def xyz_ent(): weeded_list = file_weeder([".xyz"]) weeded_list = weeded_list if preferences.folder_op else sel_files(weeded_list) if not weeded_list: return for i in weeded_list: xyz = XyzFile(read_item(i)).enantiomer() xyz.save_file()
def aproximate(xyz_1, xyz_2, vertex): """Aproximate xyz_2 to xyz_1 from trajectory vertex. Returns [xyz_1+xyz_2, xyz_2]""" def min_dist(a, b): return min(math.sqrt(sum(pow(c - d, 2) for c, d in zip(bb, aa))) for bb in b for aa in a) xyz_a = [[float(a) for a in i] for i in xyz_1.cord_strip()] xyz_b = [[float(a) + b * 50 for a, b in zip(i, vertex)] for i in xyz_2.cord_strip()] for num in range(5): step_size = 1 / 2 ** num while True: if min_dist(xyz_a, xyz_b) < 2: xyz_b = [[a + b * step_size for a, b in zip(i, vertex)] for i in xyz_b] break else: xyz_b = [[a - b * step_size for a, b in zip(i, vertex)] for i in xyz_b] cordinates = [" ".join([a, *[str(c) for c in b]]) for a, b in zip(xyz_2.all_elements(), xyz_b)] return XyzFile([xyz_2.name(), xyz_2.n_atoms(), " ", *cordinates])
def xyz_insert(weeded_list):
"""Inserts geometries into both orca and gaussian input files"""
extension = ".inp" if preferences.comp_software == "orca" else preferences.gauss_ext
sub_folder = os.path.join(os.getcwd(),"inserted_input_files")
if os.path.exists(sub_folder):
print("'inserted_input_files' directory already exists in current directory!")
print("Please remove it and try again!")
return
os.mkdir(sub_folder)
for i in weeded_list:
try:
xyz = XyzFile(read_item(i))
if preferences.comp_software == "orca": comp_input = InpFile(read_item(i.replace(".xyz",extension)))
else: comp_input = GjfFile(read_item(i.replace(".xyz",extension)))
comp_input = comp_input.replace_cord(xyz)
with open(os.path.join(sub_folder,i.replace(".xyz",extension)),"w") as file:
file.write(comp_input.return_print)
except FileNotFoundError: print("file " + i.replace(".xyz",extension) + " could not be found!")
print("\nJob done!\nPlease lookup the inserted_input_files directory\n")
return
def read_strucure(self):
charge_mult = None
title = None
coordinates = []
for i, a in enumerate(self.list[self.hash_line:]):
if i > 5 and not coordinates: break
a = a.split(",")
if len(a) == 2 and not coordinates:
charge_mult = a
continue
if len(a) == 4:
if a[0] in elements and all(
is_str_float(a[n]) for n in [1, 2, 3]):
coordinates.append(" ".join(a))
elif coordinates:
break
elif coordinates:
break
return charge_mult, XyzFile(
[self.list[0],
str(len(coordinates)), title, *coordinates])
def save_inp(self,parameters,index):
if not preferences.folder_op: self.weeded_list = sel_files(self.weeded_list)
if not self.weeded_list: return
for i in self.weeded_list:
if os.path.isfile(os.path.join(os.getcwd(), (i.replace(self.original_ext, ".inp")))):
print(i.replace(self.original_ext,".inp") + " already exist on current directory!")
continue
xyz = LogFile(read_item(i)).last_xyz_obj() if self.use_logs else XyzFile(read_item(i))
inp_out = []
for idx_a, line in enumerate(parameters[0:index]):
if self.use_logs and idx_a + 1 == len(parameters[0:index]):
line = "* " + " ".join(LogFile(read_item(i)).charge_mult)
inp_out.append(line.replace("FILENAME", i.replace(self.original_ext, "")) + "\n")
for line in xyz.form_cord_block():
inp_out.append(line + "\n")
for line in parameters[index + 1:]:
inp_out.append(line + "\n")
with open(os.path.join(os.getcwd(), (i.replace(self.original_ext,".inp"))), "w",newline="\n") as file:
for line in inp_out: file.write(line)
print(i.replace(self.original_ext, ".inp"), " created!")
return
def first_xyz_obj(self):
return XyzFile([
self.name, self.n_atoms, " ",
*(" ".join(l) for l in self.first_cord_block())
])
def any_xyz_obj(self, a_idx, b_idx, title=" ", name=False):
if name == False: name = self.name
return XyzFile([
name, self.n_atoms, title,
*(" ".join(l) for l in self.xyz_cord_block(a_idx, b_idx))
])
def xyz_obj(self):
return XyzFile([
self.name(),
self.n_atoms(), " ", *[" ".join(a) for a in self.cord_block()]
])
def start():
angles, p_angles, geodes = None, None, None
xyz_1 = read_item(None, "Choose the molecule you want to solvate?", ["xyz"])
if xyz_1: xyz_1 = XyzFile(xyz_1).std_cord()
else: return
while True:
print("Choose a trajectory englobing method")
print("0 - To cancel")
print("1 - Cubic gobling")
print("2 - Icosahedron gobling")
print("3 - Give a fulerene")
usr_opt = input()
if usr_opt == "0": return
if usr_opt in ["1","2","3"]: break
if usr_opt == "1":
geodes = [[a,b,c] for a in [-1,1] for b in [-1,1] for c in [-1,1]]
elif usr_opt == "2":
k = (1 + math.sqrt(5)) / 2
geodes = [[0, 1, k], [0, -1, k], [0, -1, -k],
[0, 1, -k], [k, 0, 1], [-k, 0, 1],
[-k, 0, -1],[k, 0, -1], [1, k, 0],
[-1, k, 0], [-1, -k, 0], [1, -k, 0]]
elif usr_opt == "3":
geodes = read_item(None, "Chose a fulerene", ["xyz"])
if geodes:
geodes = XyzFile(geodes).std_cord().cord_strip()
geodes = [[float(n) for n in i] for i in geodes]
else:
print("You need a to choose a trajectory engobling method")
return
xyz_2 = read_item(None, "Chose the solvent or counterion", ["xyz"])
if xyz_2: xyz_2 = XyzFile(xyz_2).std_cord()
else: return
while True:
print("Orientation algorithm:")
print("0 - To cancel")
print("1 - Espherical ion")
print("2 - 12 Random cubic orientations")
print("3 - 24 Sistematic cubic rotations")
usr_opt = input()
if usr_opt in [str(a) for a in range(4)]: break
if usr_opt == "0":
return
elif usr_opt == "1":
angles = [0]
p_angles = [["x", 0]]
elif usr_opt == "2":
angles = random.choices([math.pi * i for i in [0, 0.5, 1, 1.5]], k=3)
rot = [["x", 0], ["x", .5], ["x", 1], ["x", 1.5], ["z", 0.5], ["z", 1.5]]
p_angles = random.choices([[i[0], math.pi * i[1]] for i in rot], k=4)
elif usr_opt == "3":
angles = [math.pi * i for i in [0, 0.5, 1, 1.5]]
rot = [["x", 0], ["x", .5], ["x", 1], ["x", 1.5], ["z", 0.5], ["z", 1.5]]
p_angles = [[i[0], math.pi * i[1]] for i in rot]
while True:
save = input("Save individual files? (y/n)")
if save in ["y", "n"]: break
rot_alg(xyz_1, xyz_2, angles, p_angles, geodes, save)
def superimpose_alg():
while True:
print("Chosse an option:")
print("0 - To cancel")
print("1 - For batch mode")
print("2 - For single structure(In screen printing)")
mode = input()
if mode in [str(n) for n in range(3)]: break
if mode == "0":
return
elif mode == "1":
if os.path.exists(os.path.join(os.getcwd(), "rotated")):
print("Rotated directory already exists in current directory!")
print("Please remove it and try again.")
return
os.mkdir(os.path.join(os.getcwd(), "rotated"))
xyz_1 = read_item(None, "Which item do you wish to compare to?", [".xyz"])
if xyz_1: xyz_1 = XyzFile(xyz_1)
else:return
while True:
num_atoms = input("compare first N atoms (0 for all):\n")
if num_atoms in [str(a) for a in range(xyz_1.n_atoms())]:
num_atoms = int(num_atoms)
break
else:
print("Invalid input for {}".format(xyz_1.name()))
for file in file_weeder(["xyz"]):
if not file == xyz_1.name():
xyz_2 = XyzFile(read_item(file))
xyz_3 = xyz_2.superimpose(xyz_1, num_atoms, True)
xyz_3.save_file(os.path.join(os.getcwd(), "rotated"))
xyz_1.std_cord(num_atoms).save_file(os.path.join(os.getcwd(), "rotated"))
elif mode == "2":
xyz_1 = read_item(None, "Which item do you wish to compare to?", [".xyz"])
if xyz_1: xyz_1 = XyzFile(xyz_1)
else: return
xyz_2 = read_item(None, "Which item do you wish to rotate?", [".xyz"])
if xyz_2: xyz_2 = XyzFile(xyz_2)
else:return
while True:
num_atoms = input("compare first N atoms (0 for all):\n")
if num_atoms in [str(a) for a in range(min([xyz_1.n_atoms(),xyz_2.n_atoms()]))]:
num_atoms = int(num_atoms)
break
else:
print("Invalid input for either or both {} and {}".format(xyz_1.name(),xyz_2.name()))
xyz_2.superimpose(xyz_1, num_atoms, True).print_file()
xyz_1.std_cord(num_atoms).print_file()
def save_gjf(self,parameters,index):
heavy_e, gjf_overwrite, folder_op = [preferences.heavy_atom,preferences.gjf_overwrite,preferences.folder_op]
ecps, basis = None, None
if not folder_op: self.weeded_list = sel_files(self.weeded_list)
if not self.weeded_list: return
if any([b in parameters for b in ["INSERT_GBS_BASIS","INSERT_GBS_ECP"]]):
print("This parameter file requires an aditional gbs file.")
print("Where should it be taken from?")
print("0 - Current folder")
print("1 - Builtins")
print("2 - User defined")
while True:
option = input()
if option in ["0","1","2"]: break
if option == "0": files_dir = os.getcwd()
elif option == "1": files_dir = self.p_files_dir
elif option == "2": files_dir = self.user_files_dir
gbs_files = file_weeder([".gbs"], cf=files_dir)
print("Chosse one basis/ecp set\n0 - Cancel")
for i, file in enumerate(gbs_files): print("{} - {}".format(i+1, file))
while True:
option = input()
if option in [str(a) for a in range(len(gbs_files)+1)]: break
print("Invalid option")
if option == "0": return
with open(os.path.join(files_dir,gbs_files[int(option)-1])) as file:
gbs_file = file.read().splitlines()
basis, ecps = self.read_gbs(gbs_file)
assert type(basis) == dict, "Basis was not read"
assert type(ecps) == dict, "Ecps were not read"
for i in self.weeded_list:
try:
gjf_out, rm_lines, = [], []
if os.path.isfile(os.path.join(os.getcwd(),(i.replace(self.original_ext,preferences.gauss_ext)))) and not gjf_overwrite:
print(i.replace(self.original_ext,preferences.gauss_ext) + " already exist on current directory!")
continue
xyz = LogFile(read_item(i)).last_xyz_obj() if self.use_logs else XyzFile(read_item(i))
for idx_a,line in enumerate(parameters[0:index]):
if self.use_logs and idx_a+1 == len(parameters[0:index]): line = " ".join(LogFile(read_item(i)).charge_mult)
gjf_out.append(line.replace("FILENAME",i.replace(self.original_ext,""))+"\n")
for line in xyz.form_cord_block():
gjf_out.append(line+"\n")
possible = [str(b + 1) for b in range(xyz.n_atoms())]
for line in parameters[index+1:]:
# SCAN like: "B S APROX" or "B S DIST"
is_mod_red = any("modredundant" in i.lower() for i in parameters[0:index])
s_line = line.split()
while len(s_line) == 3:
if s_line[0] != "B" or s_line[1] != "S": break
if s_line[2] not in ["APROX","DIST"]: break
if not is_mod_red:
print("Missing 'modredundant' keyword?")
break
if xyz.n_atoms() <2:
raise Exception(f"At least two atoms are neded in struture {xyz.name()} to perform a scan")
atom=["a","b"]
if s_line[-1] == "APROX":
print(f"Detected bond scan (APROX) for xyz file {i}.")
while not all(atom[a] in possible if atom[0] != atom[1] else False for a in [0,1]):
atom = [input("Enter atom A: "),input("Enter atom B: ")]
line = f"B {atom[0]} {atom[1]} S APROX"
elif s_line[-1] == "DIST":
print(f"Detected bond scan (DIST) for xyz file {i}.")
while not all(atom[a] in possible if atom[0] != atom[1] else False for a in [0,1]):
atom = [input("Enter atom A: "),input("Enter atom B: ")]
line = f"B {atom[0]} {atom[1]} S DIST"
s_line = line.split()
break
# SCAN like: "B 1 2 S APROX" or "B 1 2 S DIST"
while len(s_line) == 5:
if s_line[0] != "B" or s_line[3] != "S": break
if not s_line[1].isdigit(): break
if not s_line[2].isdigit(): break
if s_line[4] not in ["APROX", "DIST"]: break
if not is_mod_red:
print("Missing 'modredundant' keyword?")
break
if xyz.n_atoms() < 2:
raise Exception(f"At least two atoms are neded in struture {xyz.name()} to perform a scan")
atoms_idx = [int(s_line[1])-1, int(s_line[2])-1]
if any(True for a in atoms_idx if not a in range(xyz.n_atoms())):
raise Exception(f"Scan atom numbers are larger than the number of atoms for: {xyz.name()}")
atoms_cord = [i for idx,i in enumerate(xyz.cord_block()) if idx in atoms_idx]
dist = math.sqrt(sum((float(i)-float(atoms_cord[1][idx]))**2 for idx,i in enumerate(atoms_cord[0]) if idx > 0))
ideal_dist=sum(b[1] for idx,b in enumerate(element_radii) if b[0] in [i[0] for i in atoms_cord])/100
if s_line[-1] == "APROX":
line = line.replace("APROX",f"{1+int((dist-ideal_dist)/0.075)} -0.075")
elif s_line[-1] == "DIST":
line = line.replace("DIST",f"{1+int(ideal_dist/0.075)} 0.075")
s_line = line.split()
break
# SCAN like: "D S"
while len(s_line) == 2:
if not is_mod_red: break
if s_line[0] != "D" or s_line[1] != "S": break
print(f"Detected dihedral scan for xyz file {i}.")
if xyz.n_atoms() < 4:
raise Exception(f"At least two four atoms are neded in struture {xyz.name()} to perform a dihedral scan")
while True:
atom = [input(f"Enter atom {a}: ") for a in ["A","B","C","D"]]
atom = [a.strip() for a in atom]
if not all([len(a.split()) == 1 and a.isdigit() for a in atom]):
print("No non-numeric characters or spaces are allowed for atom numbers")
continue
if not len(set(atom)) == 4:
print("No atom should be repeated!")
continue
if not all([a in possible for a in atom]):
print("Atoms with incorrect number were found!")
continue
break
while True:
n_steps = input("Please give the number of steps to be taken: ").strip()
if n_steps.isdigit(): break
else: print("The number of steps must be an integer")
while True:
print("Please give the step size to be taken in degrees")
size = input("The number must include a dot character as a decimal place (eg. '10.0'): ").strip()
if is_str_float(size) and size.count(".") == 1: break
else: print("Please make sure the number complies with formating rules!")
line = f"D {' '.join(atom)} S {n_steps} {size}"
s_line = line.split()
break
# READOPTIMIZE + NOTATOMS
if line.replace(" ", "").lower() == "notatoms=":
print("Please enter the atoms you want to freeze on structure {} separated by comma".format(xyz.name()))
line = line + input(line)
# READOPTIMIZE + ATOMS
elif line.replace(" ", "").lower() == "noatomsatoms=":
print("Please enter the atoms you want to optimize on structure {} separated by comma".format(xyz.name()))
line = line + input(line)
# BASIS like: "LIGHT_ELEMENT_BASIS 0" or "HEAVY_ELEMENT_BASIS 0" and ECP like "HEAVY_ELEMENT_ECP 0"
elif len(s_line) == 2:
if any(True for a in ["/gen","gen ","genecp"] if a in " ".join(parameters[0:index-3]).lower()):
if s_line == ["LIGHT_ELEMENT_BASIS","0"]:
elm = [a for a in xyz.elements() if elements.index(a) < heavy_e+1]
if elm: line = line.replace("LIGHT_ELEMENT_BASIS"," ".join(elm))
else:
for a in range(3): rm_lines.append(len(gjf_out)+a)
elif s_line == ["HEAVY_ELEMENT_BASIS","0"]:
elm = [a for a in xyz.elements() if elements.index(a) > heavy_e]
if elm: line = line.replace("HEAVY_ELEMENT_BASIS"," ".join(elm))
else:
for a in range(3): rm_lines.append(len(gjf_out)+a)
if "pseudo=read" in " ".join(parameters[0:index - 3]).lower().replace(" ",""):
if s_line == ["HEAVY_ELEMENT_ECP","0"]:
elm = [a for a in xyz.elements() if elements.index(a) > heavy_e]
if elm: line = line.replace("HEAVY_ELEMENT_ECP"," ".join(elm))
else:
pattern = re.compile(r'pseudo.{0,3}=.{0,3}read',re.IGNORECASE)
eval_lines = gjf_out[0:index-3]
for idx_a,a in enumerate(eval_lines):
gjf_out[idx_a] = pattern.sub("",a)
rm_lines.append(len(gjf_out))
rm_lines.append(len(gjf_out)+1)
# BASIS like: "INSERT_GBS_BASIS"
elif "INSERT_GBS_BASIS" in line:
for element in sorted(xyz.elements(),key=lambda x: elements.index(x)):
for line_a in basis[element]:
gjf_out.append(line_a+"\n")
continue
# ECP like: "INSERT_GBS_ECP"
elif "INSERT_GBS_ECP" in line:
if "pseudo=read" in " ".join(parameters[0:index - 3]).lower().replace(" ", ""):
need_ecp = [a for a in xyz.elements() if elements.index(a) > preferences.heavy_atom]
for element in sorted(need_ecp,key=lambda x: elements.index(x)):
for line_a in ecps[element]:
gjf_out.append(line_a+"\n")
if not need_ecp:
pattern = re.compile(r'pseudo.{0,3}=.{0,3}read', re.IGNORECASE)
eval_lines = gjf_out[0:index - 3]
for idx_a, a in enumerate(eval_lines):
gjf_out[idx_a] = pattern.sub("", a)
continue
gjf_out.append(line.replace("FILENAME",i.replace(self.original_ext,""))+"\n")
gjf_out.append("\n")
with open(os.path.join(os.getcwd(),(i.replace(self.original_ext,preferences.gauss_ext))),"w") as gjf_file:
for line in [i for idx,i in enumerate(gjf_out) if idx not in rm_lines]: gjf_file.write(line)
print(i.replace(self.original_ext,preferences.gauss_ext)," created!")
except TypeError as e:
print("Error on file {}".format(i))
print(e)
return