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Merge pull request #3305 from athomps/compute-grid-new

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Compute grid for ML-SNAP
This commit is contained in:
Axel Kohlmeyer
2022-06-28 09:00:38 -04:00
committed by GitHub
parent ae18e1e01c a9f3108f29
commit f65bc76326
29 changed files with 2732 additions and 358 deletions
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2
doc/src/Commands_compute.rst
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@ -138,6 +138,8 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`smd/vol <compute_smd_vol>`
* :doc:`snap <compute_sna_atom>`
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`sna/grid <compute_sna_atom>`
* :doc:`sna/grid/local <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`

6
doc/src/Errors_warnings.rst
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@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations.
*More than one compute sna/atom*
Self-explanatory.
*More than one compute sna/grid*
Self-explanatory.
*More than one compute sna/grid/local*
Self-explanatory.
*More than one compute snad/atom*
Self-explanatory.

2
doc/src/Packages_details.rst
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@ -1801,6 +1801,8 @@ computes which analyze attributes of the potential.
* src/ML-SNAP: filenames -> commands
* :doc:`pair_style snap <pair_snap>`
* :doc:`compute sna/atom <compute_sna_atom>`
* :doc:`compute sna/grid <compute_sna_atom>`
* :doc:`compute sna/grid/local <compute_sna_atom>`
* :doc:`compute snad/atom <compute_sna_atom>`
* :doc:`compute snav/atom <compute_sna_atom>`
* examples/snap

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doc/src/compute.rst
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@ -284,6 +284,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
* :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
* :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
* :doc:`sph/e/atom <compute_sph_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms

77
doc/src/compute_sna_atom.rst
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@ -2,6 +2,8 @@
.. index:: compute snad/atom
.. index:: compute snav/atom
.. index:: compute snap
.. index:: compute sna/grid
.. index:: compute sna/grid/local
compute sna/atom command
========================
@ -15,6 +17,12 @@ compute snav/atom command
compute snap command
====================
compute sna/grid command
========================
compute sna/grid/local command
==============================
Syntax
""""""
@ -24,6 +32,9 @@ Syntax
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID sna/grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID sna/grid/local nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* sna/atom = style name of this compute command
@ -32,6 +43,7 @@ Syntax
* twojmax = band limit for bispectrum components (non-negative integer)
* 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
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* 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* or *sinner* or *dinner*
@ -78,6 +90,7 @@ Examples
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 sinner 1.35 1.6 dinner 0.25 0.3
compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0
Description
"""""""""""
@ -212,6 +225,46 @@ command:
See section below on output for a detailed explanation of the data
layout in the global array.
The compute *sna/grid* and *sna/grid/local* commands calculate
bispectrum components for a regular grid of points.
These are calculated from the local density of nearby atoms *i'*
around each grid point, as if there was a central atom *i*
at the grid point. This is useful for characterizing fine-scale
structure in a configuration of atoms, and it is used
in the `MALA package <https://github.com/casus/mala>`_
to build machine-learning surrogates for finite-temperature Kohn-Sham
density functional theory (:ref:`Ellis et al. <Ellis2021>`)
Neighbor atoms not in the group do not contribute to the
bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}`
assumes that *i* has the same type as the neighbor atom *i'*.
Compute *sna/grid* calculates a global array containing bispectrum
components for a regular grid of points.
The grid is aligned with the current box dimensions, with the
first point at the box origin, and forming a regular 3d array with
*nx*, *ny*, and *nz* points in the x, y, and z directions. For triclinic
boxes, the array is congruent with the periodic lattice vectors
a, b, and c. The array contains one row for each of the
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components. See section below on output for a detailed explanation of the data
layout in the global array.
Compute *sna/grid/local* calculates bispectrum components of a regular
grid of points similarly to compute *sna/grid* described above.
However, because the array is local, it contains only rows for grid points
that are local to the processor sub-domain. The global grid
of :math:`nx \times ny \times nz` points is still laid out in space the same as for *sna/grid*,
but grid points are strictly partitioned, so that every grid point appears in
one and only one local array. The array contains one row for each of the
local grid points, looping over the global index *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains
the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components. See section below on output for a detailed explanation of the data
layout in the global array.
The value of all bispectrum components will be zero for atoms not in
the group. Neighbor atoms not in the group do not contribute to the
bispectrum of atoms in the group.
@ -414,6 +467,21 @@ number of columns in the global array generated by *snap* are 31, and
931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N*
is the total number of atoms.
Compute *sna/grid* evaluates a global array.
The array contains one row for each of the
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components.
Compute *sna/grid/local* evaluates a local array.
The array contains one row for each of the
local grid points, looping over the global index *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains
the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components.
If the *quadratic* keyword value is set to 1, then additional columns
are generated, corresponding to the products of all distinct pairs of
bispectrum components. If the number of bispectrum components is *K*,
@ -464,8 +532,7 @@ The optional keyword defaults are *rmin0* = 0,
.. _Thompson20141:
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316, (2015).
.. _Bartok20101:
@ -486,4 +553,8 @@ of Angular Momentum, World Scientific, Singapore (1987).
.. _Cusentino2020:
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
**(Cusentino)** Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
.. _Ellis2021:
**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)