def test_liquid(self):
"""Check liquid target with existing simulation data"""
# if not sys.version_info <= (2,7):
# self.skipTest("Existing pickle file only works with Python 3")
print("Setting input file to 'single.in'")
input_file = 'single.in'
## The general options and target options that come from parsing the input file
print("Parsing inputs...")
options, tgt_opts = parse_inputs(input_file)
print("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
forcefield = FF(options)
objective = Objective(options, tgt_opts, forcefield)
## The optimizer component of the project
print("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
assert isinstance(optimizer,
Optimizer), "Expected forcebalance optimizer object"
print(str(optimizer))
## Actually run the optimizer.
print("Done setting up! Running optimizer...")
result = optimizer.Run()
print("\nOptimizer finished. Final results:")
print(str(result))
liquid_obj_value = optimizer.Objective.ObjDict['Liquid']['x']
assert liquid_obj_value < 20, "Liquid objective function should give < 20 (about 17.23) total value."
def Run_ForceBalance(input_file, debug=False, continue_=False):
""" Create instances of ForceBalance components and run the optimizer.
The triumvirate, trifecta, or trinity of components are:
- The force field
- The objective function
- The optimizer
Cipher: "All I gotta do here is pull this plug... and there you have to watch Apoc die"
Apoc: "TRINITY" *chunk*
The force field is a class defined in forcefield.py.
The objective function is a combination of target classes and a penalty function class.
The optimizer is a class defined in this file.
"""
try:
## The general options and target options that come from parsing the input file
options, tgt_opts = parse_inputs(input_file)
## Set the continue_ option.
if continue_: options['continue'] = True
## The force field component of the project
forcefield = FF(options)
## The objective function
objective = Objective(options, tgt_opts, forcefield)
## The optimizer component of the project
optimizer = Optimizer(options, objective, forcefield)
## Actually run the optimizer.
optimizer.Run()
except:
import traceback
traceback.print_exc()
if debug:
import pdb
pdb.post_mortem()
def get_optimizer(self):
""" Return the optimizer object """
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(self.input_file)
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
assert isinstance(options,
dict), "Parser gave incorrect type for options"
assert isinstance(tgt_opts,
list), "Parser gave incorrect type for tgt_opts"
for target in tgt_opts:
assert isinstance(
target, dict), "Parser gave incorrect type for target dict"
## The force field component of the project
forcefield = FF(options)
assert isinstance(forcefield,
FF), "Expected forcebalance forcefield object"
## The objective function
objective = Objective(options, tgt_opts, forcefield)
assert isinstance(objective,
Objective), "Expected forcebalance objective object"
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
assert isinstance(optimizer,
Optimizer), "Expected forcebalance optimizer object"
self.logger.debug(str(optimizer) + "\n")
return optimizer
def runTest(self):
"""Check continuation from a previous run"""
self.logger.debug("\nSetting input file to 'test_continue.in'\n")
input_file = 'test_continue.in'
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(input_file)
options['continue'] = True
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
self.assertEqual(dict,
type(options),
msg="\nParser gave incorrect type for options")
self.assertEqual(list,
type(tgt_opts),
msg="\nParser gave incorrect type for tgt_opts")
for target in tgt_opts:
self.assertEqual(
dict,
type(target),
msg="\nParser gave incorrect type for target dict")
## The force field component of the project
forcefield = FF(options)
self.assertEqual(FF,
type(forcefield),
msg="\nExpected forcebalance forcefield object")
## The objective function
objective = Objective(options, tgt_opts, forcefield)
self.assertEqual(Objective,
type(objective),
msg="\nExpected forcebalance objective object")
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
self.assertEqual(Optimizer,
type(optimizer),
msg="\nExpected forcebalance optimizer object")
self.logger.debug(str(optimizer) + "\n")
## Actually run the optimizer.
self.logger.debug("Done setting up! Running optimizer...\n")
result = optimizer.Run()
self.logger.debug("\nOptimizer finished. Final results:\n")
self.logger.debug(str(result) + '\n')
self.assertEqual(optimizer.iterinit,
2,
msg="\nInitial iteration counter is incorrect")
self.assertEqual(optimizer.iteration,
2,
msg="\nFinal iteration counter is incorrect")
def runTest(self):
"""Check voelz study runs without errors"""
self.logger.debug("\nSetting input file to 'options.in'\n")
input_file = 'options.in'
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(input_file)
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
self.assertEqual(dict,
type(options),
msg="\nParser gave incorrect type for options")
self.assertEqual(list,
type(tgt_opts),
msg="\nParser gave incorrect type for tgt_opts")
for target in tgt_opts:
self.assertEqual(
dict,
type(target),
msg="\nParser gave incorrect type for target dict")
## The force field component of the project
self.logger.debug("Creating forcefield using loaded options: ")
forcefield = FF(options)
self.logger.debug(str(forcefield) + "\n")
self.assertEqual(FF,
type(forcefield),
msg="\nExpected forcebalance forcefield object")
## The objective function
self.logger.debug(
"Creating object using loaded options and forcefield: ")
objective = Objective(options, tgt_opts, forcefield)
self.logger.debug(str(objective) + "\n")
self.assertEqual(Objective,
type(objective),
msg="\nExpected forcebalance objective object")
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
self.logger.debug(str(optimizer) + "\n")
self.assertEqual(Optimizer,
type(optimizer),
msg="\nExpected forcebalance optimizer object")
## Actually run the optimizer.
self.logger.debug("Done setting up! Running optimizer...\n")
result = optimizer.Run()
self.logger.debug("\nOptimizer finished. Final results:\n")
self.logger.debug(str(result) + '\n')
def test_continue(self):
"""Check continuation from a previous run"""
if sys.version_info < (3, 0):
pytest.skip("Existing pickle file only works with Python 3")
self.logger.debug("\nSetting input file to 'test_continue.in'\n")
input_file = 'test_continue.in'
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(input_file)
options['continue'] = True
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
assert isinstance(options,
dict), "Parser gave incorrect type for options"
assert isinstance(tgt_opts,
list), "Parser gave incorrect type for tgt_opts"
for target in tgt_opts:
assert isinstance(
target, dict), "Parser gave incorrect type for target dict"
## The force field component of the project
forcefield = FF(options)
assert isinstance(forcefield,
FF), "Expected forcebalance forcefield object"
## The objective function
objective = Objective(options, tgt_opts, forcefield)
assert isinstance(objective,
Objective), "Expected forcebalance objective object"
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
assert isinstance(optimizer,
Optimizer), "Expected forcebalance optimizer object"
self.logger.debug(str(optimizer) + '\n')
## Actually run the optimizer.
self.logger.debug("Done setting up! Running optimizer...\n")
result = optimizer.Run()
self.logger.debug("\nOptimizer finished. Final results:\n")
self.logger.debug(str(result) + '\n')
assert optimizer.iterinit == 2, "Initial iteration counter is incorrect"
assert optimizer.iteration == 2, "Final iteration counter is incorrect"
def runTest(self):
"""Check liquid target with existing simulation data"""
if not sys.version_info <= (2, 7):
self.skipTest("Existing pickle file only works with Python 3")
self.logger.debug("\nSetting input file to 'single.in'\n")
input_file = 'single.in'
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(input_file)
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
forcefield = FF(options)
objective = Objective(options, tgt_opts, forcefield)
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
self.assertEqual(Optimizer,
type(optimizer),
msg="\nExpected forcebalance optimizer object")
self.logger.debug(str(optimizer) + "\n")
## Actually run the optimizer.
self.logger.debug("Done setting up! Running optimizer...\n")
result = optimizer.Run()
self.logger.debug("\nOptimizer finished. Final results:\n")
self.logger.debug(str(result) + '\n')
liquid_obj_value = optimizer.Objective.ObjDict['Liquid']['x']
self.assertTrue(
liquid_obj_value < 20,
msg=
"\nLiquid objective function should give < 20 (about 17.23) total value."
)
def runTest(self):
"""Check water tutorial study runs without errors"""
self.logger.debug("\nSetting input file to 'very_simple.in'\n")
input_file = 'very_simple.in'
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(input_file)
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
self.assertEqual(dict,
type(options),
msg="\nParser gave incorrect type for options")
self.assertEqual(list,
type(tgt_opts),
msg="\nParser gave incorrect type for tgt_opts")
for target in tgt_opts:
self.assertEqual(
dict,
type(target),
msg="\nParser gave incorrect type for target dict")
## The force field component of the project
forcefield = FF(options)
self.assertEqual(FF,
type(forcefield),
msg="\nExpected forcebalance forcefield object")
## The objective function
objective = Objective(options, tgt_opts, forcefield)
self.assertEqual(Objective,
type(objective),
msg="\nExpected forcebalance objective object")
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
self.assertEqual(Optimizer,
type(optimizer),
msg="\nExpected forcebalance optimizer object")
self.logger.debug(str(optimizer) + "\n")
## Actually run the optimizer.
self.logger.debug("Done setting up! Running optimizer...\n")
result = optimizer.Run()
self.logger.debug("\nOptimizer finished. Final results:\n")
self.logger.debug(str(result) + '\n')
self.assertNdArrayEqual(
EXPECTED_WATER_RESULTS,
result,
delta=0.001,
msg=
"\nCalculation results have changed from previously calculated values.\n"
"If this seems reasonable, update EXPECTED_WATER_RESULTS in test_system.py with these values"
)
# Fail if calculation takes longer than previously to converge
self.assertGreaterEqual(ITERATIONS_TO_CONVERGE, Counter(), msg="\nCalculation took longer than expected to converge (%d iterations vs previous of %d)" %\
(ITERATIONS_TO_CONVERGE, Counter()))
def runTest(self):
"""Check implicit hydration free energy study (Hydration target) converges to expected results"""
self.logger.debug("\nSetting input file to 'optimize.in'\n")
input_file = 'optimize.in'
## The general options and target options that come from parsing the input file
self.logger.debug("Parsing inputs...\n")
options, tgt_opts = parse_inputs(input_file)
self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" %
(str(options), str(tgt_opts)))
self.assertEqual(dict,
type(options),
msg="\nParser gave incorrect type for options")
self.assertEqual(list,
type(tgt_opts),
msg="\nParser gave incorrect type for tgt_opts")
for target in tgt_opts:
self.assertEqual(
dict,
type(target),
msg="\nParser gave incorrect type for target dict")
## The force field component of the project
self.logger.debug("Creating forcefield using loaded options: ")
forcefield = FF(options)
self.logger.debug(str(forcefield) + "\n")
self.assertEqual(FF,
type(forcefield),
msg="\nExpected forcebalance forcefield object")
## The objective function
self.logger.debug(
"Creating object using loaded options and forcefield: ")
objective = Objective(options, tgt_opts, forcefield)
self.logger.debug(str(objective) + "\n")
self.assertEqual(Objective,
type(objective),
msg="\nExpected forcebalance objective object")
## The optimizer component of the project
self.logger.debug("Creating optimizer: ")
optimizer = Optimizer(options, objective, forcefield)
self.logger.debug(str(optimizer) + "\n")
self.assertEqual(Optimizer,
type(optimizer),
msg="\nExpected forcebalance optimizer object")
## Actually run the optimizer.
self.logger.debug("Done setting up! Running optimizer...\n")
result = optimizer.Run()
self.logger.debug("\nOptimizer finished. Final results:\n")
self.logger.debug(str(result) + '\n')
self.assertNdArrayEqual(
EXPECTED_ETHANOL_RESULTS,
forcefield.create_pvals(result),
delta=0.02,
msg=
"\nCalculation results have changed from previously calculated values.\n"
"If this seems reasonable, update EXPECTED_ETHANOL_RESULTS in test_system.py with these values"
)