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def setUp(self):
self.options=forcebalance.parser.gen_opts_defaults.copy()
self.options.update({
'root': os.getcwd() + '/test/files',
'penalty_additive': 0.01,
'jobtype': 'NEWTON',
'forcefield': ['water.itp']})
os.chdir(self.options['root'])
self.logger.debug("\nUsing the following options:\n%s\n" % str(self.options))
self.tgt_opts = [ forcebalance.parser.tgt_opts_defaults.copy() ]
self.tgt_opts[0].update({"type" : "ABINITIO_GMX", "name" : "cluster-06"})
self.ff = forcebalance.forcefield.FF(self.options)
self.objective = forcebalance.objective.Objective(self.options, self.tgt_opts,self.ff)
def setUp(self):
self.logger.debug("\nBuilding options for target...\n")
self.options=forcebalance.parser.gen_opts_defaults.copy()
self.tgt_opt=forcebalance.parser.tgt_opts_defaults.copy()
self.ff = None # Forcefield this target is fitting
self.options.update({'root': os.getcwd() + '/test/files'})
os.chdir(self.options['root'])
def setUp(self):
# options used in 001_water_tutorial
self.logger.debug("\nSetting up options...\n")
self.options=forcebalance.parser.gen_opts_defaults.copy()
self.options.update({
'root': os.getcwd() + '/test/files',
'penalty_additive': 0.01,
'jobtype': 'NEWTON',
'forcefield': ['water.itp']})
self.logger.debug(str(self.options) + '\n')
os.chdir(self.options['root'])
self.logger.debug("Creating forcefield using above options... ")
self.ff = forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.logger.debug("ok\n")
def test_parse_inputs_returns_tuple(self):
"""Check parse_inputs() returns type"""
output = forcebalance.parser.parse_inputs('test/files/very_simple.in')
self.assertEqual(type(output), tuple,
msg = "\nExpected parse_inputs() to return a tuple, but got a %s instead" % type(output).__name__)
self.assertEqual(type(output[0]), dict,
msg = "\nExpected parse_inputs()[0] to be an options dictionary, got a %s instead" % type(output).__name__)
self.assertEqual(type(output[1]), list,
msg = "\nExpected parse_inputs()[1] to be a target list, got a %s instead" % type(output[1]).__name__)
self.assertEqual(type(output[1][0]), dict,
msg = "\nExpected parse_inputs()[1][0] to be a target dictionary, got a %s instead" % type(output[1]).__name__)
def open(self):
filters = [('Forcebalance input files', '*.in'),('Show all', '*')]
inputfile = tkfile.askopenfilename(title="Open ForceBalance input file...", filetypes=filters)
if inputfile=='': return
cwd=os.getcwd()
os.chdir(os.path.dirname(inputfile))
opts, tgt_opts = forcebalance.parser.parse_inputs(inputfile)
self.objectsPane.add(OptionObject(opts, os.path.split(inputfile)[1]))
for target in tgt_opts:
self.objectsPane.add(TargetObject(target))
self.objectsPane.add(ForcefieldObject(opts))
self.objectsPane.update()
os.chdir(cwd)
def __init__(self, filename=None):
super(CalculationObject,self).__init__(type='calculation')
self.properties['options']=[]
self.properties['targets']=[]
self.properties['forcefield']=None
self.properties['result']=None
self.properties['_expand']=True
self.properties['_expand_targets']=True
cwd=os.getcwd()
os.chdir(os.path.dirname(filename))
self.opts, self.tgt_opts = forcebalance.parser.parse_inputs(filename)
self.properties['options'] = OptionObject(self.opts, os.path.basename(filename))
self.properties['name'] = self.properties['options']['name']
for target in self.tgt_opts:
self.properties['targets'].append(TargetObject(target))
if filename:
self.properties['forcefield'] = ForcefieldObject(self.opts)
os.chdir(cwd)
def display(self, verbose=0):
s=''
default_keys=[]
for key in self.opts.iterkeys():
if key not in forcebalance.parser.tgt_opts_defaults.keys() or self.opts[key] != forcebalance.parser.tgt_opts_defaults[key]:
s+= "%s : %s\n" % (key, str(self.opts[key]))
else: default_keys.append(key)
if verbose:
s+= "\n--- options remaining at default ---\n"
for default_key in default_keys:
s+= "%s : %s\n" % (default_key, str(self.opts[default_key]))
return s
def __init__(self, opts=None, name="unknown options file"):
super(OptionObject,self).__init__()
if not opts: self.opts = forcebalance.parser.gen_opts_defaults
else: self.opts = opts
self.properties['name'] = name
def isDefault(self, option):
return option in forcebalance.parser.gen_opts_defaults.keys() and self.opts[option] == forcebalance.parser.gen_opts_defaults[option]