair_coeff command is used with the <I>tersoff</I> style
|
||||
which specifies a Tersoff potential file with parameters for all
|
||||
needed elements. These are mapped to LAMMPS atom types by specifying
|
||||
|
|
@ -132,7 +147,8 @@ it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1 and m
|
|||
Note that in the current Tersoff implementation in LAMMPS, m must be
|
||||
specified as either 3 or 1. Tersoff used a slightly different but
|
||||
equivalent form for alloys, which we will refer to as Tersoff_2
|
||||
potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
|
||||
potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>. The <I>tersoff/table</I> style implements
|
||||
Teroff_2 parameterization only.
|
||||
</P>
|
||||
<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
|
||||
gamma_ijk = omega_ik, lambda3 = 0 and the value of
|
||||
|
|
|
|||
|
|
@ -7,12 +7,16 @@
|
|||
:line
|
||||
|
||||
pair_style tersoff command :h3
|
||||
pair_style tersoff/table command :h3
|
||||
pair_style tersoff/cuda :h3
|
||||
pair_style tersoff/omp :h3
|
||||
pair_style tersoff/table/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style tersoff :pre
|
||||
pair_style tersoff/cuda :pre
|
||||
pair_style tersoff/omp :pre
|
||||
pair_style style :pre
|
||||
|
||||
style = {tersoff} or {tersoff/table} or {tersoff/cuda} or {tersoff/omp} or {tersoff/table/omp}
|
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[Examples:]
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||||
|
|
@ -20,6 +24,9 @@ pair_style tersoff
|
|||
pair_coeff * * Si.tersoff Si
|
||||
pair_coeff * * SiC.tersoff Si C Si :pre
|
||||
|
||||
pair_style tersoff/table
|
||||
pair_coeff * * SiCGe.tersoff Si(D) :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {tersoff} style computes a 3-body Tersoff potential
|
||||
|
|
@ -31,6 +38,12 @@ where f_R is a two-body term and f_A includes three-body interactions.
|
|||
The summations in the formula are over all neighbors J and K of atom I
|
||||
within a cutoff distance = R + D.
|
||||
|
||||
The {tersoff/table} style uses tabulated forms for the two-body,
|
||||
environment and angular functions. Linear interpolation is performed
|
||||
between adjacent table entries. The table length is chosen to be
|
||||
accurate within 10^-6 with respect to the {tersoff} style energy.
|
||||
The {tersoff/table} should give better performance in terms of speed.
|
||||
|
||||
Only a single pair_coeff command is used with the {tersoff} style
|
||||
which specifies a Tersoff potential file with parameters for all
|
||||
needed elements. These are mapped to LAMMPS atom types by specifying
|
||||
|
|
@ -127,7 +140,8 @@ it reduces to the form of "Albe et al."_#Albe when beta = 1 and m = 1.
|
|||
Note that in the current Tersoff implementation in LAMMPS, m must be
|
||||
specified as either 3 or 1. Tersoff used a slightly different but
|
||||
equivalent form for alloys, which we will refer to as Tersoff_2
|
||||
potential "(Tersoff_2)"_#Tersoff_2.
|
||||
potential "(Tersoff_2)"_#Tersoff_2. The {tersoff/table} style implements
|
||||
Teroff_2 parameterization only.
|
||||
|
||||
LAMMPS parameter values for Tersoff_2 can be obtained as follows:
|
||||
gamma_ijk = omega_ik, lambda3 = 0 and the value of
|
||||
|
|
|
|||
Loading…
Reference in New Issue