Commit 63c45e3f authored by cmaffeo2's avatar cmaffeo2
Browse files

Changed name of SegmentModel command for updating splines

parent da45cd89
......@@ -1416,7 +1416,11 @@ class SegmentModel(ArbdModel):
assert( len(locParticles) == 0 )
assert( len([b for s in self.segments for b in s.beads]) == 0 )
def _update_segment_positions(self, bead_coordinates): # TODO: rename to update_splines
def _update_segment_positions(self, bead_coordinates):
print("WARNING: called deprecated command '_update_segment_positions; use 'update_splines' instead")
return self.update_splines(bead_coordinates)
def update_splines(self, bead_coordinates):
""" Set new function for each segments functions
contour_to_position and contour_to_orientation """
......
......@@ -51,7 +51,7 @@ def multiresolution_simulation( model, output_name,
except:
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
output_prefix = "%s-1" % output_name
model._update_segment_positions(coordinates)
model.update_splines(coordinates)
model.simulate( outputPrefix = output_prefix, numSteps=0.95*coarse_steps, **simargs )
else:
output_prefix = "%s-1" % output_name
......@@ -68,7 +68,7 @@ def multiresolution_simulation( model, output_name,
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
simargs['timestep'] = 50e-6
simargs['outputPeriod'] = fine_output_period
model._update_segment_positions(coordinates)
model.update_splines(coordinates)
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
......@@ -81,7 +81,7 @@ def multiresolution_simulation( model, output_name,
""" Freeze twist """
output_prefix = "%s-3" % output_name
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model._update_segment_positions(coordinates)
model.update_splines(coordinates)
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=False )
model.simulate( outputPrefix = output_prefix, numSteps=fine_steps, **simargs )
......@@ -94,7 +94,7 @@ def multiresolution_simulation( model, output_name,
""" Atomic simulation """
output_prefix = "%s-4" % output_name
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model._update_segment_positions(coordinates)
model.update_splines(coordinates)
model._clear_beads()
model._generate_atomic_model(scale=backbone_scale)
model.atomic_simulate( outputPrefix = output_prefix )
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment