Previous Version Research Articles

MQCT 2024: A program for calculations of inelastic scattering of two molecules (new version announcement)

This is a revised and updated version of the package MQCT. The package includes routines for the calculations of ro-vibrational state-to-state transition cross sections for molecule + molecule collisions, using the mixed quantum/classical theory approach. One important addition to the package is an efficient and accurate adiabatic-trajectory approximation method (AT-MQCT), which enables calculations for larger and more complex molecules. An efficient parallel IO is implemented for state-to-state transition matrix, which now permits to handle very large matrixes, but also helps to truncate these matrixes by neglecting insignificant matrix elements and to balance the load on different CPUs during the matrix calculations and during the trajectory propagation. A stable recursive approach is added for computation of Wigner 3j-symbols, which expands the range of rotational states of molecules up to j∼ 100. Examples of input files are provided for all ten system types covered by the package, along with updated user manual. New version program summaryProgram title: MQCT 2024CPC Library link to program files:https://doi.org/10.17632/sg36r35njz.2Developer's repository link:https://github.com/MarquetteQuantum/MQCTCode Ocean capsule:https://codeocean.com/capsule/1260072/tree/v1Licensing provisions: GNU GPL v3.0Programming language: FORTRANJournal reference of previous version: Comput. Phys. Commun. 252 (2020) 107155Does the new version supersede the previous version?: YesReasons for the new version:1)Recently, we developed and tested the adiabatic-trajectory method [1–3] within MQCT framework, which appears to be both efficient and accurate, and is likely to become a “workhorse” for inelastic scattering calculations in molecule + molecule systems. In the new version of the package this method is made available as an option, AT-MQCT.2)Since MQCT trajectory calculations became more affordable with AT-MQCT, we started doing calculations with larger and larger rotational basis sets and quickly encountered several new problems. The major one was an extremely slow serial IO of the state-to-state transition matrix to a single file, which is now replaced by a parallel IO to multiple files written to a separate directory. Very large matrixes (up to 1010 non-zero matrix elements) are now handled efficiently.3)Another problem was an incorrect calculation of Wigner 3j-symbols for the rotational states around j∼ 40 and above. In the revised version a new stable subroutine is employed that uses a recursive method and works properly at least up to j=100.4)Several “bugs” were caught and fixed, with one major in the Monte-Carlo sampling of MQCT trajectories. Now users can add a batch of new trajectories to the previously sampled batch. In addition, users can monitor the convergence of Monte-Carlo sampling in detail. These options work for all levels of theory, including AT-MQCT. Several errors were found in the equations for calculations of state-to-state transition matrix using the expansion of potential energy surface, and in symmetrization of matrix elements for the case of identical collision partners. All these have been corrected.Summary of revisions: Several technical revisions concern the treatment of diatomic molecules in the code: A bug was found and fixed in the PES interface that converts the units of vibrational coordinate (the diatomic bond distance). Now the PES can be expressed in either Angstrom or Bohr, as specified in the input file. Integration of matrix elements over the vibrational coordinate is modified to use an equidistant grid by default (Gauss-Legendre method is still available as option). And the same for integration over Euler angles α and γ (for all system types). Integration over β uses Gauss-Legendre quadrature only. The format of ro-vibrational wavefunctions pre-computed externally and supplied as input is made more intuitive, as described in the manual. Finally, a new method for the sampling of orbital quantum number ℓ is implemented, which skips some values of ℓ and obtains results by interpolation of the data at the retained values of ℓ (for all system types, as described in the manual). Last version of the code is always available at https://github.com/MarquetteQuantum/MQCT.Supplementary material: Updated and expanded MQCT user guideNature of problem: Calculations of rotationally and vibrationally inelastic scattering of two molecules, with possible applications in astrophysics and atmospheric chemistrySolution method: Mixed quantum/classical theory (MQCT) approach References[1]B. Mandal, A. Semenov and D. Babikov, J. Phys. Chem. A 124 (2020) 9877-9888[2]B. Mandal, C. Joy, A. Semenov and D. Babikov, ACS Earth Space Chem. 6 (2022) 521-529[3]B. Mandal, C. Joy, D. Bostan, A. Eng and D. Babikov, J. Phys. Chem. Lett. 14 (2023) 817–824.

The PopuList: A Database of Populist, Far-Left, and Far-Right Parties Using Expert-Informed Qualitative Comparative Classification (EiQCC)

AbstractWith a proliferation of scholarly work focusing on populist, far-left, and far-right parties, questions have arisen about the correct ways to ideologically classify such parties. To ensure transparency and uniformity in research, the discipline could benefit from a systematic procedure. In this letter, we discuss how we have employed the method of ‘Expert-informed Qualitative Comparative Classification’ (EiQCC) to construct the newest version of The PopuList (3.0) – a database of populist, far-left, and far-right parties in Europe since 1989. This method takes into account the in-depth knowledge of national party experts while allowing for systematic comparative analysis across cases and over time. We also examine how scholars have made use of the previous versions of the dataset, explain how the new version of The PopuList differs from previous ones, and compare it to other data. We conclude with a discussion of the strengths and limitations of The PopuList dataset.

Improved phenotypic classification of male infertility to promote discovery of genetic causes.

An increasing number of genes are being described in the context of non-syndromic male infertility. Linking the underlying genetic causes of non-syndromic male infertility with clinical data from patients is important to establish new genotype-phenotype correlations. This process can be facilitated by using universal nomenclature, but no standardized vocabulary is available in the field of non-syndromic male infertility. The International Male Infertility Genomics Consortium aimed at filling this gap, providing a standardized vocabulary containing nomenclature based on the Human Phenotype Ontology (HPO). The "HPO tree" was substantially revised compared with the previous version and is based on the clinical work-up of infertile men, including physical examination and hormonal assessment. Some causes of male infertility can already be suspected based on the patient's clinical history, whereas in other instances, a testicular biopsy is needed for diagnosis. We assembled 49 HPO terms that are linked in a logical hierarchy and showed examples of morphological features of spermatozoa and testicular histology of infertile men with identified genetic diagnoses to describe the phenotypes. This work will help to record patients' phenotypes systematically and facilitate communication between geneticists and andrologists. Collaboration across institutions will improve the identification of patients with the same phenotypes, which will promote the discovery of novel genetic causes for non-syndromic male infertility.

Simple Bayesian reconstruction and forecasting of stream water temperature for ecologists-A tool using air temperature, optionally flow, in a time series decomposition approach.

Mitigating the impacts of global warming on wildlife entails four practical steps. First, we need to study how processes of interest vary with temperature. Second, we need to build good temperature scenarios. Third, processes can be forecast accordingly. Only then can we perform the fourth step, testing mitigating measures. While having good temperature data is essential, this is not straightforward for stream ecologists and managers. Water temperature (WT) data are often short and incomplete and future projections are currently not routinely available. There is a need for generic models which address this data gap with good resolution and current models are partly lacking. Here, we expand a previously published hierarchical Bayesian model that was driven by air temperature (AT) and flow (Q) as a second covariate. The new model can hindcast and forecast WT time series at a daily time step. It also allows a better appraisal of real uncertainties in the warming of water temperatures in rivers compared to the previous version, stemming from its hybrid structure between time series decomposition and regression. This model decomposes all-time series using seasonal sinusoidal periodic signals and time varying means and amplitudes. It then links the contrasted frequency signals of WT (daily and six month) through regressions to that of AT and optionally Q for better resolution. We apply this model to two contrasting case study rivers. For one case study, AT only is available as a covariate. This expanded model further improves the already good fitting and predictive capabilities of its earlier version while additionally highlighting warming uncertainties. The code is available online and can easily be run for other temperate rivers.

Polyrate 2023: A computer program for the calculation of chemical reaction rates for polyatomics. New version announcement

Polyrate 2023: A computer program for the calculation of chemical reaction rates for polyatomics. New version announcement

The current sepsis guidelines-What do you need to know?

The current international sepsis guidelines from 2021 are based on the work of apanel of 60international experts from various fields. They include a total of 93recommendations, some of which include new aspects compared to the 2016 version of the guidelines. This article provides asubjective compilation by two internal medicine intensivists who highlight some aspects, especially of changes within the guidelines compared to the previous version. The focus is on the fields of screening, sepsis bundles, fluid and vasopressor treatment and adjuvant treatment. In addition, for the first time these guidelines address the important issue of long-term sequelae for sepsis survivors and their environment.

Psychometric assessment of the 10-item, revised experience of close relationship (ECR-R-10) in nonclinical and clinical populations of adults and older adults in Thailand

The experiences of close relationships-revised (ECR-R) is a widely used 36-item self-report measurement for measuring adult attachment. However, various short versions of the ECR-R have been developed and tested psychometrically. Given the cultural impact, a short version of the Thai ECR-R should be derived from the existing Thai version of the ECR-R. This study aimed to develop a 10-item version of the ECR-R that demonstrates comparable psychometric properties to the previous Thai version and the 18-item ECR-R. This study included four studies with a total of 1,322 participants. In study 1, 434 adults in a nonclinical setting were used for the development of the 10-item Thai ECR-R and tested in an independent sample. Studies 2, 3, and 4 were conducted on 312 adults in the clinical setting, 227 older adults in the nonclinical, and 123 older adults in clinical settings. The Cronbach alphas and corrected correlations between the ECR-R-18 and the ECR-R-10 in each study were calculated. Confirmatory factor analysis of the first-order two-factor solution model with fit statistics was examined with each sample. Correlations of the ECR-R-18 and the ECR-R-10 with other measurements were presented and compared. Known-group validity and measurement invariance test were also examined. The Cronbach alphas of the ECR-R-10 among all samples were acceptable, ranging between .77 and .85 for avoidance subscales and between .82 and .86 for anxiety subscales. The corrected correlation between the ECR-R-18 and ECR-R-10 was between .61 (p < .001) and .82 (p < .001). The values of the comparative fit index and Tucker-Lewis index for the model of ECR-R-10 were between .903 and .985, whereas the root-mean-square error of approximation was between .082 and .036, indicating that the model fits were acceptable. The ECR-R-10 was related to the measurements with a similar construct; however, no difference in the magnitude of correlation was observed between ECR-R-18 and ECR-R-10. Known group validity was established. Measurement invariance was successfully established across different age and gender groups, although it was only partially achieved with respect to clinical status. The ECR-R-10 provided equal or superior psychometric properties to the ECR-R-18 across age groups and settings. As it is a briefer scale, the ECR-R-10 can be practically used in general and clinical samples to reduce the burden of assessment, especially with older adults. Further investigation is needed to test the scale's temporal stability.

The “Human Emotions” and the new “Perrotta Human Emotions Model” (PHEM-2): Structural and functional updates to the first model

Background: The first version of the Perrotta Human Emotions Model (PHEM) responded to the need for better structuring, in a functional framework, of emotions and sentiments, giving the proper role to anxiety, according to a neurobiological perspective, in a strategic scheme, but needs structural and functional corrections. Methods: Clinical interview, based on narrative-anamnestic and documentary evidence, and battery of psychometric tests. Results: Statistical comparison of data obtained by administering PHEM-1 versus data obtained by administering PHEM-2 reported an R = 0.999, with p = ≤0.001, as is the case when testing clinical utility by assessing it using MMPI-2-RF and PICI-2. Conclusion: This research confirms the clinical usefulness of administering the PHEM-2, compared with the previous version, during psychotherapeutic encounters conducted according to the brief or otherwise integrated strategic approach.

Brief report comparing the Scale of Emotional Development - Short (SED-S) with other scales for emotional development.

Different instruments were devised for assessing emotional development (ED) level in persons with an intellectual disability (ID), that is, the Scale of Emotional Development - Short (SED-S), the Scheme for Appraisal of Emotional Development (SAED), the Scale for Emotional Development - Second Revision (SED-R2 ) and the Schaal voor Emotionele Ontwikkeling - Lukas (SEO-Lukas). The aim of this study was to compare the level of emotional functioning as assessed with the SED-S with the SAED, SED-R2 and SEO-Lukas. Emotional development was measured in adults with ID with the SED-S (N=186) and the SAED (n=85), the SED-R2 (n=50) and the SEO-Lukas (n=51). Correlation analysis and Cohen's kappas were calculated between the SED-S and the three respective scales. Internal consistencies (Cronbach's alpha) of the four scales were determined. The SED-S results correlated most with the SEO-Lukas (γ=1; кω=0.936) followed by the SAED (γ=0.809; кω=0.343) and least by the SED-R2 (γ=0.665; кω=0.182). The stage of ED assessed with the SED-S was lower than the ED results measured with the SAED, but higher than with the SED-R2 and most similar to the SEO-Lukas. Cronbach's alphas were high, ranging from 0.853 to 0.975. Given the respective differences between the scales, the SED-S may equalise the results as compared with previous versions.

Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications

High-quality reference genome assemblies, representative of global heterotic patterns, offer an ideal platform to accurately characterize and utilize genetic variation in the primary gene pool of hybrid crops. Here we report three platinum grade de-novo, near gap-free, chromosome-level reference genome assemblies from the active breeding germplasm in pearl millet with a high degree of contiguity, completeness, and accuracy. An improved Tift genome (Tift23D2B1-P1-P5) assembly has a contig N50 ~ 7,000-fold (126 Mb) compared to the previous version and better alignment in centromeric regions. Comparative genome analyses of these three lines clearly demonstrate a high level of collinearity and multiple structural variations, including inversions greater than 1 Mb. Differential genes in improved Tift genome are enriched for serine O-acetyltransferase and glycerol-3-phosphate metabolic process which play an important role in improving the nutritional quality of seed protein and disease resistance in plants, respectively. Multiple marker-trait associations are identified for a range of agronomic traits, including grain yield through genome-wide association study. Improved genome assemblies and marker resources developed in this study provide a comprehensive framework/platform for future applications such as marker-assisted selection of mono/oligogenic traits as well as whole-genome prediction and haplotype-based breeding of complex traits.

Primary Central Nervous System Lymphoma

Histopathologic classifications of primary central nervous system lymphoma(PCNSL)are covered by two WHO classifications; WHO classification of Tumors: Central Nervous System Tumours(WHO-CNS)and WHO classification of Tumors: Haematolymphoid Tumours(WHO-HAEM). The International Consensus Classification(ICC)is another recent comprehensive classification of hematolymphoid tumors that covers these disease entities. While these classifications mainly share the same principles for categorizing these tumors, there are several differences that should be noted owing to the nature of WHO-CNS(which covers only the lymphomas manifesting in the CNS, and the anatomic sites are described in the titles of some entities)and the introduction of new entities in the latest version(5th)of the WHO-HAEM(WHO-HAEM5). In the WHO-HAEM5, two novel entities related to the perception of PCNSLs are introduced: primary large B-cell lymphoma of immune-privileged sites and lymphomas arising in immune deficiency/dysregulation. These entities are largely based on the underlying biology shared by lymphomas that arise from different sites, including the central nervous system, and they combine and re-classify several types that had been defined separately according to their sites and etiologies in previous versions. Classifications of PCNSLs in future revisions of the WHO-CNS might be described as parts of these novel entities, and nomenclatures of some diagnostic entities may be subject to change accordingly. This review will mainly focus on the classification of lymphomas described in the 5th edition of WHO-CNS, along with its comparison with WHO-HAEM and ICC.

PROBLEMATIKA PELAFALAN MANTRA PŪJĀ TRI SANDHYĀ (PERSPEKTIF PENDIDIKAN)

The coaching of the Pūjā Tri Sandhyā mantra is still an emphasis in the learning process in non-formal boarding schools until now, but problems in reciting this mantra are still often found in students. The problems that arise are not only related to the differences in the mantras of the 1991 PHDI standard version and the previous version, but more serious problems related to the emergence of new word pronunciations. This phenomenon is very important to study in order to obtain a clear picture of the causes of this problem so that it can become a reference for interested parties in formulating appropriate solutions. This study uses a qualitative approach that implements observation, interviews, and documentation to collect representative data. The results of the study show that the factors causing the problems of reciting the Pūjā Tri Sandhyā mantra which have not been fully resolved to date are the lack of Sanskrit language development and the tendency of students to imitate this mantra without any correction. The orientation of the learning pattern at the pasraman does not emphasize how to chant mantras in accordance with Sanskrit provisions but tends to increase śraddhā and devotional service in the form of prayer habits.

Web Accessibility: A Revisit of U.S. State and Territory COVID-19 Websites After Two Years

This study is a longitudinal replication of a website accessibility study conducted in 2021 to compare if COVID-19 sites had improved, declined, or stayed the same in terms of accessibility. Two automated accessibility checker tools, MAUVE++ and WAVE, were used to assess the accessibility of all available U.S. state and territory COVID-19 websites. Each state and territory's home page, testing page, and vaccine page were examined, and accessibility ratings were determined. The number of errors and the overall accessibility ratings were compared between the current (2023) and previous (2021) versions of the sites, both archived using the WayBack Machine. Multi-level modelling methods were employed to analyze the data. The results indicated that the most inaccessible components were those requiring visual interaction, and there were no significant changes in the overall accessibility of websites over the years. A closer examination of individual Success Criteria revealed a significant increase in violation rate of 1.4.11 (non-text contrast) from 2021 to 2023. Overall, this research suggests that there has been a lack of improvement in accessibility of the chosen COVID-19 websites over the past two years, and it has also identified areas that need to be improved.

Continuity, Considerations, and Future Directions for the Healthy Eating Index-Toddlers-2020.

The Dietary Guidelines for Americans, 2020-2025 includes guidance for infants and toddlers aged birth to 24 months. To assess alignment with this new guidance, the Healthy Eating Index (HEI)-Toddlers-2020 was developed for toddlers 12 through 23 months old. This monograph focuses on the continuity, considerations, and future directions of this new index for toddlers in the context of evolving dietary guidance. There is considerable continuity between the HEI-Toddlers-2020 and previous versions of the HEI. The same process, guiding principles, and features (with caveats) are repeated in the new index. However, there are unique considerations for measurement, analysis, and interpretation for the HEI-Toddlers-2020 that this article addresses, while identifying future directions for the HEI-Toddlers-2020. The continued evolution of dietary guidance for infants, toddlers, and young children will provide additional opportunities for index-based metrics: considering inclusion of multidimensional layers in dietary patterns, defining a healthy eating trajectory, bridging healthy eating across different life stages, and communicating the constructs of balance among dietary constituents.

Lee-Yang-inspired functional including contributions to fourth order in effective field theory

In the last years, a new family of energy density functionals directly inspired by effective field theory (EFT) has been developed, among which the ELYO (extended Lee-Yang Orsay) functional. In this paper, a new extension of ELYO that includes the recently calculated fourth-order EFT terms is presented. Compared to the previous version, the description of neutron-drop energies slightly degrades for a harmonic trap ħω = 10 MeV—yet remaining reasonable—, but improves for ħω = 5 MeV. Furthermore, the obtained neutron effective mass agrees significantly better with ab-initio estimates.

Tropospheric ozone data assimilation in the NASA GEOS Composition Forecast modeling system (GEOS-CF v2.0) using satellite data for ozone vertical profiles (MLS), total ozone columns (OMI), and thermal infrared radiances (AIRS, IASI)

The NASA Goddard Earth Observing System Composition Forecast system (GEOS-CF) provides global near-real-time analyses and forecasts of atmospheric composition. The current version of GEOS-CF builds on the GEOS general circulation model with Forward Processing assimilation of meteorological data (GEOS-FP) and includes detailed GEOS-Chem tropospheric and stratospheric chemistry. Here we add 3D variational data assimilation in GEOS-CF to assimilate satellite observations of ozone including MLS vertical profiles, OMI total columns, and AIRS and IASI hyperspectral 9.6 μm radiances. We focus our evaluations on the troposphere. We find that the detailed tropospheric chemistry in GEOS-CF significantly improves the simulated background ozone fields relative to previous versions of the GEOS model, allowing for specification of smaller background errors in assimilation and resulting in smaller assimilation increments to correct the simulated ozone. Assimilation increments are largest in the upper troposphere and are consistent between satellite data sets. The OMI and MLS ozone data generally provide more information than the AIRS and IASI radiances except at high latitudes where the radiances provide more information. Comparisons to independent ozonesonde and aircraft (ATom-4) observations for 2018 show significant GEOS-CF improvement from the assimilation, particularly in the extratropical upper troposphere.

ARCHITECT HBsAg Next assay is positioned better to resolve and refine challenging weak reactive clinical samples.

Ultrasensitive HBsAg assays are replacing the previous versions. Unlike the sensitivity, the specificity, and its positioning to resolve weak-reactives (WR) are not studied. We investigated the ability of ARCHITECT HBsAg-Next (HBsAg-Nx) assay to resolve WR and sought its clinical validation and correlation with confirmatory/reflex testing. Among 99,761 samples between Jan 2022 - 2023, 248 reactive samples in HBsAg-Qual-II were compared with HBsAg-Nx assay. Sufficient samples were further subjected to neutralization (n=108) and reflex (anti-HBc total/anti-HBs antibody) testing. Out of 248 initial reactive samples in HBsAg-Qual-II, 180 (72.58%) were repeat reactive, and 68 (27.42%) were negative, whereas in HBsAg-Nx, 89 (35.89%) were reactive and 159 (64.11%) were negative (p<0.0001). Comparing the results of two assays (Qual-II/Next), 57.67% (n=143) were concordant (++/-) and 105 (42.33%) were discordant (p=0.0025). Testing of HBsAg-Qual-II + & HBsAg-Nx - samples revealed that 85.71% (n=90) were anti-HBc total negative and 98.08% (n=51) were not neutralized as well as significant proportion (89%) had no clinical correlation. The proportion of samples neutralized was significantly different between ≤5 S/Co (26.59%) and >5 S/Co (71.42%) (p=0.0002). All samples (n=26) with enhanced reactivity in HBsAg-Nx were effectively neutralized, while samples with no increase in reactivity, 89% (n=72) failed neutralization (p=<0.001). HBsAg-Nx assay is positioned better to resolve and refine challenging WR samples than Qual-II which correlated well with confirmatory/reflex tests and clinical disease. This superior internal benchmarking significantly reduced the cost and quantum of retesting, confirmatory/reflex testing in the diagnosis of HBV infection.

Implementation of a ternary lattice Boltzmann model in LAMMPS

The properties of multicomponent fluids are governed by the interplay of phase behavior, fluid dynamics, and interfacial thermodynamics. A mixture formulation that leverages this interplay is an important aspect in many fabrication processes based on emulsion templating. The lattice Boltzmann method (LBM) has become a popular approach for simulating hydrodynamic effects in complex fluids and soft matter. Here we present an implementation of a ternary lattice Boltzmann model that allows to simulate a mixture of three immiscible fluids. We build on the LATBOLTZ extension of the open-source package LAMMPS and implement a ternary free energy model recently introduced by Semprebon et al. [Phys. Rev. E 93, 033305 (2016)]. We validate the static and dynamic properties by simulating liquid lenses, double emulsions, and ternary mixtures. From the simulations, we obtain the complete morphology diagram of the ternary mixture in composition space. We further discuss an application of the method to phase segregation of ternary films. The implementation of the ternary LBM in LAMMPS opens vast opportunities for mesoscale simulations of interfacial phenomena and non-equilibrium transport processes in multicomponent fluid mixtures. Program summaryProgram Title: fix lb/multicomponentCPC Library link to program files:https://doi.org/10.17632/gn8znmyxrh.1Developer's repository link:https://github.com/uschille/lammps/tree/ternary-lbmLicensing provisions: GPLv2Programming language: C++Journal reference of previous version: C. Denniston, N. Afrasiabian, M.G. Cole-André, F.E. Mackay, S.T.T Ollila, T. Whitehead. LAMMPS lb/fluid fix version 2: Improved hydrodynamics forces implemented into LAMMPS through a lattice-Boltzmann fluid. Comput. Phys. Commun.275, 108318 (2022).Does the new version supersede the previous version?: NoReasons for the new version: The lb/multicomponent fix provides new capabilities for simulating ternary fluid mixtures.Summary of revisions: An implementation of the ternary free-energy lattice Boltzmann model [1] has been added to the LATBOLTZ extension of LAMMPS. The new functionality is available through the script command fix lb/multicomponent.Nature of problem: Multicomponent fluids involve non-local interactions that give rise to fluid-fluid surface tension and a non-ideal pressure tensor. This requires a modification of the standard lattice Boltzmann method.Solution method: The implementation extends the existing lattice Boltzmann code in LAMMPS [2] and introduces data structures and methods for the ternary algorithm introduced in [1]. The code carries out the streaming and collision steps for three fluid components using the appropriate equilibrium distributions. The equilibrium distribution is calculated based on thermodynamic quantities derived from the free energy.Additional comments including restrictions and unusual features: The current version of the lb/multicomponent fix is restricted to the D3Q19 lattice.

Ocean biogeochemistry in the coupled ocean–sea ice–biogeochemistry model FESOM2.1–REcoM3

Abstract. The cycling of carbon in the oceans is affected by feedbacks driven by changes in climate and atmospheric CO2. Understanding these feedbacks is therefore an important prerequisite for projecting future climate. Marine biogeochemistry models are a useful tool but, as with any model, are a simplification and need to be continually improved. In this study, we coupled the Finite-volumE Sea ice–Ocean Model (FESOM2.1) to the Regulated Ecosystem Model version 3 (REcoM3). FESOM2.1 is an update of the Finite-Element Sea ice–Ocean Model (FESOM1.4) and operates on unstructured meshes. Unlike standard structured-mesh ocean models, the mesh flexibility allows for a realistic representation of small-scale dynamics in key regions at an affordable computational cost. Compared to the previous coupled model version of FESOM1.4–REcoM2, the model FESOM2.1–REcoM3 utilizes a new dynamical core, based on a finite-volume discretization instead of finite elements, and retains central parts of the biogeochemistry model. As a new feature, carbonate chemistry, including water vapour correction, is computed by mocsy 2.0. Moreover, REcoM3 has an extended food web that includes macrozooplankton and fast-sinking detritus. Dissolved oxygen is also added as a new tracer. In this study, we assess the ocean and biogeochemical state simulated with FESOM2.1–REcoM3 in a global set-up at relatively low spatial resolution forced with JRA55-do (Tsujino et al., 2018) atmospheric reanalysis. The focus is on the recent period (1958–2021) to assess how well the model can be used for present-day and future climate change scenarios on decadal to centennial timescales. A bias in the global ocean–atmosphere preindustrial CO2 flux present in the previous model version (FESOM1.4–REcoM2) could be significantly reduced. In addition, the computational efficiency is 2–3 times higher than that of FESOM1.4–REcoM2. Overall, it is found that FESOM2.1–REcoM3 is a skilful tool for ocean biogeochemical modelling applications.

A new version of PyWolf for the propagation of partially coherent light in media other than free space

PyWolf is an open-source software capable of performing numerical simulations of partially coherent light propagation from two-dimensional light sources using parallel computation. In the original version of PyWolf, the graphical user interface (GUI) would only show free-space propagation as the only option for propagating partially coherent light, even though users could add their own source models and other objects such as lenses and apertures, which was recognized by PyWolf's GUI. We introduce here the new version of PyWolf, PyWolf 2.0, which among other improvements, enables users to easily add their own propagation medium, which can be used throughout the simulation in different propagation planes. New version program summaryProgram Title: PyWolfCPC Library link to program files:https://doi.org/10.17632/frjscxypkd.2Developer's repository link:https://github.com/tiagoecmagalhaes/PyWolfLicensing provisions: GPLv3Programming language: PythonSupplementary material: Detailed description of the main changes with an example.Journal reference of previous version: Comput. Phys. Commun. 276 (2022) 108336.Reasons for the new version: In the previous paper [1] describing the original version of PyWolf, the propagation kernel was limited to free space, even though optical elements such as lenses and apertures could be added. For propagation in other media (e.g., turbulent medium), users had to substitute the free space propagation by the desired propagation medium since PyWolf always uses the same propagator, which is present in a single Python script.Summary of revisions: Propagation model selection was added to PyWolf's graphical user interface (GUI), enabling users to select the propagation medium of interest. It also enables input parameters (e.g., refractive index) for each propagation model. PyWolf checks for the Python scripts present in the “propagation models” folder at startup and displays them in the GUI, similar to what is done, for instance, for the source models. Then, during the simulation, instead of using the same free space propagators, PyWolf will use the ones that are defined in the selected propagation model. Four examples of propagation models are present in the current version, namely, free space, constant refractive index (besides 1), Kolmogorov, and Tatarskii models [2,3]. Depending on the model used, some propagation quantities may not be valid. For instance, in the current implementation for free space propagation, both the spectral density and degree of coherence are valid, however, that is not the case for the current implementations of the Kolmogorov and Tatarskii models, where only the spectral density is valid. Besides this main feature added to PyWolf, other small issues have been improved and corrected, namely: (i) PyWolf now initiates without needing PyOpenCl platforms or devices; (ii) some errors associated with the importation of packages have been corrected; and (iii) phase correction in the FFT algorithm for odd arrays which can affect the propagation image.Nature of problem: Numerical simulations of the propagation of partially coherent light from planar sources in the Fresnel or far field approximations. Computation time can be improved by using optimized versions of the fast Fourier transform algorithm, but the computation time of other tasks can also be improved through parallel computation. PyWolf aims at using parallel computation to perform time-consuming calculations in the propagation of the cross-spectral density function [4,5].Solution method: The open-source toolkit PyOpenCL is used to perform parallel computation on time-consuming calculations. The user can easily modify and add more features to the software, such as source and propagation models. A graphical user interface is also built using PyQt5 which enables the user to set input parameters, including the user's custom models, view the simulation results, export data, and save and load sessions.