Merge pull request #2589 from akohlmey/check-python-version-match

Add version check for liblammps vs. python module

cmake/CMakeLists.txt

@@ -662,8 +662,8 @@ if(BUILD_SHARED_LIBS)
   endif()
   if (Python_EXECUTABLE)
     add_custom_target(
-      install-python
-      ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      install-python ${CMAKE_COMMAND} -E remove_directory build
+      COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
       -p ${LAMMPS_PYTHON_DIR}/lammps
       -l ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}

doc/src/Developer_notes.rst

@@ -90,7 +90,7 @@ The fix must also do the following:
 The fix must also specify whether (by default) to include or exclude
 these contributions to the global/peratom energy/virial of the system.
 For the fix to include the contributions, set either of both of these
-variables in the contructor:
+variables in the constructor:
 
 * *thermo_energy* = 1, for global and peratom energy
 * *thermo_virial* = 1, for global and peratom virial

doc/src/Python_module.rst

@@ -26,6 +26,23 @@ There are multiple Python interface classes in the :py:mod:`lammps` module:
 
 .. _mpi4py_url: https://mpi4py.readthedocs.io
 
+.. admonition:: Version check
+   :class: note
+
+   The :py:mod:`lammps` module stores the version number of the LAMMPS
+   version it is installed from.  When initializing the
+   :py:class:`lammps <lammps.lammps>` class, this version is checked to
+   be the same as the result from :py:func:`lammps.version`, the version
+   of the LAMMPS shared library that the module interfaces to.  If the
+   they are not the same an AttributeError exception is raised since a
+   mismatch of versions (e.g.  due to incorrect use of the
+   ``LD_LIBRARY_PATH`` or ``PYTHONPATH`` environment variables can lead
+   to crashes or data corruption and otherwise incorrect behavior.
+
+.. automodule:: lammps
+   :members:
+   :noindex:
+
 ----------
 
 The ``lammps`` class API

doc/src/fix_cmap.rst

@@ -103,7 +103,7 @@ uninterrupted fashion.
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by
 this fix to add the potential energy of the CMAP interactions to both
 the global potential energy and peratom potential energies of the
-sysstem as part of :doc:`thermodynamic output <thermo_style>` or
+system as part of :doc:`thermodynamic output <thermo_style>` or
 output by the :doc:`compute pe/atom <compute_pe_atom>` command.  The
 default setting for this fix is :doc:`fix_modify energy yes
 <fix_modify>`.

doc/src/fix_colvars.rst

@@ -115,7 +115,7 @@ in a pair of double quotes ("), or can span multiple lines when bracketed
 by a pair of triple double quotes (""", like python embedded documentation).
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the Covars
+:doc:`output commands <Howto_output>`.  The scalar is the Colvars
 energy mentioned above.  The scalar value calculated by this fix is
 "extensive".
 

doc/src/fix_flow_gauss.rst

@@ -165,8 +165,9 @@ LAMMPS was built with that package.  See the :doc:`Build package
 Related commands
 """"""""""""""""
 
-:doc:`fix addforce <fix_addforce>`, :doc:`compute temp/profile
-     <compute_temp_profile>`, :doc:`velocity <velocity>`
+:doc:`fix addforce <fix_addforce>`,
+:doc:`compute temp/profile <compute_temp_profile>`,
+:doc:`velocity <velocity>`
 
 Default
 """""""

doc/src/fix_modify.rst

@@ -83,7 +83,7 @@ appropriate fix.
 
 .. note::
 
-   For most fixes that suppport the *energy* keyword, the default
+   For most fixes that support the *energy* keyword, the default
    setting is *no*.  For a few it is *yes*, when a user would expect
    that to be the case.  The doc page of each fix gives the default.
 
@@ -108,7 +108,7 @@ option to include or exclude the contribution from fixes.
 
 .. note::
 
-   For most fixes that suppport the *virial* keyword, the default
+   For most fixes that support the *virial* keyword, the default
    setting is *no*.  For a few it is *yes*, when a user would expect
    that to be the case.  The doc page of each fix gives the default.
 

doc/src/fix_orient.rst

@@ -149,7 +149,7 @@ No information about this fix is written to :doc:`binary restart files
 
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by
 this fix to add the potential energy of atom interactions with the
-grain bounadry driving force to the global potential energy of the
+grain boundary driving force to the global potential energy of the
 system as part of :doc:`thermodynamic output <thermo_style>`.  The
 default setting for this fix is :doc:`fix_modify energy no
 <fix_modify>`.

doc/src/fix_orient_eco.rst

@@ -103,7 +103,7 @@ files <restart>`.
 
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by
 this fix to add the potential energy of atom interactions with the
-grain bounadry driving force to the global potential energy of the
+grain boundary driving force to the global potential energy of the
 system as part of :doc:`thermodynamic output <thermo_style>`.  The
 default setting for this fix is :doc:`fix_modify energy no
 <fix_modify>`.

doc/src/fix_precession_spin.rst

@@ -141,7 +141,7 @@ No information about this fix is written to :doc:`binary restart files
 <restart>`.
 
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-this fix to add the energy assocatiated with the spin precession
+this fix to add the energy associated with the spin precession
 torque to the global potential energy of the system as part of
 :doc:`thermodynamic output <thermo_style>`.  The default setting for
 this fix is :doc:`fix_modify energy no <fix_modify>`.

doc/src/fix_tgnh_drude.rst

@@ -240,7 +240,7 @@ compute temperature on a subset of atoms.
    keyword will be unaffected by the *temp* setting.
 
 The cumulative energy change in the system imposed by these fixes, due
-to thermostatting and/or barostating, are included in the
+to thermostatting and/or barostatting, are included in the
 :doc:`thermodynamic output <thermo_style>` keywords *ecouple* and
 *econserve*.  See the :doc:`thermo_style <thermo_style>` doc page for
 details.

doc/src/fix_wall_ees.rst

@@ -131,7 +131,7 @@ The :doc:`fix_modify <fix_modify>` *energy* option is supported by
 these fixes to add the energy of interaction between atoms and all the
 specified walls or region wall to the global potential energy of the
 system as part of :doc:`thermodynamic output <thermo_style>`.  The
-default settings for thes fixes are :doc:`fix_modify energy no
+default settings for these fixes are :doc:`fix_modify energy no
 <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by

doc/utils/sphinx-config/false_positives.txt

@@ -508,6 +508,7 @@ cpp
 cpu
 createatoms
 createAtoms
+CreateIDs
 crespi
 Crespi
 Critchley
@@ -788,6 +789,7 @@ ees
 eFF
 efield
 effm
+eflag
 eflux
 eg
 Eggebrecht
@@ -2681,6 +2683,7 @@ rfile
 rg
 Rg
 Rhaphson
+Rhe
 rheological
 rheology
 rhodo
@@ -3335,6 +3338,7 @@ verlet
 Verlet
 versa
 ves
+vflag
 vhi
 vibrational
 Vij

python/lammps/__init__.py

@@ -1,4 +1,38 @@
+"""
+LAMMPS module global members:
+
+.. data:: __version__
+
+   Numerical representation of the LAMMPS version this
+   module was taken from.  Has the same format as the
+   result of :py:func:`lammps.version`.
+"""
+
 from .constants import *
 from .core import *
 from .data import *
 from .pylammps import *
+
+# convert module string version to numeric version
+def get_version_number():
+    from datetime import datetime
+    from sys import version_info
+    vstring = None
+    if version_info.major == 3 and version_info.minor >= 8:
+        from importlib.metadata import version
+        try:
+            vstring = version('lammps')
+        except: pass
+    else:
+        from pkg_resources import get_distribution
+        try:
+            vstring = get_distribution('lammps').version
+        except: pass
+
+    if not vstring:
+        return 0
+
+    d = datetime.strptime(vstring, "%d%b%Y")
+    return d.year*10000 + d.month*100 + d.day
+
+__version__ = get_version_number()

python/lammps/core.py

@@ -381,6 +381,13 @@ class lammps(object):
     self._installed_packages = None
     self._available_styles = None
 
+    # check if liblammps version matches the installed python module version
+    # but not for in-place usage, i.e. when the version is 0
+    import lammps
+    if lammps.__version__ > 0 and lammps.__version__ != self.lib.lammps_version(self.lmp):
+        raise(AttributeError("LAMMPS Python module installed for LAMMPS version %d, but shared library is version %d" \
+                % (lammps.__version__, self.lib.lammps_version(self.lmp))))
+
     # add way to insert Python callback for fix external
     self.callback = {}
     self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))

src/Makefile

@@ -272,11 +272,13 @@ mpi-stubs:
 	@cd STUBS; $(MAKE) clean; $(MAKE)
 
 # install LAMMPS shared lib and Python wrapper for Python usage
-# include python package settings to
-#   automatically adapt name of python interpreter
+# include python package settings to automatically adapt name of
+# the python interpreter. must purge build folder to not install
+# unwanted outdated files.
 
 sinclude ../lib/python/Makefile.lammps
 install-python:
+	@rm -rf ../python/build
 	@$(PYTHON) ../python/install.py -v ../src/version.h \
 		-p ../python/lammps -l ../src/liblammps.so