def __init__(self, filename):
self.filename = filename
self.xml = io.fromFile(filename)
self.obs_list = self.getObservationList()
self.obs_lists = []
for el in self.obs_list.getchildren():
self.obs_lists.append(el)
self.obs_file = self.getObservationFilename()
self.coordinates = []
self.names = []
def write_new_xml(testname, testlog):
"""Adds the needed magic to a new xml file."""
print("Renaming: {0}.xml to {0}_orig.xml".format(testname), file=testlog)
os.rename(testname + ".xml", testname + "_orig.xml")
xml = aio.fromFile(testname + "_orig.xml", True)
# vis by list of cycles
try:
vis = asearch.getElementByNamePath(xml, "visualization")
except aerrors.MissingXMLError:
pass
else:
for i in range(len(vis)):
vis.pop(vis[0].get('name'))
vis.setParameter("cycles", "Array(int)", find_vis_cycles(testname))
vis.setParameter("file name base", "string", "visdump")
try:
viss = asearch.getElementByNamePath(xml, "visualization surface")
except aerrors.MissingXMLError:
pass
else:
for i in range(len(viss)):
viss.pop(viss[0].get('name'))
viss.setParameter("cycles", "Array(int)", find_vis_cycles(testname))
viss.setParameter("file name base", "string", "visdump_surface")
# update timestep controller, nonlinear solvers
for ti in asearch.generateElementByNamePath(xml, "time integrator"):
asearch.generateElementByNamePath(
ti, "limit iterations").next().setValue(100)
asearch.generateElementByNamePath(
ti, "diverged tolerance").next().setValue(1.e10)
asearch.getElementByNamePath(
ti, "timestep controller type").setValue("from file")
ts_hist = ti.sublist("timestep controller from file parameters")
ts_hist.setParameter("file name", "string",
"../data/{0}_dts.h5".format(testname))
print("Writing: {0}.xml".format(testname), file=testlog)
aio.toFile(xml, "{0}.xml".format(testname))
snow_distribution(xml)
end_time_units(xml)
import verbose_object
verbose_object.fixVerboseObject(xml)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description="Fix a number of changes from ATS input spec 0.86 to 0.88")
parser.add_argument("infile", help="input filename")
group = parser.add_mutually_exclusive_group()
group.add_argument("-i",
"--inplace",
action="store_true",
help="fix file in place")
group.add_argument("-o", "--outfile", help="output filename")
args = parser.parse_args()
print("Converting file: %s", args.infile)
xml = aio.fromFile(args.infile, True)
update(xml)
if args.inplace:
aio.toFile(xml, args.infile)
else:
aio.toFile(xml, args.outfile)
sys.exit(0)
mesh = xml_search.getElementByNamePath(xml, "Mesh")
for label in changes_mesh:
for param in xml_search.generateElementByNamePath(mesh, label):
param.set('name', label.lower())
mesh.set('name', "mesh")
domain = xml_search.getElementByNamePath(xml, "Domain")
xml.remove(domain)
if __name__ == "__main__":
fnames = [f for f in sys.argv if f.endswith('.xml')]
for f in fnames:
try:
xml = xml_io.fromFile(f)
except xml_errors.NotNativeSpecError:
pass
except RuntimeError,msg:
print "Attempted to convert invalid xml file:", f
print " Error:", msg
else:
lower_case(xml)
xml_io.toFile(xml, f)
def flatten_pks(xml):
try:
cycle_driver = asearch.childByName(xml, "cycle driver")
except aerrors.MissingXMLError():
pass
else:
return
pks = asearch.childByName(xml, "PKs")
cd_pks = coordinator_to_cycle_driver(xml)
flat_pks = ParameterList("PKs")
flatten(pks, flat_pks, cd_pks)
pks.extend(flat_pks)
if __name__ == "__main__":
if "-h" in sys.argv or "--help" in sys.argv or "--h" in sys.argv:
print "Usage: python flatten_pks.py INFILE OUTFILE"
sys.exit(0)
outfile = sys.argv.pop(-1)
infile = sys.argv.pop(-1)
if (infile == "-i"):
infile = outfile
xml = aio.fromFile(infile)
flatten_pks(xml)
aio.toFile(xml, outfile)
sys.exit(0)
def update(xml):
flatten_pks.flatten_pks(xml)
fixEvaluator(xml, "ponded_depth", "surface-ponded_depth")
fixEvaluator(xml, "ponded_depth_bar", "surface-ponded_depth_bar")
compressibility(xml)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description="Fix a number of changes from ATS input spec 0.86 to 0.9x")
parser.add_argument("infile", help="input filename")
group = parser.add_mutually_exclusive_group()
group.add_argument("-i",
"--inplace",
action="store_true",
help="fix file in place")
group.add_argument("-o", "--outfile", help="output filename")
args = parser.parse_args()
xml = aio.fromFile(args.infile)
update(xml)
if args.inplace:
aio.toFile(xml, args.infile)
else:
aio.toFile(xml, args.outfile)
sys.exit(0)
seepage_face_bcs(xml)
primary_variable(xml)
mesh_list(xml)
vis(xml)
snow_depth(xml)
snow_distribution(xml)
seb(xml)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Fix a number of changes from ATS input spec 0.86 to 0.9x")
parser.add_argument("infile", help="input filename")
group = parser.add_mutually_exclusive_group()
group.add_argument("-i", "--inplace", action="store_true", help="fix file in place")
group.add_argument("-o", "--outfile", help="output filename")
args = parser.parse_args()
print "Converting file: %s"%args.infile
xml = aio.fromFile(args.infile, True)
update(xml)
if args.inplace:
aio.toFile(xml, args.infile)
else:
aio.toFile(xml, args.outfile)
sys.exit(0)
mesh.set('name', "mesh")
try:
domain = xml_search.getElementByNamePath(xml, "Domain")
except xml_errors.MissingXMLError:
pass
else:
xml.remove(domain)
if __name__ == "__main__":
fnames = [f for f in sys.argv if f.endswith('.xml')]
for f in fnames:
try:
xml = xml_io.fromFile(f)
except xml_errors.NotNativeSpecError:
pass
except RuntimeError,msg:
print "Attempted to convert invalid xml file:", f
print " Error:", msg
else:
lower_case(xml)
xml_io.toFile(xml, f)
cd_pks = coordinator_to_cycle_driver(xml)
flat_pks = ParameterList("PKs")
flatten(pks, flat_pks, cd_pks)
pks.extend(flat_pks)
if __name__ == "__main__":
if "-h" in sys.argv or "--help" in sys.argv or "--h" in sys.argv:
print "Usage: python flatten_pks.py INFILE OUTFILE"
sys.exit(0)
outfile = sys.argv.pop(-1)
infile = sys.argv.pop(-1)
if (infile == "-i"):
infile = outfile
xml = aio.fromFile(infile)
flatten_pks(xml)
aio.toFile(xml, outfile)
sys.exit(0)
