+Syntax: +
+angle_style sdk ++
angle_style sdk/omp ++
Examples: +
+angle_style sdk +angle_coeff 1 300.0 107.0 ++
Description: +
+The sdk 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 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. 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 command as in the example above: +
+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: +
+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 lj/sdk, +pair_style lj/sdk/coul/long +
+Default: none +
+ diff --git a/doc/angle_sdk.txt b/doc/angle_sdk.txt new file mode 100644 index 0000000000..3c70d42236 --- /dev/null +++ b/doc/angle_sdk.txt @@ -0,0 +1,58 @@ +"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 sdk command :h3 + +[Syntax:] + +angle_style sdk :pre +angle_style sdk/omp :pre + +[Examples:] + +angle_style sdk +angle_coeff 1 300.0 107.0 :pre + +[Description:] + +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 {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 +"angle_coeff"_angle_coeff.html command as in the example above: + +K (energy/radian^2) +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:] + +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 lj/sdk"_pair_sdk.html, +"pair_style lj/sdk/coul/long"_pair_sdk.html + +[Default:] none diff --git a/doc/pair_coul_diel.html b/doc/pair_coul_diel.html new file mode 100644 index 0000000000..405d3956d2 --- /dev/null +++ b/doc/pair_coul_diel.html @@ -0,0 +1,118 @@ + +Syntax: +
+pair_style coul/diel cutoff ++
cutoff = global cutoff (distance units) +
+Examples: +
+pair_style coul/diel 3.5 +pair_coeff 1 4 78. 1.375 0.112 ++
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 +
+
+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) +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) and of ionic surfactants (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) or (Jusufi). +
+The following coefficients must be defined for each pair of atom +types via the pair_coeff command as in the example +above, or in the data file or restart files read by the +read_data or read_restart +commands: +
+The global cutoff (r_c) specified in the pair_style command is used. +
+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 shift +option for the energy of the Gauss-potential portion of the pair +interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style does not support the pair_modify +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 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 for more info. +
+Related commands: +
+pair_coeff +pair_style gauss/cut +
+Default: none +
+(Stiles) Stiles , Hubbard, and Kayser, J Chem Phys, 77, +6189 (1982). +
+ + +(Lenart) Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, +044509 (2007). +
+ + +(Jusufi) Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, +13783 (2008). +
+ diff --git a/doc/pair_coul_diel.txt b/doc/pair_coul_diel.txt new file mode 100644 index 0000000000..e6ba96f64b --- /dev/null +++ b/doc/pair_coul_diel.txt @@ -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). diff --git a/doc/pair_sdk.html b/doc/pair_sdk.html new file mode 100644 index 0000000000..d382c03a9c --- /dev/null +++ b/doc/pair_sdk.html @@ -0,0 +1,166 @@ + +Syntax: +
+pair_style style args ++
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) ++
Examples: +
+pair_style lj/sdk 2.5 +pair_coeff 1 1 lj12_6 1 1.1 2.8 ++
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 ++
Description: +
+The lj/sdk styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, +given by +
+
+as required for the SDK Coarse-grained MD parametrization discussed in +(Shinoda) and (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 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 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 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. +
+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 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 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 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 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 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, 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 command. +
+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 for more info. +
+Related commands: +
+ +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_sdk.txt b/doc/pair_sdk.txt new file mode 100644 index 0000000000..476fd06fef --- /dev/null +++ b/doc/pair_sdk.txt @@ -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). +