diff --git a/doc/source/written/background/parsing.rst b/doc/source/written/background/parsing.rst index 8ea74bd2..d8c2aaf4 100644 --- a/doc/source/written/background/parsing.rst +++ b/doc/source/written/background/parsing.rst @@ -1,3 +1,5 @@ +.. _parsers_and_containers: + Parsing code output and using containers ======================================== diff --git a/doc/source/written/background/phonon_dos.rst b/doc/source/written/background/phonon_dos.rst index 199da24c..84dad4ab 100644 --- a/doc/source/written/background/phonon_dos.rst +++ b/doc/source/written/background/phonon_dos.rst @@ -1,3 +1,5 @@ +.. _pdos_from_vacf: + Velocity autocorrelation function and phonon DOS ================================================ diff --git a/doc/source/written/features.rst b/doc/source/written/features.rst index ba9e7f12..1cbbe210 100644 --- a/doc/source/written/features.rst +++ b/doc/source/written/features.rst @@ -3,50 +3,53 @@ Features ======== -* container classes for single unit cells (:class:`~pwtools.crys.Structure`) +* Container classes for single unit cells (:class:`~pwtools.crys.Structure`) and structure sequences such as molecular dynamics trajectories, relaxation - runs or NEB paths (:class:`~pwtools.crys.Trajectory`) + runs or NEB paths (:class:`~pwtools.crys.Trajectory`). See + :ref:`parsers_and_containers`. -* classes to set up calculations (parameter studies) based on template input - files for any kind of computational backend (:mod:`~pwtools.batch`) +* Classes to set up calculations (parameter studies) based on template input + files for any kind of computational backend (:mod:`~pwtools.batch`). See + :ref:`param_study`. -* simple sqlite3 interface with convenience data extraction methods - (:mod:`~pwtools.sql`) +* Simple sqlite3 interface with convenience data extraction methods + (:mod:`~pwtools.sql`). -* parsing of PWscf (QE_), CPMD_ , CP2K_ and LAMMPS_ - output into Python objects for easy access (:mod:`~pwtools.parse`) +* Parsing of PWscf (QE_), CPMD_ , CP2K_ and LAMMPS_ + output into Python objects for easy access (:mod:`~pwtools.parse`). See + :ref:`parsers_and_containers`. -* structure io: read cif, pdb, write axsf, cif, xyz (:mod:`~pwtools.io`) +* Structure io: read cif, pdb, write axsf, cif, xyz (:mod:`~pwtools.io`) -* pythonic interface to external molecular viewers for interactive use: - xcrysden_, avogadro_, jmol_, VMD_ (:mod:`~pwtools.visualize`) +* Pythonic interface to external molecular viewers for interactive use: + xcrysden_, avogadro_, jmol_, VMD_ (:mod:`~pwtools.visualize`). -* interface to the Elk_ code's EOS fitting tool and own implementation (Vinet - EOS) (:mod:`~pwtools.eos`) +* EOS fitting tools (:mod:`~pwtools.eos`) -* thermodynamic properties in the quasi-harmonic approximation from phonon - density of states, QHA implementation (:mod:`~pwtools.thermo`) +* Thermodynamic properties in the quasi-harmonic approximation from phonon + density of states, QHA implementation (:mod:`~pwtools.thermo`). See + :ref:`qha`. * MD analysis: radial pair distribution function (own implementation and VMD_ - interface), RMS, RMSD (:mod:`~pwtools.crys`) + interface), RMS, RMSD (:mod:`~pwtools.crys`). -* velocity autocorrelation function and phonon DOS from MD trajectories - (:mod:`~pwtools.pydos`) +* Velocity autocorrelation function and phonon DOS from MD trajectories + (:mod:`~pwtools.pydos`). See :ref:`pdos_from_vacf`. -* unit cell related tools: super cell building, coordinate transformation, - k-grid tools, ... (:mod:`~pwtools.crys`) +* Unit cell related tools: super cell building, coordinate transformation, + k-grid tools, ... (:mod:`~pwtools.crys`). -* thin wrappers for spglib_ functions (:mod:`~pwtools.symmetry`) +* Thin wrappers for spglib_ functions (:mod:`~pwtools.symmetry`) -* functions and classes to extend numpy/scipy, e.g. N-dim polynomial fitting +* Functions and classes to extend numpy/scipy, e.g. N-dim polynomial fitting and a number of convenient 1D classes (polynomial, spline) with a common - API (:mod:`~pwtools.num`) + API (:mod:`~pwtools.num`). * N-dim radial basis function interpolation and fitting (:mod:`~pwtools.rbf`) -* basic signal processing / fft related tools (:mod:`~pwtools.signal`) +* Basic signal processing / fft related tools (:mod:`~pwtools.signal`) -* tools to handle matplotlib plots in scripts (:mod:`~pwtools.mpl`) +* Tools to handle matplotlib plots in scripts (:mod:`~pwtools.mpl`) * QE and LAMMPS calculators for ASE (:mod:`~pwtools.calculators`)