def flush(self):
""" Write all buffers to file. """
if not len(self.__step) < 1:
# Make sure only master writes.
if MPICommons.isMaster():
# Write data to file.
with open(self._trajectory_filename, 'a') as trajectory:
for i in range(len(self.__step)):
step = self.__step[i]
time = self.__time[i]
n_atoms = len(self.__atom_id_types[i])
trajectory.write("STEP %i\n" % (step))
trajectory.write(" %i\n" % (n_atoms))
trajectory.write(" TIME %.2f\n" % (time))
for j in range(n_atoms):
t = self.__atom_id_types[i][j]
c = self.__atom_id_coordinates[i][j]
trajectory.write(" %16s %.3f %.3f %.3f %i\n" %
(t, c[0], c[1], c[2], j))
# While the other processes wait.
MPICommons.barrier()
# Reset the buffers.
self.__atom_id_types = []
self.__atom_id_coordinates = []
self.__time = []
self.__step = []
def __writeHeader(self, configuration):
"""
Write the header to the file.
:param configuration: The configuration of the system.
"""
# Make sure only master writes.
if MPICommons.isMaster():
# Open the file and write the meta information.
with open(self._trajectory_filename, 'w') as trajectory:
# Version.
trajectory.write("KMCLib XYZ FORMAT VERSION 2013.10.15\n\n")
# Cellvectors.
cell_vectors = configuration.lattice().unitCell().cellVectors()
trajectory.write("CELL VECTORS\n")
trajectory.write("a: %15.10e %15.10e %15.10e\n"%(cell_vectors[0][0], cell_vectors[0][1], cell_vectors[0][2]))
trajectory.write("b: %15.10e %15.10e %15.10e\n"%(cell_vectors[1][0], cell_vectors[1][1], cell_vectors[1][2]))
trajectory.write("c: %15.10e %15.10e %15.10e\n\n"%(cell_vectors[2][0], cell_vectors[2][1], cell_vectors[2][2]))
# Repetitions.
repetitions = configuration.lattice().repetitions()
trajectory.write("REPETITIONS %i %i %i\n\n"%(repetitions[0], repetitions[2], repetitions[2]))
# Periodicity.
periodicity = configuration.lattice().periodic()
trajectory.write("PERIODICITY %s %s %s\n\n"%(str(periodicity[0]), str(periodicity[1]), str(periodicity[2])))
# While the other processes wait.
MPICommons.barrier()
def flush(self):
""" Write all buffers to file. """
if not len(self.__step) < 1:
# Make sure only master writes.
if MPICommons.isMaster():
# Write data to file.
with open(self._trajectory_filename, 'a') as trajectory:
for i in range(len(self.__step)):
step = self.__step[i]
time = self.__time[i]
n_atoms = len(self.__atom_id_types[i])
trajectory.write("STEP %i\n"%(step))
trajectory.write(" %i\n"%(n_atoms))
trajectory.write(" TIME %15.10e\n"%(time))
for j in range(n_atoms):
t = self.__atom_id_types[i][j]
c = self.__atom_id_coordinates[i][j]
trajectory.write(" %16s %15.10e %15.10e %15.10e %i\n"%(t, c[0], c[1], c[2], j))
# While the other processes wait.
MPICommons.barrier()
# Reset the buffers.
self.__atom_id_types = []
self.__atom_id_coordinates = []
self.__time = []
self.__step = []
def __writeHeader(self, configuration):
"""
Write the header to the file.
:param configuration: The configuration of the system.
"""
# Make sure only master writes.
if MPICommons.isMaster():
# Open the file and write the meta information.
with open(self._trajectory_filename, 'w') as trajectory:
# Version.
trajectory.write("KMCLib XYZ FORMAT VERSION 2013.10.15\n\n")
# Cellvectors.
cell_vectors = configuration.lattice().unitCell().cellVectors()
trajectory.write("CELL VECTORS\n")
trajectory.write("a: %15.10e %15.10e %15.10e\n"%(cell_vectors[0][0], cell_vectors[0][1], cell_vectors[0][2]))
trajectory.write("b: %15.10e %15.10e %15.10e\n"%(cell_vectors[1][0], cell_vectors[1][1], cell_vectors[1][2]))
trajectory.write("c: %15.10e %15.10e %15.10e\n\n"%(cell_vectors[2][0], cell_vectors[2][1], cell_vectors[2][2]))
# Repetitions.
repetitions = configuration.lattice().repetitions()
trajectory.write("REPETITIONS %i %i %i\n\n"%(repetitions[0], repetitions[1], repetitions[2]))
# Periodicity.
periodicity = configuration.lattice().periodic()
trajectory.write("PERIODICITY %s %s %s\n\n"%(str(periodicity[0]), str(periodicity[1]), str(periodicity[2])))
# While the other processes wait.
MPICommons.barrier()
def tearDown(self):
""" The tearDown method for test fixtures. """
# Make sure to stop simultaneously.
MPICommons.barrier()
for f in self.__files_to_remove:
# Make sure only master delets files, while slaves wait.
if MPICommons.isMaster():
os.remove(f)
MPICommons.barrier()
def prettyPrint(msg, output=None):
"""
Utility function for printing an output string to screen.
:param msg: The message to print.
:type msg: str
:param out: The stream to write to. Defaults to sys.stdout.
"""
# Set the default.
if output is None:
output = sys.stdout
# Write.
if MPICommons.isMaster():
output.write(msg)
output.write("\n")
MPICommons.barrier()
def prettyPrint(msg, output=None):
"""
Utility function for printing an output string to screen.
:param msg: The message to print.
:type msg: str
:param out: The stream to write to. Defaults to sys.stdout.
"""
# Set the default.
if output is None:
output = sys.stdout
# Write.
if MPICommons.isMaster():
output.write(msg)
output.write("\n")
MPICommons.barrier()
def __writeToFile(self, simulation_time_buffer, step_buffer, types_buffer):
"""
Append the types and time information to the trajectory.
The trajectory if flushed to file if the flush time limit has passed.
:param simulation_time_buffer: A list of simulation times to be written to disk.
:param step_buffer: A list of step numbers to be written.
:param types_buffer: The types buffer given as a list of lists of strings.
"""
# Save to file.
# Make sure only master writes.
if MPICommons.isMaster():
with open(self.__trajectory_filename, 'a') as trajectory:
for (sim_time, step, types) in zip(simulation_time_buffer, step_buffer, types_buffer):
trajectory.write( "times.append(%f)\n"%sim_time )
trajectory.write( "steps.append(%i)\n"%step )
# Write the types.
types_str = "types.append(["
indent = " "*14
row_length = len(types_str)
for t in types[:-1]:
row_length += len(t) + 2
types_str += "\"" + t + "\"" + ","
# Berak the row if above 70 positions.
if row_length >= 70:
types_str += "\n" + indent
row_length = len(indent)
# Add the last type.
types_str += "\"" + types[-1] + "\"" + "])\n"
# Write it to file.
trajectory.write(types_str)
# While the others wait.
MPICommons.barrier()
# Update the time.
self.__time_last_dump = time.time()
def __writeToFile(self, simulation_time_buffer, step_buffer, types_buffer):
"""
Append the types and time information to the trajectory.
The trajectory if flushed to file if the flush time limit has passed.
:param simulation_time_buffer: A list of simulation times to be written to disk.
:param step_buffer: A list of step numbers to be written.
:param types_buffer: The types buffer given as a list of lists of strings.
"""
# Save to file.
# Make sure only master writes.
if MPICommons.isMaster():
with open(self._trajectory_filename, 'a') as trajectory:
for (sim_time, step, types) in zip(simulation_time_buffer,
step_buffer, types_buffer):
trajectory.write("times.append(%18.10e)\n" % sim_time)
trajectory.write("steps.append(%i)\n" % step)
# Write the types.
types_str = "types.append(["
indent = " " * 14
row_length = len(types_str)
for t in types[:-1]:
row_length += len(t) + 2
types_str += "\"" + t + "\"" + ","
# Berak the row if above 70 positions.
if row_length >= 70:
types_str += "\n" + indent
row_length = len(indent)
# Add the last type.
types_str += "\"" + types[-1] + "\"" + "])\n"
# Write it to file.
trajectory.write(types_str)
# While the others wait.
MPICommons.barrier()
def __writeHeader(self, sites):
"""
Write the header to the file.
:param sites: The sites in the system.
"""
# Make sure only master writes.
if MPICommons.isMaster():
# Open the file and write the meta information.
with open(self._trajectory_filename, 'w') as trajectory:
trajectory.write("# KMCLib Trajectory\n")
trajectory.write("version=\"2013.1.0\"\n")
trajectory.write("creation_time=\"%s\"\n" % (time.ctime()))
# Write the sites.
sites_str = "sites=["
indent = " " * 7
for i, site in enumerate(sites):
sites_str += "[%15.6f,%15.6f,%15.6f]" % (site[0], site[1],
site[2])
# Handle the last site differently.
if i == len(sites) - 1:
sites_str += "]\n"
else:
sites_str += ",\n" + indent
trajectory.write(sites_str)
# Write the empty lists.
trajectory.write("times=[]\n")
trajectory.write("steps=[]\n")
trajectory.write("types=[]\n")
# While the other processes wait.
MPICommons.barrier()
def __writeHeader(self, sites):
"""
Write the header to the file.
:param sites: The sites in the system.
"""
# Make sure only master writes.
if MPICommons.isMaster():
# Open the file and write the meta information.
with open(self._trajectory_filename, 'w') as trajectory:
trajectory.write( "# KMCLib Trajectory\n" )
trajectory.write( "version=\"2013.1.0\"\n" )
trajectory.write( "creation_time=\"%s\"\n"%(time.ctime()) )
# Write the sites.
sites_str = "sites=["
indent = " "*7
for i,site in enumerate(sites):
sites_str += "[%15.6f,%15.6f,%15.6f]"%(site[0],site[1],site[2])
# Handle the last site differently.
if i == len(sites)-1:
sites_str += "]\n"
else:
sites_str += ",\n" + indent
trajectory.write( sites_str )
# Write the empty lists.
trajectory.write("times=[]\n")
trajectory.write("steps=[]\n")
trajectory.write("types=[]\n")
# While the other processes wait.
MPICommons.barrier()
def __writeToFile(self, simulation_time_buffer, step_buffer, types_buffer):
"""
Append the types and time information to the trajectory.
The trajectory if flushed to file if the flush time limit has passed.
:param simulation_time_buffer: A list of simulation times to be written to disk.
:param step_buffer: A list of step numbers to be written.
:param types_buffer: The types buffer given as a list of lists of strings.
"""
# Save to file.
# Make sure only master writes.
if MPICommons.isMaster():
with open(self._trajectory_filename, 'a') as trajectory:
for (sim_time, step, types) in zip(simulation_time_buffer,
step_buffer, types_buffer):
trajectory.write("times.append(%18.10e)\n" % sim_time)
trajectory.write("steps.append(%i)\n" % step)
# Write the types.
types_str = "types.append(["
indent = " " * 14
row_length = len(types_str)
if isinstance(types[:-1][0], str):
for t in types[:-1]:
row_length += len(t) + 2
types_str += "\"" + t + "\"" + ","
# Berak the row if above 70 positions.
if row_length >= 70:
types_str += "\n" + indent
row_length = len(indent)
# Add the last type.
types_str += "\"" + types[-1] + "\"" + "])\n"
# With bucket types.
else:
bucket_types = toShortBucketsFormat(types)
# For all sites except the last.
for bt in bucket_types[:-1]:
# Start the types for this site.
types_str += "["
for t in bt[:-1]:
types_str += "(" + str(
t[0]) + ",\"" + t[1] + "\"),"
if len(bt) > 0:
t = bt[-1]
types_str += "(" + str(
t[0]) + ",\"" + t[1] + "\")"
types_str += "],\n" + indent
else:
types_str += "],\n" + indent
# For the last site.
bt = bucket_types[-1]
types_str += "["
for t in bt[:-1]:
types_str += "(" + str(
t[0]) + ",\"" + t[1] + "\"),"
if len(bt) > 0:
t = bt[-1]
types_str += "(" + str(
t[0]) + ",\"" + t[1] + "\")]"
else:
types_str += "]"
types_str += "])\n"
# Write it to file.
trajectory.write(types_str)
# While the others wait.
MPICommons.barrier()
def testAppend(self):
""" Test appending to the trajectory. """
# Setup input.
sites = [[0.0,1.0,2.3],
[1.0,0.0,2.3],
[1.0,1.0,0.3],
[1.0,1.0,2.3],
[3.4,4.5,4.3],
[3.4,4.3,4.3],
[3.4,5.5,4.3],
[3.7,7.5,6.5]]
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory_file.py")
self.__files_to_remove.append(trajectory_filename)
# Construct.
t = Trajectory(trajectory_filename, sites)
# Append times, steps and typers.
t.append(1.10045, 12,
["A", "A", "A", "A", "A", "A"] )
# Since this was the first time it should have triggered a dump to file.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Needed to prevent test failure.
MPICommons.barrier()
# Check the types.
ret_types = local_dict['types']
ref_types = [["A", "A", "A", "A", "A", "A"]]
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045]
self.assertEqual( ret_times, ref_times )
# Appending again directly makes no dump.
t.append(1.1993, 14,
["B", "B", "B", "B", "B", "B"] )
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Needed to prevent test failure.
MPICommons.barrier()
# Check.
ret_types = local_dict['types']
self.assertEqual( ret_types, ref_types )
ret_steps = local_dict['steps']
self.assertEqual( ret_steps, ref_steps )
ret_times = local_dict['times']
self.assertEqual( ret_times, ref_times )
# But if we dump again and set the time limit to zero we will trigger a dump.
t._Trajectory__max_buffer_time = 0.0
t.append(1.199, 19,
["C", "C", "C", "C", "C", "C"] )
# Reset the time to some thing large.
t._Trajectory__max_buffer_time = 100000000000.0
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Check the types.
ret_types = local_dict['types']
ref_types = [["A","A","A","A","A","A"],
["B","B","B","B","B","B"],
["C","C","C","C","C","C"]]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12,14,19]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045, 1.1993, 1.199]
self.assertEqual( ret_times, ref_times )
# The buffers are reset after each dump. If we make the
# max size limit smaller than the size of the appended types
# list this must trigger a dump.
types = ["A","A","A","A","A","B"]
size = sys.getsizeof(types)
t._Trajectory__max_buffer_size = size
# Append.
t.append(1.1995, 43, types )
# Check.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
ret_types = local_dict['types']
ref_types = [["A","A","A","A","A","A"],
["B","B","B","B","B","B"],
["C","C","C","C","C","C"]]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Append.
t.append(1.1995, 43, types )
t.append(1.1995, 43, types )
t.append(1.1995, 43, types )
# This last one triggers the dump.
t.append(1.1995, 43, types )
# Check.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
ret_types = local_dict['types']
ref_types = [["A","A","A","A","A","A"],
["B","B","B","B","B","B"],
["C","C","C","C","C","C"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"]]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
def setUp(self):
""" The setUp method for test fixtures. """
self.__files_to_remove = []
# Make sure to start simultaneously.
MPICommons.barrier()
def tearDown(self):
""" The tearDown method for test fixtures. """
for f in self.__files_to_remove:
if MPICommons.isMaster():
os.remove(f)
MPICommons.barrier()
def flush(self):
""" Write all buffers to file. """
if not len(self.__step) < 1:
# Make sure only master writes.
if MPICommons.isMaster():
# Write data to file.
with open(self._trajectory_filename, 'a') as trajectory:
for i in range(len(self.__step)):
step = self.__step[i]
time = self.__time[i]
n_atoms = len(self.__atom_id_types[i])
# calculate the super-cell length
H = 5.0
#supercell headers for CFG file for atomeye
trajectory.write("Number of particles = %i\n\n" %
(n_atoms))
trajectory.write("A = 1 Angstrom\n")
trajectory.write("H0(1,1) = %f A\n" % (H))
trajectory.write("H0(1,2) = 0 . 0 A\n")
trajectory.write("H0(1,3) = 0 . 0 A\n")
trajectory.write("H0(2,1) = 0 . 0 A\n")
trajectory.write("H0(2,2) = %f A\n" % (H))
trajectory.write("H0(2,3) = 0 . 0 A\n")
trajectory.write("H0(3,1) = 0 . 0 A\n")
trajectory.write("H0(3,2) = 0 . 0 A\n")
trajectory.write("H0(3,3) = %f A\n" % (H))
trajectory.write("#\n")
for j in range(n_atoms):
t = self.__atom_id_types[i][j]
c = self.__atom_id_coordinates[i][j]
#reduce the coordinates
"""if c[0] < 0.0:
s1 = 1- (c[0] - math.floor(c[0]))
print ("reduced<: %.2f"%(s1)
elif c[0] > 5.0:
s1 = c[0] - math.floor(c[0])
print ("reduced>: %.2f"%(s1)
"""
s1 = c[0] / H
s2 = c[1] / H
s3 = c[2] / H
#print("X: %f Y: %f Z: %f"%(s1, s2, s3))
#change the mass atomic number depending on type of atoms there
if t == 'Fe':
mass = 55.845
elif t == 'V':
mass = 1.0
# write the cfg file with reduced coordinates
trajectory.write(
"%.2f %s %.2f %.2f %.2f 0.0 0.0 0.0\n" %
(mass, t, s1, s2, s3))
# While the other processes wait.
MPICommons.barrier()
# Reset the buffers.
self.__atom_id_types = []
self.__atom_id_coordinates = []
self.__time = []
self.__step = []
def __writeToFile(self, simulation_time_buffer, step_buffer, types_buffer):
"""
Append the types and time information to the trajectory.
The trajectory if flushed to file if the flush time limit has passed.
:param simulation_time_buffer: A list of simulation times to be written to disk.
:param step_buffer: A list of step numbers to be written.
:param types_buffer: The types buffer given as a list of lists of strings.
"""
# Save to file.
# Make sure only master writes.
if MPICommons.isMaster():
with open(self._trajectory_filename, 'a') as trajectory:
for (sim_time, step, types) in zip(simulation_time_buffer, step_buffer, types_buffer):
trajectory.write( "times.append(%18.10e)\n"%sim_time )
trajectory.write( "steps.append(%i)\n"%step )
# Write the types.
types_str = "types.append(["
indent = " "*14
row_length = len(types_str)
if isinstance(types[:-1][0], str):
for t in types[:-1]:
row_length += len(t) + 2
types_str += "\"" + t + "\"" + ","
# Berak the row if above 70 positions.
if row_length >= 70:
types_str += "\n" + indent
row_length = len(indent)
# Add the last type.
types_str += "\"" + types[-1] + "\"" + "])\n"
# With bucket types.
else:
bucket_types = toShortBucketsFormat(types)
# For all sites except the last.
for bt in bucket_types[:-1]:
# Start the types for this site.
types_str += "["
for t in bt[:-1]:
types_str += "(" + str(t[0]) + ",\"" + t[1] + "\"),"
if len(bt) > 0:
t = bt[-1]
types_str += "(" + str(t[0]) + ",\"" + t[1] + "\")"
types_str += "],\n" + indent
else:
types_str += "],\n" + indent
# For the last site.
bt = bucket_types[-1]
types_str += "["
for t in bt[:-1]:
types_str += "(" + str(t[0]) + ",\"" + t[1] + "\"),"
if len(bt) > 0:
t = bt[-1]
types_str += "(" + str(t[0]) + ",\"" + t[1] + "\")]"
else:
types_str += "]"
types_str += "])\n"
# Write it to file.
trajectory.write(types_str)
# While the others wait.
MPICommons.barrier()
def __init__(self,
trajectory_filename,
sites,
max_buffer_size=None,
max_buffer_time=None):
"""
Constructor for the Trajectory.
:param trajectory_filename: The file name to write trajectory information to.
:type trajectory_filename: str
:param sites: The lattice sites of the configuration as an Nx3 list.
:param max_buffer_size: The max size of the the buffer in memory
before writing to file.
:type max_buffer_size: int
:param max_buffer_time: The max time limit between dumps to file.
:type max_buffer_time: float
"""
# Set the defaults.
if max_buffer_size is None:
self.__max_buffer_size = 1024*1024*10 # <- Max buffer size in bytes (10 MB)
else:
self.__max_buffer_size = max_buffer_size
if max_buffer_time is None:
self.__max_buffer_time = 30*60.0 # <- Max time in seconds (30 min)
else:
self.__max_buffer_time = max_buffer_time
# Note that this object is not in the interface, so input is allready checked.
self.__trajectory_filename = trajectory_filename
# Open the file and write the meta information.
# Make sure only master writes.
if MPICommons.isMaster():
with open(self.__trajectory_filename, 'w') as trajectory:
trajectory.write( "# KMCLib Trajectory\n" )
trajectory.write( "version=\"2013.1.0\"\n" )
trajectory.write( "creation_time=\"%s\"\n"%(time.ctime()) )
# Write the sites.
sites_str = "sites=["
indent = " "*7
for i,site in enumerate(sites):
sites_str += "[%15.6f,%15.6f,%15.6f]"%(site[0],site[1],site[2])
# Handle the last site differently.
if i == len(sites)-1:
sites_str += "]\n"
else:
sites_str += ",\n" + indent
trajectory.write( sites_str )
# Write the empty lists.
trajectory.write("times=[]\n")
trajectory.write("steps=[]\n")
trajectory.write("types=[]\n")
# While the other processes wait.
MPICommons.barrier()
# Init the member data.
self.__types_buffer = []
self.__simulation_time_buffer = []
self.__step_buffer = []
# Set the time counter to zero.
self.__time_last_dump = 0.0
def testWriteToFile(self):
""" Test writing the buffers to file. """
# Setup input.
sites = [[0.0,1.0,2.3],
[1.0,0.0,2.3],
[1.0,1.0,0.3],
[1.0,1.0,2.3],
[3.4,4.5,4.3],
[3.4,4.3,4.3],
[3.4,5.5,4.3],
[3.7,7.5,6.5]]
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory_file.py")
self.__files_to_remove.append(trajectory_filename)
# Construct.
t = Trajectory(trajectory_filename, sites)
# Write times, steps and typers.
times = [1.10045, 2.334156, 3.4516410]
steps = [12, 25, 52]
types = [["ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps",
"here", "is", "Next", "Long", "List", "Offffffff", "Names", "now", "this", "one", "is", "longer", "still"],
["A", "B", "C", "D", "E", "F", "G", "H"],
["1", "2", "4", "5", "6", "5" ,"43", "243r2424"]]
# Needed to prevent test failure.
MPICommons.barrier()
# Check that the time is zero before we start.
self.assertAlmostEqual( t._Trajectory__time_last_dump, 0.0, 10 )
t._Trajectory__writeToFile(times, steps, types)
# Needed to prevent test failure.
MPICommons.barrier()
# Check that the time stamp was updated.
self.assertTrue( 1357651850 < t._Trajectory__time_last_dump )
last_time = t._Trajectory__time_last_dump
# Check the info stored in the file.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Check the types.
ret_types = local_dict['types']
ref_types = [['ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps',
'here', 'is', 'Next', 'Long', 'List', 'Offffffff',
'Names', 'now', 'this', 'one', 'is', 'longer', 'still'],
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'],
['1', '2', '4', '5', '6', '5', '43', '243r2424']]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12, 25, 52]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045, 2.334156, 3.451641]
self.assertEqual( ret_times, ref_times )
# Sleep for two seconds before we add again.
time.sleep(1)
t._Trajectory__writeToFile(times, steps, types)
# Check the time.
self.assertTrue( (t._Trajectory__time_last_dump - last_time > 1) )
# Now, check the file again.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Check the types.
ret_types = local_dict['types']
ref_types = [['ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps',
'here', 'is', 'Next', 'Long', 'List', 'Offffffff',
'Names', 'now', 'this', 'one', 'is', 'longer', 'still'],
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'],
['1', '2', '4', '5', '6', '5', '43', '243r2424'],
['ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps',
'here', 'is', 'Next', 'Long', 'List', 'Offffffff',
'Names', 'now', 'this', 'one', 'is', 'longer', 'still'],
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'],
['1', '2', '4', '5', '6', '5', '43', '243r2424']]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12, 25, 52, 12, 25, 52]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045, 2.334156, 3.451641, 1.10045, 2.334156, 3.451641]
self.assertEqual( ret_times, ref_times )
