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three switchyard changes #48

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7 changes: 4 additions & 3 deletions rsbeams/rsdata/switchyard.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def read_opal(file_name, step_number=None, species_name='Species'):
particle_data = np.empty((mp_count, 6))
for i, coord in enumerate(['x', 'px', 'y', 'py', 'z', 'pz']):
particle_data[:, i] = pcdata[loc+'/'+coord]
total_charge = pcdata[loc].attrs['CHARGE']
total_charge = pcdata[loc].attrs['CHARGE'][0]


# TODO: This shouldn't be specific to electrons
Expand Down Expand Up @@ -185,6 +185,7 @@ def write_opal(self, file_name, species_name):
"""
coordinates = self.species[species_name].coordinates
N = self.species[species_name].macroparticle_count
coordinates[:, 4] -= np.mean(coordinates[:, 4])

np.savetxt(file_name, coordinates, header='{}'.format(N), comments='')
return 0
Expand Down Expand Up @@ -216,7 +217,7 @@ def write_genesis(self, file_name, species_name, version='2.0'):
P = self.species[species_name].pt

vers_str = '? VERSION = '+version
charge_str = '? CHARGE = '+str(self.species[species_name].total_charge)
charge_str = '? CHARGE = '+str(abs(self.species[species_name].total_charge))
size_str = '? SIZE = '+str(len(X))
clmns_str = '? COLUMNS X PX Y PY T P'

Expand Down Expand Up @@ -254,4 +255,4 @@ def write(self, filename, code, species_name=None, **kwargs):

def _get_step_number(key, prefix='Step#'):
result = key.split(prefix)[-1]
return result
return result