def set_output(self, name, outputType, filename, nSteps):
"""Set an output file for coordinates from the dynamics model.
Parameters
------------
name : string
A string identifying this output type.
outputType : string
A string identifying the output file type.
filename : string
A string with the filename to write dynamics output.
nSteps : int
The number of model timesteps bewteen which to write.s
"""
# assert outputType in __knownOutput__, "The output type specified was not recognized."
__knownOutputTypes__ = ['dcd', 'xyz', 'custom', 'xyz/mpiio', "atom"]
assert outputType in __knownOutputTypes__, "outputType that was provided was not understood."
for out in self.output:
assert out.name != name, "Output class names must be unique."
# now append the collective variable to the walker list.
self.output.append(outputClass.outputClass(name, outputType, filename, nSteps))
dump = self.output[-1]
if dump.type == "custom":
self.command("dump " + dump.name + " all " + " ".join([dump.type, str(dump.nSteps), dump.destination, "x y z"]))
else:
self.command("dump " + dump.name + " all " + " ".join([dump.type, str(dump.nSteps), dump.destination]))
def setOutput(self, name, outputType, filename, nSteps):
"""
This routine sets up a mechanism for writing system information to file directly from the dynamics engine. This is equivalent to output constructed
"""
# assert outputType in __knownOutput__, "The output type specified was not recognized."
__knownOutputTypes__ = ['text', 'h5py', 'binary']
assert outputType in __knownOutputTypes__, "outputType that was provided was not understood."
for out in self.output:
assert out.name != name, "Output class names must be unique."
# now append the collective variable to the walker list.
self.output.append(outputClass.outputClass(name, outputType, filename, nSteps))
def set_output(self, name, outputType, filename, nSteps):
"""
This routine sets up a mechanism for writing system information to file directly from the dynamics engine. This is equivalent to output constructed
"""
# assert outputType in __knownOutput__, "The output type specified was not recognized."
__knownOutputTypes__ = ['dcd', 'xyz', 'custom', 'xyz/mpiio', "atom"]
assert outputType in __knownOutputTypes__, "outputType that was provided was not understood."
for out in self.output:
assert out.name != name, "Output class names must be unique."
# now append the collective variable to the walker list.
self.output.append(outputClass.outputClass(name, outputType, filename, nSteps))
dump = self.output[-1]
if dump.type == "custom":
self.command("dump " + dump.name + " all " + " ".join([dump.type, str(dump.nSteps), dump.destination, "x y z"]))
else:
self.command("dump " + dump.name + " all " + " ".join([dump.type, str(dump.nSteps), dump.destination]))
