Thermostat - Revision history

Doye at 11:14, 12 June 2019

2019-06-12T11:14:19Z

← Older revision		Revision as of 11:14, 12 June 2019
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	A completely Brownian dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.		A completely Brownian dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.

	Increasing the value of <tt>pt</tt> makes the dynamics more damped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be ~~speeded~~ up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.		Increasing the value of <tt>pt</tt> makes the dynamics more damped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be sped up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.

Doye at 11:13, 12 June 2019

2019-06-12T11:13:35Z

← Older revision		Revision as of 11:13, 12 June 2019
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	A completely Brownian dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.		A completely Brownian dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.

	Increasing the value of <tt>pt</tt> makes the dynamics more ~~dumped~~, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be speeded up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.		Increasing the value of <tt>pt</tt> makes the dynamics more damped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be speeded up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.

Romano at 16:06, 19 March 2013

2013-03-19T16:06:36Z

← Older revision		Revision as of 16:06, 19 March 2013
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	* '''diff_coeff''' the overall monomer diffusion coefficient resulting from the thermostat. The code internally sets <tt>pt</tt> to get this value. Specifying <tt>pt</tt> will override this, regardless which comes first in the input file.		* '''diff_coeff''' the overall monomer diffusion coefficient resulting from the thermostat. The code internally sets <tt>pt</tt> to get this value. Specifying <tt>pt</tt> will override this, regardless which comes first in the input file.

	The algorithm works as follows: the system is evolved for a number of steps equal to <tt>newtonian_steps</tt> according to Newton's equations of motion. ~~Than~~ for each particle a random number is extracted; if it is larger than the value for <tt>pt</tt> (either set explicitly or derived		The algorithm works as follows: the system is evolved for a number of steps equal to <tt>newtonian_steps</tt> according to Newton's equations of motion. Then for each particle a random number is extracted; if it is larger than the value for <tt>pt</tt> (either set explicitly or derived
	from <tt>diff_coeff</tt>) the particle is left untouched. If the random number extracted is lower than the value of <tt>pt</tt>, each of the components of the the velocity and angular momentum of the particle are refreshed according to		from <tt>diff_coeff</tt>) the particle is left untouched. If the random number extracted is lower than the value of <tt>pt</tt>, each of the components of the the velocity and angular momentum of the particle are refreshed according to
	the Maxwell distribution dictated by the value of the temperature.		the Maxwell distribution dictated by the value of the temperature.

Romano at 11:35, 18 September 2012

2012-09-18T11:35:56Z

← Older revision		Revision as of 11:35, 18 September 2012
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	Then the velocity and momentum of each particle are refreshed, with a given		Then the velocity and momentum of each particle are refreshed, with a given
	fixed probability. The new velocities and momenta are chosen according to		fixed probability. The new velocities and momenta are chosen according to
	the Maxwell distribution of the temperature at which the simulation is ~~ran~~.		the Maxwell distribution of the temperature at which the simulation is run.
	This approximates a Brownian dynamics on time scales much longer than the		This approximates a Brownian dynamics on time scales much longer than the
	refresh interval.		refresh interval.

Romano at 11:31, 18 September 2012

2012-09-18T11:31:28Z

← Older revision		Revision as of 11:31, 18 September 2012
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	the Maxwell distribution dictated by the value of the temperature.		the Maxwell distribution dictated by the value of the temperature.

	A completely ~~Browninan~~ dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.		A completely Brownian dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.

	Increasing the value of <tt>pt</tt> makes the dynamics more dumped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be speeded up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.		Increasing the value of <tt>pt</tt> makes the dynamics more dumped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be speeded up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.

Rovigatti at 09:43, 20 April 2012

2012-04-20T09:43:45Z

← Older revision		Revision as of 09:43, 20 April 2012
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	The thermostat implemented in the simulation code is a simple thermostat		The best thermostat implemented in the simulation code (''john'' thermostat) is a simple thermostat
	that emulates Brownian dynamics. The system is evolved integrating Newton's		that emulates Brownian dynamics. The system is evolved integrating Newton's
	equations of motion ('NVE' ensemble) for a given (small) number of steps.		equations of motion ('NVE' ensemble) for a given (small) number of steps.

Rovigatti at 09:38, 20 April 2012

2012-04-20T09:38:42Z

← Older revision		Revision as of 09:38, 20 April 2012
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	he thermostat implemented in the simulation code is a simple thermostat		The thermostat implemented in the simulation code is a simple thermostat
	that emulates Brownian dynamics. The system is evolved integrating Newton's		that emulates Brownian dynamics. The system is evolved integrating Newton's
	equations of motion ('NVE' ensemble) for a given (small) number of steps.		equations of motion ('NVE' ensemble) for a given (small) number of steps.

Romano: New page: he thermostat implemented in the simulation code is a simple thermostat that emulates Brownian dynamics. The system is evolved integrating Newton's equations of motion ('NVE' ensemble) for...

2012-04-18T01:50:56Z

New page: he thermostat implemented in the simulation code is a simple thermostat that emulates Brownian dynamics. The system is evolved integrating Newton's equations of motion ('NVE' ensemble) for...

New page

he thermostat implemented in the simulation code is a simple thermostat
that emulates Brownian dynamics. The system is evolved integrating Newton's
equations of motion ('NVE' ensemble) for a given (small) number of steps.
Then the velocity and momentum of each particle are refreshed, with a given
fixed probability. The new velocities and momenta are chosen according to
the Maxwell distribution of the temperature at which the simulation is ran.
This approximates a Brownian dynamics on time scales much longer than the
refresh interval.

* '''dt''' time steps of the integration
* '''newtonian steps''' number of steps between refresh attempts
* '''pt''' the probability with which each particle gets its velocity and momentum refreshed at each attempt.
* '''diff_coeff''' the overall monomer diffusion coefficient resulting from the thermostat. The code internally sets <tt>pt</tt> to get this value. Specifying <tt>pt</tt> will override this, regardless which comes first in the input file.

The algorithm works as follows: the system is evolved for a number of steps equal to <tt>newtonian_steps</tt> according to Newton's equations of motion. Than for each particle a random number is extracted; if it is larger than the value for <tt>pt</tt> (either set explicitly or derived
from <tt>diff_coeff</tt>) the particle is left untouched. If the random number extracted is lower than the value of <tt>pt</tt>, each of the components of the the velocity and angular momentum of the particle are refreshed according to
the Maxwell distribution dictated by the value of the temperature.

A completely Browninan dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.

Increasing the value of <tt>pt</tt> makes the dynamics more dumped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be speeded up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.