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Add apip to documentation of read_dump and compute property/atom.

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This commit is contained in:
David Immel
2025-06-06 14:41:52 +02:00
parent 9a65ab2c4d
commit ccc078f036
2 changed files with 27 additions and 1 deletions
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25
doc/src/compute_property_atom.rst
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@ -34,6 +34,8 @@ Syntax
i_name, d_name, i2_name[I], d2_name[I],
vfrac, s0, espin, eradius, ervel, erforce,
rho, drho, e, de, cv, buckling,
apip_lambda, apip_lambda_input, apip_e_fast,
apip_e_precise
.. parsed-literal::
@ -70,6 +72,13 @@ Syntax
*i2_name[I]* = Ith column of custom integer array with name
*d2_name[I]* = Ith column of custom floating-point array with name
.. parsed-literal::
APIP package per-atom properties:
*apip_lambda* = switching parameter
*apip_lambda_input* = input used to calculate the switching parameter
*apip_e_fast,apip_e_precise* = potential energies mixed by the adaptive-precision potential
.. parsed-literal::
PERI package per-atom properties:
@ -162,6 +171,22 @@ segment particles and define the end points of each line segment.
*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
triangular particles and define the corner points of each triangle.
The accessible quantities from the :doc:`APIP package <Howto_apip>` are
explained in the doc pages of this package in detail.
In short: *apip_lambda* is the switching parameter :math:`\lambda\in[0,1]`,
that is calculated from *apip_lambda_input* and that mixes the energies
of a fast (*apip_e_fast*) and a precise (*apip_e_precise*) potential
into an adaptive-precision energy.
.. note::
The energy according to the fast and the precise potential are only
computed for the subset of atoms, for which it is required, i.e.,
for an atom :math:`i` with :math:`\lambda_i=1` one does not need
:math:`E_i^\text{precise}` and with :math:`\lambda_i=0` one does
not need :math:`E_i^\text{fast}`.
In addition, the various per-atom quantities listed above for specific
packages are only accessible by this command.

3
doc/src/read_dump.rst
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@ -16,12 +16,13 @@ Syntax
.. parsed-literal::
field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz*
field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz* or *apip_lambda*
*x*,\ *y*,\ *z* = atom coordinates
*vx*,\ *vy*,\ *vz* = velocity components
*q* = charge
*ix*,\ *iy*,\ *iz* = image flags in each dimension
*fx*,\ *fy*,\ *fz* = force components
*apip_lambda* = switching parameter of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
* zero or more keyword/value pairs may be appended
* keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*