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Merge pull request #3597 from lammps/dump-grid-dimension

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Add ITEM: DIMENSION to dump grid output
This commit is contained in:
Axel Kohlmeyer
2023-01-13 17:42:35 -05:00
committed by GitHub
parent b3396f109b 651e95654c
commit acb59c8b74
2 changed files with 25 additions and 11 deletions
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32
doc/src/dump.rst
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@ -363,22 +363,32 @@ attributes is given below.
.. versionadded:: 22Dec2022 .. versionadded:: 22Dec2022
For style *grid* the extent of the Nx by Ny by Nz grid that overlays For style *grid* the dimension of the simulation domain and size of
the simulation domain is output with each snapshot: the Nx by Ny by Nz grid that overlays the simulation domain are also
output with each snapshot:
.. parsed-literal:: .. parsed-literal::
ITEM: GRID EXTENT ITEM: DIMENSION
dim
ITEM: GRID SIZE
nx ny nz nx ny nz
For 2d simulations, nz will be 1. There will also be an "ITEM: GRID The value dim will be 2 or 3 for 2d or 3d simulations. It is included
DATA" line which includes column descriptors for the per grid cell so that post-processing tools like `OVITO <https://www.ovito.org>`,
data. Each subsequent line (Nx * Ny * Nz lines) will list the data which can visualize grid-based quantities know how to draw each grid
for a single grid cell. If grid cell IDs are included in the output cell. The grid size will match the input script parameters for
via the :doc:`compute property/grid <compute_property_grid>` command, grid(s) created by the computes or fixes which are referenced by the
then the IDs will range from 1 to N = Nx*Ny*Nz. The ordering of IDs the dump command. For 2d simulations (and grids), nz will always
is with the x index varying fastest, then the y index, and the z index be 1.
varying slowest.
There will also be an "ITEM: GRID DATA" line which includes column
descriptors for the per grid cell data. Each subsequent line (Nx *
Ny * Nz lines) will list the data for a single grid cell. If grid
cell IDs are included in the output via the :doc:`compute
property/grid <compute_property_grid>` command, then the IDs will
range from 1 to N = Nx*Ny*Nz. The ordering of IDs is with the x index
varying fastest, then the y index, and the z index varying slowest.
For style *local*, local output generated by :doc:`computes <compute>` For style *local*, local output generated by :doc:`computes <compute>`
and :doc:`fixes <fix>` is used to generate lines of output that is and :doc:`fixes <fix>` is used to generate lines of output that is

4
src/dump_grid.cpp
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@ -377,6 +377,7 @@ void DumpGrid::header_binary(bigint ndump)
fwrite(&boxyhi,sizeof(double),1,fp); fwrite(&boxyhi,sizeof(double),1,fp);
fwrite(&boxzlo,sizeof(double),1,fp); fwrite(&boxzlo,sizeof(double),1,fp);
fwrite(&boxzhi,sizeof(double),1,fp); fwrite(&boxzhi,sizeof(double),1,fp);
fwrite(&domain->dimension,sizeof(int),1,fp);
fwrite(&nxgrid,sizeof(int),1,fp); fwrite(&nxgrid,sizeof(int),1,fp);
fwrite(&nygrid,sizeof(int),1,fp); fwrite(&nygrid,sizeof(int),1,fp);
fwrite(&nzgrid,sizeof(int),1,fp); fwrite(&nzgrid,sizeof(int),1,fp);
@ -409,6 +410,7 @@ void DumpGrid::header_binary_triclinic(bigint ndump)
fwrite(&boxxy,sizeof(double),1,fp); fwrite(&boxxy,sizeof(double),1,fp);
fwrite(&boxxz,sizeof(double),1,fp); fwrite(&boxxz,sizeof(double),1,fp);
fwrite(&boxyz,sizeof(double),1,fp); fwrite(&boxyz,sizeof(double),1,fp);
fwrite(&domain->dimension,sizeof(int),1,fp);
fwrite(&nxgrid,sizeof(int),1,fp); fwrite(&nxgrid,sizeof(int),1,fp);
fwrite(&nygrid,sizeof(int),1,fp); fwrite(&nygrid,sizeof(int),1,fp);
fwrite(&nzgrid,sizeof(int),1,fp); fwrite(&nzgrid,sizeof(int),1,fp);
@ -438,6 +440,7 @@ void DumpGrid::header_item(bigint /*ndump*/)
"{:>1.16e} {:>1.16e}\n" "{:>1.16e} {:>1.16e}\n"
"{:>1.16e} {:>1.16e}\n", "{:>1.16e} {:>1.16e}\n",
boundstr,boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi); boundstr,boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi);
fmt::print(fp,"ITEM: DIMENSION\n{}\n",domain->dimension);
fmt::print(fp,"ITEM: GRID SIZE nx ny nz\n{} {} {}\n",nxgrid,nygrid,nzgrid); fmt::print(fp,"ITEM: GRID SIZE nx ny nz\n{} {} {}\n",nxgrid,nygrid,nzgrid);
fmt::print(fp,"ITEM: GRID CELLS {}\n",columns); fmt::print(fp,"ITEM: GRID CELLS {}\n",columns);
} }
@ -458,6 +461,7 @@ void DumpGrid::header_item_triclinic(bigint /*ndump*/)
"{:>1.16e} {:>1.16e} {:>1.16e}\n" "{:>1.16e} {:>1.16e} {:>1.16e}\n"
"{:>1.16e} {:>1.16e} {:>1.16e}\n", "{:>1.16e} {:>1.16e} {:>1.16e}\n",
boundstr,boxxlo,boxxhi,boxxy,boxylo,boxyhi,boxxz,boxzlo,boxzhi,boxyz); boundstr,boxxlo,boxxhi,boxxy,boxylo,boxyhi,boxxz,boxzlo,boxzhi,boxyz);
fmt::print(fp,"ITEM: DIMENSION\n{}\n",domain->dimension);
fmt::print(fp,"ITEM: GRID SIZE nx ny nz\n{} {} {}\n",nxgrid,nygrid,nzgrid); fmt::print(fp,"ITEM: GRID SIZE nx ny nz\n{} {} {}\n",nxgrid,nygrid,nzgrid);
fmt::print(fp,"ITEM: GRID CELLS {}\n",columns); fmt::print(fp,"ITEM: GRID CELLS {}\n",columns);
} }