Output File Formats in MD++ - Revision history

Caiwei: /* Use writevelocity */

2009-08-17T18:50:32Z

Use writevelocity

← Older revision		Revision as of 18:50, 17 August 2009
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	input = 0.5 scalevelocity		input = 0.5 scalevelocity

			after reading the .cn file.

	===Use writeall===		===Use writeall===

Caiwei: /* Basic atomic information */

2009-08-17T18:47:33Z

Basic atomic information

← Older revision		Revision as of 18:47, 17 August 2009
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	<math>\mathbf{r}_i = \mathbf{H} \cdot \mathbf{s}_i </math>		<math>\mathbf{r}_i = \mathbf{H} \cdot \mathbf{s}_i </math>

	where <math>\mathbf{H}</math> is the matrix described in the previous sub-section. The unit of both <math>\mathbf{r}_i</math> and <math>\mathbf{H}</math> is Angstrom. Hence the scaled coordinates are dimensionless (unit = 1).		where <math>\mathbf{H}</math> is the matrix described in the previous sub-section. The unit of both <math>\mathbf{r}_i</math> and <math>\mathbf{H}</math> is Angstrom. Hence the scaled coordinates are dimensionless (unit 1).

	The default setting is sufficient for quasi-static (energy minimization) simulations involving a single species without any fixed atoms.		The default setting is sufficient for quasi-static (energy minimization) simulations involving a single species without any fixed atoms.

Caiwei: /* Use writevelocity */

2009-08-17T18:46:56Z

Use writevelocity

← Older revision		Revision as of 18:46, 17 August 2009
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	The last three numbers contain the information of the scaled velocities of atom <math>i</math>. The scaled velocities are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.		The last three numbers contain the information of the scaled velocities of atom <math>i</math>. The scaled velocities are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.

	'''Important''': In MD++, the internal variable <math>\hat{v}^s_{x_i}</math> is not the scaled velocity itself. Instead, <math>\hat{v}^s_{x_i} = v^s_{x_i} \cdot \Delta t</math>, where <math>v^s_{x_i}</math> is the scaled velocity (unit 1/picosecond) and <math>\Delta t</math> is the integrator's timestep (unit picosecond). Therefore, <math>\hat{v}^s_{x_i}</math> is also dimensionless (unit 1). (In MD++, the internal variable <math>\hat{a}^s_{x_i}</math> to represent acceleration is also dimensionless. It is defined as <math>\hat{a}^s_{x_i} = a^s_{x_i} \cdot \frac{\Delta t^2}{2}</math>, where <math>a^s_{x_i}</math> is the scaled acceleration (unit 1/picosecond<math>^2</math>).) This also means that the <tt>timestep</tt> variable (unit picosecond) need to be specified correctly before reading a .cn file that contains velocities. If you want to use a different time step from that implied by the .cn file, you need to use scale the 'velocity' values by, ~~e.g.,~~		'''Important''': In MD++, the internal variable <math>\hat{v}^s_{x_i}</math> is not the scaled velocity itself. Instead, <math>\hat{v}^s_{x_i} = v^s_{x_i} \cdot \Delta t</math>, where <math>v^s_{x_i}</math> is the scaled velocity (unit 1/picosecond) and <math>\Delta t</math> is the integrator's timestep (unit picosecond). Therefore, <math>\hat{v}^s_{x_i}</math> is also dimensionless (unit 1). (In MD++, the internal variable <math>\hat{a}^s_{x_i}</math> to represent acceleration is also dimensionless. It is defined as <math>\hat{a}^s_{x_i} = a^s_{x_i} \cdot \frac{\Delta t^2}{2}</math>, where <math>a^s_{x_i}</math> is the scaled acceleration (unit 1/picosecond<math>^2</math>).) This also means that the <tt>timestep</tt> variable (unit picosecond) need to be specified correctly before reading a .cn file that contains velocities. If you want to use a different time step from that implied by the .cn file, say, half as before, you need to use scale the 'velocity' values by,

	input = 0.5 scalevelocity		input = 0.5 scalevelocity

Caiwei: /* Use writevelocity */

2009-08-17T18:46:04Z

Use writevelocity

← Older revision		Revision as of 18:46, 17 August 2009
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	<math>s_{x_i} \ s_{y_i} \ s_{z_i} \ \hat{v}^s_{x_i} \ \hat{v}^s_{y_i} \ \hat{v}^s_{z_i} </math>		<math>s_{x_i} \ s_{y_i} \ s_{z_i} \ \hat{v}^s_{x_i} \ \hat{v}^s_{y_i} \ \hat{v}^s_{z_i} </math>

	The last three numbers ~~are contains~~ the information of the scaled velocities of atom <math>i</math>. The scaled velocities are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.		The last three numbers contain the information of the scaled velocities of atom <math>i</math>. The scaled velocities are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.

	'''Important''': In MD++, the <math>\hat{v}s_{x_i}</math> ~~variable~~ is not the scaled velocity itself. Instead, <math>\hat{v}s_{x_i} = ~~vs_~~{x_i} \cdot \Delta t</math>, where <math>~~vs_~~{x_i}</math> is the scaled velocity (unit 1/picosecond) and <math>\Delta t</math> is the integrator's timestep (unit picosecond). Therefore, <math>\hat{v}s_{x_i}</math> is also dimensionless (unit 1). (In MD++, the internal variable <math>\hat{a}^s_{x_i}</math> to represent acceleration is also dimensionless. It is defined as <math>\hat{a}^s_{x_i} = a^s_{x_i} \Delta t^2</math>, where <math>a^s_{x_i}</math> is the ~~true~~ scaled acceleration (unit 1/picosecond<math>^2</math>).) This also means that the <tt>timestep</tt> variable (unit picosecond) need to be specified correctly before reading a .cn file that contains velocities. If you want to use a different time step from that implied by the .cn file, you need to use the ~~<tt>scalevelocity</tt>~~ ~~function~~.		'''Important''': In MD++, the internal variable <math>\hat{v}^s_{x_i}</math> is not the scaled velocity itself. Instead, <math>\hat{v}^s_{x_i} = v^s_{x_i} \cdot \Delta t</math>, where <math>v^s_{x_i}</math> is the scaled velocity (unit 1/picosecond) and <math>\Delta t</math> is the integrator's timestep (unit picosecond). Therefore, <math>\hat{v}^s_{x_i}</math> is also dimensionless (unit 1). (In MD++, the internal variable <math>\hat{a}^s_{x_i}</math> to represent acceleration is also dimensionless. It is defined as <math>\hat{a}^s_{x_i} = a^s_{x_i} \cdot \frac{\Delta t^2}{2}</math>, where <math>a^s_{x_i}</math> is the scaled acceleration (unit 1/picosecond<math>^2</math>).) This also means that the <tt>timestep</tt> variable (unit picosecond) need to be specified correctly before reading a .cn file that contains velocities. If you want to use a different time step from that implied by the .cn file, you need to use scale the 'velocity' values by, e.g.,

			input = 0.5 scalevelocity

	===Use writeall===		===Use writeall===

Caiwei: /* Use writevelocity */

2009-08-17T18:40:31Z

Use writevelocity

← Older revision		Revision as of 18:40, 17 August 2009
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	When <tt>writevelocity = 1</tt>, each line in the saved .cn file (from line 2 to line <math>NP + 1</math>) has the following format.		When <tt>writevelocity = 1</tt>, each line in the saved .cn file (from line 2 to line <math>NP + 1</math>) has the following format.

	<math>s_{x_i} \ s_{y_i} \ s_{z_i} \ ~~vs_~~{x_i} \ ~~vs_~~{y_i} \ ~~vs_~~{z_i} </math>		<math>s_{x_i} \ s_{y_i} \ s_{z_i} \ \hat{v}^s_{x_i} \ \hat{v}^s_{y_i} \ \hat{v}^s_{z_i} </math>

	The last three numbers are the scaled velocities of atom <math>i</math>. ~~They~~ are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.		The last three numbers are contains the information of the scaled velocities of atom <math>i</math>. The scaled velocities are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.

			'''Important''': In MD++, the <math>\hat{v}s_{x_i}</math> variable is not the scaled velocity itself. Instead, <math>\hat{v}s_{x_i} = vs_{x_i} \cdot \Delta t</math>, where <math>vs_{x_i}</math> is the scaled velocity (unit 1/picosecond) and <math>\Delta t</math> is the integrator's timestep (unit picosecond). Therefore, <math>\hat{v}s_{x_i}</math> is also dimensionless (unit 1). (In MD++, the internal variable <math>\hat{a}^s_{x_i}</math> to represent acceleration is also dimensionless. It is defined as <math>\hat{a}^s_{x_i} = a^s_{x_i} \Delta t^2</math>, where <math>a^s_{x_i}</math> is the true scaled acceleration (unit 1/picosecond<math>^2</math>).) This also means that the <tt>timestep</tt> variable (unit picosecond) need to be specified correctly before reading a .cn file that contains velocities. If you want to use a different time step from that implied by the .cn file, you need to use the <tt>scalevelocity</tt> function.

	===Use writeall===		===Use writeall===

Caiwei: /* Basic atomic information */

2009-08-17T18:23:47Z

Basic atomic information

← Older revision		Revision as of 18:23, 17 August 2009
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	<math>\mathbf{r}_i = \mathbf{H} \cdot \mathbf{s}_i </math>		<math>\mathbf{r}_i = \mathbf{H} \cdot \mathbf{s}_i </math>

	where <math>\mathbf{H}</math> is the matrix described in the previous sub-section.		where <math>\mathbf{H}</math> is the matrix described in the previous sub-section. The unit of both <math>\mathbf{r}_i</math> and <math>\mathbf{H}</math> is Angstrom. Hence the scaled coordinates are dimensionless (unit = 1).

	The default setting is sufficient for quasi-static (energy minimization) simulations involving a single species without any fixed atoms.		The default setting is sufficient for quasi-static (energy minimization) simulations involving a single species without any fixed atoms.


	===Use writevelocity===		===Use writevelocity===

Caiwei at 06:19, 17 August 2009

2009-08-17T06:19:30Z

← Older revision		Revision as of 06:19, 17 August 2009
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	* <math>{\rm image[}i{\rm ]}</math> has the default value -1. If it is not -1, it means atom <math>i</math> is not a real atom but a (periodic) image of another atom, whose index is stored in <math>{\rm image[}i{\rm ]}</math>. This means that if atom <math>{\rm image[}i{\rm ]}</math> moves in one step of the simulation, MD++ will move atom <math>i</math> by the same amount before going to the next step.		* <math>{\rm image[}i{\rm ]}</math> has the default value -1. If it is not -1, it means atom <math>i</math> is not a real atom but a (periodic) image of another atom, whose index is stored in <math>{\rm image[}i{\rm ]}</math>. This means that if atom <math>{\rm image[}i{\rm ]}</math> moves in one step of the simulation, MD++ will move atom <math>i</math> by the same amount before going to the next step.




	==Property .out File==		==Property .out File==

Caiwei at 06:19, 17 August 2009

2009-08-17T06:19:03Z

← Older revision		Revision as of 06:19, 17 August 2009
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	MD++ cannot read the output .out file. This file can be plotted using other programs such as Matlab and Gnuplot.		MD++ cannot read the output .out file. This file can be plotted using other programs such as Matlab and Gnuplot.



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	We can also configure MD++ to write .cfg files periodicaly in an MD simulation by setting <tt>savecfg = 1</tt> and, e.g., <tt>savecfgfreq = 10</tt> before calling <tt>run</tt>.		We can also configure MD++ to write .cfg files periodicaly in an MD simulation by setting <tt>savecfg = 1</tt> and, e.g., <tt>savecfgfreq = 10</tt> before calling <tt>run</tt>.




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	To really run this example, you need to prepare other VASP input files, such as INCAR, KPOINTS, POTCAR, etc. in your local directory. Of course, you can always copy the POSCAR file created by MD++ to a different folder for a future VASP run. This allows us to relax an atomic configuration using an empirical potential first before relaxing it using VASP.		To really run this example, you need to prepare other VASP input files, such as INCAR, KPOINTS, POTCAR, etc. in your local directory. Of course, you can always copy the POSCAR file created by MD++ to a different folder for a future VASP run. This allows us to relax an atomic configuration using an empirical potential first before relaxing it using VASP.



	==LAMMPS File==		==LAMMPS File==

Caiwei: /* Use writeall */

2009-08-17T06:15:48Z

Use writeall

← Older revision		Revision as of 06:15, 17 August 2009
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	* <math>{\rm topol[}i{\rm ]}</math> stores the central symetry deviation (CSD) parameter of atom <math>i</math> or other parameters computed by visualization algorithms. By default, it is not computed. To turn on the calculation of this field in energy minimzation or MD simulations, set <tt>plot_color_axis = 2</tt>. You can also ask MD++ to compute the <math>{\rm topol[}i{\rm ]}</math> value for the current configuration by calling <tt>calcentralsymmetry</tt>. (For an example, see [http://micro.stanford.edu/~caiwei/CSD-Book/ Computer Simulations of Dislocations] section 3.3.)		* <math>{\rm topol[}i{\rm ]}</math> stores the central symetry deviation (CSD) parameter of atom <math>i</math> or other parameters computed by visualization algorithms. By default, it is not computed. To turn on the calculation of this field in energy minimzation or MD simulations, set <tt>plot_color_axis = 2</tt>. You can also ask MD++ to compute the <math>{\rm topol[}i{\rm ]}</math> value for the current configuration by calling <tt>calcentralsymmetry</tt>. (For an example, see [http://micro.stanford.edu/~caiwei/CSD-Book/ Computer Simulations of Dislocations] section 3.3.)


	* <math>{\rm species[}i{\rm ]}</math> stores the element type of atom <math>i</math>. For a binary system, <math>{\rm species[}i{\rm ]}</math> is either 0 or 1. For a ternary system, <math>{\rm species[}i{\rm ]}</math> is either 0, 1 or 2. The interatomic potential function uses this field to decide which function to use, e.g. to compute the interaction between two given atoms.		* <math>{\rm species[}i{\rm ]}</math> stores the element type of atom <math>i</math>. For a binary system, <math>{\rm species[}i{\rm ]}</math> is either 0 or 1. For a ternary system, <math>{\rm species[}i{\rm ]}</math> is either 0, 1 or 2. The interatomic potential function uses this field to decide which function to use, e.g. to compute the interaction between two given atoms.

Caiwei: /* Use writeall */

2009-08-17T06:14:59Z

Use writeall

← Older revision		Revision as of 06:14, 17 August 2009
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	The last 6 numbers are additional attributes of atom <math>i</math> in MD++.		The last 6 numbers are additional attributes of atom <math>i</math> in MD++.

	* <math>{\rm epot[}i{\rm ]}</math> is the local potential energy of atom <math>i</math>. The sum <math>{\rm epot[}i{\rm ]}</math> for all atoms equals to the potential energy of the system.		* <math>{\rm epot[}i{\rm ]}</math> is the local potential energy of atom <math>i</math>. The sum <math>{\rm epot[}i{\rm ]}</math> for all atoms equals to the potential energy of the system. <math>{\rm epot[}i{\rm ]}</math> is sometimes used in the visualization when <tt>plot_color_axis = 1</tt>. (For an example, see [http://micro.stanford.edu/~caiwei/CSD-Book/ Computer Simulations of Dislocations] section 3.3.)

	* <math>{\rm fixed[}i{\rm ]}</math> has the default value 0. If it equals to 1, then atom <math>i</math> is fixed. Its position will not change in energy minimization or Molecular Dynamics simulations. If it equals to -1, then this atom is "removed". It will not be included in the evaluation of potential energy, and it will not exert any force on other atoms. (This is a useful way to remove an atom without changing the indices of other atoms.)		* <math>{\rm fixed[}i{\rm ]}</math> has the default value 0. If it equals to 1, then atom <math>i</math> is fixed. Its position will not change in energy minimization or Molecular Dynamics simulations. If it equals to -1, then this atom is "removed". It will not be included in the evaluation of potential energy, and it will not exert any force on other atoms. (This is a useful way to remove an atom without changing the indices of other atoms.)

	* <math>{\rm topol[}i{\rm ]}</math> stores the central symetry deviation (CSD) parameter of atom <math>i</math> or other parameters computed by visualization algorithms. By default, it is not computed. To turn on the calculation of this field in energy minimzation or MD simulations, set <tt>plot_color_axis = 2</tt>. You can also ask MD++ to compute the <math>{\rm topol[}i{\rm ]}</math> value for the current configuration by calling <tt>calcentralsymmetry</tt>.		* <math>{\rm topol[}i{\rm ]}</math> stores the central symetry deviation (CSD) parameter of atom <math>i</math> or other parameters computed by visualization algorithms. By default, it is not computed. To turn on the calculation of this field in energy minimzation or MD simulations, set <tt>plot_color_axis = 2</tt>. You can also ask MD++ to compute the <math>{\rm topol[}i{\rm ]}</math> value for the current configuration by calling <tt>calcentralsymmetry</tt>. (For an example, see [http://micro.stanford.edu/~caiwei/CSD-Book/ Computer Simulations of Dislocations] section 3.3.)


	* <math>{\rm species[}i{\rm ]}</math> stores the element type of atom <math>i</math>. For a binary system, <math>{\rm species[}i{\rm ]}</math> is either 0 or 1. For a ternary system, <math>{\rm species[}i{\rm ]}</math> is either 0, 1 or 2. The interatomic potential function uses this field to decide which function to use, e.g. to compute the interaction between two given atoms.		* <math>{\rm species[}i{\rm ]}</math> stores the element type of atom <math>i</math>. For a binary system, <math>{\rm species[}i{\rm ]}</math> is either 0 or 1. For a ternary system, <math>{\rm species[}i{\rm ]}</math> is either 0, 1 or 2. The interatomic potential function uses this field to decide which function to use, e.g. to compute the interaction between two given atoms.
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	* <math>{\rm image[}i{\rm ]}</math> has the default value -1. If it is not -1, it means atom <math>i</math> is not a real atom but a (periodic) image of another atom, whose index is stored in <math>{\rm image[}i{\rm ]}</math>. This means that if atom <math>{\rm image[}i{\rm ]}</math> moves in one step of the simulation, MD++ will move atom <math>i</math> by the same amount before going to the next step.		* <math>{\rm image[}i{\rm ]}</math> has the default value -1. If it is not -1, it means atom <math>i</math> is not a real atom but a (periodic) image of another atom, whose index is stored in <math>{\rm image[}i{\rm ]}</math>. This means that if atom <math>{\rm image[}i{\rm ]}</math> moves in one step of the simulation, MD++ will move atom <math>i</math> by the same amount before going to the next step.




	==Property .out File==		==Property .out File==