From a3c3e6cb4b8370ece4beda44463aeb674f91d1f7 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 8 Jul 2015 14:41:23 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13544
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/mass.html | 7 ++++---
doc/mass.txt | 7 ++++---
doc/pair_bop.html | 29 +++++++++++++++++++++--------
doc/pair_bop.txt | 29 +++++++++++++++++++++--------
4 files changed, 50 insertions(+), 22 deletions(-)
diff --git a/doc/mass.html b/doc/mass.html
index afdc4c6cc9..1fa0e43775 100644
--- a/doc/mass.html
+++ b/doc/mass.html
@@ -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)
diff --git a/doc/mass.txt b/doc/mass.txt
index c024da20a9..4b75132ccf 100644
--- a/doc/mass.txt
+++ b/doc/mass.txt
@@ -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)
diff --git a/doc/pair_bop.html b/doc/pair_bop.html
index ec1ff3172b..a8ed6a2f4d 100644
--- a/doc/pair_bop.html
+++ b/doc/pair_bop.html
@@ -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).
diff --git a/doc/pair_bop.txt b/doc/pair_bop.txt
index 11dddb2d86..d1c7e77392 100644
--- a/doc/pair_bop.txt
+++ b/doc/pair_bop.txt
@@ -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).
--
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