def write_hdf5(bemio_obj, out_file=None):
"""
Function that writes NEMOH, WAMIT, or NEMOH data to a standard human
readable data format that uses the HDF5 format. This data can easily be
input into various codes, such as MATLAB, Python, C++, etc. The data can
easily be viewed using `HDFVIEW <https://www.hdfgroup.org/products/java/hdfview/>`_.
Parameters:
data_object : {bemio.io.NemohOutput, bamio.io.WamitOutput, bemio.io.AqwaOutput}
A data object created using the bemio.io data readers
out_file : str, optional
The name of the output file. The file should have the .h5 file
extension
Examples:
This example assumes there is a wamit output file called wamit.out that
is read using the bemio.io.wamit.read function
>>> from bemio.io.wamit import read
>>> from bemio.io.output import write_hdf5
>>> wamit_data = read(out_file=wamit.out)
>>> write_hdf5(wamit_data)
Writing HDF5 data to ./wamit.h5
"""
if out_file is None:
out_file = bemio_obj.files["hdf5"]
print "Writing HDF5 data to " + out_file
with h5py.File(out_file, "w") as f:
for key, key in enumerate(bemio_obj.body.keys()):
# Body properities
cg = f.create_dataset("body" + str(key + 1) + "/properties/cg", data=bemio_obj.body[key].cg)
cg.attrs["units"] = "m"
cg.attrs["description"] = "Center of gravity"
cb = f.create_dataset("body" + str(key + 1) + "/properties/cb", data=bemio_obj.body[key].cb)
cb.attrs["units"] = "m"
cb.attrs["description"] = "Center of buoyancy"
vol = f.create_dataset("body" + str(key + 1) + "/properties/disp_vol", data=bemio_obj.body[key].disp_vol)
vol.attrs["units"] = "m^3"
vol.attrs["description"] = "Displaced volume"
name = f.create_dataset("body" + str(key + 1) + "/properties/name", data=bemio_obj.body[key].name)
name.attrs["description"] = "Name of rigid body"
num = f.create_dataset("body" + str(key + 1) + "/properties/body_number", data=bemio_obj.body[key].body_num)
num.attrs["description"] = "Number of rigid body from the BEM simulation"
# Hydro coeffs
# Radiation IRF
try:
irf_rad_k_correct_loc = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/impulse_response_fun/K",
data=bemio_obj.body[key].rd.irf.K,
)
irf_rad_k_correct_loc.attrs["units"] = ""
irf_rad_k_correct_loc.attrs["description"] = "Impulse response function"
irf_rad_t_correct_loc = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/impulse_response_fun/t",
data=bemio_obj.body[key].rd.irf.t,
)
irf_rad_t_correct_loc.attrs["units"] = "seconds"
irf_rad_t_correct_loc.attrs["description"] = "Time vector for the impulse response function"
irf_rad_w_correct_loc = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/impulse_response_fun/w",
data=bemio_obj.body[key].rd.irf.w,
)
irf_rad_w_correct_loc.attrs["units"] = "seconds"
irf_rad_w_correct_loc.attrs[
"description"
] = "Interpolated frequencies used to compute the impulse response function"
irf_rad_l_correct_loc = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/impulse_response_fun/L",
data=bemio_obj.body[key].rd.irf.L,
)
irf_rad_l_correct_loc.attrs["units"] = ""
irf_rad_l_correct_loc.attrs["description"] = "Time derivative of the impulse response function"
for m in xrange(bemio_obj.body[key].am.all.shape[0]):
for n in xrange(bemio_obj.body[key].am.all.shape[1]):
irf_rad_l_comp_correct_loc = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/impulse_response_fun/components/L/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array(
[bemio_obj.body[key].rd.irf.t, bemio_obj.body[key].rd.irf.L[m, n, :]]
).transpose(),
)
irf_rad_l_comp_correct_loc.attrs["units"] = ""
irf_rad_l_comp_correct_loc.attrs["description"] = "Components of the IRF"
irf_rad_k_comp_correct_loc = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/impulse_response_fun/components/K/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array(
[bemio_obj.body[key].rd.irf.t, bemio_obj.body[key].rd.irf.K[m, n, :]]
).transpose(),
)
irf_rad_k_comp_correct_loc.attrs["units"] = ""
irf_rad_k_comp_correct_loc.attrs["description"] = "Components of the ddt(IRF): K"
except:
print "\tRadiation IRF functions for " + bemio_obj.body[key].name + " were not written."
# Excitation IRF
try:
irf_ex_f = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/impulse_response_fun/f",
data=bemio_obj.body[key].ex.irf.f,
)
irf_ex_f.attrs["units"] = ""
irf_ex_f.attrs["description"] = "Impulse response function"
irf_ex_t = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/impulse_response_fun/w",
data=bemio_obj.body[key].ex.irf.w,
)
irf_ex_w = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/impulse_response_fun/t",
data=bemio_obj.body[key].ex.irf.t,
)
for m in xrange(bemio_obj.body[key].ex.mag.shape[0]):
for n in xrange(bemio_obj.body[key].ex.mag.shape[1]):
irf_ex_f_comp = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/excitation/impulse_response_fun/components/f/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array(
[bemio_obj.body[key].ex.irf.t, bemio_obj.body[key].ex.irf.f[m, n, :]]
).transpose(),
)
irf_ex_f_comp.attrs["units"] = ""
irf_ex_f_comp.attrs["description"] = "Components of the ddt(IRF): f"
except:
print "\tExcitation IRF functions for " + bemio_obj.body[key].name + " were not written."
try:
ssRadfA = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/state_space/A/all",
data=bemio_obj.body[key].rd.ss.A,
)
ssRadfA.attrs["units"] = ""
ssRadfA.attrs["description"] = "State Space A Coefficient"
ssRadfB = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/state_space/B/all",
data=bemio_obj.body[key].rd.ss.B,
)
ssRadfB.attrs["units"] = ""
ssRadfB.attrs["description"] = "State Space B Coefficient"
ssRadfC = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/state_space/C/all",
data=bemio_obj.body[key].rd.ss.C,
)
ssRadfC.attrs["units"] = ""
ssRadfC.attrs["description"] = "State Space C Coefficient"
ssRadfD = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/state_space/D/all",
data=bemio_obj.body[key].rd.ss.D,
)
ssRadfD.attrs["units"] = ""
ssRadfD.attrs["description"] = "State Space D Coefficient"
r2t = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/state_space/r2t",
data=bemio_obj.body[key].rd.ss.r2t,
)
r2t.attrs["units"] = ""
r2t.attrs["description"] = "State space curve fitting R**2 value"
it = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/state_space/it",
data=bemio_obj.body[key].rd.ss.it,
)
it.attrs["units"] = ""
it.attrs["description"] = "Order of state space realization"
for m in xrange(bemio_obj.body[key].am.all.shape[0]):
for n in xrange(bemio_obj.body[key].am.all.shape[1]):
ss_A = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/state_space/A/components/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=bemio_obj.body[key].rd.ss.A[m, n, :, :],
)
ss_A.attrs["units"] = ""
ss_A.attrs["description"] = "Components of the State Space A Coefficient"
ss_B = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/state_space/B/components/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=bemio_obj.body[key].rd.ss.B[m, n, :, :],
)
ss_B.attrs["units"] = ""
ss_B.attrs["description"] = "Components of the State Space B Coefficient"
ss_C = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/state_space/C/components/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=bemio_obj.body[key].rd.ss.C[m, n, :, :],
)
ss_C.attrs["units"] = ""
ss_C.attrs["description"] = "Components of the State Space C Coefficient"
ss_D = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/state_space/D/components/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=bemio_obj.body[key].rd.ss.D[m, n],
)
ss_D.attrs["units"] = ""
ss_D.attrs["description"] = "Components of the State Space C Coefficient"
except:
print "\tRadiation state space coefficients for " + bemio_obj.body[key].name + " were not written."
k = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/linear_restoring_stiffness", data=bemio_obj.body[key].k
)
k.attrs["units"] = ""
k.attrs["description"] = "Hydrostatic stiffness matrix"
exMag = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/mag", data=bemio_obj.body[key].ex.mag
)
exMag.attrs["units"] = ""
exMag.attrs["description"] = "Magnitude of excitation force"
exPhase = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/phase", data=bemio_obj.body[key].ex.phase
)
exPhase.attrs["units"] = "rad"
exPhase.attrs["description"] = "Phase angle of excitation force"
exRe = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/re", data=bemio_obj.body[key].ex.re
)
exRe.attrs["units"] = ""
exRe.attrs["description"] = "Real component of excitation force"
exIm = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/im", data=bemio_obj.body[key].ex.im
)
exIm.attrs["units"] = ""
exIm.attrs["description"] = "Imaginary component of excitation force"
for m in xrange(bemio_obj.body[key].ex.mag.shape[0]):
for n in xrange(bemio_obj.body[key].ex.mag.shape[1]):
irf_ex_f_comp = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/excitation//components/mag/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array([bemio_obj.body[key].T, bemio_obj.body[key].ex.mag[m, n, :]]).transpose(),
)
irf_ex_f_comp = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/excitation//components/phase/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array([bemio_obj.body[key].T, bemio_obj.body[key].ex.phase[m, n, :]]).transpose(),
)
irf_ex_f_comp = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/excitation//components/re/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array([bemio_obj.body[key].T, bemio_obj.body[key].ex.re[m, n, :]]).transpose(),
)
irf_ex_f_comp = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/excitation//components/im/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array([bemio_obj.body[key].T, bemio_obj.body[key].ex.im[m, n, :]]).transpose(),
)
# Scattering and FK forces
try:
ex_sc_Mag = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/scattering/mag",
data=bemio_obj.body[key].ex.sc.mag,
)
ex_sc_Mag.attrs["units"] = ""
ex_sc_Mag.attrs["description"] = "Magnitude of excitation force"
ex_sc_Phase = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/scattering/phase",
data=bemio_obj.body[key].ex.sc.phase,
)
ex_sc_Phase.attrs["units"] = "rad"
ex_sc_Phase.attrs["description"] = "Phase angle of excitation force"
ex_sc_Re = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/scattering/re", data=bemio_obj.body[key].ex.sc.re
)
ex_sc_Re.attrs["units"] = ""
ex_sc_Re.attrs["description"] = "Real component of excitation force"
ex_sc_Im = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/scattering/im", data=bemio_obj.body[key].ex.sc.im
)
ex_sc_Im.attrs["units"] = ""
ex_sc_Im.attrs["description"] = "Imaginary component of excitation force"
ex_fk_Mag = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/froud_krylof/mag",
data=bemio_obj.body[key].ex.fk.mag,
)
ex_fk_Mag.attrs["units"] = ""
ex_fk_Mag.attrs["description"] = "Magnitude of excitation force"
ex_fk_Phase = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/froud_krylof/phase",
data=bemio_obj.body[key].ex.fk.phase,
)
ex_fk_Phase.attrs["units"] = "rad"
ex_fk_Phase.attrs["description"] = "Phase angle of excitation force"
ex_fk_Re = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/froud_krylof/re",
data=bemio_obj.body[key].ex.fk.re,
)
ex_fk_Re.attrs["units"] = ""
ex_fk_Re.attrs["description"] = "Real component of excitation force"
ex_fk_Im = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/excitation/froud_krylof/im",
data=bemio_obj.body[key].ex.fk.im,
)
ex_fk_Im.attrs["units"] = ""
ex_fk_Im.attrs["description"] = "Imaginary component of excitation force"
except:
pass
# Write added mass information
amInf = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/added_mass/inf_freq", data=bemio_obj.body[key].am.inf
)
amInf.attrs["units for translational degrees of freedom"] = "kg"
amInf.attrs["description"] = "Infinite frequency added mass"
am = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/added_mass/all", data=bemio_obj.body[key].am.all
)
am.attrs["units for translational degrees of freedom"] = "kg"
am.attrs["units for rotational degrees of freedom"] = "kg-m^2"
am.attrs["description"] = "Added mass. Frequency is the third dimension of the data structure."
for m in xrange(bemio_obj.body[key].am.all.shape[0]):
for n in xrange(bemio_obj.body[key].am.all.shape[1]):
amComp = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/added_mass/components/" + str(m + 1) + "_" + str(n + 1),
data=np.array([bemio_obj.body[key].T, bemio_obj.body[key].am.all[m, n, :]]).transpose(),
)
amComp.attrs["units"] = ""
amComp.attrs["description"] = "Added mass components as a function of frequency"
radComp = f.create_dataset(
"body"
+ str(key + 1)
+ "/hydro_coeffs/radiation_damping/components/"
+ str(m + 1)
+ "_"
+ str(n + 1),
data=np.array([bemio_obj.body[key].T, bemio_obj.body[key].rd.all[m, n, :]]).transpose(),
)
radComp.attrs["units"] = ""
radComp.attrs["description"] = "Radiation damping components as a function of frequency"
rad = f.create_dataset(
"body" + str(key + 1) + "/hydro_coeffs/radiation_damping/all", data=bemio_obj.body[key].rd.all
)
rad.attrs["units"] = ""
rad.attrs["description"] = "Radiation damping. Frequency is the thrid dimension of the data structure."
# Simulation parameters
g = f.create_dataset("simulation_parameters/g", data=bemio_obj.body[key].g)
g.attrs["units"] = "m/s^2"
g.attrs["description"] = "Gravitational acceleration"
rho = f.create_dataset("simulation_parameters/rho", data=bemio_obj.body[key].rho)
rho.attrs["units"] = "kg/m^3"
rho.attrs["description"] = "Water density"
T = f.create_dataset("simulation_parameters/T", data=bemio_obj.body[key].T)
T.attrs["units"] = "s"
T.attrs["description"] = "Wave periods"
w = f.create_dataset("simulation_parameters/w", data=bemio_obj.body[key].w)
w.attrs["units"] = "rad/s"
w.attrs["description"] = "Wave frequencies"
water_depth = f.create_dataset("simulation_parameters/water_depth", data=bemio_obj.body[key].water_depth)
water_depth.attrs["units"] = "m"
water_depth.attrs["description"] = "Water depth"
wave_dir = f.create_dataset("simulation_parameters/wave_dir", data=bemio_obj.body[key].wave_dir)
wave_dir.attrs["units"] = "rad"
wave_dir.attrs["description"] = "Wave direction"
scaled = f.create_dataset("simulation_parameters/scaled", data=bemio_obj.body[key].scaled)
scaled.attrs["description"] = "True: The data is scaled by rho*g, False: The data is not scaled by rho*g"
bemio_version = f.create_dataset("bemio_information/version", data=base())
rawOut = f.create_dataset("bem_data/output", data=bemio_obj.body[key].bem_raw_data)
rawOut.attrs["description"] = "Raw output from BEM code"
code = f.create_dataset("bem_data/code", data=bemio_obj.body[key].bem_code)
code.attrs["description"] = "BEM code"
def write_hdf5(bemio_obj, out_file=None):
'''
Function that writes NEMOH, WAMIT, or NEMOH data to a standard human
readable data format that uses the HDF5 format. This data can easily be
input into various codes, such as MATLAB, Python, C++, etc. The data can
easily be viewed using `HDFVIEW <https://www.hdfgroup.org/products/java/hdfview/>`_.
Parameters:
data_object : {bemio.io.NemohOutput, bamio.io.WamitOutput, bemio.io.AqwaOutput}
A data object created using the bemio.io data readers
out_file : str, optional
The name of the output file. The file should have the .h5 file
extension
Examples:
This example assumes there is a wamit output file called wamit.out that
is read using the bemio.io.wamit.read function
>>> from bemio.io.wamit import read
>>> from bemio.io.output import write_hdf5
>>> wamit_data = read(out_file=wamit.out)
>>> write_hdf5(wamit_data)
Writing HDF5 data to ./wamit.h5
'''
if out_file is None:
out_file = bemio_obj.files['hdf5']
print 'Writing HDF5 data to ' + out_file
with h5py.File(out_file, "w") as f:
for key, key in enumerate(bemio_obj.body.keys()):
# Body properities
cg = f.create_dataset('body' + str(key + 1) + '/properties/cg',
data=bemio_obj.body[key].cg)
cg.attrs['units'] = 'm'
cg.attrs['description'] = 'Center of gravity'
cb = f.create_dataset('body' + str(key + 1) + '/properties/cb',
data=bemio_obj.body[key].cb)
cb.attrs['units'] = 'm'
cb.attrs['description'] = 'Center of buoyancy'
vol = f.create_dataset('body' + str(key + 1) +
'/properties/disp_vol',
data=bemio_obj.body[key].disp_vol)
vol.attrs['units'] = 'm^3'
vol.attrs['description'] = 'Displaced volume'
name = f.create_dataset('body' + str(key + 1) + '/properties/name',
data=bemio_obj.body[key].name)
name.attrs['description'] = 'Name of rigid body'
num = f.create_dataset('body' + str(key + 1) +
'/properties/body_number',
data=bemio_obj.body[key].body_num)
num.attrs[
'description'] = 'Number of rigid body from the BEM simulation'
# Hydro coeffs
# Radiation IRF
try:
irf_rad_k_correct_loc = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/impulse_response_fun/K',
data=bemio_obj.body[key].rd.irf.K)
irf_rad_k_correct_loc.attrs['units'] = ''
irf_rad_k_correct_loc.attrs[
'description'] = 'Impulse response function'
irf_rad_t_correct_loc = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/impulse_response_fun/t',
data=bemio_obj.body[key].rd.irf.t)
irf_rad_t_correct_loc.attrs['units'] = 'seconds'
irf_rad_t_correct_loc.attrs[
'description'] = 'Time vector for the impulse response function'
irf_rad_w_correct_loc = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/impulse_response_fun/w',
data=bemio_obj.body[key].rd.irf.w)
irf_rad_w_correct_loc.attrs['units'] = 'seconds'
irf_rad_w_correct_loc.attrs[
'description'] = 'Interpolated frequencies used to compute the impulse response function'
irf_rad_l_correct_loc = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/impulse_response_fun/L',
data=bemio_obj.body[key].rd.irf.L)
irf_rad_l_correct_loc.attrs['units'] = ''
irf_rad_l_correct_loc.attrs[
'description'] = 'Time derivative of the impulse response function'
for m in xrange(bemio_obj.body[key].am.all.shape[0]):
for n in xrange(bemio_obj.body[key].am.all.shape[1]):
irf_rad_l_comp_correct_loc = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/impulse_response_fun/components/L/'
+ str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].rd.irf.t,
bemio_obj.body[key].rd.irf.L[m, n, :]
]).transpose())
irf_rad_l_comp_correct_loc.attrs['units'] = ''
irf_rad_l_comp_correct_loc.attrs[
'description'] = 'Components of the IRF'
irf_rad_k_comp_correct_loc = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/impulse_response_fun/components/K/'
+ str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].rd.irf.t,
bemio_obj.body[key].rd.irf.K[m, n, :]
]).transpose())
irf_rad_k_comp_correct_loc.attrs['units'] = ''
irf_rad_k_comp_correct_loc.attrs[
'description'] = 'Components of the ddt(IRF): K'
except:
print '\tRadiation IRF functions for ' + bemio_obj.body[
key].name + ' were not written.'
# Excitation IRF
try:
irf_ex_f = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/impulse_response_fun/f',
data=bemio_obj.body[key].ex.irf.f)
irf_ex_f.attrs['units'] = ''
irf_ex_f.attrs['description'] = 'Impulse response function'
irf_ex_t = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/impulse_response_fun/w',
data=bemio_obj.body[key].ex.irf.w)
irf_ex_w = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/impulse_response_fun/t',
data=bemio_obj.body[key].ex.irf.t)
for m in xrange(bemio_obj.body[key].ex.mag.shape[0]):
for n in xrange(bemio_obj.body[key].ex.mag.shape[1]):
irf_ex_f_comp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/impulse_response_fun/components/f/'
+ str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].ex.irf.t,
bemio_obj.body[key].ex.irf.f[m, n, :]
]).transpose())
irf_ex_f_comp.attrs['units'] = ''
irf_ex_f_comp.attrs[
'description'] = 'Components of the ddt(IRF): f'
except:
print '\tExcitation IRF functions for ' + bemio_obj.body[
key].name + ' were not written.'
try:
ssRadfA = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/A/all',
data=bemio_obj.body[key].rd.ss.A)
ssRadfA.attrs['units'] = ''
ssRadfA.attrs['description'] = 'State Space A Coefficient'
ssRadfB = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/B/all',
data=bemio_obj.body[key].rd.ss.B)
ssRadfB.attrs['units'] = ''
ssRadfB.attrs['description'] = 'State Space B Coefficient'
ssRadfC = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/C/all',
data=bemio_obj.body[key].rd.ss.C)
ssRadfC.attrs['units'] = ''
ssRadfC.attrs['description'] = 'State Space C Coefficient'
ssRadfD = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/D/all',
data=bemio_obj.body[key].rd.ss.D)
ssRadfD.attrs['units'] = ''
ssRadfD.attrs['description'] = 'State Space D Coefficient'
r2t = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/r2t',
data=bemio_obj.body[key].rd.ss.r2t)
r2t.attrs['units'] = ''
r2t.attrs[
'description'] = 'State space curve fitting R**2 value'
it = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/it',
data=bemio_obj.body[key].rd.ss.it)
it.attrs['units'] = ''
it.attrs['description'] = 'Order of state space realization'
for m in xrange(bemio_obj.body[key].am.all.shape[0]):
for n in xrange(bemio_obj.body[key].am.all.shape[1]):
ss_A = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/A/components/'
+ str(m + 1) + '_' + str(n + 1),
data=bemio_obj.body[key].rd.ss.A[m, n, :, :])
ss_A.attrs['units'] = ''
ss_A.attrs[
'description'] = 'Components of the State Space A Coefficient'
ss_B = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/B/components/'
+ str(m + 1) + '_' + str(n + 1),
data=bemio_obj.body[key].rd.ss.B[m, n, :, :])
ss_B.attrs['units'] = ''
ss_B.attrs[
'description'] = 'Components of the State Space B Coefficient'
ss_C = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/C/components/'
+ str(m + 1) + '_' + str(n + 1),
data=bemio_obj.body[key].rd.ss.C[m, n, :, :])
ss_C.attrs['units'] = ''
ss_C.attrs[
'description'] = 'Components of the State Space C Coefficient'
ss_D = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/state_space/D/components/'
+ str(m + 1) + '_' + str(n + 1),
data=bemio_obj.body[key].rd.ss.D[m, n])
ss_D.attrs['units'] = ''
ss_D.attrs[
'description'] = 'Components of the State Space C Coefficient'
except:
print '\tRadiation state space coefficients for ' + bemio_obj.body[
key].name + ' were not written.'
k = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/linear_restoring_stiffness',
data=bemio_obj.body[key].k)
k.attrs['units'] = ''
k.attrs['description'] = 'Hydrostatic stiffness matrix'
exMag = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/excitation/mag',
data=bemio_obj.body[key].ex.mag)
exMag.attrs['units'] = ''
exMag.attrs['description'] = 'Magnitude of excitation force'
exPhase = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/excitation/phase',
data=bemio_obj.body[key].ex.phase)
exPhase.attrs['units'] = 'rad'
exPhase.attrs['description'] = 'Phase angle of excitation force'
exRe = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/excitation/re',
data=bemio_obj.body[key].ex.re)
exRe.attrs['units'] = ''
exRe.attrs['description'] = 'Real component of excitation force'
exIm = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/excitation/im',
data=bemio_obj.body[key].ex.im)
exIm.attrs['units'] = ''
exIm.attrs[
'description'] = 'Imaginary component of excitation force'
for m in xrange(bemio_obj.body[key].ex.mag.shape[0]):
for n in xrange(bemio_obj.body[key].ex.mag.shape[1]):
irf_ex_f_comp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation//components/mag/' +
str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].T,
bemio_obj.body[key].ex.mag[m, n, :]
]).transpose())
irf_ex_f_comp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation//components/phase/' +
str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].T,
bemio_obj.body[key].ex.phase[m, n, :]
]).transpose())
irf_ex_f_comp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation//components/re/' +
str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].T,
bemio_obj.body[key].ex.re[m, n, :]
]).transpose())
irf_ex_f_comp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation//components/im/' +
str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].T,
bemio_obj.body[key].ex.im[m, n, :]
]).transpose())
# Scattering and FK forces
try:
ex_sc_Mag = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/scattering/mag',
data=bemio_obj.body[key].ex.sc.mag)
ex_sc_Mag.attrs['units'] = ''
ex_sc_Mag.attrs[
'description'] = 'Magnitude of excitation force'
ex_sc_Phase = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/scattering/phase',
data=bemio_obj.body[key].ex.sc.phase)
ex_sc_Phase.attrs['units'] = 'rad'
ex_sc_Phase.attrs[
'description'] = 'Phase angle of excitation force'
ex_sc_Re = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/scattering/re',
data=bemio_obj.body[key].ex.sc.re)
ex_sc_Re.attrs['units'] = ''
ex_sc_Re.attrs[
'description'] = 'Real component of excitation force'
ex_sc_Im = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/scattering/im',
data=bemio_obj.body[key].ex.sc.im)
ex_sc_Im.attrs['units'] = ''
ex_sc_Im.attrs[
'description'] = 'Imaginary component of excitation force'
ex_fk_Mag = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/froud_krylof/mag',
data=bemio_obj.body[key].ex.fk.mag)
ex_fk_Mag.attrs['units'] = ''
ex_fk_Mag.attrs[
'description'] = 'Magnitude of excitation force'
ex_fk_Phase = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/froud_krylof/phase',
data=bemio_obj.body[key].ex.fk.phase)
ex_fk_Phase.attrs['units'] = 'rad'
ex_fk_Phase.attrs[
'description'] = 'Phase angle of excitation force'
ex_fk_Re = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/froud_krylof/re',
data=bemio_obj.body[key].ex.fk.re)
ex_fk_Re.attrs['units'] = ''
ex_fk_Re.attrs[
'description'] = 'Real component of excitation force'
ex_fk_Im = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/excitation/froud_krylof/im',
data=bemio_obj.body[key].ex.fk.im)
ex_fk_Im.attrs['units'] = ''
ex_fk_Im.attrs[
'description'] = 'Imaginary component of excitation force'
except:
pass
# Write added mass information
amInf = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/added_mass/inf_freq',
data=bemio_obj.body[key].am.inf)
amInf.attrs['units for translational degrees of freedom'] = 'kg'
amInf.attrs['description'] = 'Infinite frequency added mass'
am = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/added_mass/all',
data=bemio_obj.body[key].am.all)
am.attrs['units for translational degrees of freedom'] = 'kg'
am.attrs['units for rotational degrees of freedom'] = 'kg-m^2'
am.attrs[
'description'] = 'Added mass. Frequency is the third dimension of the data structure.'
for m in xrange(bemio_obj.body[key].am.all.shape[0]):
for n in xrange(bemio_obj.body[key].am.all.shape[1]):
amComp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/added_mass/components/' + str(m + 1) +
'_' + str(n + 1),
data=np.array([
bemio_obj.body[key].T,
bemio_obj.body[key].am.all[m, n, :]
]).transpose())
amComp.attrs['units'] = ''
amComp.attrs[
'description'] = 'Added mass components as a function of frequency'
radComp = f.create_dataset(
'body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/components/' +
str(m + 1) + '_' + str(n + 1),
data=np.array([
bemio_obj.body[key].T,
bemio_obj.body[key].rd.all[m, n, :]
]).transpose())
radComp.attrs['units'] = ''
radComp.attrs[
'description'] = 'Radiation damping components as a function of frequency'
rad = f.create_dataset('body' + str(key + 1) +
'/hydro_coeffs/radiation_damping/all',
data=bemio_obj.body[key].rd.all)
rad.attrs['units'] = ''
rad.attrs[
'description'] = 'Radiation damping. Frequency is the thrid dimension of the data structure.'
# Simulation parameters
g = f.create_dataset('simulation_parameters/g',
data=bemio_obj.body[key].g)
g.attrs['units'] = 'm/s^2'
g.attrs['description'] = 'Gravitational acceleration'
rho = f.create_dataset('simulation_parameters/rho',
data=bemio_obj.body[key].rho)
rho.attrs['units'] = 'kg/m^3'
rho.attrs['description'] = 'Water density'
T = f.create_dataset('simulation_parameters/T',
data=bemio_obj.body[key].T)
T.attrs['units'] = 's'
T.attrs['description'] = 'Wave periods'
w = f.create_dataset('simulation_parameters/w',
data=bemio_obj.body[key].w)
w.attrs['units'] = 'rad/s'
w.attrs['description'] = 'Wave frequencies'
water_depth = f.create_dataset('simulation_parameters/water_depth',
data=bemio_obj.body[key].water_depth)
water_depth.attrs['units'] = 'm'
water_depth.attrs['description'] = 'Water depth'
wave_dir = f.create_dataset('simulation_parameters/wave_dir',
data=bemio_obj.body[key].wave_dir)
wave_dir.attrs['units'] = 'rad'
wave_dir.attrs['description'] = 'Wave direction'
scaled = f.create_dataset('simulation_parameters/scaled',
data=bemio_obj.body[key].scaled)
scaled.attrs[
'description'] = 'True: The data is scaled by rho*g, False: The data is not scaled by rho*g'
bemio_version = f.create_dataset('bemio_information/version',
data=base())
rawOut = f.create_dataset('bem_data/output',
data=bemio_obj.body[key].bem_raw_data)
rawOut.attrs['description'] = 'Raw output from BEM code'
code = f.create_dataset('bem_data/code',
data=bemio_obj.body[key].bem_code)
code.attrs['description'] = 'BEM code'
"""A setuptools based setup module for bemio
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
from bemio.__version__ import base
setup(
name='bemio',
version=base(),
description='bemio',
long_description='Boundary Element Method Input/Output',
url='https://github.com/WEC-Sim/bemio',
author='Michael Lawson, Yi-Hsiang Yu, Carlos Michelen',
author_email='*****@*****.**',
license='Apache 2.0',
classifiers=[
'Development Status :: Release',
'Intended Audience :: Ocean research community',
'License ::Apache 2.0',
'Programming Language :: Python :: 2.7'