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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8978 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2012-10-19 15:39:31 +00:00
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3
doc/Section_accelerate.html
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@ -98,8 +98,7 @@ simply trying them out.
<LI>processor mapping via processors numa command
<LI>load-balancing: balance and fix balance
<LI>processor command for layout
<LI>OMP when lots of cores
<LI>proxy/OMP for PPPM
<LI>OMP when lots of cores
</UL>
<HR>

3
doc/Section_accelerate.txt
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@ -94,8 +94,7 @@ verlet/split
processor mapping via processors numa command
load-balancing: balance and fix balance
processor command for layout
OMP when lots of cores
proxy/OMP for PPPM :ul
OMP when lots of cores :ul
:line

21
doc/Section_commands.html
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@ -473,16 +473,15 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/proxy/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/pppm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/pppm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/proxy/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/proxy/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/pppm/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/proxy/omp</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/pppm/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/pppm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/pppm/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD></TR>
@ -636,7 +635,7 @@ package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/cuda</A></TD><TD ><A HREF = "kspace_style.html">pppm/gpu</A></TD><TD ><A HREF = "kspace_style.html">pppm/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/cg/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/tip4p/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/proxy</A></TD><TD ><A HREF = "kspace_style.html">pppm/tip4p/proxy</A>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/cg/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/tip4p/omp</A>
</TD></TR></TABLE></DIV>
</HTML>

8
doc/Section_commands.txt
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@ -805,7 +805,6 @@ package"_Section_accelerate.html.
"lj/charmm/coul/long/cuda"_pair_charmm.html,
"lj/charmm/coul/long/gpu"_pair_charmm.html,
"lj/charmm/coul/long/omp"_pair_charmm.html,
"lj/charmm/coul/long/proxy/omp"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/charmm/coul/pppm/omp"_pair_charmm.html,
"lj/class2/coul/cut/cuda"_pair_class2.html,
@ -814,7 +813,6 @@ package"_Section_accelerate.html.
"lj/class2/coul/long/gpu"_pair_class2.html,
"lj/class2/coul/pppm/omp"_pair_class2.html,
"lj/class2/coul/long/omp"_pair_class2.html,
"lj/class2/coul/long/proxy/omp"_pair_class2.html,
"lj/class2/cuda"_pair_class2.html,
"lj/class2/gpu"_pair_class2.html,
"lj/class2/omp"_pair_class2.html,
@ -829,7 +827,6 @@ package"_Section_accelerate.html.
"lj/cut/coul/long/cuda"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
"lj/cut/coul/long/omp"_pair_lj.html,
"lj/cut/coul/long/proxy/omp"_pair_lj.html,
"lj/cut/coul/long/opt"_pair_lj.html,
"lj/cut/coul/pppm/omp"_pair_lj.html,
"lj/cut/cuda"_pair_lj.html,
@ -839,7 +836,6 @@ package"_Section_accelerate.html.
"lj/cut/opt"_pair_lj.html,
"lj/cut/tip4p/long/omp"_pair_lj.html,
"lj/cut/tip4p/long/opt"_pair_lj.html,
"lj/cut/tip4p/long/proxy/omp"_pair_lj.html,
"lj/expand/cuda"_pair_lj_expand.html,
"lj/expand/gpu"_pair_lj_expand.html,
"lj/expand/omp"_pair_lj_expand.html,
@ -1063,6 +1059,4 @@ package"_Section_accelerate.html.
"pppm/gpu"_kspace_style.html,
"pppm/omp"_kspace_style.html,
"pppm/cg/omp"_kspace_style.html,
"pppm/tip4p/omp"_kspace_style.html,
"pppm/proxy"_kspace_style.html,
"pppm/tip4p/proxy"_kspace_style.html :tb(c=4,ea=c)
"pppm/tip4p/omp"_kspace_style.html :tb(c=4,ea=c)

19
doc/kspace_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>kspace_style style value
</PRE>
<UL><LI>style = <I>none</I> or <I>ewald</I> or <I>ewald/disp</I> or <I>ewald/omp</I> or <I>pppm</I> or <I>pppm/cg</I> or <I>pppm/disp</I> or <I>pppm/tip4p</I> or <I>pppm/disp/tip4p</I> or <I>pppm/gpu</I> or <I>pppm/omp</I> or <I>pppm/cg/omp</I> or <I>pppm/tip4p/omp</I> or <I>pppm/proxy</I> or <I>pppm/tip4p/proxy</I> or <I>msm</I>
<UL><LI>style = <I>none</I> or <I>ewald</I> or <I>ewald/disp</I> or <I>ewald/omp</I> or <I>pppm</I> or <I>pppm/cg</I> or <I>pppm/disp</I> or <I>pppm/tip4p</I> or <I>pppm/disp/tip4p</I> or <I>pppm/gpu</I> or <I>pppm/omp</I> or <I>pppm/cg/omp</I> or <I>pppm/tip4p/omp</I> or <I>msm</I>
<PRE> <I>none</I> value = none
<I>ewald</I> value = accuracy
@ -43,10 +43,6 @@
accuracy = desired relative error in forces
<I>pppm/tip4p/omp</I> value = accuracy
accuracy = desired relative error in forces
<I>pppm/proxy</I> value = accuracy
accuracy = desired relative error in forces
<I>pppm/tip4p/proxy</I> value = accuracy
accuracy = desired relative error in forces
<I>msm</I> value = accuracy
accuracy = desired relative error in forces
</PRE>
@ -82,8 +78,7 @@ matching keyword to the name of the KSpace style, as in this table:
<TR ALIGN="center"><TD >coul/long </TD><TD > ewald or pppm</TD></TR>
<TR ALIGN="center"><TD >coul/msm </TD><TD > msm</TD></TR>
<TR ALIGN="center"><TD >lj/long or buck/long </TD><TD > disp (for dispersion)</TD></TR>
<TR ALIGN="center"><TD >tip4p/long </TD><TD > tip4p</TD></TR>
<TR ALIGN="center"><TD >proxy </TD><TD > proxy
<TR ALIGN="center"><TD >tip4p/long </TD><TD > tip4p
</TD></TR></TABLE></DIV>
<HR>
@ -125,16 +120,6 @@ adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with <A HREF = "pair_style.html">pair styles</A> with a
<I>long/tip4p</I> in their style name.
</P>
<P>The <I>pppm/proxy</I> and <I>pppm/tip4p/proxy</I> styles are special variants
for calculations in hybrid OpenMP/MPI parallel mode. They are
functionally equivalent to <I>pppm</I> and <I>pppm/tip4p</I>, but the force
computation is executed as a single thread concurrently with a
multi-threaded non-bonded calculation for a pair style with <I>pppm/omp</I>
suffix. For calcuations across many multi-core nodes, this can have a
performance benefit over performing the real and reciprocal space part
separately, specifically when otherwise the time spent on the pair
style would slightly less than in <I>pppm</I> without threading.
</P>
<HR>
<P>The <I>pppm/disp</I> and <I>pppm/disp/tip4p</I> styles add a long-range

19
doc/kspace_style.txt
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@ -12,7 +12,7 @@ kspace_style command :h3
kspace_style style value :pre
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {pppm/proxy} or {pppm/tip4p/proxy} or {msm} :ulb,l
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} :ulb,l
{none} value = none
{ewald} value = accuracy
accuracy = desired relative error in forces
@ -39,10 +39,6 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
{pppm/tip4p/omp} value = accuracy
accuracy = desired relative error in forces
{pppm/proxy} value = accuracy
accuracy = desired relative error in forces
{pppm/tip4p/proxy} value = accuracy
accuracy = desired relative error in forces
{msm} value = accuracy
accuracy = desired relative error in forces :pre
:ule
@ -76,8 +72,7 @@ Pair style : KSpace style
coul/long : ewald or pppm
coul/msm : msm
lj/long or buck/long : disp (for dispersion)
tip4p/long : tip4p
proxy : proxy :tb(s=:,ea=c)
tip4p/long : tip4p :tb(s=:,ea=c)
:line
@ -118,16 +113,6 @@ adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with "pair styles"_pair_style.html with a
{long/tip4p} in their style name.
The {pppm/proxy} and {pppm/tip4p/proxy} styles are special variants
for calculations in hybrid OpenMP/MPI parallel mode. They are
functionally equivalent to {pppm} and {pppm/tip4p}, but the force
computation is executed as a single thread concurrently with a
multi-threaded non-bonded calculation for a pair style with {pppm/omp}
suffix. For calcuations across many multi-core nodes, this can have a
performance benefit over performing the real and reciprocal space part
separately, specifically when otherwise the time spent on the pair
style would slightly less than in {pppm} without threading.
:line
The {pppm/disp} and {pppm/disp/tip4p} styles add a long-range

22
doc/pair_charmm.html
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@ -31,8 +31,6 @@
</H3>
<H3>pair_style lj/charmm/coul/long/omp command
</H3>
<H3>pair_style lj/charmm/coul/long/proxy/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
@ -93,19 +91,13 @@ which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
</P>
<P>Styles <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/long/proxy/omp</I>
compute the same formulas as style <I>lj/charmm/coul/charmm</I> except that
an additional damping factor is applied to the Coulombic term, as in
the discussion for pair style <I>lj/cut/coul/long</I>. Only one Coulombic
cutoff is specified for <I>lj/charmm/coul/long</I>; if only 2 arguments are
used in the pair_style command, then the outer LJ cutoff is used as
the single Coulombic cutoff. Style <I>lj/charmm/coul/long/proxy/omp</I> is
a variant for use with K-space style <A HREF = "kspace_style.html"><I>pppm/proxy</I></A>
and OpenMP multi-threading and will perform the corresponding
reciprocal space calculation concurrently with the pair calculation in
a separate thread. For certain parallel setups, this may have a
performance benefit over performing k-space style and pair style
separately and one after the other.
<P>Styles <I>lj/charmm/coul/long</I> computes the same formulas as style
<I>lj/charmm/coul/charmm</I> except that an additional damping factor is
applied to the Coulombic term, as in the discussion for pair style
<I>lj/cut/coul/long</I>. Only one Coulombic cutoff is specified for
<I>lj/charmm/coul/long</I>; if only 2 arguments are used in the pair_style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples

21
doc/pair_charmm.txt
View File

@ -17,7 +17,6 @@ pair_style lj/charmm/coul/long/cuda command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/long/proxy/omp command :h3
[Syntax:]
@ -78,19 +77,13 @@ which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
Styles {lj/charmm/coul/long} and {lj/charmm/coul/long/proxy/omp}
compute the same formulas as style {lj/charmm/coul/charmm} except that
an additional damping factor is applied to the Coulombic term, as in
the discussion for pair style {lj/cut/coul/long}. Only one Coulombic
cutoff is specified for {lj/charmm/coul/long}; if only 2 arguments are
used in the pair_style command, then the outer LJ cutoff is used as
the single Coulombic cutoff. Style {lj/charmm/coul/long/proxy/omp} is
a variant for use with K-space style "{pppm/proxy}"_kspace_style.html
and OpenMP multi-threading and will perform the corresponding
reciprocal space calculation concurrently with the pair calculation in
a separate thread. For certain parallel setups, this may have a
performance benefit over performing k-space style and pair style
separately and one after the other.
Styles {lj/charmm/coul/long} computes the same formulas as style
{lj/charmm/coul/charmm} except that an additional damping factor is
applied to the Coulombic term, as in the discussion for pair style
{lj/cut/coul/long}. Only one Coulombic cutoff is specified for
{lj/charmm/coul/long}; if only 2 arguments are used in the pair_style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples

10
doc/pair_class2.html
View File

@ -31,8 +31,6 @@
</H3>
<H3>pair_style lj/class2/coul/long/omp command
</H3>
<H3>pair_style lj/class2/coul/long/proxy/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
@ -103,14 +101,6 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
</P>
<P>Style <I>lj/class2/coul/long/proxy/omp</I> is a variant for use with
K-space style <A HREF = "kspace_style.html"><I>pppm/proxy</I></A> and OpenMP
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
</P>
<HR>
<P>If the pair_coeff command is not used to define coefficients for a

9
doc/pair_class2.txt
View File

@ -17,7 +17,6 @@ pair_style lj/class2/coul/long command :h3
pair_style lj/class2/coul/long/cuda command :h3
pair_style lj/class2/coul/long/gpu command :h3
pair_style lj/class2/coul/long/omp command :h3
pair_style lj/class2/coul/long/proxy/omp command :h3
[Syntax:]
@ -88,14 +87,6 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
Style {lj/class2/coul/long/proxy/omp} is a variant for use with
K-space style "{pppm/proxy}"_kspace_style.html and OpenMP
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
:line
If the pair_coeff command is not used to define coefficients for a

14
doc/pair_lj.html
View File

@ -51,14 +51,10 @@
</H3>
<H3>pair_style lj/cut/coul/long/omp command
</H3>
<H3>pair_style lj/cut/coul/long/proxy/omp command
</H3>
<H3>pair_style lj/cut/tip4p/long command
</H3>
<H3>pair_style lj/cut/tip4p/long/omp command
</H3>
<H3>pair_style lj/cut/tip4p/long/proxy/omp command
</H3>
<H3>pair_style lj/cut/tip4p/long/opt command
</H3>
<P><B>Syntax:</B>
@ -227,16 +223,6 @@ can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
</P>
<P>Styles <I>lj/cut/coul/long/proxy/omp</I> and <I>lj/cut/tip4p/long/proxy/omp</I>
are variants of <I>lj/cut/coul/long/omp</I> and <I>lj/cut/tip4p/long/omp</I> for
use with k-space styles <A HREF = "kspace_style.html"><I>pppm/proxy</I></A> and
<A HREF = "kspace_style.html"><I>pppm/tip4p/proxy</I></A>, respectively and OpenMP
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally

12
doc/pair_lj.txt
View File

@ -27,10 +27,8 @@ pair_style lj/cut/coul/long/cuda command :h3
pair_style lj/cut/coul/long/gpu command :h3
pair_style lj/cut/coul/long/opt command :h3
pair_style lj/cut/coul/long/omp command :h3
pair_style lj/cut/coul/long/proxy/omp command :h3
pair_style lj/cut/tip4p/long command :h3
pair_style lj/cut/tip4p/long/omp command :h3
pair_style lj/cut/tip4p/long/proxy/omp command :h3
pair_style lj/cut/tip4p/long/opt command :h3
[Syntax:]
@ -198,16 +196,6 @@ can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
Styles {lj/cut/coul/long/proxy/omp} and {lj/cut/tip4p/long/proxy/omp}
are variants of {lj/cut/coul/long/omp} and {lj/cut/tip4p/long/omp} for
use with k-space styles "{pppm/proxy}"_kspace_style.html and
"{pppm/tip4p/proxy}"_kspace_style.html, respectively and OpenMP
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
:line
Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally