atom_style style args-
args = none for any style except hybrid hybrid args = list of one or more sub-styles @@ -57,7 +57,8 @@ velocities, atom IDs and types.
Typically, simulations require only a single (non-hybrid) atom style. If some atoms in the simulation do not have all the properties defined @@ -84,7 +85,8 @@ section. "molecular" package. The granular style is part of the "granular" package. The dpd style is part of the "dpd" package. The dipole style is part of the "dipole" package. The ellipsoid style is part -of the "ellipsoid" package. They are only enabled if LAMMPS was built +of the "ellipsoid" package. The peri style is part of the "peri" +package for Peridynamics. They are only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
diff --git a/doc/atom_style.txt b/doc/atom_style.txt index 0e66524405..54c79c12d0 100644 --- a/doc/atom_style.txt +++ b/doc/atom_style.txt @@ -13,7 +13,7 @@ atom_style command :h3 atom_style style args :pre style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \ - {dpd} or {ellipsoid} or {full} or {granular} or {molecular} or \ + {dpd} or {ellipsoid} or {full} or {granular} or {molecular} or {peri} \ {hybrid} :ul args = none for any style except {hybrid} {hybrid} args = list of one or more sub-styles :pre @@ -55,7 +55,8 @@ velocities, atom IDs and types. {ellipsoid} = quaternion for particle orientation, angular velocity/momentum {full} = molecular + charge - e.g. biomolecules, charged polymers {granular} = granular atoms with rotational properties -{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers :ul +{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers +{peri} = mass, volume - e.g. mesocopic Peridynamics :ul Typically, simulations require only a single (non-hybrid) atom style. If some atoms in the simulation do not have all the properties defined @@ -82,7 +83,8 @@ The {angle}, {bond}, {full}, and {molecular} styles are part of the "molecular" package. The {granular} style is part of the "granular" package. The {dpd} style is part of the "dpd" package. The {dipole} style is part of the "dipole" package. The {ellipsoid} style is part -of the "ellipsoid" package. They are only enabled if LAMMPS was built +of the "ellipsoid" package. The {peri} style is part of the "peri" +package for Peridynamics. They are only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html new file mode 100644 index 0000000000..7b119c6b5a --- /dev/null +++ b/doc/compute_damage_atom.html @@ -0,0 +1,55 @@ + +Syntax: +
+compute ID group-ID damage/atom ++
Examples: +
+compute 1 all damage/atom ++
Description: +
+Define a computation that calculates the per-atom damage for each atom +in a group. Please see the PDLAMMPS user +guide for a formal +definition of "damage" and more details about Peridynamics as it is +implemented in LAMMPS. +
+The value of the damage will be 0.0 for atoms not in the specified +compute group. +
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
+Restrictions: +
+The damage/peri style is part of the "peri" package. It is only +enabled if LAMMPS was built with that package. See the Making +LAMMPS section for more info. +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt new file mode 100644 index 0000000000..8021625f5a --- /dev/null +++ b/doc/compute_damage_atom.txt @@ -0,0 +1,50 @@ +"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 + +compute damage/peri command :h3 + +[Syntax:] + +compute ID group-ID damage/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +damage/atom = style name of this compute command :ul + +[Examples:] + +compute 1 all damage/atom :pre + +[Description:] + +Define a computation that calculates the per-atom damage for each atom +in a group. Please see the "PDLAMMPS user +guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal +definition of "damage" and more details about Peridynamics as it is +implemented in LAMMPS. + +The value of the damage will be 0.0 for atoms not in the specified +compute group. + +[Output info:] + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + +[Restrictions:] + +The {damage/peri} style is part of the "peri" 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:] + +"dump custom"_dump.html + +[Default:] none diff --git a/doc/compute_damage_peri.html b/doc/compute_damage_peri.html new file mode 100644 index 0000000000..c9a4f66775 --- /dev/null +++ b/doc/compute_damage_peri.html @@ -0,0 +1,56 @@ + +Syntax: +
+compute ID group-ID damage/peri ++
Examples: +
+compute 1 all damage/peri ++
Description: +
+Define a computation that calculates the per-atom damage +for each atom in a group. +Please see the +PDLAMMPS user guide for +more +details. +
+The value of the damage will be 0.0 for atoms not in the +specified compute group. +
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
+Restrictions: The damage/peri style is part of the "peridynamic" package. It +is only +enabled if LAMMPS was built with that package (which it is not by +default). See the Making LAMMPS section for +more info. +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index 1364171b34..61c4f7840f 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -129,6 +129,7 @@ the pair_style command, and coefficients specified by the associatedSyntax: +
+pair_style peri/pmb ++
Examples: +
+pair_style peri/pmb +pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 ++
Description: +
+The peri/pmb style implements the peridynamic bond-based prototype +microelastic brittle (PMB) model. Please see the +PDLAMMPS user guide for more +details. +
+The syntax for the pair_coeff command is: +
+pair_coeff type1 type2 c horizon s00 alpha ++
The following coefficients must be defined for each pair of atoms types via +the pair_coeff command as in the examples above. +
+Restrictions: +
+The peri/pmb style is part of the "peridynamic" package. It is only +enabled if LAMMPS was built with that package (which it is not by +default). See the Making LAMMPS section for +more info. +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/pair_peri_pmb.txt b/doc/pair_peri_pmb.txt new file mode 100644 index 0000000000..98b74ebeeb --- /dev/null +++ b/doc/pair_peri_pmb.txt @@ -0,0 +1,52 @@ +"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 peri/pmb command :h3 + +[Syntax:] + +pair_style peri/pmb :pre + +[Examples:] + +pair_style peri/pmb +pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre + +[Description:] + +The {peri/pmb} style implements the peridynamic bond-based prototype +microelastic brittle (PMB) model. Please see the +"PDLAMMPS"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf user guide for more +details. + +The syntax for the pair_coeff command is: + +pair_coeff type1 type2 c horizon s00 alpha :pre + +The following coefficients must be defined for each pair of atoms types via +the pair_coeff command as in the examples above. + +c (peridynamic PMB "spring constant") +horizon (peridynamic horizon) +s00 (used when calculating if bond should break) +alpha (used when calculating if bond should break) :ul + +:line + +[Restrictions:] + +The {peri/pmb} style is part of the "peridynamic" package. It is only +enabled if LAMMPS was built with that package (which it is not by +default). See the "Making LAMMPS"_Section_start.html#2_3 section for +more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none diff --git a/doc/pair_style.html b/doc/pair_style.html index 1364ac6cb3..1b676641da 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -131,6 +131,7 @@ the pair_style command, and coefficients specified by the associatedtype value = atom type type/fraction values = type fraction seed @@ -44,7 +44,9 @@ bond value = bond type for all bonds between selected atoms angle value = angle type for all angles between selected atoms dihedral value = dihedral type for all dihedrals between selected atoms - improper value = improper type for all impropers between selected atoms + improper value = improper type for all impropers between selected atoms + rmass value = particle mass (mass units) + vfrac value = particle volume (volume units)@@ -148,9 +150,18 @@ etc) was set by the bond types (angle types, etc) field in the header of the data file read by the read_data command. +
Keyword rmass sets the mass of each atom, for simulations where each +atom stores its own mass. This is distinct from the mass +command, which sets the mass by atom type. When used with atom style +peri, this command sets the density of each particle, +not its mass. +
+Keyword vfrac sets the volume for all selected particles. This is +only supported by atom style peri. +
Restrictions:
-You cannot set an atom attribute (e.g. mol or q) if the +
You cannot set an atom attribute (e.g. mol or q or vfrac) if the atom_style does not have that attribute.
This command requires inter-processor communication to coordinate the diff --git a/doc/set.txt b/doc/set.txt index ac6c7b71d8..7404e94153 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -18,7 +18,8 @@ one or more keyword/value pairs may be appended :l keyword = {type} or {type/fraction} or {mol} or \ {x} or {y} or {z} or {vx} or {vy} or {vz} or \ {charge} or {dipole} or {dipole/random} or {quat/random} or \ - {bond} or {angle} or {dihedral} or {improper} :l + {bond} or {angle} or {dihedral} or {improper} or \ + {rmass} or {vfrac} :l {type} value = atom type {type/fraction} values = type fraction seed type = new atom type @@ -40,7 +41,9 @@ keyword = {type} or {type/fraction} or {mol} or \ {bond} value = bond type for all bonds between selected atoms {angle} value = angle type for all angles between selected atoms {dihedral} value = dihedral type for all dihedrals between selected atoms - {improper} value = improper type for all impropers between selected atoms :pre + {improper} value = improper type for all impropers between selected atoms + {rmass} value = particle mass (mass units) + {vfrac} value = particle volume (volume units) :pre :ule [Examples:] @@ -143,9 +146,18 @@ etc) was set by the {bond types} ({angle types}, etc) field in the header of the data file read by the "read_data"_read_data.html command. +Keyword {rmass} sets the mass of each atom, for simulations where each +atom stores its own mass. This is distinct from the "mass"_mass.html +command, which sets the mass by atom type. When used with "atom style +peri"_atom_style.html, this command sets the density of each particle, +not its mass. + +Keyword {vfrac} sets the volume for all selected particles. This is +only supported by "atom style peri"_atom_style.html. + [Restrictions:] -You cannot set an atom attribute (e.g. {mol} or {q}) if the +You cannot set an atom attribute (e.g. {mol} or {q} or {vfrac}) if the "atom_style"_atom_style.html does not have that attribute. This command requires inter-processor communication to coordinate the diff --git a/doc/units.html b/doc/units.html index a80168afd1..c4e31e89fe 100644 --- a/doc/units.html +++ b/doc/units.html @@ -15,7 +15,7 @@
units style-
Examples:
@@ -86,11 +86,27 @@ results from a unitless LJ simulation into physical quantities.For style si, these are the units: +
+This command also sets the timestep size and neighbor skin distance to default values for each style. For style lj these are dt = 0.005 tau and skin = 0.3 sigma. For style real these are dt = 1.0 fmsec and skin = 2.0 Angstroms. For style metal these are dt = 0.001 psec -and skin = 2.0 Angstroms. +and skin = 2.0 Angstroms. For style si these are dt = 1.0e-8 sec and +skin = 0.001 meters.
Restrictions:
diff --git a/doc/units.txt b/doc/units.txt index 7119f52881..8ad56aba8a 100644 --- a/doc/units.txt +++ b/doc/units.txt @@ -12,7 +12,7 @@ units command :h3 units style :pre -style = {lj} or {real} or {metal} :ul +style = {lj} or {real} or {metal} or {si} :ul [Examples:] @@ -83,11 +83,27 @@ charge = multiple of electron charge (+1.0 is a proton) dipole = charge*Angstroms electric field = volts/Angstrom :ul +For style {si}, these are the units: + +mass = kilograms +distance = meters +time = seconds +energy = Joules +velocity = meters/second +force = Newtons +temperature = degrees K +pressure = Pascals +viscosity = Pascal*second +charge = Coulombs +dipole = Coulombs*meters +electric field = volts/meter :ul + This command also sets the timestep size and neighbor skin distance to default values for each style. For style {lj} these are dt = 0.005 tau and skin = 0.3 sigma. For style {real} these are dt = 1.0 fmsec and skin = 2.0 Angstroms. For style {metal} these are dt = 0.001 psec -and skin = 2.0 Angstroms. +and skin = 2.0 Angstroms. For style {si} these are dt = 1.0e-8 sec and +skin = 0.001 meters. [Restrictions:]