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NEWS
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=================
= ESPRESSO NEWS =
=================
ESPResSo 4.0
============
ESPResSo 4.0 is the first release of ESPResSo with a Python interface.
I.e., the language in which simulation scripts are written is now Python,
and support for the TCL-interface has been dropped.
We recommend all users switch to ESPResSo 4.0, there will be no more fixes to
TCL-based versions.
Transitioning from TCL-based versions
-------------------------------------
The following can serve as a starting point for the new interface:
* The "Introduction" chapter in the user's guide
* The tutorials provided with ESPResSo
Both can be found at http://espressomd.org/wordpress/documentation
Please note that, starting from ESPResSo 4.0, enabling additional features in myconfig.hpp no longer changes the behavior of a simulation scripts. Features such as particle rotation and virtual sites have to be activated explicitly in the simulation scripts.
New features:
-------------
* Reaction ensemble methods for the modelling of chemical reactions, including constant pH and Wang-Landau schemes
* Polarisable particles via the Drude-oscillator scheme
* Steepest-descent energy minimization scheme
* Methods for active particles (swimmer_reaction, dipolar swimmers)
* GPU-accelerated P3M method for electrostatic interactions
* GPU-accelerated direct summation and Barnes-Hutt schemes for dipolar interactions under open boundary conditions
* Support for the electrostatic and magnetostatics method provided by the ScaFaCoS library
* Immersed boundary method for soft immersed objects in an LB fluid
* Virtual sites acting as inertialess tracers in an LB fluid usable as part of the immersed boundary method or independently
* Online cluster analysis based on criteria for pairs of particles
* New bonded quartic and Coulomb interactions
* Possibility to tune the skin parameter
* Support for saving to the h5md file format for molecular dynamics data.
* Connection to the MD Analysis Python package
* A rotate_system command was added, which rotates the particle positions around the system's center of mass
Visualisation
-------------
Espresso contains two online visualizers, one based on Mayavi, one on the OpenGl Python module.
Support for online visualization in VMD has been dropped, but particle data can be stored in file formats which VMD can read (vcf/vtf, h5md).
User-visible changes
--------------------
* When the ROTATION feature is compiled in, the rotation of a particle around each of its Cartesian axes in the body-fixed frame can be enabled
* The rotational degrees of freedom of virtual sites is now integrated. Virtual sites no longer use the quaternion attributes to store their relative orientation
* Alternatively, the orientation of the virtual site can be specified relative to that of the particle it is derived from.
* The random number generator was changed to Mersenne Twister as implemented by C++11.
* Espresso now depends on the Boost library including Boost-Mpi and a C++11 capable compiler
* The build system is now based on CMake.
Removed features
----------------
The following features are not part of the ESPResSo 4.0 release, but support is expected to be re-added in a subsequent release.
* Generalized hybrid Monte Carlo thermostat
* Virtual sites located at the center of mass of a group of particles
* Metadynamics, umbrella sampling and parallel tempering
* Non-equilibrium molecular dynamics (shear boundary conditions implemented by moving slabs of particles at the boundaries)
* The memd/maggs electrostatic solver
* The com_force feature
* The Shan Chen lattice Boltzmann extension
* Lees-Edwards (shear) boundary conditions
* The chain rdf analysis
The following functionality is removed permanently:
* Blockfile support, which is replaced by support for the h5md format as well as checkpointing based on the pickle Python module.
* Some of the convenience functions for particle creation such as salt and counterions, as these can be replaced by a very few lines of Python in the simulation script.
* The lj_angle and angledist (not-quite)-pair potentials
* The following analysis methods:
diffusion_profile, cwvac, p_inst, ..._mol, cel_gpb, dipmom_normal, MSD, angularmomentum, cluster_size_dist, mol, lipid_orient_order, get_lipid_orients, current, wall_stuff,
necklace, bilayer, modes2d
* The uwerr error estimator
Known issues and limitations
----------------------------
The numbers refer to issue numbers at http://github.com/espressomd/espresso
* Lattice Boltzmann interpolated velocities are only accurate up to one
lattice cell next to a boundary (#1865)
* Adding boundaries in the electrokinetics method resets species densities
to their initial values (#1899)
* The collision detection feature does not support checkpointing (#1943)
* Changing interaction parameters does not automatically update the value of
the force property stored on the particles. Forces are re-calculated in
the next integration step. (#1973)
* The domain decomposition cell system does not always choose the node grid
yielding the best performance in parallel simulations (#1970)
* The dipolar P3M method can only be tuned once in a simulation script,
unless method parameters are explicitly reset to 0 before the second tuning
(#1937)
* In rare cases, P3M produces an rs mesh overflow warning (#2067)
* The H5MD file writer cannot handle bounds that involve more than two bond
partners (#1715)
* Pickle checkpoints are not guaranteed to be compatible between
different ESPResSo versions (#1181)
* Switching from the GPU-Based MMM1D and MMM2D methods to a different
electrostatic method within a single simulation script may not work (#396)
* The membrane_collision interaction of the object in fluid framework may
use an outward direction which is outdated by one time step (#2214)
ESPResSo 3.3
============
New user-visible features
-------------------------
* SHANCHEN: a bicomponent lattice Boltzmann fluid, with support for rigid
boundaries and coupling to particle dynamics.
* ELECTROKINETICS: An algorithm to treat species of ions on a mean-field
level. Implementation takes advantage of a GPU.
* MMM1DGPU: The mmm1d electrostatics algorithm is now available as GPU version.
* Support of P3M on GPU.
* Provide the preliminary Python interface. Configure with
--with-python-interface.
* Allow the p3m to dump the mesh in x, y, and z (before it only dumped
the mesh in x). This allows for the dumping of the p3m in blockfile
format in the case of non-cubic boxes. It will also now be possible
to tune the settings of a non-cubic mesh.
* Stomatocyte lb-boundary and constraint implemented.
* MEMD electrostatics can now handle spatially varying dielectrc
constants.
* Pore constraint / lbboundary can have a two outer radii now to create nozzles.
* Slitpore constraint and dielectric for IL based supercaps implemented.
* New command time_integration to get the runtime of the integration
loop.
* New harmonic well that runs on the GPU.
Known bugs
----------
* The implementation of dielectric contrasts in conjunction with ELC
seems to have an error. Please do not use it if you do not know
exactly what you are doing until we have fixe the problem.
User-visible changes
--------------------
* Added new arguments "recalc_forces" and "reuse_forces" to the
command "integrate". These arguments can be used to enforce or
suppress the recalculation of the forces at the beginning of the
call to "integrate". This is important for doing checkpoints, where
the forces have to be stored and reloaded.
* Removed command "invalidate_system".
* Comfixed now works with periodic boundary conditions.
* The pressure contribution due to rigid bodies constructed by means of the
virtual sites relative mechanism is included, both for pressure and stress
tensor. Note that the corresponding contribution for rigid bonds is still
not implemented.
* The configure option "--with-myconfig" has been removed. Instead,
the configure variable "MYCONFIG" can be set to give the name of a
myconfig file.
* Generic LJ can now be turned into a soft potential.
* Renamed torque to torque_{lab,body}, improved torque handling in
blockfiles. Clearer distinction between the reference frames for
torque and angular momentum.
* Lattice-Boltzmann now has a additional 3-point coupling scheme.
* The noise type in thermalized Lattice-Boltzmann is now selectable via Tcl.
* Interaction with a wall can be restricted to the outside.
* Removed compiler switch GRANDCANONICAL.
* Removed outdated ADRESS code.
* external_potential tabulated to include arbitrary potentials applied to all
particles.
* thermostat inter_dpd ignore_fixed_particles 1 allows the user to swith on DPD
with fixed particles.
* New Observable concept that includes running averages and other observables
with history
Changes visible for developers
------------------------------
* Feature GHOSTS_HAVE_BONDS allows for ghost particles to also store the bonds.
* The code has been switched to using a C++ compiler.
* Introduced object-oriented interfaces for forces/constraints/external fields:
SystemInterface and Actor.
* Improved Lattice structure
* Generic TclAppend function
ESPResSo 3.2
============
New user-visible features
-------------------------
* Added a new immersed boundaries code that allows to simulate
extended, flexible objects in conjunction with the LB code. This is
described in the UG in the new chapter "Object-in-fluid".
* The script tools/blockfile2vtf.tcl can be used to convert ESPResSo
blockfiles into VTF files.
* Two new short-ranged nonbonded potentials have been added:
* HAT: the classical conservative DPD interaction, a simple force
ramp.
* GAUSSIAN: A Gaussian potential.
* The feature CATALYTIC_REACTIONS and the command "reaction" model a
simple chemical reaction: when a particle of the reactant type comes
into the vincinity of a particle of the catalysator type, the
reactant is transformed into a particle of the product type.
* The feature GHMC implements a generalized hybrid Monte-Carlo
thermostat.
* The feature GRANDCANONICAL provided functions to simplify grandcanonical
simulations in espresso. To that end it provides functions to find and
delete random particles of a certain type.
* Added new feature ROTATION_PER_PARTICLE that allows to choose
whether a particle has rotational degrees of freedom or not.
User-visible changes
--------------------
* Removed non-working tools and samples.
* Bond angle potentials are now defined on the Tcl-level instead of on
the feature-level, i.e. to choose the type of the bond-angle
potential, you should use the corresponding Tcl command instead of a
feature. To allow for any bond angle potential, activate the feature
BOND_ANGLE.
* We have removed the forcecaps for the different interaction
types. Instead, there is now a single global forcecap, plus it is
possible to define individual forcecaps on a particle pair level.
* By default, CUDA is now automatically detected and activated when it
is there and usable.
* The functions for galilei transformations have been overhauled and
renamed. The old functions are deprecated.
* DPD (as thermostat) now works without any other interaction, so a pure
DPD fluid is possible.
ESPResSo 3.1.2
==============
* Fixed bugs #38475, #37725, #36434.
* Added workaround for bug in VTF reader plugin of VMD 1.9.1 that made
all particles look the same when ELECTROSTATICS is turned on.
* Added Tcl-scripts of the tutorials to the distribution.
* Added forgotten part of the UG on the correlators.
* Removed buggy readline code tclline.tcl. Fixes #36432.
* Removed Ewald code from ESPResSo that never worked and was never
documented.
ESPResSo 3.1.1
==============
* The Espresso binary now outputs the header to STDERR instead of STDOUT.
* Fixed bugs #36431, #37120, #37214, #37374, #37306, #35767.
* Fixed generation of myconfig-sample.h.
* Fixed AdResS example.
* Added new logo.
* The documentation sources are now left out of the distribution
package, only the PDF files are included. This fixes problems when
calling "make doc" in a distribution package (#35958).
ESPResSo 3.1.0
==============
New user-visible features
-------------------------
* While so far, observables were typically computed and stored on the
Tcl-level after a call to "integrate", a new observable concept now
allows to compute observables while the C-core is running. This is
particularly useful for observables that have to be computed very
frequently, as for example in the case of time-correlations
(e.g. the RMSD of particles).
The new concept is documented in the User's Guide in Section 8.4
("Correlations and observables").
* The new feature COLLISION_DETECTION allows to dynamically add new
bonds between colliding particles.
* Added new feature LANGEVIN_PER_PARTICLE that allows to set the
Langevin parameters temperature and gamma per particle.
* Added new constraint and LB boundary condition "rhomboid".
* Lattice-Boltzmann:
* nonzero velocity boundary conditions are available
* forces on boundaries can be calculated
* wall constraints work
* Added basic tutorial on Lennard-Jones liquid, made second tutorial
(simple charged systems) better available (all in doc/tutorials/)
* The ICC* algorithm is now ready to use. It is used with the command
"iccp3m" and allows to take into account dielectric boundaries of
arbitrary shape. The command "dielectric" allows to create the
boundaries in a similar fashion as constraints and lbboundaries.
User-visible changes
--------------------
* The blockfile C-library has been removed. In theory, there was a
library usable from C that could be used to read and write
blockfiles. Since several years, it was broken, so apparently it
wasn't used anyway.
* The NPT barostat now works in many more combinations of
algorithms than so far (e.g. MMM2D, ELC, ...)
* The Lattice-Boltzmann CPU implementation now works when Verlet lists
are used.
* Removed unneccessary overhead of neutral particles in simulations
with P3M.
* Removed unneccessary overhead of activated but ununsed interaction
features.
* Some changes in the Verlet list construction yield a performance
gain of up to 90% in systems where the interaction ranges differ
significantly, or where some particle types do not interact at all
(phantom particles).
* Renamed Coulomb method maggs to MEMD (inter coulomb maggs => inter
coulomb memd).
Changes visible for developers
------------------------------
* code_info does now not only show the main package version, but also
the exact git commit id and whether or not the code was modified
("dirty"). Also, the distribution package provides this information.
* The various features are now defined in the file
src/features.def. From this file, a couple of Python scripts
automatically generate myconfig-sample.h and what was config.h and
config.c. Also, this allows to check whether all features are
documented, tested and defined.
Note that due to this change, ESPResSo development now requires
Python.
* The domain decomposition, P3M, LB and MEMD now use MPI cartesian
communicators. This will hopefully speed up the simulations on some
platforms.
* Split interaction code into .c and .h files.
* Split off the Tcl interface (into src/tcl/) from the C core code (in
src/)
* Added ESPResSo logos, cover issue images, and some other material to
the repo (doc/).
* Started new LaTeX-Developer's Guide (DG), and moved all "Related
pages" from the doxygen docs. The doxygen stuff still exists and is
available via doc/doxygen/.
ESPResSo 3.0.2
==============
* Fixed features ADRESS and VIRTUAL_SITES_COM that did not work for a while.
* Fixed bugs #33489, #34238.
* Fixed a few bugs that were never reported via the bug tracker,
mainly in the documentation.
ESPResSo 3.0.1
==============
* Fixed bugs #33375,#33376,#32005
* Fixed a few bugs that were never reported via the bug tracker.
ESPResSo 3.0.0
===============
User-visible changes
--------------------
* The Lattice-Boltzmann implementation in ESPResSo has been
significantly overhauled and it has been documented for the first
time.
* A CUDA implementation for NVIDIA GPUs of the Lattice-Boltzmann
algorithm is included.
* The Maggs algorithm (or Maxwell Equation Molecular Dynamics, MEMD)
for computing electrostatic interactions has been included and
documented. The algorithm is a fast and scalable alternative for P3M
or other such algorithms.
* The P3M algorithm for electrostatic and dipolar (magnetostatic)
interactions has been extended.
* Electrostatic P3M allows for non-cubic boxes.
* The electrostatic P3M pressure tensor is computed correctly now.
* Dipolar P3M has been parallelized (electrostatics P3M was
parallelized already!)
* The MDLC method (magnetic dipolar layer correction) has been
parallelized.
* The virtual sites feature has been significantly extended and
documented. Virtual sites are particles that can interact with
other particles but whose positions are not integrated via the
normal integrator. Instead, the positions are determined by the
positions of other, "real" particles. Virtual sites can either be
set into the center of mass of a set of real particles (feature
VIRTUAL_SITES_COM), or it can be set to an arbitrary location
relative to another particle (VIRTUAL_SITES_RELATIVE). This allows
to create rigid structures within ESPResSo.
* The User's Guide has been significantly updated and extended.
* Some constraints can now be made penetrable and reflecting.
* "Espresso" is now the actual binary instead of a wrapper shell
script that automatically calls MPI. This means that it is necessary
to call "mpiexec" or "mpirun" youself to run ESPResSo in an MPI
environment.
* The directory where the scripts are installed is now compiled into
the binary, i.e. it is not necessary anymore to set the environment
variable ESPRESSO_SCRIPTS. Still, it will heed the environment
variable if it is set.
* The build system has been overhauled and simplified.
* Running "make check" will run the testsuite with a single number
of processors, which gives a significant speedup. "configure" will
try to determine the available number of CPUs/cores. If it can't,
it will use 1 by default.
* MPI recognition has changed. The build system first needs to find
out how to compile an MPI binary. If it doesn't find out
automatically, you can help it by setting the variable MPICC or
LDFLAGS correctly. Furthermore, it needs to know how to run an MPI
binary. If "mpiexec" is available, everything is fine. If it is
not, you can provide a script "mympiexec.sh" that behaves like
mpiexec.
* So far, when you built in the source directory, all files ended up
in a subdirectory "obj.XXX", where XXX was some description of the
processor you used. This non-standard behavior has been removed.
Instead, the files are generated directly in the source directory
when compiling there.
If you want to compile several binaries from a single source
directory, you can use build directories as described in the
User's Guide.
* A number of functions have been deprecated, as they are not
maintained anymore. Plase do not use them in your code and replace
them with appropriate alternatives if you use them in your code!
The following functions are deprecated:
checkpoint_*, polyBlock*, calcOb*, calcObs*, plot*, polyConf*
* FFTW2 is no longer supported.
Organizational changes
----------------------
* The home page of ESPReSso has been relocated to
http://espressomd.org
* The mailing list and source code repository have been moved to GNU
Savannah. Furthermore, we have a bugtracker now. The development
homepage is
https://savannah.nongnu.org/projects/espressomd
* The maintenance of ESPResSo has been relocated from Torsten Stühn
from the Max-Planck-Institute for Polymer Research at Mainz to
Olaf Lenz <[email protected]>
from the Institute for Computational Physics at Stuttgart University.
* The old "ESPResSo license" was removed, as it was not really a
license, but only contained additions that were either non-binding
or already contained in the GPL.
* The license was upgraded to GPLv3.
* The package was adapted to GNU standards. RELEASE_NOTES was moved
aside to old/RELEASE_NOTES, instead, we will have the files
ChangeLog and NEWS. NEWS will contain a description of the most
noteworthy changes since the last release.
Changes visible for developers
------------------------------
* The source code repository has been moved from CVS to git, and it
has moved to GNU Savannah (see above) and github. The main
development code repository is
https://github.com/espressomd/espresso
* We have an automated build server (Jenkins) at
http://espressomd.org/jenkins/
that automatically builds and checks the ESPResSo package whenever
new code is pushed to the main development repository. Every night,
a number of additional tests are performed
* The .c/.h/.cu source files have been moved to the subdirectory
src/. The Espresso binary is still placed in the top-level build
directory. myconfig.h may be placed eitther in the src/ or top-level
dirs.
* The automatically generated files configure and Makefile.in are not
part of the repository anymore. A developer can generate them using
the command "bootstrap.sh", which requires the GNU autotools
(autoconf and automake).
* All functions that represent the interface to Tcl should follow the
same naming conventions. These are described here:
git log 3d4d6f31655a8d96e47c8f80e10f27f6b764f8df
* Adding a new MPI function to communication.c has been significantly
simplified. It is enough to add the function in the C file at a
single location.
========================================================================
For older changes to ESPResSo, see ./old/RELEASE_NOTES.
========================================================================
Copyright (C) 2010,2011,2012,2013,2014 The ESPResSo project
Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved. This file is offered as-is,
without any warranty.