Geometry input documentation
============================

Specify one of the supported geometry actions.
Defaults to `Fixed` if none specified.


Used to initialize class :class:`qimpy.dft.geometry.Geometry`.

YAML template:
--------------

.. parsed-literal::

   :yamlparam:`qimpy.dft.geometry.Geometry:fixed`:                     :yamlcomment:`# Electronic optimization only at a fixed geometry:`
                             
   :yamlparam:`qimpy.dft.geometry.Geometry:relax`:                     :yamlcomment:`# Geometry relaxation of ions, and optionally, also the lattice:`
     :yamlparam:`qimpy.dft.geometry.Relax:n-iterations`: 20         :yamlcomment:`# Maximum number of iterations.`
     :yamlparam:`qimpy.dft.geometry.Relax:energy-threshold`: 5e-05  :yamlcomment:`# Convergence threshold on energy change in Eh.`
     :yamlparam:`qimpy.dft.geometry.Relax:fmax-threshold`: 0.0005   :yamlcomment:`# Convergence threshold on maximum force in Eh/a0.`
     :yamlparam:`qimpy.dft.geometry.Relax:stress-threshold`: 1e-05  :yamlcomment:`# Convergence threshold on |stress| (stress tensor norm) in Eh/a0^3.`
     :yamlparam:`qimpy.dft.geometry.Relax:n-consecutive`: 1         :yamlcomment:`# Number of consecutive iterations each threshold must be satisfied.`
     :yamlparam:`qimpy.dft.geometry.Relax:method`: l-bfgs           :yamlcomment:`# Relaxation algorithm: L-BFGS, CG or Gradient.`
     :yamlparam:`qimpy.dft.geometry.Relax:cg-type`: polak-ribiere   :yamlcomment:`# CG variant: Polak-Ribiere, Fletcher-Reeves or Hestenes-Stiefel.`
     :yamlparam:`qimpy.dft.geometry.Relax:line-minimize`: auto      :yamlcomment:`# Line minimization scheme: Auto, Constant, Quadratic, Wolfe.`
     :yamlparam:`qimpy.dft.geometry.Relax:n-history`: 15            :yamlcomment:`# Maximum history size (only used for L-BFGS).`
     :yamlparam:`qimpy.dft.geometry.Relax:converge-on`: all         :yamlcomment:`# Converge on 'any', 'all' or a specific number of thresholds.`
     :yamlparam:`qimpy.dft.geometry.Relax:drag-wavefunctions`: :yamlkey:`yes`  :yamlcomment:`# Whether to drag atomic components of wavefunctions.`
     :yamlparam:`qimpy.dft.geometry.Relax:save-history`: :yamlkey:`yes`        :yamlcomment:`# Whether to save history along the trajectory.`
                             
   :yamlparam:`qimpy.dft.geometry.Geometry:dynamics`:                  :yamlcomment:`# Molecular dynamics of ions, and optionally, also the lattice:`
     :yamlparam:`qimpy.dft.geometry.Dynamics:dt`: [:yamltype:`float`]              :yamlcomment:`# Time step.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:n-steps`: [:yamltype:`int`]           :yamlcomment:`# Number of MD steps.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:thermostat`:              :yamlcomment:`# Thermostat/barostat method:`
       :yamlparam:`qimpy.dft.geometry.thermostat.Thermostat:nve`:                   :yamlcomment:`# No thermostat (or barostat), i.e. NVE ensemble:`
                             
       :yamlparam:`qimpy.dft.geometry.thermostat.Thermostat:nose-hoover`:           :yamlcomment:`# Nose-Hoover thermostat and/or barostat:`
         :yamlparam:`qimpy.dft.geometry.thermostat.NoseHoover:chain-length-T`: 3    :yamlcomment:`# Nose-Hoover chain length for thermostat.`
         :yamlparam:`qimpy.dft.geometry.thermostat.NoseHoover:chain-length-P`: 3    :yamlcomment:`# Nose-Hoover chain length for barostat.`
                             
       :yamlparam:`qimpy.dft.geometry.thermostat.Thermostat:berendsen`:             :yamlcomment:`# Berendsen velocity-rescaling thermostat and/or barostat:`
         :yamlparam:`qimpy.dft.geometry.thermostat.Berendsen:B0`: 2.200 GPa        :yamlcomment:`# Characteristic bulk modulus for Berendsen barostat.`
                             
       :yamlparam:`qimpy.dft.geometry.thermostat.Thermostat:langevin`:              :yamlcomment:`# Langevin stochastic thermostat and/or barostat:`
                             
     :yamlparam:`qimpy.dft.geometry.Dynamics:seed`: 1234               :yamlcomment:`# Random seed for initial velocities.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:T0`: 298.000 K            :yamlcomment:`# Initial temperature / temperature set point.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:P0`: 1.000 bar            :yamlcomment:`# Pressure set point for NPT, if lattice.movable is True.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:stress0`: :yamlkey:`null`            :yamlcomment:`# Stress set point for N-stress-T, if lattice.movable is True.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:t-damp-T`: 50.000 fs      :yamlcomment:`# Thermostat damping time.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:t-damp-P`: 100.000 fs     :yamlcomment:`# Barostat damping time.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:drag-wavefunctions`: :yamlkey:`yes`  :yamlcomment:`# Whether to drag atomic components of wavefunctions.`
     :yamlparam:`qimpy.dft.geometry.Dynamics:save-history`: :yamlkey:`yes`        :yamlcomment:`# Whether to save history along the trajectory.`
                             

Component classes:
------------------

.. toctree::
    :maxdepth: 1

    Fixed <qimpy.dft.geometry.Fixed>
    Relax <qimpy.dft.geometry.Relax>
    Dynamics <qimpy.dft.geometry.Dynamics>

Parameters:
-----------

fixed
+++++

*Type:* :doc:`Fixed <qimpy.dft.geometry.Fixed>`, *Default:*  :yamlkey:`null`

Electronic optimization only at a fixed geometry.

relax
+++++

*Type:* :doc:`Relax <qimpy.dft.geometry.Relax>`, *Default:*  :yamlkey:`null`

Geometry relaxation of ions, and optionally, also the lattice.

dynamics
++++++++

*Type:* :doc:`Dynamics <qimpy.dft.geometry.Dynamics>`, *Default:*  :yamlkey:`null`

Molecular dynamics of ions, and optionally, also the lattice.