adding references to LWF and scdm , workaround mkdocs imcompatibility with recent jinja2, clean typora tmp file

doc/.gitignore

@@ -1,7 +1,6 @@
 # The following md files have been copied from ~abinit and should be `git ignored`
-INSTALL_gpu.md
-INSTALL_EasyBuild.md
 INSTALL_CentOS.md
+INSTALL_EasyBuild.md
 INSTALL_MacOS.md
 INSTALL_Ubuntu.md
 INSTALL_gpu.md
@@ -9,8 +8,7 @@ INSTALL_gpu.md
 developers/autoconf_examples.md
 variables/index.md
 variables/external_parameters.md
-variables/multibinit.md
-variables/aim.md
+variables/atdep.md
 variables/basic.md
 variables/bse.md
 variables/dev.md
@@ -28,9 +26,10 @@ variables/paw.md
 variables/rlx.md
 variables/vdw.md
 variables/w90.md
-variables/optic.md
-variables/atdep.md
 variables/anaddb.md
+variables/aim.md
+variables/multibinit.md
+variables/optic.md
 variables/varset_stats.md
 topics/Abipy.md
 topics/APPA.md

doc/abiref.bib

@@ -9131,3 +9131,51 @@ url = {https://doi.org/10.1107/S0021889802008580},
  year = {2022},
  month = feb,
 }
+
+@article{damle2015compressed,
+  title={Compressed representation of Kohn--Sham orbitals via selected columns of the density matrix},
+  author={Damle, Anil and Lin, Lin and Ying, Lexing},
+  journal={Journal of Chemical Theory and Computation},
+  volume={11},
+  number={4},
+  pages={1463--1469},
+  year={2015},
+  publisher={ACS Publications}
+}
+@article{damle2018disentanglement,
+  title={Disentanglement via entanglement: A unified method for Wannier localization},
+  author={Damle, Anil and Lin, Lin},
+  journal={Multiscale Modeling \& Simulation},
+  volume={16},
+  number={3},
+  pages={1392--1410},
+  year={2018},
+  publisher={SIAM}
+}
+
+
+@article{damle2017scdm,
+  title={SCDM-k: Localized orbitals for solids via selected columns of the density matrix},
+  author={Damle, Anil and Lin, Lin and Ying, Lexing},
+  journal={Journal of Computational Physics},
+  volume={334},
+  pages={1--15},
+  year={2017},
+  publisher={Elsevier}
+}
+
+
+@article{rabe1995localized,
+  title = {{Localized basis for effective lattice Hamiltonians: Lattice Wannier functions}},
+  author = {Rabe, K. M. and Waghmare, U. V.},
+  journal = {Phys. Rev. B},
+  volume = {52},
+  issue = {18},
+  pages = {13236--13246},
+  numpages = {0},
+  year = {1995},
+  month = {Nov},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevB.52.13236},
+  url = {https://link.aps.org/doi/10.1103/PhysRevB.52.13236}
+}

doc/tutorial/lattice_wannier.md

@@ -4,7 +4,7 @@ authors: HeXu
 
 # Tutorials on constructing Lattice Wannier functions (LWF's). 
 
-This tutorial introduces the methods for constructing lattice Wannier funtions (LWF's). You'll learn how to use the SCDM-k (selected columns of the density matrix in k-space) method for constructing the LWF's. And how to plot the band structure of the LWF's and compare it with the full phonon band structures. 
+This tutorial introduces the methods for constructing lattice Wannier funtions (LWF's)[[cite:rabe1995localized]]. You'll learn how to use the SCDM-k (selected columns of the density matrix in k-space) [[cite:damle2015compressed]] [[cite:amle2017scdm]] [[cite:damle2018disentanglement]] method for constructing the LWF's. And how to plot the band structure of the LWF's and compare it with the full phonon band structures. 
 
 The LWF is a close analogy to the electron Wannier functions.  Each LWF is formed by a group of atomic displacement within a certain range. Together they form a localized basis set for the atomic distortions, which could span the (sub)space for the atomic vibrations (phonons). One typical use case is to build effective Hamiltonian of atomic displacement. In many phenomenons, only a few distortion modes are important. For example,  in a structural phase transition the soft modes are often related, whereas the phonons with much higher frequency are probably less relevant. Thus if the LWF's can well represent the relevant phonon modes, it could reduce the number of degrees of freedom in the study of such phenomenons. 
 

requirements.txt

@@ -3,6 +3,7 @@ html2text
 # Pinned versions for website deployment
 mkdocs==1.1.2
 mkdocs-material==7.0.6
+jinja2<3.1.0
 
 pymdown-extensions==8.2
 python-markdown-math