remove docs for unexisting command compute pace/extrapolation
This commit is contained in:
Yury Lysogorskiy
@ -96,7 +96,6 @@ KOKKOS, o = OPENMP, t = OPT.
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* :doc:`nbond/atom <compute_nbond_atom>`
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* :doc:`omega/chunk <compute_omega_chunk>`
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* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
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* :doc:`pace/extrapolation <compute_pace_extrapolation>`
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* :doc:`pair <compute_pair>`
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* :doc:`pair/local <compute_pair_local>`
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* :doc:`pe <compute_pe>`
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@ -240,7 +240,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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* :doc:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
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* :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
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* :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
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* :doc:`pace/extrapolation <compute_pace_extrapolation>` - calculate extrapolation grade for pair style pace/extrapolation
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* :doc:`pair <compute_pair>` - values computed by a pair style
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* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
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* :doc:`pe <compute_pe>` - potential energy
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@ -1,69 +0,0 @@
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.. index:: compute pace/extrapolation
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compute pace/extrapolation command
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==================================
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Syntax
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""""""
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.. parsed-literal::
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compute ID all pace/extrapolation
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* ID is documented in :doc:`compute <compute>` command
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* pace/extrapolation = style name of this compute command
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute pace_gamma all pace/extrapolation
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Description
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"""""""""""
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Define a computation that calculates both per-atom and per-structure extrapolation grades for PACE interatomic potential.
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Pair style :doc:`pair_style pace/extrapolation <pair_pace>` must be instantiated before.
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Extrapolation grades are computed by `pair_style pace/extrapolation` every *gamma_freq* steps (see :doc:`pair_style pace/extrapolation <pair_pace>`),
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but `compute pace/extrapolation` will invoke extra calculations with this pair style if necessary.
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For better performance, it is recommended to use the same values of *gamma_freq* and
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the frequency of compute style callers, i.e. `dump` or `thermo`.
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.. code-block:: LAMMPS
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compute pace_gamma all pace/extrapolation
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# per-structure extrapolation grade c_pace_gamma
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thermo_style custom step etotal temp press c_pace_gamma
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# per-atom extrapolation grade c_pace_gamma
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dump 1 all custom 100 my.dump id type mass x y z c_pace_gamma
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Output info
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"""""""""""
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This compute calculates both per-atom vector and per-structure scalar,
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which can be accessed by any command that uses per-atom and/or per-structure values from a compute as input.
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See the :doc:`Howto output <Howto_output>` page for an overview of
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LAMMPS output options.
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All values are unitless.
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Restrictions
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""""""""""""
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Pair style :doc:`pair_style pace/extrapolation <pair_pace>` must be instantiated before.
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group-ID always corresponds to the group atoms used by `pair_style pace/extrapolation` and by default is `all`.
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Related commands
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""""""""""""""""
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:doc:`pair_style pace/extrapolation <pair_pace>`, :doc:`dump custom <dump>`, :doc:`thermo custom <thermo>`
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Default
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"""""""
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`compute pace_gamma all pace/extrapolation`
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@ -1,45 +0,0 @@
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.. index:: dump pace/extrapolation
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dump pace/extrapolation command
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================================
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Syntax
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""""""
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.. parsed-literal::
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dump ID group-ID pace/extrapolation N file args
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* ID = user-assigned name for the dump
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* group-ID = ID of the group of atoms to be dumped
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* N = dump every this many timesteps (use 1 to potentially dump on every step, see below)
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* file = name of file to write dump info to
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* args = list of arguments (see :doc:`dump custom <dump>`)
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Examples
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""""""""
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.. code-block:: LAMMPS
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dump pace all pace/extrapolation 1 extrapolation.dat id type mass x y z c_pace_gamma
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dump pace all pace/extrapolation 1 extrapolation.lammpsbin id type mass x y z c_pace_gamma
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Description
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"""""""""""
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Dump a snapshot of atom coordinates if extrapolation grade, computed by
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:doc:`compute pace/extrapolation <compute_pace_extrapolation>`, exceeds *gamma_lower_bound* threshold,
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provided in :doc:`pair_style pace/extrapolation <pair_pace>`.
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.. note::
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To be able to use this dump, you need to setup :doc:`pair_style pace/extrapolation <pair_pace>`
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and :doc:`compute pace/extrapolation <compute_pace_extrapolation>` beforehand
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----------
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Related commands
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""""""""""""""""
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:doc:`pair_style pace/extrapolation <pair_pace>`, :doc:`compute pace/extrapolation <compute_pace_extrapolation>`
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@ -28,14 +28,7 @@ Syntax
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.. code-block:: LAMMPS
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pair_style pace/extrapolation gamma_lower_bound gamma_upper_bound gamma_freq
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* one or more arguments may be appended
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.. parsed-literal::
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*gamma_lower_bound* = minimal value of extrapolation grade considered as moderate extrapolation
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*gamma_upper_bound* = maximal value of extrapolation grade considered as moderate extrapolation
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*gamma_freq* value = frequency of computing extrapolation grade (in steps)
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pair_style pace/extrapolation
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Examples
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""""""""
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@ -46,7 +39,7 @@ Examples
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pair_style pace product chunksize 2048
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pair_coeff * * Cu-PBE-core-rep.ace Cu
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pair_style pace/extrapolation 1.5 10 20
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pair_style pace/extrapolation
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pair_coeff * * Cu.yaml Cu.asi Cu
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Description
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@ -106,37 +99,32 @@ In order to compute extrapolation grade one needs to provide:
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#. Active Set Inverted (ASI) file for corresponding potential (`.asi` format)
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Calculation of extrapolation grades requires matrix-vector multiplication for each atom
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and can be slower than the usual `pair_style pace recursive`,
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therefore it make sense *not* to do it on every step.
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Extrapolation grade calculation frequency is controlled by *gamma_freq* parameter.
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On all other steps `pair_style pace recursive` is used.
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The maximal value of *gamma* for all atoms in a structure determines the extrapolation grade for structure.
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Both per-atom and per-structure extrapolation grades are accessible via `compute pace/extrapolation`:
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and is slower than the usual `pair_style pace recursive`, therefore it is *not* computed by default.
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Extrapolation grade calculation is involved by `fix pair`, which requests to compute `gamma`, as shown in example below:
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.. code-block:: LAMMPS
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compute pace_gamma all pace/extrapolation
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pair_style pace/extrapolation
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pair_coeff * * Cu.yaml Cu.asi Cu
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# show maximal extrapolation grade per-structure
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thermo_style custom step etotal temp press c_pace_gamma
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fix pace_gamma all pair 10 pace/extrapolation gamma 1
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# dump structure with per-atom extrapolation grades
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dump 1 all custom 100 my.dump id type mass x y z c_pace_gamma
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If maximal extrapolation grade per-structure exceeds *gamma_lower_bound* but less than *gamma_upper_bound*,
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the structure is considered as extrapolative and can be stored with `dump pace/extrapolation`:
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.. code-block:: LAMMPS
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compute pace_gamma all pace/extrapolation
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dump pace all pace/extrapolation 1 extrapolation.dat id type mass x y z c_pace_gamma
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Please note, that even if you provide dump frequency equal to one, dump will write structure
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only if extrapolation grades are computed on current timestep *and* maximal extrapolation grade exceeds *gamma_lower_bound*.
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If extrapolation grade exceeds *gamma_upper_bound*, simulation will be aborted.
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compute max_pace_gamma all reduce max f_pace_gamma
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variable dump_skip equal "c_max_pace_gamma < 5"
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dump pace_dump all custom 20 extrapolative_structures.dump id x y z f_pace_gamma
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dump_modify pace_dump skip v_dump_skip
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variable max_pace_gamma equal c_max_pace_gamma
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fix extreme_extrapolation all halt 10 v_max_pace_gamma > 25
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Here extrapolation grade gamma is computed every 10 steps and is stored in `f_pace_gamma` per-atom variable.
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The largest value of extrapolation grade among all atoms in a structure is reduced to `c_max_pace_gamma` variable.
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Only if this value exceeds extrapolation threshold 5, then the structure will be dumped into `extrapolative_structures.dump`
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file, but not more often than every 20 steps.
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On all other steps `pair_style pace recursive` will be used.
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----------
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@ -179,16 +167,12 @@ Related commands
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""""""""""""""""
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:doc:`pair_style snap <pair_snap>`,
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:doc:`compute pace/extrapolation <compute_pace_extrapolation>`,
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:doc:`dump pace/extrapolation <dump_pace_extrapolation>`,
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:doc:`fix pair <fix_pair>`
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Default
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"""""""
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recursive, chunksize = 4096,
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gamma_lower_bound = 1.5,
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gamma_upper_bound = 10,
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gamma_freq = 1
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.. _Drautz20191:
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