def main(self, params, options, args):
"""Execute the script."""
from dials.algorithms.refinement import RefinerFactory
from dials.model.serialize import load
import cPickle as pickle
from time import time
import sys
# Check the number of arguments is correct
if len(args) != 3:
self.config().print_help()
return
# Hack the phil parameters to control the number of reflections
params.refinement.reflections.use_all_reflections = False
params.refinement.reflections.random_seed = None
# and also to make the target achieved criterion more stringent
params.refinement.target.bin_size_fraction = 0.1
# print header for output table
print "Nref RMSDx RMSDy RMSDphi Steps Target_acheived Time"
#for n in range(1,170,2):
for n in [e * 0.1 for e in range(1,100)]:
# Set nref to use
params.refinement.reflections.reflections_per_degree = n
# Get the refiner from the input parameters
refine = RefinerFactory.from_parameters(params, options.verbosity)
# Try to load the models
sweep = load.sweep(args[0])
crystal = load.crystal(args[1])
reflections = pickle.load(open(args[2], 'rb'))
# Refine the geometry
start_time = time()
try:
refined = refine(sweep, crystal, reflections)
except Exception as e:
print "ERROR occurred"
continue
time_taken = time() - start_time
print refined.history.num_reflections[-1],
print "%.6f %.6f %.8f" % refine.rmsds(),
print "%d" % refined.get_num_steps(),
print refined.test_for_termination(),
print "%.3f" % time_taken
# flush the buffer so we can see some output
sys.stdout.flush()
return
def main(self, params, options, args):
"""Execute the script."""
from dials.algorithms.refinement import RefinerFactory
from dials.model.serialize import load
import cPickle as pickle
from time import time
import sys
# Check the number of arguments is correct
if len(args) != 3:
self.config().print_help()
return
# Hack the phil parameters to control the number of reflections
params.refinement.reflections.use_all_reflections = False
params.refinement.reflections.random_seed = None
# and also to make the target achieved criterion more stringent
params.refinement.target.bin_size_fraction = 0.1
# print header for output table
print("Nref RMSDx RMSDy RMSDphi Steps Target_acheived Time")
# for n in range(1,170,2):
for n in [e * 0.1 for e in range(1, 100)]:
# Set nref to use
params.refinement.reflections.reflections_per_degree = n
# Get the refiner from the input parameters
refine = RefinerFactory.from_parameters(params, options.verbosity)
# Try to load the models
sweep = load.sweep(args[0])
crystal = load.crystal(args[1])
reflections = pickle.load(open(args[2], "rb"))
# Refine the geometry
start_time = time()
try:
refined = refine(sweep, crystal, reflections)
except Exception as e:
print("ERROR occurred")
continue
time_taken = time() - start_time
print(refined.history.num_reflections[-1], end=" ")
print("%.6f %.6f %.8f" % refine.rmsds(), end=" ")
print("%d" % refined.get_num_steps(), end=" ")
print(refined.test_for_termination(), end=" ")
print("%.3f" % time_taken)
# flush the buffer so we can see some output
sys.stdout.flush()
return
