ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6809 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2011-08-25 17:01:01 +00:00
parent a3add0b021
commit a8cf1de735
338 changed files with 1081 additions and 1063 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
doc/Section_python.txt
View File

@ -18,11 +18,11 @@ either from a Python script or interactively from a Python prompt.
language which can be used to wrap software like LAMMPS and other
packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See "this
section"_Section_howto.html#4_10 of the manual and the couple
section"_Section_howto.html#howto_10 of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See "this section"_Section_start.html#start_4 about how
to build LAMMPS as a library, and "this
section"_Section_howto.html#4_19 for a description of the library
section"_Section_howto.html#howto_19 for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
is exposed to Python. It is designed to be easy to add functions to.
@ -86,13 +86,13 @@ setup discussion. The next to last sub-section describes the Python
syntax used to invoke LAMMPS. The last sub-section describes example
Python scripts included in the python directory.
11.1 "Extending Python with a serial version of LAMMPS"_#11_1
11.2 "Creating a shared MPI library"_#11_2
11.3 "Extending Python with a parallel version of LAMMPS"_#11_3
11.4 "Extending Python with MPI"_#11_4
11.5 "Testing the Python-LAMMPS interface"_#11_5
11.6 "Using LAMMPS from Python"_#11_6
11.7 "Example Python scripts that use LAMMPS"_#11_7 :ul
11.1 "Extending Python with a serial version of LAMMPS"_#py_1
11.2 "Creating a shared MPI library"_#py_2
11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
11.4 "Extending Python with MPI"_#py_4
11.5 "Testing the Python-LAMMPS interface"_#py_5
11.6 "Using LAMMPS from Python"_#py_6
11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
Before proceeding, there are 2 items to note.
@ -131,7 +131,7 @@ LAMMPS wrapper.
:line
:line
11.1 Extending Python with a serial version of LAMMPS :link(11_1),h4
11.1 Extending Python with a serial version of LAMMPS :link(py_1),h4
From the python directory in the LAMMPS distribution, type
@ -161,7 +161,7 @@ If these commands are successful, a {lammps.py} and
:line
11.2 Creating a shared MPI library :link(11_2),h4
11.2 Creating a shared MPI library :link(py_2),h4
A shared library is one that is dynamically loadable, which is what
Python requires. On Linux this is a library file that ends in ".so",
@ -192,7 +192,7 @@ stand-alone code.
:line
11.3 Extending Python with a parallel version of LAMMPS :link(11_3),h4
11.3 Extending Python with a parallel version of LAMMPS :link(py_3),h4
From the python directory, type
@ -230,7 +230,7 @@ will be put in the appropriate directory.
:line
11.4 Extending Python with MPI :link(11_4),h4
11.4 Extending Python with MPI :link(py_4),h4
There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
@ -305,7 +305,7 @@ and see one line of output for each processor you ran on.
:line
11.5 Testing the Python-LAMMPS interface :link(11_5),h4
11.5 Testing the Python-LAMMPS interface :link(py_5),h4
Before using LAMMPS in a Python program, one more step is needed. The
interface to LAMMPS is via the Python ctypes package, which loads the
@ -398,7 +398,7 @@ Python on a single processor, not in parallel.
:line
:line
11.6 Using LAMMPS from Python :link(11_6),h4
11.6 Using LAMMPS from Python :link(py_6),h4
The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a
@ -494,7 +494,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See "this section"_Section_howto.html#4_15 of the manual for a
See "this section"_Section_howto.html#howto_15 of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
"computes"_compute.html and "fixes"_fix.html for a description of what
@ -589,7 +589,7 @@ Python script. Isn't ctypes amazing? :l,ule
:line
:line
11.7 Example Python scripts that use LAMMPS :link(11_7),h4
11.7 Example Python scripts that use LAMMPS :link(py_7),h4
These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of