diff --git a/doc/Section_python.html b/doc/Section_python.html index 46c4ab97837676c230d40da4e6adfbbd5699aa25..9b97533af18aff05fb025ddba9a89cc1fee92c86 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -58,12 +58,13 @@ operations within LAMMPS, such as running a simulation for a reasonable number of timesteps, then the overhead cost of invoking LAMMPS thru Python will be negligible. </P> -<P>Before using LAMMPS from a Python script, you have to do two things. -You need to set two environment variables. And you need to build -LAMMPS as a dynamic shared library, so it can be loaded by Python. -Both these steps are discussed below. If you wish to run LAMMPS in -parallel from Python, you also need to extend your Python with MPI. -This is also discussed below. +<P>Before using LAMMPS from a Python script, you need to do two things. +You need to build LAMMPS as a dynamic shared library, so it can be +loaded by Python. And you need to tell Python how to find the library +and the Python wrapper file python/lammps.py. Both these steps are +discussed below. If you wish to run LAMMPS in parallel from Python, +you also need to extend your Python with MPI. This is also discussed +below. </P> <P>The Python wrapper for LAMMPS uses the amazing and magical (to me) "ctypes" package in Python, which auto-generates the interface code @@ -131,7 +132,7 @@ python/lammps.py file. </P> <P>You can invoke install.py from the python directory as </P> -<PRE>% python install.py <B>libdir</B> <B>pydir</B> +<PRE>% python install.py [libdir] [pydir] </PRE> <P>The optional libdir is where to copy the LAMMPS shared library to; the default is /usr/local/lib. The optional pydir is where to copy the @@ -146,12 +147,12 @@ non-standard locations, such as within your own user space, you will need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables accordingly, as above. </P> -<P>If the instally.py script does not allow you to copy files into system +<P>If the install.py script does not allow you to copy files into system directories, prefix the python command with "sudo". If you do this, make sure that the Python that root runs is the same as the Python you run. E.g. you may need to do something like </P> -<PRE>% sudo /usr/local/bin/python install.py <B>libdir</B> <B>pydir</B> +<PRE>% sudo /usr/local/bin/python install.py [libdir] [pydir] </PRE> <P>You can also invoke install.py from the make command in the src directory as @@ -275,8 +276,8 @@ If the load fails, the most common error to see is <PRE>OSError: Could not load LAMMPS dynamic library </PRE> <P>which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMMPS shared library -or one of the auxiliary shared libraries it depends on. +typically occurs if the system can't find the LAMMPS shared library or +one of the auxiliary shared libraries it depends on. </P> <P>Python (actually the operating system) isn't verbose about telling you why the load failed, so carefully go through the steps above regarding diff --git a/doc/Section_python.txt b/doc/Section_python.txt index 3c29fe6fe6d21c829ce940a2be76810532156414..47e53fc8a860c2272e69d8e1dce9f1a38aef6660 100644 --- a/doc/Section_python.txt +++ b/doc/Section_python.txt @@ -55,12 +55,13 @@ operations within LAMMPS, such as running a simulation for a reasonable number of timesteps, then the overhead cost of invoking LAMMPS thru Python will be negligible. -Before using LAMMPS from a Python script, you have to do two things. -You need to set two environment variables. And you need to build -LAMMPS as a dynamic shared library, so it can be loaded by Python. -Both these steps are discussed below. If you wish to run LAMMPS in -parallel from Python, you also need to extend your Python with MPI. -This is also discussed below. +Before using LAMMPS from a Python script, you need to do two things. +You need to build LAMMPS as a dynamic shared library, so it can be +loaded by Python. And you need to tell Python how to find the library +and the Python wrapper file python/lammps.py. Both these steps are +discussed below. If you wish to run LAMMPS in parallel from Python, +you also need to extend your Python with MPI. This is also discussed +below. The Python wrapper for LAMMPS uses the amazing and magical (to me) "ctypes" package in Python, which auto-generates the interface code @@ -127,7 +128,7 @@ python/lammps.py file. You can invoke install.py from the python directory as -% python install.py [libdir] [pydir] :pre +% python install.py \[libdir\] \[pydir\] :pre The optional libdir is where to copy the LAMMPS shared library to; the default is /usr/local/lib. The optional pydir is where to copy the @@ -142,12 +143,12 @@ non-standard locations, such as within your own user space, you will need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables accordingly, as above. -If the instally.py script does not allow you to copy files into system +If the install.py script does not allow you to copy files into system directories, prefix the python command with "sudo". If you do this, make sure that the Python that root runs is the same as the Python you run. E.g. you may need to do something like -% sudo /usr/local/bin/python install.py [libdir] [pydir] :pre +% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre You can also invoke install.py from the make command in the src directory as @@ -271,8 +272,8 @@ If the load fails, the most common error to see is OSError: Could not load LAMMPS dynamic library :pre which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMMPS shared library -or one of the auxiliary shared libraries it depends on. +typically occurs if the system can't find the LAMMPS shared library or +one of the auxiliary shared libraries it depends on. Python (actually the operating system) isn't verbose about telling you why the load failed, so carefully go through the steps above regarding diff --git a/doc/Section_start.html b/doc/Section_start.html index e225c3394aa365253363ba3a72222f879e23f349..2951ab50966783c602afe24807e5b85a4d59c271 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -850,7 +850,7 @@ should be the file /usr/local/lib/libmpich.so. the environment variable LD_LIBRARY_PATH. So you may wish to copy the file src/liblammps.so or src/liblammps_g++.so (for example) to a place the system can find it by default, such as /usr/local/lib, or you may -wish to add the lammps src directory to LD_LIBRARY_PATH, so that the +wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the current version of the shared library is always available to programs that use it. </P> diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 5712e9123650ce7c08f0a538f25f50ac84b5ec18..7551850b9f68a0d54fcfe90cb2d81727028161cd 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -844,7 +844,7 @@ The operating system finds shared libraries to load at run-time using the environment variable LD_LIBRARY_PATH. So you may wish to copy the file src/liblammps.so or src/liblammps_g++.so (for example) to a place the system can find it by default, such as /usr/local/lib, or you may -wish to add the lammps src directory to LD_LIBRARY_PATH, so that the +wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the current version of the shared library is always available to programs that use it.