+These are angle styles contributed by users, which can be used if +LAMMPS is built with the appropriate package. +
+| cg/cmm + |
Dihedral_style potentials. See the diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index b7b4f7fb87..468ef02a66 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -521,6 +521,9 @@ These are pair styles contributed by users, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#2_3. "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/coul"_pair_lj_coul.html :tb(c=4,ea=c) :line @@ -554,6 +557,11 @@ itself for a full description: "cosine/squared"_angle_cosine_squared.html, "harmonic"_angle_harmonic.html :tb(c=4,ea=c,w=100) +These are angle styles contributed by users, which can be used if +"LAMMPS is built with the appropriate package"_Section_start.html#2_3. + +"cg/cmm"_angle_cmm.html :tb(c=4,ea=c) + :line Dihedral_style potentials. See the diff --git a/doc/angle_cmm.html b/doc/angle_cmm.html new file mode 100644 index 0000000000..d994d98a6d --- /dev/null +++ b/doc/angle_cmm.html @@ -0,0 +1,65 @@ + +
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 new file mode 100644 index 0000000000..69eaa1dbe7 --- /dev/null +++ b/doc/angle_cmm.txt @@ -0,0 +1,60 @@ +"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#2_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 new file mode 100644 index 0000000000..239c495a26 --- /dev/null +++ b/doc/pair_cmm.html @@ -0,0 +1,176 @@ + +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). 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. +
+Mixing, shift, table, tail correction, per-atom energy/stress, +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 can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +
+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. They are only enabled if LAMMPS was built with that +package. The cg/cmm/coul/long style also requires the "kspace" +package to be built (which is enabled by default). See the Making +LAMMPS section for more info. +
+On some 64-bit machines, compiling with -O3 appears to break the +Coulombic tabling option used by the cg/cmm/coul/long style. See +the "Additional build tips" section of the Making LAMMPS documentation +pages for workarounds on this issue. +
+Related commands: +
+pair_coeff, angle_style cg/cmm +
+Default: none +
+(Shinoda) Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). +
+ diff --git a/doc/pair_cmm.txt b/doc/pair_cmm.txt new file mode 100644 index 0000000000..495e652707 --- /dev/null +++ b/doc/pair_cmm.txt @@ -0,0 +1,167 @@ +"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/coul/cut command :h3 +pair_style cg/cmm/coul/long 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. 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 + +[Mixing, shift, table, tail correction, per-atom energy/stress, +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 can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +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. They are only enabled if LAMMPS was built with that +package. The {cg/cmm/coul/long} style also requires the "kspace" +package to be built (which is enabled by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +On some 64-bit machines, compiling with -O3 appears to break the +Coulombic tabling option used by the {cg/cmm/coul/long} style. See +the "Additional build tips" section of the Making LAMMPS documentation +pages for workarounds on this issue. + +[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).