diff --git a/doc/mass.html b/doc/mass.html index 24dca99fac..b787a9aed7 100644 --- a/doc/mass.html +++ b/doc/mass.html @@ -30,10 +30,15 @@ mass 2* 62.5 also be set in the read_data data file. See the units command for what mass units to use.

-

Most atom styles require masses to be specified. One exception is -atom_style granular, where masses are defined for -individual atoms, not types. Pair_style eam defines -the masses of atom types in the EAM potential file. +

Most atom styles require per-type masses to be specified. One +exception is atom_style granular or atom_style +peri, where masses are defined for individual atoms, +not types. These are defined in the file read by the +read_data command, or set to default values by the +create_atoms command, or set to new values by the +set density command. Also note that pair_style +eam defines the masses of atom types in the EAM +potential file.

I can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be diff --git a/doc/mass.txt b/doc/mass.txt index 468aa742be..2dc7495615 100644 --- a/doc/mass.txt +++ b/doc/mass.txt @@ -27,10 +27,15 @@ Set the mass for all atoms of one or more atom types. Mass values can also be set in the "read_data"_read_data.html data file. See the "units"_units.html command for what mass units to use. -Most atom styles require masses to be specified. One exception is -"atom_style granular"_atom_style.html, where masses are defined for -individual atoms, not types. "Pair_style eam"_pair_eam.html defines -the masses of atom types in the EAM potential file. +Most atom styles require per-type masses to be specified. One +exception is "atom_style granular"_atom_style.html or "atom_style +peri"_atom_style.html, where masses are defined for individual atoms, +not types. These are defined in the file read by the +"read_data"_read_data.html command, or set to default values by the +"create_atoms"_create_atoms.html command, or set to new values by the +"set density"_set.html command. Also note that "pair_style +eam"_pair_eam.html defines the masses of atom types in the EAM +potential file. I can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be diff --git a/doc/read_data.html b/doc/read_data.html index fc013a5204..d3b7f50cbb 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -279,10 +279,10 @@ of analysis.

@@ -141,6 +143,18 @@ xy plane are generated.

For the dipole and quat keywords, the atom style being used must support the use of dipoles or quaternions.

+

Keyword diameter sets the size of all selected particles. +

+

Keyword density sets the density of all selected particles, which +combined with its density determines their mass. +

+

Keyword volume sets the effective size of all selected particles. +

+

For the diameter and density and volume keywords, the atom +style being used must support the use of those +parameters. For example, granular particles store a diameter and +density. Peridynamic particles store a volume and density. +

Keywords bond, angle, dihedral, and improper, set the bond type (angle type, etc) of all bonds (angles, etc) of selected atoms to the specified value from 1 to nbondtypes (nangletypes, etc). All @@ -150,19 +164,10 @@ 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 or vfrac) if the -atom_style does not have that attribute. +

You cannot set an atom attribute (e.g. mol or q or volume) if +the atom_style does not have that attribute.

This command requires inter-processor communication to coordinate the setting of bond types (angle types, etc). This means that your system diff --git a/doc/set.txt b/doc/set.txt index 7404e94153..82edc5c17d 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -18,8 +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} or \ - {rmass} or {vfrac} :l + {diameter} or {density} or {volume} or + {bond} or {angle} or {dihedral} or {improper} :l {type} value = atom type {type/fraction} values = type fraction seed type = new atom type @@ -38,12 +38,13 @@ keyword = {type} or {type/fraction} or {mol} or \ theta = rotation angle in degrees {quat/random} value = seed seed = random # seed (positive integer) for quaternion orientations + {diameter} value = particle diameter (distance units) + {density} value = particle mass (mass/distance^3 units) + {volume} value = particle volume (distance^3 units) {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 - {rmass} value = particle mass (mass units) - {vfrac} value = particle volume (volume units) :pre + {improper} value = improper type for all impropers between selected atoms :pre :ule [Examples:] @@ -137,6 +138,18 @@ xy plane are generated. For the {dipole} and {quat} keywords, the "atom style"_atom_style.html being used must support the use of dipoles or quaternions. +Keyword {diameter} sets the size of all selected particles. + +Keyword {density} sets the density of all selected particles, which +combined with its density determines their mass. + +Keyword {volume} sets the effective size of all selected particles. + +For the {diameter} and {density} and {volume} keywords, the "atom +style"_atom_style.html being used must support the use of those +parameters. For example, granular particles store a diameter and +density. Peridynamic particles store a volume and density. + Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond type (angle type, etc) of all bonds (angles, etc) of selected atoms to the specified value from 1 to nbondtypes (nangletypes, etc). All @@ -146,19 +159,10 @@ 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} or {vfrac}) if the -"atom_style"_atom_style.html does not have that attribute. +You cannot set an atom attribute (e.g. {mol} or {q} or {volume}) if +the "atom_style"_atom_style.html does not have that attribute. This command requires inter-processor communication to coordinate the setting of bond types (angle types, etc). This means that your system