Dynamics input documentation
============================


Specify molecular dynamics parameters.


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

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

.. parsed-literal::

   :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

    Thermostat <qimpy.dft.geometry.thermostat.Thermostat>

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

dt
++

*Type:* :yamltype:`float`

Time step.

n-steps
+++++++

*Type:* :yamltype:`int`

Number of MD steps.

thermostat
++++++++++

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

Thermostat/barostat method.
Specify name of thermostat eg. 'nose-hoover' if using default options
for that thermostat method, and dictionary of parameters if not.

seed
++++

*Type:* :yamltype:`int`, *Default:*  1234

Random seed for initial velocities.

T0
++

*Type:* :yamltype:`Unit` or :yamltype:`float`, *Default:*  298.000 K

Initial temperature / temperature set point.

P0
++

*Type:* :yamltype:`Unit` or :yamltype:`float`, *Default:*  1.000 bar

Pressure set point for NPT, if lattice.movable is :yamlkey:`yes`.
Note that this is overridden by `stress0`, if that is specified.

stress0
+++++++

*Type:* <class 'numpy.ndarray'> or <class 'torch.Tensor'> or :yamltype:`null`, *Default:*  :yamlkey:`null`

Stress set point for N-stress-T, if lattice.movable is :yamlkey:`yes`.
If specified and lattice.movable, strain tensor will fluctuate
during dynamics, instead of only volume in NPT mode.
(Set to :yamlkey:`null` and specify `P0` instead for NPT mode.)

t-damp-T
++++++++

*Type:* :yamltype:`Unit` or :yamltype:`float`, *Default:*  50.000 fs

Thermostat damping time.

t-damp-P
++++++++

*Type:* :yamltype:`Unit` or :yamltype:`float`, *Default:*  100.000 fs

Barostat damping time.

drag-wavefunctions
++++++++++++++++++

*Type:* :yamltype:`bool`, *Default:*  :yamlkey:`yes`

Whether to drag atomic components of wavefunctions.

save-history
++++++++++++

*Type:* :yamltype:`bool`, *Default:*  :yamlkey:`yes`

Whether to save history along the trajectory.
Saved quantities include positions, forces, velocities, temperature,
pressure, potential and total stress (if available),
and lattice (if movable).