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disable certain options in fix ttm/grid for distributed grids

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This commit is contained in:
Steve Plimpton
2022-08-30 16:00:13 -06:00
parent ac2cf8c4ed
commit f2b6027b02
5 changed files with 52 additions and 111 deletions
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3
doc/src/fix_ave_grid.rst
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@ -479,4 +479,5 @@ Related commands
Default
"""""""
The option defaults are norm = all, ave = one, and bias = none.
The option defaults are discard = yes, norm = all, ave = one, and bias
= none.

64
doc/src/fix_ttm.rst
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@ -183,19 +183,22 @@ embedded within a larger continuum representation of the electronic
subsystem.
The *set* keyword specifies a *Tinit* temperature value to initialize
the value stored on all grid points.
the value stored on all grid points. By default the temperatures
are all zero when the grid is created.
The *infile* keyword specifies an input file of electronic temperatures
for each grid point to be read in to initialize the grid. By default
the temperatures are all zero when the grid is created. The input file
is a text file which may have comments starting with the '#' character.
Each line contains four numeric columns: ix,iy,iz,Temperature. Empty
or comment-only lines will be ignored. The
number of lines must be equal to the number of user-specified grid
points (Nx by Ny by Nz). The ix,iy,iz are grid point indices ranging
from 0 to nxnodes-1 inclusive in each dimension. The lines can appear
in any order. For example, the initial electronic temperatures on a 1
by 2 by 3 grid could be specified in the file as follows:
for each grid point to be read in to initialize the grid, as an alternative
to using the *set* keyword.
The input file is a text file which may have comments starting with
the '#' character. Each line contains four numeric columns:
ix,iy,iz,Temperature. Empty or comment-only lines will be
ignored. The number of lines must be equal to the number of
user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are grid
point indices ranging from 0 to nxnodes-1 inclusive in each dimension.
The lines can appear in any order. For example, the initial
electronic temperatures on a 1 by 2 by 3 grid could be specified in
the file as follows:
.. parsed-literal::
@ -229,11 +232,20 @@ the same as the input temperature file. It will contain a comment in
the first line reporting the date the file was created, the LAMMPS
units setting in use, grid size and the current timestep.
Note that the atomic temperature for atoms in each grid cell can also
be computed and output by the :doc:`fix ave/chunk <fix_ave_chunk>`
command using the :doc:`compute chunk/atom <compute_chunk_atom>`
command to create a 3d array of chunks consistent with the grid used
by this fix.
.. note::
The fix ttm/grid command does not support the *outfile* keyword.
Instead you can use the :doc:`dump grid <dump>` command to output
the electronic temperature on the distributed grid to a dump file.
For the fix ttm and fix ttm/mod commands, the corresponding atomic
temperature for atoms in each grid cell can be computed and output by
the :doc:`fix ave/chunk <fix_ave_chunk>` command using the
:doc:`compute chunk/atom <compute_chunk_atom>` command to create a 3d
array of chunks consistent with the grid used by this fix. For the
fix ttm/grid command the same thing can be done using the :doc:`fix
ave/grid <fix_ave_grid>` command and its per-grid values can be output
via the :doc:`dump grid <dump>` command.
----------
@ -339,13 +351,16 @@ ignored. The lines with the even numbers are treated as follows:
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
These fixes write the state of the electronic subsystem and the energy
exchange between the subsystems to :doc:`binary restart files
<restart>`. See the :doc:`read_restart <read_restart>` command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion. Note that the restart script must define the
same size grid as the original script.
The fix ttm and fix ttm/mod commands write the state of the electronic
subsystem and the energy exchange between the subsystems to
:doc:`binary restart files <restart>`. The fix ttm/grid command does
not yet support writing of its distributed grid to a restart file.
See the :doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion. Note
that the restart script must define the same size grid as the original
script.
Because the state of the random number generator is not saved in the
restart files, this means you cannot do "exact" restarts with this
@ -373,7 +388,8 @@ The vector values calculated are "extensive".
Th fix ttm/grid command also calculates a per-grid vector which store
the electron temperature for each grid cell in temperature :doc:`units
<units>`. The length of the vector (distributed across all
<units>`. which can be accessed by various :doc:`output commands
<Howto_output>`. The length of the vector (distributed across all
processors) is Nx * Ny * Nz. For access by other commands, the name
of the grid produced by fix ttm/grid is "grid". The name of its data
is "data".

5
examples/ttm/in.ttm.grid
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@ -40,4 +40,9 @@ thermo 100
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
thermo_modify format float "%20.16g"
compute 10 all property/grid 5 5 5 id xc yc zc
fix ave all ave/grid 100 5 500 5 5 5 f_twotemp:grid:data
dump ave all grid 500 tmp.dump.ave &
c_10:grid:data[*] f_ave:grid:data
run 1000

90
src/EXTRA-FIX/fix_ttm_grid.cpp
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@ -57,11 +57,8 @@ FixTTMGrid::FixTTMGrid(LAMMPS *lmp, int narg, char **arg) :
pergrid_flag = 1;
pergrid_freq = 1;
/*
NOTE: uncomment this when ready to release
if (outfile) error->all(FLERR,"Fix ttm/grid does not support outfile option - "
"use dump grid instead");
*/
"use dump grid command instead");
skin_original = neighbor->skin;
}
@ -364,30 +361,6 @@ void FixTTMGrid::read_electron_temperatures(const std::string &filename)
memory->destroy3d_offset(T_initial_set, nzlo_in, nylo_in, nxlo_in);
}
/* ----------------------------------------------------------------------
write out current electron temperatures to user-specified file
only written by proc 0
NOTE: remove this function when ready to release
------------------------------------------------------------------------- */
void FixTTMGrid::write_electron_temperatures(const std::string &filename)
{
if (comm->me == 0) {
FPout = fopen(filename.c_str(), "w");
if (!FPout) error->one(FLERR, "Fix ttm/grid could not open output file");
fmt::print(FPout,
"# DATE: {} UNITS: {} COMMENT: Electron temperature "
"{}x{}x{} grid at step {}. Created by fix {}\n",
utils::current_date(), update->unit_style, nxgrid, nygrid, nzgrid, update->ntimestep,
style);
}
grid->gather(Grid3d::FIX, this, 1, sizeof(double), 1, nullptr, MPI_DOUBLE);
if (comm->me == 0) fclose(FPout);
}
/* ----------------------------------------------------------------------
subset of grid assigned to each proc may have changed
called by load balancer when proc subdomains are adjusted
@ -500,27 +473,8 @@ void FixTTMGrid::deallocate_grid()
void FixTTMGrid::write_restart(FILE *fp)
{
int rsize = nxgrid * nygrid * nzgrid + 4;
double *rlist;
memory->create(rlist, rsize, "ttm/grid:rlist");
int n = 0;
rlist[n++] = nxgrid;
rlist[n++] = nygrid;
rlist[n++] = nzgrid;
rlist[n++] = seed;
// gather rest of rlist on proc 0 as global grid values
//grid->gather(Grid3d::FIX, this, 1, sizeof(double), 0, &rlist[4], MPI_DOUBLE);
if (comm->me == 0) {
int size = rsize * sizeof(double);
fwrite(&size, sizeof(int), 1, fp);
fwrite(rlist, sizeof(double), rsize, fp);
}
memory->destroy(rlist);
error->all(FLERR,"Fix ttm/grid command does not yet support "
"writing a distributed grid to a restart file");
}
/* ----------------------------------------------------------------------
@ -529,42 +483,8 @@ void FixTTMGrid::write_restart(FILE *fp)
void FixTTMGrid::restart(char *buf)
{
int ix, iy, iz;
int n = 0;
auto rlist = (double *) buf;
// check that restart grid size is same as current grid size
int nxgrid_old = static_cast<int>(rlist[n++]);
int nygrid_old = static_cast<int>(rlist[n++]);
int nzgrid_old = static_cast<int>(rlist[n++]);
if (nxgrid_old != nxgrid || nygrid_old != nygrid || nzgrid_old != nzgrid)
error->all(FLERR, "Must restart fix ttm/grid with same grid size");
// change RN seed from initial seed, to avoid same Langevin factors
// just increment by 1, since for RanMars that is a new RN stream
seed = static_cast<int>(rlist[n++]) + 1;
delete random;
random = new RanMars(lmp, seed + comm->me);
// extract this proc's local grid values from global grid in rlist
int iglobal;
for (iz = nzlo_in; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
iglobal = nygrid * nxgrid * iz + nxgrid * iy + ix;
T_electron[iz][iy][ix] = rlist[n + iglobal];
}
// communicate new T_electron values to ghost grid points
grid->forward_comm(Grid3d::FIX, this, 1, sizeof(double), 0,
grid_buf1, grid_buf2, MPI_DOUBLE);
error->all(FLERR,"Fix ttm/grid command does not yet support "
"reading a distributed grid from a restart file");
}
/* ----------------------------------------------------------------------

1
src/EXTRA-FIX/fix_ttm_grid.h
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@ -70,7 +70,6 @@ class FixTTMGrid : public FixTTM {
void allocate_grid() override;
void deallocate_grid() override;
void read_electron_temperatures(const std::string &) override;
void write_electron_temperatures(const std::string &) override;
};
} // namespace LAMMPS_NS