docs: refresh project landing pages (#5951)

## Summary

- Replace the repository README with a Markdown-first landing page that
prominently highlights pretrained DPA models and the current DeePMD-kit
feature set.
- Route feature-level calls to action to the hosted documentation while
keeping runnable examples in the repository.
- Preserve the theme-aware logo plus the DOI and live citation-count
badges for the three general software publications.
- Refresh the documentation homepage with responsive Sphinx Design
cards, model guidance, data-to-dynamics navigation, and the complete
general software citations.
- Keep the change isolated to `README.md` and `doc/index.rst` to avoid
conflicts with other documentation work.

## Validation

- `ruff check .`
- `ruff format .`
- Repository Markdown and whitespace hooks
- `git diff --check`
- Minimal Sphinx 9.1 HTML build with `sphinx-design`
- Verified all hosted documentation links and citation badge endpoints
referenced by the README return HTTP 200

Fixes #5240

Coding agent: Codex
Codex version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning effort: xhigh

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Documentation**
* Rewrote the README with an accessible overview of capabilities, model
families, supported backends, workflows, installation, quick starts,
pretrained models, integrations, licensing, and references.
* Replaced the documentation landing page with structured guidance for
installation, training, deployment, physics features, and recent
developments.
* Improved navigation with card-based sections, clearer guide
categories, project details, generated indices, and search access.
* **References**
* Added citations for the Deep Potential representation and DeePCG
coarse-grained model.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <njzjz@qq.com>
Co-authored-by: njzjz-bot <njzjz.bot@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: njzjz-bot (driven by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.6-terra))[bot] <48687836+njzjz-bot@users.noreply.github.com>
Co-authored-by: Duo <50307526+iProzd@users.noreply.github.com>
Co-authored-by: njzjz-bot <njzjz-bot@users.noreply.github.com>

Author: 5 people

CITATIONS.bib

@@ -86,6 +86,22 @@ @article{Zeng_JChemTheoryComput_2025_v21_p4375
   },
 }
 
+@article{Han_CommunComputPhys_2018_v23_p629,
+  annote       = {Deep Potential},
+  title        = {
+    {Deep Potential: A General Representation of a Many-Body Potential Energy
+    Surface}
+  },
+  author       = {Jiequn Han and Linfeng Zhang and Roberto Car and Weinan E},
+  journal      = {Commun. Comput. Phys.},
+  year         = 2018,
+  volume       = 23,
+  number       = 3,
+  pages        = {629--639},
+  doi          = {10.4208/cicp.OA-2017-0213},
+  url          = {https://arxiv.org/abs/1707.01478},
+}
+
 @article{Lu_CompPhysCommun_2021_v259_p107624,
   annote       = {GPU support},
   title        = {
@@ -120,6 +136,18 @@ @article{Zhang_PhysRevLett_2018_v120_p143001
   doi          = {10.1103/PhysRevLett.120.143001},
 }
 
+@article{Zhang_JChemPhys_2018_v149_p34101,
+  annote       = {coarse-grained model (DeePCG)},
+  title        = {{DeePCG: Constructing Coarse-Grained Models via Deep Neural Networks}},
+  author       = {Linfeng Zhang and Jiequn Han and Han Wang and Roberto Car and Weinan E},
+  journal      = {J. Chem. Phys.},
+  year         = 2018,
+  volume       = 149,
+  number       = 3,
+  pages        = 034101,
+  doi          = {10.1063/1.5027645},
+}
+
 @incollection{Zhang_BookChap_NIPS_2018_v31_p4436,
   annote       = {DeepPot-SE (se\_e2\_a, se\_e2\_r, se\_e3, se\_atten)},
   title        = {
@@ -196,6 +224,35 @@ @article{Zhang_npjComputMater_2024_v10_p293
   doi          = {10.1038/s41524-024-01493-2},
 }
 
+@article{Zhang_npjComputMater_2026_DPA3,
+  annote       = {DPA-3 descriptor (dpa3)},
+  author       = {
+    Duo Zhang and Anyang Peng and Chun Cai and Wentao Li and Yuanchang Zhou and
+    Jinzhe Zeng and Mingyu Guo and Chengqian Zhang and Bowen Li and Hong Jiang
+    and Tong Zhu and Weile Jia and Linfeng Zhang and Han Wang
+  },
+  title        = {{A Graph Neural Network for the Era of Large Atomistic Models}},
+  journal      = {npj Comput. Mater.},
+  year         = 2026,
+  doi          = {10.1038/s41524-026-02146-2},
+}
+
+@misc{Li_2026_DPA4,
+  annote       = {DPA-4 descriptor (dpa4, sezm)},
+  author       = {
+    Tiancheng Li and Wentao Li and Anyang Peng and Jianming Xue and Linfeng
+    Zhang and Duo Zhang and Han Wang
+  },
+  title        = {
+    {{DPA4}: Pushing the Accuracy-Cost Frontier of Interatomic Potentials with
+    {EMFA} {SO(2)} Convolution}
+  },
+  publisher    = {arXiv},
+  year         = 2026,
+  doi          = {10.48550/arXiv.2606.02419},
+  url          = {https://arxiv.org/abs/2606.02419},
+}
+
 @article{Zhang_PhysPlasmas_2020_v27_p122704,
   annote       = {frame-specific parameters (e.g. electronic temperature)},
   author       = {
@@ -262,6 +319,18 @@ @article{Sommers_PhysChemChemPhys_2020_v22_p10592
   doi          = {10.1039/D0CP01893G},
 }
 
+@misc{Ahart_2026_DeepPolaron,
+  annote       = {atomic charge population (DeepPopulation)},
+  author       = {Christian S. Ahart and Denan Li and Jochen Blumberger and Shi Liu},
+  title        = {
+    {Polaron Transport in {TiO}$_{2}$ from Machine Learning Molecular Dynamics}
+  },
+  publisher    = {arXiv},
+  year         = 2026,
+  doi          = {10.48550/arXiv.2606.01763},
+  url          = {https://arxiv.org/abs/2606.01763},
+}
+
 @article{Zeng_JChemTheoryComput_2023_v19_p1261,
   annote       = {fit relative energies},
   author       = {Jinzhe Zeng and Yujun Tao and Timothy J Giese and Darrin M York},

README.md

@@ -15,6 +15,24 @@ Cite DeePMD-kit and methods
    Zeng_JChemPhys_2023_v159_p054801
    Zeng_JChemTheoryComput_2025_v21_p4375
 
+.. _cite-deep-potential:
+
+- If the original Deep Potential model is used,
+
+.. bibliography::
+   :filter: False
+
+   Han_CommunComputPhys_2018_v23_p629
+
+.. _cite-deepcg:
+
+- If the DeePCG coarse-grained model is used,
+
+.. bibliography::
+   :filter: False
+
+   Zhang_JChemPhys_2018_v149_p34101
+
 - If GPU version is used,
 
 .. bibliography::
@@ -57,6 +75,24 @@ Cite DeePMD-kit and methods
 
    Zhang_npjComputMater_2024_v10_p293
 
+.. _cite-dpa3:
+
+- If DPA-3 descriptor (`dpa3`) is used,
+
+.. bibliography::
+   :filter: False
+
+   Zhang_npjComputMater_2026_DPA3
+
+.. _cite-dpa4:
+
+- If DPA-4 descriptor (`dpa4`, `sezm`) is used,
+
+.. bibliography::
+   :filter: False
+
+   Li_2026_DPA4
+
 - If frame-specific parameters (`fparam`, e.g. electronic temperature) is used,
 
 .. bibliography::
@@ -85,6 +121,15 @@ Cite DeePMD-kit and methods
 
    Sommers_PhysChemChemPhys_2020_v22_p10592
 
+.. _cite-deeppopulation:
+
+- If fitting atomic charge populations with DeepPopulation,
+
+.. bibliography::
+   :filter: False
+
+   Ahart_2026_DeepPolaron
+
 - If fitting density of states,
 
 .. bibliography::