def load_all_K_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
filename_must_not_contain=[],
filename_must_contain=[],
reps='all'):
"""
Will load all the K files in a specified folder. This will output an
Ordered Dictionary with filenames as keys and data as values.
Inputs:
* folder = the folder to look for sigma files in
* min_step = first step to read
* max_step = last step to read
* stride = stride to take when reading
* ignore_steps = which steps to ignore
* filename_must_contain = any strings the filename must contain (list)
* filename_must_not_contain = any strings the filename must not contain
(list)
* reps = which replicas to get data for
"""
filename_must_contain.append("K")
filename_must_contain.append("list")
return Utils.load_all_in_folder(
folder=folder,
func=load_K,
args=[min_step, max_step, stride, ignore_steps],
filename_must_not_contain=filename_must_not_contain,
filename_must_contain=filename_must_contain,
reps=reps)
def load_all_tintf_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
reps='all'):
return Utils.load_all_in_folder(
folder=folder,
func=load_tintf,
args=[min_step, max_step, stride, ignore_steps],
filename_must_contain=['t_int_frc', 'xyz'],
filename_must_not_contain=[],
reps=reps)
def load_all_ad_frc_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
reps='all'):
"""
Loads all adiabatic forces in a folder
"""
return Utils.load_all_in_folder(
folder=folder,
func=load_ad_frc,
args=[min_step, max_step, stride, ignore_steps],
filename_must_contain=['frc', 'xyz', 'ad'],
filename_must_not_contain=[],
reps=reps)
def load_all_pos_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
reps='all'):
"""
Loads all forces in a folder
"""
return Utils.load_all_in_folder(
folder=folder,
func=load_pos,
args=[min_step, max_step, stride, ignore_steps],
filename_must_contain=['pos', 'xyz'],
filename_must_not_contain=['init'],
reps=reps)
def load_all_QM_0_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
reps='all'):
"""
Will load all the QM_0 files in 1 folder.
"""
return Utils.load_all_in_folder(
folder=folder,
func=load_QM_0,
args=[min_step, max_step, stride, ignore_steps],
filename_must_contain=['QM_0', 'xyz'],
filename_must_not_contain=['force'],
reps=reps)
def load_all_coeff_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
filename_must_not_contain=[],
filename_must_contain=[],
reps='all'):
return Utils.load_all_in_folder(
folder=folder,
func=load_coeff,
args=[min_step, max_step, stride, ignore_steps],
filename_must_not_contain=filename_must_not_contain,
filename_must_contain=filename_must_contain,
reps=reps)
def load_all_ham_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
reps='all'):
allHamFiles = [i for i in os.listdir(folder) if 'run-ham' in i]
filepath = folder + allHamFiles[0]
num_basis = find_num_basis(filepath)
metadata = XYZ.get_xyz_step_metadata2(filepath)
return Utils.load_all_in_folder(
folder=folder,
func=load_ham,
args=[num_basis, metadata, min_step, max_step, stride, ignore_steps],
filename_must_contain=['ham', 'xyz'],
filename_must_not_contain=[],
reps=reps)
def load_all_ener_time_in_folder(folder, reps):
"""
Will load all ener files in a folder. This means the kinetic, potential and
conserved energies and the time taken.
Inputs:
* folder => the folder to look in [str]
* reps => Which reps to load (can be 'all') [str] or [list of int]
Outpus:
* dictionary of each file with parse energy data. Filename is key and
data is value.
"""
return Utils.load_all_in_folder(folder=folder,
func=load_ener_time_data,
filename_must_contain=['csv', 'ener'],
filename_must_not_contain=['ad'],
reps=reps)
def load_all_Rlk_in_folder(folder,
min_step=0,
max_step='all',
stride=1,
ignore_steps=[],
reps='all'):
rlk_data = Utils.load_all_in_folder(
folder=folder,
func=load_Qlk,
args=[min_step, max_step, stride, ignore_steps],
filename_must_contain=['rlk', 'xyz'],
filename_must_not_contain=[],
reps=reps)
keys = list(rlk_data.keys())
if len(keys) > 1:
files = '\n\t*'.join(keys)
raise SystemExit("Found more than 1 Rlk file!\n\n\t*%s" % files)
rlk_data = rlk_data[keys[0]]
return rlk_data
def load_all_ener_ad(folder, reps, max_time='all', min_time=0):
return Utils.load_all_in_folder(folder,
load_ener_ad,
args=[max_time, min_time],
filename_must_contain=['csv', 'ad_ener'],
reps=reps)
def load_all_ener_dat(folder, reps, max_time):
return Utils.load_all_in_folder(folder,
load_ener_dat,
args=[max_time],
filename_must_contain=['dat', 'ener'],
reps=reps)