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[ESPResSo-users] Espresso 4.0.1 released

From: Rudolf Weeber
Subject: [ESPResSo-users] Espresso 4.0.1 released
Date: Tue, 29 Jan 2019 14:00:37 +0100
User-agent: Mutt/1.9.4 (2018-02-28)

Dear Espresso users,

the Espresso team is pleased to announce the release of Espresso 4.0.1.
The source can be downloaded at
Please see the release notes below.

Many thanks to all contributors!
Regards, Rudolf

This release provides a number of corrections for Espresso 4.0.
We recommend that this release be used for all production simulations.
The interface has not been changed between Espresso 4.0 and 4.0.1
However, some bugs were discovered which can affect simulation results.
Below, please find the list of changes. The numbers in brackets refer to 
ticket numbers on

Physics related corrections:
  * The GPU lattice Boltzmann method produced incorrect results when
    EXTERNAL_FORCES was not declared in myconfig.hpp.
    This issue was present since around June 2018 (#2241)

  * The temperature fluctuations for the GPU lattice Boltzmann implementation
    were larger than the ones for the Cpu lattice Boltzmann implementation.
    The cause was likely weak or incorrect random number generation.
    It is not clear since when this issue existed.
    It has been resolved by using library code for a counter-based
    random number generator (Philox) rather than the existing custom code.

  * Particles which were moved with the configuration changing moves (MC) 
implemented in the reaction ensemble 
    module did not get assigned a random velocity. This was not a problem if 
you were looking at observables 
    which do not depend on velocity.
  * Particles which were created in the Reaction Ensemble module were assigned 
a random velocity which was not distributed according to the Maxwell-Boltzmann 
distribution. This was not a problem if you were looking at observables which 
do not depend on velocity. If you looked at velocity dependent observables but 
used a thermostat for thermalization before taking a sample you are also fine.  

  * Under some conditions, the torque on self-propelled particles 
    in a lattice-Boltzmann fluid was incorrect due to a sign error in the 
    ENGINE feature. This was the case since the introduction of the feature

  * The SimplePore shape was incorrect (#2379)
  * The parameters passed from Python to some features were narrowed to single 
    precision. I.e., the values used were only accurate up to the 7th-8th 
    significant digit. Further calculations with those values still were
    done using double precision.
    Classes backed by the script interface were affected. This includes
    shapes, LB boundaries, pair criteria and the collision detection.
    This issue was likely present since the introduction of Python support
    for the relevant features. (#2379)
  * Forces on LB boundaries retrieved via the LbBoundary.get_force() method
    in a Python script were incorrect for the CPU LB implementation.
    The GPU implementation was not affected.
    It is not clear, when the issue was introduced. (#2366)

  * In highly dense systems, the Widdom insertion scheme reported wrong values

  * Fixed the Gay-Berne potential for sigma != 1. Downgraded the GAY_BERNE 
feature to an experimental feature due to insufficient testing (#2424)

Further general corrections and improvements:
* Fix restoring checkpointed simulations which contain exclusions (#2418)

* Allow neutral systems in reaction ensemble (#2378)

* Support re-tuning the dipolar P3M method (#2351, #1937)
* Support checkpointing of the collision detection parameters (#2342)
* Virtual sites tracers: don't complain about missing lb for non-virtual 
  part (#2341)
* Prevent access to non-existent lb nodes from Python
* Opengl wildcard imports + mac fix  (#2295)

* Fix segfaults in virtual sites based collision detection schemes on more than 
one processor core (#2195)

* Fixed find_current_cell() and particle deletion (#2410, #2441)

* Fixed coordinate folding for corner cases (0 - epsilon on 32 bit 
architectures) (#2415)

Documentation and tutorials corrections and improvements: 

* Mention how to read h5md files in the docs (#2353)

* Correct docs for setting the skin (#2340)

* Corrections to the Lennard-Jones tutorial (#2339)

* doc: Fixed Gay-Bern formula (#2234)

* Update PDF of tutorial 6 with bibliography (#2285)

Build system and platform related corrections and improvements:

* Fix Cython detection on Fedora 29 (#2371)

* Properly detect CUDA libraries if multiple are available (#2352)

* Guard tests and compilation for different feature sets
  in myconfig.hpp (#2344, #2326, #2350, #2349, #2335, #2337, #2266)

* install libH5mdCore (#2277)
* Fix MPI on Ubuntu 18.04 with CUDA (#2271)
* Fix PARTIAL_PERIODIC on big-endian platforms (#2259)

* Fixes for OpenSUSE rpm build (#2255)

* ctest: add ARGS option to custom 'make check' (#2252)
* cmake: workaround for cmake bug#18349 (#2244)

* Remove some superfluous executable bits (#2242)
* Silence arm32 warnings (#2267)
* Fix unit test without SSE instructions (#2265)

* Turn off ScaFaCoS support by default. Has to be enabled explicitly using 
-DWITH_SCAFACOS=on in CMake. (#2417)

* Fix builds with the Gnu Scientific Library in non-standard locations (#2429)

* Resolve some floating point rounding issues on I386 32-bit (#2454)

Improved testing:

* Test the LB thermostat (#2391, #2362)
* Better stability of the LB test (#2360)
* testsuite: fix checkpoint test (#2336)
* Test the installation routine (#2268)

* Improved testing of the cylindrical lb profile observables (#2272)
* testsuite: Check planar shear profile of LB (#2263)

* Test builds without optional dependencies (#2406)

* Test builds on non-Amd64 architectures (#2401)

* Improved test coverage of the Wang-Landau reaction ensemble (#2404)

* Testing of the electrostatic pressure (#2409)

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