texcleaner 0.3.0__py3-none-any.whl

texclean/__init__.py

@@ -0,0 +1,24 @@
+"""
+TeXClean - A GUI front-end for cleaning LaTeX track changes.
+
+Supports cleaning track changes from:
+- trackchanges.sty
+- changes.sty
+- arXiv submission preparation
+"""
+
+from .version import __version__
+from .wrapper import (
+    clean_trackchanges,
+    clean_changes,
+    clean_arxiv,
+    generate_output_filename
+)
+
+__all__ = [
+    "clean_trackchanges",
+    "clean_changes",
+    "clean_arxiv",
+    "generate_output_filename",
+    "__version__",
+]

texclean/__main__.py

@@ -0,0 +1,4 @@
+from .app import main
+
+if __name__ == "__main__":
+    main()

texclean/app.py

@@ -0,0 +1,308 @@
+#!/usr/bin/env python
+"""
+app.py - GUI front-end for cleaning LaTeX track changes
+
+A simple Tkinter application to clean LaTeX documents of track changes markup
+from TrackChanges, Changes, or arXiv submission packages.
+"""
+
+import os
+import threading
+import tkinter as tk
+from tkinter import ttk, filedialog, messagebox, scrolledtext
+
+from .wrapper import (
+    clean_trackchanges,
+    clean_changes,
+    clean_arxiv,
+    generate_output_filename,
+    detect_cleaning_module
+)
+from .version import __version__
+
+
+class TeXCleanApp:
+    def __init__(self, root):
+        self.root = root
+        self.root.title(f"TeXClean v{__version__} - LaTeX Track Changes Cleaner")
+        self.root.geometry("700x500")
+        self.root.resizable(True, True)
+
+        self.input_path = tk.StringVar()
+
+        self.create_widgets()
+
+    def create_widgets(self):
+        self.notebook = ttk.Notebook(self.root)
+        self.notebook.pack(fill=tk.BOTH, expand=True, padx=10, pady=10)
+
+        self.trackchanges_tab = ttk.Frame(self.notebook)
+        self.arxiv_tab = ttk.Frame(self.notebook)
+
+        self.notebook.add(self.trackchanges_tab, text="Track Changes Cleaner")
+        self.notebook.add(self.arxiv_tab, text="arXiv Cleaner")
+
+        self._create_trackchanges_tab()
+        self._create_arxiv_tab()
+
+    def _create_trackchanges_tab(self):
+        main_frame = ttk.Frame(self.trackchanges_tab, padding="10")
+        main_frame.pack(fill=tk.BOTH, expand=True)
+
+        title_label = ttk.Label(
+            main_frame,
+            text="Clean LaTeX Track Changes",
+            font=("TkDefaultFont", 14, "bold")
+        )
+        title_label.pack(pady=(0, 20))
+
+        input_frame = ttk.LabelFrame(main_frame, text="Input File", padding="5")
+        input_frame.pack(fill=tk.X, pady=5)
+        input_frame.columnconfigure(0, weight=1)
+
+        self.trackchanges_entry = ttk.Entry(input_frame, textvariable=self.input_path)
+        self.trackchanges_entry.pack(side=tk.LEFT, fill=tk.X, expand=True, padx=(0, 5))
+
+        browse_btn = ttk.Button(input_frame, text="Browse...", command=self._browse_trackchanges_input)
+        browse_btn.pack(side=tk.RIGHT)
+
+        helper_label = ttk.Label(
+            input_frame,
+            text="Select a .tex file",
+            font=("TkDefaultFont", 9, "italic"),
+            foreground="gray"
+        )
+        helper_label.pack(anchor=tk.W, pady=(2, 0))
+
+        self.trackchanges_clean_btn = ttk.Button(
+            main_frame,
+            text="Detect & Clean",
+            command=self._start_trackchanges_cleaning
+        )
+        self.trackchanges_clean_btn.pack(pady=20)
+
+        log_label = ttk.Label(main_frame, text="Log Output:", font=("TkDefaultFont", 10, "bold"))
+        log_label.pack(anchor=tk.W, pady=(10, 5))
+
+        self.trackchanges_log = scrolledtext.ScrolledText(
+            main_frame,
+            height=12,
+            width=80,
+            state=tk.DISABLED,
+            wrap=tk.WORD
+        )
+        self.trackchanges_log.pack(fill=tk.BOTH, expand=True, pady=5)
+
+        self.trackchanges_progress = ttk.Progressbar(main_frame, mode="indeterminate")
+        self.trackchanges_progress.pack(fill=tk.X, pady=5)
+
+    def _create_arxiv_tab(self):
+        main_frame = ttk.Frame(self.arxiv_tab, padding="10")
+        main_frame.pack(fill=tk.BOTH, expand=True)
+
+        title_label = ttk.Label(
+            main_frame,
+            text="Clean for arXiv Submission",
+            font=("TkDefaultFont", 14, "bold")
+        )
+        title_label.pack(pady=(0, 20))
+
+        input_frame = ttk.LabelFrame(main_frame, text="Project Folder", padding="5")
+        input_frame.pack(fill=tk.X, pady=5)
+        input_frame.columnconfigure(0, weight=1)
+
+        self.arxiv_entry = ttk.Entry(input_frame)
+        self.arxiv_entry.pack(side=tk.LEFT, fill=tk.X, expand=True, padx=(0, 5))
+
+        browse_btn = ttk.Button(input_frame, text="Browse...", command=self._browse_arxiv_input)
+        browse_btn.pack(side=tk.RIGHT)
+
+        helper_label = ttk.Label(
+            input_frame,
+            text="Select a project folder",
+            font=("TkDefaultFont", 9, "italic"),
+            foreground="gray"
+        )
+        helper_label.pack(anchor=tk.W, pady=(2, 0))
+
+        self.arxiv_clean_btn = ttk.Button(
+            main_frame,
+            text="Clean for arXiv",
+            command=self._start_arxiv_cleaning
+        )
+        self.arxiv_clean_btn.pack(pady=20)
+
+        log_label = ttk.Label(main_frame, text="Log Output:", font=("TkDefaultFont", 10, "bold"))
+        log_label.pack(anchor=tk.W, pady=(10, 5))
+
+        self.arxiv_log = scrolledtext.ScrolledText(
+            main_frame,
+            height=12,
+            width=80,
+            state=tk.DISABLED,
+            wrap=tk.WORD
+        )
+        self.arxiv_log.pack(fill=tk.BOTH, expand=True, pady=5)
+
+        self.arxiv_progress = ttk.Progressbar(main_frame, mode="indeterminate")
+        self.arxiv_progress.pack(fill=tk.X, pady=5)
+
+    def _browse_trackchanges_input(self):
+        file_path = filedialog.askopenfilename(
+            title="Select LaTeX File",
+            filetypes=[("LaTeX files", "*.tex"), ("All files", "*.*")]
+        )
+        if file_path:
+            self.input_path.set(file_path)
+
+    def _browse_arxiv_input(self):
+        folder = filedialog.askdirectory(title="Select LaTeX Project Folder")
+        if folder:
+            self.arxiv_entry.delete(0, tk.END)
+            self.arxiv_entry.insert(0, folder)
+
+    def _log(self, message, log_widget):
+        log_widget.config(state=tk.NORMAL)
+        log_widget.insert(tk.END, message)
+        log_widget.see(tk.END)
+        log_widget.config(state=tk.DISABLED)
+
+    def _clear_log(self, log_widget):
+        log_widget.config(state=tk.NORMAL)
+        log_widget.delete(1.0, tk.END)
+        log_widget.config(state=tk.DISABLED)
+
+    def _validate_tex_input(self, input_path):
+        if not input_path:
+            return False, "Please select an input file."
+        if not os.path.exists(input_path):
+            return False, f"Path not found: {input_path}"
+        if not os.path.isfile(input_path):
+            return False, "Error: This operation requires a .tex file."
+        if not input_path.lower().endswith(".tex"):
+            return False, "Error: The selected file must have a .tex extension."
+        return True, ""
+
+    def _validate_folder_input(self, folder_path):
+        if not folder_path:
+            return False, "Please select a project folder."
+        if not os.path.exists(folder_path):
+            return False, f"Folder not found: {folder_path}"
+        if not os.path.isdir(folder_path):
+            return False, "Error: This operation requires a folder."
+        return True, ""
+
+    def _start_trackchanges_cleaning(self):
+        input_path = self.input_path.get().strip()
+
+        valid, error_msg = self._validate_tex_input(input_path)
+        if not valid:
+            messagebox.showerror("Input Error", error_msg)
+            return
+
+        detected = detect_cleaning_module(input_path)
+
+        if detected is None:
+            result = messagebox.askyesno(
+                "No Track Changes Detected",
+                "No track changes markup (trackchanges or changes package) was detected in the file.\n\n"
+                "Would you like to try cleaning anyway?"
+            )
+            if not result:
+                return
+            detected = "trackchanges"
+        else:
+            module_name = "TrackChanges (trackchanges.sty)" if detected == "trackchanges" else "Changes (changes.sty)"
+            result = messagebox.askyesno(
+                "Confirm Detected Module",
+                f"Detected '{module_name}' signatures in the file.\n\n"
+                f"Is this correct and would you like to proceed with cleaning?"
+            )
+            if not result:
+                return
+
+        self._clear_log(self.trackchanges_log)
+        self.trackchanges_clean_btn.config(state=tk.DISABLED)
+        self.trackchanges_progress.start(10)
+        self._log(f"Detected module: {detected}\n", self.trackchanges_log)
+        self._log("Starting cleaning...\n", self.trackchanges_log)
+
+        thread = threading.Thread(
+            target=self._run_trackchanges_cleaning,
+            args=(input_path, detected)
+        )
+        thread.daemon = True
+        thread.start()
+
+    def _run_trackchanges_cleaning(self, input_path, detected_module):
+        def callback(message):
+            self.root.after(0, self._log, message, self.trackchanges_log)
+
+        try:
+            output_path = generate_output_filename(input_path, "-cleaned")
+
+            if detected_module == "trackchanges":
+                success, message = clean_trackchanges(input_path, output_path, callback)
+            else:
+                success, message = clean_changes(input_path, output_path, callback)
+
+            callback("\n" + message + "\n")
+
+            if success:
+                self.root.after(0, lambda: messagebox.showinfo("Success", message))
+            else:
+                self.root.after(0, lambda: messagebox.showerror("Error", message))
+
+        except Exception as e:
+            error_msg = f"Unexpected error: {str(e)}"
+            self.root.after(0, self._log, error_msg, self.trackchanges_log)
+            self.root.after(0, lambda: messagebox.showerror("Error", error_msg))
+
+        finally:
+            self.root.after(0, self.trackchanges_progress.stop)
+            self.root.after(0, lambda: self.trackchanges_clean_btn.config(state=tk.NORMAL))
+
+    def _start_arxiv_cleaning(self):
+        folder_path = self.arxiv_entry.get().strip()
+
+        valid, error_msg = self._validate_folder_input(folder_path)
+        if not valid:
+            messagebox.showerror("Input Error", error_msg)
+            return
+
+        self._clear_log(self.arxiv_log)
+        self.arxiv_clean_btn.config(state=tk.DISABLED)
+        self.arxiv_progress.start(10)
+
+        thread = threading.Thread(target=self._run_arxiv_cleaning, args=(folder_path,))
+        thread.daemon = True
+        thread.start()
+
+    def _run_arxiv_cleaning(self, folder_path):
+        def callback(message):
+            self.root.after(0, self._log, message, self.arxiv_log)
+
+        try:
+            success, message = clean_arxiv(folder_path, callback=callback)
+
+            callback("\n" + message + "\n")
+
+            if success:
+                self.root.after(0, lambda: messagebox.showinfo("Success", message))
+            else:
+                self.root.after(0, lambda: messagebox.showerror("Error", message))
+
+        except Exception as e:
+            error_msg = f"Unexpected error: {str(e)}"
+            self.root.after(0, self._log, error_msg, self.arxiv_log)
+            self.root.after(0, lambda: messagebox.showerror("Error", error_msg))
+
+        finally:
+            self.root.after(0, self.arxiv_progress.stop)
+            self.root.after(0, lambda: self.arxiv_clean_btn.config(state=tk.NORMAL))
+
+
+def main():
+    root = tk.Tk()
+    app = TeXCleanApp(root)
+    root.mainloop()

texclean/scripts/changes/0-text.tex

@@ -0,0 +1,225 @@
+
+\title{Chemical Reactions \deleted{between} \added{in} H-N-Silicate \added{Systems} at High P--T: Implications for nitrogen partitioning between \replaced{envelope}{atmospheres} and interior\deleted{s} of sub-Neptunes}
+\author{Spoke person: Taehyun Kim}
+\maketitle
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Abstract ($<2000$ character)}
+
+%\begin{cbox}
+%The abstract should be written as goal $\rightarrow$ introduction $\rightarrow$ detailed plan.  I changed the order of sentences to fit this flow.  Please use this flow next time.
+%\end{cbox}
+
+
+% 2114
+We request beamtime to investigate reaction\deleted{s} between olivine\added{/feropericlase} and \replaced{N-H}{H$_2$-N$_2$} fluids \added{at high P-T} to \replaced{understand partitioning of nitrogen between the envelope and the interior of sub-Neptune exoplanets.}{improve our understanding of sub-Neptune interiors.} 
+
+\replaced{Recent JWST measurements have identified}{Atmospheric models identify} NH$_3$, HCN, and N$_2$ \deleted{as important nitrogen-bearing species} in \replaced{hydrogen}{H$_2$}-rich \added{atmosphere of exoplanets} \deleted{planets} \cite{heng_ANALYTICAL_2016, bean_Nature_2021, radecka_Nitrogen_2025}. 
+\replaced{While possible ingassing of nitrogen under this condition can impact the interpretation of the observation and the modeling of sub-Neptunes}{However}, \deleted{the} \added{partitioning} \deleted{behavior} of nitrogen \added{between the atmosphere and the interior} under \deleted{the} highly reducing conditions \replaced{expected in}{of} \replaced{hydrogen-rich environment of sub-Neptunes}{sub-Neptune interiors} remains poorly \replaced{understood}{constrained}. 
+\deleted{In the presence of abundant H$_2$, N$_2$ may participate in reactions that form nitrides, N-bearing alloys, and N-H-bearing species.}
+
+Our recent experiments at \replaced{13IDD}{13-ID-D} \added{have} revealed that \replaced{H$_2$/H$_2$O}{H$_2$-rich (or H$_2$O-rich)} fluids \added{can} react extensively with silicates and oxides, producing metallic alloys, hydrides, SiH$_4$, and \replaced{hydrous phases}{H$_2$O-bearing phases}, \added{revealing large exchange of elements between the envelope and the interior} \cite{nisr_Large_2020, kim_Atomicscale_2021, kim_Stability_2023, horn_Building_2025}. 
+These studies \deleted{focused on H$_2$-, H$_2$O-, and H$_2$-H$_2$O-bearing systems and} \added{have also} demonstrated that \replaced{synchrotron high-pressure experiments can provide critical data for understanding exoplanets and early terrestrial planets (like Earth).}{atmosphere-interior interactions can modify planetary mineralogy and atmosphere chemistry.}
+
+Our preliminary experiments \added{at 13IDD beamline} \replaced{showed}{indicate} that \replaced{N-H}{H$_2$-N$_2$} fluids \added{can} react with silicates and oxides to form nitrides and \replaced{Fe-N alloys}{N-bearing Fe alloys} \added{at 10~GPa and over 3000~K} (Fig.~\ref{Olivine-N2-H2}). 
+\added{At lower temperatures}, \added{retainment of N-H bonding in a fluid phase was found}\deleted{exhibit N-H bonding environments consistent with NH$_3$-bearing species}. 
+These observations suggest that nitrogen \replaced{can}{may} be \deleted{re}distributed between \replaced{the envelope and the interior}{atmospheric and interior reservoirs} through fluid-silicate reactions. 
+\deleted{We therefore propose a systematic investigation of {H$_2$-N$_2$-silicate (and H$_2$-N$_2$-oxide) reactions} over an expanded pressure-temperature range relevant to sub-Neptune exoplanets.}
+
+
+\deleted{The primary objectives are to determine the stability of silicates in H$_2$-N$_2$ fluids and  to identify reaction products formed  under high-pressure and high-temperature conditions.} 
+\added{In the proposed beamtimes} at \replaced{13IDD}{13-ID-D}, we will \replaced{investigate the reaction and its pressure and temperature-dependent variations}{monitor reactions} using in situ X-ray diffraction in a laser-heated diamond-anvil cell at {3--30~GPa and 1500--4000~K} conditions relevant to the \replaced{envelope}{atmosphere}-interior boundary of sub-Neptune exoplanets. 
+\added{After the synchrotron experiments,} Raman spectroscopy and electron microscopy will \added{be conducted, which will} provide \replaced{additional}{complementary} \replaced{data}{constraints} on reaction products and phase distributions. 
+\replaced{The resulting dataset will provide}{The expected results include: changes in silicate composition,} {silicate stability under N-H fluid,} nitride formation, \added{Fe-N alloy formation,} \deleted{nitrogen partitioning,} and the \added{N-H bearing molecule} formation \deleted{ of N-bearing phases in sub-Neptune interiors}\added{at different P-T conditions, providing key (yet currently missing) data for understanding size and age dependent changes in the chemical interaction.}
+\added{Therefore, the proposed data will advance our understanding on atmosphere-interior interactions in early terrestrial planets and sub-Neptune exoplanets}.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{What is the scientific or technical purpose and importance of the proposed research?  ($<2000$ character)}
+
+% 1835
+Sub-Neptunes are among the most abundant classes of exoplanets discovered to date. 
+Their low bulk densities (2--4~g/cm$^3$) \replaced{can be}{are commonly} explained by \replaced{envelopes rich in either hydrogen or water}{H$_2$-rich atmospheres} overlying silicate and metallic interiors \added{(gas dwarfs and water worlds, respectively)} \cite{bean_Nature_2021}.
+\added{The conditions and compositions in these settings are dramatically different from those of terrestrial planets, requiring new data to understand the astrophysical data of the exoplanet class.}
+
+Recent high\replaced{ P-T}{-pressure and high-temperature} studies have \deleted{investigated reactions between silicates and H2-rich fluids under conditions relevant to the atmosphere-interior boundary of sub-Neptunes. These experiments} demonstrated that \replaced{envelope materials can react with materials of the interior under the conditions, producing}{atmosphere-interior interactions can produce} metal alloys, hydrides, and H$_2$O\replaced{.}{,} 
+\replaced{Such reaction can modify the compositions of}{thereby modifying} both \replaced{atmosphere and interior}{atmospheric composition and interior mineralogy} \cite{horn_Building_2025, kim_Stability_2023, miozzi_Experiments_2025}. 
+However, previous studies focused primarily on pure \replaced{hydrogen fluid interacting with silicates}{H$_2$ systems}, whereas \replaced{astrophysical surveys have revealed much more complex atmosphere compositions of exoplanets, including abundant presence of nitrogen}{atmospheric models have emphasized the importance of nitrogen chemistry} \cite{radecka_Nitrogen_2025}.
+
+To our knowledge, \replaced{interaction between N-H}{H$_2$-N$_2$} fluids \added{and silicates} have not been systematically investigated \replaced{at relevant conditions for the planets}{in laser-heated DAC experiments involving silicates or oxides}. %\sidecomment{Note that by writing N$_2$-H$_2$ you are assuming that nitrogen and hydrogen will exist in these specific forms, not the other forms, such as NH3 or even ingassed forms.}
+It is unknown whether \replaced{nitrogen}{N$_2$} remains in the fluid phase \added{of the envelope}, \added{or} forms nitrides, \replaced{Fe-N}{partitions into metallic} alloys, or \replaced{dissolves into silicates (therefore ingassed)}{is incorporated into silicate structures} under the highly reducing conditions expected in \added{hydrogen-rich environment of} sub-Neptune\replaced{s}{ interiors}.
+
+Our preliminary experiments suggest that nitrogen \replaced{can}{may} be incorporated into planetary interiors\deleted{ rather than remaining entirely in atmosphere} (Fig.~\ref{Olivine-N2-H2}). 
+The formation of nitrides \replaced{and Fe-N}{N-bearing} alloys \deleted{or} \deleted{NH$_3$-bearing species} \deleted{would} \replaced{implies}{imply} \replaced{strong}{active} nitrogen exchange between \replaced{the envelope and the interior}{atmospheres and interiors}, \deleted{potentially} affecting \deleted{both planetary} evolution and \replaced{interpretation of the measured atmosphere spectra of these planets}{observable atmospheric compositions}.
+
+The primary objective\replaced{ of our proposed experiments is to understand nitrogen partitioning between fluid and silicates at high P-T.}{s of the proposed research are to determine the stability of silicates in N-bearing, H-rich fluids and to identify reaction products.}
+\added{In our recent studies} \cite{horn_Building_2025}, \added{we also found that the experiment designed and executed for exoplanets can also provide new insights on early evolution of terrestrial planets (including Earth)} \cite{young_Earth_2023}. %\sidecomment{cite Young 2023 Nature paper here.}
+\added{Considering importance of nitrogen for Earth's atmosphere, our new data can potentially impact our understanding of how the atmosphere chemistry can be affected by underlying geology in early terrestrial planets.}
+\deleted{The {resulting data} will provide {the first systematic experimental constraints} on {phase stability,} reaction {pathways, and nitrogen-bearing products} in {H$_2$-N$_2$}-silicate systems at 5-30 GPa and 1500-4000 K.}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Why do you need the APS for this research?  ($<2000$ character)}
+
+% 983
+\replaced{The proposed chemical system will produce low-Z materials with}{We propose X-ray diffraction measurements on} weak\deleted{ly} \added{X-ray} scattering \added{factors.} \deleted{, low-Z materials} 
+The \deleted{anticipated} reaction products \replaced{include}{are expected to consist primarily of} \deleted{low-Z phases, including} nitrides, hydrides, and silicates.
+\added{Furthermore, the amount of the materials will be extremely small} under high-pressure and high-temperature conditions in a diamond-anvil cell. 
+\replaced{To overcome these factors,}{which require} the high brilliance \added{X-ray beam} available at APS \added{is critical} for reliable phase identification\deleted{with intense diffraction peaks}.
+\replaced{The small apertures of diamond-anvil cells require high energy X-ray beam for ensuring detection of low d-spacing critical for accurate identification of phases and determination of unit-cell volumes.}{Successful execution of these experiments requires both high X-ray flux and high X-ray energy (higher than 30 keV).} 
+
+
+Our experimental plan also includes very short heating durations (1-2 \replaced{seconds}{s}). 
+\added{The reason is that during longer laser heating in fluid, silicate melts can migrate away from the heated area.}
+\added{Therefore, short heating duration is required.}
+To monitor reactions during these \added{short} heating events, \deleted{the} X-ray beam must be sufficiently intense to produce \added{high-quality} diffraction patterns of weakly scattering nitride, hydride, and silicate phases\deleted{ generated during 1-2 s heating events}. 
+\replaced{T}{In addition, t}he laser-heated region is typically less than 20 $\mu$m in diameter at high pressure, necessitating a highly collimated X-ray beam with a size of \replaced{less than}{approximately 1-} 2 $\mu$m.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Describe why you are choosing your requested beamline ($<2000$ character)}
+
+% 1435
+\added{Beamline} \replaced{13IDD}{13-IDD} is designed \added{and optimized} for high-pressure experiments. 
+The beamline provides high-brilliance X-ray\replaced{s}{ beam} with focusing optics, coupled with state-of-the-art experimental instrumentation for in situ laser heating in a diamond-anvil cell. 
+The laser heating system at \replaced{13IDD}{13-IDD} is a crucial component for conducting our proposed experiments\deleted{,} \replaced{where}{which require heating} silicates \added{will be heated} in \replaced{hydrogen}{H2}-rich fluids to temperatures approaching 4000 K.
+
+\replaced{The beamline}{13-IDD} features \deleted{a unique} pulsed-laser heating mode and burst (ramp) heating mode, essential for achieving sufficiently high temperatures for melting all the materials \replaced{including silicates and fluid medium}{involved} at high pressures. 
+These two heating methods are particularly useful for reaching temperatures above 3000 K, where continuous laser heating could induce severe fluid convection problems, thereby lowering laser coupling efficiency. 
+In other words, these dedicated heating techniques enable us to obtain data on chemical reactions without suffering from dynamic instability in the sample chamber during \deleted{partial} melting.
+
+\replaced{The beamline}{13-IDD} also \replaced{provides}{has} an extremely well-collimated X-ray beam on the scale of 1-2 \replaced{micrometers}{microns}, and the X-ray beam size can \deleted{now} be \added{further} reduced to a few hundred nanometers. 
+This smaller beam size helps to minimize the \replaced{impact from the radial}{horizontal} thermal gradient in the heated area. 
+Additionally, the user-friendly interface of the software programs allow\deleted{s} users to obtain and analyze high-quality XRD images and temperature data \replaced{efficiently during beamtime}{under high-temperature and high-pressure conditions}.
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{How many visits during the proposal lifespan do you expect to need? ($<2000$ character)} 
+
+%2093
+We request \replaced{12}{9} shifts for this project, with 3 shifts allocated per visit. 
+\deleted{However, the proposed work can also be completed with 2 shifts per visit if necessary.} 
+We plan to prepare four to five \replaced{diamond-anvil cells (DACs)}{DACs} per visit, depending on the number of shifts allocated.
+
+For the first visit, we will prepare two DACs containing ferropericlase \replaced{in a}{+} N$_2$-67\%H$_2$ medium and two DACs containing olivine \replaced{in a}{+} N$_2$-67\%H$_2$ medium. 
+\added{A gas loading system at ASU is capable of loading gas mixtures and we will prepare these samples before the beamtime trip} \cite{fu_Core_2023}.
+Based on our previous experience \added{for similar experiments at 13IDD}, approximately 5 hours are required per DAC, including sample alignment, laser heating, and post-heating 2D XRD mapping \replaced{(5 hours per DAC and 4 DACs, totaling 20 hours)}{(5 hours x 4 DACs = 20 hours)}. 
+The target pressures for the first visit will be 5\replaced{--}{ and }14 GPa, with temperatures ranging from 1500 to 4000 K. 
+An additional 4 hours will be required to collect 2D XRD maps of \added{the} recovered samples at \deleted{lower pressures and/or} ambient pressure.
+
+During the second visit, we will investigate higher-pressure conditions (15-30 GPa)\deleted{, where more complex phase relations and reaction products are expected}. 
+We will prepare two DACs containing ferropericlase \replaced{in a }{+} N$_2$-67\%H$_2$ medium and two DACs containing olivine \replaced{in a }{+} N$_2$-67\%H$_2$ medium. 
+
+\added{During the third visit, we will target very high temperature (4000~K) at very low pressures (2-5 GPa), which is important for understanding smaller young sub-Neptune exoplanets.
+The same two compositions we discussed above will be investigated.}
+Because pressure instabilities may occur during laser heating \added{to extremely high temperatures} at low pressures, we will prepare one or two \added{more} backup DACs. 
+\replaced{If needed, we will further}{and} reduce heating durations\deleted{ when necessary}. 
+\deleted{If heating experiments at temperatures up to 4000 K are successfully completed at higher pressures, we will use the backup DACs to explore lower-pressure conditions (2-5 GPa) with moderate heating temperatures (1500-2000 K). These conditions are relevant to smaller sub-Neptunes, where the atmosphere-interior boundary is expected to occur at lower pressures.}
+
+During the \replaced{fourth}{third} visit, we will focus on verifying the reproducibility of \replaced{the results obtained in first three visits}{newly identified phases and reaction products} \added{and completing the dataset sufficient for understanding pressure- and temperature-dependent variation in chemical reactions in the N-H-silicate system}. 
+\replaced{If previously unknown phases are observed in first three visits, we will synthesize them and measure their equations of state in this beamtime.}{We will also conduct additional measurements to determine the equations of state of newly synthesized materials whenever sufficient diffraction data are available.}
+\deleted{In addition, we will investigate less-explored pressure-temperature conditions identified during the first and second visits and follow up on any intriguing reaction products or phase assemblages.}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Describe/provide a list of samples ($<2000$ character)} 
+
+% 390
+
+We will use natural San Carlos olivine ((Mg$_{0.9}$Fe$_{0.1}$)$_2$SiO$_4$), \replaced{which have been also used in our previous experiments}{consistent with that used in the principal investigator's previous studies} \cite{kim_Atomicscale_2021, kim_Solubility_2022}. 
+\added{For ferropericlase,} we will \deleted{also} use \deleted{synthetic ferropericlase} (Mg$_{0.75}$Fe$_{0.25}$)O \added{synthesized in} a multi-anvil press at FORCE, ASU. 
+\added{Combining these two compositions, we will be able to isolate the effects of Si in the chemical reaction and cover a wide range of Mg/Si ratios for the limited beamtimes.}
+
+\replaced{Nitrogen and hydrogen will be mixed in 1:3 ratio in our gas loading system at ASU.
+The gas mixture will be captured together with the silicate/oxide samples to 1500~bars in DACs before the beamtime trips.}{A N$_2$-H$_2$ mixed gas (33 mol\% N$_2$ and 67 mol\% H$_2$) will be used as the reactive fluid during high-pressure and high-temperature experiments.}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Overview of the experimental plan and procedures, including sample usage  ($<2000$ character)} 
+
+
+We will use \added{diamond anvil} culet diameters of 300 and 400 $\mu$m for laser-heating experiments at 15-30 and 5-14 GPa, respectively. 
+A thin foil ($\sim$\replaced{10}{15} $\mu$m thick) of compressed olivine or ferropericlase powder will be loaded into a drilled gasket hole (typically 200-300 $\mu$m in diameter) together with a N$_2$-H$_2$ gas \added{mixture as a medium}. 
+\replaced{Sample}{Four} spacer\replaced{ grains}{s} will be used to support the foil and prevent direct contact with the diamond anvils. 
+The gases will be loaded using \replaced{a}{the} gas-loading system at ASU.
+
+During heating to \deleted{extreme} temperatures \added{over} \deleted{(}$\sim$4000 K\deleted{)} at \deleted{relatively} low\added{er} pressures (e.g., 5 GPa), \replaced{mechanical relaxation of the DACs can occur}{the DAC may partially open}, \replaced{which can result in loss of pressure and therefore}{resulting in} leakage of the pressure medium. 
+Such failures \added{can} occur primarily during \replaced{long}{prolonged} heating. 
+Therefore, we will \replaced{reduce}{minimize} heating durations and use \added{smaller} gasket holes \deleted{that are relatively small compared to the culet diameter} to reduce the risk of \added{potential} sample loss \added{during extreme high temperature heating}.
+
+Ruby fluorescence will be used for \added{measuring} pressure\deleted{ calibration}. 
+We will employ both burst-mode and continuous laser-heating methods and evaluate their relative effectiveness based on the experimental results \added{during our first visit}. 
+\replaced{An}{The} EIGER2 X CdTe 9M detector \added{at the beamline} will enable rapid acquisition of high-quality diffraction patterns during and after heating, with particular emphasis on identifying nitrides, \replaced{Fe-N}{N-bearing metallic} alloys, hydrides, and other reaction products formed during heating. 
+Two-dimensional XRD maps will be collected after heating at high pressure\added{s} and \deleted{again} after decompression to ambient pressure.
+
+Following \added{the} laser heating, Raman spectra will be \replaced{measured}{collected} using the GSECARS Raman system to characterize reaction products both at high pressure and after recovery to ambient conditions. 
+To maximize efficiency during beamtime, one group member will conduct Raman measurements while \replaced{the other researcher}{the principal investigator} performs laser-heating experiments on another DAC. 
+After beamtime, \added{the} recovered samples will be characterized using \added{an} FIB-SEM-EDS \added{instrument} at ASU to determine composition\deleted{s} and microstructure\deleted{s}, providing \replaced{additional}{complementary} information\deleted{to the synchrotron XRD and Raman datasets}.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Describe the team's previous experimental experience with synchrotron radiation ($<2000$ character)}
+
+Taehyun Kim, the principal investigator (PI), has conducted LHDAC experiments at \replaced{13IDD}{13-IDD} at GSECARS, \replaced{16IDB}{16-IDB} at HPCAT, and P02.2 at PETRA III, and has performed numerous XRD experiments at ALS, SSRL, and PLS-II.
+
+Sang-Heon Dan Shim, the PI's advisor, has conducted numerous XRD experiments at APS, CHESS, NSLS, SSRL, and ALS over the past \replaced{30}{28} years.
+
+Allison Pease and Alem Tukic, members of Shim's group, have carried out synchrotron X-ray diffraction experiments at APS, including at \replaced{13IDD}{13-IDD}.
+
+Taehyun Kim and Sang-Heon Dan Shim have already conducted similar experiments as proposed here in recent years at the \replaced{13IDD}{13-IDD} beamline \cite{kim_Stability_2023, horn_Building_2025}.
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{List publications resulting from work done at the APS  ($<2000$ character)}
+
+%\inlinecomment{Please identify the beamline(s) where the work was done.}
+
+Selected recent publication based on past APS work includes:
+
+Fu, S., Chariton, S., Prakapenka, V. B., and Shim, S.-H. (2023). Core origin of seismic velocity anomalies at Earth's core-mantle boundary. Nature. https://doi.org/10.1038/s41586-023-05713-5. 
+
+Kim, T., O'Rourke, J. G., Lee, J., Chariton, S., Prakapenka, V., Husband, R. J., et al. (2023). A hydrogen-enriched layer in the topmost outer core sourced from deeply subducted water. Nature Geoscience. https://doi.org/10.1038/s41561-023-01324-x
+
+Kim, T., Wei, X., Chariton, S., Prakapenka, V. B., Ryu, Y.-J., Yang, S., and Shim, S.-H. (2023). Stability of hydrides in sub-Neptune exoplanets with thick hydrogen-rich atmospheres. Proceedings of the National Academy of Sciences, 120(52), e2309786120. https://doi.org/10.1073/pnas.2309786120
+
+Ko, B., Greenberg, E., Prakapenka, V., Alp, E. E., Bi, W., Meng, Y., et al. (2022). Calcium dissolution in bridgmanite in the Earth's deep mantle. Nature. https://doi.org/10.1038/s41586-022-05237-4
+
+Horn, H. W., Prakapenka, V., Chariton, S., Speziale, S., and Shim, S.-H. (2023). Reaction between hydrogen and ferrous/ferric oxides at high pressures and high temperatures - implications for sub-Neptunes and super-Earths. The Planetary Science Journal, 4(2), 30. https://doi.org/10.3847/PSJ/acab03
+
+\added{Wei, X., Chariton, S., Prakapenka, V. B., Fei, Y. and Shim S. (2026). Effects of hydrogen on Fe-S alloys and their implications for the martian core. JGR Planets 131, e2025JE009217.}
+
+These studies were conducted at 13IDD. 
+In addition to these papers, we have two submissions from experiments performed at GSECARS, APS.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\clearpage
+
+\begin{figure}
+\centering\includegraphics[width=0.7\textwidth]{figs/fig.jpg}
+\caption{
+Preliminary results for the \replaced{N-H-olivine}{olivine-H$_2$-N$_2$} reaction. 
+(a) \added{An} XRD pattern collected after heating to 3300 K at 10 GPa. 
+\replaced{The colored vertical bars}{Colored lines} indicate the diffraction positions of $\beta$-Si$_3$N$_4$, an Fe-N alloy phase, MgO, and residual olivine. 
+The sample was laser-heated at ASU, and synchrotron XRD data were collected at Beamline 12.2.2 of the ALS. 
+Diffraction peaks from olivine were \replaced{detected}{also observed} because the X-ray beam size \replaced{was too large at the ALS beamline, highlighting the importance of the high-resolution setup at 13IDD for this investigation}{exceeded the heated region}. 
+(b) Raman spectrum \replaced{measured at a lower temperature region}{collected near the edge of the heated region} after laser heating. 
+\replaced{The observed peaks}{Broad bands between 3100 and 3500 cm$^{-1}$} are consistent with N-H stretching vibrations \added{reported in previous study} \deleted{(c) Reference Raman spectra from Chidester and Strobel (2011)} \cite{chidester_Ammonia_2011} \added{(c)}. 
+\deleted{The positions of the N-H stretching modes closely match those observed in panel (b), supporting the presence of N-H-bearing species.} 
+(d) \added{A} cross-sectional SEM image \replaced{from} {corresponding to} the XRD data \added{area} \deleted{shown} in panel (a). 
+\deleted{A hole is observed at the center of the heated region.} 
+\added{The} elemental maps (e, f) were collected from the boxed area \added{revealing Fe alloy phase and silicon nitride from the reaction between N-H fluid and olivine melt.} \deleted{EDS elemental distribution maps of Fe (red), Mg (green), Si (cyan), O (yellow), and N (dark blue). The spatial correlation between Si and N also supports the formation of Si$_3$N$_4$ during the reaction between olivine and H$_2$-N$_2$ fluids.
+}
+}\label{Olivine-N2-H2}
+\end{figure}
+
+%\begin{cbox}
+%{I had to reduce the figure file size by 100 times to prevent latex crashing.  Make sure your figure file size is always less than 5 MB.}
+%\end{cbox}
+
+\clearpage
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\inlinecomment{Literature references (DOIs or citations) - 2000 character limit}
+
+\bibliographystyle{proposal2-doi-only}
+\bibliography{./bibs/KimLibrary}