From a8f5cc01f6e03835a464241cfb7491ab1f3d80de Mon Sep 17 00:00:00 2001
From: "T.Tian" <alchem0x2a@gmail.com>
Date: Wed, 23 Oct 2024 18:13:29 +0800
Subject: [PATCH] update references

---
 paper/fig/fig_sparc_api_overview.svg |  8 +--
 paper/paper.bib                      | 76 +++++++++++++++++++++++++++-
 paper/paper.md                       | 73 ++++++++++++++------------
 3 files changed, 120 insertions(+), 37 deletions(-)

diff --git a/paper/fig/fig_sparc_api_overview.svg b/paper/fig/fig_sparc_api_overview.svg
index e529cfa2..a502d76c 100644
--- a/paper/fig/fig_sparc_api_overview.svg
+++ b/paper/fig/fig_sparc_api_overview.svg
@@ -2198,7 +2198,7 @@ AIBwgg8AIJzgAwAIJ/gAAMJ9ACZwEZHB4cT7AAAAAElFTkSuQmCC
          id="text19611"><tspan
            sodipodi:role="line"
            id="tspan19609"
-           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:mono;-inkscape-font-specification:mono;fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Mono';-inkscape-font-specification:'Fira Mono';fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
            x="9.287055"
            y="261.46112">sparc.io</tspan></text><text
          xml:space="preserve"
@@ -2225,7 +2225,7 @@ AIBwgg8AIJzgAwAIJ/gAAMJ9ACZwEZHB4cT7AAAAAElFTkSuQmCC
          id="text19615"><tspan
            sodipodi:role="line"
            id="tspan19613"
-           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:mono;-inkscape-font-specification:mono;fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Mono';-inkscape-font-specification:'Fira Mono';fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
            x="73.207031"
            y="261.46112">sparc.api</tspan></text><text
          xml:space="preserve"
@@ -2252,7 +2252,7 @@ AIBwgg8AIJzgAwAIJ/gAAMJ9ACZwEZHB4cT7AAAAAElFTkSuQmCC
          id="text19619"><tspan
            sodipodi:role="line"
            id="tspan19617"
-           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:mono;-inkscape-font-specification:mono;fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Mono';-inkscape-font-specification:'Fira Mono';fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
            x="124.00703"
            y="261.46112">sparc.calculator</tspan></text><text
          xml:space="preserve"
@@ -2284,7 +2284,7 @@ AIBwgg8AIJzgAwAIJ/gAAMJ9ACZwEZHB4cT7AAAAAElFTkSuQmCC
        id="text19623"><tspan
          sodipodi:role="line"
          id="tspan19621"
-         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:mono;-inkscape-font-specification:mono;fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
+         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Mono';-inkscape-font-specification:'Fira Mono';fill:#4a4174;fill-opacity:1;stroke-width:0.264583"
          x="114.03883"
          y="225.03543">sparc.docparser</tspan></text><rect
        style="fill:#ffc9b5;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:0.499999;stroke-linecap:square;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
diff --git a/paper/paper.bib b/paper/paper.bib
index 44b874c3..952ffeb8 100644
--- a/paper/paper.bib
+++ b/paper/paper.bib
@@ -259,7 +259,7 @@ @article{bonomi_plumed_2019
  	volume = {16},
  	rights = {2019 Springer Nature America, Inc.},
  	issn = {1548-7105},
- 	url = {https://www.nature.com/articles/s41592-019-0506-8},
+ 	url = {http://dx.doi.org/10.1038/s41592-019-0506-8},
  	doi = {10.1038/s41592-019-0506-8},
  	pages = {670--673},
  	number = {8},
@@ -644,3 +644,77 @@ @article{smith_psi4_2020
   url	       = {http://dx.doi.org/10.1063/5.0006002},
   publisher    = {AIP Publishing}
 }
+
+@article{musielewicz_finetuna_2022,
+  author       = {Musielewicz, Joseph and Wang, Xiaoxiao and Tian,
+                  Tian and Ulissi, Zachary},
+  title	       = {FINETUNA: fine-tuning accelerated molecular
+                  simulations},
+  journal      = {Machine Learning: Science and Technology},
+  year	       = 2022,
+  volume       = 3,
+  number       = 3,
+  month	       = sep,
+  pages	       = {03LT01},
+  issn	       = {2632-2153},
+  doi	       = {10.1088/2632-2153/ac8fe0},
+  url	       = {http://dx.doi.org/10.1088/2632-2153/ac8fe0},
+  publisher    = {IOP Publishing}
+}
+
+@misc{ilyes_mace_2023,
+  author       = {Batatia, Ilyes and Benner, Philipp and Chiang, Yuan
+                  and Elena, Alin M. and Kovács, Dávid P. and
+                  Riebesell, Janosh and Advincula, Xavier R. and Asta,
+                  Mark and Avaylon, Matthew and Baldwin, William
+                  J. and Berger, Fabian and Bernstein, Noam and
+                  Bhowmik, Arghya and Blau, Samuel M. and Cărare, Vlad
+                  and Darby, James P. and De, Sandip and Della Pia,
+                  Flaviano and Deringer, Volker L. and Elijošius,
+                  Rokas and El-Machachi, Zakariya and Falcioni, Fabio
+                  and Fako, Edvin and Ferrari, Andrea C. and
+                  Genreith-Schriever, Annalena and George, Janine and
+                  Goodall, Rhys E. A. and Grey, Clare P. and Grigorev,
+                  Petr and Han, Shuang and Handley, Will and Heenen,
+                  Hendrik H. and Hermansson, Kersti and Holm,
+                  Christian and Jaafar, Jad and Hofmann, Stephan and
+                  Jakob, Konstantin S. and Jung, Hyunwook and Kapil,
+                  Venkat and Kaplan, Aaron D. and Karimitari, Nima and
+                  Kermode, James R. and Kroupa, Namu and Kullgren,
+                  Jolla and Kuner, Matthew C. and Kuryla, Domantas and
+                  Liepuoniute, Guoda and Margraf, Johannes T. and
+                  Magdău, Ioan-Bogdan and Michaelides, Angelos and
+                  Moore, J. Harry and Naik, Aakash A. and Niblett,
+                  Samuel P. and Norwood, Sam Walton and O'Neill, Niamh
+                  and Ortner, Christoph and Persson, Kristin A. and
+                  Reuter, Karsten and Rosen, Andrew S. and Schaaf,
+                  Lars L. and Schran, Christoph and Shi, Benjamin
+                  X. and Sivonxay, Eric and Stenczel, Tamás K. and
+                  Svahn, Viktor and Sutton, Christopher and Swinburne,
+                  Thomas D. and Tilly, Jules and van der Oord, Cas and
+                  Varga-Umbrich, Eszter and Vegge, Tejs and Vondrák,
+                  Martin and Wang, Yangshuai and Witt, William C. and
+                  Zills, Fabian and Csányi, Gábor},
+  title	       = {A foundation model for atomistic materials
+                  chemistry},
+  year	       = 2024,
+  doi	       = {10.48550/ARXIV.2401.00096},
+  url	       = {https://arxiv.org/abs/2401.00096},
+  keywords     = {Chemical Physics (physics.chem-ph), Materials
+                  Science (cond-mat.mtrl-sci), FOS: Physical sciences,
+                  FOS: Physical sciences},
+  publisher    = {arXiv},
+  copyright    = {Creative Commons Attribution Non Commercial No
+                  Derivatives 4.0 International}
+}
+
+@misc{fairchem_2024,
+  author = {},
+  title = {fairchem by FAIR Chemistry},
+  year = {2024},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  howpublished = {\url{https://github.com/FAIR-Chem/fairchem}},
+  url={https://github.com/FAIR-Chem/fairchem},
+  commit = {f22dbdf5498912e519459831ac58668566e38e67}
+}
diff --git a/paper/paper.md b/paper/paper.md
index 9bace9de..6c33aa26 100644
--- a/paper/paper.md
+++ b/paper/paper.md
@@ -102,15 +102,16 @@ allowing for the flexible treatment of systems in
 any dimensionality.
 
 In the past few years, the SPARC-X project
-([https://github.com/SPARC-X](https://github.com/SPARC-X)) has
-led 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. The philosophy of the SPARC-X project is to provide codes that are highly
-efficient and portable (i.e. straightforward to install and use across various computational
-environments). The codes also seek to be user-friendly and developer-friendly
-to facilitate the implementation of new algorithms. In line with this, SPARC-X offers real-space DFT
-algorithms through two implementations: 1) Matlab-based M-SPARC
-[@xu_m-sparc-1.0_2020; @zhang_m-sparc-2.0_2023] for algorithm
+([https://github.com/SPARC-X](https://github.com/SPARC-X)) has led
+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. The philosophy of the SPARC-X project is to provide codes that
+are highly efficient and portable (i.e. straightforward to install and
+use across various computational environments). The codes also seek to
+be user-friendly and developer-friendly to facilitate the
+implementation of new algorithms. In line with this, SPARC-X offers
+real-space DFT algorithms through two implementations: 1) Matlab-based
+M-SPARC [@xu_m-sparc-1.0_2020; @zhang_m-sparc-2.0_2023] for algorithm
 prototyping and small-system simulations, with no external
 dependencies other than Matlab itself, and 2) C/C++ based SPARC
 [@xu_sparc-1.0_2021; @zhang_sparc-2.0_2024] for large-scale production
@@ -122,33 +123,41 @@ interactions, and advanced exchange-correlation (xc) functionals
 method [@suryanarayana_sparc_sq_2018], cyclic/helical symmetry
 [@sharma_sparc_cyclix_2021], real-space density functional
 perturbation theory (DFPT) [@sharma_sparc_dfpt_2023], orbital-free DFT
-(ODFT) [@ghosh_sparc_ofdft_2016],
-on-the-fly machine-learning force fields (OTF-MLFF)
-[@kumar_ofdft_delta_ml_2023; @timmerman_sparc_mlff_2024; @kumar_sparc_mlff_2024]. The rapid
+(ODFT) [@ghosh_sparc_ofdft_2016], on-the-fly machine-learning force
+fields (OTF-MLFF) [@kumar_ofdft_delta_ml_2023;
+@timmerman_sparc_mlff_2024; @kumar_sparc_mlff_2024]. The rapid
 development of SPARC has led to the need for a fully functional and
 user-friendly interface that facilitates the use of SPARC with
-high-throughput workflows.  To address this, we introduce the SPARC-X-API,
-a Python interface designed to bridge the SPARC code with a
-wide range of scientific workflows. The SPARC-X-API builds upon the
+high-throughput workflows.  To address this, we introduce the
+SPARC-X-API, a Python interface designed to bridge the SPARC code with
+a wide range of scientific workflows. The SPARC-X-API builds upon the
 Python wrapper originally shipped with SPARC version 1.0
 [@xu_sparc-1.0_2021], offering an API compatible with the widely-used
-ASE (ASE [@larsen_ase_2017]) standard and
-updated with the latest versions of SPARC. With ASE's support for
-various popular DFT methods, including both plane-wave (e.g. VASP
-[@kresse_vasp_1996], Quantum ESPRESSO [@giannozzi_qe_2017], and Abinit
-[@gonze_abinit_2020]), and real-space (e.g. GPAW
-[@enkovaara_gpaw_1_2011; @mortensen_gpaw_2_2024] and Octopus
-[@tancogne_dejean_octopus_2020]) implementations, SPARC-X-API enables
-seamless integration of SPARC into existing workflows, allowing users
-to incorporate real-space DFT calculations with minimal adjustments. A summary of the role
+ASE (ASE [@larsen_ase_2017]) standard and updated with the latest
+versions of SPARC. With ASE's support for various popular DFT methods,
+including both plane-wave (e.g. VASP [@kresse_vasp_1996], Quantum
+ESPRESSO [@giannozzi_qe_2017], and Abinit [@gonze_abinit_2020]), and
+real-space (e.g. GPAW [@enkovaara_gpaw_1_2011; @mortensen_gpaw_2_2024]
+and Octopus [@tancogne_dejean_octopus_2020]) implementations,
+SPARC-X-API enables seamless integration of SPARC into existing
+workflows, allowing users to incorporate real-space DFT calculations
+with minimal adjustments.  The modular design of SPARC-X-API makes it
+straightforward to be plugged into complex computational workflows,
+for example high-throughput dynamics simulations by i-PI
+[@litman_i-pi-3.0_2024] and PLUMED [@article{bonomi_plumed_2019], as
+well as active machine learning frameworks including FineTuna
+[@musielewicz_finetuna_2022], powered by state-of-art neural network
+interatomic potentials such as FAIR-Chem
+(https://github.com/FAIR-Chem/fairchem)[https://github.com/FAIR-Chem/fairchem]
+and MACE-MP [@ilyes_mace_2023] model series.  A summary of the role
 SPARC-X-API in the SPARC-X project is shown in
-\autoref{fig:sparc-overview}.
-In addition to the capabilities inherited from ASE, SPARC-X-API seeks
-to enhance the user experience in a few key aspects, including 1)
-supporting SPARC-specific features in an ASE-comatible API, 2) a
-parameter validation mechanism based on SPARC's `LaTeX` documentation,
-and 3) a versatile socket communication layer for efficient
-high-throughput calculations. Details will be discussed in the Features and Functionalities section.
+\autoref{fig:sparc-overview}.  In addition to the capabilities
+inherited from ASE, SPARC-X-API seeks to enhance the user experience
+in a few key aspects, including 1) supporting SPARC-specific features
+in an ASE-comatible API, 2) a parameter validation mechanism based on
+SPARC's `LaTeX` documentation, and 3) a versatile socket communication
+layer for efficient high-throughput calculations. Details will be
+discussed in the Features and Functionalities section.
 
 <!-- Firstly, the -->
 <!-- design of the API is closely aligned with the ASE interfaces of other -->
@@ -181,7 +190,7 @@ high-throughput calculations. Details will be discussed in the Features and Func
 
 ![Overview of SPARC-X-API in the SPARC-X project system
 \label{fig:sparc-overview}
-](fig/fig_sparc_api_overview.svg){ width=100% }
+](fig/fig_sparc_api_overview.svg){ width=90% }