Hoomd - Revision history

Admin: /* Step 1 - Particle Position Updates */

2017-12-05T03:37:33Z

Step 1 - Particle Position Updates

← Older revision		Revision as of 03:37, 5 December 2017
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	===Step 1 - Particle Position Updates===		===Step 1 - Particle Position Updates===

			TwoStepBD step one: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepBD.cc#L62

			TwoStepLangevin step one: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevin.cc#L86

	===Step 2 - Particle Accel Updates===		===Step 2 - Particle Accel Updates===

Admin: /* Two Integration Steps */

2017-12-05T03:31:30Z

Two Integration Steps

← Older revision		Revision as of 03:31, 5 December 2017
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	* Step 1 (Langevin and BD) - update the particle positions dx/dt		* Step 1 (Langevin and BD) - update the particle positions dx/dt
	* Step 2 (Langevin only) - update the particle accelerations dv/dt		* Step 2 (Langevin only) - update the particle accelerations dv/dt

			===Step 1 - Particle Position Updates===

			===Step 2 - Particle Accel Updates===

	=References=		=References=

Admin: /* Two Step Integrator */

2017-12-05T03:30:50Z

Two Step Integrator

← Older revision		Revision as of 03:30, 5 December 2017
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	The setDeltaT() method is actually called by the Python script creating the C++ objects.		The setDeltaT() method is actually called by the Python script creating the C++ objects.

			===Two Integration Steps===

			The two integration steps are:
			* Step 1 (Langevin and BD) - update the particle positions dx/dt
			* Step 2 (Langevin only) - update the particle accelerations dv/dt

	=References=		=References=

Admin: /* Integration Method parent class */

2017-12-05T03:28:27Z

Integration Method parent class

← Older revision		Revision as of 03:28, 5 December 2017
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	From this class, we see that the time step is initialized at 0 [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc#L30 here], then changed with the setDeltaT() method [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc#L56 here]		From this class, we see that the time step is initialized at 0 [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc#L30 here], then changed with the setDeltaT() method [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc#L56 here]

			The setDeltaT() method is actually called by the Python script creating the C++ objects.

	=References=		=References=

Admin: /* Two Step Integrator */

2017-12-05T03:21:57Z

Two Step Integrator

← Older revision		Revision as of 03:21, 5 December 2017
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	hoomd md directory: https://github.com/charlesreid1/hoomd-blue/tree/master/hoomd/md		hoomd md directory: https://github.com/charlesreid1/hoomd-blue/tree/master/hoomd/md

			===Inheritance===

	TwoStepLangevin inherits from TwoStepLangevinBase (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevin.h TwoStepLangevin.h])		TwoStepLangevin inherits from TwoStepLangevinBase (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevin.h TwoStepLangevin.h])

	TwoStepLangevinBase inherits from IntegrationMethodTwoStep (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevinBase.h TwoStepLangevinBase.h])		TwoStepLangevinBase inherits from IntegrationMethodTwoStep (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevinBase.h TwoStepLangevinBase.h])

			===Integration Method parent class===

	IntegrationMethodTwoStep.h: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.h		IntegrationMethodTwoStep.h: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.h

	IntegrationMethodTwoStep.cc: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc		IntegrationMethodTwoStep.cc: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc

			From this class, we see that the time step is initialized at 0 [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc#L30 here], then changed with the setDeltaT() method [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc#L56 here]

	=References=		=References=

Admin: /* Tabs Open */

2017-12-05T03:19:28Z

Tabs Open

← Older revision		Revision as of 03:19, 5 December 2017
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	=References=		=References=

	==Tabs ~~Open~~==		==Tabs==

	* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/?at=maint		* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/?at=maint

Admin: /* Two Step Integrator */

2017-12-05T03:19:15Z

Two Step Integrator

← Older revision		Revision as of 03:19, 5 December 2017
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	TwoStepLangevin inherits from TwoStepLangevinBase (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevin.h TwoStepLangevin.h])		TwoStepLangevin inherits from TwoStepLangevinBase (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevin.h TwoStepLangevin.h])

	TwoStepLangevinBase inherits from IntegrationMethodTwoStep (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevinBase.h TwoStepLangevinBase.h]		TwoStepLangevinBase inherits from IntegrationMethodTwoStep (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevinBase.h TwoStepLangevinBase.h])

	IntegrationMethodTwoStep.h: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.h		IntegrationMethodTwoStep.h: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.h

Admin: /* Brownian Equation */

2017-12-05T03:19:02Z

Brownian Equation

← Older revision		Revision as of 03:19, 5 December 2017
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	** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.cc?at=maint&fileviewer=file-view-default		** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.cc?at=maint&fileviewer=file-view-default

			==Two Step Integrator==

			hoomd md directory: https://github.com/charlesreid1/hoomd-blue/tree/master/hoomd/md

			TwoStepLangevin inherits from TwoStepLangevinBase (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevin.h TwoStepLangevin.h])

			TwoStepLangevinBase inherits from IntegrationMethodTwoStep (via [https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/TwoStepLangevinBase.h TwoStepLangevinBase.h]

			IntegrationMethodTwoStep.h: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.h

			IntegrationMethodTwoStep.cc: https://github.com/charlesreid1/hoomd-blue/blob/master/hoomd/md/IntegrationMethodTwoStep.cc

	=References=		=References=

Admin: /* Brownian Equation */

2017-12-03T23:50:13Z

Brownian Equation

← Older revision		Revision as of 23:50, 3 December 2017
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	** Header file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.h?at=maint&fileviewer=file-view-default		** Header file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.h?at=maint&fileviewer=file-view-default
	** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.cc?at=maint&fileviewer=file-view-default		** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.cc?at=maint&fileviewer=file-view-default



			=References=

			==Tabs Open==

			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/?at=maint
			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/integrate.py?at=maint&fileviewer=file-view-default#integrate.py-1075

			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepLangevin.h?at=maint&fileviewer=file-view-default
			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepLangevin.cc?at=maint&fileviewer=file-view-default
			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48/hoomd/md/?at=maint
			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.cc?at=maint&fileviewer=file-view-default
			* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.h?at=maint&fileviewer=file-view-default
			* https://hoomd-blue.readthedocs.io/en/stable/module-md-integrate.html#hoomd.md.integrate.brownian
			* https://hoomd-blue.readthedocs.io/en/stable/module-hoomd-group.html#module-hoomd.group

Admin: /* Molecular Dynamics (md) Module */

2017-12-02T04:48:29Z

Molecular Dynamics (md) Module

← Older revision		Revision as of 04:48, 2 December 2017
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	Code for solving the Langevin equation is in integrate.py, in a class called langevin.		Code for solving the Langevin equation is in integrate.py, in a class called langevin.

			Link to hoomd documentation on Langevin equation:
			* https://hoomd-blue.readthedocs.io/en/stable/module-md-integrate.html#hoomd.md.integrate.langevin

	Link to hoomd source code:		Link to hoomd source code:
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	** Header file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepLangevin.h?at=maint&fileviewer=file-view-default		** Header file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepLangevin.h?at=maint&fileviewer=file-view-default
	** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepLangevin.cc?at=maint&fileviewer=file-view-default		** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepLangevin.cc?at=maint&fileviewer=file-view-default

	~~Link to hoomd documentation on Langevin equation:~~
	* https://hoomd-blue.readthedocs.io/en/stable/module-md-integrate.html#hoomd.md.integrate.langevin

	===Brownian Equation===		===Brownian Equation===

	Code for solving the Brownian dynamics equation of motion is in integrate.py, in a class called brownian.		Code for solving the Brownian dynamics equation of motion is in integrate.py, in a class called brownian.

	~~Link to hoomd source code, brownian class:~~
	* https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/integrate.py?at=maint&fileviewer=file-view-default#integrate.py-975

	Link to hoomd documentation on brownian equation:		Link to hoomd documentation on brownian equation:
	* https://hoomd-blue.readthedocs.io/en/stable/module-md-integrate.html#hoomd.md.integrate.brownian		* https://hoomd-blue.readthedocs.io/en/stable/module-md-integrate.html#hoomd.md.integrate.brownian

			Link to hoomd source code, brownian class:
			* Brownian class in Python: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/integrate.py?at=maint&fileviewer=file-view-default#integrate.py-975
			* TwoStepBD class in C++:
			** Header file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.h?at=maint&fileviewer=file-view-default
			** Source file: https://bitbucket.org/glotzer/hoomd-blue/src/5007cf262c48aa72210bf93266aa175898ebb254/hoomd/md/TwoStepBD.cc?at=maint&fileviewer=file-view-default