Add PDOS and atomic solver modules

.gitignore

@@ -17,3 +17,10 @@ dev_tests/
 /doc/.LaTeX/Manual.pdf*
 /doc/.LaTeX/**/*.synctex*
 /README.html
+
+# Python cache
+__pycache__/
+*.pyc
+.ipynb_checkpoints/
+outputs/
+.DS_Store

ChangeLog

@@ -2,6 +2,13 @@
 -Date
 -Name
 -changes
+--------------
+November 07, 2025
+Name: Qihao Cheng
+Changes: utils/pdos/, utils/atom/
+1. Add projected density of states (PDOS) post-processing module, including configuration file, example scripts, and sample outputs.
+2. Add atomic utilities and related submodules (mesh, pseudo, scf, xc, etc.) for standalone atomic DFT calculations.
+
 --------------
 October 03, 2025
 Name: Sayan Bhowmik

src/initialization.c

@@ -3722,7 +3722,7 @@ void write_output_init(SPARC_OBJ *pSPARC) {
     }
 
     fprintf(output_fp,"***************************************************************************\n");
-    fprintf(output_fp,"*                       SPARC (version October 03, 2025)                      *\n");
+    fprintf(output_fp,"*                       SPARC (version November 07, 2025)                 *\n");
     fprintf(output_fp,"*   Copyright (c) 2020 Material Physics & Mechanics Group, Georgia Tech   *\n");
     fprintf(output_fp,"*           Distributed under GNU General Public License 3 (GPL)          *\n");
     fprintf(output_fp,"*                   Start time: %s                  *\n",c_time_str);

utils/atom/__init__.py

@@ -0,0 +1,22 @@
+"""
+Atomic DFT Solver Package
+
+This package provides a comprehensive implementation of Atomic Density Functional Theory
+solver using finite element method.
+
+Main class:
+    AtomicDFTSolver: Main solver class for atomic DFT calculations
+
+Example:
+    >>> from delta.atomic_dft import AtomicDFTSolver
+    >>> solver = AtomicDFTSolver(atomic_number=13, xc_functional="GGA_PBE")
+    >>> results = solver.solve()
+"""
+
+__version__ = "0.1.0"
+
+# Main solver class
+from .solver import AtomicDFTSolver
+
+# Make AtomicDFTSolver easily accessible
+__all__ = ["AtomicDFTSolver"]

utils/atom/delta/__init__.py

@@ -0,0 +1 @@
+from .pipeline import DeltaLearningPipeline  # noqa: F401

utils/atom/delta/dataset.py

@@ -0,0 +1,13 @@
+from __future__ import annotations
+import numpy as np
+from typing import Dict, Any
+
+def save_delta_npz(path: str, snapshot, ref_v: Dict[str, np.ndarray], other_v: Dict[str, np.ndarray]) -> None:
+    """Persist Δ-learning data to NPZ."""
+    np.savez_compressed(
+        path,
+        r=snapshot.r_quad, rho=snapshot.rho,
+        vx_ref=ref_v.get("vx"), vc_ref=ref_v.get("vc"),
+        vx_other=other_v.get("vx"), vc_other=other_v.get("vc"),
+        meta=snapshot.meta
+    )

utils/atom/delta/pipeline.py

@@ -0,0 +1,12 @@
+from __future__ import annotations
+from typing import Tuple, Dict, Any
+
+class DeltaLearningPipeline:
+    """High-level Δ-learning pipeline at fixed density snapshots. Placeholder."""
+    def __init__(self, solver, xc_evaluator):
+        self.solver = solver
+        self.xc_eval = xc_evaluator
+
+    def run_once(self, xc_ref: str, xc_other: str, include_tau: bool = False) -> Tuple[Any, Dict[str, Any], Dict[str, Any], Dict[str, Any]]:
+        """Return (snapshot, ref_v, other_v, delta)."""
+        raise NotImplementedError

utils/atom/mesh/__init__.py

@@ -0,0 +1,2 @@
+from .builder import Quadrature1D, Mesh1D, LagrangeShapeFunctions  # noqa: F401
+from .operators import RadialOperatorsBuilder  # noqa: F401