Update APIP naming in documentation.
This commit is contained in:
David Immel
@ -22,7 +22,7 @@ OPT.
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* :doc:`append/atoms <fix_append_atoms>`
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* :doc:`atc <fix_atc>`
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* :doc:`atom/swap <fix_atom_swap>`
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* :doc:`apip_atom_weight <fix_apip_atom_weight>`
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* :doc:`atom_weight/apip <fix_atom_weight_apip>`
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* :doc:`ave/atom <fix_ave_atom>`
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* :doc:`ave/chunk <fix_ave_chunk>`
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* :doc:`ave/correlate <fix_ave_correlate>`
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@ -90,7 +90,8 @@ OPT.
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* :doc:`imd <fix_imd>`
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* :doc:`indent <fix_indent>`
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* :doc:`ipi <fix_ipi>`
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* :doc:`lambda <fix_lambda>`
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* :doc:`lambda/apip <fix_lambda_apip>`
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* :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>`
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* :doc:`langevin (k) <fix_langevin>`
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* :doc:`langevin/drude <fix_langevin_drude>`
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* :doc:`langevin/eff <fix_langevin_eff>`
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@ -99,7 +100,6 @@ OPT.
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* :doc:`lb/momentum <fix_lb_momentum>`
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* :doc:`lb/viscous <fix_lb_viscous>`
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* :doc:`lineforce <fix_lineforce>`
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* :doc:`lambda_thermostat <fix_lambda_thermostat>`
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* :doc:`manifoldforce <fix_manifoldforce>`
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* :doc:`mdi/qm <fix_mdi_qm>`
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* :doc:`mdi/qmmm <fix_mdi_qmmm>`
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@ -126,9 +126,9 @@ OPT.
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* :doc:`ilp/tmd (t) <pair_ilp_tmd>`
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* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
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* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
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* :doc:`lambda/zone <pair_lambda_zone>`
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* :doc:`lambda_input <pair_lambda_input>`
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* :doc:`lambda_input/csp <pair_lambda_input>`
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* :doc:`lambda/input/apip <pair_lambda_input_apip>`
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* :doc:`lambda/input/csp/apip <pair_lambda_input_apip>`
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* :doc:`lambda/zone/apip <pair_lambda_zone_apip>`
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* :doc:`lcbop <pair_lcbop>`
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* :doc:`lebedeva/z <pair_lebedeva_z>`
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* :doc:`lennard/mdf <pair_mdf>`
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@ -242,8 +242,8 @@ OPT.
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* :doc:`pace (k) <pair_pace>`
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* :doc:`pace/extrapolation (k) <pair_pace>`
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* :doc:`pace/apip <pair_pace_apip>`
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* :doc:`pace/apip/fast <pair_pace_apip>`
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* :doc:`pace/apip/precise <pair_pace_apip>`
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* :doc:`pace/fast/apip <pair_pace_apip>`
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* :doc:`pace/precise/apip <pair_pace_apip>`
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* :doc:`pedone (o) <pair_pedone>`
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* :doc:`pod (k) <pair_pod>`
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* :doc:`peri/eps <pair_peri>`
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@ -51,24 +51,24 @@ following components:
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.. tab:: dynamic switching parameter
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#. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
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#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/apip/fast <pair_pace_apip>`.
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#. A precise potential: :doc:`pace/apip/precise <pair_pace_apip>`.
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#. :doc:`pair_style lambda_input <pair_lambda_input>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
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#. :doc:`fix lambda <fix_lambda>` to calculate the switching parameter :math:`\lambda_i`.
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#. :doc:`pair_style lambda/zone <pair_lambda_zone>` to calculate the spatial transition zone of the switching parameter.
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#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
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#. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
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#. :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
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#. :doc:`fix lambda/apip <fix_lambda_apip>` to calculate the switching parameter :math:`\lambda_i`.
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#. :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>` to calculate the spatial transition zone of the switching parameter.
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#. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
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#. :doc:`fix lambda_thermostat <fix_lambda_thermostat>` to conserve the energy when switching parameters change.
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#. :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.
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#. :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>` to conserve the energy when switching parameters change.
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#. :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.
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#. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
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.. tab:: constant switching parameter
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#. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
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#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/apip/fast <pair_pace_apip>`.
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#. A precise potential: :doc:`pace/apip/precise <pair_pace_apip>`.
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#. :doc:`set <fix_lambda>` command to set the switching parameter :math:`\lambda_i`.
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#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
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#. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
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#. :doc:`set <set>` command to set the switching parameter :math:`\lambda_i`.
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#. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
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#. :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.
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#. :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.
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#. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
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----------
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@ -92,15 +92,15 @@ Example
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atom_style apip
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comm_style tiled
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pair_style hybrid/overlay eam/fs/apip pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda/zone 12.0
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pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
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pair_coeff * * eam/fs/apip Cu.eam.fs Cu
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pair_coeff * * pace/apip Cu.yace Cu
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pair_coeff * * lambda_input/csp
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pair_coeff * * lambda/zone
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pair_coeff * * pace/precise/apip Cu.yace Cu
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pair_coeff * * lambda/input/csp/apip
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pair_coeff * * lambda/zone/apip
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fix 2 all lambda 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
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fix 3 all lambda_thermostat N_rescaling 200
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fix 4 all apip_atom_weight 100 eam ace lambda_input lambda all
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fix 2 all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
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fix 3 all lambda_thermostat/apip N_rescaling 200
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fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
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variable myweight atom f_4
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@ -129,15 +129,15 @@ Example
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atom_style apip
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comm_style tiled
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pair_style hybrid/overlay eam/fs/apip pace/apip/precise
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pair_style hybrid/overlay eam/fs/apip pace/precise/apip
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pair_coeff * * eam/fs/apip Cu.eam.fs Cu
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pair_coeff * * pace/apip Cu.yace Cu
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pair_coeff * * pace/precise/apip Cu.yace Cu
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# calculate lambda somehow
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variable lambda atom ...
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set group all lambda v_lambda
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set group all apip_lambda v_lambda
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fix 4 all apip_atom_weight 100 eam ace lambda_input lambda all
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fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
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variable myweight atom f_4
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@ -229,12 +229,12 @@ The APIP package requires also the installation of ML-PACE, which has
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* ``src/APIP``: filenames -> commands
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* :doc:`Howto APIP <Howto_apip>`
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* ``examples/PACKAGES/apip``
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* :doc:`fix apip_atom_weight <fix_apip_atom_weight>`
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* :doc:`fix lambda <fix_lambda>`
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* :doc:`fix lambda_thermostat <fix_lambda_thermostat>`
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* :doc:`fix atom_weight/apip <fix_atom_weight_apip>`
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* :doc:`fix lambda/apip <fix_lambda_apip>`
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* :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`
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* :doc:`pair_style eam/apip <pair_eam_apip>`
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* :doc:`pair_style lambda/zone <pair_lambda_zone>`
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* :doc:`pair_style lambda_input <pair_lambda_input>`
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* :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`
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* :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`
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* :doc:`pair_style pace/apip <pair_pace_apip>`
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----------
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@ -118,7 +118,7 @@ the Additional Information section below.
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- :ref:`MOLECULE <PKG-MOLECULE>`
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- bead-spring polymers with stiffness
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* - *apip*
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- *atomic* + lambda, lambda_required, lambda_input, lambda_const, lambda_input_ta, e_simple, e_complex, f_const_lambda, f_dyn_lambda
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- *atomic* + apip_lambda, apip_lambda_required, apip_lambda_input, apip_lambda_const, apip_lambda_input_ta, apip_e_fast, apip_e_precise, apip_f_const_lambda, apip_f_dyn_lambda
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- :ref:`APIP <PKG-APIP>`
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- adaptive-precision interatomic potentials(APIP), see :doc:`APIP howto <Howto_apip>`
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* - *atomic*
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@ -201,7 +201,7 @@ accelerated styles exist.
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* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
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* :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
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* :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
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* :doc:`apip_atom_weight <fix_apip_atom_weight>` - compute atomic load of an :doc:`APIP potential <Howto_apip>` for load balancing
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* :doc:`atom_weight/apip <fix_atom_weight_apip>` - compute atomic load of an :doc:`APIP potential <Howto_apip>` for load balancing
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* :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
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* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
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* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
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@ -269,7 +269,7 @@ accelerated styles exist.
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* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
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* :doc:`indent <fix_indent>` - impose force due to an indenter
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* :doc:`ipi <fix_ipi>` - enable LAMMPS to run as a client for i-PI path-integral simulations
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* :doc:`lambda <fix_lambda>` - compute switching parameter, that controls the precision of an :doc:`APIP potential <Howto_apip>`
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* :doc:`lambda/apip <fix_lambda_apip>` - compute switching parameter, that controls the precision of an :doc:`APIP potential <Howto_apip>`
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* :doc:`langevin <fix_langevin>` - Langevin temperature control
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* :doc:`langevin/drude <fix_langevin_drude>` - Langevin temperature control of Drude oscillators
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* :doc:`langevin/eff <fix_langevin_eff>` - Langevin temperature control for the electron force field model
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@ -278,7 +278,7 @@ accelerated styles exist.
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* :doc:`lb/momentum <fix_lb_momentum>` - :doc:`fix momentum <fix_momentum>` replacement for use with a lattice-Boltzmann fluid
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* :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
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* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
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* :doc:`lambda_thermostat <fix_lambda_thermostat>` - apply energy conserving correction for an :doc:`APIP potential <Howto_apip>`
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* :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>` - apply energy conserving correction for an :doc:`APIP potential <Howto_apip>`
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* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
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* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
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* :doc:`mdi/qmmm <fix_mdi_qmmm>` - LAMMPS operates as client for QM/MM simulation with a quantum code via the MolSSI Driver Interface (MDI)
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@ -1,6 +1,6 @@
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.. index:: fix apip_atom_weight
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.. index:: fix atom_weight/apip
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fix apip_atom_weight command
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fix atom_weight/apip command
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============================
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Syntax
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@ -8,15 +8,15 @@ Syntax
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.. code-block:: LAMMPS
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fix ID group-ID apip_atom_weight nevery fast_potential precise_potential lambda_input lambda group_lambda_input [no_rescale]
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fix ID group-ID atom_weight/apip nevery fast_potential precise_potential lambda_input lambda_zone group_lambda_input [no_rescale]
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* apip_atom_weight = style name of this fix command
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* atom_weight/apip = style name of this fix command
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* nevery = perform load calculation every this many steps
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* fast_potential = *eam* or *ace* for time measurements of the corresponding pair_style or float for constant time
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* precise_potential = *ace* for a time measurement of the pair_style pace/apip or float for constant time
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* lambda_input = *lambda_input* for a time measurement of pair_style lambda_input or float for constant time
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* lambda = *lambda/zone* for a time measurement of pair_style lambda/zone or float for constant time
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* lambda_input = *lambda/input* for a time measurement of pair_style lambda/input/apip or float for constant time
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* lambda_zone = *lambda/zone* for a time measurement of pair_style lambda/zone/apip or float for constant time
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* group_lambda_input = group-ID of the group for which lambda_input is computed
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* no_rescale = do not rescale the work per processor to the measured total force-computation time
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@ -25,9 +25,9 @@ Examples
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.. code-block:: LAMMPS
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fix 2 all apip_atom_weight 50 eam ace lambda_input lambda/zone all
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fix 2 all apip_atom_weight 50 1e-05 0.0004 4e-06 4e-06 all
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fix 2 all apip_atom_weight 50 ace ace 4e-06 4e-06 all no_rescale
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fix 2 all atom_weight/apip 50 eam ace lambda/input lambda/zone all
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fix 2 all atom_weight/apip 50 1e-05 0.0004 4e-06 4e-06 all
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fix 2 all atom_weight/apip 50 ace ace 4e-06 4e-06 all no_rescale
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Description
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"""""""""""
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@ -44,10 +44,10 @@ and :doc:`pace/apip <pair_pace_apip>` is calculated only
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for a subset of atoms.
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The switching parameter that determines per atom, which potential energy is
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used, can be also calculated by
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:doc:`pair_style lambda_input <pair_lambda_input>`.
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:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
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A spatial switching zone, that ensures a smooth transition between two
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different interatomic potentials, can be calculated by
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:doc:`pair_style lambda/zone <pair_lambda_zone>`.
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:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
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Thus, there are up to four force-subroutines, that are computed only for a
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subset of atoms and combined via the pair_style :doc:`hybrid/overlay <pair_hybrid>`.
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For all four force-subroutines, the average work per atom is be measured
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@ -66,7 +66,7 @@ as input for :doc:`fix balance <fix_balance>`:
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.. code-block:: LAMMPS
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variable nevery equal 10
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fix weight_atom all apip_atom_weight ${nevery} eam ace lambda_input lambda/zone all
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fix weight_atom all atom_weight/apip ${nevery} eam ace lambda/input lambda/zone all
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variable myweight atom f_weight_atom
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fix balance all balance ${nevery} 1.1 rcb weight var myweight
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@ -94,8 +94,8 @@ values in the vector are as follows:
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#. average compute time for one atom using the fast pair_style
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#. average compute time for one atom using the precise pair_style
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#. average compute time of lambda_input for one atom
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#. average compute time of lambda/zone for one atom
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#. average compute time of lambda/input/apip for one atom
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#. average compute time of lambda/zone/apip for one atom
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The compute times are computed as average of all processors that
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measured at least one computation of the corresponding style.
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@ -124,10 +124,10 @@ Related commands
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""""""""""""""""
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:doc:`fix balance <fix_balance>`,
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:doc:`fix lambda <fix_lambda>`,
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:doc:`fix lambda_thermostat <fix_lambda_thermostat>`,
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:doc:`pair_style lambda/zone <pair_lambda_zone>`,
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:doc:`pair_style lambda_input <pair_lambda_input>`,
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:doc:`fix lambda/apip <fix_lambda_apip>`,
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:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
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:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
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:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
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:doc:`pair_style eam/apip <pair_eam_apip>`,
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:doc:`pair_style pace/apip <pair_pace_apip>`,
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@ -1,17 +1,17 @@
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.. index:: fix lambda
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.. index:: fix lambda/apip
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fix lambda command
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==============================
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fix lambda/apip command
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=======================
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID lambda thr_lo thr_hi keyword args ...
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fix ID group-ID lambda/apip thr_lo thr_hi keyword args ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* lambda = style name of this fix command
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* lambda/apip = style name of this fix command
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* thr_lo = value below which :math:`\lambda_i^\text{input}` results in a switching parameter of 1
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* thr_hi = value above which :math:`\lambda_i^\text{input}` results in a switching parameter of 0
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* zero or one keyword/args pairs may be appended
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@ -45,8 +45,8 @@ Examples
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.. code-block:: LAMMPS
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fix 2 all lambda 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
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fix 2 mobile lambda 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01 group_ignore_lambda_input immobile lambda_non_group fast
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fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
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fix 2 mobile lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01 group_ignore_lambda_input immobile lambda_non_group fast
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Description
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"""""""""""
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@ -63,7 +63,7 @@ according to a fast interatomic potential like EAM,
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interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
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switching parameter that decides which potential energy is used.
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This fix calculates the switching parameter :math:`\lambda_i` based on the
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input provided from :doc:`pair_style lambda_input <pair_lambda_input>`.
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input provided from :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
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The calculation of the switching parameter is described in detail in
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:ref:`(Immel) <Immel2025_3>`.
|
||||
@ -80,7 +80,7 @@ can be set via *time_averaged_zone*.
|
||||
.. note::
|
||||
|
||||
:math:`\lambda^\text{input}_{i}` is calculated by
|
||||
:doc:`pair_style lambda_input <pair_lambda_input>`, which needs to be included
|
||||
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`, which needs to be included
|
||||
in the input script as well.
|
||||
|
||||
The time averaged input :math:`\lambda^\text{input}_{\text{avg},i}` is then
|
||||
@ -131,7 +131,7 @@ neighboring atoms of atom :math:`i`.
|
||||
.. note::
|
||||
|
||||
:math:`\lambda_{\text{min},i}` is calculated by
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`, which needs to be included
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`, which needs to be included
|
||||
in the input script as well.
|
||||
|
||||
The switching parameter is smoothed by the calculation of the time average
|
||||
@ -173,21 +173,21 @@ A code example for the calculation of the switching parameter for an
|
||||
adaptive-precision potential is given in the following:
|
||||
The adaptive-precision potential is created
|
||||
by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
|
||||
and :doc:`pair_style pace/apip/precise <pair_pace_apip>`.
|
||||
and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
|
||||
The input, from which the switching parameter is calculated, is provided
|
||||
by :doc:`pair lambda_input/csp <pair_lambda_input>`.
|
||||
by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
|
||||
The switching parameter is calculated by this fix, whereas the spatial
|
||||
transition zone of the switching parameter is calculated by
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`.
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay eam/fs/apip pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda 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_precise.yace Cu
|
||||
pair_coeff * * lambda_input/csp
|
||||
pair_coeff * * lambda
|
||||
fix 2 all lambda 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
|
||||
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
|
||||
pair_coeff * * lambda/input/csp/apip
|
||||
pair_coeff * * lambda/zone/apip
|
||||
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
|
||||
|
||||
|
||||
----------
|
||||
@ -233,12 +233,12 @@ LAMMPS was built with that package. See the :doc:`Build package
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`,
|
||||
:doc:`pair_style lambda_input <pair_lambda_input>`,
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
|
||||
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
|
||||
:doc:`pair_style eam/apip <pair_eam_apip>`,
|
||||
:doc:`pair_style pace/apip <pair_pace_apip>`,
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`
|
||||
:doc:`fix lambda_thermostat <fix_lambda_thermostat>`,
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
|
||||
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -1,17 +1,17 @@
|
||||
.. index:: fix lambda_thermostat
|
||||
.. index:: fix lambda_thermostat/apip
|
||||
|
||||
fix lambda_thermostat command
|
||||
=============================
|
||||
fix lambda_thermostat/apip command
|
||||
==================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix ID group-ID lambda_thermostat keyword values ...
|
||||
fix ID group-ID lambda_thermostat/apip keyword values ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* lambda_thermostat = style name of this fix command
|
||||
* lambda_thermostat/apip = style name of this fix command
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *seed* or *store_atomic_forces* or *N_rescaling*
|
||||
|
||||
@ -29,10 +29,10 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 2 all lambda_thermostat
|
||||
fix 2 all lambda_thermostat N_rescaling 100
|
||||
fix 2 all lambda_thermostat seed 42
|
||||
fix 2 all lambda_thermostat seed 42 store_atomic_forces 1000
|
||||
fix 2 all lambda_thermostat/apip
|
||||
fix 2 all lambda_thermostat/apip N_rescaling 100
|
||||
fix 2 all lambda_thermostat/apip seed 42
|
||||
fix 2 all lambda_thermostat/apip seed 42 store_atomic_forces 1000
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -157,12 +157,12 @@ LAMMPS was built with that package. See the :doc:`Build package
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix lambda <fix_lambda>`,
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`,
|
||||
:doc:`pair_style lambda_input <pair_lambda_input>`,
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
|
||||
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
|
||||
:doc:`pair_style eam/apip <pair_eam_apip>`,
|
||||
:doc:`pair_style pace/apip <pair_pace_apip>`,
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -24,11 +24,11 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay eam/fs/apip pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda 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_precise.yace Cu
|
||||
pair_coeff * * lambda_input/csp
|
||||
pair_coeff * * lambda
|
||||
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
|
||||
pair_coeff * * lambda/input/csp/apip
|
||||
pair_coeff * * lambda/zone/apip
|
||||
|
||||
|
||||
Description
|
||||
@ -58,14 +58,14 @@ interatomic potential (APIP) according to :ref:`(Immel) <Immel2025_5>` is given
|
||||
E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
|
||||
|
||||
whereas the switching parameter :math:`\lambda_i` is computed
|
||||
dynamically during a simulation by :doc:`fix lambda <fix_lambda>`
|
||||
dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
|
||||
or set prior to a simulation via :doc:`set <set>`.
|
||||
|
||||
The pair style *eam/fs/apip* computes the potential energy
|
||||
:math:`\lambda_i E_i^\text{EAM}` and the
|
||||
corresponding force and should be combined
|
||||
with a precise potential like
|
||||
:doc:`pair_style pace/apip/precise <pair_pace_apip>` that computes the
|
||||
:doc:`pair_style pace/precise/apip <pair_pace_apip>` that computes the
|
||||
potential energy :math:`(1-\lambda_i) E_i^\text{(precise)}` and the
|
||||
corresponding force via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
|
||||
|
||||
@ -103,12 +103,12 @@ Related commands
|
||||
|
||||
:doc:`pair_style eam <pair_eam>`,
|
||||
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
|
||||
:doc:`fix lambda <fix_lambda>`,
|
||||
:doc:`fix lambda_thermostat <fix_lambda_thermostat>`,
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`,
|
||||
:doc:`pair_style lambda_input <pair_lambda_input>`,
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
|
||||
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
|
||||
:doc:`pair_style pace/apip <pair_pace_apip>`,
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -1,30 +1,30 @@
|
||||
.. index:: pair_style lambda_input
|
||||
.. index:: pair_style lambda_input/csp
|
||||
.. index:: pair_style lambda/input/apip
|
||||
.. index:: pair_style lambda/input/csp/apip
|
||||
|
||||
pair_style lambda_input command
|
||||
===============================
|
||||
pair_style lambda/input/apip command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lambda_input cutoff
|
||||
pair_style lambda/input/apip cutoff
|
||||
|
||||
* lambda_input = style name of this pair style
|
||||
* lambda/input/apip = style name of this pair style
|
||||
* cutoff = global cutoff (distance units)
|
||||
|
||||
pair_style lambda_input/csp command
|
||||
===================================
|
||||
pair_style lambda/input/csp/apip command
|
||||
========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lambda_input/csp lattice keyword args
|
||||
pair_style lambda/input/csp/apip lattice keyword args
|
||||
|
||||
* lambda_input/csp = style name of this pair style
|
||||
* lambda/input/csp/apip = style name of this pair style
|
||||
* lattice = *fcc* or *bcc* or integer
|
||||
|
||||
.. parsed-literal::
|
||||
@ -48,16 +48,16 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lambda_input/csp fcc
|
||||
pair_style lambda_input/csp fcc cutoff 5.0
|
||||
pair_style lambda_input/csp bcc cutoff 5.0 N_buffer 2
|
||||
pair_style lambda_input/csp 14
|
||||
pair_style lambda/input/csp/apip fcc
|
||||
pair_style lambda/input/csp/apip fcc cutoff 5.0
|
||||
pair_style lambda/input/csp/apip bcc cutoff 5.0 N_buffer 2
|
||||
pair_style lambda/input/csp/apip 14
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This pair_styles calculates :math:`\lambda_i^\text{input}(t)`, which
|
||||
is required for :doc:`fix lambda <fix_lambda>`.
|
||||
is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
|
||||
|
||||
The pair_style lambda_input sets :math:`\lambda_i^\text{input}(t) = 0`.
|
||||
|
||||
@ -74,30 +74,30 @@ the calculation of the contributions from the pair j,j+N/2 to the CSP as
|
||||
discussed in :ref:`(Immel) <Immel2025_6>`.
|
||||
|
||||
The computation of :math:`\lambda_i^\text{input}(t)` is done by this
|
||||
pair_style instead of by :doc:`fix lambda <fix_lambda>`, as this computation
|
||||
pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
|
||||
takes time and this pair_style can be included in the load-balancing via
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`.
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
|
||||
|
||||
A code example for the calculation of the switching parameter for an adaptive-
|
||||
precision potential is given in the following:
|
||||
The adaptive-precision potential is created
|
||||
by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
|
||||
and :doc:`pair_style pace/apip/precise <pair_pace_apip>`.
|
||||
and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
|
||||
The input, from which the switching parameter is calculated, is provided
|
||||
by this pair_style.
|
||||
The switching parameter is calculated by :doc:`fix lambda <fix_lambda>`,
|
||||
The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
whereas the spatial
|
||||
transition zone of the switching parameter is calculated by
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`.
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay eam/fs/apip pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda 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_precise.yace Cu
|
||||
pair_coeff * * lambda_input/csp
|
||||
pair_coeff * * lambda
|
||||
fix 2 all lambda 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
|
||||
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
|
||||
pair_coeff * * lambda/input/csp/apip
|
||||
pair_coeff * * lambda/zone/apip
|
||||
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
|
||||
|
||||
----------
|
||||
|
||||
@ -128,12 +128,12 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute centro/atom <compute_centro_atom>`,
|
||||
:doc:`fix lambda <fix_lambda>`,
|
||||
:doc:`fix lambda_thermostat <fix_lambda_thermostat>`,
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`,
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
|
||||
:doc:`pair_style eam/apip <pair_eam_apip>`,
|
||||
:doc:`pair_style pace/apip <pair_pace_apip>`,
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: pair_style lambda/zone
|
||||
.. index:: pair_style lambda/zone/apip
|
||||
|
||||
pair_style lambda/zone command
|
||||
==============================
|
||||
pair_style lambda/zone/apip command
|
||||
===================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lambda/zone cutoff
|
||||
pair_style lambda/zone/apip cutoff
|
||||
|
||||
* lambda/zone = style name of this pair style
|
||||
* lambda/zone/apip = style name of this pair style
|
||||
* cutoff = global cutoff (distance units)
|
||||
|
||||
Examples
|
||||
@ -18,52 +18,52 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lambda/zone 12.0
|
||||
pair_style lambda/zone/apip 12.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This pair_style calculates :math:`\lambda_{\text{min},i}`, which
|
||||
is required for :doc:`fix lambda <fix_lambda>`.
|
||||
is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
|
||||
The meaning of :math:`\lambda_{\text{min},i}` is documented in
|
||||
:doc:`fix lambda <fix_lambda>`, as this pair_style is for use with
|
||||
:doc:`fix lambda <fix_lambda>` only.
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>`, as this pair_style is for use with
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>` only.
|
||||
|
||||
This pair_style requires only the global cutoff as argument.
|
||||
The remaining quantities, that are required to calculate
|
||||
:math:`\lambda_{\text{min},i}` are extracted from
|
||||
:doc:`fix lambda <fix_lambda>` and, thus,
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>` and, thus,
|
||||
do not need to be passed to this pair_style as arguments.
|
||||
|
||||
.. warning::
|
||||
|
||||
The cutoff given as argument to this pair style is only relevant for the
|
||||
neighbor list creation. The radii, which define :math:`r_{\lambda,\text{hi}}` and :math:`r_{\lambda,\text{lo}}` are defined by :doc:`fix lambda <fix_lambda>`.
|
||||
neighbor list creation. The radii, which define :math:`r_{\lambda,\text{hi}}` and :math:`r_{\lambda,\text{lo}}` are defined by :doc:`fix lambda/apip <fix_lambda_apip>`.
|
||||
|
||||
The computation of :math:`\lambda_{\text{min},i}` is done by this
|
||||
pair_style instead of by :doc:`fix lambda <fix_lambda>`, as this computation
|
||||
pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
|
||||
takes time and this pair_style can be included in the load-balancing via
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`.
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
|
||||
|
||||
A code example for the calculation of the switching parameter for an
|
||||
adaptive-precision interatomic potential (APIP) is given in the following:
|
||||
The adaptive-precision potential is created
|
||||
by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
|
||||
and :doc:`pair_style pace/apip/precise <pair_pace_apip>`.
|
||||
and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
|
||||
The input, from which the switching parameter is calculated, is provided
|
||||
by :doc:`pair lambda_input/csp <pair_lambda_input>`.
|
||||
The switching parameter is calculated by :doc:`fix lambda <fix_lambda>`,
|
||||
by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
|
||||
The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
whereas the spatial transition zone of the switching parameter is calculated
|
||||
by this pair style.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
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_precise.yace Cu
|
||||
pair_coeff * * lambda_input/csp
|
||||
pair_coeff * * lambda/zone
|
||||
fix 2 all lambda 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
|
||||
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
|
||||
pair_coeff * * lambda/input/csp/apip
|
||||
pair_coeff * * lambda/zone/apip
|
||||
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
|
||||
|
||||
----------
|
||||
|
||||
@ -93,12 +93,12 @@ LAMMPS was built with that package. See the :doc:`Build package
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix lambda <fix_lambda>`,
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`
|
||||
:doc:`pair_style lambda_input <pair_lambda_input>`,
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
|
||||
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
|
||||
:doc:`pair_style eam/apip <pair_eam_apip>`,
|
||||
:doc:`pair_style pace/apip <pair_pace_apip>`,
|
||||
:doc:`fix lambda_thermostat <fix_lambda_thermostat>`,
|
||||
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -1,15 +1,15 @@
|
||||
.. index:: pair_style pace/apip
|
||||
.. index:: pair_style pace/apip/fast
|
||||
.. index:: pair_style pace/apip/precise
|
||||
.. index:: pair_style pace/fast/apip
|
||||
.. index:: pair_style pace/precise/apip
|
||||
|
||||
pair_style pace/apip command
|
||||
==============================
|
||||
============================
|
||||
|
||||
pair_style pace/apip/fast command
|
||||
===================================
|
||||
pair_style pace/fast/apip command
|
||||
=================================
|
||||
|
||||
pair_style pace/apip/precise command
|
||||
======================================
|
||||
pair_style pace/precise/apip command
|
||||
====================================
|
||||
|
||||
Constant precision variant: *pace*
|
||||
|
||||
@ -19,8 +19,8 @@ Syntax
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style pace/apip ... keyword values ...
|
||||
pair_style pace/apip/fast ... keyword values ...
|
||||
pair_style pace/apip/precise ... keyword values ...
|
||||
pair_style pace/fast/apip ... keyword values ...
|
||||
pair_style pace/precise/apip ... keyword values ...
|
||||
|
||||
* one or more keyword/value pairs may be appended
|
||||
|
||||
@ -33,17 +33,17 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay pace/apip/fast pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda 12.0
|
||||
pair_coeff * * pace/apip/fast Cu_fast.yace Cu
|
||||
pair_coeff * * pace/apip/precise Cu_precise.yace Cu
|
||||
pair_coeff * * lambda_input/csp
|
||||
pair_coeff * * lambda
|
||||
pair_style hybrid/overlay pace/fast/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
|
||||
pair_coeff * * pace/fast/apip Cu_fast.yace Cu
|
||||
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
|
||||
pair_coeff * * lambda/input/csp/apip
|
||||
pair_coeff * * lambda/zone/apip
|
||||
|
||||
pair_style hybrid/overlay eam/fs/apip pace/apip/precise lambda_input/csp fcc cutoff 5.0 lambda 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_precise.yace Cu
|
||||
pair_coeff * * lambda_input/csp
|
||||
pair_coeff * * lambda
|
||||
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
|
||||
pair_coeff * * lambda/input/csp/apip
|
||||
pair_coeff * * lambda/zone/apip
|
||||
|
||||
|
||||
Description
|
||||
@ -64,24 +64,24 @@ interatomic potential (APIP) according to
|
||||
E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
|
||||
|
||||
whereas the switching parameter :math:`\lambda_i` is computed
|
||||
dynamically during a simulation by :doc:`fix lambda <fix_lambda>`
|
||||
dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
|
||||
or set prior to a simulation via :doc:`set <set>`.
|
||||
|
||||
The pair style *pace/apip/precise* computes the potential energy
|
||||
The pair style *pace/precise/apip* computes the potential energy
|
||||
:math:`(1-\lambda_i) E_i^\text{(pace)}` and the
|
||||
corresponding force and should be combined
|
||||
with a fast potential that computes the potential energy
|
||||
:math:`\lambda_i E_i^\text{(fast)}` and the corresponding force
|
||||
via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
|
||||
|
||||
The pair style *pace/apip/fast* computes the potential energy
|
||||
The pair style *pace/fast/apip* computes the potential energy
|
||||
:math:`\lambda_i E_i^\text{(pace)}` and the
|
||||
corresponding force and should be combined
|
||||
with a precise potential that computes the potential energy
|
||||
:math:`(1-\lambda_i) E_i^\text{(precise)}` and the corresponding force
|
||||
via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
|
||||
|
||||
The pair_styles *pace/apip/fast* and *pace/apip/precise*
|
||||
The pair_styles *pace/fast/apip* and *pace/precise/apip*
|
||||
commands may be followed by the optional keywords of
|
||||
:doc:`pair_style pace <pair_pace>`, which are described
|
||||
:doc:`here <pair_pace>`.
|
||||
@ -120,12 +120,12 @@ Related commands
|
||||
|
||||
:doc:`pair_style pace <pair_pace>`,
|
||||
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
|
||||
:doc:`fix lambda <fix_lambda>`,
|
||||
:doc:`fix lambda_thermostat <fix_lambda_thermostat>`,
|
||||
:doc:`pair_style lambda/zone <pair_lambda_zone>`,
|
||||
:doc:`pair_style lambda_input <pair_lambda_input>`,
|
||||
:doc:`fix lambda/apip <fix_lambda_apip>`,
|
||||
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
|
||||
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
|
||||
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
|
||||
:doc:`pair_style eam/apip <pair_eam_apip>`,
|
||||
:doc:`fix apip_atom_weight <fix_apip_atom_weight>`
|
||||
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -219,9 +219,9 @@ accelerated styles exist.
|
||||
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
|
||||
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
|
||||
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
|
||||
* :doc:`lambda/zone <pair_lambda_zone>` - transition zone of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
|
||||
* :doc:`lambda_input <pair_lambda_input>` - constant as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
|
||||
* :doc:`lambda_input/csp <pair_lambda_input>` - CSP as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
|
||||
* :doc:`lambda/input/apip <pair_lambda_input_apip>` - constant as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
|
||||
* :doc:`lambda/input/csp/apip <pair_lambda_input_apip>` - CSP as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
|
||||
* :doc:`lambda/zone/apip <pair_lambda_zone_apip>` - transition zone of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
|
||||
* :doc:`lcbop <pair_lcbop>` - long-range bond-order potential (LCBOP)
|
||||
* :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis
|
||||
* :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function
|
||||
@ -335,8 +335,8 @@ accelerated styles exist.
|
||||
* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
|
||||
* :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
|
||||
* :doc:`pace/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
|
||||
* :doc:`pace/apip/fast <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as fast potential
|
||||
* :doc:`pace/apip/precise <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
|
||||
* :doc:`pace/fast/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as fast potential
|
||||
* :doc:`pace/precise/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
|
||||
* :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential (non-Coulomb part)
|
||||
* :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
|
||||
* :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential
|
||||
|
||||
@ -32,7 +32,7 @@ Syntax
|
||||
*volume* or *image* or *bond* or *angle* or *dihedral* or
|
||||
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
|
||||
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
|
||||
*edpd/temp* or *edpd/cv* or *cc* or *epsilon* or *lambda* or
|
||||
*edpd/temp* or *edpd/cv* or *cc* or *epsilon* or *apip_lambda* or
|
||||
*i_name* or *d_name* or *i2_name* or *d2_name*
|
||||
|
||||
.. parsed-literal::
|
||||
@ -143,7 +143,7 @@ Syntax
|
||||
index = index of a chemical species (1 to Nspecies)
|
||||
cc = chemical concentration of tDPD particles for a species (mole/volume units)
|
||||
*epsilon* value = dielectric constant of the medium where the atoms reside
|
||||
*lambda* value = fast or precise or float
|
||||
*apip_lambda* value = fast or precise or float
|
||||
fast = switching parameter of fast potential (1) (APIP package)
|
||||
precise = switching parameter of fast potential (0) (APIP package)
|
||||
float = constant float or atom-style variable (between 0 and 1) (APIP package)
|
||||
@ -573,7 +573,7 @@ charges, one needs to use the set command with the *charge*
|
||||
keyword. Care must be taken to ensure that the real and scaled charges,
|
||||
and dielectric constants are consistent.
|
||||
|
||||
Keyword *lambda* sets the switching parameter of an
|
||||
Keyword *apip_lambda* sets the switching parameter of an
|
||||
adaptive-precision interatomic potential (:doc:`APIP <Howto_apip>`).
|
||||
The precise potential is used for an atom when its switching parameter
|
||||
:math:`\lambda` is 0. The fast potential is used for an atom when its
|
||||
|
||||
Reference in New Issue
Block a user