def merge_field_nodes(fdir, lap, conf):
fstr = fdir + '/fields-*_' + str(lap) + '.h5'
print(fstr)
files = glob.glob(fstr)
files.sort(key=natural_keys)
print(files)
fname_merged = fdir + '/fields_' + str(lap) + '.h5'
f5 = h5py.File(fname_merged, 'w')
fvars = ['bx', 'by', 'bz', 'ex', 'ey', 'ez', 'jx', 'jy', 'jz', 'rho']
for fvar in fvars:
print("processing {}".format(fvar))
arr = combine_tiles(files[0], fvar, conf, isp=None)
for ff in files[1:]:
print(" file: {}".format(ff))
arrN = combine_tiles(ff, fvar, conf, isp=None)
arr += arrN
dset = f5.create_dataset(fvar, data=arr)
f5.close()
def merge_analysis_nodes(fdir, lap, isps, conf):
fstr = fdir + '/analysis-*_' + str(lap) + '.h5'
print(fstr)
files = glob.glob(fstr)
files.sort(key=natural_keys)
print(files)
fname_merged = fdir + '/analysis_' + str(lap) + '.h5'
f5 = h5py.File(fname_merged, 'w')
fvars = [
'rho',
'edens',
#'temp',
#'Vx',
#'Vy',
#'Vz',
#'momx',
#'momy',
#'momz',
#'pressx',
#'pressy',
#'pressz',
#'shearxy',
#'shearxz',
#'shearyz',
]
for fvar in fvars:
print("processing {}".format(fvar))
for isp in isps:
print(" isp {}".format(isp))
arr = combine_tiles(files[0], fvar, conf, isp=isp)
for ff in files[1:]:
print(" file: {}".format(ff))
arrN = combine_tiles(ff, fvar, conf, isp=None)
arr += arrN
dset = f5.create_dataset(fvar + '_' + str(isp), data=arr)
f5.close()
def test_write_fields2D(self):
##################################################
# write
conf = Conf()
conf.Nx = 3
conf.Ny = 4
conf.Nz = 1
conf.NxMesh = 5
conf.NyMesh = 6
conf.NzMesh = 1
conf.outdir = "io_test_2D/"
if not os.path.exists( conf.outdir ):
os.makedirs(conf.outdir)
grid = pycorgi.twoD.Grid(conf.Nx, conf.Ny)
grid.set_grid_lims(conf.xmin, conf.xmax, conf.ymin, conf.ymax)
loadTiles2D(grid, conf)
ref = fill_ref(grid, conf)
fill_yee(grid, ref, conf)
pyrunko.vlv.twoD.write_yee(grid, 0, conf.outdir)
##################################################
# read using analysis tools
arrs = combine_tiles(conf.outdir+"fields-0_0.h5", "ex", conf)
Nx = grid.get_Nx()
Ny = grid.get_Ny()
Nz = grid.get_Nz()
NxM = conf.NxMesh
NyM = conf.NyMesh
NzM = conf.NzMesh
for i in range(grid.get_Nx()):
for j in range(grid.get_Ny()):
for k in range(grid.get_Nz()):
#if n.get_mpi_grid(i,j) == n.rank:
if True:
for q in range(conf.NxMesh):
for r in range(conf.NyMesh):
for s in range(conf.NzMesh):
self.assertAlmostEqual( arrs[i*NxM + q, j*NyM + r, k*NzM + s],
ref[i*NxM + q, j*NyM + r, k*NzM + s, 0], places=6)
##################################################
# test reading back
node2 = pycorgi.twoD.Grid(conf.Nx, conf.Ny)
node2.set_grid_lims(conf.xmin, conf.xmax, conf.ymin, conf.ymax)
loadTiles2D(node2, conf)
pyrunko.vlv.twoD.read_yee(node2, 0, "io_test_2D")
yee1 = getYee2D(grid, conf)
yee2 = getYee2D(node2, conf)
for i in range(grid.get_Nx()):
for j in range(grid.get_Ny()):
for k in range(grid.get_Nz()):
#if n.get_mpi_grid(i,j) == n.rank:
if True:
for q in range(conf.NxMesh):
for r in range(conf.NyMesh):
for s in range(conf.NzMesh):
for m in ["jx", "jy", "jz", "ex", "ey", "ez", "bx", "by", "bz", "rho"]:
self.assertAlmostEqual(
yee1[m][i*NxM + q, j*NyM + r],
yee2[m][i*NxM + q, j*NyM + r],
places=6)
bx = []
by = []
bz = []
jx = []
jy = []
jz = []
dens = []
start = 0
end = len(files_F)
interval = 1
for step in range(start, end, interval):
print("reading {} and {}".format(files_F[step], files_A[step]))
exi = combine_tiles(files_F[step], "ex", conf)[:, :, 0]
eyi = combine_tiles(files_F[step], "ey", conf)[:, :, 0]
ezi = combine_tiles(files_F[step], "ez", conf)[:, :, 0]
jxi = combine_tiles(files_F[step], "jx", conf)[:, :, 0]
jyi = combine_tiles(files_F[step], "jy", conf)[:, :, 0]
jzi = combine_tiles(files_F[step], "jz", conf)[:, :, 0]
bxi = combine_tiles(files_F[step], "bx", conf)[:, :, 0]
byi = combine_tiles(files_F[step], "by", conf)[:, :, 0]
bzi = combine_tiles(files_F[step], "bz", conf)[:, :, 0]
densi = combine_tiles(files_F[step], "rho", conf)[:, :, 0]
print("shape ex")
print(np.shape(exi))