xml Class Reference

---

Detailed Description

Writes simulation snapshots in the HOOMD XML format.

Every period time steps, a new file will be created. The state of the particles at that time step is written to the file in the HOOMD XML format.

See also:

XML File Format

Public Member Functions
def	__init__
	Initialize the hoomd_xml writer.
def	set_params
	Change xml write parameters.
def	write
	Write a file at the current time step.
def	disable
	Disables the analyzer.
def	enable
	Enables the analyzer.
def	set_period
	Changes the period between analyzer executions.

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Member Function Documentation

def __init__	(		self,
			filename = "dump",
			period = None
	)

Initialize the hoomd_xml writer.

Parameters:

	filename	(optional) Base of the file name
	period	(optional) Number of time steps between file dumps

Examples:

 dump.xml(filename="atoms.dump", period=1000)
 xml = dump.xml(filename="particles", period=1e5)
 xml = dump.xml()

If period is set, a new file will be created every period steps. The time step at which the file is created is added to the file name in a fixed width format to allow files to easily be read in order. I.e. the write at time step 0 with filename="particles" produces the file particles.0000000000.xml

By default, only particle positions are output to the dump files. This can be changed with set_params().

If period is not specified, then no periodic updates will occur. Instead, the write() command must be executed to write an output file.

period can be a function: see Variable period specification for details

def disable

(

self

)

[inherited]

Disables the analyzer.

Examples:

 analyzer.disable()

Executing the disable command will remove the analyzer from the system. Any run() command executed after disabling an analyzer will not use that analyzer during the simulation. A disabled analyzer can be re-enabled with enable()

To use this command, you must have saved the analyzer in a variable, as shown in this example:

 analyzer = analyzer.some_analyzer()
 # ... later in the script
 analyzer.disable()

def enable

(

self

)

[inherited]

Enables the analyzer.

Examples:

 analyzer.enable()

See disable() for a detailed description.

def set_params	(		self,
			all = None,
			position = None,
			image = None,
			velocity = None,
			mass = None,
			diameter = None,
			type = None,
			wall = None,
			bond = None
	)

Change xml write parameters.

Parameters:

	all	(if true) Enables the output of all optional parameters below
	position	(if set) Set to True/False to enable/disable the output of particle positions in the xml file
	image	(if set) Set to True/False to enable/disable the output of particle images in the xml file
	velocity	(if set) Set to True/False to enable/disable the output of particle velocities in the xml file
	mass	(if set) Set to True/False to enable/disable the output of particle masses in the xml file
	diameter	(if set) Set to True/False to enable/disable the output of particle diameters in the xml file
	type	(if set) Set to True/False to enable/disable the output of particle types in the xml file
	wall	(if set) Set to True/False to enable/disable the output of walls in the xml file
	bond	(if set) Set to True/False to enable/disable the output of bonds in the xml file

Using set_params() requires that the dump was saved in a variable when it was specified.

 xml = dump.xml(filename="particles", period=1e5)

Examples:

 xml.set_params(type=False)
 xml.set_params(position=False, type=False, velocity=True)
 xml.set_params(type=True, position=True)
 xml.set_params(position=True, wall=True)
 xml.set_params(bond=True)
 xml.set_params(all=True)

def set_period	(		self,
			period
	)			[inherited]

Changes the period between analyzer executions.

Parameters:

period

New period to set

Examples:

 analyzer.set_period(100)
 analyzer.set_period(1)

While the simulation is running, the action of each analyzer is executed every period time steps.

To use this command, you must have saved the analyzer in a variable, as shown in this example:

 analyzer = analyze.some_analyzer()
 # ... later in the script
 analyzer.set_period(10)

def write	(		self,
			filename
	)

Write a file at the current time step.

Parameters:

filename

File name to write to

The periodic file writes can be temporarily overridden and a file with any file name written at the current time step.

Executing write() requires that the dump was saved in a variable when it was specified.

 xml = dump.xml()

Examples:

 xml.write(filename="start.xml")