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In this article we describe the implementation of an online-coupled gas-phase chemistry model in the turbulence-resolving PALM model system 6.0 (formerly an abbreviation for Parallelized Large-eddy Simulation Model and now an independent name). The new chemistry model is implemented in the PALM model as part of the PALM-4U (PALM for urban applications) components, which are designed for application of the PALM model in the urban environment (Maronga et al., 2020). The latest version of the Kinetic PreProcessor (KPP, 2.2.3) has been utilized for the numerical integration of gas-phase chemical reactions. A number of tropospheric gas-phase chemistry mechanisms of different complexity have been implemented ranging from the photostationary state (PHSTAT) to mechanisms with a strongly simplified volatile organic compound (VOC) chemistry (e.g. the SMOG mechanism from KPP) and the Carbon Bond Mechanism 4 (CBM4; Gery et al., 1989), which includes a more comprehensive, but still simplified VOC chemistry. Further mechanisms can also be easily added by the user. In this work, we provide a detailed description of the chemistry model, its structure and input requirements along with its various features and limitations. A case study is presented to demonstrate the application of the new chemistry model in the urban environment. The computation domain of the case study comprises part of Berlin, Germany. Emissions are considered using street-type-dependent emission factors from traffic sources. Three chemical mechanisms of varying complexity and one no-reaction (passive) case have been applied, and results are compared with observations from two permanent air quality stations in Berlin that fall within the computation domain. Even though the feedback of the model's aerosol concentrations on meteorology is not yet considered in the current version of the model, the results show the importance of online photochemistry and dispersion of air pollutants in the urban boundary layer for high spatial and temporal resolutions. The simulated NOx and O3 species show reasonable agreement with observations. The agreement is better during midday and poorest during the evening transition hours and at night. The CBM4 and SMOG mechanisms show better agreement with observations than the steady-state PHSTAT mechanism. © 2021 Copernicus GmbH. All rights reserved.

Large-eddy simulation (LES) provides a physically sound approach to study complex turbulent processes within the atmospheric boundary layer including urban boundary layer flows. However, such flow problems often involve a large separation of turbulent scales, requiring a large computational domain and very high grid resolution near the surface features, leading to prohibitive computational costs. To overcome this problem, an online LES–LES nesting scheme is implemented into the PALM model system 6.0. The hereby documented and evaluated nesting method is capable of supporting multiple child domains, which can be nested within their parent domain either in a parallel or recursively cascading configuration. The nesting system is evaluated by first simulating a purely convective boundary layer flow system and then three different neutrally stratified flow scenarios with increasing order of topographic complexity. The results of the nested runs are compared with corresponding non-nested high- and low-resolution results. The results reveal that the solution accuracy within the high-resolution nest domain is clearly improved as the solutions approach the non-nested high-resolution reference results. In obstacle-resolving LES, the two-way coupling becomes problematic as anterpolation introduces a regional discrepancy within the obstacle canopy of the parent domain. This is remedied by introducing canopy-restricted anterpolation where the operation is only performed above the obstacle canopy. The test simulations make evident that this approach is the most suitable coupling strategy for obstacle-resolving LES. The performed simulations testify that nesting can reduce the CPU time up to 80 % compared to the fine-resolution reference runs, while the computational overhead from the nesting operations remained below 16 % for the two-way coupling approach and significantly less for the one-way alternative.

Large-Eddy Simulation (LES) allow to simulate pollutant dispersion at a fine-scale turbulence-resolving scale with explicitly resolved turbulent transport around building structures and in street canyons. The microscale urban climate model with atmospheric chemistry PALM-4U (i.e. PALM for Urban applications; Maronga et al., 2019, Met. Z., https://doi.org/10.1127/metz/2019/0909) has been developed within the collaborative project MOSAIK (Model-based city planning and application in climate change). With such a large-eddy simulation (LES) model, pollutant dispersion around buildings and within street canyons can be simulated, with explicitly resolving the turbulent transport in urban environments.Cyclic boundaries are frequently applied in LES in order to obtain lateral boundary conditions for the turbulent quantities. In addition to the default cyclic boundary conditions, PALM-4U allows also time-dependent boundary conditions from regional models to account for variable weather conditions and regional scale pollutant transport. Turbulent fluctuations, which are not included in the boundary conditions from the regional simulation but are needed as additional boundary conditions for the LES model are produced by a turbulence generator (Maronga et al, 2019, GMDD, https://doi.org/10.5194/gmd-2019-103).PALM-4U simulations with and without time dependent boundary conditions from regional simulations with WRF-Chem are performed for different setups in order to test the impact of the domain configuration. The simulations indicate that cyclic boundary conditions can lead to unrealistic accumulation of pollutants over urban areas with strong sources, which is not the case when time-dependent boundary conditions are applied. However, even though a turbulence generator is applied, explicit setting of time-dependent boundary conditions requires large model domains, in order to obtain fully developed turbulence within the domain of interest, increasing the computational demand of the simulation.

Large-Eddy Simulation (LES) models are so far barely applied to dispersion and chemical transformation of pollutants in urban air quality studies. Within the joint project MOSAIK (Modellbasierte Stadtplanung und Anwendung im Klimawandel/Model-based city planning and application in climate change) a new LES based state-of-the-art microscale urban climate model PALM-4U, has been developed. The new model includes both gas phase and aerosol chemistry. For practical applications, our approach is to go beyond the simulation of single street canyons to chemical transformation, advection and deposition of air pollutants in the larger urban canopy. First LES results of a test case for an urban quarter of Berlin (Germany) are presented.

To accurately simulate dispersion, chemical transformation and removal of air pollutants in the urban canopy layer, fine-scale turbulence-resolving simulations are required that can explicitly resolve building structures and street canyons. Large-Eddy Simulation (LES) models explicitly resolve the dominant scales of turbulence in the atmospheric boundary layer and therefore, have the potential to capture the turbulent motion within street canyons as well as the observed short term fluctuations of pollutant concentrations. LES models including chemical transformation of pollutants are so far barely applied for urban air quality studies. Within the joint project MOSAIK (Model-based city planning and application in climate change) a new urban microscale model including gas Phase chemistry and aerosols, PALM-4U, has been developed. The state-of-the-art LES model PALM (Maronga et al, 2015, Geosci. Model Dev., 8, doi:10.5194/gmd-8-2515-2015) is used as core model for PALM-4U. In order to obtain the necessary flexibility in the choice of the chemistry mechanisms the gas-phase chemistry was implemented using the Kinetic PreProcessor KPP. Due to the very high computational demands of an LES-based model, compromises are required with respect to the degree of detail of the gas-phase chemistry mechanisms. A number of chemical mechanisms with varying complexity and detail that ranges from a strongly reduced mechanism which includes only a simple O3-NO2-NO-VOC-HOx chemistry and a small number of products to large mechanisms which are typically used in regional air quality models were implemented into PALM-4U. The performance of different gas-phase chemistry schemes of different complexity within the LES model PALM-4U is tested and compared.

In this paper we present the current version of the Parallelized Large-Eddy Simulation Model (PALM) whose core has been developed at the Institute of Meteorology and Climatology at Leibniz Universität Hannover (Germany). PALM is a Fortran 95-based 5 code with some Fortran 2003 extensions and has been applied for the simulation of a variety of atmospheric and oceanic boundary layers for more than 15 years. PALM is optimized for use on massively parallel computer architectures and was recently ported to general-purpose graphics processing units. In the present paper we give a detailed description of the current version of the model and its features, such as an embedded 10 Lagrangian cloud model and the possibility to use Cartesian topography. Moreover, we discuss recent model developments and future perspectives for LES applications. DFG/RA/617/3 DFG/RA/617/6 DFG/RA/617/16 DFG/RA/617/27-1

Large-Eddy Simulation (LES) of atmospheric boundary layer (ABL) is becoming an important research method for urban air-quality studies. Until very recently, it was impossible to include detailed structures, such as buildings in ABL LES. Nowadays, it is possible, but such LES is still limited to a relatively small areas because typically about 1 m resolution is required. However, for several reasons an ABL LES domain should cover a large area leading to huge computational task. A means to overcome this is to concentrate resolution to the primary area of interest by means of model nesting. The idea of nesting is to simultaneously run a series of two or more LES in domains with different sizes and resolutions. In this work, two-way nesting is implemented in the parallelized LES model PALM. The nesting system is tested for several test cases including a convective boundary layer with zero mean wind, several neutral boundary layers over both flat terrain and terrain with an array of obstacles.

The computational power and availability of graphics processing units (GPUs) and many integrated core (MIC) processors on high performance computing (HPC) systems is rapidly evolving. However, HPC applications need to be ported to take advantage of such hardware. This paper is a report on our experience of porting the MPI+OpenMP parallelised large-eddy simulation model (PALM) to multi-GPU as well as to MIC processor environments using OpenACC and OpenMP. PALM is written in Fortran, entails 140 kLOC and runs on HPC farms of up to 43,200 cores. The main porting challenges are the size and complexity of PALM, its inconsistent modularisation and no unit-tests. We report the methods used to identify performance issues as well as our experiences with state-of-the-art profiling tools. Moreover, we outline the required porting steps, describe the problems and bottlenecks we encountered and present separate performance tests for both architectures. We however, do not provide benchmark information.