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Completed inner cutoff, KOKKOS still in progress

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This commit is contained in:
Aidan Thompson
2022-04-21 17:30:12 -06:00
parent e8cacc4380
commit 4de9ab85ce
17 changed files with 286 additions and 188 deletions
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21
doc/src/compute_sna_atom.rst
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@ -33,7 +33,7 @@ Syntax
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
* w_1, w_2,... = list of neighbor weights, one for each type
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag*
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner*
.. parsed-literal::
@ -59,8 +59,12 @@ Syntax
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = per-atom bispectrum descriptors are summed over atoms
*1* = per-atom bispectrum descriptors are not summed over atoms
*switchinnerflag* values = *sinnerlist* *dinnerlist*
*switchinnerflag* value = *0* or *1*
*0* = do not use inner switching function
*1* = use inner switching function
*sinner* values = *sinnerlist*
*sinnerlist* = *ntypes* values of *Sinner* (distance units)
*dinner* values = *dinnerlist*
*dinnerlist* = *ntypes* values of *Dinner* (distance units)
Examples
@ -73,7 +77,7 @@ Examples
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
compute snap all snap 1.4 0.95 6 2.0 1.0
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1.35 1.6 0.25 0.3
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3
Description
"""""""""""
@ -312,7 +316,8 @@ the resulting bispectrum rows are :math:`B_{i,k}` instead of just
:math:`B_k`. In this case, the entries in the final column for these rows
are set to zero.
The keyword *switchinnerflag* activates an additional radial switching
The keyword *switchinnerflag* with value 1
activates an additional radial switching
function similar to :math:`f_c(r)` above, but acting to switch off
smoothly contributions from neighbor atoms at short separation distances.
This is useful when SNAP is used in combination with a simple
@ -328,9 +333,9 @@ factor :math:`f_{inner}(r)` defined as follows:
where the switching region is centered at :math:`S_{inner}` and it extends a distance :math:`D_{inner}`
to the left and to the right of this.
The keyword is followed by the *ntypes*
values for :math:`S_{inner}` and the *ntypes*
values for :math:`D_{inner}`.
With this option, additional keywords *sinner* and *dinner* must be used,
each followed by *ntypes*
values for :math:`S_{inner}` and :math:`D_{inner}`, respectively.
When the central atom and the neighbor atom have different types,
the values of :math:`S_{inner}` and :math:`D_{inner}` are
the arithmetic means of the values for both types.
@ -453,7 +458,7 @@ Default
The optional keyword defaults are *rmin0* = 0,
*switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0,
*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = off,
*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = 0,
----------

4
doc/src/pair_snap.rst
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@ -136,7 +136,7 @@ keyword/value pair. The required keywords are *rcutfac* and
*twojmax*\ . Optional keywords are *rfac0*, *rmin0*,
*switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*,
*bnormflag*, *wselfallflag*, *switchinnerflag*,
*Sinner*, *Dinner*, *chunksize*, and *parallelthresh*\ .
*sinner*, *dinner*, *chunksize*, and *parallelthresh*\ .
The default values for these keywords are
@ -197,7 +197,7 @@ pair_coeff command, to avoid ambiguity in the number of coefficients.
The keyword *switchinnerflag* activates an additional switching function
that smoothly turns off contributions to the SNAP potential from neighbor
atoms at short separations. If *switchinnerflag* is set to 1 then
the additional keywords *Sinner* and *Dinner* must also be provided.
the additional keywords *sinner* and *dinner* must also be provided.
Each of these is followed by *nelements* values, where *nelements*
is the number of unique elements appearing in appearing in the LAMMPS
pair_coeff command. The element order should correspond to the order