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A dissipative particle dynamics (DPD) model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow…
PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…
Modeling physical systems in a generative manner offers several advantages, including the ability to handle partial observations, generate diverse solutions, and address both forward and inverse problems. Recently, diffusion models have…
We describe a simple method for simulating the dynamics of small grains in a dusty gas, relevant to micron-sized grains in the interstellar medium and grains of centimetre size and smaller in protoplanetary discs. The method involves…
To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…
Multiparticle collision dynamics (MPCD) is a relatively new algorithm of fluid flow simulations that has been applied mostly to flows around simple objects. One might ask how it behaves in more complex flows. Therefore, we extend MPCD to…
This article presents an innovative open-source software named ModelFLOWs-app, written in Python, which has been created and tested to generate precise and robust hybrid reduced order models (ROMs) fully data-driven. By integrating modal…
We present PyAtoms, an interactive open-source software that rapidly simulates atomic-scale scanning tunneling microscopy (STM) and other scanning probe microscopy (SPM) images of two-dimensional (2D) layered materials, moir\'{e} systems,…
Our work is motivated by the analysis of ash plume dynamics, arising in the study of volcanic eruptions. Such phenomena are characterized by large Reynolds number (exceeding $10^7$) and a large number of polydispersed particles~[1]. Thus,…
We present a multiscale simulation algorithm for amorphous materials, which we illustrate and validate in a canonical case of dense granular flow. Our algorithm is based on the recently proposed Spot Model, where particles in a dense random…
PyPartMC is a Pythonic interface to PartMC, a stochastic, particle-resolved aerosol model implemented in Fortran. Both PyPartMC and PartMC are free, libre, and open-source. PyPartMC reduces the number of steps and mitigates the effort…
partycls is a Python framework for cluster analysis of systems of interacting particles. By grouping particles that share similar structural or dynamical properties, partycls enables rapid and unsupervised exploration of the system's…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
We outline the development of a general-purpose Python-based data analysis tool for OpenFOAM. Our implementation relies on the construction of OpenFOAM applications that have bindings to data analysis libraries in Python. Double precision…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
The collision kernel of droplets in warm clouds is a crucially important quantity for the parameterization of precipitation in weather and climate models. Nevertheless, its accurate representation remains a challenge, specifically in the…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
Here, we review the basic concepts and applications of the phase-field-crystal (PFC) method, which is one of the latest simulation methodologies in materials science for problems, where atomic- and microscales are tightly coupled. The PFC…