def saveOutputHTML(self):
"""
Save the current reaction model to a pretty HTML file.
"""
logging.info('Saving current model to HTML file...')
from rmgpy.rmg.output import saveOutputHTML
saveOutputHTML(os.path.join(self.outputDirectory, 'output.html'), self.reactionModel)
def main(chemkin, dictionary, output, foreign):
model = CoreEdgeReactionModel()
model.core.species, model.core.reactions = loadChemkinFile(chemkin, dictionary, readComments=not foreign)
outputPath = os.path.join(output, 'output.html')
speciesPath = os.path.join(output, 'species')
if not os.path.isdir(speciesPath):
os.makedirs(speciesPath)
saveOutputHTML(outputPath, model)
def main(chemkin, dictionary, output, foreign):
model = CoreEdgeReactionModel()
model.core.species, model.core.reactions = loadChemkinFile(
chemkin, dictionary, readComments=not foreign, checkDuplicates=foreign)
outputPath = os.path.join(output, 'output.html')
speciesPath = os.path.join(output, 'species')
if not os.path.isdir(speciesPath):
os.makedirs(speciesPath)
saveOutputHTML(outputPath, model)
def saveHTMLFile(path):
"""
Save an output HTML file from the contents of a RMG-Java output folder
"""
from rmgpy.rmg.model import CoreEdgeReactionModel
from rmgpy.rmg.output import saveOutputHTML
chemkinPath= path + '/chemkin/chem.inp'
dictionaryPath = path + 'RMG_Dictionary.txt'
model = CoreEdgeReactionModel()
model.core.species, model.core.reactions = loadChemkinFile(chemkinPath,dictionaryPath)
outputPath = path + 'output.html'
speciesPath = path + '/species/'
if not os.path.isdir(speciesPath):
os.makedirs(speciesPath)
saveOutputHTML(outputPath, model)
def initialize(self, args):
"""
Initialize an RMG job using the command-line arguments `args` as returned
by the :mod:`argparse` package.
"""
# Save initialization time
self.initializationTime = time.time()
# Log start timestamp
logging.info('RMG execution initiated at ' + time.asctime() + '\n')
# Print out RMG header
self.logHeader()
# Set directories
self.outputDirectory = args.output_directory
self.scratchDirectory = args.scratch_directory
# Read input file
self.loadInput(args.file[0])
# Check input file
self.checkInput()
# See if memory profiling package is available
try:
import os
import psutil
except ImportError:
logging.info('Optional package dependency "psutil" not found; memory profiling information will not be saved.')
# See if spreadsheet writing package is available
if self.saveConcentrationProfiles:
try:
xlwt
except NameError:
logging.warning('Package dependency "xlwt" not loaded; reaction system concentration profiles will not be saved, despite saveConcentrationProfiles = True option.')
self.saveConcentrationProfiles = False
# Make output subdirectories
self.makeOutputSubdirectory('plot')
self.makeOutputSubdirectory('species')
self.makeOutputSubdirectory('pdep')
self.makeOutputSubdirectory('chemkin')
self.makeOutputSubdirectory('solver')
# Load databases
self.loadDatabase()
# Set wall time
if args.walltime == '0':
self.wallTime = 0
else:
data = args.walltime[0].split(':')
if len(data) == 1:
self.wallTime = int(data[-1])
elif len(data) == 2:
self.wallTime = int(data[-1]) + 60 * int(data[-2])
elif len(data) == 3:
self.wallTime = int(data[-1]) + 60 * int(data[-2]) + 3600 * int(data[-3])
elif len(data) == 4:
self.wallTime = int(data[-1]) + 60 * int(data[-2]) + 3600 * int(data[-3]) + 86400 * int(data[-4])
else:
raise ValueError('Invalid format for wall time; should be HH:MM:SS.')
# Delete previous HTML file
from rmgpy.rmg.output import saveOutputHTML
saveOutputHTML(os.path.join(self.outputDirectory, 'output.html'), self.reactionModel)
# Initialize reaction model
if args.restart:
self.loadRestartFile(os.path.join(self.outputDirectory,'restart.pkl'))
else:
# Seed mechanisms: add species and reactions from seed mechanism
# DON'T generate any more reactions for the seed species at this time
for seedMechanism in self.seedMechanisms:
self.reactionModel.addSeedMechanismToCore(seedMechanism, react=False)
# Reaction libraries: add species and reactions from reaction library to the edge so
# that RMG can find them if their rates are large enough
for library, option in self.reactionLibraries:
self.reactionModel.addReactionLibraryToEdge(library)
# Add nonreactive species (e.g. bath gases) to core first
# This is necessary so that the PDep algorithm can identify the bath gas
self.reactionModel.enlarge([spec for spec in self.initialSpecies if not spec.reactive])
# Then add remaining reactive species
for spec in self.initialSpecies:
spec.generateThermoData(self.database)
self.reactionModel.enlarge([spec for spec in self.initialSpecies if spec.reactive])
# Save a restart file if desired
if self.saveRestartPeriod:
self.saveRestartFile(os.path.join(self.outputDirectory,'restart.pkl'), self.reactionModel)
# Create pathway calculation folder
if not os.path.exists(pathwayFolder):
os.makedirs(pathwayFolder)
shutil.copy(mechFileCti, os.path.join(pathwayFolder, mechFileCti))
shutil.move(pathwayFile, os.path.join(pathwayFolder, pathwayFile))
# Generate HTML file
if not os.path.isfile(os.path.join(mechFolder, mechHTML)):
print 'create reaction model...'
model = CoreEdgeReactionModel()
print 'load chemkin file...'
model.core.species, model.core.reactions = loadChemkinFile(
os.path.join(mechFolder, mechFileInp),
os.path.join(mechFolder, spcFile))
print 'save HTML file...'
saveOutputHTML(os.path.join(mechFolder, mechHTML), model)
print 'finished!'
# Copy the 'species' folder generated during the generation of HTML file to the 'pathway' folder. Rename the copy as 'structure'
structureDir = os.path.join(pathwayFolder, structureFolder)
if not os.path.exists(structureDir):
shutil.copytree(os.path.join(mechFolder, spcFolder), structureDir)
for filename in os.listdir(structureDir):
if filename.endswith(').png'):
filename = os.path.join(structureDir, filename)
im = Image.open(filename)
# f = 200.0/max(im.width, im.height)
f = 3
im = im.resize((int(im.width * f), int(im.height * f)))
im.save(filename)
