Commit 0afdb0b9 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1966 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 192008e7

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

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

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

doc/read_data.txt

+4 −4
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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

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) 

</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

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