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See detaili-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations
Kapil, Venkat; Rossi, Mariana; Marsalek, Ondrej et al

in Computer Physics Communications (2018)

Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by ... [more ▼]

Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives. [less ▲]

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See detailThe Flexible Rare Event Sampling Harness System (FRESHS)
Kratzer, Kai; Berryman, Josh UL; Taudt, Aaron et al

in Computer Physics Communications (2014)

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling ... [more ▼]

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling (FFS) and Stochastic Process Rare Event Sampling (SPRES) have been implemented. These two methods together make rare event sampling available for both quasi-static and full non-equilibrium regimes. Our framework provides a plugin system for software implementing the underlying physics of the system of interest. At present, example plugins exist for our framework to steer the popular MD packages GROMACS, LAMMPS and ESPResSo, but due to the simple interface of our plugin system, it is also easy to attach other simulation software or self-written code. Use of our framework does not require recompilation of the simulation program. The modular structure allows the flexible implementation of further sampling methods or physics engines and creates a basis for objective comparison of different sampling algorithms. Our code is designed to make optimal use of available compute resources. System states are managed using standard database technology so as to allow checkpointing, scaling and flexible analysis. The communication within the framework uses plain TCP/IP networking and is therefore suited to high-performance parallel hardware as well as to distributed or even heterogeneous networks of inexpensive machines. For FFS we implemented an automatic interface placement that ensures optimal, nearly constant flux through the interfaces. We introduce ‘ghost’ (or ‘look-ahead’) runs that remedy the bottleneck which occurs when progressing to the next interface. FRESHS is open-source, providing a publicly available parallelized rare event sampling system. [less ▲]

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See detailIsotropic-isotropic phase separation in mixtures of rods and spheres: Some aspects of Monte Carlo simulation in the grand canonical ensemble
Jungblut, S.; Binder, K.; Schilling, Tanja UL

in Computer Physics Communications (2008), 179(1-3), 13-16

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See detailNucleation in suspensions of anisotropic colloids
Schilling, Tanja UL; Frenkel, Daan

in Computer Physics Communications (2005), 169(1-3), 117-121

We report Monte Carlo studies of liquid crystal nucleation in two types of anisotropic colloidal systems: hard rods and hard ellipsoids. In both cases we find that nucleation pathways differ strongly from ... [more ▼]

We report Monte Carlo studies of liquid crystal nucleation in two types of anisotropic colloidal systems: hard rods and hard ellipsoids. In both cases we find that nucleation pathways differ strongly from the pathways in systems of spherical particles. Short hard rods show an effect of self-poisoning. This part of the article is based on a previous publication [T. Schilling, D. Frenkel, Self-poisoning of crystal nuclei in hard-rod liquids, Phys. Rev. Lett. 92 (2004) 085505]. When a crystallite forms, its surfaces are covered preferentially by rods which align perpendicular to the surface. Therefore subsequent growth is stunted. Hard, almost spherical ellipsoids can be compressed to very high densities without crystallization—in contrast to hard spheres, which crystallize easily. When forced to crystallize, ellipsoids form very loosely aggregated nuclei. In both cases nucleation pathways are complex and it is therefore difficult to define an appropriate reaction coordinate. The common strategies of investigation of nucleation problems (i.e. definition of a coordinate and then sampling barrier crossing with well-known techniques) fail in these systems. [less ▲]

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