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Update APIP naming in documentation.

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This commit is contained in:
David Immel
2025-06-05 20:05:37 +02:00
parent 20f123ddd1
commit 6c798f1847
15 changed files with 192 additions and 192 deletions
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doc/src/Howto_apip.rst
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@ -51,24 +51,24 @@ following components:
.. tab:: dynamic switching parameter
#. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/apip/fast <pair_pace_apip>`.
#. A precise potential: :doc:`pace/apip/precise <pair_pace_apip>`.
#. :doc:`pair_style lambda_input <pair_lambda_input>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
#. :doc:`fix lambda <fix_lambda>` to calculate the switching parameter :math:`\lambda_i`.
#. :doc:`pair_style lambda/zone <pair_lambda_zone>` to calculate the spatial transition zone of the switching parameter.
#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
#. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
#. :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
#. :doc:`fix lambda/apip <fix_lambda_apip>` to calculate the switching parameter :math:`\lambda_i`.
#. :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>` to calculate the spatial transition zone of the switching parameter.
#. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
#. :doc:`fix lambda_thermostat <fix_lambda_thermostat>` to conserve the energy when switching parameters change.
#. :doc:`fix apip_atom_weight <fix_apip_atom_weight>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
#. :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>` to conserve the energy when switching parameters change.
#. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
#. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
.. tab:: constant switching parameter
#. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/apip/fast <pair_pace_apip>`.
#. A precise potential: :doc:`pace/apip/precise <pair_pace_apip>`.
#. :doc:`set <fix_lambda>` command to set the switching parameter :math:`\lambda_i`.
#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
#. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
#. :doc:`set <set>` command to set the switching parameter :math:`\lambda_i`.
#. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
#. :doc:`fix apip_atom_weight <fix_apip_atom_weight>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
#. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
#. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
----------
@ -92,15 +92,15 @@ Example
atom_style apip
comm_style tiled
pair_style hybrid/overlay eam/fs/apip pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda/zone 12.0
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/apip Cu.yace Cu
pair_coeff * * lambda_input/csp
pair_coeff * * lambda/zone
pair_coeff * * pace/precise/apip Cu.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix 2 all lambda 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
fix 3 all lambda_thermostat N_rescaling 200
fix 4 all apip_atom_weight 100 eam ace lambda_input lambda all
fix 2 all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
fix 3 all lambda_thermostat/apip N_rescaling 200
fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
variable myweight atom f_4
@ -129,15 +129,15 @@ Example
atom_style apip
comm_style tiled
pair_style hybrid/overlay eam/fs/apip pace/apip/precise
pair_style hybrid/overlay eam/fs/apip pace/precise/apip
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/apip Cu.yace Cu
pair_coeff * * pace/precise/apip Cu.yace Cu
# calculate lambda somehow
variable lambda atom ...
set group all lambda v_lambda
set group all apip_lambda v_lambda
fix 4 all apip_atom_weight 100 eam ace lambda_input lambda all
fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
variable myweight atom f_4