Merge branch 'brucefan1983:master' into expand_group_method

Author: luowh35

Dockerfile

@@ -1,52 +1,36 @@
 # Base image
-FROM nvidia/cuda:11.7.1-devel-ubuntu20.04
+FROM nvidia/cuda:13.1.1-devel-ubuntu24.04
 
 # Base packages
 ARG DEBIAN_FRONTEND=noninteractive
 ENV TZ=Europe/Gothenburg
-RUN \
-  apt-get update -qy && \
-  apt-get upgrade -qy && \
-  apt-get install -qy \
-    git \
-    graphviz \
-    pandoc \
-    python3-pip \
-    zip
 
-RUN \
-  pip3 install --upgrade \
-    pip \
-  && \
-  pip3 install --upgrade \
-    coverage \
-    flake8 \
-    nbmake \
-    pytest \
-    setuptools_scm \
-    twine \
-    xdoctest
+RUN apt-get update -qy && \
+    apt-get install -y --no-install-recommends \
+      git \
+      graphviz \
+      pandoc \
+      python3-pip \
+      zip && \
+    rm -rf /var/lib/apt/lists/*
 
-# Packages needed for calorine (compare setup.py)
-RUN \
-  pip3 install \
-    ase \
-    matplotlib \
-    numpy \
-    pandas \
-    pybind11
+RUN pip3 install --break-system-packages --no-cache-dir \
+      coverage \
+      flake8 \
+      nbmake \
+      pytest \
+      setuptools_scm \
+      twine \
+      xdoctest \
+      ase \
+      matplotlib \
+      numpy \
+      pandas \
+      pybind11 \
+      sphinx_autodoc_typehints \
+      sphinx-rtd-theme \
+      sphinx_sitemap \
+      sphinxcontrib-bibtex \
+      nbsphinx
 
-# Packages for building documentation
-RUN \
-  pip3 install --upgrade \
-    sphinx_autodoc_typehints \
-    sphinx-rtd-theme \
-    sphinx_sitemap \
-    sphinxcontrib-bibtex \
-    cloud_sptheme \
-    nbsphinx \
-  && \
-  pip3 install --upgrade \
-    jinja2==3.0.3
-
-CMD /bin/bash
+CMD ["/bin/bash"]

doc/gpumd/input_files/kpoints_in.rst

@@ -47,5 +47,6 @@ or
  0.5 0 0.5 X
 
 Here,
+
 * The first three columns represent the coordinates of high symmetry points. The last column corresponds to names.
-* A blank line must be used to indicate a breakpoint or the start of a second path.
+* A blank line must be used to indicate a breakpoint or the start of a second path.

doc/gpumd/output_files/index.rst

@@ -113,7 +113,7 @@ Output files
      - :ref:`compute_phonon <kw_compute_phonon>`
      - Phonon frequency squared :math:`\omega^2(\boldsymbol{k})` for the input :math:`\boldsymbol{k}`-points
      - Overwrite
-   * - :ref:`viscosity_out <viscosity_out>`
+   * - :ref:`viscosity.out <viscosity_out>`
      - :ref:`compute_viscosity <kw_compute_viscosity>`
      - Viscosity and stress auto-correlation function
      - Append

doc/publications.bib

@@ -925,6 +925,19 @@ @article{FanZhaFan25
 doi = {10.1038/s41524-025-01705-3}
 }
 
+@article{FenCheYin25,
+  title = {Searching superhard {C} and {BxCyNz} via full-space inverse design approach},
+  author = {Feng, Kaiwei and Cheng, Guanjian and Yin, Wan-Jian},
+  journal = {Phys. Rev. Mater.},
+  volume = {9},
+  issue = {12},
+  pages = {123603},
+  numpages = {10},
+  year = {2025},
+  publisher = {American Physical Society},
+  doi = {10.1103/8qyx-sqtn}
+}
+
 @article{FenLiuBai24,
 title = {Nontrivial impact of interlayer coupling on thermal conductivity: Opposing trends in in-plane and out-of-plane phonons},
 author = {Feng, H. F. and Liu, B. and Bai, J. L. and Zhang, X. and Song, Z. X. and Guo, Zhi-Xin},
@@ -1108,6 +1121,17 @@ @article{GaoLinXia25
 doi = {10.1016/j.tws.2025.113751}
 }
 
+@article{GaoYuaCao25,
+title = {Melt structure of {NiCrW} superalloy near liquidus studied by experiment and molecular dynamics simulation},
+journal = {Materials Letters},
+volume = {389},
+pages = {138405},
+year = {2025},
+issn = {0167-577X},
+doi = {10.1016/j.matlet.2025.138405},
+author = {Zhongtang Gao and Yilin Yuan and Teng Cao and Jiahao Yang and Zhiming Gao and Yuan Yu}
+}
+
 @article{GenZhaWan26,
 author = {Geng, Xingze and Zhang, Wentao and Wang, Lin-Wang and Meng, Xiangying},
 title = {Origin of the machine learning forces field errors across metal elements},
@@ -1200,11 +1224,12 @@ @article{HaoLooDin26
   doi = {10.1103/76nt-hw3h}
 }
 
-@article{HeMaChu25,
-title = {Polytypical Phase Transformation of Topologically Close-Packed Phase Enabled Toughening in Multi-Principal-Element Eutectic Alloy},
+@article{HeMaChu26,
+title = {Polytypic phase transformation of topologically close-packed phase enabled toughening in multi-principal-element eutectic alloy},
 journal = {Acta Materialia},
+volume = {306},
 pages = {121737},
-year = {2025},
+year = {2026},
 issn = {1359-6454},
 doi = {10.1016/j.actamat.2025.121737},
 author = {Q.F. He and S.H. Ma and D.H. Chung and H. Wang and Z.Q. Chen and Z.Y. Ding and Q. Yu and J.H. Luan and Q. Wang and F. Zhang and H.B. Lou and Q.S. Zeng and J.F. Gu and S.J. Zhao and Y. Yang}
@@ -1975,6 +2000,16 @@ @article{LiuYinHe25
 doi = {10.1016/j.commatsci.2025.113686},
 }
 
+@article{LiuYuZhu26,
+title = {Uncovering the thermal expansion in high-entropy ceramics by machine learning},
+journal = {Journal of Materiomics},
+pages = {101205},
+year = {2026},
+issn = {2352-8478},
+doi = {10.1016/j.jmat.2026.101205},
+author = {Yiwen Liu and Hulei Yu and Lei Zhuang and Yanhui Chu}
+}
+
 @Article{LiuZha25,
 author={Liu, Jie and Zhang, Lin},
 title={A physics-informed machine learning perspective to present the structures and properties of titanium matrixes and nanoclusters through atomic modeling},
@@ -2990,6 +3025,14 @@ @article{TanZheSon24
     doi = {10.1063/5.0206028}
 }
 
+@article{TaoZhaTan26,
+author = {Tao, Feng and Zhang, Xiaoliang and Tang, Dawei and Maruyama, Shigeo and Feng, Ya},
+title = {Bose-{Einstein} Phonon Statistics Explain Drastic Thermal Conductivity Reduction in {SWCNT} Bundles},
+journal = {Nano Letters},
+year = {2026},
+doi = {10.1021/acs.nanolett.5c06521}
+}
+
 @article{TiaCheQin26,
 title = {Atomic-level engineering anisotropic thermal transport for directional heat dissipation in silicon electronics},
 journal = {Materials Today Physics},
@@ -3412,6 +3455,17 @@ @article{WeiSonHou25
 doi = {10.1016/j.actamat.2025.121529}
 }
 
+@article{WeiWanShu26,
+title = {Decoupled influence of chemical compositions and nanotopographies on the hydrophilicity of nanotextured {Ti}-6{Al}-4{V} implants: {Insights} from molecular dynamics simulations},
+journal = {Journal of Colloid and Interface Science},
+volume = {704},
+pages = {139464},
+year = {2026},
+issn = {0021-9797},
+doi = {10.1016/j.jcis.2025.139464},
+author = {Sujing Wei and Xueliang Wang and Tianyu Shu}
+}
+
 @article{WenChoYu25,
 author = {Wen, Yue and Cho, Jeongho and Yu, Linfeng and Zhao, Yi-Ming and Wang, Jingxuan and Shen, Lei and Qin, Guangzhao and Yoon, Seok Min and Lim, Jongwoo and Shin, Sunmi},
 title = {Thermal conductivity of individual single-crystalline {F₁₆CuPc} nanoribbons},
@@ -3856,6 +3910,17 @@ @article{YanFanZhu26
 doi = {10.1021/acs.jcim.5c02335}
 }
 
+@article{YanHuaWan26,
+title = {Study on the microstructure and wear resistance of {CoCrFeMnNiMoYₓ} high entropy alloys based on molecular dynamics simulation},
+journal = {Tribology International},
+volume = {213},
+pages = {111084},
+year = {2026},
+issn = {0301-679X},
+doi = {10.1016/j.triboint.2025.111084},
+author = {Xinyi Yang and Bensheng Huang and Xiaowei Wang and Yongyou Zhu and Jianneng Zheng}
+}
+
 @article{YanSiShe25,
 author = {Rui Yang  and Qiaoling Si  and Qiang Sheng  and Mingyang Yang  and Mu Du  and Hu Zhang  and Xiao-Lei Shi  and Guihua Tang  and Zhi-Gang Chen },
 title = {Atomic armor for thermal stability in nanoporous structures},
@@ -4060,6 +4125,17 @@ @article{YuaGuoYi25
   doi = {10.1103/PhysRevB.111.184310}
 }
 
+@article{YuBiLiu26,
+title = {Machine learning molecular dynamics investigation on cation diffusion mechanisms in {Ni}0.2{Cu}0.3{Zn}0.5{Fe}2{O}4 ferrite and its homogeneous interfaces},
+journal = {Solid State Ionics},
+volume = {439},
+pages = {117164},
+year = {2026},
+issn = {0167-2738},
+doi = {10.1016/j.ssi.2026.117164},
+author = {Shihong Yu and Peng Bi and Jingsong Liu and Enzhu Li and Yong Yi}
+}
+
 @article{YuDonYan24,
 title = {Dynamic mesophase transition induces anomalous suppressed and anisotropic phonon thermal transport},
 author = {Yu, Linfeng and Dong, Kexin and Yang, Qi and Zhang, Yi and Fan, Zheyong and Zheng, Xiong and Wang, Huimin and Qin, Zhenzhen and Qin, Guangzhao},