def test_avi_simple(self):
folder = os.path.join(os.path.dirname(rmgpy.__file__),'tools','data','flux')
inputFile = os.path.join(folder,'input_simple.py')
chemkinFile = os.path.join(folder, 'chemkin', 'chem.inp')
dictFile = os.path.join(folder, 'chemkin', 'species_dictionary.txt')
settings = {'maximumNodeCount': 50,
'maximumEdgeCount': 50,
'concentrationTolerance': 1e-6,
'speciesRateTolerance': 1e-6,
'maximumNodePenWidth': 10.0,
'maximumEdgePenWidth': 10.0,
'radius': 2,
'centralReactionCount': 2,
'timeStep': 10**0.1}
createFluxDiagram(inputFile, chemkinFile, dictFile,
centralSpeciesList=[1], superimpose=True, settings=settings)
outputdir = os.path.join(folder,'flux')
simfile = os.path.join(outputdir,'1','flux_diagram.avi')
speciesdir = os.path.join(folder,'species')
self.assertTrue(os.path.isfile(simfile))
shutil.rmtree(outputdir)
shutil.rmtree(speciesdir)
def test_avi_simple(self):
folder = os.path.join(os.path.dirname(rmgpy.__file__), 'tools', 'data',
'flux')
inputFile = os.path.join(folder, 'input_simple.py')
chemkinFile = os.path.join(folder, 'chemkin', 'chem.inp')
dictFile = os.path.join(folder, 'chemkin', 'species_dictionary.txt')
settings = {
'maximumNodeCount': 50,
'maximumEdgeCount': 50,
'concentrationTolerance': 1e-6,
'speciesRateTolerance': 1e-6,
'maximumNodePenWidth': 10.0,
'maximumEdgePenWidth': 10.0,
'timeStep': 10**0.1
}
createFluxDiagram(inputFile,
chemkinFile,
dictFile,
centralSpecies='ethane',
settings=settings)
outputdir = os.path.join(folder, 'flux')
simfile = os.path.join(outputdir, '1', 'flux_diagram.avi')
speciesdir = os.path.join(folder, 'species')
self.assertTrue(os.path.isfile(simfile))
shutil.rmtree(outputdir)
shutil.rmtree(speciesdir)
def generateFlux(request):
"""
Allows user to upload a set of RMG condition files and/or chemkin species concentraiton output
to generate a flux diagram video.
"""
from rmgpy.tools.fluxdiagram import createFluxDiagram
flux = FluxDiagram()
path = ''
flux.deleteDir()
if request.method == 'POST':
flux.createDir()
form = FluxDiagramForm(request.POST, request.FILES, instance=flux)
if form.is_valid():
form.save()
input = os.path.join(flux.path, 'input.py')
chemkin = os.path.join(flux.path, 'chem.inp')
dict = os.path.join(flux.path, 'species_dictionary.txt')
chemkinOutput = ''
if 'ChemkinOutput' in request.FILES:
chemkinOutput = os.path.join(flux.path, 'chemkin_output.out')
java = form.cleaned_data['Java']
settings = {}
settings['maximumNodeCount'] = form.cleaned_data['MaxNodes']
settings['maximumEdgeCount'] = form.cleaned_data['MaxEdges']
settings['timeStep'] = form.cleaned_data['TimeStep']
settings['concentrationTolerance'] = form.cleaned_data[
'ConcentrationTolerance']
settings['speciesRateTolerance'] = form.cleaned_data[
'SpeciesRateTolerance']
createFluxDiagram(input,
chemkin,
dict,
savePath=flux.path,
java=java,
settings=settings,
chemkinOutput=chemkinOutput)
# Look at number of subdirectories to determine where the flux diagram videos are
subdirs = [
name for name in os.listdir(flux.path)
if os.path.isdir(os.path.join(flux.path, name))
]
subdirs.remove('species')
return render_to_response('fluxDiagram.html', {
'form': form,
'path': subdirs
},
context_instance=RequestContext(request))
else:
form = FluxDiagramForm(instance=flux)
return render_to_response('fluxDiagram.html', {
'form': form,
'path': path
},
context_instance=RequestContext(request))
def main():
inputFile, chemkinFile, dictFile, speciesPath, chemkinOutput, useJava, dflag, settings = parse_arguments(
)
createFluxDiagram(inputFile,
chemkinFile,
dictFile,
speciesPath=speciesPath,
java=useJava,
settings=settings,
chemkinOutput=chemkinOutput,
diffusionLimited=dflag)
def test_avi_liquid(self):
folder = os.path.join(os.path.dirname(rmgpy.__file__), 'tools', 'data', 'flux')
inputFile = os.path.join(folder, 'input_liquid.py')
chemkinFile = os.path.join(folder, 'chemkin', 'chem.inp')
dictFile = os.path.join(folder, 'chemkin', 'species_dictionary.txt')
createFluxDiagram(inputFile, chemkinFile, dictFile, diffusionLimited=False)
outputdir = os.path.join(folder, 'flux')
simfile = os.path.join(outputdir, '1', 'flux_diagram.avi')
speciesdir = os.path.join(folder, 'species')
self.assertTrue(os.path.isfile(simfile))
shutil.rmtree(outputdir)
shutil.rmtree(speciesdir)
def test_avi_liquid(self):
folder = os.path.join(os.path.dirname(rmgpy.__file__), 'tools', 'data', 'flux')
inputFile = os.path.join(folder, 'input_liquid.py')
chemkinFile = os.path.join(folder, 'chemkin', 'chem.inp')
dictFile = os.path.join(folder, 'chemkin', 'species_dictionary.txt')
createFluxDiagram(inputFile, chemkinFile, dictFile, diffusionLimited=False)
outputdir = os.path.join(folder, 'flux')
simfile = os.path.join(outputdir, '1', 'flux_diagram.avi')
speciesdir = os.path.join(folder, 'species')
self.assertTrue(os.path.isfile(simfile))
shutil.rmtree(outputdir)
shutil.rmtree(speciesdir)
def main():
(inputFile, chemkinFile, dictFile, speciesPath, chemkinOutput, useJava,
dflag, checkDuplicates, settings, centralSpeciesList, superimpose,
saveStates, readStates) = parse_arguments()
createFluxDiagram(inputFile,
chemkinFile,
dictFile,
speciesPath=speciesPath,
java=useJava,
settings=settings,
chemkinOutput=chemkinOutput,
diffusionLimited=dflag,
centralSpeciesList=centralSpeciesList,
superimpose=superimpose,
saveStates=saveStates,
readStates=readStates,
checkDuplicates=checkDuplicates)
def main():
(inputFile,
chemkinFile,
dictFile,
speciesPath,
chemkinOutput,
useJava,
dflag,
checkDuplicates,
settings,
centralSpeciesList,
superimpose,
saveStates,
readStates) = parse_arguments()
createFluxDiagram(inputFile, chemkinFile, dictFile, speciesPath=speciesPath, java=useJava, settings=settings,
chemkinOutput=chemkinOutput, diffusionLimited=dflag, centralSpeciesList=centralSpeciesList,
superimpose=superimpose, saveStates=saveStates, readStates=readStates,
checkDuplicates=checkDuplicates)
def generateFlux(request):
"""
Allows user to upload a set of RMG condition files and/or chemkin species concentraiton output
to generate a flux diagram video.
"""
from rmgpy.tools.fluxdiagram import createFluxDiagram
flux = FluxDiagram()
path = ''
flux.deleteDir()
if request.method == 'POST':
flux.createDir()
form = FluxDiagramForm(request.POST, request.FILES,instance=flux)
if form.is_valid():
form.save()
input = os.path.join(flux.path,'input.py')
chemkin = os.path.join(flux.path,'chem.inp')
dict = os.path.join(flux.path,'species_dictionary.txt')
chemkinOutput = ''
if 'ChemkinOutput' in request.FILES:
chemkinOutput = os.path.join(flux.path,'chemkin_output.out')
java = form.cleaned_data['Java']
settings = {}
settings['maximumNodeCount'] = form.cleaned_data['MaxNodes']
settings['maximumEdgeCount'] = form.cleaned_data['MaxEdges']
settings['timeStep'] = form.cleaned_data['TimeStep']
settings['concentrationTolerance'] = form.cleaned_data['ConcentrationTolerance']
settings['speciesRateTolerance'] = form.cleaned_data['SpeciesRateTolerance']
createFluxDiagram(input, chemkin, dict, savePath=flux.path, java=java, settings=settings, chemkinOutput=chemkinOutput)
# Look at number of subdirectories to determine where the flux diagram videos are
subdirs = [name for name in os.listdir(flux.path) if os.path.isdir(os.path.join(flux.path, name))]
subdirs.remove('species')
return render(request, 'fluxDiagram.html', {'form': form, 'path':subdirs})
else:
form = FluxDiagramForm(instance=flux)
return render(request, 'fluxDiagram.html', {'form': form,'path':path})
def main():
inputFile, chemkinFile, dictFile, speciesPath, chemkinOutput, useJava, dflag, settings = parse_arguments()
createFluxDiagram(inputFile, chemkinFile, dictFile, speciesPath=speciesPath, java=useJava, settings=settings,
chemkinOutput=chemkinOutput, diffusionLimited=dflag)