def get_values(filename, filetype):
"""Get values of interest from given file of given type."""
box_a = 0.0
box_b = 0.0
box_c = 0.0
alpha = 0.0
beta = 0.0
gamma = 0.0
energy = 0.0
density = 0.0
volume = 0.0
temp = 0.0
if filetype == "pwout":
molsys = read_pw_out(filename)
molsys.ts_boxes[-1].box_cart2lat()
box = molsys.ts_boxes[-1]
box_a = box.ltc_a
box_b = box.ltc_b
box_c = box.ltc_c
alpha = np.degrees(box.ltc_alpha)
beta = np.degrees(box.ltc_beta)
gamma = np.degrees(box.ltc_gamma)
energy = molsys.pw_other_info["ENERGIES"][-1]
density = molsys.pw_other_info["DENSITIES"][-1]
volume = molsys.pw_other_info["VOLUMES"][-1]
temp = 0.0 # ab initio is always at 0 K
elif filetype == "lmplog":
molsys = ag_lmplog.LmpLog()
molsys.read_lmplog(filename)
box_a = molsys.data[-1]["Cella"][-1]
box_b = molsys.data[-1]["Cellb"][-1]
box_c = molsys.data[-1]["Cellc"][-1]
alpha = molsys.data[-1]["CellAlpha"][-1]
beta = molsys.data[-1]["CellBeta"][-1]
gamma = molsys.data[-1]["CellGamma"][-1]
energy = molsys.data[-1]["PotEng"][-1]
density = molsys.data[-1]["Density"][-1]
volume = molsys.data[-1]["Volume"][-1]
temp = molsys.data[-1]["Temp"][-1]
elif filetype == "cif":
box = get_cell_from_cif(filename)
cif_others = get_other_stuff_from_cif(filename)
box_a = box.ltc_a
box_b = box.ltc_b
box_c = box.ltc_c
alpha = np.degrees(box.ltc_alpha)
beta = np.degrees(box.ltc_beta)
gamma = np.degrees(box.ltc_gamma)
density = cif_others["density"]
volume = cif_others["cell_volume"]
temp = cif_others["cell_measurement_temperature"]
else:
raise Warning("Only pwout, lmplog and cif are valid keywords")
keys = ("a", "b", "c", "alpha", "beta", "gamma", "temp", "volume",
"density", "energy")
values = (box_a, box_b, box_c, alpha, beta, gamma, temp, volume, density,
energy)
return OrderedDict(list(zip(keys, values)))
def _append_data(data, lmplog, fstart=1, thermo="PotEng"):
"""
fstart : int
frame to start recording from
"""
cur_log = agl.LmpLog()
cur_log.read_lmplog(lmplog)
# potential energy of the whole system (solvent included if part of system)
cur_data = cur_log.data[-1][thermo][fstart:]
data.extend(cur_data)
def find_best_frame(lmplogs, dcds, thermo="c_pe_solvate_complete", percentage_to_check=80):
"""
Find the frame with the lowest energy / value for use in the requenching procedure.
Parameters
----------
lmplogs : tuple or list
lammps-log files with thermo information.
dcds : tuple or list
dcd files with coordinates which correspond the given data of the
log files (same number of frames is mandatory)
Returns
-------
total_min_dcd : str
name of dcd file with the lowest energy / value
total_min_idx : int
index of frame with the lowest energy / value
total_min_val : int or float
lowest value found over all lmplogs for thermo
"""
#total_min_val = 1e20
#total_min_idx = None
#total_min_dcd = ""
total_data = []
# read the whole dataset, i.e. all lmplog files
for lmplog in lmplogs:
cur_log = agl.LmpLog()
cur_log.read_lmplog(lmplog)
# flatten list if more than one run was done
# neglect the first frame since it is redundant in the log file
cur_data = [i[thermo][1:] for i in cur_log.data]
cur_data = [item for i in cur_data for item in i]
total_data.append(cur_data)
del cur_data
# find minimum value in the last X % of the data
total_data_flattened = [item for i in total_data for item in i]
last_frames_to_check = int(percentage_to_check / 100 * len(total_data_flattened))
data_to_check = total_data_flattened[-last_frames_to_check:]
min_val = min(data_to_check)
for cur_data, dcd in zip(total_data, dcds):
if min_val in cur_data:
return (dcd, cur_data.index(min_val), min_val)
else:
raise Exception("This should not have happened :/")
def read_file(self, filename, filetype):
"""Get values of interest from given file of given type."""
if filetype == "pwout":
molsys = read_pw_out(filename)
molsys.ts_boxes[-1].box_cart2lat()
# get box and convert angles to degrees
self.box = molsys.ts_boxes[-1]
self.box.ltc_alpha = np.degrees(molsys.ts_boxes[-1].ltc_alpha)
self.box.ltc_beta = np.degrees(molsys.ts_boxes[-1].ltc_beta)
self.box.ltc_gamma = np.degrees(molsys.ts_boxes[-1].ltc_gamma)
self.energy = molsys.pw_other_info["ENERGIES"][-1]
self.density = molsys.pw_other_info["DENSITIES"][-1]
self.volume = molsys.pw_other_info["VOLUMES"][-1]
# ab initio is always at 0 K
self.temp = 0.0
self.natoms = len(molsys.ts_coords[-1])
elif filetype == "lmplog":
molsys = ag_lmplog.LmpLog()
molsys.read_lmplog(filename)
# box stuff
self.box = mdb.Box()
self.box.ltc_a = molsys.data[-1]["Cella"][-1]
self.box.ltc_b = molsys.data[-1]["Cellb"][-1]
self.box.ltc_c = molsys.data[-1]["Cellc"][-1]
self.box.ltc_alpha = molsys.data[-1]["CellAlpha"][-1]
self.box.ltc_beta = molsys.data[-1]["CellBeta"][-1]
self.box.ltc_gamma = molsys.data[-1]["CellGamma"][-1]
# other
self.energy = molsys.data[-1]["PotEng"][-1]
self.density = molsys.data[-1]["Density"][-1]
self.volume = molsys.data[-1]["Volume"][-1]
self.temp = molsys.data[-1]["Temp"][-1]
with open(filename) as fin:
line = fin.readline()
while line != '':
if line.startswith("Loop time of"):
self.natoms = int(line.split()[-2])
line = fin.readline()
elif filetype == "cif":
# box stuff
self.box = get_cell_from_cif(filename)
cif_others = get_other_stuff_from_cif(filename)
self.box.ltc_alpha = np.degrees(self.box.ltc_alpha)
self.box.ltc_beta = np.degrees(self.box.ltc_beta)
self.box.ltc_gamma = np.degrees(self.box.ltc_gamma)
# other
self.density = cif_others["density"]
self.volume = cif_others["cell_volume"]
self.temp = cif_others["cell_measurement_temperature"]
else:
raise Warning("Only pwout, lmplog and cif are valid keywords")
if filetype == "lmplog" or filetype == "pwout":
self.nmols = int(self.natoms / self.atoms_p_molecule)
else:
self.nmols = cif_others["cell_formula_units"]
iterations_on = (0, 107)
#iterations_off = (0, 107, 115)
dreiding = "off"
for iteration in iterations_on:
# get box from original (multiplied and untouched) supercell in order to get the
# factors of each unit cell it was built from
# using the box from the last snapshot could lead to inconsistencies due to rounding
#original_supercell = agum.Unification()
#original_supercell.read_lmpdat(lmpdat_supercell.format(iteration, polymorph))
#original_supercell.ts_boxes[0].box_lmp2lat()
lammps_polymorphs = {}
FF_SINGLE_MOLECULE = ag_lmplog.LmpLog()
FF_SINGLE_MOLECULE.read_lmplog(path_single.format(iteration))
# convert to kcal*mol-1
FF_SINGLE_MOLECULE.data[-1]["PotEng"][-1] *= 23
for index, polymorph in enumerate(("I", "II", "III", "IV", "V")):
if iteration == 0 or dreiding == "off":
# no dreiding force field for stock gaff force field
cur_file = path_scell_dreiding_off.format(iteration, polymorph)
else:
cur_file = path_scell_dreiding_on.format(iteration, polymorph)
#print(cur_file)
cur_polymorph = Polymorph(30)
cur_polymorph.read_file(cur_file, "lmplog")