git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12343 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_accelerate.html

@@ -176,8 +176,8 @@ discussed below.
 package. These styles support vectorized single and mixed precision
 calculations, in addition to full double precision.  In extreme cases,
 this can provide speedups over 3.5x on CPUs.  The package also
-supports acceleration with offload to Intel corprocessors (Xeon
+supports acceleration with offload to Intel(R) Xeon Phi(TM) coprocessors.
-Phi). This can result in additional speedup over 2x depending on the
+This can result in additional speedup over 2x depending on the
 hardware configuration.
 </P>
 <P>Styles with a "kk" suffix are part of the KOKKOS package, and can be
@@ -977,10 +977,10 @@ LAMMPS.
 </H4>
 <P>The USER-INTEL package was developed by Mike Brown at Intel
 Corporation. It provides a capability to accelerate simulations by
-offloading neighbor list and non-bonded force calculations to Intel
+offloading neighbor list and non-bonded force calculations to Intel(R)
-coprocessors (Xeon Phi).  Additionally, it supports running
+Xeon Phi(TM) coprocessors.  Additionally, it supports running
 simulations in single, mixed, or double precision with vectorization,
-even if a coprocessor is not present, i.e. on an Intel CPU.  The same
+even if a coprocessor is not present, i.e. on an Intel(R) CPU.  The same
 C++ code is used for both cases.  When offloading to a coprocessor,
 the routine is run twice, once with an offload flag.
 </P>
@@ -1006,19 +1006,19 @@ LINKFLAGS variables.  You also need to add -DLAMMPS_MEMALIGN=64 and
 </P>
 <P>If you are compiling on the same architecture that will be used for
 the runs, adding the flag <I>-xHost</I> will enable vectorization with the
-Intel compiler.  In order to build with support for an Intel
+Intel(R) compiler.  In order to build with support for an Intel(R)
 coprocessor, the flag <I>-offload</I> should be added to the LINKFLAGS line
 and the flag <I>-DLMP_INTEL_OFFLOAD</I> should be added to the CCFLAGS
 line.
 </P>
 <P>The files src/MAKE/Makefile.intel and src/MAKE/Makefile.intel_offload
 are included in the src/MAKE directory with options that perform well
-with the Intel compiler. The latter Makefile has support for offload
+with the Intel(R) compiler. The latter Makefile has support for offload
 to coprocessors and the former does not.
 </P>
-<P>It is recommended that Intel Compiler 2013 SP1 update 1 be used for
+<P>It is recommended that Intel(R) Compiler 2013 SP1 update 1 be used for
 compiling. Newer versions have some performance issues that are being
-addressed. If using Intel MPI, version 5 or higher is recommended.
+addressed. If using Intel(R) MPI, version 5 or higher is recommended.
 </P>
 <P>The rest of the compilation is the same as for any other package that
 has no additional library dependencies, e.g.
@@ -1034,7 +1034,7 @@ them.
 </P>
 <P>The total number of MPI tasks used by LAMMPS (one or multiple per
 compute node) is set in the usual manner via the mpirun or mpiexec
-commands, and is independent of the Intel package.
+commands, and is independent of the USER-INTEL package.
 </P>
 <P>Input script requirements to run using pair styles with a <I>intel</I>
 suffix are as follows:
@@ -1054,10 +1054,10 @@ use all single or all double precision, the <A HREF = "package.html">package
 intel</A> command must be used in the input script with a
 "single" or "double" keyword specified.
 </P>
-<P><B>Running with an Intel coprocessor:</B>
+<P><B>Running with an Intel(R) coprocessor:</B>
 </P>
 <P>The USER-INTEL package supports offload of a fraction of the work to
-Intel coprocessors (Xeon Phi).  This is accomplished by setting a
+Intel(R) Xeon Phi(TM) coprocessors.  This is accomplished by setting a
 balance fraction on the <A HREF = "package.html">package intel</A> command. A
 balance of 0 runs all calculations on the CPU.  A balance of 1 runs
 all calculations on the coprocessor.  A balance of 0.5 runs half of
@@ -1075,8 +1075,8 @@ adding a short warm-up run (10-20 steps) will allow the load-balancer
 to find a setting that will carry over to additional runs.
 </P>
 <P>The default for the <A HREF = "package.html">package intel</A> command is to have
-all the MPI tasks on a given compute node use a single coprocessor
+all the MPI tasks on a given compute node use a single Xeon Phi(TM) coprocessor
-(Xeon Phi). In general, running with a large number of MPI tasks on
+In general, running with a large number of MPI tasks on
 each node will perform best with offload.  Each MPI task will
 automatically get affinity to a subset of the hardware threads
 available on the coprocessor.  For example, if your card has 61 cores,
@@ -1087,7 +1087,7 @@ tuning of the number of threads to use per MPI task or the number of
 threads to use per core can be accomplished with keywords to the
 <A HREF = "package.html">package intel</A> command.
 </P>
-<P>If LAMMPS is using offload to a coprocessor (Xeon Phi), a diagnostic
+<P>If LAMMPS is using offload to a Intel(R) Xeon Phi(TM) coprocessor, a diagnostic
 line during the setup for a run is printed to the screen (not to log
 files) indicating that offload is being used and the number of
 coprocessor threads per MPI task.  Additionally, an offload timing
@@ -1095,7 +1095,7 @@ summary is printed at the end of each run.  When using offload, the
 <A HREF = "atom_modify.html">sort</A> frequency for atom data is changed to 1 so
 that the per-atom data is sorted every neighbor build.
 </P>
-<P>To use multiple coprocessors (Xeon Phis) on each compute node, the
+<P>To use multiple coprocessors on each compute node, the
 <I>offload_cards</I> keyword can be specified with the <A HREF = "package.html">package
 intel</A> command to specify the number of coprocessors to
 use.

doc/Section_accelerate.txt

@@ -172,8 +172,8 @@ Styles with an "intel" suffix are part of the USER-INTEL
 package. These styles support vectorized single and mixed precision
 calculations, in addition to full double precision.  In extreme cases,
 this can provide speedups over 3.5x on CPUs.  The package also
-supports acceleration with offload to Intel corprocessors (Xeon
+supports acceleration with offload to Intel(R) Xeon Phi(TM) coprocessors.
-Phi). This can result in additional speedup over 2x depending on the
+This can result in additional speedup over 2x depending on the
 hardware configuration.
 
 Styles with a "kk" suffix are part of the KOKKOS package, and can be
@@ -973,10 +973,10 @@ LAMMPS.
 
 The USER-INTEL package was developed by Mike Brown at Intel
 Corporation. It provides a capability to accelerate simulations by
-offloading neighbor list and non-bonded force calculations to Intel
+offloading neighbor list and non-bonded force calculations to Intel(R)
-coprocessors (Xeon Phi).  Additionally, it supports running
+Xeon Phi(TM) coprocessors.  Additionally, it supports running
 simulations in single, mixed, or double precision with vectorization,
-even if a coprocessor is not present, i.e. on an Intel CPU.  The same
+even if a coprocessor is not present, i.e. on an Intel(R) CPU.  The same
 C++ code is used for both cases.  When offloading to a coprocessor,
 the routine is run twice, once with an offload flag.
 
@@ -1002,19 +1002,19 @@ LINKFLAGS variables.  You also need to add -DLAMMPS_MEMALIGN=64 and
 
 If you are compiling on the same architecture that will be used for
 the runs, adding the flag {-xHost} will enable vectorization with the
-Intel compiler.  In order to build with support for an Intel
+Intel(R) compiler.  In order to build with support for an Intel(R)
 coprocessor, the flag {-offload} should be added to the LINKFLAGS line
 and the flag {-DLMP_INTEL_OFFLOAD} should be added to the CCFLAGS
 line.
 
 The files src/MAKE/Makefile.intel and src/MAKE/Makefile.intel_offload
 are included in the src/MAKE directory with options that perform well
-with the Intel compiler. The latter Makefile has support for offload
+with the Intel(R) compiler. The latter Makefile has support for offload
 to coprocessors and the former does not.
 
-It is recommended that Intel Compiler 2013 SP1 update 1 be used for
+It is recommended that Intel(R) Compiler 2013 SP1 update 1 be used for
 compiling. Newer versions have some performance issues that are being
-addressed. If using Intel MPI, version 5 or higher is recommended.
+addressed. If using Intel(R) MPI, version 5 or higher is recommended.
 
 The rest of the compilation is the same as for any other package that
 has no additional library dependencies, e.g.
@@ -1030,7 +1030,7 @@ them.
 
 The total number of MPI tasks used by LAMMPS (one or multiple per
 compute node) is set in the usual manner via the mpirun or mpiexec
-commands, and is independent of the Intel package.
+commands, and is independent of the USER-INTEL package.
 
 Input script requirements to run using pair styles with a {intel}
 suffix are as follows:
@@ -1050,10 +1050,10 @@ use all single or all double precision, the "package
 intel"_package.html command must be used in the input script with a
 "single" or "double" keyword specified.
 
-[Running with an Intel coprocessor:]
+[Running with an Intel(R) coprocessor:]
 
 The USER-INTEL package supports offload of a fraction of the work to
-Intel coprocessors (Xeon Phi).  This is accomplished by setting a
+Intel(R) Xeon Phi(TM) coprocessors.  This is accomplished by setting a
 balance fraction on the "package intel"_package.html command. A
 balance of 0 runs all calculations on the CPU.  A balance of 1 runs
 all calculations on the coprocessor.  A balance of 0.5 runs half of
@@ -1071,8 +1071,8 @@ adding a short warm-up run (10-20 steps) will allow the load-balancer
 to find a setting that will carry over to additional runs.
 
 The default for the "package intel"_package.html command is to have
-all the MPI tasks on a given compute node use a single coprocessor
+all the MPI tasks on a given compute node use a single Xeon Phi(TM) coprocessor
-(Xeon Phi). In general, running with a large number of MPI tasks on
+In general, running with a large number of MPI tasks on
 each node will perform best with offload.  Each MPI task will
 automatically get affinity to a subset of the hardware threads
 available on the coprocessor.  For example, if your card has 61 cores,
@@ -1083,7 +1083,7 @@ tuning of the number of threads to use per MPI task or the number of
 threads to use per core can be accomplished with keywords to the
 "package intel"_package.html command.
 
-If LAMMPS is using offload to a coprocessor (Xeon Phi), a diagnostic
+If LAMMPS is using offload to a Intel(R) Xeon Phi(TM) coprocessor, a diagnostic
 line during the setup for a run is printed to the screen (not to log
 files) indicating that offload is being used and the number of
 coprocessor threads per MPI task.  Additionally, an offload timing
@@ -1091,7 +1091,7 @@ summary is printed at the end of each run.  When using offload, the
 "sort"_atom_modify.html frequency for atom data is changed to 1 so
 that the per-atom data is sorted every neighbor build.
 
-To use multiple coprocessors (Xeon Phis) on each compute node, the
+To use multiple coprocessors on each compute node, the
 {offload_cards} keyword can be specified with the "package
 intel"_package.html command to specify the number of coprocessors to
 use.

doc/Section_example.html

@@ -59,7 +59,7 @@ section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
 <TR><TD >gpu</TD><TD >      use of the GPU package for GPU acceleration</TD></TR>
 <TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
 <TR><TD >indent</TD><TD >	  spherical indenter into a 2d solid</TD></TR>
-<TR><TD >intel</TD><TD >    use of the USER-INTEL package for CPU or Xeon Phi acceleration</TD></TR>
+<TR><TD >intel</TD><TD >    use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
 <TR><TD >kim</TD><TD >      use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
 <TR><TD >line</TD><TD >     line segment particles in 2d rigid bodies</TD></TR>
 <TR><TD >meam</TD><TD >	  MEAM test for SiC and shear (same as shear examples)</TD></TR>

doc/Section_example.txt

@@ -55,7 +55,7 @@ friction: frictional contact of spherical asperities between 2d surfaces
 gpu:      use of the GPU package for GPU acceleration
 hugoniostat: Hugoniostat shock dynamics
 indent:	  spherical indenter into a 2d solid
-intel:    use of the USER-INTEL package for CPU or Xeon Phi acceleration
+intel:    use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
 line:     line segment particles in 2d rigid bodies
 meam:	  MEAM test for SiC and shear (same as shear examples)

doc/Section_intro.html

@@ -109,7 +109,7 @@ it to LAMMPS.
 <LI>  open-source distribution
 <LI>  highly portable C++
 <LI>  optional libraries used: MPI and single-processor FFT
-<LI>  GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
+<LI>  GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
 <LI>  easy to extend with new features and functionality
 <LI>  runs from an input script
 <LI>  syntax for defining and using variables and formulas

doc/Section_intro.txt

@@ -105,7 +105,7 @@ General features :h4
   open-source distribution
   highly portable C++
   optional libraries used: MPI and single-processor FFT
-  GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
+  GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
   easy to extend with new features and functionality
   runs from an input script
   syntax for defining and using variables and formulas

doc/Section_packages.html

@@ -125,7 +125,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
 <TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_7">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
 <TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "fix_adapt.html">fix adapt/fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
-<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "Section_accelerate.html#acc_9">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "Section_accelerate.html#acc_9">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR>
@@ -390,6 +390,22 @@ Contact him directly if you have questions.
 </P>
 <HR>
 
+<H4>USER-INTEL package 
+</H4>
+<P>This package provides options for performing neighbor list and
+non-bonded force calculations in single, mixed, or double precision
+and also a capability for accelerating calculations with an
+Intel(R) Xeon Phi(TM) coprocessor.
+</P>
+<P>See this section of the manual to get started:
+</P>
+<P><A HREF = "Section_accelerate.html#acc_9">Section_accelerate</A>
+</P>
+<P>The person who created this package is W. Michael Brown at Intel
+(michael.w.brown at intel.com).  Contact him directly if you have questions.
+</P>
+<HR>
+
 <H4>USER-LB package 
 </H4>
 <P>This package contains a LAMMPS implementation of a background

doc/Section_packages.txt

@@ -117,7 +117,7 @@ USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars
 USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_Section_accelerate.html#acc_7, USER/cuda, -, lib/cuda
 USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
 USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "fix adapt/fep"_fix_adapt.html, USER/fep, -, -
-USER-INTEL, Vectorized CPU and Intel coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_Section_accelerate.html#acc_9, examples/intel, -, -
+USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_Section_accelerate.html#acc_9, examples/intel, -, -
 USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
 USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
@@ -377,6 +377,22 @@ Contact him directly if you have questions.
 
 :line
 
+USER-INTEL package :h4
+
+This package provides options for performing neighbor list and
+non-bonded force calculations in single, mixed, or double precision
+and also a capability for accelerating calculations with an
+Intel(R) Xeon Phi(TM) coprocessor.
+ 
+See this section of the manual to get started:
+
+"Section_accelerate"_Section_accelerate.html#acc_9
+
+The person who created this package is W. Michael Brown at Intel
+(michael.w.brown at intel.com).  Contact him directly if you have questions.
+
+:line
+
 USER-LB package :h4
 
 This package contains a LAMMPS implementation of a background

doc/Section_start.html

@@ -1493,8 +1493,8 @@ default GPU settings, as if the command "package gpu force/neigh 0 0
 changed by using the <A HREF = "package.html">package gpu</A> command in your script
 if desired.
 </P>
-<P>For the Intel package, using this command-line switch also invokes the
+<P>For the USER-INTEL package, using this command-line switch also invokes the
-default Intel settings, as if the command "package intel * mixed
+default USER-INTEL settings, as if the command "package intel * mixed
 balance -1" were used at the top of your input script.  These settings
 can be changed by using the <A HREF = "package.html">package intel</A> command in
 your script if desired.  If the USER-OMP package is installed, the

doc/Section_start.txt

@@ -1487,8 +1487,8 @@ default GPU settings, as if the command "package gpu force/neigh 0 0
 changed by using the "package gpu"_package.html command in your script
 if desired.
 
-For the Intel package, using this command-line switch also invokes the
+For the USER-INTEL package, using this command-line switch also invokes the
-default Intel settings, as if the command "package intel * mixed
+default USER-INTEL settings, as if the command "package intel * mixed
 balance -1" were used at the top of your input script.  These settings
 can be changed by using the "package intel"_package.html command in
 your script if desired.  If the USER-OMP package is installed, the

doc/package.html

@@ -249,7 +249,7 @@ terms and single precision for everything else), or <I>double</I> (intel
 styles use double precision for all calculations).
 </P>
 <P>Additional keyword-value pairs are available that are used to
-determine how work is offloaded to an Intel coprocessor. If LAMMPS is
+determine how work is offloaded to an Intel(R) coprocessor. If LAMMPS is
 built without offload support, these values are ignored. The
 additional settings are as follows:
 </P>

doc/package.txt

@@ -243,7 +243,7 @@ terms and single precision for everything else), or {double} (intel
 styles use double precision for all calculations).
 
 Additional keyword-value pairs are available that are used to
-determine how work is offloaded to an Intel coprocessor. If LAMMPS is
+determine how work is offloaded to an Intel(R) coprocessor. If LAMMPS is
 built without offload support, these values are ignored. The
 additional settings are as follows:
 

doc/suffix.html

@@ -51,7 +51,7 @@ run on one or more GPUs or multicore CPU/GPU nodes
 
 <LI>USER-INTEL = a collection of pair styles and neighbor routines
 optimized to run in single, mixed, or double precision on CPUs and
-Intel coprocessors (Xeon Phi). 
+Intel(R) Xeon Phi(TM) coprocessors. 
 
 <LI>KOKKOS = a collection of atom, pair, and fix styles optimized to run
 using the Kokkos library on various kinds of hardware, including GPUs

doc/suffix.txt

@@ -48,7 +48,7 @@ run on one or more GPUs or multicore CPU/GPU nodes :l
 
 USER-INTEL = a collection of pair styles and neighbor routines
 optimized to run in single, mixed, or double precision on CPUs and
-Intel coprocessors (Xeon Phi). :l
+Intel(R) Xeon Phi(TM) coprocessors. :l
 
 KOKKOS = a collection of atom, pair, and fix styles optimized to run
 using the Kokkos library on various kinds of hardware, including GPUs