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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7626 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-01-31 22:57:34 +00:00
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8
doc/Section_intro.html
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@ -155,13 +155,13 @@ commands)
<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
<LI> water potentials: TIP3P, TIP4P, SPC
<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
<LI> <A HREF = "http://openkim.org">KIM archive</A> of potentials
<LI> long-range Coulombics and dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
<LI> force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
<LI> handful of GPU-enabled pair styles
<LI> handful of GPU-enabled pair styles
<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
<LI> overlaid potentials: superposition of multiple pair potentials
</UL>
<P> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
</P>
<H4>Atom creation
</H4>
<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,

5
doc/Section_intro.txt
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@ -154,13 +154,14 @@ commands)
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
"KIM archive"_http://openkim.org of potentials
long-range Coulombics and dispersion: Ewald, Wolf, \
PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
handful of GPU-enabled pair styles :ul
handful of GPU-enabled pair styles
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
overlaid potentials: superposition of multiple pair potentials :ul
Atom creation :h4
("read_data"_read_data.html, "lattice"_lattice.html,

6
doc/Section_packages.html
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@ -50,7 +50,8 @@ packages, more details are provided.
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">howto</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6<A HREF = "pair_kim.html">>howto</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > pair_style kim</A></TD><TD > kim</TD><TD > lib/kim</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
@ -77,6 +78,9 @@ Jonathan Higdon's group at UIUC.
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
</P>
<P>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package.

4
doc/Section_packages.txt
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@ -46,6 +46,7 @@ DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dip
FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
GPU, GPU-enabled potentials, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu
GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, -
KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), pair_style kim"_pair_kim.html, kim, lib/kim
KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
@ -71,6 +72,9 @@ Jonathan Higdon's group at UIUC.
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
command implemented as part of the package.

23
doc/Section_start.html
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@ -637,10 +637,10 @@ type "make package" to see all of the package-related make options.
<P>A few of the standard and user packages require additional auxiliary
libraries to be compiled first. If you get a LAMMPS build error about
a missing library, this is likely the reason. The source code for
these libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these or see
<A HREF = "Section_packages.html">Section_packages</A> of the doc pages.
a missing library, this is likely the reason. The source code or
hooks to these libraries is included in the LAMMPS distribution under
the "lib" directory. Look at the lib/README file for a list of these
or see <A HREF = "Section_packages.html">Section_packages</A> of the doc pages.
</P>
<P>Each lib directory has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done
@ -649,13 +649,16 @@ in this manner:
<PRE>make -f Makefile.g++
</PRE>
<P>in the appropriate directory, e.g. in lib/reax. Some of the libraries
do not build this way. Again, see the libary README file for details.
do not build this way. Some of the directories do not even have
source code for the library, since you are expected to download and
build it separately. Again, see the libary README file for details.
</P>
<P>In any event, you will need to use a Makefile that is a match for your
system. If one of the provided Makefiles is not appropriate for your
system you will need to edit or add one. For example, in the case of
Fortran-based libraries, your system must have a Fortran compiler, the
settings for which will need to be listed in the Makefile.
<P>If you are building the library, you will need to use a Makefile that
is a match for your system. If one of the provided Makefiles is not
appropriate for your system you will need to edit or add one. For
example, in the case of Fortran-based libraries, your system must have
a Fortran compiler, the settings for which will need to be listed in
the Makefile.
</P>
<P>When you have built one of these libraries, there are 2 things to
check:

23
doc/Section_start.txt
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@ -631,10 +631,10 @@ type "make package" to see all of the package-related make options.
A few of the standard and user packages require additional auxiliary
libraries to be compiled first. If you get a LAMMPS build error about
a missing library, this is likely the reason. The source code for
these libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these or see
"Section_packages"_Section_packages.html of the doc pages.
a missing library, this is likely the reason. The source code or
hooks to these libraries is included in the LAMMPS distribution under
the "lib" directory. Look at the lib/README file for a list of these
or see "Section_packages"_Section_packages.html of the doc pages.
Each lib directory has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done
@ -643,13 +643,16 @@ in this manner:
make -f Makefile.g++ :pre
in the appropriate directory, e.g. in lib/reax. Some of the libraries
do not build this way. Again, see the libary README file for details.
do not build this way. Some of the directories do not even have
source code for the library, since you are expected to download and
build it separately. Again, see the libary README file for details.
In any event, you will need to use a Makefile that is a match for your
system. If one of the provided Makefiles is not appropriate for your
system you will need to edit or add one. For example, in the case of
Fortran-based libraries, your system must have a Fortran compiler, the
settings for which will need to be listed in the Makefile.
If you are building the library, you will need to use a Makefile that
is a match for your system. If one of the provided Makefiles is not
appropriate for your system you will need to edit or add one. For
example, in the case of Fortran-based libraries, your system must have
a Fortran compiler, the settings for which will need to be listed in
the Makefile.
When you have built one of these libraries, there are 2 things to
check: