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Kokkos versions of bispectrum and Gaussian descriptors on grid
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| Original file line number | Diff line number | Diff line change |
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| .. index:: compute gaussian/grid/local | ||
| .. index:: compute gaussian/grid/local/kk | ||
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| compute gaussian/grid/local command | ||
| =================================== | ||
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| Accelerator Variants: *gaussian/grid/local/kk* | ||
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| Syntax | ||
| """""" | ||
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| .. code-block:: LAMMPS | ||
| compute ID group-ID gaussian/grid/local grid nx ny nz rcutfac R_1 R_2 ... sigma_1 sigma_2 | ||
| * ID, group-ID are documented in :doc:`compute <compute>` command | ||
| * gaussian/grid/local = style name of this compute command | ||
| * *grid* values = nx, ny, nz, number of grid points in x, y, and z directions (positive integer) | ||
| * *rcutfac* = scale factor applied to all cutoff radii (positive real) | ||
| * *R_1, R_2,...* = list of cutoff radii, one for each type (distance units) | ||
| * *sigma_1, sigma_2,...* = Gaussian widths, one for each type (distance units) | ||
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| Examples | ||
| """""""" | ||
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| .. code-block:: LAMMPS | ||
| compute mygrid all gaussian/grid/local grid 40 40 40 4.0 0.5 0.5 0.4 0.4 | ||
| Description | ||
| """"""""""" | ||
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| Define a computation that calculates a Gaussian representation of the ionic | ||
| structure. This representation is used for the efficient evaluation | ||
| of quantities related to the structure factor in a grid-based workflow, | ||
| such as the ML-DFT workflow MALA :ref:`(Ellis) <Ellis2021b>`, for which it was originally | ||
| implemented. Usage of the workflow is described in a separate publication :ref:`(Fiedler) <Fiedler2023>`. | ||
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| For each LAMMPS type, a separate sum of Gaussians is calculated, using | ||
| a separate Gaussian broadening per type. The computation | ||
| is always performed on the numerical grid, no atom-based version of this | ||
| compute exists. The Gaussian representation can only be executed in a local | ||
| fashion, thus the output array only contains rows for grid points | ||
| that are local to the processor subdomain. The layout of the grid is the same | ||
| as for the see :doc:`sna/grid/local <compute_sna_atom>` command. | ||
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| Namely, 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 values of the Gaussians | ||
| (one floating point number per type per grid point). | ||
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| ---------- | ||
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| .. include:: accel_styles.rst | ||
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| ---------- | ||
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| Output info | ||
| """"""""""" | ||
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| Compute *gaussian/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. The array contains math :math:`ntypes+6` columns, | ||
| where *ntypes* is the number of LAMMPS types. The first three columns are | ||
| the global indexes *ix*, *iy*, and *iz*, followed by the *x*, *y*, | ||
| and *z* coordinates of the grid point, followed by the *ntypes* columns | ||
| containing the values of the Gaussians for each type. | ||
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| Restrictions | ||
| """""""""""" | ||
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| These computes are part of the ML-SNAP package. They are only enabled | ||
| if LAMMPS was built with that package. See the :doc:`Build package | ||
| <Build_package>` page for more info. | ||
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| Related commands | ||
| """""""""""""""" | ||
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| :doc:`compute sna/grid/local <compute_sna_atom>` | ||
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| ---------- | ||
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| .. _Ellis2021b: | ||
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| **(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, `Phys. Rev. B, 104, 035120, (2021) <https://doi.org/10.1103/PhysRevB.104.035120>`_ | ||
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| .. _Fiedler2023: | ||
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| **(Fiedler)** Fiedler, Modine, Schmerler, Vogel, Popoola, Thompson, Rajamanickam, and Cangi, | ||
| `npj Comp. Mater., 9, 115 (2023) <https://doi.org/10.1038/s41524-023-01070-z>`_ | ||
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| # Demonstrate calculation of Gaussian descriptors on a grid | ||
| # for a cell with two atoms of type 1 and type 2. | ||
| # The output in dump.glocal shows that for grid points | ||
| # sitting on an atom of type 1 or 2: | ||
| # val1 = 1.0/(0.1355*sqrt(2.0*pi))**3 = 25.5219 | ||
| # val2 = 1.0/(0.2 *sqrt(2.0*pi))**3 = 7.93670 | ||
| # These values are extracted to the log file | ||
| # | ||
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| variable nrep index 1 | ||
| variable a index 3.316 | ||
| variable ngrid index 2 | ||
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| units metal | ||
| atom_modify map hash | ||
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| # generate the box and atom positions using a BCC lattice | ||
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| variable nx equal ${nrep} | ||
| variable ny equal ${nrep} | ||
| variable nz equal ${nrep} | ||
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| boundary p p p | ||
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| lattice custom $a & | ||
| a1 1 0 0 & | ||
| a2 0 1 0 & | ||
| a3 0 0 1 & | ||
| basis 0 0 0 & | ||
| basis 0.5 0.5 0.5 & | ||
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| region box block 0 ${nx} 0 ${ny} 0 ${nz} | ||
| create_box 2 box | ||
| create_atoms 1 box basis 1 1 basis 2 2 | ||
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| mass * 180.88 | ||
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| # define atom compute and grid compute | ||
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| variable rcutfac equal 4.67637 | ||
| variable radelem1 equal 0.5 | ||
| variable radelem2 equal 0.5 | ||
| variable sigmaelem1 equal 0.1355 | ||
| variable sigmaelem2 equal 0.2 | ||
| variable gaussian_options string & | ||
| "${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}" | ||
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| # build zero potential to force ghost atom creation | ||
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| pair_style zero ${rcutfac} | ||
| pair_coeff * * | ||
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| # define atom and grid computes | ||
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| compute mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} & | ||
| ${gaussian_options} | ||
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| # define output | ||
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| dump 1 all local 1000 dump.glocal c_mygridlocal[*] | ||
| dump 2 all custom 1000 dump.gatom id x y z | ||
| compute val1 all reduce max c_mygridlocal[7] inputs local | ||
| compute val2 all reduce max c_mygridlocal[8] inputs local | ||
| thermo_style custom step c_val1 c_val2 | ||
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| # run | ||
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| run 0 |
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