git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10154 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/pair_adp.html

@@ -68,6 +68,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of extended <I>setfl</I> elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways to
+specify the path for the potential file.
+</P>
 <P>As an example, the potentials/AlCu.adp file, included in the
 potentials directory of the LAMMPS distrbution, is an extended <I>setfl</I>
 file which has tabulated ADP values for w elements and their alloy

doc/pair_adp.txt

@@ -64,6 +64,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of extended {setfl} elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways to
+specify the path for the potential file.
+
 As an example, the potentials/AlCu.adp file, included in the
 potentials directory of the LAMMPS distrbution, is an extended {setfl}
 file which has tabulated ADP values for w elements and their alloy

doc/pair_airebo.html

@@ -104,6 +104,9 @@ pair_coeff command, where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of AIREBO elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, if your LAMMPS simulation has 4 atom types and you want
 the 1st 3 to be C, and the 4th to be H, you would use the following
 pair_coeff command:

doc/pair_airebo.txt

@@ -98,6 +98,9 @@ pair_coeff command, where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of AIREBO elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, if your LAMMPS simulation has 4 atom types and you want
 the 1st 3 to be C, and the 4th to be H, you would use the following
 pair_coeff command:

doc/pair_bop.html

@@ -136,6 +136,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of BOP elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine the CdTe.bop file has BOP values for Cd
 and Te.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Cd, and the 4th to be Te, you would use the following

doc/pair_bop.txt

@@ -130,6 +130,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of BOP elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine the CdTe.bop file has BOP values for Cd
 and Te.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Cd, and the 4th to be Te, you would use the following

doc/pair_comb.html

@@ -94,10 +94,11 @@ This can be used when a <I>comb</I> potential is used as part of the
 that will be used with other potentials.
 </P>
 <P>The <I>ffield.comb</I> potential file is in the <I>potentials</I> directory of
-the LAMMPS distribution.  Lines that are not blank or comments
-(starting with #) define parameters for a triplet of elements.  The 49
-parameters in a single entry correspond to coefficients in the formula
-above:
+the LAMMPS distribution.  See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page
+for alternate ways to specify the path for the potential file.  Lines
+that are not blank or comments (starting with #) define parameters for
+a triplet of elements.  The 49 parameters in a single entry correspond
+to coefficients in the formula above:
 </P>
 <UL><LI>element 1 (the center atom in a 3-body interaction)
 <LI>element 2 (the atom bonded to the center atom)

doc/pair_comb.txt

@@ -90,10 +90,11 @@ This can be used when a {comb} potential is used as part of the
 that will be used with other potentials.
 
 The {ffield.comb} potential file is in the {potentials} directory of
-the LAMMPS distribution.  Lines that are not blank or comments
-(starting with #) define parameters for a triplet of elements.  The 49
-parameters in a single entry correspond to coefficients in the formula
-above:
+the LAMMPS distribution.  See the "pair_coeff"_pair_coeff.html doc page
+for alternate ways to specify the path for the potential file.  Lines
+that are not blank or comments (starting with #) define parameters for
+a triplet of elements.  The 49 parameters in a single entry correspond
+to coefficients in the formula above:
 
 element 1 (the center atom in a 3-body interaction)
 element 2 (the atom bonded to the center atom)

doc/pair_eam.html

@@ -140,12 +140,14 @@ single argument:
 </PRE>
 <P>will read the cuu3 potential file and use the tabulated Cu values for
 F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
-1,2 and 2,1 are ignored).  In effect, this makes atom types 1 and 2 in
-LAMMPS be Cu atoms.  Different single-element files can be assigned to
-different atom types to model an alloy system.  The mixing to create
-alloy potentials for type pairs with I != J is done automatically the
-same way that the serial DYNAMO code originally did it; you do not
-need to specify coefficients for these type pairs.
+1,2 and 2,1 are ignored).  See the <A HREF = "pair_coeff.html">pair_coeff</A> doc
+page for alternate ways to specify the path for the potential file.
+In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms.
+Different single-element files can be assigned to different atom types
+to model an alloy system.  The mixing to create alloy potentials for
+type pairs with I != J is done automatically the same way that the
+serial DYNAMO code originally did it; you do not need to specify
+coefficients for these type pairs.
 </P>
 <P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS
 distribution have an ".eam" suffix.  A DYNAMO single-element <I>funcfl</I>
@@ -215,9 +217,11 @@ where N is the number of LAMMPS atom types:
 </UL>
 <P>As an example, the potentials/NiAlH_jea.eam.alloy file is a <I>setfl</I>
 file which has tabulated EAM values for 3 elements and their alloy
-interactions: Ni, Al, and H.  If your LAMMPS simulation has 4 atoms
-types and you want the 1st 3 to be Ni, and the 4th to be Al, you would
-use the following pair_coeff command:
+interactions: Ni, Al, and H.  See the <A HREF = "pair_coeff.html">pair_coeff</A> doc
+page for alternate ways to specify the path for the potential file.
+If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
+be Ni, and the 4th to be Al, you would use the following pair_coeff
+command:
 </P>
 <PRE>pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al 
 </PRE>
@@ -334,13 +338,14 @@ same as for style <I>eam/alloy</I>, e.g.
 <PRE>pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al 
 </PRE>
 <P>where there are N additional arguments after the filename, where N is
-the number of LAMMPS atom types.  The N values determine the mapping
-of LAMMPS atom types to EAM elements in the file, as described above
-for style <I>eam/alloy</I>.  As with <I>eam/alloy</I>, if a mapping value is
-NULL, the mapping is not performed.  This can be used when an <I>eam/fs</I>
-potential is used as part of the <I>hybrid</I> pair style.  The NULL values
-are used as placeholders for atom types that will be used with other
-potentials.
+the number of LAMMPS atom types.  See the <A HREF = "pair_coeff.html">pair_coeff</A>
+doc page for alternate ways to specify the path for the potential
+file.  The N values determine the mapping of LAMMPS atom types to EAM
+elements in the file, as described above for style <I>eam/alloy</I>.  As
+with <I>eam/alloy</I>, if a mapping value is NULL, the mapping is not
+performed.  This can be used when an <I>eam/fs</I> potential is used as
+part of the <I>hybrid</I> pair style.  The NULL values are used as
+placeholders for atom types that will be used with other potentials.
 </P>
 <P>FS EAM files include more information than the DYNAMO <I>setfl</I> format
 files read by <I>eam/alloy</I>, in that i,j density functionals for all

doc/pair_eam.txt

@@ -121,12 +121,14 @@ pair_coeff *2 1*2 cuu3.eam :pre
 
 will read the cuu3 potential file and use the tabulated Cu values for
 F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
-1,2 and 2,1 are ignored).  In effect, this makes atom types 1 and 2 in
-LAMMPS be Cu atoms.  Different single-element files can be assigned to
-different atom types to model an alloy system.  The mixing to create
-alloy potentials for type pairs with I != J is done automatically the
-same way that the serial DYNAMO code originally did it; you do not
-need to specify coefficients for these type pairs.
+1,2 and 2,1 are ignored).  See the "pair_coeff"_pair_coeff.html doc
+page for alternate ways to specify the path for the potential file.
+In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms.
+Different single-element files can be assigned to different atom types
+to model an alloy system.  The mixing to create alloy potentials for
+type pairs with I != J is done automatically the same way that the
+serial DYNAMO code originally did it; you do not need to specify
+coefficients for these type pairs.
 
 {Funcfl} files in the {potentials} directory of the LAMMPS
 distribution have an ".eam" suffix.  A DYNAMO single-element {funcfl}
@@ -196,9 +198,11 @@ N element names = mapping of {setfl} elements to atom types :ul
 
 As an example, the potentials/NiAlH_jea.eam.alloy file is a {setfl}
 file which has tabulated EAM values for 3 elements and their alloy
-interactions: Ni, Al, and H.  If your LAMMPS simulation has 4 atoms
-types and you want the 1st 3 to be Ni, and the 4th to be Al, you would
-use the following pair_coeff command:
+interactions: Ni, Al, and H.  See the "pair_coeff"_pair_coeff.html doc
+page for alternate ways to specify the path for the potential file.
+If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
+be Ni, and the 4th to be Al, you would use the following pair_coeff
+command:
 
 pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al :pre
 
@@ -315,13 +319,14 @@ same as for style {eam/alloy}, e.g.
 pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al :pre
 
 where there are N additional arguments after the filename, where N is
-the number of LAMMPS atom types.  The N values determine the mapping
-of LAMMPS atom types to EAM elements in the file, as described above
-for style {eam/alloy}.  As with {eam/alloy}, if a mapping value is
-NULL, the mapping is not performed.  This can be used when an {eam/fs}
-potential is used as part of the {hybrid} pair style.  The NULL values
-are used as placeholders for atom types that will be used with other
-potentials.
+the number of LAMMPS atom types.  See the "pair_coeff"_pair_coeff.html
+doc page for alternate ways to specify the path for the potential
+file.  The N values determine the mapping of LAMMPS atom types to EAM
+elements in the file, as described above for style {eam/alloy}.  As
+with {eam/alloy}, if a mapping value is NULL, the mapping is not
+performed.  This can be used when an {eam/fs} potential is used as
+part of the {hybrid} pair style.  The NULL values are used as
+placeholders for atom types that will be used with other potentials.
 
 FS EAM files include more information than the DYNAMO {setfl} format
 files read by {eam/alloy}, in that i,j density functionals for all
@@ -360,7 +365,6 @@ are listed.
 
 :line
 
-
 Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
 the same as the corresponding style without the suffix.  They have
 been optimized to run faster, depending on your available hardware, as

doc/pair_edip.html

@@ -48,6 +48,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of EDIP elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine a file Si.edip has EDIP values for Si.
 </P>
 <P>EDIP files in the <I>potentials</I> directory of the LAMMPS

doc/pair_edip.txt

@@ -44,6 +44,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of EDIP elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine a file Si.edip has EDIP values for Si.
 
 EDIP files in the {potentials} directory of the LAMMPS

doc/pair_lcbop.html

@@ -35,6 +35,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of LCBOP elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, if your LAMMPS simulation has 4 atom types and you want
 the 1st 3 to be C you would use the following pair_coeff command:
 </P>

doc/pair_lcbop.txt

@@ -32,6 +32,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of LCBOP elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, if your LAMMPS simulation has 4 atom types and you want
 the 1st 3 to be C you would use the following pair_coeff command:
 

doc/pair_meam.html

@@ -72,6 +72,9 @@ command, where N is the number of LAMMPS atom types:
 <LI>MEAM parameter file
 <LI>N element names = mapping of MEAM elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential files.
+</P>
 <P>As an example, the potentials/library.meam file has generic MEAM
 settings for a variety of elements.  The potentials/sic.meam file has
 specific parameter settings for a Si and C alloy system.  If your

doc/pair_meam.txt

@@ -69,6 +69,9 @@ Elem1, Elem2, ...
 MEAM parameter file
 N element names = mapping of MEAM elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential files.
+
 As an example, the potentials/library.meam file has generic MEAM
 settings for a variety of elements.  The potentials/sic.meam file has
 specific parameter settings for a Si and C alloy system.  If your

doc/pair_meam_spline.html

@@ -60,6 +60,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of spline-based MEAM elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine the Ti.meam.spline file has values for Ti.  If
 your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potentials, you would use the following pair_coeff

doc/pair_meam_spline.txt

@@ -56,6 +56,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of spline-based MEAM elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine the Ti.meam.spline file has values for Ti.  If
 your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potentials, you would use the following pair_coeff

doc/pair_meam_sw_spline.html

@@ -64,6 +64,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of spline-based MEAM+SW elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine the Ti.meam.sw.spline file has values for Ti.
 If your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potential, you would use the following pair_coeff

doc/pair_meam_sw_spline.txt

@@ -60,6 +60,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of spline-based MEAM+SW elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine the Ti.meam.sw.spline file has values for Ti.
 If your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potential, you would use the following pair_coeff

doc/pair_sw.html

@@ -45,6 +45,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of SW elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine a file SiC.sw has Stillinger-Weber values for
 Si and C.  If your LAMMPS simulation has 4 atoms types and you want
 the 1st 3 to be Si, and the 4th to be C, you would use the following

doc/pair_sw.txt

@@ -40,6 +40,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of SW elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine a file SiC.sw has Stillinger-Weber values for
 Si and C.  If your LAMMPS simulation has 4 atoms types and you want
 the 1st 3 to be Si, and the 4th to be C, you would use the following

doc/pair_tersoff.html

@@ -60,6 +60,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of Tersoff elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine the SiC.tersoff file has Tersoff values for Si
 and C.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Si, and the 4th to be C, you would use the following

doc/pair_tersoff.txt

@@ -53,6 +53,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of Tersoff elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine the SiC.tersoff file has Tersoff values for Si
 and C.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Si, and the 4th to be C, you would use the following

doc/pair_tersoff_zbl.html

@@ -61,6 +61,9 @@ where N is the number of LAMMPS atom types:
 <UL><LI>filename
 <LI>N element names = mapping of Tersoff/ZBL elements to atom types 
 </UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
 <P>As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
 for Si and C.  If your LAMMPS simulation has 4 atoms types and you
 want the 1st 3 to be Si, and the 4th to be C, you would use the

doc/pair_tersoff_zbl.txt

@@ -57,6 +57,9 @@ where N is the number of LAMMPS atom types:
 filename
 N element names = mapping of Tersoff/ZBL elements to atom types :ul
 
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
 As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
 for Si and C.  If your LAMMPS simulation has 4 atoms types and you
 want the 1st 3 to be Si, and the 4th to be C, you would use the