jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6228 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-05-27 17:59:03 +00:00
parent fcf8b1bf34
commit c2aca39265
26 changed files with 378 additions and 404 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
doc/Section_accelerate.html
View File

@ -39,7 +39,7 @@ on how to turn off/on the suffix associated with this switch within
your input script.
</P>
<P>Styles with an "opt" suffix are part of the OPT package and typically
run 5% to 25% faster on modern cache-based CPUs.
speed-up the pairwise portion of your simulation by 5-25%.
</P>
<P>Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
@ -71,20 +71,27 @@ packages, since they are both designed to use NVIDIA GPU hardware.
<H4><A NAME = "10_1"></A>10.1 OPT package
</H4>
<P>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie and Vincent Natoli (Stone Ridge
Technologies).
</P>
<HR>
<H4><A NAME = "10_2"></A>10.2 GPU package
</H4>
<P>The GPU package was developed by Mike Brown at ORNL.
</P>
<P>A few LAMMPS <A HREF = "pair_style.html">pair styles</A> can be run on graphical
processing units (GPUs). We plan to add more over time. Currently,
they only support NVIDIA GPU cards. To use them you need to install
certain NVIDIA CUDA software on your system:
</P>
<UL><LI>Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
<LI>Go to http://www.nvidia.com/object/cuda_get.html
<LI>Install a driver and toolkit appropriate for your system (SDK is not necessary)
<LI>Follow the instructions in README in lammps/lib/gpu to build the library
<LI>Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties
<UL><LI>Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0 Go
<LI>to http://www.nvidia.com/object/cuda_get.html Install a driver and
<LI>toolkit appropriate for your system (SDK is not necessary) Follow the
<LI>instructions in README in lammps/lib/gpu to build the library Run
<LI>lammps/lib/gpu/nvc_get_devices to list supported devices and
<LI>properties
</UL>
<H4>GPU configuration
</H4>
@ -208,6 +215,9 @@ latter requires that your GPU card supports double precision.
<H4><A NAME = "10_3"></A>10.3 USER-CUDA package
</H4>
<P>The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany.
</P>
<HR>
<H4><A NAME = "10_4"></A>10.4 Comparison of GPU and USER-CUDA packages

22
doc/Section_accelerate.txt
View File

@ -36,7 +36,7 @@ on how to turn off/on the suffix associated with this switch within
your input script.
Styles with an "opt" suffix are part of the OPT package and typically
run 5% to 25% faster on modern cache-based CPUs.
speed-up the pairwise portion of your simulation by 5-25%.
Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
@ -68,20 +68,27 @@ packages, since they are both designed to use NVIDIA GPU hardware.
10.1 OPT package :h4,link(10_1)
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie and Vincent Natoli (Stone Ridge
Technologies).
:line
10.2 GPU package :h4,link(10_2)
The GPU package was developed by Mike Brown at ORNL.
A few LAMMPS "pair styles"_pair_style.html can be run on graphical
processing units (GPUs). We plan to add more over time. Currently,
they only support NVIDIA GPU cards. To use them you need to install
certain NVIDIA CUDA software on your system:
Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
Go to http://www.nvidia.com/object/cuda_get.html
Install a driver and toolkit appropriate for your system (SDK is not necessary)
Follow the instructions in README in lammps/lib/gpu to build the library
Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties :ul
Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0 Go
to http://www.nvidia.com/object/cuda_get.html Install a driver and
toolkit appropriate for your system (SDK is not necessary) Follow the
instructions in README in lammps/lib/gpu to build the library Run
lammps/lib/gpu/nvc_get_devices to list supported devices and
properties :ul
GPU configuration :h4
@ -205,6 +212,9 @@ latter requires that your GPU card supports double precision.
10.3 USER-CUDA package :h4,link(10_3)
The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany.
:line
10.4 Comparison of GPU and USER-CUDA packages :h4,link(10_4)

15
doc/Section_commands.html
View File

@ -426,9 +426,8 @@ potentials. Click on the style itself for a full description:
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated pair styles, which can be used if LAMMPS is
@ -436,10 +435,10 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96_cut.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A>
</TD></TR></TABLE></DIV>
<HR>
@ -525,7 +524,7 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/cuda</A><A HREF = "kspace_style.html">pppm/gpu</A>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/cuda</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/gpu</A>
</TD></TR></TABLE></DIV>
</HTML>

7
doc/Section_commands.txt
View File

@ -639,10 +639,8 @@ These are pair styles contributed by users, which can be used if
"buck/coul"_pair_buck_coul.html,
"cg/cmm"_pair_cmm.html,
"cg/cmm/gpu"_pair_cmm.html,
"cg/cmm/coul/cut"_pair_cmm.html,
"cg/cmm/coul/long"_pair_cmm.html,
"cg/cmm/coul/long/gpu"_pair_cmm.html,
"eam/cd"_pair_eam.html,
"eff/cut"_pair_eff.html,
"lj/coul"_pair_lj_coul.html,
@ -653,6 +651,8 @@ built with the "appropriate accelerated
package"_Section_accelerate.html.
"gayberne/gpu"_pair_gayberne.html,
"cg/cmm/gpu"_pair_cmm.html,
"cg/cmm/coul/long/gpu"_pair_cmm.html,
"lj/charmm/coul/long/gpu"_pair_charmm.html,
"lj/cut/coul/cut/gpu"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
@ -762,6 +762,5 @@ These are accelerated Kspace solvers, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"pppm/cuda"_kspace_style.html
"pppm/cuda"_kspace_style.html,
"pppm/gpu"_kspace_style.html :tb(c=4,ea=c,w=100)

80
doc/Section_start.html
View File

@ -513,9 +513,9 @@ the various options.
<A NAME = "2_3_3"></A><B><I>Packages that require extra LAMMPS libraries:</I></B>
<P>A few packages (standard or user) require that additional libraries be
<P>A few standard or user packages require that additional libraries be
compiled first, which LAMMPS will link to when it builds. The source
code for these libraries are included in the LAMMPS distribution under
code for these libraries is included in the LAMMPS distribution under
the "lib" directory. Look at the README files in the lib directories
(e.g. lib/reax/README) for instructions on how to build each library.
</P>
@ -528,56 +528,60 @@ link with the library file.
</P>
<P>The "atc" library in lib/atc is used by the user-atc package. It
provides continuum field estimation and molecular dynamics-finite
element coupling methods.
element coupling methods. It was written by Reese Jones, Jeremy
Templeton and Jonathan Zimmerman at Sandia.
</P>
<P>The "cuda" library in lib/cuda is used by the user-cuda package. It
contains code to enable portions of LAMMPS to run on NVIDIA GPUs
was written by Christian Trott at U of Technology Ilmenau in Germany.
It contains code to enable portions of LAMMPS to run on NVIDIA GPUs
associated with your CPUs. Currently, only NVIDIA GPUs are supported.
Building this library requires NVIDIA Cuda tools to be installed on
your system. See <A HREF = "Section_accelerate.html#10_3">this section</A> of the
manual for more information about using this package effectively and
how it differs from the gpu package.
</P>
<P>The "gpu" library in lib/gpu is used by the gpu package. It contains
code to enable portions of LAMMPS to run on GPUs associated with your
CPUs. Currently, only NVIDIA GPUs are supported, but eventually this
may be extended to OpenCL. Building this library requires NVIDIA Cuda
tools to be installed on your system. See <A HREF = "Section_accelerate.html#10_2">this
<P>The "gpu" library in lib/gpu is used by the gpu package. It was
written by Mike Brown at ORNL. It contains code to enable portions of
LAMMPS to run on GPUs associated with your CPUs. Currently, only
NVIDIA GPUs are supported, but eventually this may be extended to
OpenCL. Building this library requires NVIDIA Cuda tools to be
installed on your system. See <A HREF = "Section_accelerate.html#10_2">this
section</A> of the manual for more
information about using this package effectively and how it differs
from the user-cuda package.
</P>
<P>The "meam" library in lib/meam is used by the meam package.
computes the modified embedded atom method potential, which is a
generalization of EAM potentials that can be used to model a wider
variety of materials. This MEAM implementation was written by Greg
Wagner at Sandia. It requires a F90 compiler to build. The C++ to
FORTRAN function calls in pair_meam.cpp assumes that FORTRAN object
names are converted to C object names by appending an underscore
character. This is generally the case, but on machines that do not
conform to this convention, you will need to modify either the C++
code or your compiler settings.
<P>The "meam" library in lib/meam is used by the meam package. It was
written by Greg Wagner at Sandia. It computes the modified embedded
atom method potential, which is a generalization of EAM potentials
that can be used to model a wider variety of materials. This MEAM
implementation was written by Greg Wagner at Sandia. It requires a
F90 compiler to build. The C++ to FORTRAN function calls in
pair_meam.cpp assumes that FORTRAN object names are converted to C
object names by appending an underscore character. This is generally
the case, but on machines that do not conform to this convention, you
will need to modify either the C++ code or your compiler settings.
</P>
<P>The "poems" library in lib/poems is used by the poems package.
computes the constrained rigid-body motion of articulated (jointed)
multibody systems. POEMS was written and is distributed by Prof Kurt
Anderson's group at Rensselaer Polytechnic Institute (RPI).
<P>The "poems" library in lib/poems is used by the poems package. It was
written by Rudra Mukherjee at JPL. It computes the constrained
rigid-body motion of articulated (jointed) multibody systems. POEMS
is distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI).
</P>
<P>The "reax" library in lib/reax is used by the reax package. It
computes the Reactive Force Field (ReaxFF) potential, developed by
Adri van Duin in Bill Goddard's group at CalTech. This implementation
in LAMMPS uses many of Adri's files and was developed by Aidan
Thompson at Sandia and Hansohl Cho at MIT. It requires a F77 or F90
compiler to build. The C++ to FORTRAN function calls in pair_reax.cpp
assume that FORTRAN object names are converted to C object names by
appending an underscore character. This is generally the case, but on
machines that do not conform to this convention, you will need to
modify either the C++ code or your compiler settings. The name
conversion is handled by the preprocessor macro called FORTRAN in
pair_reax_fortran.h. Different definitions of this macro can be
obtained by adding a machine-specific macro definition to the CCFLAGS
variable in your Makefile e.g. -D_IBM. See pair_reax_fortran.h for
more info.
<P>The "reax" library in lib/reax is used by the reax package. It was
written by Aidan Thompson at Sandia. It computes the Reactive Force
Field (ReaxFF) potential, developed by Adri van Duin in Bill Goddard's
group at CalTech. This implementation in LAMMPS uses many of Adri's
files and was developed by Aidan Thompson at Sandia and Hansohl Cho at
MIT. It requires a F77 or F90 compiler to build. The C++ to FORTRAN
function calls in pair_reax.cpp assume that FORTRAN object names are
converted to C object names by appending an underscore character. This
is generally the case, but on machines that do not conform to this
convention, you will need to modify either the C++ code or your
compiler settings. The name conversion is handled by the preprocessor
macro called FORTRAN in pair_reax_fortran.h. Different definitions of
this macro can be obtained by adding a machine-specific macro
definition to the CCFLAGS variable in your Makefile e.g. -D_IBM. See
pair_reax_fortran.h for more info.
</P>
<P>As described in the README file in each lib directory, each library is
typically built by typing something like

80
doc/Section_start.txt
View File

@ -506,9 +506,9 @@ the various options.
[{Packages that require extra LAMMPS libraries:}] :link(2_3_3)
A few packages (standard or user) require that additional libraries be
A few standard or user packages require that additional libraries be
compiled first, which LAMMPS will link to when it builds. The source
code for these libraries are included in the LAMMPS distribution under
code for these libraries is included in the LAMMPS distribution under
the "lib" directory. Look at the README files in the lib directories
(e.g. lib/reax/README) for instructions on how to build each library.
@ -521,56 +521,60 @@ Here is a bit of information about each library:
The "atc" library in lib/atc is used by the user-atc package. It
provides continuum field estimation and molecular dynamics-finite
element coupling methods.
element coupling methods. It was written by Reese Jones, Jeremy
Templeton and Jonathan Zimmerman at Sandia.
The "cuda" library in lib/cuda is used by the user-cuda package. It
contains code to enable portions of LAMMPS to run on NVIDIA GPUs
was written by Christian Trott at U of Technology Ilmenau in Germany.
It contains code to enable portions of LAMMPS to run on NVIDIA GPUs
associated with your CPUs. Currently, only NVIDIA GPUs are supported.
Building this library requires NVIDIA Cuda tools to be installed on
your system. See "this section"_Section_accelerate.html#10_3 of the
manual for more information about using this package effectively and
how it differs from the gpu package.
The "gpu" library in lib/gpu is used by the gpu package. It contains
code to enable portions of LAMMPS to run on GPUs associated with your
CPUs. Currently, only NVIDIA GPUs are supported, but eventually this
may be extended to OpenCL. Building this library requires NVIDIA Cuda
tools to be installed on your system. See "this
The "gpu" library in lib/gpu is used by the gpu package. It was
written by Mike Brown at ORNL. It contains code to enable portions of
LAMMPS to run on GPUs associated with your CPUs. Currently, only
NVIDIA GPUs are supported, but eventually this may be extended to
OpenCL. Building this library requires NVIDIA Cuda tools to be
installed on your system. See "this
section"_Section_accelerate.html#10_2 of the manual for more
information about using this package effectively and how it differs
from the user-cuda package.
The "meam" library in lib/meam is used by the meam package.
computes the modified embedded atom method potential, which is a
generalization of EAM potentials that can be used to model a wider
variety of materials. This MEAM implementation was written by Greg
Wagner at Sandia. It requires a F90 compiler to build. The C++ to
FORTRAN function calls in pair_meam.cpp assumes that FORTRAN object
names are converted to C object names by appending an underscore
character. This is generally the case, but on machines that do not
conform to this convention, you will need to modify either the C++
code or your compiler settings.
The "meam" library in lib/meam is used by the meam package. It was
written by Greg Wagner at Sandia. It computes the modified embedded
atom method potential, which is a generalization of EAM potentials
that can be used to model a wider variety of materials. This MEAM
implementation was written by Greg Wagner at Sandia. It requires a
F90 compiler to build. The C++ to FORTRAN function calls in
pair_meam.cpp assumes that FORTRAN object names are converted to C
object names by appending an underscore character. This is generally
the case, but on machines that do not conform to this convention, you
will need to modify either the C++ code or your compiler settings.
The "poems" library in lib/poems is used by the poems package.
computes the constrained rigid-body motion of articulated (jointed)
multibody systems. POEMS was written and is distributed by Prof Kurt
Anderson's group at Rensselaer Polytechnic Institute (RPI).
The "poems" library in lib/poems is used by the poems package. It was
written by Rudra Mukherjee at JPL. It computes the constrained
rigid-body motion of articulated (jointed) multibody systems. POEMS
is distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI).
The "reax" library in lib/reax is used by the reax package. It
computes the Reactive Force Field (ReaxFF) potential, developed by
Adri van Duin in Bill Goddard's group at CalTech. This implementation
in LAMMPS uses many of Adri's files and was developed by Aidan
Thompson at Sandia and Hansohl Cho at MIT. It requires a F77 or F90
compiler to build. The C++ to FORTRAN function calls in pair_reax.cpp
assume that FORTRAN object names are converted to C object names by
appending an underscore character. This is generally the case, but on
machines that do not conform to this convention, you will need to
modify either the C++ code or your compiler settings. The name
conversion is handled by the preprocessor macro called FORTRAN in
pair_reax_fortran.h. Different definitions of this macro can be
obtained by adding a machine-specific macro definition to the CCFLAGS
variable in your Makefile e.g. -D_IBM. See pair_reax_fortran.h for
more info.
The "reax" library in lib/reax is used by the reax package. It was
written by Aidan Thompson at Sandia. It computes the Reactive Force
Field (ReaxFF) potential, developed by Adri van Duin in Bill Goddard's
group at CalTech. This implementation in LAMMPS uses many of Adri's
files and was developed by Aidan Thompson at Sandia and Hansohl Cho at
MIT. It requires a F77 or F90 compiler to build. The C++ to FORTRAN
function calls in pair_reax.cpp assume that FORTRAN object names are
converted to C object names by appending an underscore character. This
is generally the case, but on machines that do not conform to this
convention, you will need to modify either the C++ code or your
compiler settings. The name conversion is handled by the preprocessor
macro called FORTRAN in pair_reax_fortran.h. Different definitions of
this macro can be obtained by adding a machine-specific macro
definition to the CCFLAGS variable in your Makefile e.g. -D_IBM. See
pair_reax_fortran.h for more info.
As described in the README file in each lib directory, each library is
typically built by typing something like

13
doc/fix_gpu.html
View File

@ -74,13 +74,12 @@ calculations can be performed on the CPU while the GPU is performing
force calculations for the GPU-enabled pair style.
</P>
<P>In order to use GPU acceleration, a GPU enabled style must be selected
in the input script in addition to this fix. Currently, this is
in the input script in addition to this fix. Currently, this is
limited to a few <A HREF = "pair_style.html">pair styles</A> and the PPPM <A HREF = "kspace_style.html">kspace
style</A>.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>See <A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
details about using the GPU package.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
@ -97,9 +96,9 @@ the <A HREF = "run.html">run</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>The fix must be the first fix specified for a given run. The force/neigh
<I>mode</I> should not be used with a triclinic box or <A HREF = "pair_hybrid.html">hybrid</A>
pair styles.
<P>The fix must be the first fix specified for a given run. The
force/neigh <I>mode</I> should not be used with a triclinic box or
<A HREF = "pair_hybrid.html">hybrid</A> pair styles.
</P>
<P>The <I>split</I> setting must be positive when using
<A HREF = "pair_hybrid.html">hybrid</A> pair styles.

13
doc/fix_gpu.txt
View File

@ -65,13 +65,12 @@ calculations can be performed on the CPU while the GPU is performing
force calculations for the GPU-enabled pair style.
In order to use GPU acceleration, a GPU enabled style must be selected
in the input script in addition to this fix. Currently, this is
in the input script in addition to this fix. Currently, this is
limited to a few "pair styles"_pair_style.html and the PPPM "kspace
style"_kspace_style.html.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
See "this section"_doc/Section_accerate.html of the manual for more
details about using the GPU package.
[Restart, fix_modify, output, run start/stop, minimize info:]
@ -88,9 +87,9 @@ the "run"_run.html command.
[Restrictions:]
The fix must be the first fix specified for a given run. The force/neigh
{mode} should not be used with a triclinic box or "hybrid"_pair_hybrid.html
pair styles.
The fix must be the first fix specified for a given run. The
force/neigh {mode} should not be used with a triclinic box or
"hybrid"_pair_hybrid.html pair styles.
The {split} setting must be positive when using
"hybrid"_pair_hybrid.html pair styles.

25
doc/kspace_style.html
View File

@ -77,7 +77,7 @@ long-range potentials.
(triclinic symmetry) simulation boxes.
</P>
<P>The <I>pppm/gpu/single</I> and <I>pppm/gpu/double</I> styles are GPU-enabled
version of <I>pppm</I>. See more details below.
version of <I>pppm</I>. See more details below.
</P>
<HR>
@ -99,24 +99,23 @@ options of the K-space solvers that can be set.
</P>
<HR>
<P>The <I>pppm/gpu/single</I> style performs single precision
charge assignment and force interpolation calculations on the GPU.
The <I>pppm/gpu/double</I> style performs the mesh calculations on the GPU
in double precision. FFT solves are calculated on the CPU in both
cases. If either <I>pppm/gpu/single</I> or <I>pppm/gpu/double</I> are used with
a GPU-enabled pair style, part of the PPPM calculation can be performed
<P>The <I>pppm/gpu/single</I> style performs single precision charge
assignment and force interpolation calculations on the GPU. The
<I>pppm/gpu/double</I> style performs the mesh calculations on the GPU in
double precision. In both cases, FFT solves are calculated on the CPU.
If either <I>pppm/gpu/single</I> or <I>pppm/gpu/double</I> are used with a
GPU-enabled pair style, part of the PPPM calculation can be performed
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
</P>
<P>More details about GPU settings and various possible hardware
configurations are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>See <A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
details.
</P>
<P>Additional requirements in your input script to run with GPU-enabled
<P>Additional requirements in your input script to run with GPU-enabled
PPPM styles are as follows:
</P>
<P><A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls
the essential GPU selection and initialization steps.
<P>The <A HREF = "fix_gpu.html">fix gpu</A> command must be used. The fix controls the
GPU selection and initialization steps.
</P>
<P><B>Restrictions:</B>
</P>

25
doc/kspace_style.txt
View File

@ -72,7 +72,7 @@ Currently, only the {ewald/n} style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
The {pppm/gpu/single} and {pppm/gpu/double} styles are GPU-enabled
version of {pppm}. See more details below.
version of {pppm}. See more details below.
:line
@ -94,24 +94,23 @@ options of the K-space solvers that can be set.
:line
The {pppm/gpu/single} style performs single precision
charge assignment and force interpolation calculations on the GPU.
The {pppm/gpu/double} style performs the mesh calculations on the GPU
in double precision. FFT solves are calculated on the CPU in both
cases. If either {pppm/gpu/single} or {pppm/gpu/double} are used with
a GPU-enabled pair style, part of the PPPM calculation can be performed
The {pppm/gpu/single} style performs single precision charge
assignment and force interpolation calculations on the GPU. The
{pppm/gpu/double} style performs the mesh calculations on the GPU in
double precision. In both cases, FFT solves are calculated on the CPU.
If either {pppm/gpu/single} or {pppm/gpu/double} are used with a
GPU-enabled pair style, part of the PPPM calculation can be performed
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
More details about GPU settings and various possible hardware
configurations are in "this section"_Section_start.html#2_8 of the
manual.
See "this section"_doc/Section_accerate.html of the manual for more
details.
Additional requirements in your input script to run with GPU-enabled
Additional requirements in your input script to run with GPU-enabled
PPPM styles are as follows:
"fix gpu"_fix_gpu.html must be used. The fix controls
the essential GPU selection and initialization steps.
The "fix gpu"_fix_gpu.html command must be used. The fix controls the
GPU selection and initialization steps.
[Restrictions:]

33
doc/pair_charmm.html
View File

@ -52,6 +52,7 @@ pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<PRE>pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_style lj/charmm/coul/long/opt 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
@ -91,13 +92,11 @@ applied to the Coulombic term, as in the discussion for pair style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
</P>
<P>Style <I>lj/charmm/coul/long/gpu</I> is a GPU-enabled version of style <I>lj/charmm/coul/long</I>.
See more details below.
<P>Style <I>lj/charmm/coul/long/gpu</I> is a GPU-enabled version of style
<I>lj/charmm/coul/long</I>. See more details below.
</P>
<P>Style <I>lj/charmm/coul/long/opt</I> is an optimized version of style
<I>lj/charmm/coul/long</I> that should give identical answers. Depending
on system size and the processor you are running on, it may be 5-25%
faster (for the pairwise portion of the run time).
<I>lj/charmm/coul/long</I>. See more details below.
</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
@ -123,23 +122,23 @@ the pair_style command.
</P>
<HR>
<P>The <I>lj/charmm/coul/long/gpu</I> style is identical to the <I>lj/charmm/coul/long</I>
style, except that each processor off-loads its pairwise calculations to
a GPU chip. Depending on the hardware available on your system this can
provide a significant speed-up. See the <A HREF = "Section_start.html#2_8">Running on
GPUs</A> section of the manual for more details
about hardware and software requirements for using GPUs.
<P>The <I>lj/charmm/coul/long/opt</I> style is identical to the
<I>lj/charmm/coul/long</I> style, except that it is written in an optimized
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>The <I>lj/charmm/coul/long/gpu</I> style is identical to the
<I>lj/charmm/coul/long</I> style, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a significant speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
</P>
<P>Additional requirements in your input script to run with style
<I>lj/charmm/coul/long/gpu</I> are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>

33
doc/pair_charmm.txt
View File

@ -44,6 +44,7 @@ pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_style lj/charmm/coul/long/opt 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
@ -83,13 +84,11 @@ applied to the Coulombic term, as in the discussion for pair style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
Style {lj/charmm/coul/long/gpu} is a GPU-enabled version of style {lj/charmm/coul/long}.
See more details below.
Style {lj/charmm/coul/long/gpu} is a GPU-enabled version of style
{lj/charmm/coul/long}. See more details below.
Style {lj/charmm/coul/long/opt} is an optimized version of style
{lj/charmm/coul/long} that should give identical answers. Depending
on system size and the processor you are running on, it may be 5-25%
faster (for the pairwise portion of the run time).
{lj/charmm/coul/long}. See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -115,23 +114,23 @@ the pair_style command.
:line
The {lj/charmm/coul/long/gpu} style is identical to the {lj/charmm/coul/long}
style, except that each processor off-loads its pairwise calculations to
a GPU chip. Depending on the hardware available on your system this can
provide a significant speed-up. See the "Running on
GPUs"_Section_start.html#2_8 section of the manual for more details
about hardware and software requirements for using GPUs.
The {lj/charmm/coul/long/opt} style is identical to the
{lj/charmm/coul/long} style, except that it is written in an optimized
fashion for faster CPU execution. See "this
section"_doc/Section_accerate.html of the manual for more details.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
The {lj/charmm/coul/long/gpu} style is identical to the
{lj/charmm/coul/long} style, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a significant speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Additional requirements in your input script to run with style
{lj/charmm/coul/long/gpu} are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
:line

35
doc/pair_cmm.html
View File

@ -65,8 +65,8 @@ given by
<P>as required for the CMM Coarse-grained MD parametrization discussed in
<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
</P>
<P>Style <I>cg/cmm/gpu</I> is a GPU-enabled version of style <I>cg/cmm</I>.
See more details below.
<P>Style <I>cg/cmm/gpu</I> is a GPU-enabled version of style <I>cg/cmm</I>. See
more details below.
</P>
<P>Style <I>cg/cmm/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
@ -96,8 +96,8 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>cg/cmm/coul/long/gpu</I> is a GPU-enabled version of style <I>cg/cmm/coul/long</I>.
See more details below.
<P>Style <I>cg/cmm/coul/long/gpu</I> is a GPU-enabled version of style
<I>cg/cmm/coul/long</I>. See more details below.
</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
@ -129,24 +129,19 @@ pair_style command.
</P>
<HR>
<P>The <I>cg/cmm/gpu</I> and <I>cg/cmm/coul/long/gpu</I> styles
are identical to the <I>cg/cmm</I> and <I>cg/cmm/coul/long</I>
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
<P>The <I>cg/cmm/gpu</I> and <I>cg/cmm/coul/long/gpu</I> styles are identical to
the <I>cg/cmm</I> and <I>cg/cmm/coul/long</I> styles, except that each processor
off-loads its pairwise calculations to a GPU. Depending on the
hardware available on your system this can provide a speed-up. See
<A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
details.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>Additional requirements in your input script to run with GPU-enabled
styles are as follows:
</P>
<P>Additional requirements in your input script to run with GPU-enabled styles
are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>

35
doc/pair_cmm.txt
View File

@ -56,8 +56,8 @@ given by
as required for the CMM Coarse-grained MD parametrization discussed in
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
Style {cg/cmm/gpu} is a GPU-enabled version of style {cg/cmm}.
See more details below.
Style {cg/cmm/gpu} is a GPU-enabled version of style {cg/cmm}. See
more details below.
Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
@ -87,8 +87,8 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {cg/cmm/coul/long/gpu} is a GPU-enabled version of style {cg/cmm/coul/long}.
See more details below.
Style {cg/cmm/coul/long/gpu} is a GPU-enabled version of style
{cg/cmm/coul/long}. See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -120,24 +120,19 @@ pair_style command.
:line
The {cg/cmm/gpu} and {cg/cmm/coul/long/gpu} styles
are identical to the {cg/cmm} and {cg/cmm/coul/long}
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
The {cg/cmm/gpu} and {cg/cmm/coul/long/gpu} styles are identical to
the {cg/cmm} and {cg/cmm/coul/long} styles, except that each processor
off-loads its pairwise calculations to a GPU. Depending on the
hardware available on your system this can provide a speed-up. See
"this section"_doc/Section_accerate.html of the manual for more
details.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
Additional requirements in your input script to run with GPU-enabled
styles are as follows:
Additional requirements in your input script to run with GPU-enabled styles
are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
:line

25
doc/pair_eam.html
View File

@ -62,10 +62,8 @@ nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
</P>
<P>Style <I>eam/opt</I> is an optimized version of style <I>eam</I> that should
give identical answers. Depending on system size and the processor
you are running on, it may be 5-25% faster (for the pairwise portion
of the run time).
<P>Style (eam/opt</I> is an optimized version of style <I>eam</I>. See
more details below.
</P>
<P>The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
@ -185,10 +183,8 @@ above, <I>setfl</I> files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than <I>funcfl</I> files for
modeling alloys.
</P>
<P>Style <I>eam/alloy/opt</I> is an optimized version of style <I>eam/alloy</I>
that should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
<P>Style (eam/alloy/opt</I> is an optimized version of style <I>eam/alloy</I>.
See more details below.
</P>
<P>For style <I>eam/alloy</I>, potential values are read from a file that is
in the DYNAMO multi-element <I>setfl</I> format, except that element names
@ -310,10 +306,8 @@ so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
</P>
<P>Style <I>eam/fs/opt</I> is an optimized version of style <I>eam/fs</I> that
should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
<P>Style (eam/fs/opt</I> is an optimized version of style <I>eam/fs</I>. See
more details below.
</P>
<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
reads a DYNAMO <I>setfl</I> file that has been extended to include
@ -377,6 +371,13 @@ are listed.
</P>
<HR>
<P>The <I>eam/opt</I>, <I>eam/alloy/opt</I>, and <I>eam/fs/opt</I> styles are identical
to the <I>eam</I>, <I>eam/alloy</I>, and <I>eam/fs</I> styles, except that they are
written in an optimized fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to

25
doc/pair_eam.txt
View File

@ -53,10 +53,8 @@ nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
Style {eam/opt} is an optimized version of style {eam} that should
give identical answers. Depending on system size and the processor
you are running on, it may be 5-25% faster (for the pairwise portion
of the run time).
Style (eam/opt} is an optimized version of style {eam}. See
more details below.
The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
@ -176,10 +174,8 @@ above, {setfl} files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than {funcfl} files for
modeling alloys.
Style {eam/alloy/opt} is an optimized version of style {eam/alloy}
that should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
Style (eam/alloy/opt} is an optimized version of style {eam/alloy}.
See more details below.
For style {eam/alloy}, potential values are read from a file that is
in the DYNAMO multi-element {setfl} format, except that element names
@ -301,10 +297,8 @@ so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
Style {eam/fs/opt} is an optimized version of style {eam/fs} that
should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
Style (eam/fs/opt} is an optimized version of style {eam/fs}. See
more details below.
The associated "pair_coeff"_pair_coeff.html command for style {eam/fs}
reads a DYNAMO {setfl} file that has been extended to include
@ -368,6 +362,13 @@ are listed.
:line
The {eam/opt}, {eam/alloy/opt}, and {eam/fs/opt} styles are identical
to the {eam}, {eam/alloy}, and {eam/fs} styles, except that they are
written in an optimized fashion for faster CPU execution. See "this
section"_doc/Section_accerate.html of the manual for more details.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to

17
doc/pair_gayberne.html
View File

@ -140,23 +140,18 @@ pair_coeff sigma to 1.0 as well.
<HR>
<P>The <I>gayberne/gpu</I> style is identical to the <I>gayberne</I> style, except
that each processor off-loads its pairwise calculations to a GPU chip.
that each processor off-loads its pairwise calculations to a GPU.
Depending on the hardware available on your system this can provide a
significant speed-up, especially for the relatively expensive
computations inherent in Gay-Berne interactions. See the <A HREF = "Section_start.html#2_8">Running on
GPUs</A> section of the manual for more details
about hardware and software requirements for using GPUs.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
computations inherent in Gay-Berne interactions. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
</P>
<P>Additional requirements in your input script to run with style
<I>gayberne/gpu</I> are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>

17
doc/pair_gayberne.txt
View File

@ -135,23 +135,18 @@ pair_coeff sigma to 1.0 as well.
:line
The {gayberne/gpu} style is identical to the {gayberne} style, except
that each processor off-loads its pairwise calculations to a GPU chip.
that each processor off-loads its pairwise calculations to a GPU.
Depending on the hardware available on your system this can provide a
significant speed-up, especially for the relatively expensive
computations inherent in Gay-Berne interactions. See the "Running on
GPUs"_Section_start.html#2_8 section of the manual for more details
about hardware and software requirements for using GPUs.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
computations inherent in Gay-Berne interactions. See "this
section"_doc/Section_accerate.html of the manual for more details.
Additional requirements in your input script to run with style
{gayberne/gpu} are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
:line

44
doc/pair_lj.html
View File

@ -107,10 +107,8 @@ given by
<P>Style <I>lj/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut</I>.
See more details below.
</P>
<P>Style <I>lj/cut/opt</I> is an optimized version of style <I>lj/cut</I> that
should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
<P>Style <I>lj/cut/opt</I> is an optimized version of style <I>lj/cut</I>. See
more details below.
</P>
<P>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
@ -123,8 +121,8 @@ specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>Style <I>lj/cut/coul/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut/coul/cut</I>.
See more details below.
<P>Style <I>lj/cut/coul/cut/gpu</I> is a GPU-enabled version of style
<I>lj/cut/coul/cut</I>. See more details below.
</P>
<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
to the Coulombic term, given by
@ -142,8 +140,8 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>lj/cut/coul/long/gpu</I> is a GPU-enabled version of style <I>lj/cut/coul/long</I>.
See more details below.
<P>Style <I>lj/cut/coul/long/gpu</I> is a GPU-enabled version of style
<I>lj/cut/coul/long</I>. See more details below.
</P>
<P>Style <I>lj/cut/coul/long/tip4p</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
@ -191,24 +189,24 @@ Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P>The <I>lj/cut/gpu</I>, <I>lj/cut/coul/cut/gpu</I>, and <I>lj/cut/coul/long/gpu</I> styles
are identical to the <I>lj/cut</I>, <I>lj/cut/coul/cut</I>, and <I>lj/cut/coul/long</I>
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
<P>The <I>lj/cut/opt</I> style is identical to the <I>lj/cut</I> style, except that
it is written in an optimized fashion for faster CPU execution. See
<A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
details.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>The <I>lj/cut/gpu</I>, <I>lj/cut/coul/cut/gpu</I>, and <I>lj/cut/coul/long/gpu</I>
styles are identical to the <I>lj/cut</I>, <I>lj/cut/coul/cut</I>, and
<I>lj/cut/coul/long</I> styles, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
</P>
<P>Additional requirements in your input script to run with GPU-enabled styles
are as follows:
<P>Additional requirements in your input script to run with GPU-enabled
styles are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls
the essential GPU selection and initialization steps.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>

44
doc/pair_lj.txt
View File

@ -96,10 +96,8 @@ Rc is the cutoff.
Style {lj/cut/gpu} is a GPU-enabled version of style {lj/cut}.
See more details below.
Style {lj/cut/opt} is an optimized version of style {lj/cut} that
should give identical answers. Depending on system size and the
processor you are running on, it may be 5-25% faster (for the pairwise
portion of the run time).
Style {lj/cut/opt} is an optimized version of style {lj/cut}. See
more details below.
Style {lj/cut/coul/cut} adds a Coulombic pairwise interaction given by
@ -112,8 +110,8 @@ specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
Style {lj/cut/coul/cut/gpu} is a GPU-enabled version of style {lj/cut/coul/cut}.
See more details below.
Style {lj/cut/coul/cut/gpu} is a GPU-enabled version of style
{lj/cut/coul/cut}. See more details below.
Style {lj/cut/coul/debye} adds an additional exp() damping factor
to the Coulombic term, given by
@ -131,8 +129,8 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {lj/cut/coul/long/gpu} is a GPU-enabled version of style {lj/cut/coul/long}.
See more details below.
Style {lj/cut/coul/long/gpu} is a GPU-enabled version of style
{lj/cut/coul/long}. See more details below.
Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
@ -180,24 +178,24 @@ Coulombic cutoff specified in the pair_style command.
:line
The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and {lj/cut/coul/long/gpu} styles
are identical to the {lj/cut}, {lj/cut/coul/cut}, and {lj/cut/coul/long}
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
The {lj/cut/opt} style is identical to the {lj/cut} style, except that
it is written in an optimized fashion for faster CPU execution. See
"this section"_doc/Section_accerate.html of the manual for more
details.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and {lj/cut/coul/long/gpu}
styles are identical to the {lj/cut}, {lj/cut/coul/cut}, and
{lj/cut/coul/long} styles, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Additional requirements in your input script to run with GPU-enabled styles
are as follows:
Additional requirements in your input script to run with GPU-enabled
styles are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls
the essential GPU selection and initialization steps.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
:line

25
doc/pair_lj96_cut.html
View File

@ -54,23 +54,18 @@ cutoff specified in the pair_style command is used.
</P>
<HR>
<P>The <I>lj96/cut/gpu</I> style is identical to the <I>lj96/cut</I> style, except that
each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
<P>The <I>lj96/cut/gpu</I> style is identical to the <I>lj96/cut</I> style, except
that each processor off-loads its pairwise calculations to a GPU.
Depending on the hardware available on your system this can provide a
speed-up. See <A HREF = "doc/Section_accerate.html">this section</A> of the manual
for more details.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>Additional requirements in your input script to run with the
<I>lj96/cut/gpu</I> style are as follows:
</P>
<P>Additional requirements in your input script to run with the <I>lj96/cut/gpu</I>
style are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps
</P>
<HR>

25
doc/pair_lj96_cut.txt
View File

@ -50,23 +50,18 @@ cutoff specified in the pair_style command is used.
:line
The {lj96/cut/gpu} style is identical to the {lj96/cut} style, except that
each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
The {lj96/cut/gpu} style is identical to the {lj96/cut} style, except
that each processor off-loads its pairwise calculations to a GPU.
Depending on the hardware available on your system this can provide a
speed-up. See "this section"_doc/Section_accerate.html of the manual
for more details.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
Additional requirements in your input script to run with the
{lj96/cut/gpu} style are as follows:
Additional requirements in your input script to run with the {lj96/cut/gpu}
style are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps
:line

23
doc/pair_lj_expand.html
View File

@ -59,22 +59,17 @@ See more details below.
<HR>
<P>The <I>lj/expand/gpu</I> style is identical to the <I>lj/expand</I> style,
except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
except that each processor off-loads its pairwise calculations to a
GPU. Depending on the hardware available on your system this can
provide a speed-up. See <A HREF = "doc/Section_accerate.html">this section</A> of
the manual for more details.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>Additional requirements in your input script to run with GPU-enabled
styles are as follows:
</P>
<P>Additional requirements in your input script to run with GPU-enabled styles
are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls
the essential GPU selection and initialization steps.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>

23
doc/pair_lj_expand.txt
View File

@ -54,22 +54,17 @@ See more details below.
:line
The {lj/expand/gpu} style is identical to the {lj/expand} style,
except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
except that each processor off-loads its pairwise calculations to a
GPU. Depending on the hardware available on your system this can
provide a speed-up. See "this section"_doc/Section_accerate.html of
the manual for more details.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
Additional requirements in your input script to run with GPU-enabled
styles are as follows:
Additional requirements in your input script to run with GPU-enabled styles
are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls
the essential GPU selection and initialization steps.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
:line

38
doc/pair_morse.html
View File

@ -54,33 +54,31 @@ commands:
<P>The last coefficient is optional. If not specified, the global morse
cutoff is used.
</P>
<P>Style <I>morse/opt</I> is an optimized version of style <I>morse</I> that should
give identical answers. Depending on system size and the processor
you are running on, it may be 5-25% faster (for the pairwise portion
of the run time).
<P>Style (morse/opt</I> is an optimized version of style <I>eam</I>. See
more details below.
</P>
<P>Style <I>morse/gpu</I> is a GPU-enabled version of style <I>morse</I>.
See more details below.
</P>
<HR>
<P>The <I>morse/gpu</I> style is identical to the <I>morse</I> style,
except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
<P>The <I>morse/opt</I> style is identical to the <I>morse/cut</I> style, except
that it is written in an optimized fashion for faster CPU execution.
See <A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
details.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
<P>The <I>morse/gpu</I> style is identical to the <I>morse</I> style, except that
each processor off-loads its pairwise calculations to a GPU.
Depending on the hardware available on your system this can provide a
speed-up. See <A HREF = "doc/Section_accerate.html">this section</A> of the manual
for more details.
</P>
<P>Additional requirements in your input script to run with GPU-enabled styles
are as follows:
<P>Additional requirements in your input script to run with GPU-enabled
styles are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls
the essential GPU selection and initialization steps.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>
@ -112,8 +110,8 @@ to be specified in an input script that reads a restart file.
<P><B>Restrictions:</B>
</P>
<P>The <I>morse/opt</I> style is part of the "opt" package. The <I>morse/gpu</I>
style is part of the "gpu" package. They are only
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
style is part of the "gpu" package. They are only enabled if LAMMPS
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>

38
doc/pair_morse.txt
View File

@ -47,33 +47,31 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global morse
cutoff is used.
Style {morse/opt} is an optimized version of style {morse} that should
give identical answers. Depending on system size and the processor
you are running on, it may be 5-25% faster (for the pairwise portion
of the run time).
Style (morse/opt} is an optimized version of style {eam}. See
more details below.
Style {morse/gpu} is a GPU-enabled version of style {morse}.
See more details below.
:line
The {morse/gpu} style is identical to the {morse} style,
except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
The {morse/opt} style is identical to the {morse/cut} style, except
that it is written in an optimized fashion for faster CPU execution.
See "this section"_doc/Section_accerate.html of the manual for more
details.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
The {morse/gpu} style is identical to the {morse} style, except that
each processor off-loads its pairwise calculations to a GPU.
Depending on the hardware available on your system this can provide a
speed-up. See "this section"_doc/Section_accerate.html of the manual
for more details.
Additional requirements in your input script to run with GPU-enabled styles
are as follows:
Additional requirements in your input script to run with GPU-enabled
styles are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls
the essential GPU selection and initialization steps.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
:line
@ -105,8 +103,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
The {morse/opt} style is part of the "opt" package. The {morse/gpu}
style is part of the "gpu" package. They are only
enabled if LAMMPS was built with those packages. See the "Making
style is part of the "gpu" package. They are only enabled if LAMMPS
was built with those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]