Exemplo n.º 1
0
	def func_05(mode="print",idx=None):
		"""Insert xyz geometries into input"""
		if preferences.comp_software == "orca":
			if mode == "print":	print(f"{idx} - Insert .xyz geometries into the corresponding .inp files")
			elif mode == "run":	xyz_insert(file_weeder([".xyz"]))
		elif preferences.comp_software == "gaussian":
			if mode == "print":	print(f"{idx} - Insert .xyz geometries into the corresponding {preferences.gauss_ext} files")
			elif mode == "run":	xyz_insert(file_weeder([".xyz"]))
Exemplo n.º 2
0
	def func_06(mode="print",idx=None):
		"""Analyze relative free energies"""
		if preferences.comp_software == "orca":
			if mode == "print":	print(f"{idx} - Extract free energies from .log files*")
			elif mode == "run": e_analysis(file_weeder([".log"]))
		elif preferences.comp_software == "gaussian":
			if mode == "print":	print(f"{idx} - Extract free energies from .log files")
			elif mode == "run": e_analysis(file_weeder([".log"]))
Exemplo n.º 3
0
def deduplicate():
    print("Analyzing energies...")
    energies = [[
        b.name,
        float(b.scf_done[-1][1]), b.normal_termin,
        b.last_xyz_obj()
    ] for i in file_weeder([".log"]) for b in [LogFile(read_item(i))]]
    unique = energies
    if not unique:
        print("No log files to be analyzed")
        return
    black_list, folder_mov = [], []
    print("Starting analysis...")
    for file in sorted(unique, key=lambda x: (x[2], -x[1]), reverse=True):
        if file[0] in black_list: continue
        black_list.append(file[0])
        sim_en = [
            i for i in unique
            if i[0] not in black_list and i[1] + 1 > file[1] > i[1] - 1
        ]
        if sim_en:
            duplicates = []
            for obj in sim_en:
                if obj[3].superimpose(file[3], ret="max_d", conv=6):
                    print("{} is a duplicate of {}".format(
                        obj[3].name(), file[3].name()))
                    duplicates.append(obj[3].name())
                    black_list.append(obj[3].name())
            if duplicates: folder_mov.append([file[3].name(), duplicates])
    for folder in folder_mov:
        subfolder = os.path.join(
            os.getcwd(),
            "duplicates_of_{}".format(folder[0].replace(".log", "")))
        try:
            os.mkdir(subfolder)
        except FileExistsError:
            pass
        print("Moving duplicates of {} to the following directory:\n{}".format(
            folder[0], subfolder))
        for file in folder[1]:
            for alt_file in file_weeder([file.replace(".log", ".")]):
                try:
                    shutil.move(os.path.join(os.getcwd(), alt_file),
                                os.path.join(subfolder, alt_file))
                    print("Moved: {}".format(alt_file))
                except PermissionError:
                    print("Error while moving log files:")
                    print(
                        "Maybe {} already exists in the following directory:\n{}"
                        .format(alt_file, subfolder))
                except FileNotFoundError:
                    print("File {} not found in the following directory:\n{}".
                          format(alt_file, subfolder))
    print("Done!")
Exemplo n.º 4
0
	def func_03(self,mode="print",idx=None):
		"""Validade inputs and possibly create pbs files"""
		if preferences.comp_software == "orca":
			if mode == "print":
				if self.pbs: print(f'{idx} - Create .pbs files and a submission script from .inp files')
				else: print(f'{idx} - Validate .inp files')
			elif mode == "run":
				validate_input(file_weeder([".inp"]))
		elif preferences.comp_software == "gaussian":
			if mode == "print":
				if self.pbs: print(f"{idx} - Create .pbs files and a submission script from {preferences.gauss_ext} files")
				else: print(f"{idx} - Validate {preferences.gauss_ext} files")
			elif mode == "run":	validate_input(file_weeder([preferences.gauss_ext]))
Exemplo n.º 5
0
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()
Exemplo n.º 6
0
def log_to_xyz_scan():
	weeded_list = sel_files(file_weeder([".log"]))
	for item in weeded_list:
		log = LogFile(read_item(item))
		if log.calc_type.lower() == "red": xyzs = log.scan_geoms(); ext_name = "_scan_traject.xyz"
		elif log.calc_type.lower() == "irc": xyzs = log.irc(); ext_name = "_irc_traject.xyz"
		elif log.calc_type.lower() in ["opt","ts"]: xyzs = log.opt(); ext_name = "_opt_traject.xyz"
		else: print("The file is not a scan, opt or irc log file"); continue
		if len(xyzs) < 2:
			print("The file contains less than 2 steps")
			is_terse_irc = all([len(xyzs) < 2, log.calc_type == "IRC",
				log.raw_route.lower().startswith("#t") or log.raw_route.lower().startswith("# t ")])
			if is_terse_irc:
				print("WARNING! Error above may have been caused by the following:")
				print("IRC calculations with the #T keyword may not archive intermediate geometries")
				print("#N or #P keywords are recommended instead")
			continue
		max_e = max(float(i.title()) for i in xyzs)
		min_e = min(float(i.title()) for i in xyzs)
		c=[0,"percentage","kcal"]
		print("{:5}{:^90}{:>8}".format("Entry"," >---> Relative Energy >---> "," kcal"))
		for entry in [float(i.title()) for i in xyzs]:
			c[0]=c[0]+1
			c[1]= "|"*int(90*((float(entry)-min_e)/(max_e-min_e)) if max_e != min_e else 0)
			c[2]= (float(entry)-min_e)*627.5
			print("{:<5}{:<90}".format(c[0],c[1]),"{:>6.5f}".format(c[2]) if ext_name == "_opt_traject.xyz" else "{:>6.2f}".format(c[2]))
		file_name = item.replace(".log",ext_name)
		with open(file_name,mode="w",newline="\n") as file: file.write("\n".join([a for i in xyzs for a in i.return_print()]))
Exemplo n.º 7
0
	def __init__(self,use_logs=False):
		self.use_logs = use_logs
		self.original_ext = ".log" if use_logs else ".xyz"
		self.template_ext = ".GAUSSIAN" if preferences.comp_software == "gaussian" else ".ORCA"
		self.extension = preferences.gauss_ext if preferences.comp_software == "gaussian" else ".inp"
		self.weeded_list = file_weeder([self.original_ext])
		self.p_files_dir = os.path.join(os.path.dirname(__file__),"builtin_templates")
		self.user_files_dir = os.path.join(os.path.dirname(__file__), "par_templates")
		self.submit_parameters()
Exemplo n.º 8
0
def input_to_xyz():
	extension = preferences.gauss_ext if preferences.comp_software == "gaussian" else ".inp"
	weeded_list = file_weeder([extension])
	weeded_list = weeded_list if preferences.folder_op else sel_files(weeded_list)
	if not weeded_list: return
	for i in weeded_list:
		if preferences.comp_software == "orca":
			xyz = InpFile(read_item(i)).xyz_obj()
			xyz.save_file()
		elif preferences.comp_software == "gaussian":
			xyz = GjfFile(read_item(i)).xyz_obj()
			xyz.save_file()
Exemplo n.º 9
0
	def submit_parameters(self):
		l_files = file_weeder([self.template_ext])
		if len(l_files) == 1:
			print("Reading parameters from {} in current folder".format(l_files[0]))
			parameters = read_item(l_files[0])
			self.find_idx(parameters)
		elif len(l_files) > 1:
			l_files.insert(0, None)
			option = True
			print("Chose a parameter file:")
			for idx, i in enumerate(l_files):
				if i is None: print("  0 - Cancel")
				else: print("{:>3} - {}".format(idx, i))
			while option == True: option = {str(idx): i for idx, i in enumerate(l_files)}.get(input(), True)
			if option is None: return
			else: parameters = read_item(option); self.find_idx(parameters)
		else:
			print("Could not find {} file on current file".format(self.template_ext))
			option = True
			while option == True:
				print("Chose an option:")
				print("0 - To cancel")
				print("1 - Use builtins")
				print("2 - User defined")
				option = {str(i): str(i) for i in range(3)}.get(input(), True)
			if option == "0": return
			else:
				folder = self.p_files_dir if option == "1" else self.user_files_dir
				p_files = file_weeder([self.template_ext], cf=folder)
				p_files.insert(0, None)
				print(f"Reading {self.template_ext} files from:\n{folder}\nChoose a parameter file:")
				option_2 = True
				for idx, i in enumerate(p_files):
					if i == None: print("  0 - Cancel")
					else: print("{:>3} - {}".format(idx, i))
				while option_2 == True: option_2 = {str(idx): i for idx, i in enumerate(p_files)}.get(input(), True)
				if option_2 == None: return
				else:
					shutil.copy(os.path.join(folder, option_2), os.path.join(os.getcwd(), "PARAMETERS{}".format(self.template_ext)))
					self.try_again()
Exemplo n.º 10
0
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()
Exemplo n.º 11
0
def rel_scf(list=False):
    energies = []
    for i in file_weeder([".log"]):
        log = LogFile(read_item(i))
        energies.append([log.name, log.scf_done[-1][1], log.normal_termin])
    if len(energies) == 0:
        print("No .log files in current folder")
        return
    energies = [[i[0], float(i[1]), i[2]] for i in energies]
    energies.sort(key=lambda x: x[1])
    min_e = energies[0][1]
    energies = [[i[0], (i[1] - min_e) * 627.509, i[2]] for i in energies]
    if list == False:
        print("\n".join(["{:>30}{:>15f}{:>5}".format(*l) for l in energies]))
    elif list == True:
        return energies
Exemplo n.º 12
0
def log_to_xyz():
	weeded_list = file_weeder([".log"])
	weeded_list = weeded_list if preferences.folder_op else sel_files(weeded_list)
	if not weeded_list: return
	while True:
		print("Which geometry do you want?")
		print("0 - Cancel")
		print("1 - Last")
		print("2 - Lowest energy")
		print("3 - First")
		geom = input()
		if geom == "0": return
		if geom in ["1","2","3"]: break
		else: print("Invalid option!")
	for i in weeded_list:
		try:
			if geom == "1":	LogFile(read_item(i)).last_xyz_obj().save_file()
			elif geom == "2": LogFile(read_item(i)).low_e_xyz_obj().save_file()
			elif geom == "3": LogFile(read_item(i)).first_xyz_obj().save_file()
		except Exception as e:
			print("Error on file: {}".format(i))
			print(e)
Exemplo n.º 13
0
def deploy():
	scripts_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)),"scripts")
	while True:
		options = file_weeder([".py"], scripts_dir)
		options = [a for a in options if a != "__init__.py"]
		options.insert(0, "To cancel")
		print("Which script do you want to paste in the current folder?")
		for idx, i in enumerate(options):
			print("{:>3} - {}".format(idx, i))
		option = input()
		if option in [str(a) for a in range(len(options))]:
			break
	if option == "0":
		return
	else:
		with open(os.path.join(scripts_dir,options[int(option)])) as file:
			script = file.readlines()
		script = [a.replace("sub_s_name",preferences.sub_s_name) for a in script]
		script = [a.replace(".gjf", preferences.gauss_ext) for a in script]
		with open((os.path.join(os.getcwd(), options[int(option)])), "w", newline="\n") as file_b:
			for line in script:
				file_b.write(str(line))
Exemplo n.º 14
0
def log_freq_xyz():
	weeded_list = sel_files(file_weeder([".log"]))
	for i in weeded_list:
		log = LogFile(read_item(i))
		if not log.last_freq:
			print("No frequencies found in file:{}!".format(i))
			continue
		option = None
		while True:
			print("Analizing file: {}".format(i))
			print("Chose a frequency to split (0-To cancel/m-For more)")
			for idx,item in enumerate(log.last_freq.frequencies(),start=1):
				print("{:>5}:{:>15}".format(idx,item))
				if option == "m": continue
				if idx > 2: break
			option=input()
			if option == "m": continue
			elif option in [str(a+1) for a in range(len(log.last_freq.frequencies()))]: break
			elif option == "0": break
			else: print("Invalid option, try again!")
		if option == "0": continue
		print("Give a multiplier (recomended multiplier = 1) ")
		while True:
			try:
				mult=float(input().replace(",","."))
				break
			except ValueError:
				print("Not a valid number")
		left = log.last_xyz_obj().displace(-mult,log.last_freq.displ_for_freq_idx(int(option)-1))
		left.list[0] = i.replace(".log","_l.xyz")
		left.save_file()
		right = log.last_xyz_obj().displace(mult,log.last_freq.displ_for_freq_idx(int(option)-1))
		right.list[0] = i.replace(".log","_r.xyz")
		right.save_file()
		print("\nJob Done!\n")
	print("Finished !")
Exemplo n.º 15
0
	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