update refs

paper/paper.bib

@@ -251,3 +251,69 @@ @article{bonomi_plumed_2019
  note = {Publisher: Nature Publishing Group},
  keywords = {Culture, Software},
  }
+
+@article{mortensen_gpaw_original_2005,
+ author = {Mortensen, J. J. and Hansen, L. B. and Jacobsen,
+ K. W.},
+ title = {Real-space grid implementation of the projector
+ augmented wave method},
+ journal = {Physical Review B},
+ year = 2005,
+ volume = 71,
+ number = 3,
+ month = jan,
+ issn = {1550-235X},
+ doi = {10.1103/physrevb.71.035109},
+ url = {http://dx.doi.org/10.1103/PhysRevB.71.035109},
+ publisher = {American Physical Society (APS)}
+}
+
+@article{enkovaara_gpaw_1_2011,
+ author = {Enkovaara, Jussi and Romero, Nichols A. and Shende,
+ Sameer and Mortensen, Jens J.},
+ title = {GPAW - massively parallel electronic structure
+ calculations with Python-based software},
+ journal = {Procedia Computer Science},
+ year = 2011,
+ volume = 4,
+ pages = {17–25},
+ issn = {1877-0509},
+ doi = {10.1016/j.procs.2011.04.003},
+ url = {http://dx.doi.org/10.1016/j.procs.2011.04.003},
+ publisher = {Elsevier BV}
+}
+
+@article{mortensen_gpaw_2_2024,
+ author = {Mortensen, Jens Jørgen and Larsen, Ask Hjorth and
+ Kuisma, Mikael and Ivanov, Aleksei V. and
+ Taghizadeh, Alireza and Peterson, Andrew and Haldar,
+ Anubhab and Dohn, Asmus Ougaard and Schäfer,
+ Christian and Jónsson, Elvar Örn and Hermes, Eric
+ D. and Nilsson, Fredrik Andreas and Kastlunger,
+ Georg and Levi, Gianluca and Jónsson, Hannes and
+ Häkkinen, Hannu and Fojt, Jakub and Kangsabanik,
+ Jiban and Sødequist, Joachim and Lehtomäki, Jouko
+ and Heske, Julian and Enkovaara, Jussi and Winther,
+ Kirsten Trøstrup and Dulak, Marcin and Melander,
+ Marko M. and Ovesen, Martin and Louhivuori, Martti
+ and Walter, Michael and Gjerding, Morten and
+ Lopez-Acevedo, Olga and Erhart, Paul and Warmbier,
+ Robert and Würdemann, Rolf and Kaappa, Sami and
+ Latini, Simone and Boland, Tara Maria and Bligaard,
+ Thomas and Skovhus, Thorbjørn and Susi, Toma and
+ Maxson, Tristan and Rossi, Tuomas and Chen, Xi and
+ Schmerwitz, Yorick Leonard A. and Schiøtz, Jakob and
+ Olsen, Thomas and Jacobsen, Karsten Wedel and
+ Thygesen, Kristian Sommer},
+ title = {GPAW: An open Python package for electronic
+ structure calculations},
+ journal = {The Journal of Chemical Physics},
+ year = 2024,
+ volume = 160,
+ number = 9,
+ month = mar,
+ issn = {1089-7690},
+ doi = {10.1063/5.0182685},
+ url = {http://dx.doi.org/10.1063/5.0182685},
+ publisher = {AIP Publishing}
+}

paper/paper.md

@@ -1,5 +1,5 @@
 ---
-title: 'SPARC-X-API: Versatile Python Interface for Atomistic Ab-initio Real-space Calculations'
+title: 'SPARC-X-API: Versatile Python Interface for Real-space Density Functional Theory Calculations'
 tags:
  - Density Functional Theories
  - Atomistic Simulations
@@ -40,16 +40,158 @@ bibliography: paper.bib
 
 # Summary
 
+Density Functional Theory (DFT) is the de facto gold standard for
+electronic structure calculations in chemistry and materials
+science. While plane-wave DFT remains the most widely used, real-space
+DFT provides advantages in handling complex boundary conditions and
+scaling to very large systems. The SPARC-X project
+(https://github.com/SPARC-X) has pioneered highly efficient real-space
+DFT codes available in both Matlab [@xu_m-sparc-1.0_2020;
+@zhang_m-sparc-2.0_2023] and C [@xu_sparc-1.0_2021;
+@zhang_sparc-2.0_2024]. However, the specific input formats for SPARC
+have often made it challenging for users accustomed to plane-wave DFT
+to transition to real-space methods. To address this, we introduce
+SPARC-X-API, a Python interface designed to bridge the SPARC-X project
+with broader computational frameworks. Built on the atomic simulation
+environment (ASE [@larsen_ase_2017]) standard, SPARC-X-API allows
+users to handle SPARC file formats, and run SPARC calculations using
+the same interface as with other computational packages. SPARC-X-API
+provides additional features beyond the standard ASE package,
+including 1) support of complex boundary conditions, 2) a JSON schema
+for validating and converting calculation parameters, and 3) a
+comprehensive calculator interface with advanced socket-communication
+support. SPARC-X-API provides a smooth transition for users from
+plane-wave DFT, making the access to real-space DFT calculations more
+available and flexible for a wider range of users and computational
+workflows.
 
+# Statement of Need
 
+Kohn-Sham Density Functional Theory (DFT) has unargubaly become the
+cornerstone of electronic simulations in chemical and materials
+sciences due to its simplicity and applications across a wide range of
+systems. The popularity of DFT over other first-principle methods in
+materials simulation largely stems from the simplicity of the
+plane-wave pseudopotential implementation, where convergence is
+controlled by simply the plane-wave cutoff energy, and solving the
+Kohn-Sham equations can be benefited from highly-optimized Fast
+Fourier Transform (FFT) packages. While many non-theoretical
+researchers may associate DFT exclusively with plane-wave
+implementations, this approach has notable limitations. The periodic
+nature of the Fourier basis enforces the use of periodic boundary
+conditions, making the simulation setup of isolated and semi-finite
+systems non-straightforward. Additionally, the global nature of the
+Fourier basis causes plane-wave codes to scale poorly with increasing
+numbers of parallel processes. A compelling alternative to overcome
+these limitations is to solve the Kohn-Sham equations using a
+finite-difference approach on real-space grids. Real-space DFT
+naturally supports both periodic and Dirichlet boundary conditions,
+allowing for the flexible treatment of systems in any
+dimensionality. Furthermore, the locality of the finite-difference
+grids makes real-space DFT methods inherently scalable, paving the way
+for the development of linearly-scaling solutions to the Kohn-Sham
+equations.
 
-# Statement of Need
+<!-- Need review @TT 2024.09.30 --> Despite the advantages of
+real-space DFT, plane-wave implementations remain dominant in the
+field of computational chemistry and materials science, largely due to
+the greater accessibility of plane-wave DFT codes and their more
+established programmable interfaces. While real-space DFT offers
+significant benefits, there are currently few widely used packages
+that provide comprehensive real-space DFT capabilities.
+
+The only notable exception has been GPAW
+[@mortensen_gpaw_original_2005; @enkovaara_gpaw_1_2011;
+@mortensen_gpaw_2_2024], which originally focused on real-space
+finite-difference methods. However, in recent years, the development
+of GPAW has shifted its focus toward plane-wave implementations
+[@@mortensen_gpaw_2_2024], leaving its finite-difference capabilities
+underdeveloped and missing key functionality. In contrast, the SPARC-X
+project (https://github.com/SPARC-X) has pioneered efforts to develop
+an open-source, real-space DFT code that is both user-friendly and
+competitive with state-of-the-art plane-wave codes.
+
+SPARC-X offers real-space DFT algorithms through two implementations:
+M-SPARC [@xu_m-sparc-1.0_2020; @zhang_m-sparc-2.0_2023] for
+prototyping and small-system simulations, and SPARC
+[@xu_sparc-1.0_2021; @zhang_sparc-2.0_2024] for large-scale production
+calculations that can accommodate a wide range of system
+sizes. Although SPARC has demonstrated its computational efficiency
+and features a rich set of algorithms, its adoption has been limited
+by the lack of a user-friendly interface that can connect the code to
+a broader audience of users and computational tools.
+
+To address this, we introduce SPARC-X-API, a Python-based interface
+designed to bridge the SPARC-X code with a broader range of scientific
+workflows. Built on the Atomic Simulation Environment (ASE
+[@larsen_ase_2017]) standard, SPARC-X-API provides seamless file
+read/write support for SPARC files and a feature-complete calculator
+interface to the SPARC code. With SPARC-X-API, researchers can easily
+incorporate real-space DFT into their workflows using familiar tools
+and interfaces, making real-space DFT more accessible to a wider range
+of users.
+
+<!-- statement of SPARC-X-API v0.1 -->
+
+<!-- SPARC-X-API philosophy -->
+
+
+# Features and Functionalities
+
+SPARC-X-API offers two key functionalities:
+
+- File I/O: Through the sparc.io submodule, SPARC-X-API implements
+ file read/write support for SPARC file formats, including .inpt and
+ .ion files. SPARC-X-API operates on the directory level, treating
+ each calculation directory as a "SPARC bundle." From version 1.0
+ onwards, SPARC-X-API is fully integrated with ASE (version 3.23),
+ automatically registering SPARC as an external I/O format.
+- Calculator Interface: The sparc.calculator submodule provides a full
+ ASE-compatible calculator interface for running SPARC calculations,
+ enabling integration with ASE workflows. <!-- IO and socker -->
+
+Unique Features of SPARC-X-API:
+
+1) Support for Bundled File Formats: Unlike typical single-file DFT implementations, SPARC requires both .inpt and .ion files. SPARC-X-API's design simplifies this by reading and writing at the directory level, streamlining the handling of SPARC bundles.
+
+2) JSON Schema for Parameter Validation: SPARC-X-API ensures parameter
+consistency through a JSON schema derived from SPARC's LaTeX
+documentation. This guarantees compatibility with SPARC's source code,
+offering a robust mechanism for validating and converting parameters.
+3) Unit Conversions: SPARC-X-API manages the conversion between atomic
+units (Hartree, Bohr) used in SPARC and the eV/Å units in ASE.
+
+## Socket-Communication Calculator Interface
+SPARC-X-API’s socket-communication layer allows for efficient and
+flexible workflows by reducing the overhead of file I/O. This feature
+is particularly useful for iterative calculations, such as structural
+optimizations and saddle point searches, where traditional file-based
+communication can become a bottleneck.
 
+Key advantages:
 
+Efficiency: Eliminates intermediate file I/O by streaming data
+directly between processes. Speed: Enhances performance in iterative
+calculations, critical for large-scale simulations. Flexibility:
+Enables real-time modification of calculation parameters without
+restarting processes. SPARC-X-API implements a backward-compatible
+i-PI protocol, allowing both low-level and high-level interfacing with
+SPARC's DFT code.
 
-# Brief Description of the Program Use and Features
+# Code Release and Maintenance
+SPARC-X-API maximizes accessibility for users by providing streamlined
+installation via the conda-forge channel, where the sparc-x-api
+package can be installed with default ONCV pseudopotentials. It also
+integrates continuous integration (CI) and continuous deployment (CD)
+workflows for:
 
+- Unit testing and code coverage
+- Fetching the latest SPARC documentation for updating the JSON schema
+- Validating all test examples from the SPARC repository
 
+These workflows ensure that SPARC-X-API remains up-to-date with
+ongoing SPARC developments while separating parameter updates from the
+main SPARC maintainers’ efforts.
 
 # Acknowledgements