4.0.0

This feature release adds new functionality to ESPResSo. This is also the first release of ESPResSo with a Python interface. Support for the TCL-interface has been dropped.

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

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

• 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)