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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	src/KSPACE/msm.cpp
	src/KSPACE/msm_cg.cpp
	src/KSPACE/pppm.cpp
	src/KSPACE/pppm_cg.cpp
	src/KSPACE/pppm_disp.cpp
	src/KSPACE/pppm_disp_tip4p.cpp
	src/KSPACE/pppm_stagger.cpp
	src/KSPACE/pppm_tip4p.cpp
This commit is contained in:
Axel Kohlmeyer
2014-08-26 12:33:31 -04:00
parent d6dfdd6cb1 b74fcc80ac
commit 54576e2b35
29 changed files with 162 additions and 95 deletions
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36
doc/Section_accelerate.html
View File

@ -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
Phi). This can result in additional speedup over 2x depending on the
supports acceleration with offload to Intel(R) Xeon Phi(TM) coprocessors.
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
coprocessors (Xeon Phi). Additionally, it supports running
offloading neighbor list and non-bonded force calculations to Intel(R)
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>
@ -1004,21 +1004,25 @@ flags to enable OpenMP support (<I>-openmp</I>) to both the CCFLAGS and
LINKFLAGS variables. You also need to add -DLAMMPS_MEMALIGN=64 and
-restrict to CCFLAGS.
</P>
<P>Note that currently you must use the Intel C++ compiler (icc/icpc) to
build the package. In the future, using other compilers (e.g. g++)
may be possible.
</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 +1038,7 @@ 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 +1058,10 @@ 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 +1079,8 @@ 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
(Xeon Phi). In general, running with a large number of MPI tasks on
all the MPI tasks on a given compute node use a single Xeon Phi(TM) coprocessor
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 +1091,7 @@ 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 +1099,7 @@ 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.

36
doc/Section_accelerate.txt
View File

@ -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
Phi). This can result in additional speedup over 2x depending on the
supports acceleration with offload to Intel(R) Xeon Phi(TM) coprocessors.
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
@ -976,10 +976,10 @@ 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
coprocessors (Xeon Phi). Additionally, it supports running
offloading neighbor list and non-bonded force calculations to Intel(R)
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.
@ -1003,21 +1003,25 @@ flags to enable OpenMP support ({-openmp}) to both the CCFLAGS and
LINKFLAGS variables. You also need to add -DLAMMPS_MEMALIGN=64 and
-restrict to CCFLAGS.
Note that currently you must use the Intel C++ compiler (icc/icpc) to
build the package. In the future, using other compilers (e.g. g++)
may be possible.
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.
@ -1033,7 +1037,7 @@ 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:
@ -1053,10 +1057,10 @@ 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
@ -1074,8 +1078,8 @@ 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
(Xeon Phi). In general, running with a large number of MPI tasks on
all the MPI tasks on a given compute node use a single Xeon Phi(TM) coprocessor
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,
@ -1086,7 +1090,7 @@ 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
@ -1094,7 +1098,7 @@ 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.

2
doc/Section_example.html
View File

@ -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>

2
doc/Section_example.txt
View File

@ -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)

2
doc/Section_intro.html
View File

@ -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

2
doc/Section_intro.txt
View File

@ -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

18
doc/Section_packages.html
View File

@ -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

18
doc/Section_packages.txt
View File

@ -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

4
doc/Section_start.html
View File

@ -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
default Intel settings, as if the command "package intel * mixed
<P>For the USER-INTEL package, using this command-line switch also invokes the
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

4
doc/Section_start.txt
View File

@ -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
default Intel settings, as if the command "package intel * mixed
For the USER-INTEL package, using this command-line switch also invokes the
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

37
doc/fix_langevin.html
View File

@ -239,20 +239,29 @@ group. As a result, the center-of-mass of a system with zero initial
momentum will not drift over time.
</P>
<P>The keyword <I>gjf</I> can be used to run the <A HREF = "#Gronbech-Jensen">Gronbech-Jensen/Farago
</A> time-discretization of the Langevin model. The
effective random force is composed of the average of two random forces
representing half-contributions from the previous and current time
intervals. This discretization has been shown to be consistent with
the underlying physical model of Langevin dynamics and produces the
correct Boltzmann distribution of positions for large timesteps,
up to the numerical stability limit. In common with all
methods based on Verlet integration, the discretized velocities
generated by the time integration scheme are not exactly conjugate
to the positions. As a result the temperature computed from the
discretized velocities will be systematically lower than the
target temperature, by an amount that grows with the timestep.
Nonetheless, the distribution of positions will be consistent
with the target temperature.
</A> time-discretization of the Langevin model. As
described in the papers cited below, the purpose of this method is to
enable longer timesteps to be used (up to the numerical stability
limit of the integrator), while still producing the correct Boltzmann
distribution of atom positions. It is implemented within LAMMPS, by
changing how the the random force is applied so that it is composed of
the average of two random forces representing half-contributions from
the previous and current time intervals. In common with all methods
based on Verlet integration, the discretized velocities generated by
this method in conjunction with velocity-Verlet time integration are
not exactly conjugate to the positions. As a result the temperature
(computed from the discretized velocities) will be systematically
lower than the target temperature, by a small amount which grows with
the timestep. Nonetheless, the distribution of atom positions will
still be consistent with the target temperature. For molecules containing
C-H bonds, configurational properties generated with dt = 2.5 fs and
tdamp = 100 fs are indistinguishable from dt = 0.5 fs.
Because the velocity distribution systematically decreases with increasing
timestep, the method should not be used to
generate properties that depend on the velocity distribution, such as
the velocity autocorrelation function (VACF). In the above example, the
velocity distribution at dt = 2.5fs generates an average temperature of 220 K,
instead of 300 K.
</P>
<HR>

37
doc/fix_langevin.txt
View File

@ -227,20 +227,29 @@ group. As a result, the center-of-mass of a system with zero initial
momentum will not drift over time.
The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago
"_#Gronbech-Jensen time-discretization of the Langevin model. The
effective random force is composed of the average of two random forces
representing half-contributions from the previous and current time
intervals. This discretization has been shown to be consistent with
the underlying physical model of Langevin dynamics and produces the
correct Boltzmann distribution of positions for large timesteps,
up to the numerical stability limit. In common with all
methods based on Verlet integration, the discretized velocities
generated by the time integration scheme are not exactly conjugate
to the positions. As a result the temperature computed from the
discretized velocities will be systematically lower than the
target temperature, by an amount that grows with the timestep.
Nonetheless, the distribution of positions will be consistent
with the target temperature.
"_#Gronbech-Jensen time-discretization of the Langevin model. As
described in the papers cited below, the purpose of this method is to
enable longer timesteps to be used (up to the numerical stability
limit of the integrator), while still producing the correct Boltzmann
distribution of atom positions. It is implemented within LAMMPS, by
changing how the the random force is applied so that it is composed of
the average of two random forces representing half-contributions from
the previous and current time intervals. In common with all methods
based on Verlet integration, the discretized velocities generated by
this method in conjunction with velocity-Verlet time integration are
not exactly conjugate to the positions. As a result the temperature
(computed from the discretized velocities) will be systematically
lower than the target temperature, by a small amount which grows with
the timestep. Nonetheless, the distribution of atom positions will
still be consistent with the target temperature. For molecules containing
C-H bonds, configurational properties generated with dt = 2.5 fs and
tdamp = 100 fs are indistinguishable from dt = 0.5 fs.
Because the velocity distribution systematically decreases with increasing
timestep, the method should not be used to
generate properties that depend on the velocity distribution, such as
the velocity autocorrelation function (VACF). In the above example, the
velocity distribution at dt = 2.5fs generates an average temperature of 220 K,
instead of 300 K.
:line

2
doc/package.html
View File

@ -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>

2
doc/package.txt
View File

@ -244,7 +244,7 @@ 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:

2
doc/suffix.html
View File

@ -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

2
doc/suffix.txt
View File

@ -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

2
src/KSPACE/msm.cpp
View File

@ -1429,7 +1429,7 @@ void MSM::particle_map()
int flag = 0;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
for (int i = 0; i < nlocal; i++) {

2
src/KSPACE/msm_cg.cpp
View File

@ -310,7 +310,7 @@ void MSMCG::particle_map()
int i;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
for (int j = 0; j < num_charged; j++) {
i = is_charged[j];

5
src/KSPACE/pppm.cpp
View File

@ -1877,7 +1877,7 @@ void PPPM::particle_map()
int flag = 0;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
for (int i = 0; i < nlocal; i++) {
@ -1897,9 +1897,8 @@ void PPPM::particle_map()
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
ny+nlower < nylo_out || ny+nupper > nyhi_out ||
nz+nlower < nzlo_out || nz+nupper > nzhi_out) {
nz+nlower < nzlo_out || nz+nupper > nzhi_out)
flag = 1;
}
}
if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM");

2
src/KSPACE/pppm_cg.cpp
View File

@ -283,7 +283,7 @@ void PPPMCG::particle_map()
double **x = atom->x;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int j = 0; j < num_charged; j++) {

2
src/KSPACE/pppm_disp.cpp
View File

@ -4210,7 +4210,7 @@ void PPPMDisp::particle_map(double delx, double dely, double delz,
int nlocal = atom->nlocal;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int i = 0; i < nlocal; i++) {

2
src/KSPACE/pppm_disp_tip4p.cpp
View File

@ -79,7 +79,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
int nlocal = atom->nlocal;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int i = 0; i < nlocal; i++) {

2
src/KSPACE/pppm_stagger.cpp
View File

@ -680,7 +680,7 @@ void PPPMStagger::particle_map()
int nlocal = atom->nlocal;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int i = 0; i < nlocal; i++) {

2
src/KSPACE/pppm_tip4p.cpp
View File

@ -74,7 +74,7 @@ void PPPMTIP4P::particle_map()
int nlocal = atom->nlocal;
if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int i = 0; i < nlocal; i++) {

2
src/MPIIO/dump_atom_mpiio.cpp
View File

@ -98,7 +98,7 @@ void DumpAtomMPIIO::openfile()
}
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);

2
src/MPIIO/dump_custom_mpiio.cpp
View File

@ -119,7 +119,7 @@ void DumpCustomMPIIO::openfile()
}
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);

2
src/MPIIO/dump_xyz_mpiio.cpp
View File

@ -118,7 +118,7 @@ void DumpXYZMPIIO::openfile()
}
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);

2
src/MPIIO/restart_mpiio.cpp
View File

@ -59,7 +59,7 @@ void RestartMPIIO::openForRead(char *filename)
void RestartMPIIO::openForWrite(char *filename)
{
int err = MPI_File_open(world, filename, MPI_MODE_APPEND | MPI_MODE_WRONLY,
int err = MPI_File_open(world, filename, MPI_MODE_WRONLY,
MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS) {
char str[MPI_MAX_ERROR_STRING+128];

24
src/USER-INTEL/README
View File

@ -1,6 +1,6 @@
--------------------------------
LAMMPS Intel Package
LAMMPS Intel(R) Package
--------------------------------
W. Michael Brown (Intel)
@ -12,14 +12,15 @@ This package is based on the USER-OMP package and provides LAMMPS styles that:
1. include support for single and mixed precision in addition to double.
2. include modifications to support vectorization for key routines
3. include modifications to support offload to Xeon Phi coprocessors
3. include modifications to support offload to Intel(R) Xeon Phi(TM)
coprocessors
-----------------------------------------------------------------------------
When using the suffix command with "intel", intel styles will be used if they
exist; if they do not, and an omp version exists, that style will be used.
This is accomplished through the files *ompinto_intel.h that are created
in the src directory when the intel package is installed. For example,
exist; if they do not, and the USER-OMP package is installed and an omp version
exists, that style will be used. For example, in the case the USER-OMP package
is installed,
kspace_style pppm/intel 1e-4
@ -31,5 +32,14 @@ because no pppm style has been implemented for the Intel package.
-----------------------------------------------------------------------------
In order to use offload to Xeon Phi, the flag -DLMP_INTEL_OFFLOAD should be
set in the Makefile. Offload requires the use of Intel compilers.
In order to use offload to Intel(R) Xeon Phi(TM) coprocessors, the flag
-DLMP_INTEL_OFFLOAD should be set in the Makefile. Offload requires the use of
Intel compilers.
-----------------------------------------------------------------------------
The files in this package must be compiled with the Intel C++
compiler, i.e. icc/icpc.