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PaNOSC-ViNYL / SimEx

Start-to-end photon experiment simulation platform
https://simex.readthedocs.io/
GNU General Public License v3.0
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pysingfel: H5pyDeprecationWarning #185

Open JunCEEE opened 4 years ago

JunCEEE commented 4 years ago

hdf version: 1.10.5, When excute:

diffractor.backengine()
diffractor = SingFELPhotonDiffractor(parameters=diffraction_parameters,
                                     input_path='pmi',
                                     output_path="diffr")

Got error:

/home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/radiationDamage.py:56: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. photon_energy = f.get('/history/parent/detail/params/photonEnergy').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/radiationDamage.py:80: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. focus_xFWHM = f.get('/history/parent/detail/misc/xFWHM').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/radiationDamage.py:81: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. focus_yFWHM = f.get('/history/parent/detail/misc/yFWHM').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:57: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. atomPos = f.get(datasetname + '/r').value # atom position -> N x 3 array /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:58: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. ionList = f.get(datasetname + '/xyz').value # length = N, contain atom type id for each atom /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:64: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. atomType = f.get(datasetname + '/T').value # atom type array, each type is represented by an integer /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:66: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. ffTable = f.get(datasetname + '/ff').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:69: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. self.qSample = f.get(datasetname + '/halfQ').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:71: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. self.comptonQSample = f.get(datasetname + '/Sq_halfQ').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:73: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. self.sBound = f.get(datasetname + '/Sq_bound').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/particle.py:74: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. self.nFree = f.get(datasetname + '/Sq_free').value /home/juncheng/.conda/envs/simex/lib/python3.6/pysingfel/radiationDamage.py:96: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. n_phot += f.get(datasetname).value