11. System manipulation

11.1. Changing the box volume

This is implemented in espressomd.system.System.change_volume_and_rescale_particles() with the parameters d_new for the new length and dir for the coordinates to work on and "xyz" for isotropic.

Changes the volume of either a cubic simulation box to the new volume or its given x-/y-/z-/xyz-extension to the new box-length, and isotropically adjusts the particles coordinates as well. The function returns the new volume of the deformed simulation box.

11.2. Stopping particles

To stop particles you can use the functionality implemented in the espressomd.galilei module. The corresponding class espressomd.galilei.GalileiTransform which is wrapped inside the espressomd.system.System instance as espressomd.system.System.galilei has two functions:

11.3. Fixing the center of mass

This interaction type applies a constraint on particles of the specified types such that during the integration the center of mass of these particles is fixed. This is accomplished as follows: The sum of all the forces acting on particles of type are calculated. These include all the forces due to other interaction types and also the thermostat. Next a force equal in magnitude, but in the opposite direction is applied to all the particles. This force is divided on the particles of type relative to their respective mass. Under periodic boundary conditions, this fixes the itinerant center of mass, that is, the one obtained from the unfolded coordinates.

Center of mass fixing can be activated via espressomd.system.System:

system.comfixed.types = list_of_types_to_fix

11.4. Capping the force during warmup

Non-bonded interactions are often used to model the hard core repulsion between particles. Most of the potentials in the section are therefore singular at zero distance, and forces usually become very large for distances below the particle size. This is not a problem during the simulation, as particles will simply avoid overlapping. However, creating an initial dense random configuration without overlap is often difficult. By artificially capping the forces, it is possible to simulate a system with overlaps. By gradually raising the cap value, possible overlaps become unfavorable, and the system equilibrates to an overlap-free configuration.

Force capping can be activated via espressomd.system.System:

system.force_cap = F_max

This command will limit the magnitude of the force to \(r F_\mathrm{max}\). Energies are not affected by the capping, so the energy can be used to identify the remaining overlap. Torques are also not affected by the capping. Force capping is switched off by setting \(F_\mathrm{max}=0\).

For simple systems, it is often more convenient to use the Steepest descent algorithm instead of writing a tailored warmup loop in Python. The steepest descent algorithm will integrate the system while capping both the maximum displacement and maximum rotation.

11.5. Galilei Transform and Particle Velocity Manipulation

The following class espressomd.galilei.GalileiTransform may be useful in affecting the velocity of the system.

system = espressomd.System(box_l=[1, 1, 1])
gt = system.galilei

  • Particle motion and rotation

    gt.kill_particle_motion()

    This command halts all particles in the current simulation, setting their velocities to zero, as well as their angular momentum if the option rotation is specified and the feature ROTATION has been compiled in.

  • Forces and torques acting on the particles

    gt.kill_particle_forces()

    This command sets all forces on the particles to zero, as well as all torques if the option torque is specified and the feature ROTATION has been compiled in.

  • The center of mass of the system

    gt.system_CMS()

    Returns the center of mass of the whole system. It currently does not factor in the density fluctuations of the lattice-Boltzmann fluid.

  • The center-of-mass velocity

    gt.system_CMS_velocity()

    Returns the velocity of the center of mass of the whole system.

  • The Galilei transform

    gt.galilei_transform()

    Subtracts the velocity of the center of mass of the whole system from every particle’s velocity, thereby performing a Galilei transform into the reference frame of the center of mass of the system. This transformation is useful for example in combination with the DPD thermostat, since there, a drift in the velocity of the whole system leads to an offset in the reported temperature.