Make group - Revision history

Uttiyo: /* Group style atomtype */

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Group style atomtype

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Group style id

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Group style block

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Examples

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Example

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Example

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Examples

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Example

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Examples

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Example

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 =Group style <code>atomtype</code>=
-This style is used to group atoms by their types. The <code>Number_specific_to_group_style</code> should be greater than 1 and can be maximum equal to the number of species of atoms in the simulation box. The <code>Entries_specific_to_group_style</code> are just the symbols of the elements or species. This may be required only when the simulation system consists of many types of atoms.
+This style is used to group atoms by their types. The <code>Number_specific_to_group_style</code> should be at least equal to 1 and can be maximum equal to the number of species of atoms in the simulation box. The <code>Entries_specific_to_group_style</code> are just the symbols of the elements or species. This may be required only when the simulation system consists of many types of atoms.
 ===Example===
   make_group = grp2 atomtype 1 H

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 =Group style <code>id</code>=
-This style is used to make a group a atoms with the mentioned IDs. The <code>Number_specific_to_group_style</code> is the number of IDs that will be provided and the <code>Entries_specific_to_group_style</code> are the IDs.
+This style is used to make a group of atoms with the mentioned atom IDs. The <code>Number_specific_to_group_style</code> is the number of IDs that will be provided and the <code>Entries_specific_to_group_style</code> are the IDs of the atoms.
 ===Example===
   make_group = grp1 id 5 21 33 212 300 100

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 =Group style <code>block</code>=
-This style is used to define a block of atoms. The block is built with the specified lower and upper limits of values along the x-, y- and z-axes (i.e., xlow, xhigh, ylow, yhigh, etc.) specified in the input. Here <code>Number_specific_to_group_style</code> is the number of values that will be provided to define block (or blocks together). One block is defined by 6 limits, so when a block style group is being made this number should be at least equal to 6. The <code>Entries_specific_to_group_style</code> are real numbers denoting the limits of the block (or blocks together).
+This style is used to define a block of atoms. The block is built with the lower and upper limits of values along the x-, y- and z-axes (i.e., xlow, xhigh, ylow, yhigh, etc.) specified in the input. Here <code>Number_specific_to_group_style</code> is the number of values that will be provided to define block (or blocks together). One block is defined by 6 limits, so when a block style group is being made this number should be equal to a multiple of 6. The <code>Entries_specific_to_group_style</code> are real numbers denoting the limits of the block (or blocks together).
 ===Examples===
   make_group = blk1 block 6 xlow xhigh ylow yhigh zlow zhigh

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 =Group style <code>subtract</code>=
 This style is used to form a group of the atoms which is only in one group and none of the other groups. Here again, the <code>Number_specific_to_group_style</code> should be at least equal to 2, followed those many <code>Entries_specific_to_group_style</code>, which are the IDs of the groups. The present group will be made with those atoms which are in the group mentioned first and in none of the subsequent groups.
-==Examples==
+===Examples===
   make_group = sub1 subtract 2 all blk3
 This makes a group named sub1 containing all atoms in the simulation box which are not in the group blk3.

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 =Group style <code>sphere</code>=
 This style is used to define a group of atoms which fall within a sphere of a given radius.  The <code>Number_specific_to_group_style</code> here is 4 and the <code>Entries_specific_to_group_style</code> are first the radius of the sphere and then followed by the x, y and z coordinates of the centre of the sphere.
-==Example==
+===Example===
   make_group = sph1 sphere 4 3.2 4.2 5.0 4.2
 This makes a group sph1 for the atoms which are within a sphere of radius 3.2 Å and centred at (4.2, 5.0, 4.2).

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 =Group style <code>add</code>=
 This style is used to add the atoms in two or more groups to the group that is presently being defined. So, necessarily the <code>Number_specific_to_group_style</code> should be at least equal to 2, followed those many <code>Entries_specific_to_group_style</code>, which are now just the IDs of the groups whose atoms should be  added into the present group. The groups to be considered for adding should be already defined before performing this operation.
-==Example==
+===Example===
   make_group = blk123 add 3 blk1 blk2 blk3
 This will make group blk123 contain all the atoms that are in groups blk1, blk2 and blk3.

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 =Group style <code>dynamic</code>=
 This style is used to designate an already defined group as dynamic, meaning that the atoms in this group will be checked if they still belong to the geometrical region that was originally defined for them as the MD time has evolved. This check is performed at an interval of MD steps provided through the <code>Number_specific_to_group_style</code>. The update of the specified group is performed at the specified interval after the inter-atomic forces have been computed. Note that defining groups as dynamic is computation expensive and doing too frequent an update of the dynamic groups will also increase computation times.
-==Examples==
+===Examples===
   make_group =  blk2 dynamic 1000
   make_group =  sph1 dynamic 100
 In example 1, the group blk2 of style block defined earlier will be checked for update of its constituent atoms, which means it will be remade, after every 1000 MD time-steps. In example 2, the group sph1 of style sphere defined earlier will undergo the same update after every 100 steps.
 =Summary=