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Commit 4961e40b authored by Lauri Himanen's avatar Lauri Himanen
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Fixed issue with restarted calculations, fixed bugs in reading MD files with... 

Fixed issue with restarted calculations, fixed bugs in reading MD files with non-unity print frequencies.
parent d361b1ad
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parser/parser-cp2k/cp2kparser/parser.py
View file @ 4961e40b
......@@ -32,12 +32,15 @@ class CP2KParser(ParserInterface):
# this information.
regex_version = re.compile(r" CP2K\| version string:\s+CP2K version ([\d\.]+)")
regex_run_type = re.compile(r"\s+GLOBAL\| Run type\s+(.+)")
n_lines = 50
n_lines = 100
version_id = None
run_type = None
with open(self.parser_context.main_file, 'r') as outputfile:
for i_line in range(n_lines):
line = next(outputfile)
try:
line = next(outputfile)
except StopIteration:
break
result_version = regex_version.match(line)
result_run_type = regex_run_type.match(line)
if result_version:
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
View file @ 4961e40b
......@@ -127,11 +127,28 @@ class CP2KCommonParser(CommonParser):
],
),
SM( " CELL\|",
adHoc=self.adHoc_x_cp2k_section_cell(),
adHoc=self.adHoc_x_cp2k_section_cell,
),
]
)
# SimpleMatcher for the restart information
def restart(self):
return SM( re.escape(" * RESTART INFORMATION *"),
sections=["x_cp2k_section_restart_information"],
subMatchers=[
SM( re.escape(" *******************************************************************************")),
SM( re.escape(" * *")),
SM( re.escape(" * RESTART FILE NAME: (?P<x_cp2k_restart_file_name>{})\s+*".format(self.regexs.word))),
SM( re.escape(" * *")),
SM( re.escape(" * RESTARTED QUANTITIES: *")),
SM( re.escape(" * (?P<x_cp2k_restarted_quantity>{})\s+*".format(self.regexs.word)),
repeats=True,
),
SM( re.escape(" *******************************************************************************"))
]
)
# SimpleMatcher for the footer that is common to all run types
def footer(self):
return SM( " - DBCSR STATISTICS -",
......@@ -168,32 +185,32 @@ class CP2KCommonParser(CommonParser):
]
),
SM( r" \*\*\* SCF run converged in\s+(\d+) steps \*\*\*",
adHoc=self.adHoc_single_point_converged()
adHoc=self.adHoc_single_point_converged
),
SM( r" \*\*\* SCF run NOT converged \*\*\*",
adHoc=self.adHoc_single_point_not_converged()
adHoc=self.adHoc_single_point_not_converged
),
SM( r" Electronic kinetic energy:\s+(?P<x_cp2k_electronic_kinetic_energy__hartree>{})".format(self.regexs.float)),
SM( r" **************************** NUMERICAL STRESS ********************************".replace("*", "\*"),
# endReStr=" **************************** NUMERICAL STRESS END *****************************".replace("*", "\*"),
adHoc=self.adHoc_stress_calculation(),
adHoc=self.adHoc_stress_calculation,
),
SM( r" ENERGY\| Total FORCE_EVAL \( \w+ \) energy \(a\.u\.\):\s+(?P<x_cp2k_energy_total__hartree>{0})".format(self.regexs.float),
),
SM( r" ATOMIC FORCES in \[a\.u\.\]"),
SM( r" # Atom Kind Element X Y Z",
adHoc=self.adHoc_atom_forces(),
adHoc=self.adHoc_atom_forces,
),
SM( r" (?:NUMERICAL )?STRESS TENSOR \[GPa\]",
sections=["x_cp2k_section_stress_tensor"],
subMatchers=[
SM( r"\s+X\s+Y\s+Z",
adHoc=self.adHoc_stress_tensor(),
adHoc=self.adHoc_stress_tensor,
),
SM( " 1/3 Trace\(stress tensor\):\s+(?P<x_cp2k_stress_tensor_one_third_of_trace__GPa>{})".format(self.regexs.float)),
SM( " Det\(stress tensor\)\s+:\s+(?P<x_cp2k_stress_tensor_determinant__GPa3>{})".format(self.regexs.float)),
SM( " EIGENVECTORS AND EIGENVALUES OF THE STRESS TENSOR",
adHoc=self.adHoc_stress_tensor_eigenpairs()),
adHoc=self.adHoc_stress_tensor_eigenpairs),
]
)
]
......@@ -201,7 +218,7 @@ class CP2KCommonParser(CommonParser):
# SimpleMatcher the stuff that is done to initialize a quickstep calculation
def quickstep_header(self):
return SM( " *******************************************************************************".replace("*", "\*"),
return SM( re.escape(" ** ... make the atoms dance **"),
forwardMatch=True,
sections=["x_cp2k_section_quickstep_settings"],
subMatchers=[
......@@ -216,7 +233,7 @@ class CP2KCommonParser(CommonParser):
],
),
SM( " DFT\+U\|",
adHoc=self.adHoc_dft_plus_u(),
adHoc=self.adHoc_dft_plus_u,
),
SM( " QS\|",
forwardMatch=True,
......@@ -301,10 +318,10 @@ class CP2KCommonParser(CommonParser):
]
),
SM( " MP2\|",
adHoc=self.adHoc_mp2()
adHoc=self.adHoc_mp2
),
SM( " RI-RPA\|",
adHoc=self.adHoc_rpa()
adHoc=self.adHoc_rpa
),
]
)
......@@ -501,113 +518,96 @@ class CP2KCommonParser(CommonParser):
#===========================================================================
# adHoc functions
def adHoc_x_cp2k_section_cell(self):
def adHoc_x_cp2k_section_cell(self, parser):
"""Used to extract the cell information.
"""
def wrapper(parser):
# Read the lines containing the cell vectors
a_line = parser.fIn.readline()
b_line = parser.fIn.readline()
c_line = parser.fIn.readline()
# Define the regex that extracts the components and apply it to the lines
regex_string = r" CELL\| Vector \w \[angstrom\]:\s+({0})\s+({0})\s+({0})".format(self.regexs.float)
regex_compiled = re.compile(regex_string)
a_result = regex_compiled.match(a_line)
b_result = regex_compiled.match(b_line)
c_result = regex_compiled.match(c_line)
# Convert the string results into a 3x3 numpy array
cell = np.zeros((3, 3))
cell[0, :] = [float(x) for x in a_result.groups()]
cell[1, :] = [float(x) for x in b_result.groups()]
cell[2, :] = [float(x) for x in c_result.groups()]
# Push the results to cache
self.cache_service["simulation_cell"] = cell
return wrapper
def adHoc_atom_forces(self):
# Read the lines containing the cell vectors
a_line = parser.fIn.readline()
b_line = parser.fIn.readline()
c_line = parser.fIn.readline()
# Define the regex that extracts the components and apply it to the lines
regex_string = r" CELL\| Vector \w \[angstrom\]:\s+({0})\s+({0})\s+({0})".format(self.regexs.float)
regex_compiled = re.compile(regex_string)
a_result = regex_compiled.match(a_line)
b_result = regex_compiled.match(b_line)
c_result = regex_compiled.match(c_line)
# Convert the string results into a 3x3 numpy array
cell = np.zeros((3, 3))
cell[0, :] = [float(x) for x in a_result.groups()]
cell[1, :] = [float(x) for x in b_result.groups()]
cell[2, :] = [float(x) for x in c_result.groups()]
# Push the results to cache
self.cache_service["simulation_cell"] = cell
def adHoc_atom_forces(self, parser):
"""Used to extract the final atomic forces printed at the end of a
calculation.
"""
def wrapper(parser):
end_str = " SUM OF ATOMIC FORCES"
end = False
force_array = []
# Loop through coordinates until the sum of forces is read
while not end:
line = parser.fIn.readline()
if line.startswith(end_str):
end = True
else:
forces = line.split()[-3:]
forces = [float(x) for x in forces]
force_array.append(forces)
force_array = np.array(force_array)
# If anything found, push the results to the correct section
if len(force_array) != 0:
# self.cache_service["atom_forces"] = force_array
self.backend.addArrayValues("x_cp2k_atom_forces", force_array, unit="forceAu")
end_str = " SUM OF ATOMIC FORCES"
end = False
force_array = []
# Loop through coordinates until the sum of forces is read
while not end:
line = parser.fIn.readline()
if line.startswith(end_str):
end = True
else:
forces = line.split()[-3:]
forces = [float(x) for x in forces]
force_array.append(forces)
force_array = np.array(force_array)
return wrapper
# If anything found, push the results to the correct section
if len(force_array) != 0:
# self.cache_service["atom_forces"] = force_array
self.backend.addArrayValues("x_cp2k_atom_forces", force_array, unit="forceAu")
def adHoc_stress_tensor(self):
def adHoc_stress_tensor(self, parser):
"""Used to extract the stress tensor printed at the end of a
calculation.
"""
def wrapper(parser):
row1 = [float(x) for x in parser.fIn.readline().split()[-3:]]
row2 = [float(x) for x in parser.fIn.readline().split()[-3:]]
row3 = [float(x) for x in parser.fIn.readline().split()[-3:]]
stress_array = np.array([row1, row2, row3])
parser.backend.addArrayValues("x_cp2k_stress_tensor", stress_array, unit="GPa")
return wrapper
row1 = [float(x) for x in parser.fIn.readline().split()[-3:]]
row2 = [float(x) for x in parser.fIn.readline().split()[-3:]]
row3 = [float(x) for x in parser.fIn.readline().split()[-3:]]
stress_array = np.array([row1, row2, row3])
parser.backend.addArrayValues("x_cp2k_stress_tensor", stress_array, unit="GPa")
def adHoc_stress_calculation(self):
def adHoc_stress_calculation(self, parser):
"""Used to skip over the stress tensor calculation details.
"""
def wrapper(parser):
end_line = " **************************** NUMERICAL STRESS END *****************************\n"
finished = False
while not finished:
line = parser.fIn.readline()
if line == end_line:
finished = True
return wrapper
def adHoc_stress_tensor_eigenpairs(self):
end_line = " **************************** NUMERICAL STRESS END *****************************\n"
finished = False
while not finished:
line = parser.fIn.readline()
if line == end_line:
finished = True
def adHoc_stress_tensor_eigenpairs(self, parser):
"""Parses the stress tensor eigenpairs.
"""
def wrapper(parser):
parser.fIn.readline()
eigenvalues = np.array([float(x) for x in parser.fIn.readline().split()])
parser.fIn.readline()
row1 = [float(x) for x in parser.fIn.readline().split()]
row2 = [float(x) for x in parser.fIn.readline().split()]
row3 = [float(x) for x in parser.fIn.readline().split()]
eigenvectors = np.array([row1, row2, row3])
parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvalues", eigenvalues, unit="GPa")
parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvectors", eigenvectors)
return wrapper
def adHoc_single_point_converged(self):
parser.fIn.readline()
eigenvalues = np.array([float(x) for x in parser.fIn.readline().split()])
parser.fIn.readline()
row1 = [float(x) for x in parser.fIn.readline().split()]
row2 = [float(x) for x in parser.fIn.readline().split()]
row3 = [float(x) for x in parser.fIn.readline().split()]
eigenvectors = np.array([row1, row2, row3])
parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvalues", eigenvalues, unit="GPa")
parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvectors", eigenvectors)
def adHoc_single_point_converged(self, parser):
"""Called when the SCF cycle of a single point calculation has converged.
"""
def wrapper(parser):
parser.backend.addValue("x_cp2k_quickstep_converged", True)
return wrapper
parser.backend.addValue("x_cp2k_quickstep_converged", True)
def adHoc_single_point_not_converged(self):
def adHoc_single_point_not_converged(self, parser):
"""Called when the SCF cycle of a single point calculation did not converge.
"""
def wrapper(parser):
parser.backend.addValue("x_cp2k_quickstep_converged", False)
return wrapper
parser.backend.addValue("x_cp2k_quickstep_converged", False)
def adHoc_x_cp2k_section_quickstep_atom_information(self):
"""Used to extract the initial atomic coordinates and names in the
......@@ -680,17 +680,16 @@ class CP2KCommonParser(CommonParser):
return wrapper
def adHoc_dft_plus_u(self):
def wrapper(parser):
self.test_electronic_structure_method = "DFT+U"
return wrapper
def adHoc_dft_plus_u(self, parser):
self.test_electronic_structure_method = "DFT+U"
def adHoc_mp2(self):
def wrapper(parser):
self.test_electronic_structure_method = "MP2"
return wrapper
def adHoc_mp2(self, parser):
self.test_electronic_structure_method = "MP2"
def adHoc_rpa(self):
def wrapper(parser):
self.test_electronic_structure_method = "RPA"
def adHoc_rpa(self, parser):
self.test_electronic_structure_method = "RPA"
def adHoc_print(self, msg):
def wrapper(parser, groups):
print(msg)
return wrapper
parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
View file @ 4961e40b
......@@ -70,20 +70,16 @@ class CP2KInputParser(AbstractBaseParser):
def parse(self, filepath):
#=======================================================================
# Preprocess to spell out variables and to include stuff from other
# files
self.preprocess_input(filepath)
#=======================================================================
# Gather the information from the input file
self.fill_input_tree(filepath)
#=======================================================================
# Parse everything in the input to cp2k specific metadata
self.fill_metadata()
#=======================================================================
# Parse the used XC_functionals and their parameters
xc = self.input_tree.get_section("FORCE_EVAL/DFT/XC/XC_FUNCTIONAL")
if xc is not None:
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
View file @ 4961e40b
......@@ -103,7 +103,7 @@ class CP2KMDParser(MainHierarchicalParser):
subMatchers=[
self.cm.quickstep_calculation(),
SM( " ENSEMBLE TYPE ="),
SM( " STEP NUMBER ="),
SM( " STEP NUMBER =\s+(?P<x_cp2k_md_step_number>{})".format(self.regexs.int)),
SM( " TIME \[fs\] =\s+(?P<x_cp2k_md_time__fs>{})".format(self.regexs.float)),
SM( " CONSERVED QUANTITY \[hartree\] =\s+(?P<x_cp2k_md_conserved_quantity__hartree>{})".format(self.regexs.float)),
SM( " CPU TIME \[s\] =\s+(?P<x_cp2k_md_cpu_time_instantaneous>{})\s+(?P<x_cp2k_md_cpu_time_average>{})".format(self.regexs.float, self.regexs.float)),
......@@ -135,6 +135,7 @@ class CP2KMDParser(MainHierarchicalParser):
forwardMatch=True,
sections=["section_method"],
subMatchers=[
self.cm.restart(),
self.cm.header(),
self.cm.quickstep_header(),
],
......@@ -260,7 +261,7 @@ class CP2KMDParser(MainHierarchicalParser):
if add_last_vel_setting == "NUMERIC" or add_last_vel_setting == "SYMBOLIC":
add_last_vel = True
last_step = self.n_steps - 1
last_step = self.n_steps
md_steps = section["x_cp2k_section_md_step"]
frame_sequence_potential_energy = []
......@@ -269,10 +270,24 @@ class CP2KMDParser(MainHierarchicalParser):
frame_sequence_kinetic_energy = []
frame_sequence_conserved_quantity = []
frame_sequence_pressure = []
ener_frames = []
single_conf_gids = []
i_md_step = 0
# Check that is the calculation starting from first frame. If not, this
# is a restarted calculation. In this case it is practically impossible
# to know from which frame number we should start reading the
# configurations, because the print settings in the previous runs may
# have been different from now, and the step numbers are hard to align.
# In this case we just parse what is found in this output file
start_step_number = md_steps[1]["x_cp2k_md_step_number"][0]
if start_step_number != 1:
self.traj_iterator = None
self.cell_iterator = None
self.vel_iterator = None
self.energy_iterator = None
for i_step in range(self.n_steps + 1):
sectionGID = backend.openSection("section_single_configuration_calculation")
......@@ -290,7 +305,7 @@ class CP2KMDParser(MainHierarchicalParser):
# Trajectory
if freqs["trajectory"][1] and self.traj_iterator is not None:
if (i_step + 1) % freqs["trajectory"][0] == 0 or (i_step == last_step and add_last_traj):
if (i_step) % freqs["trajectory"][0] == 0 or (i_step == last_step and add_last_traj):
try:
pos = next(self.traj_iterator)
except StopIteration:
......@@ -300,7 +315,7 @@ class CP2KMDParser(MainHierarchicalParser):
# Velocities
if freqs["velocities"][1] and self.vel_iterator is not None:
if (i_step + 1) % freqs["velocities"][0] == 0 or (i_step == last_step and add_last_vel):
if (i_step) % freqs["velocities"][0] == 0 or (i_step == last_step and add_last_vel):
try:
vel = next(self.vel_iterator)
except StopIteration:
......@@ -310,7 +325,7 @@ class CP2KMDParser(MainHierarchicalParser):
# Energy file
if self.energy_iterator is not None:
if (i_step + 1) % freqs["energies"][0] == 0:
if (i_step) % freqs["energies"][0] == 0:
line = next(self.energy_iterator)
time = line[1]
......@@ -326,20 +341,30 @@ class CP2KMDParser(MainHierarchicalParser):
frame_sequence_potential_energy.append(potential_energy)
frame_sequence_conserved_quantity.append(conserved_quantity)
ener_frames.append(i_step)
backend.addValue("energy_total", conserved_quantity)
backend.addValue("time_calculation", wall_time)
# Cell file
if self.cell_iterator is not None:
if (i_step + 1) % freqs["cell"][0] == 0:
if (i_step) % freqs["cell"][0] == 0:
line = next(self.cell_iterator)
cell = np.reshape(line, (3, 3))
self.backend.addArrayValues("simulation_cell", cell, unit="angstrom")
# Output file
if md_steps:
if (i_step + 1) % freqs["output"][0] == 0:
md_step = md_steps[i_md_step]
if (i_step) % freqs["output"][0] == 0:
try:
md_step = md_steps[i_md_step]
except IndexError:
# The process has stopped unexpectedly, but still we
# should report all the steps so far. So we break the
# loop and retain what was parsed.
break
# print(md_step["x_cp2k_md_step_number"])
quickstep = self.md_quicksteps[i_md_step]
if quickstep is not None:
quickstep.add_latest_value("x_cp2k_atom_forces", "atom_forces")
......@@ -358,23 +383,47 @@ class CP2KMDParser(MainHierarchicalParser):
backend.closeSection("section_single_configuration_calculation", sectionGID)
# Add the summaries to frame sequence
frame_sequence_potential_energy = convert_unit(np.array(frame_sequence_potential_energy), "hartree")
frame_sequence_kinetic_energy = convert_unit(np.array(frame_sequence_kinetic_energy), "hartree")
frame_sequence_conserved_quantity = convert_unit(np.array(frame_sequence_conserved_quantity), "hartree")
frame_sequence_time = np.array(frame_sequence_time)
frame_sequence_temperature = np.array(frame_sequence_temperature)
frame_sequence_pressure = np.array(frame_sequence_pressure)
backend.addArrayValues("frame_sequence_potential_energy", frame_sequence_potential_energy)
backend.addArrayValues("frame_sequence_kinetic_energy", frame_sequence_kinetic_energy)
backend.addArrayValues("frame_sequence_conserved_quantity", frame_sequence_conserved_quantity)
backend.addArrayValues("frame_sequence_temperature", frame_sequence_temperature)
backend.addArrayValues("frame_sequence_time", frame_sequence_time, unit="fs")
if frame_sequence_pressure.size != 0:
if len(frame_sequence_potential_energy) != 0:
frame_sequence_potential_energy = convert_unit(np.array(frame_sequence_potential_energy), "hartree")
backend.addArrayValues("frame_sequence_potential_energy", frame_sequence_potential_energy)
backend.addArrayValues("frame_sequence_potential_energy_frames", np.array(ener_frames))
mean_pot = frame_sequence_potential_energy.mean()
std_pot = frame_sequence_potential_energy.std()
backend.addArrayValues("frame_sequence_potential_energy_stats", np.array([mean_pot, std_pot]))
if len(frame_sequence_kinetic_energy) != 0:
frame_sequence_kinetic_energy = convert_unit(np.array(frame_sequence_kinetic_energy), "hartree")
backend.addArrayValues("frame_sequence_kinetic_energy", frame_sequence_kinetic_energy)
backend.addArrayValues("frame_sequence_kinetic_energy_frames", np.array(ener_frames))
mean_kin = frame_sequence_kinetic_energy.mean()
std_kin = frame_sequence_kinetic_energy.std()
backend.addArrayValues("frame_sequence_kinetic_energy_stats", np.array([mean_kin, std_kin]))
if len(frame_sequence_conserved_quantity) != 0:
frame_sequence_conserved_quantity = convert_unit(np.array(frame_sequence_conserved_quantity), "hartree")
backend.addArrayValues("frame_sequence_conserved_quantity", frame_sequence_conserved_quantity)
backend.addArrayValues("frame_sequence_conserved_quantity_frames", np.array(ener_frames))
mean_cons = frame_sequence_conserved_quantity.mean()
std_cons = frame_sequence_conserved_quantity.std()
backend.addArrayValues("frame_sequence_conserved_quantity_stats", np.array([mean_cons, std_cons]))
if len(frame_sequence_time) != 0:
frame_sequence_time = np.array(frame_sequence_time)
backend.addArrayValues("frame_sequence_time", frame_sequence_time, unit="fs")
if len(frame_sequence_temperature) != 0:
frame_sequence_temperature = np.array(frame_sequence_temperature)
backend.addArrayValues("frame_sequence_temperature", frame_sequence_temperature)
backend.addArrayValues("frame_sequence_temperature_frames", np.array(ener_frames))
mean_temp = frame_sequence_temperature.mean()
std_temp = frame_sequence_temperature.std()
backend.addArrayValues("frame_sequence_temperature_stats", np.array([mean_temp, std_temp]))
if len(frame_sequence_pressure) != 0:
frame_sequence_pressure = np.array(frame_sequence_pressure)
backend.addArrayValues("frame_sequence_pressure", frame_sequence_pressure)
mean_pressure = frame_sequence_pressure.mean()
std_pressure = frame_sequence_pressure.std()
backend.addArrayValues("frame_sequence_pressure_stats", np.array([mean_pressure, std_pressure]))
# Number of frames
backend.addValue("number_of_frames_in_sequence", self.n_steps + 1)
# Number of frames. We open a SCC for each frame, even if there is no
# information for it.
backend.addValue("number_of_frames_in_sequence", len(single_conf_gids))
# Reference to sampling method
backend.addValue("frame_sequence_to_sampling_ref", 0)
......@@ -382,32 +431,6 @@ class CP2KMDParser(MainHierarchicalParser):
# References to local frames
backend.addArrayValues("frame_sequence_local_frames_ref", np.array(single_conf_gids))
# Temperature stats
mean_temp = frame_sequence_temperature.mean()
std_temp = frame_sequence_temperature.std()
backend.addArrayValues("frame_sequence_temperature_stats", np.array([mean_temp, std_temp]))
# Potential energy stats
mean_pot = frame_sequence_potential_energy.mean()
std_pot = frame_sequence_potential_energy.std()
backend.addArrayValues("frame_sequence_potential_energy_stats", np.array([mean_pot, std_pot]))
# Kinetic energy stats
mean_kin = frame_sequence_kinetic_energy.mean()
std_kin = frame_sequence_kinetic_energy.std()
backend.addArrayValues("frame_sequence_kinetic_energy_stats", np.array([mean_kin, std_kin]))
# Conserved quantity stats
mean_cons = frame_sequence_conserved_quantity.mean()
std_cons = frame_sequence_conserved_quantity.std()
backend.addArrayValues("frame_sequence_conserved_quantity_stats", np.array([mean_cons, std_cons]))
# Pressure stats
if frame_sequence_pressure.size != 0:
mean_pressure = frame_sequence_pressure.mean()
std_pressure = frame_sequence_pressure.std()
backend.addArrayValues("frame_sequence_pressure_stats", np.array([mean_pressure, std_pressure]))
#===========================================================================
# adHoc functions
def adHoc_save_md_quickstep(self):
......
regtests/cp2k_2.6.2/errors/short_main_file/unittest.out 0 → 100644
View file @ 4961e40b
*******************************************************************************
* RESTART INFORMATION *
*******************************************************************************
* *
* RESTART FILE NAME: ./md_trajectory-restart-1.restart *
* *
* RESTARTED QUANTITIES: *
* CELL *
* COORDINATES *
* RANDOM NUMBER GENERATOR *
* VELOCITIES *
* MD COUNTERS *
* MD AVERAGES *
* BAROSTAT *
* THERMOSTAT OF BAROSTAT *
* PARTICLE THERMOSTAT *
* REAL TIME PROPAGATION *
* PINT BEAD POSITIONS *
* PINT BEAD VELOCITIES *
* PINT NOSE THERMOSTAT *
* PINT GLE THERMOSTAT *
* HELIUM BEAD POSITIONS *
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