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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13544 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-07-08 14:41:23 +00:00
parent 7b3f236f7f
commit a3c3e6cb4b
4 changed files with 50 additions and 22 deletions
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7
doc/mass.html
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@ -59,9 +59,10 @@ Per-atom masses are defined in the data file read by the
set to new values by the <A HREF = "set.html">set mass</A> or <A HREF = "set.html">set density</A>
commands.
</P>
<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> defines the masses of
atom types in the EAM potential file, in which case the mass command
is normally not used.
<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> and <A HREF = "pair_bop.html">pair_style
bop</A> commands define the masses of atom types in their
respective potential files, in which case the mass command is normally
not used.
</P>
<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
(or more) sub-styles which require per-type mass and one (or more)

7
doc/mass.txt
View File

@ -56,9 +56,10 @@ Per-atom masses are defined in the data file read by the
set to new values by the "set mass"_set.html or "set density"_set.html
commands.
Also note that "pair_style eam"_pair_eam.html defines the masses of
atom types in the EAM potential file, in which case the mass command
is normally not used.
Also note that "pair_style eam"_pair_eam.html and "pair_style
bop"_pair_bop.html commands define the masses of atom types in their
respective potential files, in which case the mass command is normally
not used.
If you define a "hybrid atom style"_atom_style.html which includes one
(or more) sub-styles which require per-type mass and one (or more)

29
doc/pair_bop.html
View File

@ -27,7 +27,7 @@
</P>
<PRE>pair_style bop
pair_coeff * * ../potentials/CdTe_bop Cd Te
pair_style bop 4.90 save
pair_style bop save
pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
comm_modify cutoff 14.70
</PRE>
@ -85,8 +85,18 @@ to either stabilize or destabilize close-packed structures. The pi
bond-order includes hopping paths of length 4. This enables the
incorporation of dihedral angles effects.
</P>
<P>One option can be specified as a keyword with the
pair_style command.
<P>IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for BOP
potentials are not set in the pair_style or pair_coeff command; they
are specified in the BOP potential files themselves. Likewise, the
BOP potential files list atomic masses; thus you do not need to use
the <A HREF = "mass.html">mass</A> command to specify them. Note that for BOP
potentials with hydrogen, you will likely want to set the mass of H
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
You can do this by using the <A HREF = "mass.html">mass</A> command after using the
<A HREF = "doc/pair_coeff.html">pair_coeff</A> command to read the BOP potential
file.
</P>
<P>One option can be specified as a keyword with the pair_style command.
</P>
<P>The <I>save</I> keyword gives you the option to calculate in advance and
store a set of distances, angles, and derivatives of angles. The
@ -296,11 +306,14 @@ the previous section but is interaction type dependent)
<P>The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
</P>
<LI>Line 1: g0, g1, g2... (These are coefficients for
the angular spline of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction.
The function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five terms
the second g0, g1, g2 (for e_1-e_1-e_2)
<LI>Line 1: g0, g1, g2... (These are coefficients for the angular spline
of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The
function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five
terms the second line will contain the remaining constants The
following lines will then contain the constants for the remainaing g0,
g1, g2... (for e_1-e_1-e_2) and the other three body
interactions
</UL>
<P>The rest of the table has the same structure as the previous section
(see above).

29
doc/pair_bop.txt
View File

@ -21,7 +21,7 @@ keyword = {save} :l
pair_style bop
pair_coeff * * ../potentials/CdTe_bop Cd Te
pair_style bop 4.90 save
pair_style bop save
pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
comm_modify cutoff 14.70 :pre
@ -79,8 +79,18 @@ to either stabilize or destabilize close-packed structures. The pi
bond-order includes hopping paths of length 4. This enables the
incorporation of dihedral angles effects.
One option can be specified as a keyword with the
pair_style command.
IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for BOP
potentials are not set in the pair_style or pair_coeff command; they
are specified in the BOP potential files themselves. Likewise, the
BOP potential files list atomic masses; thus you do not need to use
the "mass"_mass.html command to specify them. Note that for BOP
potentials with hydrogen, you will likely want to set the mass of H
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
You can do this by using the "mass"_mass.html command after using the
"pair_coeff"_doc/pair_coeff.html command to read the BOP potential
file.
One option can be specified as a keyword with the pair_style command.
The {save} keyword gives you the option to calculate in advance and
store a set of distances, angles, and derivatives of angles. The
@ -268,11 +278,14 @@ the previous section but is interaction type dependent) :l,ule
The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
Line 1: g0, g1, g2... (These are coefficients for
the angular spline of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction.
The function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five terms
the second g0, g1, g2 (for e_1-e_1-e_2) :l,ule
Line 1: g0, g1, g2... (These are coefficients for the angular spline
of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The
function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five
terms the second line will contain the remaining constants The
following lines will then contain the constants for the remainaing g0,
g1, g2... (for e_1-e_1-e_2) and the other three body
interactions :l,ule
The rest of the table has the same structure as the previous section
(see above).