<code>eph_Tinfile</code> takes the name of the file containing the parameters to construct the mesh in three dimensions for the electronic system. If this file is provided, then the corresponding electronic parameters need not be provided in input file as those will not be considered. This file has to be prepared in a standard format. This is shown below.

1st line – any comments
2nd line – any comments
3rd line – any comments
4th line – gsx gsy gsz number_of_fdm_steps
5th line – mesh_xlimit_low mesh_xlimit_high
6th line – mesh_ylimit_low mesh_ylimit_high
7th line – mesh_zlimit_low mesh_zlimit_high
8th line – i j k T_e S_e rho_e C_e K_e flag T_dyn_flag
9th line – values corresponding to column headers
10th line – values corresponding to column headers
….
….
Values are provided for the full mesh.
[Note that mesh indices i, j, k must start from 1 not 0.]

===Example (mostly used)===
#
# 3 lines of comments
#
2 2 2 1
-30.0 30.0
-30.0 30.0
-30.0 30.0
i j k T_e S_e rho_e C_e K_e flag T_dyn_flag
1 1 1 50.0 1.0 1.0 3.5E-01 0.12 0 0
2 1 1 50.0 1.0 1.0 3.5E-01 0.12 0 0
1 2 1 50.0 1.0 1.0 3.5E-01 0.12 0 0
2 2 1 50.0 1.0 1.0 3.5E-01 0.12 0 0
1 1 2 50.0 1.0 1.0 3.5E-01 0.12 0 0
2 1 2 50.0 1.0 1.0 3.5E-01 0.12 0 0
1 2 2 50.0 1.0 1.0 3.5E-01 0.12 0 0
2 2 2 50.0 1.0 1.0 3.5E-01 0.12 0 0

===Note (additional uses)===
(1) To simulate with an external source term in S_e, at least one value under the 'flag' column must be set equal to 1.

(2) To simulate (non-linear case) using temperature-dependent parameters C_e and K_e, at least one value under 'T_dyn_flag' column must be set equal to 1. Then <math>C_e(T_e)</math> and <math>K_e(T_e)</math> has to be provided through a file named as "Te-dependent_e-parameters.txt", which has a simple format as shown below:
# First 3 comment lines
# Te-dependent_e-parameters.txt file
# First N C_e(T_e) with T_e, no line gap, then M K_e(T_e) with T_e
N
10.0 3.5e-7
100.0 4.5e-7
200.0 5.5e-7
..... .....
M
10.0 0.0048
100.0 0.0248
200.0 0.0348
300.0 0.0448
400.0 0.0515
..... .....

=== Summary ===

{| class="wikitable"
|+ Summary for <code>eph_Tinfile</code> keyword
! style="text-align:left;"| Required/optional
! style="text-align:left;"| Type
! style="text-align:left;"| Accepted values
! style="text-align:left;"| Default
! style="text-align:left;"| See also
! style="text-align:left;"| Remarks
|-
| Optional
| String
| Short file names
| 'NULL'
| <code>[[nonadiabatic_processes]]</code>
| If this file is not provided the FDM mesh is constructed from given input (or default) data. Put name of file within quotes.
|}

Estop filename

2024-03-11T13:27:53Z

Uttiyo: /* Summary */

2023-11-06T14:21:33Z

Uttiyo:

<code>make_group</code> creates a group for the atoms within the simulation system which are designated by one of the various styles (presently seven) described below.
One or more atoms can be combined into groups on which different physical processes can be made to act while doing an MD simulation. For example, a thermostat can be applied to the sides of a cubic box when another process can be active on rest of the atoms inside the side walls. There are several ways by which different groups of atoms can be made. This keyword can be used more than once in the input script as more than one group may need to be defined for modeling specific setups. The general format for using the make_group command is as follows:

<code>make_group</code> = <code>group_ID</code> <code>group_Style</code> <code>Number_specific_to_group_style</code> <code>Entries_specific_to_group_style</code>

So, there are four kinds of input data that are required in order to define a group of atom(s). Each of these are explained in the following.

<code>group_ID</code> – it is the ID (or name) of the present group that is being defined. The atoms in the group will be identified by this name. For any subsequent operation on this group of atoms this group ID has to be referred. The name can be a combination of characters and numbers up to length 16.

<code>group_Style</code> – it is one of various styles by which a group of atoms can be defined. The available group styles are <code>block</code>, <code>add</code>, <code>subtract</code>, <code>id</code>, <code>sphere</code>, <code>atomtype</code>, <code>dynamic</code>. The group style <code>all</code> is already defined for all atoms in the simulation box and cannot be re-defined. Each of these group styles are explained below which will help to understand the third and fourth kinds of input data (<code>Number_specific_to_group_style</code> and <code>Entries_specific_to_group_style</code>) specific to the style.

Note: a group of all atoms with group style all and group ID all is defined by default. At present, a maximum of additional 16 groups can be made.

=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).
Examples:
# make_group = blk1 block 6 xlow xhigh ylow yhigh zlow zhigh
This will make a group named blk1 containing the atoms whose coordinates are within the limits (including the limiting values).
# make_group = blk2 block 12
xlow1 xhigh1 ylow1 yhigh1 zlow1 zhigh1
xlow2 xhigh2 ylow2 yhigh2 zlow2 zhigh2
This will make a group of atoms whose coordinates are within any of the two blocks defined by the limits.
# make_group = blk3 block 36
xlow1 xhigh1 ylow1 yhigh1 zlow1 zhigh1
xlow2 xhigh2 ylow2 yhigh2 zlow2 zhigh2
…… ……. ……. ……. ……. …….
xlow6 xhigh6 ylow6 yhigh6 zlow6 zhigh6
This makes a single group of atoms named as blk3 where six block are defined together (they can be all the sides of the simulation box, etc.)

=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:
# 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.

=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.
Example:
# make_group = grp1 id 5 21 33 212 300 100
This will make a group named grp1 with five atoms whose IDs are as given.

=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.
Example:
# 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.
# make_group = sub subtract 4 all blk1 blk2 blk3
This makes a group named sub where those atoms only are present which are not in any of the groups blk1 blk2 blk3.

=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:
# 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).

=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.
Example:
# make_group = grp2 atomtype 1 H
This makes a group named grp2 of all the H atoms in the system, provided there are multiple species in the system and H is one of them.

=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.
Example:
# 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.

<code>[[adapt_time_groupID]]</code>, <code>[[optimize_groupID]]</code>, <code>[[thermostat_groupID]]</code>, <code>[[eel_groupID]]</code>, <code>[[eph_groupID]]</code>.

=== Summary ===

{| class="wikitable"
|+ Summary for <code>adaptive_time</code> keyword
! style="text-align:left;"| Required/optional
! style="text-align:left;"| Type
! style="text-align:left;"| Accepted values
! style="text-align:left;"| Default
! style="text-align:left;"| See also
! style="text-align:left;"| Remarks
|-
| Optional
| Boolean
| <code>.true.</code> or <code>.false.</code>
| <code>.false.</code>
| <code>[[adapt_tstep_interval]]</code>, <code>[[adapt_tmin]]</code>, <code>[[adapt_tmax]]</code>, <code>[[adapt_xmax]]</code>, <code>[[adapt_emax]]</code>
| Required functionality for simulating collision cascades
|}

=== Example ===