Merge pull request #15 from rbberger/pylammps-improvements (1c3302d1) · Commits · 郑智淋 / lammps

python/lammps.py

+45 −0

Original line number	Diff line number	Diff line
		@@ -309,6 +309,9 @@ class OutputCapture(object):

		def __exit__(self, type, value, tracebac):
		os.dup2(self.stdout, self.stdout_fd)
		os.close(self.stdout)
		os.close(self.stdout_pipe_read)
		os.close(self.stdout_pipe_write)

		# check if we have more to read from the pipe
		def more_data(self, pipe):
		@@ -350,8 +353,11 @@ class AtomList(object):
		def __init__(self, lammps_wrapper_instance):
		self.lmp = lammps_wrapper_instance
		self.natoms = self.lmp.system.natoms
		self.dimensions = self.lmp.system.dimensions

		def __getitem__(self, index):
		if self.dimensions == 2:
		return Atom2D(self.lmp, index + 1)
		return Atom(self.lmp, index + 1)


		@@ -382,6 +388,12 @@ class Atom(object):
		self.lmp.eval("y[%d]" % self.index),
		self.lmp.eval("z[%d]" % self.index))

		@position.setter
		def position(self, value):
		self.lmp.set("atom", self.index, "x", value[0])
		self.lmp.set("atom", self.index, "y", value[1])
		self.lmp.set("atom", self.index, "z", value[2])

		@property
		def velocity(self):
		return (self.lmp.eval("vx[%d]" % self.index),
		@@ -399,6 +411,31 @@ class Atom(object):
		return self.lmp.eval("q[%d]" % self.index)


		class Atom2D(Atom):
		def __init__(self, lammps_wrapper_instance, index):
		super(Atom2D, self).__init__(lammps_wrapper_instance, index)

		@property
		def position(self):
		return (self.lmp.eval("x[%d]" % self.index),
		self.lmp.eval("y[%d]" % self.index))

		@position.setter
		def position(self, value):
		self.lmp.set("atom", self.index, "x", value[0])
		self.lmp.set("atom", self.index, "y", value[1])

		@property
		def velocity(self):
		return (self.lmp.eval("vx[%d]" % self.index),
		self.lmp.eval("vy[%d]" % self.index))

		@property
		def force(self):
		return (self.lmp.eval("fx[%d]" % self.index),
		self.lmp.eval("fy[%d]" % self.index))


		class PyLammps(object):
		"""
		More Python-like wrapper for LAMMPS (e.g., for iPython)
		@@ -608,6 +645,10 @@ class PyLammps(object):
		with OutputCapture() as capture:
		self.lmp.command(' '.join(cmd_args))
		output = capture.output

		if 'verbose' in kwargs and kwargs['verbose']:
		print(output)

		lines = output.splitlines()

		if len(lines) > 1:
		@@ -662,3 +703,7 @@ class IPyLammps(PyLammps):
		self.write_dump(*cmd_args)
		from IPython.core.display import Image
		return Image('snapshot.png')

		def video(self, filename):
		from IPython.display import HTML
		return HTML("<video controls><source src=\"" + filename + "\"></video>")

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