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doc/Section_howto.txt
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@ -315,7 +315,7 @@ All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in "this
section"_Section_start.html#2_6 of the manual.
section"_Section_start.html#start_6 of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
@ -351,13 +351,13 @@ runs different replicas at a series of temperature to facilitate
rare-event sampling.
These command can only be used if LAMMPS was built with the "replica"
package. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info on packages.
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
switch"_Section_start.html#2_6 to launch LAMMPS on multiple
switch"_Section_start.html#start_6 to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
@ -365,8 +365,8 @@ mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
of the "-in command-line switch"_Section_start.html#2_6 to specify the
input script which is required when running in multi-replica mode.
of the "-in command-line switch"_Section_start.html#start_6 to specify
the input script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
@ -655,10 +655,10 @@ strain induced across grain boundaries :l,ule
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
"This section"_Section_start.html#2_4 of the documentation describes
how to build LAMMPS as a library. Once this is done, you can
interface with LAMMPS either via C++, C, Fortran, or Python (or any
other language that supports a vanilla C-like interface). For
"This section"_Section_start.html#start_4 of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) "instances" of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
@ -1645,10 +1645,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
6.19 Library interface to LAMMPS :link(6_19),h4
As described in "this section"_Section_start.html#2_4, LAMMPS can be
built as a library, so that it can be called by another code, used in
a "coupled manner"_Section_howto.html#6_10 with other codes, or driven
through a "Python interface"_Section_python.html.
As described in "this section"_Section_start.html#start_4, LAMMPS can
be built as a library, so that it can be called by another code, used
in a "coupled manner"_Section_howto.html#6_10 with other codes, or
driven through a "Python interface"_Section_python.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
@ -1667,11 +1667,12 @@ void lammps_file(void *, char *);
char *lammps_command(void *, char *); :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line arguments"_#2_6 when
LAMMPS is run in stand-alone mode from the command line, and a MPI
communicator for LAMMPS to run under. It returns a ptr to the LAMMPS
object that is created, and which is used in subsequent library calls.
The lammps_open() function can be called multiple times, to create
list of strings as if they were "command-line
arguments"_Section_start.html#start_6 when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This