csml-wiki.northwestern.edu - User contributions [en]

Etiquette: Running Nice on other desktop machines

2015-09-29T22:25:44Z

Huanxin:

When using someone else's machine, it's polite to use the command '''nice''' and '''renice'''.

'''Nice''' changes the priority of a task. When using another machine, you want to set your task to a lower priority as to not interfere with the user's tasks. Priority ranges from -20 (highest) to 20 (lowest).

nice [options] [command]

Example:

nice -19 ~/run.py

UNIX priority levels are counted from negative (highest) to positive.

'''Renice''' allows you to reset the priority of a process that is already running.

renice [-n] [PID] [options]

Replace [-n] with the desired priority, and [PID] with the process ID number.

Etiquette: Running Nice on other desktop machines

2015-09-29T22:24:51Z

Huanxin:

When using someone else's machine, it's polite to use the command '''nice''' and '''renice'''.

'''Nice''' changes the priority of a task. When using another machine, you want to set your task to a lower priority as to not interfere with the user's tasks. Priority ranges from -20 (highest) to 20 (lowest).

nice [options] [command]

Example:

nice -19 ~/run.py

UNIX priority levels are counted from negative (highest) to positive

'''Renice''' allows you to reset the priority of a process that is already running.

renice [-n] [PID] [options]

Replace [-n] with the desired priority, and [PID] with the process ID number.

VMD

2015-02-27T20:47:01Z

Huanxin: /* Atom Selection */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, users can write

<code>
index >= 100 and vx < 1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding variable name in the comment line to be, for example, "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". VMD will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose an appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

Click [http://blender.stackexchange.com/questions/648/what-are-the-differences-between-orthographic-and-perspective-views here] to learn more about the difference.

VMD

2015-02-27T20:46:34Z

Huanxin: /* 3D Projection */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, users can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding variable name in the comment line to be, for example, "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". VMD will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose an appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

Click [http://blender.stackexchange.com/questions/648/what-are-the-differences-between-orthographic-and-perspective-views here] to learn more about the difference.

VMD

2015-02-27T20:39:12Z

Huanxin: /* Atom Selection */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, users can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding variable name in the comment line to be, for example, "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". VMD will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose an appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T20:34:36Z

Huanxin: /* Dynamic Color Code */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding variable name in the comment line to be, for example, "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". VMD will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose an appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T20:33:54Z

Huanxin: /* Dynamic Color Code */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding variable name in the comment line to be, for example, "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". VMD will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose the appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T20:33:28Z

Huanxin: /* Dynamic Color Code */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding variable name in the comment line to be, for example, "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". This will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose the appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T20:32:29Z

Huanxin: /* Dynamic Color Code */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc., If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding comment line of that variable name to be "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". This will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose the appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T20:31:59Z

Huanxin: /* Dynamic Color Code */

= Overview =
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

= Atom Selection =
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

= Coloring Method =

== Dynamic Color Code ==
When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc. If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding comment line of that variable name to be "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". This will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose the appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

= Miscellaneous =
== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T20:06:13Z

Huanxin:

VMD

2015-02-27T20:04:29Z

Huanxin: /* Coloring Method */

== Overview ==
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

== Atom Selection ==
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

== Coloring Method ==

== Dynamic Color Code ==

== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T18:30:38Z

Huanxin: /* Overview */

== Overview ==
[http://www.ks.uiuc.edu/Research/vmd/ VMD] is

== Atom Selection ==
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

== Coloring Method ==

== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T18:30:04Z

Huanxin: /* Overview */

== Overview ==
VMD [http://www.ks.uiuc.edu/Research/vmd/] is

== Atom Selection ==
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

== Coloring Method ==

== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-27T18:28:47Z

Huanxin:

== Overview ==
[http://www.ks.uiuc.edu/Research/vmd/] is

== Atom Selection ==
Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

<code>
index >= 100 and vx <1.5
</code>

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

== Coloring Method ==

== 3D Projection ==
Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."

VMD

2015-02-26T17:52:41Z

Huanxin: Created page with "== Overview == [http://www.ks.uiuc.edu/Research/vmd/] is == Coloring Method == == 3D Projection == Under the "Display" category, one can choose"

== Overview ==
[http://www.ks.uiuc.edu/Research/vmd/] is

== Coloring Method ==

== 3D Projection ==
Under the "Display" category, one can choose

Hardware

2014-11-21T17:47:51Z

Huanxin: /* Printers */

=== Desktop machines ===

All desktop machines run [http://www.opensuse.org OpenSuSE]. [[Installation instructions for OpenSuSE 13.1]].

=== Clusters ===

==== Minotaur ====
* 38 nodes, each containing two 4-core processors (304 cores total). 8 GB memory per node. Processor type: Intel Xeon E5472, 3.0 GHz.
* Jobs are scheduled via [http://www.adaptivecomputing.com/products/open-source/torque/ Torque]/Maui. [[Notes on Torque]].

==== Hydra ====
* 60 nodes, each containing two 6-core processors (720 cores total). 12 GB memory per node. 8 nodes (queue "fast", nodes h001-h008) have Intel Xeon X5690 3.47 GHz processors. 52 nodes (queue "default", nodes h009-h060) have Intel Xeon E5645 2.40 GHz processors.
* Jobs are scheduled via [http://www.adaptivecomputing.com/products/open-source/torque/ Torque]/Maui. [[Notes on Torque]].
* [[General Usage of Hydra]]

==== Quest ====
* Jobs are scheduled via [http://www.adaptivecomputing.com/products/open-source/torque/ Torque]/Moab. [[Notes on Torque]].
* [[General Usage of Quest]]

=== Disk space, backups, and RAID storage ===

==== Disk space allocations and nightly backups ====

Each user has a home directory located on ''ariadne''. This home directory is exported to all desktop machines, so that you see the same home filesystem on each machine. The drive is protected against hardware failure via a [[http://en.wikipedia.org/wiki/RAID_1#RAID_1 RAID-1]] setup. Furthermore, each night all new or modified files on /home are written to tape (located in ariadne). This makes it important not to store temporary data in your home folder, as it would quickly fill up the tape. Since users tend to forget this, a quota system has been enabled on ariadne, restricting each user to 15 GB. To check how much space you are using log on to ariadne and issue the command
<pre>
quota -s
</pre>

In addition, each user has significant additional storage on the scratch partitions. These drives are located in the different desktop machines and protected via RAID-1, but backups are your own responsibility. Note that these partitions are generally only mounted on the desktop machine that contains the corresponding drives. If you need a partition to be exported to a different machine, please ask.

==== Changing the nightly backup tape ====

# Press eject button on tape drive in ariadne.
# Take the tape cartridge out of the drive and put it in its box (should be on top of ariadne). Label the box. Give to Erik.
# Insert cleaning tape (on top of ariadne). It will work for less than a minute and then eject automatically.
# Put cleaning tape back in box on top of ariadne.
# Insert new DDS tape (find in cabinet). Leave empty box on top of ariadne.
# Erik: Update settings in /usr/local/lib/backup, namely ''position'' and ''tapenumber''; update logfile.

==== Recovering data from the nightly backup tape ====

Log files of all nightly backup tapes are located on ariadne, in /usr/local/lib/backup. For privacy reasons, these logfiles are only accessible to root. Once the proper file to be recovered has been identified, insert the corresponding tape into the drive on ariadne and follow these steps (all to be executed as root):

# <tt>cd /</tt> (if you change to a different directory, the recovered file will be placed relative to this directory)
# <tt>/usr/local/bin/tape-rewind</tt> (or <tt>mtst -f /dev/nst0 rewind</tt>)
# <tt>mtst -f /dev/nst0 fsf <position></tt> (see the contents file in /usr/local/lib/backup for the position number)
# <tt>tar xzvf /dev/nst0 <full_file_name_without_leading_slash></tt> This step won't work unless you omit the leading slash; also note that you can specify multiple files, separated by spaces. The 'z' option is necessary because all nightly backups are compressed. For wildcards, use --wildcards and escape '*' and '?'. For example: <tt>tar -x --wildcards -zvf /dev/nst0 \*datafiles\*</tt>
# <tt>/usr/local/bin/tape-rewoffl</tt> (or <tt>mtst -f /dev/nst0 rewoffl</tt>)

==== Archiving data using the LTO tape drive ====

==== Checking RAID status ====

<ul>

<li>Hydra
<ul>
<li>OS is on software RAID (which spans /dev/sda and /dev/sdb). An overview is obtained via
<pre>cat /proc/mdstat</pre>
Detailed information via
<pre>
mdadm --detail /dev/mdX
</pre>
where X = 1, 5, 6, 7. Also see [[Setting up e-mail notifications for Linux Software RAID]].</li>
<li>/home</li>
<li>/archive</li>
</ul>
</li>

<li>Minotaur Web interface. Log in as root to head node and use ''opera''.</li>

<li>Ariadne RAID-5 controller with 4 drives. Status can be checked by interrogating the controller:
<pre>
/opt/MegaRAID/MegaCli/MegaCli64 -AdpAllInfo -aALL | less
</pre>
In the 'Device Present' section, it is reported if any drives are critical or have failed, and what the state of the RAID is. More detailed information can also be found via
<pre>
/opt/MegaRAID/MegaCli/MegaCli64 -LDPDInfo -aAll | less
</pre>
Directly at the beginning (under 'Adapter #0') it should report 'State: Optimal'</li>

<li>Desktop machines, except pelops Hardware RAID-1. The RAID status is reported upon reboot of a machine. Press Ctrl-C (when prompted) to enter the configuration utility. From within Linux, use (as root):
<pre>
mpt-status -i 0
mpt-status -i 2
</pre>
The second command only applies to machines with a second set of hard drives (achilles, agamemnon, nestor, poseidon) 
To allow regular users to verify the RAID status, the <tt>mpt-status</tt> has been added to <tt>sudo</tt>:
<pre>
sudo mpt-status -i 0
sudo mpt-status -i 2
</pre>
</li>

<li>Pelops: Software RAID (for OS and scratch partitions). See [[#hydra|Hydra]].</li>

</ul>

=== Printers ===
There are two black and white laser printers (PS-1 and PS-2) in the lab supporting double sided printing. Currently, PS-1 is not working properly. To access printer (PS-2) wirelessly, add a new printer on your OS with IP address "luijten-ps2.ms.northwestern.edu". The default protocol should be "Line Printer Daemon -LPD".

=== Scanner ===

=== UPS ===

All our UPS units are manufactured by APC, and supported via apcupsd. Installation & configuration instructions:

<ul>

<li>Make sure sure the <tt>apcupsd</tt> package is installed, see [[Installation instructions for OpenSuSE 13.1]].</li>

<li>Connect UPS unit to USB port of the corresponding machine.</li>

<li>In <tt>/etc/apcupsd/apcupsd.conf</tt> edit these lines:
<pre>
UPSCABLE usb
UPSTYPE usb
</pre>
Also, '''comment out''' the <tt>DEVICE</tt> line.
</li>

<li>From command line, do
<pre>
chkconfig apcupsd on
</pre>
</li>

<li>Start the daemon manually:
<pre>
apcupsd
</pre>

<li>Test it:
<pre>
apcaccess
</pre>
This should produce extensive output regarding the UPS unit. 
(Note: this command also works for regular users; in that case use <tt>/usr/sbin/apcaccess</tt>.)

</li>

</ul>

Compressed data files

2014-10-29T20:29:59Z

Huanxin: fixed one small typo

Many computer simulation packages offer the option to write data files in compressed form. This is strongly recommended.

=== Advantages ===

* Save disk/tape space
* Faster writing of data (the CPU time expenditure for the compression is negligible compared to the time save by writing smaller files)
* File corruption is detected more easily
* Easier transfer to other computer systems

=== Dealing with truncated compressed files ===

A situation sometimes encountered is that a compressed file is truncated (this most frequently occurs when a program aborts and a file buffer was not flushed). Naive application of <tt>gzip -d</tt> (or <tt>gunzip</tt>) will lead to a "unexpected end of file" error message. However, it is easy to access most of the data in this file by compressing "on the fly" and redirecting the data stream to a file. For example, if <tt>output.dat.gz</tt> is truncated, use
<pre>
gzip -dc output.dat.gz > output.dat
</pre>

This will yield the same error message as <tt>gzip -d output.dat.gz</tt> but now the decompressed file contents (until close to the truncation point) will be saved to <tt>output.dat</tt>

=== Avoiding decompression of compressed files ===

Ideally, compressed data files are '''not''' decompressed during analysis. Decompression would require additional diskspace, as well as time to compress the data again after the analysis. Instead, analysis tools such as the [[Generic_Analyzer|generic analyzer]] and [[Autocorrelation|autocorrelation]] can handle compressed data directly. Indeed, even [[Gnuplot|gnuplot]] can plot compressed data files, see [[Gnuplot#General_usage_tips|gnuplot usage notes]].