Commit 33756860 authored by eric pellegrini's avatar eric pellegrini
Browse files

Bug fix in SpatailDensity with settings

Added svg support for MSD
parent f41b8285
...@@ -80,7 +80,7 @@ class MeanSquareDisplacement(IJob): ...@@ -80,7 +80,7 @@ class MeanSquareDisplacement(IJob):
settings['grouping_level']=('grouping_level',{}) settings['grouping_level']=('grouping_level',{})
settings['transmutated_atoms']=('atom_transmutation',{"dependencies":{'trajectory':'trajectory', 'atom_selection':'atom_selection'}}) settings['transmutated_atoms']=('atom_transmutation',{"dependencies":{'trajectory':'trajectory', 'atom_selection':'atom_selection'}})
settings['weights']=('weights',{}) settings['weights']=('weights',{})
settings['output_files']=('output_files', {"formats":["netcdf","ascii"]}) settings['output_files']=('output_files', {"formats":["netcdf","ascii","svg"]})
settings['running_mode']=('running_mode',{}) settings['running_mode']=('running_mode',{})
def initialize(self): def initialize(self):
...@@ -119,7 +119,9 @@ class MeanSquareDisplacement(IJob): ...@@ -119,7 +119,9 @@ class MeanSquareDisplacement(IJob):
step=self.configuration['frames']['step']) step=self.configuration['frames']['step'])
series = self.configuration['projection']["projector"](series) series = self.configuration['projection']["projector"](series)
1/0
msd = mean_square_displacement(series) msd = mean_square_displacement(series)
return index, msd return index, msd
......
...@@ -66,9 +66,9 @@ class SpatialDensity(IJob): ...@@ -66,9 +66,9 @@ class SpatialDensity(IJob):
settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')}) settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})
settings['frames'] = ('frames', {'dependencies':{'trajectory':'trajectory'}}) settings['frames'] = ('frames', {'dependencies':{'trajectory':'trajectory'}})
settings['spatial_resolution'] = ('float', {'mini':0.01, 'default':0.1}) settings['spatial_resolution'] = ('float', {'mini':0.01, 'default':0.1})
settings['reference_basis'] = ('basis_selection', {'dependencies':{'trajectory':'trajectory'}, settings['reference_basis'] = ('atoms_list', {'dependencies':{'trajectory':'trajectory'},
'nAtoms':3, 'nAtoms':3,
'default':('C284H438N84O79S7',('O','C_beta','C_delta'))}) 'default':('C284H438N84O79S7',('O','C_beta','C_delta'))})
settings['target_molecule'] = ('atom_selection', {'dependencies':{'trajectory':'trajectory'}, settings['target_molecule'] = ('atom_selection', {'dependencies':{'trajectory':'trajectory'},
'default':'atom_index 151'}) 'default':'atom_index 151'})
settings['output_files'] = ('output_files', {'formats':["netcdf","ascii"]}) settings['output_files'] = ('output_files', {'formats':["netcdf","ascii"]})
......
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