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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1966 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-07-24 23:46:15 +00:00
parent 192008e7c7
commit 0afdb0b938
6 changed files with 66 additions and 47 deletions
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13
doc/mass.html
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@ -30,10 +30,15 @@ mass 2* 62.5
also be set in the <A HREF = "read_data.html">read_data</A> data file. See the
<A HREF = "units.html">units</A> command for what mass units to use.
</P>
<P>Most atom styles require masses to be specified. One exception is
<A HREF = "atom_style.html">atom_style granular</A>, where masses are defined for
individual atoms, not types. <A HREF = "pair_eam.html">Pair_style eam</A> defines
the masses of atom types in the EAM potential file.
<P>Most atom styles require per-type masses to be specified. One
exception is <A HREF = "atom_style.html">atom_style granular</A> or <A HREF = "atom_style.html">atom_style
peri</A>, where masses are defined for individual atoms,
not types. These are defined in the file read by the
<A HREF = "read_data.html">read_data</A> command, or set to default values by the
<A HREF = "create_atoms.html">create_atoms</A> command, or set to new values by the
<A HREF = "set.html">set density</A> command. Also note that <A HREF = "pair_eam.html">pair_style
eam</A> defines the masses of atom types in the EAM
potential file.
</P>
<P>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

13
doc/mass.txt
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@ -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

8
doc/read_data.html
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@ -279,10 +279,10 @@ of analysis.
<UL><LI>atom-ID = integer ID of atom
<LI>molecule-ID = integer ID of molecule the atom belongs to
<LI>type-ID = type of atom (1-Ntype)
<LI>q = charge on atom
<LI>diameter = diameter of atom
<LI>density = density of atom
<LI>volume = volume of atom
<LI>q = charge on atom (charge units)
<LI>diameter = diameter of atom (distance units)
<LI>density = density of atom (mass/distance^3 units)
<LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = direction of dipole moment of atom
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom

8
doc/read_data.txt
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@ -256,10 +256,10 @@ The keywords have these meanings:
atom-ID = integer ID of atom
molecule-ID = integer ID of molecule the atom belongs to
type-ID = type of atom (1-Ntype)
q = charge on atom
diameter = diameter of atom
density = density of atom
volume = volume of atom
q = charge on atom (charge units)
diameter = diameter of atom (distance units)
density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = direction of dipole moment of atom
quatw,quati,quatj,quatk = quaternion components for orientation of atom :ul

35
doc/set.html
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@ -21,7 +21,8 @@
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>rmass</I> or <I>vfrac</I>
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>diameter</I> or <I>density</I> or <I>volume</I> or
<I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
<PRE> <I>type</I> value = atom type
<I>type/fraction</I> values = type fraction seed
@ -41,12 +42,13 @@
theta = rotation angle in degrees
<I>quat/random</I> value = seed
seed = random # seed (positive integer) for quaternion orientations
<I>diameter</I> value = particle diameter (distance units)
<I>density</I> value = particle mass (mass/distance^3 units)
<I>volume</I> value = particle volume (distance^3 units)
<I>bond</I> value = bond type for all bonds between selected atoms
<I>angle</I> value = angle type for all angles between selected atoms
<I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
<I>improper</I> value = improper type for all impropers between selected atoms
<I>rmass</I> value = particle mass (mass units)
<I>vfrac</I> value = particle volume (volume units)
<I>improper</I> value = improper type for all impropers between selected atoms
</PRE>
</UL>
@ -141,6 +143,18 @@ xy plane are generated.
<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
being used must support the use of dipoles or quaternions.
</P>
<P>Keyword <I>diameter</I> sets the size of all selected particles.
</P>
<P>Keyword <I>density</I> sets the density of all selected particles, which
combined with its density determines their mass.
</P>
<P>Keyword <I>volume</I> sets the effective size of all selected particles.
</P>
<P>For the <I>diameter</I> and <I>density</I> and <I>volume</I> keywords, the <A HREF = "atom_style.html">atom
style</A> 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.
</P>
<P>Keywords <I>bond</I>, <I>angle</I>, <I>dihedral</I>, and <I>improper</I>, 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 <I>bond types</I> (<I>angle types</I>, etc) field in the
header of the data file read by the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P>Keyword <I>rmass</I> sets the mass of each atom, for simulations where each
atom stores its own mass. This is distinct from the <A HREF = "mass.html">mass</A>
command, which sets the mass by atom type. When used with <A HREF = "atom_style.html">atom style
peri</A>, this command sets the density of each particle,
not its mass.
</P>
<P>Keyword <I>vfrac</I> sets the volume for all selected particles. This is
only supported by <A HREF = "atom_style.html">atom style peri</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>You cannot set an atom attribute (e.g. <I>mol</I> or <I>q</I> or <I>vfrac</I>) if the
<A HREF = "atom_style.html">atom_style</A> does not have that attribute.
<P>You cannot set an atom attribute (e.g. <I>mol</I> or <I>q</I> or <I>volume</I>) if
the <A HREF = "atom_style.html">atom_style</A> does not have that attribute.
</P>
<P>This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc). This means that your system

36
doc/set.txt
View File

@ -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