def get_data(self):
# Gets energies stored in *.txt files
file_list = [file for file in os.listdir() if file.endswith('.txt')]
for current_file in file_list:
log.i('Reading \'{}\'.'.format(current_file))
with open(current_file, 'r') as f:
text = f.readlines()
data_list = []
for line in text:
line_dict = {}
line = line.split()
line_dict['name'] = line[0][:-1]
line_dict['energy'] = float(line[-1])
data_list.append(line_dict)
# Orders data list
ordered_data_list = [None] * (len(data_list) + 1)
for molecule in data_list:
numer = int(sub("[^0-9]", "", molecule['name']))
ordered_data_list[numer] = molecule
data_list = ordered_data_list
for item in data_list:
if item is None:
data_list.remove(item)
return data_list
def get_energies_from_files(self):
log.d('Getting energies from files.')
energies_dict = {}
for folder_name in FOLDER_NAMES:
temp_file_list = [
file for file in os.listdir(folder_name)
if file.endswith('.log')
]
for molecule_name in temp_file_list:
text = None
temp_dict = {}
with open(folder_name + '/' + molecule_name, 'r') as f:
text = f.read()
if folder_name in ['1-DFTmin_opt', '2-MP2min_sp']:
energy_value = round(float(DFT_RE.findall(text)[-1]), 5)
temp_dict[folder_name] = energy_value
elif folder_name in ['3-M062Xmin_opt', '4-M062Xmax_sp']:
energy_value = round(float(M06_RE.findall(text)[-1]), 5)
temp_dict[folder_name] = energy_value
if molecule_name[:-4] not in energies_dict:
energies_dict[molecule_name[:-4]] = [temp_dict]
else:
energies_dict[molecule_name[:-4]].append(temp_dict)
log.i(f'Energies from {len(energies_dict.keys())} files recovered.')
# pp.pprint(energies_dict)
return energies_dict
def myMain():
x=input('Enter x:')
if argv[1] == 'zen':
log.level('info')
log.d('debug')
log.i('info x={}'.format(x))
log.w('warn')
log.e('error')
log.c('critical')
else:
if argv[1] == 'basic':
# see Python Docs logging.html 16.6.7. LogRecord attributes
logging.basicConfig(style='{',format="{asctime:s}:{filename:s}:{lineno:d}:{msg:s}",level='DEBUG')
logging.debug('our debug message x={}'.format(x))
logging.warn('our warn message x={}'.format(x))
else:
print("If we don't want to type logging.debug() etc, we have to create our own logger lg=logging.getLogger({})".format(__name__))
lg=logging.getLogger(__name__)
if argv[1]=='easy':
logging.basicConfig(level='INFO')
else:
lg.setLevel('WARN') # optional: defaults to all levels
lg.addHandler(logging.StreamHandler())
lg.handlers[0].setFormatter(logging.Formatter(style='{',fmt="{filename:s}:{funcName:s}():{lineno:d}:{msg:s}"))
lg.debug('our debug mesage')
lg.info('our info here')
def get_web_page(url):
'''
# Let the user know we are trying to download a webpage
# Construct a request with a User-Agent header
# Send the request and read the webpage from the response
# Convert the webpage from bytes to a string, and return it
'''
url = clean_link(url)
log.i('getting: ' + url)
handle = Request(url)
handle.add_header('User-Agent', 'SPD/1.0')
try:
webpage = urlopen(handle).read()
except HTTPError as err:
log.w('a problem occured when getting ' + url)
if err.code == 404:
message = 'the requested page could not be found'
else:
message = 'the server returned a code of ' + str(err.code)
log.w(message)
webpage = str(err.code) # pass the return code as a string
webpage = str(webpage) # convert from bytes to string
log.d(len(webpage))
soup = BeautifulSoup(webpage, 'html.parser')
return soup
def lowest_energy_molecule(self, data_list):
if self.user_input == '1':
# Converts each energy value from Hartree (Ha) to kcal/mol
for molecule in data_list:
molecule['energy'] = molecule['energy'] * 627.51
min_value = min([molecule['energy'] for molecule in data_list])
min_names = []
for molecule in data_list:
molecule_data = list(molecule.values())
if min_value in molecule_data:
min_names.append(molecule_data[0])
molecule['energy'] -= min_value
if self.user_input == '2':
# Converts each energy value from kJ/mol to kcal/mol
for molecule in data_list:
molecule['energy'] = molecule['energy'] / 4.184
min_value = min([molecule['energy'] for molecule in data_list])
min_names = []
for molecule in data_list:
molecule_data = list(molecule.values())
if min_value in molecule_data:
min_names.append(molecule_data[0])
molecule['energy'] -= min_value
if min_names[0] != '':
log.i('Minimum energy {} was found on molecule(s) {}.'.format(
min_value, min_names))
else:
log.i('Minimum energy {} was found.'.format(min_value))
return min_value, min_names
def get_web_page(url):
'''
# Let the user know we are trying to download a webpage
# Construct a request with a User-Agent header
# Send the request and read the webpage from the response
# Convert the webpage from bytes to a string, and return it
'''
url = clean_link(url)
log.i('getting: ' + url)
handle = Request(url)
handle.add_header('User-Agent', 'SPD/1.0')
try:
webpage = urlopen(handle).read()
except HTTPError as err:
log.w('a problem occured when getting ' + url)
if err.code == 404:
message = 'the requested page could not be found'
else:
message = 'the server returned a code of ' + str(err.code)
log.w(message)
webpage = str(err.code) # pass the return code as a string
webpage = str(webpage) # convert from bytes to string
log.d(len(webpage))
soup = BeautifulSoup(webpage, 'html.parser')
return soup
def lowest_energy_molecule(self, data_list):
# Converts each energy value from Hartree (Ha) to kcal/mol
for molecule in data_list:
molecule['energy'] = molecule['energy'] * 627.51
min_value = min([molecule['energy'] for molecule in data_list])
min_names = []
for molecule in data_list:
molecule_data = list(molecule.values())
if min_value in molecule_data:
min_names.append(molecule_data[0])
molecule['energy'] -= min_value
log.i('Minimum energy {} was found on file(s) {}.'.format(
min_value, min_names))
return min_value, min_names
def get_energies_from_files(self):
log.d('Getting energies from files.')
energies_dict = {}
folder_names = [
folder for folder in next(os.walk('.'))[1]
if folder[0].isnumeric()
]
folder_names.sort()
for folder_name in folder_names:
try:
temp_file_list = [
file for file in os.listdir(folder_name)
if file.endswith('.log')
]
except FileNotFoundError:
continue
for molecule_name in temp_file_list:
text = None
temp_dict = {}
with open(folder_name + '/' + molecule_name, 'r') as f:
text = f.read()
try:
if 'freq' in folder_name.lower():
free_energ = round(float(FRQ_RE.findall(text)[-1]), 8)
enthalp = round(float(ENT_RE.findall(text)[-1]), 8)
energy_value = 'Free Energy: ' + str(
free_energ) + '\nEnthalpy: ' + str(enthalp)
temp_dict[folder_name] = energy_value
elif len([
method
for method in ['dft', 'mp2min', 'm06', 'b3lyp']
if method in folder_name.lower()
]) > 0:
energy_value = round(float(DFT_RE.findall(text)[-1]),
8)
temp_dict[folder_name] = energy_value
if molecule_name[:-4] not in energies_dict:
energies_dict[molecule_name[:-4]] = [temp_dict]
else:
energies_dict[molecule_name[:-4]].append(temp_dict)
except IndexError:
log.e(f'Error on \'{folder_name+"/"+molecule_name}\'.')
temp_dict[folder_name] = 'missing value'
log.i(f'Energies from {len(energies_dict.keys())} files recovered.')
return energies_dict, folder_names
def get_data(self):
# Gets energies stored in *.txt files
file_list = [file for file in os.listdir() if file.endswith('.txt')]
if len(file_list) > 0:
for current_file in file_list:
log.i('Reading \'{}\'.'.format(current_file))
with open(current_file, 'r') as f:
text = f.readlines()
data_list = []
for line in text:
line_dict = {}
line = line.split()
line_dict['name'] = line[0]
line_dict['energy'] = float(line[-1])
data_list.append(line_dict)
else:
log.e(
'ERROR - File error: Wrong file format (must be .txt) or \'boltzmann.py\' not in same folder as chosen text file. Exiting program...'
)
quit()
print(
f'\nPlease select the appropiate units for the results:\n\t(1) Hartree (Ha)\n\t(2) kJ/mol'
)
self.user_input = input('Please input (1) or (2) and press ENTER: ')
if self.user_input == '1':
# Orders data list
ordered_data_list = [None] * (len(data_list) + 1)
for molecule in data_list:
numer = int(sub("[^0-9]", "", molecule['name']))
ordered_data_list[numer] = molecule
data_list = ordered_data_list
for item in data_list:
if item is None:
data_list.remove(item)
return data_list
def download_image(link):
'''
# Let the user know we are trying to download an image at the given link
# Prepare the command (wget) to download the image
# If wget doesn't exist, we raise a FileNotFound error
# Otherwise, if we're on Windows, modify the wget command to avoid an issue
# with GnuWin wget and SSL
# Finally, we run the constructed command to download the image
'''
global args
# --no-check-certificate is used on windows because GnuWin wget fails to
# verify all certificates for some reason
link = clean_link(link)
log.i('downloading: ' + link)
wget_command = [which('wget'), '-b', '-N', '-o', '/dev/null', link]
if (which('wget') is None):
raise WGetNotFoundException('Could not find wget')
elif operating_system() == 'Windows':
log.d('on windows, adjusting wget_command')
wget_command = [
which('wget'), '-b', '-N', '-o', 'NUL', '--no-check-certificate',
link
]
try:
while call(wget_command) != 0:
time.sleep(.05)
log.d('call is not 0')
log.i('retrying...')
except BlockingIOError:
time.sleep(.1)
log.d('BlockingIOError!')
log.w('retrying...')
download_image(link)
def download_image(link):
'''
# Let the user know we are trying to download an image at the given link
# Prepare the command (wget) to download the image
# If wget doesn't exist, we raise a FileNotFound error
# Otherwise, if we're on Windows, modify the wget command to avoid an issue
# with GnuWin wget and SSL
# Finally, we run the constructed command to download the image
'''
global args
# --no-check-certificate is used on windows because GnuWin wget fails to
# verify all certificates for some reason
link = clean_link(link)
log.i('downloading: ' + link)
wget_command = [which('wget'), '-b', '-N', '-o', '/dev/null', link]
if (which('wget') is None):
raise WGetNotFoundException('Could not find wget')
elif operating_system() == 'Windows':
log.d('on windows, adjusting wget_command')
wget_command = [which('wget'), '-b', '-N', '-o', 'NUL',
'--no-check-certificate', link]
try:
while call(wget_command) != 0:
time.sleep(.05)
log.d('call is not 0')
log.i('retrying...')
except BlockingIOError:
time.sleep(.1)
log.d('BlockingIOError!')
log.w('retrying...')
download_image(link)
def gjf_settings(self):
config_dict = {}
file_list = [file for file in os.listdir() if file.endswith('.pdb')]
if len(file_list) == 0:
log.e(
f'\'.pdb\' files not found in directory \'{os.path.basename(os.getcwd())}\'. Aborting...'
)
quit()
log.i(f'{len(file_list)} files found. Gathering settings...')
while True:
try:
log.d('How many calculations do you wish to perform?')
ncalc = int(input())
log.d(
'Do you want to set number of processors used and memory size available? Default is 8 processors and 1gb of memory. (Y/N) '
)
query = input()
nproc, mem = 8, 1
if query.lower() == 'y':
log.d('How many procesors do you wish to use? ')
nproc = int(input())
log.d('How much memory do you want to use? ')
mem = float(input())
break
except:
log.w('You have not provided a valid input, please try again.')
config_dict['ncalc'] = ncalc
config_dict['nproc'] = nproc
config_dict['mem'] = mem
config_dict['chk'] = 'chkfile.chk'
for calc_number in range(ncalc):
type_list = [
'DFTmin', 'MP2min', 'MP2max', 'M062Xmin', 'M062Xmax', 'Custom'
]
opt_list = [
'Local minimum', 'Transition State', 'Restart from Checkpoint'
]
freq_list = ['Complete', 'no Raman']
method_list = ['B3LYP', 'MP2', 'M062X']
basis_list = ['6-31G(d)', '6-311+G(d,p)']
log.d(
f'For calculation number {calc_number}, choose a calculation type preset by its number or type \'custom\' for custom settings...'
)
for val, name in enumerate(type_list):
print(f'{val:15}) {name}')
calc_type = input()
log.d(
f'For calculation number {calc_number}, do you wish optimization (Y/N):'
)
query = input()
if query.lower() == 'y':
log.d(f'Which optimization type do you wish :')
for val, name in enumerate(opt_list):
print(f'{val:15}) {name}')
opt_type = input()
log.d(
f'For calculation number {calc_number}, do you wish frequency calculations (Y/N):'
)
query = input()
if query.lower() == 'y':
log.d(f'Which frequency calculation do you wish:')
for val, name in enumerate(freq_list):
print(f'{val:15}) {name}')
opt_type = input()
if calc_type.lower() == 'custom':
log.d(
f'For calculation number {calc_number}, select calculation method:'
)
for val, name in enumerate(method_list):
print(f'{val:15}) {name}')
calc_method = input()
log.d(
f'For calculation number {calc_number}, select basis set:')
for val, name in enumerate(basis_list):
print(f'{val:15}) {name}')
basis_set = input()
log.d(
f'For calculation number {calc_number}, do you wish to specify a solvent (Y/N):'
)
query = input()
if query.lower() == 'y':
query_text1 = 'Please input solvent name:'
solvent = input(f'{query_text1:15}')
pp.pprint(config_dict)
return config_dict