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update documentation for renaming of cg/cmm to lj/sdk

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This commit is contained in:
Axel Kohlmeyer
2011-11-29 18:36:32 -05:00
parent 61622c72b3
commit 28ae26a28f
6 changed files with 84 additions and 110 deletions
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17
doc/Section_commands.txt
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@ -686,9 +686,8 @@ package"_Section_start.html#start_3.
"awpmd/cut"_pair_awpmd.html,
"buck/coul"_pair_buck_coul.html,
"cg/cmm"_pair_cmm.html,
"cg/cmm/coul/cut"_pair_cmm.html,
"cg/cmm/coul/long"_pair_cmm.html,
"lj/sdk"_pair_sdk.html,
"lj/sdk/coul/long"_pair_sdk.html,
"dipole/sf"_pair_dipole.html,
"eam/cd"_pair_eam.html,
"edip"_pair_edip.html,
@ -720,12 +719,10 @@ package"_Section_accelerate.html.
"buck/coul/omp"_pair_buck_coul.html,
"buck/cuda"_pair_buck.html,
"buck/omp"_pair_buck.html,
"cg/cmm/coul/cut/cuda"_pair_cmm.html,
"cg/cmm/coul/debye/cuda"_pair_cmm.html,
"cg/cmm/coul/long/cuda"_pair_cmm.html,
"cg/cmm/coul/long/gpu"_pair_cmm.html,
"cg/cmm/cuda"_pair_cmm.html,
"cg/cmm/gpu"_pair_cmm.html,
"lj/sdk/gpu"_pair_sdk.html,
"lj/sdk/omp"_pair_sdk.html,
"lj/sdk/coul/long/gpu"_pair_sdk.html,
"lj/sdk/coul/long/omp"_pair_sdk.html,
"colloid/omp"_pair_colloid.html,
"comb/omp"_pair_comb.html,
"coul/cut/omp"_pair_coul.html,
@ -890,7 +887,7 @@ These are angle styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cg/cmm"_angle_cmm.html,
"sdk"_angle_sdk.html,
"cosine/shift"_angle_cosine_shift.html,
"cosine/shift/exp"_angle_cosine_shift_exp.html :tb(c=4,ea=c)

37
doc/Section_packages.txt
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@ -89,7 +89,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
USER-MISC, single-file contributions, USER-MISC/README, -, -, -, -
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style cg/cmm"_pair_cmm.html, USER/cg-cmm, "cg"_cg, -
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "accelerate"_Section_accelerate.html#acc_4, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-EWALDN, Ewald for 1/R^n, Pieter in' t Veld (BASF), "kspace_style"_kspace_style.html, -, -, -
@ -199,28 +199,41 @@ have questions.
USER-CG-CMM package :h4
This package implements 4 commands which can be used in a LAMMPS input
This package implements 3 commands which can be used in a LAMMPS input
script:
pair_style cg/cmm
pair_style cg/cmm/coul/cut
pair_style cg/cmm/coul/long
angle_style cg/cmm :ul
pair_style lj/sdk
pair_style lj/sdk/coul/long
angle_style sdk :ul
These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids (to be published soon).
(SDK), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids.
See the doc pages for these commands for details.
There are example scripts for using this package in
examples/USER/cg-cmm.
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.
This is the second generation implementation reducing the
the clutter of the previous version. For many systems with
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.
For any other coulomb interactions this is now required.
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 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.

0
doc/angle_cmm.html → doc/angle_sdk.html
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32
doc/angle_cmm.txt → doc/angle_sdk.txt
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@ -6,45 +6,42 @@
:line
angle_style cg/cmm command :h3
angle_style sdk command :h3
[Syntax:]
angle_style cg/cmm :pre
angle_style sdk :pre
angle_style sdk/omp :pre
[Examples:]
angle_style cg/cmm
angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130 :pre
angle_style sdk
angle_coeff 1 300.0 107.0 :pre
[Description:]
The {cg/cmm} angle style is a combination of the harmonic angle potential,
The {sdk} angle style is a combination of the harmonic angle potential,
:c,image(Eqs/angle_harmonic.jpg)
where theta0 is the equilibrium value of the angle and K a prefactor,
with the {repulsive} part of the non-bonded {cg/cmm} pair style
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 cg/cmm"_pair_cmm.html. Relative to the pair_style
{cg/cmm}, however, the energy is shifted by {epsilon}, to avoid sudden
"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
"angle_coeff"_angle_coeff.html command as in the example above. As
with other CMM coarse grained parameters, they cannot be set in the
data file, but can be restored from restarts via the
"read_restart"_read_restart.html command:
"angle_coeff"_angle_coeff.html command as in the example above:
K (energy/radian^2)
theta0 (degrees)
cg_type (string, one of lj9_6, lj12_4, lj12_6)
epsilon (energy units)
sigma (distance units) :ul
theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
The also required {lj/sdk} parameters will be extracted automatically
from the pair_style.
[Restrictions:]
@ -55,6 +52,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html, "angle_style
harmonic"_angle_harmonic.html, "pair_style cg/cmm"_pair_cmm.html
harmonic"_angle_harmonic.html, "pair_style lj/sdk"_pair_sdk.html,
"pair_style lj/sdk/coul/long"_pair_sdk.html
[Default:] none

0
doc/pair_cmm.html → doc/pair_sdk.html
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108
doc/pair_cmm.txt → doc/pair_sdk.txt
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@ -6,82 +6,51 @@
:line
pair_style cg/cmm command :h3
pair_style cg/cmm/cuda command :h3
pair_style cg/cmm/gpu command :h3
pair_style cg/cmm/coul/cut command :h3
pair_style cg/cmm/coul/cut/cuda command :h3
pair_style cg/cmm/coul/debye/cuda command :h3
pair_style cg/cmm/coul/long command :h3
pair_style cg/cmm/coul/long/gpu command :h3
pair_style cg/cmm/coul/long/cuda command :h3
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 = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long}
style = {lj/sdk} or {lj/sdk/coul/long}
args = list of arguments for a particular style :ul
{cg/cmm} args = cutoff
{lj/sdk} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
{cg/cmm/coul/long} args = cutoff (cutoff2)
{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 cg/cmm 2.5
pair_style lj/sdk 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre
pair_style cg/cmm/coul/cut 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0
pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0 :pre
pair_style cg/cmm/coul/long 10.0
pair_style cg/cmm/coul/long 10.0 8.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0 :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 {cg/cmm} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
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 CMM Coarse-grained MD parametrization discussed in
as required for the SDK Coarse-grained MD parametrization discussed in
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the "dielectric"_dielectric.html command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
This style also contains an additional exp() damping factor
to the Coulombic term, given by
:c,image(Eqs/pair_debye.jpg)
where kappa is the Debye length (kappa=0.0 is the unscreened coulomb).
This potential is another way to mimic the screening effect of a polar
solvent.
Style {cg/cmm/coul/long} computes the same Coulombic interactions as
style {cg/cmm/coul/cut} except that an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
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.
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
@ -92,8 +61,7 @@ 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)
cutoff2 (distance units) :ul
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
@ -106,22 +74,22 @@ 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 {cg/cmm/coul/long} only the LJ cutoff can be specified since a
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}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
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, and OPT
packages respectively. They are only enabled if LAMMPS was built with
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.
@ -138,43 +106,41 @@ instructions on how to use the accelerated styles effectively.
[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 cg/cmm pair styles {cannot} be mixed,
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 cg/cmm pair styles support the
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 {cg/cmm/coul/long} pair styles support the
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 cg/cmm pair styles write their information to "binary
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 cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support
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, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
See the "run_style"_run_style.html command for details.
respa"_run_style.html command.
:line
[Restrictions:]
All of the cg/cmm pair styles are part of the USER-CG-CMM package.
The {cg/cmm/coul/long} style also requires the KSPACE package to be
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 cg/cmm"_angle_cmm.html
"pair_coeff"_pair_coeff.html, "angle_style sdk"_angle_sdk.html
[Default:] none