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]))