From 1f81fcf5e450787a2bc1eb0c493c3d94c7a6c278 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 8 Dec 2011 23:17:38 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7322 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/angle_cmm.html | 65 --------------- doc/angle_cmm.txt | 60 -------------- doc/pair_cmm.html | 203 --------------------------------------------- doc/pair_cmm.txt | 188 ----------------------------------------- 4 files changed, 516 deletions(-) delete mode 100644 doc/angle_cmm.html delete mode 100644 doc/angle_cmm.txt delete mode 100644 doc/pair_cmm.html delete mode 100644 doc/pair_cmm.txt diff --git a/doc/angle_cmm.html b/doc/angle_cmm.html deleted file mode 100644 index bfd2507f64..0000000000 --- a/doc/angle_cmm.html +++ /dev/null @@ -1,65 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

angle_style cg/cmm command -

-

Syntax: -

-
angle_style cg/cmm 
-
-

Examples: -

-
angle_style cg/cmm
-angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130 
-
-

Description: -

-

The cg/cmm angle style is a combination of the harmonic angle potential, -

-
-
-

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 -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. Relative to the pair_style -cg/cmm, 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 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 command: -

- -

Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

-

Restrictions: -

-

This angle style can only be used if LAMMPS was built with the -USER-CG-CMM package. See the Making -LAMMPS section for more info on packages. -

-

Related commands: -

-

angle_coeff, angle_style -harmonic, pair_style cg/cmm -

-

Default: none -

- diff --git a/doc/angle_cmm.txt b/doc/angle_cmm.txt deleted file mode 100644 index bbc5033ad6..0000000000 --- a/doc/angle_cmm.txt +++ /dev/null @@ -1,60 +0,0 @@ -"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 - -angle_style cg/cmm command :h3 - -[Syntax:] - -angle_style cg/cmm :pre - -[Examples:] - -angle_style cg/cmm -angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130 :pre - -[Description:] - -The {cg/cmm} 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 -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 -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: - -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 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-CG-CMM package. See the "Making -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 - -[Default:] none diff --git a/doc/pair_cmm.html b/doc/pair_cmm.html deleted file mode 100644 index 766904a07e..0000000000 --- a/doc/pair_cmm.html +++ /dev/null @@ -1,203 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

pair_style cg/cmm command -

-

pair_style cg/cmm/cuda command -

-

pair_style cg/cmm/gpu command -

-

pair_style cg/cmm/coul/cut command -

-

pair_style cg/cmm/coul/cut/cuda command -

-

pair_style cg/cmm/coul/debye/cuda command -

-

pair_style cg/cmm/coul/long command -

-

pair_style cg/cmm/coul/long/gpu command -

-

pair_style cg/cmm/coul/long/cuda command -

-

Syntax: -

-
pair_style style args 
-
- -
  cg/cmm 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)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
-

Examples: -

-
pair_style cg/cmm 2.5
-pair_coeff 1 1 lj12_6 1 1.1 2.8 
-
-
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 
-
-
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 
-
-

Description: -

-

The cg/cmm styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, -given by -

-
-
-

as required for the CMM Coarse-grained MD parametrization discussed in -(Shinoda) and (DeVane). Rc is the cutoff. -

-

Style cg/cmm/coul/cut adds a Coulombic pairwise interaction given by -

-
-
-

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 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 -

-
-
-

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 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. -

-

The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

- -

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 cg/cmm/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. -

-
- -

Styles with a cuda, gpu, 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 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 -those packages. See the Making LAMMPS -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 when you invoke LAMMPS, or you can -use the suffix command in your input script. -

-

See this section of the manual for more -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, -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 -pair_modify shift option for the energy of the -Lennard-Jones portion of the pair interaction. -

-

The cg/cmm/coul/long pair styles support the -pair_modify 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 -restart files, 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 use of the inner, middle, and outer keywords of the run_style -respa command, meaning the pairwise forces can be -partitioned by distance at different levels of the rRESPA hierarchy. -See the run_style command for details. -

-
- -

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 -built (which is enabled by default). They are only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

-

Related commands: -

-

pair_coeff, angle_style cg/cmm -

-

Default: none -

-
- - - -

(Shinoda) Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). -

- - -

(DeVane) Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008). -

- diff --git a/doc/pair_cmm.txt b/doc/pair_cmm.txt deleted file mode 100644 index b330de4915..0000000000 --- a/doc/pair_cmm.txt +++ /dev/null @@ -1,188 +0,0 @@ -"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 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 - -[Syntax:] - -pair_style style args :pre - -style = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long} -args = list of arguments for a particular style :ul - {cg/cmm} 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) - 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_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 - -[Description:] - -The {cg/cmm} 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 -"(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. - -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) -cutoff2 (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 {cg/cmm/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 -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 -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 cg/cmm 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 -"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 -"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 -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 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. - -: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 -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 - -[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). -