from lammps import lammps
lmp = lammps()
diff --git a/doc/Section_python.txt b/doc/Section_python.txt
index 3b3c28a817..4ed05e47d4 100644
--- a/doc/Section_python.txt
+++ b/doc/Section_python.txt
@@ -158,7 +158,7 @@ To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:
make yes-python
-make machine
+make machine :pre
Note that this will link LAMMPS with the Python library on your
system, which typically requires several auxiliary system libraries to
@@ -183,7 +183,7 @@ Instructions on how to build LAMMPS as a shared library are given in
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
->From the src directory, type
+From the src directory, type
make foo mode=shlib :pre
@@ -194,10 +194,11 @@ load by default. Note that if you are building multiple machine
versions of the shared library, the soft link is always set to the
most recently built version.
-If this fails, see "Section_start 5"_Section_start.html#start_5 for
-more details, especially if your LAMMPS build uses auxiliary libraries
-like MPI or FFTW which may not be built as shared libraries on your
-system.
+NOTE: If you are building LAMMPS with an MPI or FFT library or other
+auxiliary libraries (used by various packages), then all of these
+extra libraries must also be shared libraries. If the LAMMPS
+shared-library build fails with an error complaining about this, see
+"Section_start 5"_Section_start.html#start_5 for more details.
:line
@@ -610,15 +611,6 @@ lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms
:line
-NOTE: Currently, the creation of a LAMMPS object from within lammps.py
-does not take an MPI communicator as an argument. There should be a
-way to do this, so that the LAMMPS instance runs on a subset of
-processors if desired, but I don't know how to do it from Pypar. So
-for now, it runs with MPI_COMM_WORLD, which is all the processors. If
-someone figures out how to do this with one or more of the Python
-wrappers for MPI, like Pypar, please let us know and we will amend
-these doc pages.
-
The lines
from lammps import lammps
diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt
index 7025e5797a..4618b33588 100644
--- a/doc/_sources/Section_commands.txt
+++ b/doc/_sources/Section_commands.txt
@@ -455,37 +455,37 @@ with the :doc:`appropriate accelerated package `.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`adapt ` | :doc:`addforce (c) ` | :doc:`append/atoms ` | :doc:`atom/swap ` | :doc:`aveforce (c) ` | :doc:`ave/atom ` | :doc:`ave/chunk ` | :doc:`ave/correlate ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`ave/histo ` | :doc:`ave/histo/weight ` | :doc:`ave/spatial ` | :doc:`ave/time ` | :doc:`balance ` | :doc:`bond/break ` | :doc:`bond/create ` | :doc:`bond/swap ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`box/relax ` | :doc:`deform (k) ` | :doc:`deposit ` | :doc:`drag ` | :doc:`dt/reset ` | :doc:`efield ` | :doc:`enforce2d (c) ` | :doc:`evaporate ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`external ` | :doc:`freeze (c) ` | :doc:`gcmc ` | :doc:`gld ` | :doc:`gravity (co) ` | :doc:`heat ` | :doc:`indent ` | :doc:`langevin (k) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`lineforce ` | :doc:`momentum ` | :doc:`move ` | :doc:`msst ` | :doc:`neb ` | :doc:`nph (ko) ` | :doc:`nphug (o) ` | :doc:`nph/asphere (o) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`nph/sphere (o) ` | :doc:`npt (ckio) ` | :doc:`npt/asphere (o) ` | :doc:`npt/sphere (o) ` | :doc:`nve (ckio) ` | :doc:`nve/asphere (i) ` | :doc:`nve/asphere/noforce ` | :doc:`nve/body ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`nve/limit ` | :doc:`nve/line ` | :doc:`nve/noforce ` | :doc:`nve/sphere (o) ` | :doc:`nve/tri ` | :doc:`nvt (cko) ` | :doc:`nvt/asphere (o) ` | :doc:`nvt/sllod (o) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`nvt/sphere (o) ` | :doc:`oneway ` | :doc:`orient/fcc ` | :doc:`planeforce ` | :doc:`poems ` | :doc:`pour ` | :doc:`press/berendsen ` | :doc:`print ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`property/atom ` | :doc:`qeq/comb (o) ` | :doc:`qeq/dynamic ` | :doc:`qeq/fire ` | :doc:`qeq/point ` | :doc:`qeq/shielded ` | :doc:`qeq/slater ` | :doc:`reax/bonds ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`recenter ` | :doc:`restrain ` | :doc:`rigid (o) ` | :doc:`rigid/nph (o) ` | :doc:`rigid/npt (o) ` | :doc:`rigid/nve (o) ` | :doc:`rigid/nvt (o) ` | :doc:`rigid/small (o) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`rigid/small/nph ` | :doc:`rigid/small/npt ` | :doc:`rigid/small/nve ` | :doc:`rigid/small/nvt ` | :doc:`setforce (ck) ` | :doc:`shake (c) ` | :doc:`spring ` | :doc:`spring/rg ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`spring/self ` | :doc:`srd ` | :doc:`store/force ` | :doc:`store/state ` | :doc:`temp/berendsen (c) ` | :doc:`temp/csld ` | :doc:`temp/csvr ` | :doc:`temp/rescale (c) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`tfmc ` | :doc:`thermal/conductivity ` | :doc:`tmd ` | :doc:`ttm ` | :doc:`tune/kspace ` | :doc:`vector ` | :doc:`viscosity ` | :doc:`viscous (c) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`wall/colloid ` | :doc:`wall/gran ` | :doc:`wall/harmonic ` | :doc:`wall/lj1043 ` | :doc:`wall/lj126 ` | :doc:`wall/lj93 ` | :doc:`wall/piston ` | :doc:`wall/reflect (k) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`wall/region ` | :doc:`wall/srd ` | | | | | | |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`adapt ` | :doc:`addforce (c) ` | :doc:`append/atoms ` | :doc:`atom/swap ` | :doc:`aveforce (c) ` | :doc:`ave/atom ` | :doc:`ave/chunk ` | :doc:`ave/correlate ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`ave/histo ` | :doc:`ave/histo/weight ` | :doc:`ave/spatial ` | :doc:`ave/time ` | :doc:`balance ` | :doc:`bond/break ` | :doc:`bond/create ` | :doc:`bond/swap ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`box/relax ` | :doc:`deform (k) ` | :doc:`deposit ` | :doc:`drag ` | :doc:`dt/reset ` | :doc:`efield ` | :doc:`enforce2d (c) ` | :doc:`evaporate ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`external ` | :doc:`freeze (c) ` | :doc:`gcmc ` | :doc:`gld ` | :doc:`gravity (co) ` | :doc:`heat ` | :doc:`indent ` | :doc:`langevin (k) ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`lineforce ` | :doc:`momentum ` | :doc:`move ` | :doc:`msst ` | :doc:`neb ` | :doc:`nph (ko) ` | :doc:`nphug (o) ` | :doc:`nph/asphere (o) ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`nph/sphere (o) ` | :doc:`npt (ckio) ` | :doc:`npt/asphere (o) ` | :doc:`npt/sphere (o) ` | :doc:`nve (ckio) ` | :doc:`nve/asphere (i) ` | :doc:`nve/asphere/noforce ` | :doc:`nve/body ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`nve/limit ` | :doc:`nve/line ` | :doc:`nve/noforce ` | :doc:`nve/sphere (o) ` | :doc:`nve/tri ` | :doc:`nvt (cko) ` | :doc:`nvt/asphere (o) ` | :doc:`nvt/sllod (o) ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`nvt/sphere (o) ` | :doc:`oneway ` | :doc:`orient/fcc ` | :doc:`planeforce ` | :doc:`poems ` | :doc:`pour ` | :doc:`press/berendsen ` | :doc:`print ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`property/atom ` | :doc:`qeq/comb (o) ` | :doc:`qeq/dynamic ` | :doc:`qeq/fire ` | :doc:`qeq/point ` | :doc:`qeq/shielded ` | :doc:`qeq/slater ` | :doc:`rattle ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`reax/bonds ` | :doc:`recenter ` | :doc:`restrain ` | :doc:`rigid (o) ` | :doc:`rigid/nph (o) ` | :doc:`rigid/npt (o) ` | :doc:`rigid/nve (o) ` | :doc:`rigid/nvt (o) ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`rigid/small (o) ` | :doc:`rigid/small/nph ` | :doc:`rigid/small/npt ` | :doc:`rigid/small/nve ` | :doc:`rigid/small/nvt ` | :doc:`setforce (ck) ` | :doc:`shake (c) ` | :doc:`spring ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`spring/rg ` | :doc:`spring/self ` | :doc:`srd ` | :doc:`store/force ` | :doc:`store/state ` | :doc:`temp/berendsen (c) ` | :doc:`temp/csld ` | :doc:`temp/csvr ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`temp/rescale (c) ` | :doc:`tfmc ` | :doc:`thermal/conductivity ` | :doc:`tmd ` | :doc:`ttm ` | :doc:`tune/kspace ` | :doc:`vector ` | :doc:`viscosity ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`viscous (c) ` | :doc:`wall/colloid ` | :doc:`wall/gran ` | :doc:`wall/harmonic ` | :doc:`wall/lj1043 ` | :doc:`wall/lj126 ` | :doc:`wall/lj93 ` | :doc:`wall/piston ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`wall/reflect (k) ` | :doc:`wall/region ` | :doc:`wall/srd ` | | | | | |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
These are additional fix styles in USER packages, which can be used if
:ref:`LAMMPS is built with the appropriate package `.
@@ -493,7 +493,7 @@ These are additional fix styles in USER packages, which can be used if
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
| :doc:`adapt/fep ` | :doc:`addtorque ` | :doc:`atc ` | :doc:`ave/correlate/long ` | :doc:`ave/spatial/sphere ` | :doc:`colvars ` |
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
-| :doc:`drude ` | :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse ` | :doc:`eos/cv ` | :doc:`eos/table ` | :doc:`gle ` |
+| :doc:`drude ` | :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse ` | :doc:`eos/cv ` | :doc:`eos/table ` | :doc:`gle ` |
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
| :doc:`imd ` | :doc:`ipi ` | :doc:`langevin/drude