def setup_class(self):
self.project_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(self.project_dir)
import config
self.settings = config.CONFIG()
self.settings.DEBUGGING = True
import unlogger
self.logging = unlogger.UnmanicLogger.__call__()
self.logging.setup_logger(self.settings)
self.logger = self.logging.get_logger()
self.ffmpeg = FFMPEGHandle(self.settings, self.logging)
def main():
global threads
global RUN_THREADS
# Read settings
settings = config.CONFIG()
# Create our data queues
data_queues = {
"scheduledtasks": queue.Queue(),
"inotifytasks": queue.Queue(),
"progress_reports": queue.Queue(),
"logging": unmanic_logging
}
# Clear cache directory
common.clean_files_in_dir(settings.CACHE_PATH)
# Setup job queue
job_queue = JobQueue(settings, data_queues)
# Setup post-processor thread
start_post_processor(data_queues, settings, job_queue)
# Start the worker threads
worker_handle = start_workers(data_queues, settings, job_queue)
# Start new thread to handle messages from service
start_handler(data_queues, settings, job_queue)
# Start new thread to run the web UI
start_ui_server(data_queues, settings, worker_handle)
# Start scheduled thread
start_library_scanner_manager(data_queues, settings)
# Start inotify watch manager
start_inotify_watch_manager(data_queues, settings)
# Watch for the term signal
signal.signal(signal.SIGTERM, sig_handle)
while RUN_THREADS:
signal.pause()
# Received term signal. Stop everything
main_logger.info("Stopping all threads")
for thread in threads:
main_logger.info("Sending thread {} abort signal".format(
thread['name']))
thread['thread'].stop()
main_logger.info("Waiting for thread {} to stop".format(
thread['name']))
thread['thread'].join()
main_logger.info("Exit Unmanic")
def main():
# Read settings
settings = config.CONFIG(main_logger)
# Apply settings to logging
unmanic_logging.setup_logger(settings)
# Create our data queues
data_queues = {
"scheduledtasks": queue.Queue(),
"inotifytasks": queue.Queue(),
"progress_reports": queue.Queue(),
"logging": unmanic_logging
}
# Clear cache directory
common.clean_files_in_dir(settings.CACHE_PATH)
# Setup job queue
job_queue = JobQueue(settings, data_queues)
# Setup post-processor thread
start_post_processor(data_queues, settings, job_queue)
# Start the worker threads
worker_handle = start_workers(data_queues, settings, job_queue)
# Start new thread to handle messages from service
start_handler(data_queues, settings, job_queue)
# Start new thread to run the web UI
start_ui_server(data_queues, settings, worker_handle)
# start scheduled thread
start_library_scanner_manager(data_queues, settings)
# start inotify watch manager
notifier = start_inotify_watch_manager(data_queues, settings)
notifier.loop()
while True:
time.sleep(5)
# stop everything
main_logger.info("Stopping all processes")
scheduler.abort_flag.set()
handler.abort_flag.set()
scheduler.join()
handler.join()
main_logger.info("Exit")
def setup_class(self):
"""
Setup the class state for pytest.
:return:
"""
self.project_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
# sys.path.append(self.project_dir)
unmanic_logging = unlogger.UnmanicLogger.__call__(False)
unmanic_logging.get_logger()
# import config
import config
self.settings = config.CONFIG()
self.settings.DEBUGGING = True
self.ffmpeg = ffmpeg.FFMPEGHandle(self.settings)
def setup_class(self):
self.project_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
import config
from lib import unlogger
self.settings = config.CONFIG()
self.settings.DEBUGGING = True
self.logging = unlogger.UnmanicLogger.__call__()
self.logging.setup_logger(self.settings)
self.logger = self.logging.get_logger()
# Create our test queues
self.data_queues = {
"progress_reports": queue.Queue(),
"logging": self.logging
}
self.task_queue = queue.Queue(maxsize=1)
self.complete_queue = queue.Queue()
def setup_class(self):
"""
Setup the class state for pytest
:return:
"""
self.project_dir = os.path.dirname(
os.path.dirname(os.path.abspath(__file__)))
# sys.path.append(self.project_dir)
self.logging = unlogger.UnmanicLogger.__call__(False)
self.logging.get_logger()
# import config
import config
self.settings = config.CONFIG()
self.settings.DEBUGGING = True
# Create our test queues
self.data_queues = {
"progress_reports": queue.Queue(),
"logging": self.logging
}
self.task_queue = queue.Queue(maxsize=1)
self.complete_queue = queue.Queue()
import asyncio
from aiocache import Cache
from databases import Database
import config
from files_app.models import init_db
Settings = config.CONFIG()
cache = Cache()
def setup_database(db_config):
db = Database(db_config)
asyncio.get_event_loop().run_until_complete(init_db(db))
return db
db = setup_database(Settings.get_db_config())
# This file is executed on every boot (including wake-boot from deepsleep)
import esp
import network
import webrepl
esp.osdebug(None)
# wifi connect
wlan = network.WLAN(network.STA_IF)
wlan.active(True)
try:
# read config
import config
import app
app.cfg = config.CONFIG()
wlan.config(dhcp_hostname=app.cfg.hostname)
wlan.connect(app.cfg.ssid, app.cfg.pwd)
except:
wlan.connect('WG', 'voytek66')
webrepl.start()
import pytest
from io import StringIO
from main import *
import asyncio
from files_app.models import File
from pytest_mock import mocker
import time
from files_app.routes import *
import setup
import config
Settings = config.CONFIG(test=True)
@pytest.yield_fixture
async def app(mocker):
app = Sanic(__name__)
from files_app.routes import bp
app.blueprint(bp)
yield app
@pytest.fixture
def test_cli(loop, app, sanic_client):
return loop.run_until_complete(sanic_client(app))
async def test_files_returns_200(test_cli):
import tensorflow as tf
import databatch
import define
import numpy as np
import config
import pickle
import os
os.environ["PYTHONUNBUFFERED"] = "1"
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
CFG = config.CONFIG()
CFG.Print()
def init_w(s, name=None):
return tf.Variable(tf.truncated_normal(shape=s, stddev=0.1), name=name)
def init_b(s, name=None):
return tf.Variable(tf.constant(0.1, shape=s), name=name)
def conv2d(x, W, strides=[1, 1, 1, 1], downsize=False, name=None):
if downsize: strides = [1, 4, 1, 1]
return tf.nn.conv2d(x, W, strides=strides, padding="SAME", name=name)
def res_block(input,
input_channel_num,
output_channel_num,
name,
about.set_name(creditos.Info.name)
about.set_authors(creditos.Info.authors)
about.set_documenters(creditos.Info.documenters)
about.set_artists(creditos.Info.artists)
about.set_translator_credits(creditos.Info.translator)
about.set_version(creditos.Info.version)
about.set_comments(creditos.Info.description)
about.set_copyright(creditos.Info.copyright)
about.set_website(creditos.Info.website)
about.set_license(creditos.Info.license)
about.set_wrap_license(True)
about.run()
about.destroy()
if string==_("Config"):
print " menu de congifuracion"
conf=config.CONFIG()
conf.show()
#~ def carga_tooltip(self):
#~ ruta=os.path.abspath(os.path.dirname(__file__))
#~ ff=open(ruta + "/tooltips.xml","r")
#~ t=ff.readlines()
#~ for a in range(len(t)):
#~ cad_aux=t[a].strip("\n")
#~ if cad_aux=="<tool>":
#~ self.tooltip[t[a+1].strip("\n")]=t[a+2].strip("\n")
def carga_dicc(self):
"""
funcion para cargar los componentes bloques,
los valores del gtk.notebook estan determinados
por el nombre del archivo, leyendo el archivo saco el valor
def main(inputfile, outputfile, configfile=''):
torspath = os.path.dirname(os.path.realpath(sys.argv[0]))
if configfile == '':
configfile = torspath + os.path.sep + 'configfile.txt'
args = config.ARGS(inputfile)
Config = config.CONFIG(configfile, outputfile)
paths = Config.path_dic()
paths['torsscan'] = torspath
sys.path.insert(0, es.get_paths(paths, 'bin'))
sys.path.insert(0, es.get_paths(paths, 'qtc'))
sys.path.insert(0, es.get_paths(paths, 'torsscan'))
log.info(random_cute_animal())
##### Build and Run EStokTP ######
####################################
global io, ob
import obtools as ob
import iotools as io
import tctools as tc
import shutil
symnums = []
samps = None
if args.restart < 8:
index = 0
if "Opt" in args.jobs and args.restart < 1:
alljobs = args.jobs
args.jobs = ["Opt"]
es.run_level0(args, paths)
args.restart = 1
args.jobs = alljobs
if "1dTau" in args.jobs and args.restart < 4:
logging.info("========\nBEGIN LEVEL 1 and 1DHR\n========\n")
alljobs = args.jobs
negvals = True
attempt = 0
while (negvals and attempt < 3):
attempt += 1
args.jobs = ["Opt_1", "1dTau"]
negvals = False
if attempt == 1 and args.restart == 3:
pass
else:
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if io.check_file('output/estoktp.out'):
shutil.copy('output/estoktp.out', 'output/estoktp_l1.out')
args.restart = 3
for i in range(len(args.reacs)):
lowene = 0.0
lowenefile = None
if io.check_file('me_files/reac' + str(i + 1) + '_hr.me'):
hr = io.read_file('me_files/reac' + str(i + 1) +
'_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp' + str(
i + 1).zfill(2) + '_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
logging.info(xyz)
slabel = ob.get_slabel(ob.get_mol(xyz))
if slabel.split('_m')[0] == ob.get_slabel(
args.reacs[i]).split('_m')[0]:
negvals = True
if io.check_file('data/ts.dat') and i == 0:
if 'isomerization' in args.reactype.lower():
tsfile = io.read_file('data/ts.dat')
ijk = tsfile.split('ji ki')[1].split()[:3]
ijk.append(
tsfile.split('ireact2')[1].split('\n')
[1].split()[-1])
xyz = xyz.splitlines()
xyz[int(ijk[0]) +
1] = '2 ' + xyz[int(ijk[0]) + 1]
xyz[int(ijk[1]) +
1] = '3 ' + xyz[int(ijk[1]) + 1]
xyz[int(ijk[2]) +
1] = '4 ' + xyz[int(ijk[2]) + 1]
xyz[int(ijk[3]) +
1] = '1 ' + xyz[int(ijk[3]) + 1]
xyz = '\n'.join(xyz)
else:
ijk = io.read_file('data/ts.dat').split(
'ksite')[1].split()[:3]
xyz = xyz.splitlines()
xyz[int(ijk[0]) +
1] = '2 ' + xyz[int(ijk[0]) + 1]
xyz[int(ijk[1]) +
1] = '1 ' + xyz[int(ijk[1]) + 1]
xyz[int(ijk[2]) +
1] = '3 ' + xyz[int(ijk[2]) + 1]
xyz = '\n'.join(xyz)
slabel = ob.get_smiles_filename(
ob.get_slabel(args.reacs[i]))
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/' + slabel + '.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to {}'
.format(slabel + '.xyz'))
else:
log.warning(
'Lower configuration found in 1dTau. But has different smiles: {} vs. {}'
.format(slabel, ob.get_slabel(args.reacs[i])))
for l in range(len(args.prods)):
lowene = 0.
lowenefile = None
if io.check_file('me_files/prod' + str(l + 1) + '_hr.me'):
hr = io.read_file('me_files/prod' + str(l + 1) +
'_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp' + str(
i + l + 2).zfill(2) + '_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
slabel = ob.get_slabel(ob.get_mol(xyz))
if slabel.split('_m')[0] == ob.get_slabel(
args.prods[l]).split('_m')[0]:
negvals = True
slabel = ob.get_smiles_filename(
ob.get_slabel(args.prods[l]))
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/' + slabel + '.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to {}'
.format(slabel + '.xyz'))
else:
log.warning(
'Lower configuration found in 1dTau. But has different smiles: {} vs. {}'
.format(slabel, ob.get_slabel(args.prods[l])))
if args.reactype.lower() in [
'addition', 'abstraction', 'isomerization',
'addition_well', 'isomerization_well'
]:
lowene = 0.
lowenefile = None
if io.check_file('me_files/ts_hr.me'):
hr = io.read_file('me_files/ts_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp00_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
negvals = True
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/ts.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to ts.xyz'
)
if args.wellp and args.wellp.lower() != 'false':
lowene = 0.
lowenefile = None
if io.check_file('me_files/wellp_hr.me'):
hr = io.read_file('me_files/wellp_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp06_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
negvals = True
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/wellp.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to wellp.xyz'
)
if args.wellr and args.wellr.lower() != 'false':
lowene = 0.
lowenefile = None
if io.check_file('me_files/wellr_hr.me'):
hr = io.read_file('me_files/wellr_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp05_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
negvals = True
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/wellr.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to wellr.xyz'
)
args.jobs = alljobs
elif "Opt_1" in args.jobs and args.restart < 2:
log.info("========\nBEGIN LEVEL 1\n========\n")
alljobs = args.jobs
args.jobs = ["Opt_1"]
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if io.check_file('output/estoktp.out'):
shutil.copy('output/estoktp.out', 'output/estoktp_l1.out')
args.jobs = alljobs
args.restart = 2
if args.anharm.lower() != 'false' and 'd' not in args.nodes[0]:
import thermo
log.info("========\nBEGIN VPT2\n========\n")
optlevel, anlevel = thermo.get_anlevel(args.anharm, args.meths)
for n, reac in enumerate(args.reacs):
typ = 'reac'
natom = ob.get_natom(reac)
if natom > 2:
mult = ob.get_mult(reac)
if io.check_file('me_files/' + typ + str(n + 1) +
'_fr.me'):
if not 'Anh' in io.read_file('me_files/' + typ +
str(n + 1) + '_fr.me'):
anfr, fr1, anx, fr2, fr3, _ = thermo.get_anharm(
typ, str(n + 1), natom, args.nodes[0],
anlevel, args.anovrwrt, reac,
optlevel.split('/'), paths)
lines = io.read_file('me_files/' + typ +
str(n + 1) + '_fr.me')
io.write_file(
lines,
'me_files/' + typ + str(n + 1) + '_harm.me')
lines = fr1 + fr2.split(
'End'
)[0] + fr3 + '\n !************************************\n'
io.write_file(
lines,
'me_files/' + typ + str(n + 1) + '_fr.me')
for n, prod in enumerate(args.prods):
typ = 'prod'
natom = ob.get_natom(prod)
if natom > 2:
mult = ob.get_mult(prod)
if io.check_file('me_files/' + typ + str(n + 1) +
'_fr.me'):
if not 'Anh' in io.read_file('me_files/' + typ +
str(n + 1) + '_fr.me'):
anfr, fr1, anx, fr2, fr3, _ = thermo.get_anharm(
typ, str(n + 1), natom, args.nodes[0],
anlevel, args.anovrwrt, prod,
optlevel.split('/'), paths)
lines = io.read_file('me_files/' + typ +
str(n + 1) + '_fr.me')
io.write_file(
lines,
'me_files/' + typ + str(n + 1) + '_harm.me')
lines = fr1 + fr2.split(
'End'
)[0] + fr3 + '\n !************************************\n'
io.write_file(
lines,
'me_files/' + typ + str(n + 1) + '_fr.me')
if args.reactype and io.check_file('geoms/tsgta_l1.xyz'):
typ = 'ts'
mol = io.read_file('geoms/tsgta_l1.xyz')
ts = ob.get_mol(mol)
natom = ob.get_natom(ts)
mult = ob.get_mult(ts)
if io.check_file('me_files/ts_fr.me'):
if not 'Anh' in io.read_file('me_files/ts_fr.me'):
anfr, fr1, anx, fr2, fr3, _ = thermo.get_anharm(
typ, str(n + 1), natom, args.nodes[0], anlevel,
args.anovrwrt, 'ts', optlevel.split('/'), paths)
lines = io.read_file('me_files/' + typ + '_fr.me')
io.write_file(lines, 'me_files/' + typ + '_harm.me')
lines = fr1 + fr2.split(
'End'
)[0] + fr3 + '\n End\n !************************************\n'
io.write_file(lines, 'me_files/' + typ + '_fr.me')
log.info("========\nBEGIN MDHR, HL\n========\n")
if 'kTP' in args.jobs:
alljobs = args.jobs
args.jobs = []
for job in alljobs:
if job != 'kTP':
args.jobs.append(job)
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if io.check_file('me_files/ts_en.me'):
tsen = float(io.read_file('me_files/ts_en.me'))
tsen += float(io.read_file('me_files/ts_zpe.me'))
reacen = 0
proden = 0
for i, reac in enumerate(args.reacs):
if io.check_file('me_files/reac{}_en.me'.format(i + 1)):
reacen += float(
io.read_file('me_files/reac{}_en.me'.format(i +
1)))
reacen += float(
io.read_file('me_files/reac{}_zpe.me'.format(i +
1)))
if args.reactype.lower(
) == 'addition_well' or args.reactype.lower(
) == 'isomerization_well':
if io.check_file('me_files/wellp_en.me'):
proden += float(io.read_file('me_files/wellp_en.me'))
proden += float(io.read_file('me_files/wellp_zpe.me'))
else:
for i, prod in enumerate(args.prods):
if io.check_file('me_files/prod{}_en.me'.format(i +
1)):
proden += float(
io.read_file(
'me_files/prod{}_en.me'.format(i + 1)))
proden += float(
io.read_file(
'me_files/prod{}_zpe.me'.format(i + 1)))
if tsen <= reacen or tsen <= proden:
log.info('Well Depth is negative. NoTunnel is turned on')
if args.esoptions:
args.esoptions += ',NoTunnel'
else:
args.esoptions = 'NoTunnel'
log.info("========\nBEGIN kTP\n========\n")
args.jobs = alljobs
restart = 7
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
else:
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if ("1dTau" in args.jobs or 'MdTau' in args.jobs):
for i in range(len(args.reacs)):
es.check_hrs(i + 1, 'reac')
for i in range(len(args.prods)):
es.check_hrs(i + 1, 'prod')
es.me_file_abs_path()
if args.restart == 10:
io.execute([paths['bin'] + os.path.sep + 'mess', 'me_ktp.inp'])
if args.reactype and io.check_file('rate.out'):
import me_parser
#initialize the class in which to store the results
data = me_parser.paper()
data.reactions = []
# set some constants, depending upon whether the rate coefficients are to be used for CHEMKIN or something else.
data.T0 = 1.0
data.R = 1.987 # cal/mol-K. Note that PLOG formalism requires Ea in cal/mol-K!
data.N_avo = 6.0221415E23 #convert bimolecular rate coefficients from cm^3/sec to cm^3/mol/s
# set the minimum and maximum temperature
#data.Tmin = 600.0
#data.Tmax = 1200.0
# read me.out file from the command line
me_dot_out = 'rate.out'
if io.check_file(me_dot_out):
lines = io.read_file(me_dot_out, True)
if len(lines) < 2:
log.info('rate.out is empty')
## copy new plog executable to the path of the source file
#path = os.path.abspath(os.path.dirname(me_dot_out))
#
#command = 'cp /home/elliott/bin/dsarrfit.x_cfg ' + path
#log.info( command)
#os.system(command)
# parse results for the temperature, pressure, and names of channels
me_parser.get_temp_pres(data, lines)
# parse results for the pdep rate constants
me_parser.get_pdep_k(data, lines)
# fit the results to PLOG expressions
me_parser.fit_pdep(
data, nonlin_fit=False
) #replace <True> with <False> if you don't want to use the nonlinear solver (not recommended)
# print the resulting PLOG expressions to file
me_parser.print_plog(data, me_dot_out)
# plot the results: dashed line = single PLOG, solid line = double PLOG
#me_parser.plot_reactant(data, me_dot_out, show_plot=False, save_plot=True)
####### Parse results #########
########################################
import results
rs = results.RESULTS(args, paths)
args.hlen = rs.get_hlen()
args.optlevel = rs.optlevel
args.enlevel = rs.enlevel
args.taulevel = rs.taulevel
if args.parseall.lower() == 'true' or args.alltherm.lower() == 'true':
rs.get_results()
####### Build and run thermo #########
########################################
import thermo
rs.thermo = False
if args.alltherm.lower() == 'true':
rs.thermo = True
args.symnums = symnums
rs.dH0, rs.dH298, rs.hfbases, rs.anfreqs, rs.anxmat = thermo.run(
args, paths, rs.d)
if args.parseall.lower() == 'true':
rs.get_thermo_results()
return
