Research articles using Fortran

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Zero air pollution and zero carbon from all energy at low cost and without blackouts in variable weather throughout the U.S. with 100% wind-water-solar and storage
by Mark Z. Jacobson, Anna-Katharina von Krauland, Stephen J. Coughlin, Frances C. Palmer, and Miles M. Smith
Renewable Energy
Volume 184, January 2022, Pages 430-442

Abstract

This study analyzes 2050–2051 grid stability in the 50 U S. states and District of Columbia after their all-sector (electricity, transportation, buildings, industry) energy is transitioned to 100% clean, renewable Wind-Water-Solar (WWS) electricity and heat plus storage and demand response (thus to zero air pollution and zero carbon). Grid stability is analyzed in five regions; six isolated states (Texas, California, Florida, New York, Alaska, Hawaii); Texas interconnected with the Midwest, and the contiguous U.S. No blackouts occur, including during summer in California or winter in Texas. No batteries with over 4-h storage are needed. Concatenating 4-h batteries provides long-duration storage. Whereas transitioning more than doubles electricity use, it reduces total end-use energy demand by ∼57% versus business- as -usual (BAU), contributing to the 63 (43–79)% and 86 (77–90)% lower annual private and social (private + health + climate) energy costs, respectively, than BAU. Costs per unit energy in California, New York, and Texas are 11%, 21%, and 27% lower, respectively, and in Florida are 1.5% higher, when these states are interconnected regionally rather than islanded. Transitioning may create ∼4.7 million more permanent jobs than lost and requires only ∼0.29% and 0.55% of new U.S. land for footprint and spacing, respectively, less than the 1.3% occupied by the fossil industry today.

An article on CNBC (a business TV channel) says this:

Jacobson and his colleagues use three types of models for the calculations.

First, they use a spreadsheet model to project business-as-usual energy demand in each sector in each state to 2050 and then to convert the business-as-usual energy demand in 2050 to electricity provided by wind, water and solar.

Second, they use a weather model to predict the wind and solar fields in each state every 30 seconds. This weather-prediction model runs on a supercomputer and is written in Fortran computing language.

And the third component of his modeling matches the 2050 energy demand with the weather modeling of energy that can be supplied from wind, water and solar every 30 seconds. The third component is also written in Fortran, but this portion of the process can run on virtually any computer.

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BESLE: Boundary element software for 3D linear elasticity

Abstract
BESLE is the first available parallel open-source code to analyse the mechanical behaviour of heterogeneous materials using the boundary element method (BEM) in 3D and in both an elastostatic and elastodynamic setting. Unlike all the other codes that are presently available, the software presented here is capable of simulating both isotropic and anisotropic materials comprised of single or multiple domains. Furthermore, the user-interface has been designed to provide a convenient way for configuring simulations involving many complex material constituents. Results are described by the displacement and traction fields, also, the stress and strain tensors are available for post-processing. BESLE is largely implemented in Fortran-MPI, but some of the sub-packages are based on other languages such as C and C++, and as such a the software is best used on a multi-core architecture where the parallelisation can be fully exploited. The main features and functionality of BESLE are presented here, and the User’s Guide, available from the repository listed below, gives further details and outlines how users can carry out bespoke simulations.

Programming language: Fortran 90, C++/C

External libraries: LAPACK [1], BLAS [2], SCOTCH [3], ScaLAPACK [4], MUMPS [5], Voro++ [6], Triangle [7]

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64

Reshetova G., Cheverda V., Koinov V. (2021) Comparative Efficiency Analysis of MPI Blocking and Non-blocking Communications with Coarray Fortran. In: Voevodin V., Sobolev S. (eds) Supercomputing. RuSCDays 2021. Communications in Computer and Information Science, vol 1510. Springer, Cham. DOI: 10.1007/978-3-030-92864-3_25
https://link.springer.com/chapter/10.1007/978-3-030-92864-3_25

It is not Open Access, but there is also a presentation here:

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Vanderbauwhede, W. Making legacy Fortran code type safe through automated program transformation. J Supercomput 78, 2988–3028 (2022). https://doi.org/10.1007/s11227-021-03839-9

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66

Castillo-Méndez, C., & Ortiz, A. (2022). Numerical simulation data and FORTRAN code to compare the stress response of two transversely isotropic hyperelastic models in ABAQUS. Data in Brief, 41, https://doi.org/10.1016/j.dib.2022.107853

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Uğurlu, B., Kahraman, İ. and Soares, C.G., 2022. Numerical investigation of the Fourier–Kochin theory for wave-induced response estimation of floating structures. Ocean Engineering, 247, p.110562.

https://www.sciencedirect.com/science/article/pii/S0029801822000361?casa_token=aS60FAt7hpcAAAAA:iaiTxvuInuekgSPU8bRMX1YWF0SWTIHTOPyTbzAq8LS3vvFWt37BYyRck0MezsYo2ZLtOlQA1g0

Abstract

The Fourier–Kochin theory—an indirect solution approach for the boundary integral representations of free-surface flows that rely on free-surface Green function—is investigated by considering effective computation and reliable prediction. The present study addresses wave–body interaction with zero forward speed by adopting a higher-order approximation. Three distinct hull forms, the DTMB 5415, a scaled model reproduced from it, and a barge are used for practical application. The scaled frigate and barge models are used for comparative analysis to assess the performance of different computation techniques, modeling elements, and solution methods and to find the best course; the purpose of studying DTMB 5415 is to provide a realistic application based on a full-scale hull form by using the findings of the earlier benchmark studies. The analyses that cover both the rigid-body and elastic responses indicate that an adaptive approach for the computation of Fourier components has the potential to eliminate the numerical drawbacks of the presented implementation the Fourier–Kochin theory, but also stringently needs parallelism, preferably using the Single Program Multiple Data model. Using discontinuous elements for free-surface discretization when applying the Extended Boundary Integral Equation Method, the featured technique for irregular frequency suppression, is also promoted.

Excerpt

The preferred programming language for execution of the numerical solution here is Fortran, which also has native support for high-performance parallel computing, its relatively new coarray feature. Fortran follows the Single Program Multiple Data (SPMD) parallelism model. Accordingly, a single program is copied on each invoked parallel process, that is a thread or a core, which uses its own independent data—tasks are distributed and run simultaneously as parallel processes.

Fortran coarrays offer both shared-memory and distributed-memory parallel processing, similar to the Message Passing Interface, MPI, protocol. As the name implies, in a shared-memory system multiple processors access the same memory space, hence they do not need additional directives to communicate. In a typical setting, the program starts executing on one processor and the execution splits in a parallel region, where multiple processors execute a single program on different data. When the parallel region ends, execution is synchronized and only one processor continues, while others wait. Open Multi-Processing (OpenMP), the standard programming interface for shared-memory multiprocessing, supports parallelization through a set of directives. It requires low to moderate effort to deliver significant acceleration especially through loop structures with OpenMP; however, the number of processing units that a shared-memory system may have is limited. A distributed-memory computing system is a collection of independent computers, referred to as nodes, all serving as shared-memory multiprocessing units. Every processor in a node starts its own program on local memory and each node communicates with other nodes by sending and receiving messages, i.e., transfers and syncs data. MPI is the effective standard for communication and synchronization of distributed-memory systems; it operates mostly at low-level, which can make its use complicated.

The coarrays in Fortran provide a simple and an elegant tool for enabling parallelism. They are used to distribute the shared data objects among parallel processes, identified as images. Similar to an array (a data structure for representing one- or multi-dimensional data) that captures multiple values within a single object or distributes one object into multiple components with an opposite perspective, a coarray partitions a data object to the available array of images, and then recollects all parts by allowing direct communication among them. Fortran is a partitioned global address space language that the available memory, including those belonging to the remote images, appear as a local shared-memory space. Built on this, the coarrays presents an intuitive way to copy data between parallel processes much like to array operations (Curcic, 2020).

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68

A. L. Spek, J. Appl. Cryst. 2003, 36, 7-11. Single-crystal structure validation with the program PLATON; doi 10.1107/S0021889802022112 (open access).

Widely used in small molecule X-ray crystallography since about 1980, his program has been in constant development to check model data for errors in syntax, and inconsistencies either within the model in scrutiny, or in comparison with data extracted from other models already admitted to curated databases with about 500 tests (a 2020 open-access review by Spek). Though usable via a web service (checkcif), the author maintains an other dedicated web site for documentation and distribution of compiled executables. The platon.f source code he wrote is a single FORTRAN file, by 2022-02-09 counting 174697 LOC.

(Possibly an interesting speaker for how he organized and continued for decades the development of the program, all by himself.)

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Discussed at Hacker News. An associated Fortran program is GitHub - brg4/SAP_chromosome

Fundamental behaviors emerge from simulations of a living minimal cell
Cell
VOLUME 185, ISSUE 2, P345-360.E28, JANUARY 20, 2022
by Zane R. Thornburg et al.
Summary
We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.

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Wu, W., Hückelheim, J., Hovland, P.D., Siegel, S.F. (2022). “Verifying Fortran Programs with CIVL”, In: Fisman, D., Rosu, G. (eds) Tools and Algorithms for the Construction and Analysis of Systems. TACAS 2022. Lecture Notes in Computer Science, vol 13243. Springer, Cham. Verifying Fortran Programs with CIVL | SpringerLink, open access.

Abstract
Fortran is widely used in computational science, engineering, and high performance computing. This paper presents an extension to the CIVL verification framework to check correctness properties of Fortran programs. Unlike previous work that translates Fortran to C, LLVM IR, or other intermediate formats before verification, our work allows CIVL to directly consume Fortran source files. We extended the parsing, translation, and analysis phases to support Fortran-specific features such as array slicing and reshaping, and to find program violations that are specific to Fortran, such as argument aliasing rule violations, invalid use of variable and function attributes, or defects due to Fortran’s unspecified expression evaluation order. We demonstrate the usefulness of our tool on a verification benchmark suite and kernels extracted from a real world application.

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71

There is a 45 pages chapter about Fortran in that new book Quantum Mechanics: Detailed Historical, Mathematical and Computational Approaches:

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I read two of the chapter abstracts, and it struck me that Taylor and Francis dropped the ball as far as assigning a capable editor to check the English usage and word selection was concerned. For example, note this:

“The second-order differential equations are explored in details due to its importance to the wave quantum mechanics.”

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Congrats @CRquantum and co-authors on your new paper:

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Thank you @milancurcic , in that paper I use Metropolis method to sample discrete and continuous variables together, in contrast with traditional ways which sample continuous variables first and then sum over discrete variables.
I thanked basically all of you guys in the acknowledgement part. There are still some work needs to be done.
Here is another one about my PhD work, use modern Fortran + MPI + supercomputer,

That path-integral Monte Carlo is more scalable than the the EM method, basically always 95+% efficiency.

image
image908×696 14 KB

Thank you all!

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75

Banger, P., Kaur, P., Roy, A., Gautam, S.
“FORTRESS: FORTRAN programs to solve coupled Gross-Pitaevskii equations for spin-orbit coupled spin-f Bose-Einstein condensate with spin f = 1 or 2”
(2022) Computer Physics Communications, 279, art. no. 108442

DOI: 10.1016/j.cpc.2022.108442

https://doi.org/10.1016/j.cpc.2022.108442

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76

Machine Learning-based models in particle-in-cell codes for advanced physics extensions

excerpt from the paper:

The micro-framework neural-fortran (Curcic 2019) was developed with the intent of providing a library capable of performing the basic operations needed for a NN (e.g. gradient descent
optimization, fully-connected dense layer calculations) within a Fortran environment.
Further work expanded this library into the Fortran-Keras Bridge (FKB) (Ott et al.
2020). With FKB, one can train NNs in a Python environment with the Keras library
and export their parameters to files that are then read and used for inference by the FKB
Fortran.

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77

Little, M.P., Rosenberg, P.S. & Arsham, A. Alternative stopping rules to limit tree expansion for random forest models. Sci Rep 12 , 15113 (2022)

Abstract

Random forests are a popular type of machine learning model, which are relatively robust to overfitting, unlike some other machine learning models, and adequately capture non-linear relationships between an outcome of interest and multiple independent variables. There are relatively few adjustable hyperparameters in the standard random forest models, among them the minimum size of the terminal nodes on each tree. The usual stopping rule, as proposed by Breiman, stops tree expansion by limiting the size of the parent nodes, so that a node cannot be split if it has less than a specified number of observations. Recently an alternative stopping criterion has been proposed, stopping tree expansion so that all terminal nodes have at least a minimum number of observations. The present paper proposes three generalisations of this idea, limiting the growth in regression random forests, based on the variance, range, or inter-centile range. The new approaches are applied to diabetes data obtained from the National Health and Nutrition Examination Survey and four other datasets (Tasmanian Abalone data, Boston Housing crime rate data, Los Angeles ozone concentration data, MIT servo data). Empirical analysis presented herein demonstrate that the new stopping rules yield competitive mean square prediction error to standard random forest models. In general, use of the intercentile range statistic to control tree expansion yields much less variation in mean square prediction error, and mean square prediction error is also closer to the optimal. The Fortran code developed is provided in the Supplementary Material.

5 Likes
78

Nicholas F. Wogan, David C. Catling, Kevin J. Zahnle, and Mark W. Claire (2022). Rapid timescale for an oxic transition during the Great Oxidation Event and the instability of low atmospheric O2. PNAS . DOI:10.1073/pnas.2205618119.

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79

Journal of Computational Physics

Volume 473, 15 January 2023, 111772

An efficient geometric method for incompressible hydrodynamics on the sphere

by P.Cifani, M.Viviani, and K.Modin

Highlights

• Development of a scalable geometric method for two-dimensional hydrodynamics.
• Analysis of the parallel performance of the Lie-Poisson integrator on the sphere.
• Efficient computation of a discrete spherical harmonic basis.
• Simulation of the Casimir preserving spectrum of Euler’s equations.

with GitHub repo GLIFS (Geometric Lie-Poisson Isospectral Flow Solver)

3 Likes
80

Here is a work that introduced a novel set of scaled Hankel functions for real-valued arguments and complex-valued. Fortran 90 is used to obtain scaled forms of the cylindrical function that prevent numerical underflow and overflow errors associated with large real and large imaginary orders without sacrificing accuracy.

https://www.researchgate.net/publication/364305301_An_Accurate_and_Numerically_Stable_Formulation_for_Computing_the_Electromagnetic_Fields_in_Uniform_Bend_Rectangular_Waveguides

An Accurate and Numerically Stable Formulation for Computing the Electromagnetic Fields in Uniform Bend Rectangular Waveguides

Abstract: This paper describes a numerically stable formulation for the analysis of electromagnetic fields in rectangular cross-section waveguides with a curved longitudinal axis. A novel set of scaled Hankel functions for real-valued arguments and complex-valued orders is introduced for rescaling the characteristic equations associated with TE and TM fields of the exact boundary-value problem. The exponentially-scaled cylindrical functions presented here prevent numerical underflow and overflow errors associated with large real and large imaginary orders without sacrificing accuracy. The proposed methodology is validated against variable-precision arithmetic results. Numerical results are also presented for waveguides with large radii of curvature, where the present methodology is compared with perturbation ones in several examples. Dielectric-filled waveguides with small radii of curvature are investigated and our solutions is compared with finite-integration technique results.

3 Likes