forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12435 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
a0b94e9053
commit
9cefb57272
|
|
@ -11,6 +11,8 @@ Section</A>
|
|||
|
||||
<HR>
|
||||
|
||||
<P>NOTE: USER-CUDA: no newton setting needed?
|
||||
</P>
|
||||
<H3>5. Accelerating LAMMPS performance
|
||||
</H3>
|
||||
<P>This section describes various methods for improving LAMMPS
|
||||
|
|
@ -44,12 +46,12 @@ on different hardware platforms.
|
|||
understand how it currently performs and where the bottlenecks are.
|
||||
</P>
|
||||
<P>The best way to do this is run the your system (actual number of
|
||||
atoms) for a modest number of timesteps (say 100, or a few 100 at
|
||||
most) on several different processor counts, including a single
|
||||
processor if possible. Do this for an equilibrium version of your
|
||||
system, so that the 100-step timings are representative of a much
|
||||
longer run. There is typically no need to run for 1000s or timesteps
|
||||
to get accurate timings; you can simply extrapolate from short runs.
|
||||
atoms) for a modest number of timesteps (say 100 steps) on several
|
||||
different processor counts, including a single processor if possible.
|
||||
Do this for an equilibrium version of your system, so that the
|
||||
100-step timings are representative of a much longer run. There is
|
||||
typically no need to run for 1000s of timesteps to get accurate
|
||||
timings; you can simply extrapolate from short runs.
|
||||
</P>
|
||||
<P>For the set of runs, look at the timing data printed to the screen and
|
||||
log file at the end of each LAMMPS run. <A HREF = "Section_start.html#start_8">This
|
||||
|
|
@ -244,6 +246,13 @@ Technologies). It contains a handful of pair styles whose compute()
|
|||
methods were rewritten in C++ templated form to reduce the overhead
|
||||
due to if tests and other conditional code.
|
||||
</P>
|
||||
<P>Here is a quick overview of how to use the OPT package:
|
||||
</P>
|
||||
<UL><LI>include the OPT package and build LAMMPS
|
||||
<LI>use OPT pair styles in your input script
|
||||
</UL>
|
||||
<P>Details follow.
|
||||
</P>
|
||||
<P><B>Required hardware/software:</B>
|
||||
</P>
|
||||
<P>None.
|
||||
|
|
@ -255,8 +264,8 @@ due to if tests and other conditional code.
|
|||
<PRE>make yes-opt
|
||||
make machine
|
||||
</PRE>
|
||||
<P>No additional compile/link flags are needed in your lo-level
|
||||
src/MAKE/Makefile.machine.
|
||||
<P>No additional compile/link flags are needed in your machine
|
||||
Makefile in src/MAKE.
|
||||
</P>
|
||||
<P><B>Running with the OPT package:</B>
|
||||
</P>
|
||||
|
|
@ -296,6 +305,16 @@ nearly all bonded styles (bond, angle, dihedral, improper), several
|
|||
Kspace styles, and a few fix styles. The package currently
|
||||
uses the OpenMP interface for multi-threading.
|
||||
</P>
|
||||
<P>Here is a quick overview of how to use the USER-OMP package:
|
||||
</P>
|
||||
<UL><LI>specify the -fopenmp flag for compiling and linking in your machine Makefile
|
||||
<LI>include the USER-OMP package and build LAMMPS
|
||||
<LI>specify how many threads per MPI task to run with via an environment variable or the package omp command
|
||||
<LI>enable the USER-OMP package via the "-sf omp" command-line switch, or the package omp commmand
|
||||
<LI>use USER-OMP styles in your input script
|
||||
</UL>
|
||||
<P>Details follow.
|
||||
</P>
|
||||
<P><B>Required hardware/software:</B>
|
||||
</P>
|
||||
<P>Your compiler must support the OpenMP interface. You should have one
|
||||
|
|
@ -362,8 +381,7 @@ style in your input script:
|
|||
<PRE>pair_style lj/cut/omp 2.5
|
||||
fix nve/omp
|
||||
</PRE>
|
||||
<P><
|
||||
Or you can run with the "-sf omp" <A HREF = "Section_start.html#start_7">command-line
|
||||
<P>Or you can run with the "-sf omp" <A HREF = "Section_start.html#start_7">command-line
|
||||
switch</A>, which will automatically append
|
||||
"omp" to styles that support it.
|
||||
</P>
|
||||
|
|
@ -393,7 +411,7 @@ benchmark runs for a specific simulation running on a specific
|
|||
machine, paying attention to guidelines discussed in the next
|
||||
sub-section.
|
||||
</P>
|
||||
<P>A description of the multi-threading strategy used in the UESR-OMP
|
||||
<P>A description of the multi-threading strategy used in the USER-OMP
|
||||
package and some performance examples are <A HREF = "http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented
|
||||
here</A>
|
||||
</P>
|
||||
|
|
@ -502,6 +520,19 @@ NVIDIA support as well as more general OpenCL support, so that the
|
|||
same functionality can eventually be supported on a variety of GPU
|
||||
hardware.
|
||||
</UL>
|
||||
<P>Here is a quick overview of how to use the GPU package:
|
||||
</P>
|
||||
<UL><LI>build the library in lib/gpu for your GPU hardware (CUDA_ARCH) with desired precision (CUDA_PREC)
|
||||
<LI>include the GPU package and build LAMMPS
|
||||
<LI>decide how many MPI tasks per GPU to run with, i.e. set MPI tasks/node via mpirun
|
||||
<LI>specify how many GPUs per node to use (default = 1) via the package gpu command
|
||||
<LI>enable the GPU package via the "-sf gpu" command-line switch, or the package gpu commmand
|
||||
<LI>use the newton command to turn off Newton's law for pairwise interactions
|
||||
<LI>use the package gpu command to enable neighbor list building on the GPU if desired
|
||||
<LI>use GPU pair styles and kspace styles in your input script
|
||||
</UL>
|
||||
<P>Details follow.
|
||||
</P>
|
||||
<P><B>Required hardware/software:</B>
|
||||
</P>
|
||||
<P>To use this package, you currently need to have an NVIDIA GPU and
|
||||
|
|
@ -714,10 +745,20 @@ transparently.
|
|||
<LI>The package only supports use of a single MPI task, running on a
|
||||
single CPU (core), assigned to each GPU.
|
||||
</UL>
|
||||
<P>Here is a quick overview of how to use the USER-CUDA package:
|
||||
</P>
|
||||
<UL><LI>build the library in lib/cuda for your GPU hardware (arch with desired precision (precision)
|
||||
<LI>include the USER-CUDA package and build LAMMPS
|
||||
<LI>use the mpirun command to specify 1 MPI task per GPU (on each node)
|
||||
<LI>specify how many GPUs per node to use (default = 1) via the package cuda command
|
||||
<LI>enable the USER-CUDA package via the "-c on" command-line switch
|
||||
<LI>use USER-CUDA styles in your input script
|
||||
</UL>
|
||||
<P>Details follow.
|
||||
</P>
|
||||
<P><B>Required hardware/software:</B>
|
||||
</P>
|
||||
<P>To use this package, you need to have an NVIDIA GPU and
|
||||
install the NVIDIA Cuda software on your system:
|
||||
<P>To use this package, you need to have one or more NVIDIA GPUs and install the NVIDIA Cuda software on your system:
|
||||
</P>
|
||||
<P>Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
|
||||
help you to find out the Compute Capability of your card:
|
||||
|
|
@ -1260,6 +1301,24 @@ suffix to "omp" so that styles from the USER-OMP package will be used
|
|||
if available, after first testing if a style from the USER-INTEL
|
||||
package is available.
|
||||
</P>
|
||||
<P>Here is a quick overview of how to use the USER-INTEL package
|
||||
for CPU acceleration:
|
||||
</P>
|
||||
<UL><LI>specify these CCFLAGS in your machine Makefile: -fopenmp, -DLAMMPS_MEMALIGN=64, and -restrict, -xHost
|
||||
<LI>specify -fopenmp with LINKFLAGS in your machine Makefile
|
||||
<LI>include the USER-INTEL package and (optionally) USER-OMP package and build LAMMP
|
||||
<LI>if also using the USER-OMP package, specify how many threads per MPI task to run with via an environment variable or the package omp command
|
||||
<LI>use USER-INTEL styles in your input script
|
||||
</UL>
|
||||
<P>Running with the USER-INTEL package to offload to the Intel(R) Xeon Phi(TM)
|
||||
is the same except for these additional steps:
|
||||
</P>
|
||||
<UL><LI>add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Machine makefile
|
||||
<LI>add the flag -offload to the LINKFLAGS in your Machine makefile
|
||||
<LI>the package intel command can be used to adjust threads per coprocessor
|
||||
</UL>
|
||||
<P>Details follow.
|
||||
</P>
|
||||
<P><B>Required hardware/software:</B>
|
||||
</P>
|
||||
<P>To use the offload option, you must have one or more Intel(R) Xeon
|
||||
|
|
|
|||
|
|
@ -8,6 +8,8 @@ Section"_Section_howto.html :c
|
|||
|
||||
:line
|
||||
|
||||
NOTE: USER-CUDA: no newton setting needed?
|
||||
|
||||
5. Accelerating LAMMPS performance :h3
|
||||
|
||||
This section describes various methods for improving LAMMPS
|
||||
|
|
@ -40,12 +42,12 @@ Before trying to make your simulation run faster, you should
|
|||
understand how it currently performs and where the bottlenecks are.
|
||||
|
||||
The best way to do this is run the your system (actual number of
|
||||
atoms) for a modest number of timesteps (say 100, or a few 100 at
|
||||
most) on several different processor counts, including a single
|
||||
processor if possible. Do this for an equilibrium version of your
|
||||
system, so that the 100-step timings are representative of a much
|
||||
longer run. There is typically no need to run for 1000s or timesteps
|
||||
to get accurate timings; you can simply extrapolate from short runs.
|
||||
atoms) for a modest number of timesteps (say 100 steps) on several
|
||||
different processor counts, including a single processor if possible.
|
||||
Do this for an equilibrium version of your system, so that the
|
||||
100-step timings are representative of a much longer run. There is
|
||||
typically no need to run for 1000s of timesteps to get accurate
|
||||
timings; you can simply extrapolate from short runs.
|
||||
|
||||
For the set of runs, look at the timing data printed to the screen and
|
||||
log file at the end of each LAMMPS run. "This
|
||||
|
|
@ -238,6 +240,13 @@ Technologies). It contains a handful of pair styles whose compute()
|
|||
methods were rewritten in C++ templated form to reduce the overhead
|
||||
due to if tests and other conditional code.
|
||||
|
||||
Here is a quick overview of how to use the OPT package:
|
||||
|
||||
include the OPT package and build LAMMPS
|
||||
use OPT pair styles in your input script :ul
|
||||
|
||||
Details follow.
|
||||
|
||||
[Required hardware/software:]
|
||||
|
||||
None.
|
||||
|
|
@ -249,8 +258,8 @@ Include the package and build LAMMPS.
|
|||
make yes-opt
|
||||
make machine :pre
|
||||
|
||||
No additional compile/link flags are needed in your lo-level
|
||||
src/MAKE/Makefile.machine.
|
||||
No additional compile/link flags are needed in your machine
|
||||
Makefile in src/MAKE.
|
||||
|
||||
[Running with the OPT package:]
|
||||
|
||||
|
|
@ -290,6 +299,16 @@ nearly all bonded styles (bond, angle, dihedral, improper), several
|
|||
Kspace styles, and a few fix styles. The package currently
|
||||
uses the OpenMP interface for multi-threading.
|
||||
|
||||
Here is a quick overview of how to use the USER-OMP package:
|
||||
|
||||
specify the -fopenmp flag for compiling and linking in your machine Makefile
|
||||
include the USER-OMP package and build LAMMPS
|
||||
specify how many threads per MPI task to run with via an environment variable or the package omp command
|
||||
enable the USER-OMP package via the "-sf omp" command-line switch, or the package omp commmand
|
||||
use USER-OMP styles in your input script :ul
|
||||
|
||||
Details follow.
|
||||
|
||||
[Required hardware/software:]
|
||||
|
||||
Your compiler must support the OpenMP interface. You should have one
|
||||
|
|
@ -355,7 +374,7 @@ style in your input script:
|
|||
|
||||
pair_style lj/cut/omp 2.5
|
||||
fix nve/omp :pre
|
||||
<
|
||||
|
||||
Or you can run with the "-sf omp" "command-line
|
||||
switch"_Section_start.html#start_7, which will automatically append
|
||||
"omp" to styles that support it.
|
||||
|
|
@ -386,7 +405,7 @@ benchmark runs for a specific simulation running on a specific
|
|||
machine, paying attention to guidelines discussed in the next
|
||||
sub-section.
|
||||
|
||||
A description of the multi-threading strategy used in the UESR-OMP
|
||||
A description of the multi-threading strategy used in the USER-OMP
|
||||
package and some performance examples are "presented
|
||||
here"_http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1
|
||||
|
||||
|
|
@ -495,6 +514,19 @@ NVIDIA support as well as more general OpenCL support, so that the
|
|||
same functionality can eventually be supported on a variety of GPU
|
||||
hardware. :l,ule
|
||||
|
||||
Here is a quick overview of how to use the GPU package:
|
||||
|
||||
build the library in lib/gpu for your GPU hardware (CUDA_ARCH) with desired precision (CUDA_PREC)
|
||||
include the GPU package and build LAMMPS
|
||||
decide how many MPI tasks per GPU to run with, i.e. set MPI tasks/node via mpirun
|
||||
specify how many GPUs per node to use (default = 1) via the package gpu command
|
||||
enable the GPU package via the "-sf gpu" command-line switch, or the package gpu commmand
|
||||
use the newton command to turn off Newton's law for pairwise interactions
|
||||
use the package gpu command to enable neighbor list building on the GPU if desired
|
||||
use GPU pair styles and kspace styles in your input script :ul
|
||||
|
||||
Details follow.
|
||||
|
||||
[Required hardware/software:]
|
||||
|
||||
To use this package, you currently need to have an NVIDIA GPU and
|
||||
|
|
@ -707,10 +739,20 @@ Neighbor lists are constructed on the GPU. :l
|
|||
The package only supports use of a single MPI task, running on a
|
||||
single CPU (core), assigned to each GPU. :l,ule
|
||||
|
||||
Here is a quick overview of how to use the USER-CUDA package:
|
||||
|
||||
build the library in lib/cuda for your GPU hardware (arch with desired precision (precision)
|
||||
include the USER-CUDA package and build LAMMPS
|
||||
use the mpirun command to specify 1 MPI task per GPU (on each node)
|
||||
specify how many GPUs per node to use (default = 1) via the package cuda command
|
||||
enable the USER-CUDA package via the "-c on" command-line switch
|
||||
use USER-CUDA styles in your input script :ul
|
||||
|
||||
Details follow.
|
||||
|
||||
[Required hardware/software:]
|
||||
|
||||
To use this package, you need to have an NVIDIA GPU and
|
||||
install the NVIDIA Cuda software on your system:
|
||||
To use this package, you need to have one or more NVIDIA GPUs and install the NVIDIA Cuda software on your system:
|
||||
|
||||
Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
|
||||
help you to find out the Compute Capability of your card:
|
||||
|
|
@ -1253,6 +1295,24 @@ suffix to "omp" so that styles from the USER-OMP package will be used
|
|||
if available, after first testing if a style from the USER-INTEL
|
||||
package is available.
|
||||
|
||||
Here is a quick overview of how to use the USER-INTEL package
|
||||
for CPU acceleration:
|
||||
|
||||
specify these CCFLAGS in your machine Makefile: -fopenmp, -DLAMMPS_MEMALIGN=64, and -restrict, -xHost
|
||||
specify -fopenmp with LINKFLAGS in your machine Makefile
|
||||
include the USER-INTEL package and (optionally) USER-OMP package and build LAMMP
|
||||
if also using the USER-OMP package, specify how many threads per MPI task to run with via an environment variable or the package omp command
|
||||
use USER-INTEL styles in your input script :ul
|
||||
|
||||
Running with the USER-INTEL package to offload to the Intel(R) Xeon Phi(TM)
|
||||
is the same except for these additional steps:
|
||||
|
||||
add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Machine makefile
|
||||
add the flag -offload to the LINKFLAGS in your Machine makefile
|
||||
the package intel command can be used to adjust threads per coprocessor :ul
|
||||
|
||||
Details follow.
|
||||
|
||||
[Required hardware/software:]
|
||||
|
||||
To use the offload option, you must have one or more Intel(R) Xeon
|
||||
|
|
|
|||
|
|
@ -406,12 +406,13 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
|||
<TR ALIGN="center"><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph (o)</A></TD><TD ><A HREF = "fix_nphug.html">nphug (o)</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere (o)</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere (o)</A></TD><TD ><A HREF = "fix_nh.html">npt (co)</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_npt_sphere.html">npt/sphere (o)</A></TD><TD ><A HREF = "fix_nve.html">nve (cko)</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere (o)</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt (co)</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere (o)</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod (o)</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere (o)</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq.html">qeq</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>These are additional fix styles in USER packages, which can be used if
|
||||
|
|
|
|||
|
|
@ -527,6 +527,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
|||
"press/berendsen"_fix_press_berendsen.html,
|
||||
"print"_fix_print.html,
|
||||
"property/atom"_fix_property_atom.html,
|
||||
"qeq"_fix_qeq.html,
|
||||
"qeq/comb (o)"_fix_qeq_comb.html,
|
||||
"reax/bonds"_fix_reax_bonds.html,
|
||||
"recenter"_fix_recenter.html,
|
||||
|
|
|
|||
|
|
@ -0,0 +1,182 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix qeq/point command
|
||||
</H3>
|
||||
<H3>fix qeq/shielded command
|
||||
</H3>
|
||||
<H3>fix qeq/slater command
|
||||
</H3>
|
||||
<H3>fix qeq/dynamic command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID style Nevery cutoff tolerance maxiter params
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>style = <I>qeq/point</I> or <I>qeq/shielded</I> or <I>qeq/slater</I> or <I>qeq/dynamic</I>
|
||||
<LI>Nevery = perform charge equilibration every this many steps
|
||||
<LI>cutoff = global cutoff for charge-charge interactions (distance unit)
|
||||
<LI>tolerance = precision to which charges will be equilibrated
|
||||
<LI>maxiter = maximum iterations to perform charge equilibration
|
||||
<LI>params = a filename
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
|
||||
fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
|
||||
fix 1 all qeq/slater 5 10 1.0e-6 100 params
|
||||
fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Perform the charge equilibration (QEq) method as described in <A HREF = "#Rappe">(Rappe
|
||||
and Goddard)</A> and formulated in <A HREF = "#Nakano">(Nakano)</A> (also
|
||||
known as the matrix inversion method)
|
||||
and in <A HREF = "#Rick">(Rick and Stuart)</A> (also known as the extended
|
||||
Lagrangian method) based on the electronegativity equilization principle.
|
||||
These fixes can be used with any potential in LAMMPS, so long as it defines and
|
||||
uses charges on each atom and that QEq parameters are provided.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A>
|
||||
command should be used to perform charge equliibration with the <A HREF = "pair_comb.html">COMB
|
||||
potential</A>. The <A HREF = "fix_qeq_reax.html">fix qeq/reax</A>
|
||||
command can be used to perform charge equilibration with the <A HREF = "pair_reax_c.html">ReaxFF force
|
||||
field</A>, although fix qeq/shielded yields exact same
|
||||
results as fix qeq/reax if <I>Nevery</I>, cutoff</I>, and <I>tolerance</I> are the same.
|
||||
</P>
|
||||
<P>The QEq method minimizes the electrostatic energy of the system (or
|
||||
equalizes the derivative of energy with respect to charge of all the
|
||||
atoms) by adjusting the partial charge on individual atoms based on
|
||||
interactions with their neighbors within <I>cutoff</I>.
|
||||
It reqires some parameters for each atom type provided in a file
|
||||
specified by <I>params</I>. First line of the file should be the unit
|
||||
style of these parameters. These
|
||||
fixes support real, metal, si, cgs, and electron units. Using lj,
|
||||
micro, and nano units will result in an error.
|
||||
Each of the following lines should be formatted as follows:
|
||||
</P>
|
||||
<PRE>itype chi eta gamma zeta qcore
|
||||
</PRE>
|
||||
<P>where <I>itype</I> is the atom type from 1 to Ntypes, <I>chi</I> denotes the
|
||||
electronegativity in energy units, <I>eta</I> denotes the self-Coulomb
|
||||
potential in energy units, <I>gamma</I> denotes the shielded Coulomb
|
||||
constant defined by <A HREF = "#vanDuin">ReaxFF force field</A> in distance units,
|
||||
<I>zeta</I> denotes the Slater type orbital exponent defined by the
|
||||
<A HREF = "#Streitz">Streitz-Mintmire</A> potential (not yet available in LAMMPS)
|
||||
in reverse distance units, and <I>qcore</I> denotes the charge of the
|
||||
nucleus defined by the Streitz-Mintmire potential in charge units.
|
||||
</P>
|
||||
<P>The <I>qeq/point</I> style describes partial charges on atoms as point charges.
|
||||
Interaction between a pair of charged particles is 1/r, which is the simplest
|
||||
description of the interaction between charges. Only <I>chi</I> and <I>eta</I>
|
||||
parameters in the <I>params</I> file are used. Note that Coulomb catastrophe
|
||||
can occur if repulsion between the pair of charged particles is too weak.
|
||||
This style solves partial charges on atoms via the matrix inversion method.
|
||||
A tolerance of 1.0e-6 is usually a good number.
|
||||
</P>
|
||||
<P>The <I>qeq/shielded</I> style describes partial charges on atoms also as point
|
||||
charges, but uses a shielded Coulomb potential to describe
|
||||
the interaction between a pair of charged particles. Interaction through
|
||||
the shielded Coulomb is given by equation (13) of the
|
||||
<A HREF = "#vanDuin">ReaxFF force field</A> paper. The shielding accounts for charge overlap
|
||||
between charged particles at small separation. This style is the same as
|
||||
<A HREF = "fix_qeq_reax.html">fix qeq/reax</A>, and can be used with
|
||||
<A HREF = "pair_reax_c.html">pair_style reax/c</A>. Only <I>chi</I>, <I>eta</I>, and <I>gamma</I> parameters
|
||||
in the <I>params</I> file are used.
|
||||
This style solves partial charges on atoms via the matrix inversion method.
|
||||
A tolerance of 1.0e-6 is usually a good number.
|
||||
</P>
|
||||
<P>The <I>qeq/slater</I> style describes partial charges on atoms as spherical
|
||||
charge densities centered around atoms via the Slater 1<I>s</I> orbital, so that
|
||||
the interaction between a pair of charged particles is the product of two
|
||||
Slater 1<I>s</I> orbitals. The expression for the Slater 1<I>s</I> orbital is given under
|
||||
equation (6) of the <A HREF = "#Streitz">Streitz-Mintmire</A> paper. <I>chi</I>, <I>eta</I>, <I>zeta</I>,
|
||||
and <I>qcore</I> parameters in the <I>params</I> file are used.
|
||||
This style solves partial charges on atoms via the matrix inversion method.
|
||||
A tolerance of 1.0e-6 is usually a good number.
|
||||
</P>
|
||||
<P>The <I>qeq/dynamic</I> style describes partial charges on atoms as point charges
|
||||
that interact through 1/r, but the extended Lagrangian method is used to solve
|
||||
partial charges on atoms. Only <I>chi</I> and <I>eta</I> parameters in the <I>params</I> file
|
||||
are used. Note that Coulomb catastrophe can occur if repulsion between the
|
||||
pair of charged particles is too weak.
|
||||
A tolerance of 1.0e-3 is usually a good number.
|
||||
</P>
|
||||
<P>Note that <I>qeq/point</I>, <I>qeq/shielded</I>, and <I>qeq/slater</I> describe different charge
|
||||
models, whereas the matrix inversion method and the extended Lagrangian method
|
||||
(<I>qeq/dynamic</I>) are different solvers.
|
||||
</P>
|
||||
<P>Note that the <I>qeq/point</I> and the <I>qeq/dynamic</I> styles both describe charges as
|
||||
point charges that interact through 1/r relationship, but solve partial charges
|
||||
on atoms using different solvers. <I>qeq/point</I> and the <I>qeq/dynamic</I> styles should
|
||||
yield comparable results if the QEq parameters and <I>Nevery</I>, cutoff</I>,
|
||||
and <I>tolerance</I> are the same. <I>qeq/point</I> is typically faster, but <I>qeq/dynamic</I>
|
||||
scales better on larger sizes.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: To avoid the evaluation of the derivative of charge with
|
||||
respect to position, which is typically ill-defined, the system should have a
|
||||
zero net charge.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore)
|
||||
is an "art". Charges on atoms are not guaranteed to equilibrate with arbitrary
|
||||
choices of these parameters. We do not develop these QEq paramters.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about these fixes is written to <A HREF = "restart.html">binary restart
|
||||
files</A>. No global scalar or vector or per-atom
|
||||
quantities are stored by these fixes for access by various <A HREF = "Section_howto.html#howto_15">output
|
||||
commands</A>. No parameter of these fixes can
|
||||
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
||||
</P>
|
||||
<P>Thexe fixes are invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>These fixes are part of the USER-QEQ package. They are only enabled if
|
||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_qeq_reax.html">fix qeq/reax</A>
|
||||
<A HREF = "fix_qeq_comb.html">fix qeq/comb</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Rappe"></A>
|
||||
|
||||
<P><B>(Rappe and Goddard)</B> A. K. Rappe and W. A. Goddard III, J Physical Chemistry, 105,
|
||||
3358-3363 (1991).
|
||||
</P>
|
||||
<A NAME = "Nakano"></A>
|
||||
|
||||
<P><B>(Nakano)</B> A. Nakano, Computer Physics Communications, 104, 59-69 (1997).
|
||||
</P>
|
||||
<A NAME = "Rick"></A>
|
||||
|
||||
<P><B>(Rick and Stuart)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics
|
||||
101, 16141 (1994).
|
||||
</P>
|
||||
<A NAME = "Streitz"></A>
|
||||
|
||||
<P><B>(Streitz-Mintmire)</B> F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
|
||||
16, 11996 (1994)
|
||||
</P>
|
||||
<A NAME = "vanDuin"></A>
|
||||
|
||||
<P><B>(ReaxFF)</B> A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J
|
||||
Physical Chemistry, 105, 9396-9049 (2001)
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,169 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix qeq/point command :h3
|
||||
fix qeq/shielded command :h3
|
||||
fix qeq/slater command :h3
|
||||
fix qeq/dynamic command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID style Nevery cutoff tolerance maxiter params :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
style = {qeq/point} or {qeq/shielded} or {qeq/slater} or {qeq/dynamic}
|
||||
Nevery = perform charge equilibration every this many steps
|
||||
cutoff = global cutoff for charge-charge interactions (distance unit)
|
||||
tolerance = precision to which charges will be equilibrated
|
||||
maxiter = maximum iterations to perform charge equilibration
|
||||
params = a filename :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
|
||||
fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
|
||||
fix 1 all qeq/slater 5 10 1.0e-6 100 params
|
||||
fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Perform the charge equilibration (QEq) method as described in "(Rappe
|
||||
and Goddard)"_#Rappe and formulated in "(Nakano)"_#Nakano (also
|
||||
known as the matrix inversion method)
|
||||
and in "(Rick and Stuart)"_#Rick (also known as the extended
|
||||
Lagrangian method) based on the electronegativity equilization principle.
|
||||
These fixes can be used with any potential in LAMMPS, so long as it defines and
|
||||
uses charges on each atom and that QEq parameters are provided.
|
||||
|
||||
IMPORTANT NOTE: The "fix qeq/comb"_fix_qeq_comb.html
|
||||
command should be used to perform charge equliibration with the "COMB
|
||||
potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html
|
||||
command can be used to perform charge equilibration with the "ReaxFF force
|
||||
field"_pair_reax_c.html, although fix qeq/shielded yields exact same
|
||||
results as fix qeq/reax if {Nevery}, cutoff}, and {tolerance} are the same.
|
||||
|
||||
The QEq method minimizes the electrostatic energy of the system (or
|
||||
equalizes the derivative of energy with respect to charge of all the
|
||||
atoms) by adjusting the partial charge on individual atoms based on
|
||||
interactions with their neighbors within {cutoff}.
|
||||
It reqires some parameters for each atom type provided in a file
|
||||
specified by {params}. First line of the file should be the unit
|
||||
style of these parameters. These
|
||||
fixes support real, metal, si, cgs, and electron units. Using lj,
|
||||
micro, and nano units will result in an error.
|
||||
Each of the following lines should be formatted as follows:
|
||||
|
||||
itype chi eta gamma zeta qcore :pre
|
||||
|
||||
where {itype} is the atom type from 1 to Ntypes, {chi} denotes the
|
||||
electronegativity in energy units, {eta} denotes the self-Coulomb
|
||||
potential in energy units, {gamma} denotes the shielded Coulomb
|
||||
constant defined by "ReaxFF force field"_#vanDuin in distance units,
|
||||
{zeta} denotes the Slater type orbital exponent defined by the
|
||||
"Streitz-Mintmire"_#Streitz potential (not yet available in LAMMPS)
|
||||
in reverse distance units, and {qcore} denotes the charge of the
|
||||
nucleus defined by the Streitz-Mintmire potential in charge units.
|
||||
|
||||
The {qeq/point} style describes partial charges on atoms as point charges.
|
||||
Interaction between a pair of charged particles is 1/r, which is the simplest
|
||||
description of the interaction between charges. Only {chi} and {eta}
|
||||
parameters in the {params} file are used. Note that Coulomb catastrophe
|
||||
can occur if repulsion between the pair of charged particles is too weak.
|
||||
This style solves partial charges on atoms via the matrix inversion method.
|
||||
A tolerance of 1.0e-6 is usually a good number.
|
||||
|
||||
The {qeq/shielded} style describes partial charges on atoms also as point
|
||||
charges, but uses a shielded Coulomb potential to describe
|
||||
the interaction between a pair of charged particles. Interaction through
|
||||
the shielded Coulomb is given by equation (13) of the
|
||||
"ReaxFF force field"_#vanDuin paper. The shielding accounts for charge overlap
|
||||
between charged particles at small separation. This style is the same as
|
||||
"fix qeq/reax"_fix_qeq_reax.html, and can be used with
|
||||
"pair_style reax/c"_pair_reax_c.html. Only {chi}, {eta}, and {gamma} parameters
|
||||
in the {params} file are used.
|
||||
This style solves partial charges on atoms via the matrix inversion method.
|
||||
A tolerance of 1.0e-6 is usually a good number.
|
||||
|
||||
The {qeq/slater} style describes partial charges on atoms as spherical
|
||||
charge densities centered around atoms via the Slater 1{s} orbital, so that
|
||||
the interaction between a pair of charged particles is the product of two
|
||||
Slater 1{s} orbitals. The expression for the Slater 1{s} orbital is given under
|
||||
equation (6) of the "Streitz-Mintmire"_#Streitz paper. {chi}, {eta}, {zeta},
|
||||
and {qcore} parameters in the {params} file are used.
|
||||
This style solves partial charges on atoms via the matrix inversion method.
|
||||
A tolerance of 1.0e-6 is usually a good number.
|
||||
|
||||
The {qeq/dynamic} style describes partial charges on atoms as point charges
|
||||
that interact through 1/r, but the extended Lagrangian method is used to solve
|
||||
partial charges on atoms. Only {chi} and {eta} parameters in the {params} file
|
||||
are used. Note that Coulomb catastrophe can occur if repulsion between the
|
||||
pair of charged particles is too weak.
|
||||
A tolerance of 1.0e-3 is usually a good number.
|
||||
|
||||
Note that {qeq/point}, {qeq/shielded}, and {qeq/slater} describe different charge
|
||||
models, whereas the matrix inversion method and the extended Lagrangian method
|
||||
({qeq/dynamic}) are different solvers.
|
||||
|
||||
Note that the {qeq/point} and the {qeq/dynamic} styles both describe charges as
|
||||
point charges that interact through 1/r relationship, but solve partial charges
|
||||
on atoms using different solvers. {qeq/point} and the {qeq/dynamic} styles should
|
||||
yield comparable results if the QEq parameters and {Nevery}, cutoff},
|
||||
and {tolerance} are the same. {qeq/point} is typically faster, but {qeq/dynamic}
|
||||
scales better on larger sizes.
|
||||
|
||||
IMPORTANT NOTE: To avoid the evaluation of the derivative of charge with
|
||||
respect to position, which is typically ill-defined, the system should have a
|
||||
zero net charge.
|
||||
|
||||
IMPORTANT NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore)
|
||||
is an "art". Charges on atoms are not guaranteed to equilibrate with arbitrary
|
||||
choices of these parameters. We do not develop these QEq paramters.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about these fixes is written to "binary restart
|
||||
files"_restart.html. No global scalar or vector or per-atom
|
||||
quantities are stored by these fixes for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of these fixes can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
|
||||
Thexe fixes are invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These fixes are part of the USER-QEQ package. They are only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix qeq/reax"_fix_qeq_reax.html
|
||||
"fix qeq/comb"_fix_qeq_comb.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Rappe)
|
||||
[(Rappe and Goddard)] A. K. Rappe and W. A. Goddard III, J Physical Chemistry, 105,
|
||||
3358-3363 (1991).
|
||||
|
||||
:link(Nakano)
|
||||
[(Nakano)] A. Nakano, Computer Physics Communications, 104, 59-69 (1997).
|
||||
|
||||
:link(Rick)
|
||||
[(Rick and Stuart)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics
|
||||
101, 16141 (1994).
|
||||
|
||||
:link(Streitz)
|
||||
[(Streitz-Mintmire)] F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
|
||||
16, 11996 (1994)
|
||||
|
||||
:link(vanDuin)
|
||||
[(ReaxFF)] A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J
|
||||
Physical Chemistry, 105, 9396-9049 (2001)
|
||||
Loading…
Reference in New Issue