Docs: Add overview of CLI utilities; optimisation TODO

CLIUTILS.md

@@ -0,0 +1,43 @@
+Overview of QPMS command line utilities
+=======================================
+
+The utilities are located in the `misc` directory. Run the
+utility with `-h` argument to get more info.
+
+
+Rectangular and square 2D lattices
+----------------------------------
+
+These scripts deal with simple 2D rectangular lattices,
+finite or infinite, one scatterer per unit cell. 
+\f$ D_{2h} \f$ or \f$ D_{4h} \f$ symmetric adapted bases
+are used where applicable.
+
+### Finite lattices
+
+ * `finiterectlat-modes.py`:  Search for resonances using Beyn's algorithm.
+ * `finiterectlat-scatter.py`:  Plane wave scattering.
+ * `finiterectlat-constant-driving.py`: Rectangular array response to
+   a driving where a subset of particles are excited by basis VSWFs with the
+   same phase.
+
+### Infinite lattices
+
+ * `rectlat_simple_modes.py`: Search for lattice modes using Beyn's algorithm.
+ * `infiniterectlat-k0realfreqsvd.py`: 
+    Evaluate the lattice mode problem singular values at the Γ point for a real frequency interval.
+    Useful as a starting point in lattice mode search before using Beyn's algorithm.
+ * `infiniterectlat-scatter.py`: Plane wave scattering.
+
+
+General 2D lattices
+-------------------
+
+### Infinite lattices
+
+These can contain several scatterers per unit cell. Symmetry adapted bases currently not implemented.
+
+ * `lat2d_modes.py`: Search for lattice modes using Beyn's algorithm.
+ * `lat2d_realfreqsvd.py`: 
+    Evaluate the lattice mode problem singular values at the Γ point for a real frequency interval.
+    Useful as a starting point in lattice mode search before using Beyn's algorithm.

Doxyfile

@@ -753,7 +753,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = qpms notes finite_systems.md README.md README.Triton.md finite_systems.md lattices.md TODO.md
+INPUT                  = qpms notes misc finite_systems.md CLIUTILS.md README.md README.Triton.md finite_systems.md lattices.md TODO.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -773,7 +773,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          =
+FILE_PATTERNS          = 
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -1462,7 +1462,7 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax
+MATHJAX_RELPATH        = https://uslugi.necada.org/js/mathjax
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example

README.md

@@ -112,6 +112,13 @@ Tutorials
 
 See also the examples directory in the source repository.
 
+
+Command line utilities
+----------------------
+
+  * [Overview of the Python command line utilities][cliutils]
+
+
 Acknowledgments
 ================
 
@@ -128,7 +135,7 @@ Bug reports
 ===========
 
 If you believe that some parts of QPMS behave incorrectly, please mail
-a bug report to <marek@necada.org>. To ensure that your message is not
+a bug report to [marek@necada.org][authormail]. To ensure that your message is not
 considered spam, please start the subject line with `QPMS`.
 
 If you were able to fix a bug yourself, please include the patch as well,
@@ -143,7 +150,7 @@ documentation, code quality, or new features.
 
 You can send patches prepared using the 
 [`git format-patch`](https://git-scm.com/docs/git-format-patch) tool
-to <marek@necada.org>. 
+to [marek@necada.org][authormail].
 
 If you plan to contribute with major changes to the codebase, it is 
 recommended to discuss that first (see the contact information below).
@@ -152,10 +159,10 @@ recommended to discuss that first (see the contact information below).
 Contact & discussion
 ====================
 
-You can contact the main author e.g. via [e-mail](marek@necada.org) 
+You can contact the main author e.g. via [e-mail][authormail]
 or [Telegram](https://t.me/necadam).
 
-You are also warmly welcome to the [QPMS user chat](https://t.me/QPMScattering)
+You are also warmly welcome to the [QPMS user chat][telegramchat]
 in Telegram!
 
 
@@ -164,9 +171,12 @@ in Telegram!
 [OpenBLAS]: https://www.openblas.net/
 [GSL]: https://www.gnu.org/software/gsl/
 [cmake]: https://cmake.org
-[tRITON-README]: README.Triton.md
+[TRITON-README]: README.Triton.md
 [tutorial-finite]: finite_systems.md
 [tutorial-infinite]: lattices.md
 [doxygen]: http://doxygen.nl/
 [QD]: https://www.aalto.fi/en/department-of-applied-physics/quantum-dynamics-qd
 [lepaper]: https://arxiv.org/abs/2006.12968
+[telegramchat]: https://t.me/QPMScattering
+[authormail]: mailto:marek@necada.org
+[cliutils]: CLIUTILS.md

TODO.md

@@ -40,3 +40,16 @@ Nice but less important features
 
 - Static, thread-safe caches of constant coefficients + API without the current "calculators".
 
+
+Optimisations
+-------------
+
+- Leaving out the irrelevant elements if a "rectangular" block of the translations matrix is needed.
+- Ewald sums with "non-parallel" shifts (are about 20 times slower than the purely parallel ones).
+- Reusing intermediate results (profiling needed)
+  * Bessel, Legendre functions (see also branch `finite_lattice_speedup`)
+  * Lattice points (sorting and scaling)
+  * Γ/Δ functions (for periodic lattices)
+- More parallelisation.
+- Possibly pre-calculation of the (precise) coefficients in Bessel and Legendre functions (using gmp)
+- Asymptotic approximations of the Bessel functions for far fields.

qpms/přehled

@@ -4,8 +4,6 @@ qpms_p.py (až na změny souřadnic???)
 
 ## Nové věci
 lattices2d.py
-scripts_common.py
-timetrack.py
 tmatrices.py
 types.py
 svwf.c
@@ -69,15 +67,6 @@ G0L_analytical
 G0T_analytical
 G0_sum_1_slow
 
-# scripts_common.py
-## funkce
-make_action_sharedlist
-add_argparse_k_output_options
-add_argparse_unitcell_definitions
-add_argparse_infinite_lattice_options
-add_argparse_output_options
-add_argparse_common_options
-arg_preprocess_particles
 
 # timetrack.py