4.1.1
This bugfix release provides a number of corrections for the ESPResSo 4.1 line.
The interface is mostly unchanged between ESPResSo 4.1.0 and 4.1.1; the two exceptions are limited to these experimental features:
Integrator.set_isotropic_npt()
: input valuedirection=[0,0,0]
now throws an error instead of being silently changed to[1,1,1]
ParticleHandle.swimming
: deprecated value'rotational_friction'
is now disabled
These changes are unlikely to affect production simulations.
General corrections and improvements:
- Restore checkpointing mechanism for the steepest descent and NPT integrators, LB and NPT thermostats (#3245)
- Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and lower are no longer supported (#3236)
- Fix
Integrator.set_isotropic_npt()
: remove the silent conversion of the incorrect input parameterdirection=[0,0,0]
to[1,1,1]
in the core; the function now throws an exception for fixed-volume boxes; this change is unlikely to break pypresso scripts since not providing a value todirection
or providing[1,1,1]
were the two standard ways to set up a box with all directions allowed to rescale (#3253) - Fix
Integrator.set_vv()
: this function failed to set the velocity Verlet integrator if the NPT integrator was active; this is now resolved (#3274) - Fix the random segmentation fault triggered by the removal of a particle with a bond or a virtual site relationship to another particle (#3288)
- Fix
system.part.writevtk()
: the function now writes down all particles when usingtypes="all"
(#3290) - Disable the deprecated and broken ENGINE shear torque calculation feature; the feature will be completely removed from the core in the upcoming 4.2 release (#3277)
- Fix unit conversion for the LB fluid viscosity (#3287)
Documentation and tutorials corrections and improvements:
- Add more detailed installation instructions for ESPResSo and its Python dependencies on MacOS X (#3236)
- Add links to Dockerfiles providing installation instructions for ESPResSo and its Python dependencies on CentOS 7, Fedora 30, Debian 10 and OpenSUSE Leap 15.1 (#3244)
- Add instructions to read PDB files with
MDAnalysis
, which is one of the recommended tools to read/write molecular dynamics topologies and trajectories in ESPResSo; the PdbParser feature will be removed in the upcoming 4.2 release (#3257) - Add a new tutorial on the constant pH method; the reaction ensemble tutorial will be removed in the upcoming 4.2 release (#3184)
Build system and platform-related corrections and improvements:
- Fix a PYTHONPATH error when ESPResSo is built in a directory containing whitespace characters (#3238)
- Fix several issues with the command
make install
that lead to import errors in Python (incorrect runtime path, missing shared objects, name collision for submodulecluster_analysis
) and deprecate themake install DESTDIR=/path/to/espresso
command in favor of the standardcmake .. -DCMAKE_INSTALL_PREFIX=/path/to/espresso
command (#3228), install espressomd module in a platform-dependent python path, typicallylib{,64}/python3.X/{dist,site}-packages
(#3258) - Fix an issue in mpiio that triggered an assertion in systems with no bonds when ESPResSo is built with stdlibc++ range checking enabled (#3234)
- Fix the pypresso script to correctly parse filepaths containing whitespaces passed after a pypresso flag, such as
--gdb
, and make conditional statements cross-platform (#3292)
Improved testing: