Miguel Caro: /* Example */

2021-07-30T11:41:51Z

Example

Miguel Caro at 11:37, 30 July 2021

2021-07-30T11:37:37Z

Miguel Caro: Created page with "box_scaling_factor determines the change in lattice vectors taking place throughout a molecular dynamics simulation. It needs to be used in combination with `sc..."`


2021-07-30T11:36:59Z
Created page with "box_scaling_factor determines the change in lattice vectors taking place throughout a molecular dynamics simulation. It needs to be used in combination with <code>sc..."
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[[box_scaling_factor]] determines the change in lattice vectors taking place throughout a [[molecular dynamics]] simulation. It needs to be used in combination with <code>[[scale_box]] = .true.</code>. The lattice vectors change according to the following equation:



<math>\textbf{v} (i_\text{step}) = \frac{i_\text{step}}{N_\text{steps}} [[1+t_{xx}, t_{xy}, t_{xz}], [t_{yx}, 1+t_{yy}, t_{yz}], [t_{zx}, t_{zy}, 1+t_{zz}]] \, \textbf{v}_0,</math>



where <math>i_\text{step}</math> is the current time step, <math>N_\text{steps}</math> is the total number of time steps, <math>\textbf{v}_0</math> is a lattice vector at the beginning of the simulation, and the ''t''s are the scaling factors. The symmetry of the transformation is determined by how many elements, 1, 3 or 9, the user provides:



* 1 element, e.g., <code>box_scaling_factor = 1.2</code>, specifies an isotropic (homogeneous) transformation of the box, with <math>t_{xx} = t_{yy} = t_{zz} = 0.2</math> in the example;

* 3 elements, e.g., <code>box_scaling_factor = 1.1 1.2 1.3</code>, specifies an orthorhombic (diagonal) transformation of the box, with <math>t_{xx} = 0.1</math>, <math>t_{yy} = 0.2</math> and <math>t_{zz} = 0.3</math> in the example;

* 9 elements, e.g., <code>box_scaling_factor = 1.1 0.2 0.3 0.4 1.5 0.6 0.7 0.8 1.9</code>, specifies a triclinic (general) transformation of the box, with <math>t_{xx} = 0.1</math>, <math>t_{xy} = 0.2</math>, <math>t_{xz} = 0.3</math>, <math>t_{yx} = 0.4</math>, <math>t_{yy} = 0.5</math>, <math>t_{yz} = 0.6</math>, <math>t_{zx} = 0.7</math>, <math>t_{zy} = 0.8</math> and <math>t_{zz} = 0.9</math> in the example;



=== Important considerations ===



* For the ''diagonal'' components of the transformation matrix, the user defines <math>1+t</math> rather than ''t''. 

* The atomic positions are scaled together with the lattice vectors.

* The off-diagonal factors (<math>t_{ij}, i \neq j</math>) can be positive or negative; the diagonal factors (<math>1+t_{ii}</math>) should be positive, otherwise the volume of the box would collapse to zero during the simulation.



=== Summary ===



{| class="wikitable"

|+ Summary for <code>box_scaling_factor</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

|-

| Optional

| Real or real array of dimension 3 or real array of dimension 9

| Any real scalar or real array of dimension 3 or 9

| <code>1. 0. 0. 0. 1. 0. 0. 0. 1.</code>

| [[MD options]], <code>[[scale_box]]</code>, <code>[[barostat]]</code>

|}



=== Example ===



 [[scale_box]] = .true.

 [[box_rescaling_factor]] = 1.2

← Older revision		Revision as of 11:41, 30 July 2021
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	[[scale_box]] = .true.		[[scale_box]] = .true.
−	[[~~box_rescaling_factor~~]] = 1.2	+	[[box_scaling_factor]] = 1.2

← Older revision		Revision as of 11:37, 30 July 2021
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−	[[box_scaling_factor]] determines the change in lattice vectors taking place throughout a [[molecular dynamics]] simulation. It needs to be used in combination with <code>[[scale_box]] = .true.</code>. The lattice vectors change according to the following equation:	+	<code>[[box_scaling_factor]]</code> determines the change in lattice vectors taking place throughout a [[molecular dynamics]] simulation. It needs to be used in combination with <code>[[scale_box]] = .true.</code>. The lattice vectors change according to the following equation:

	<math>\textbf{v} (i_\text{step}) = \frac{i_\text{step}}{N_\text{steps}} [[1+t_{xx}, t_{xy}, t_{xz}], [t_{yx}, 1+t_{yy}, t_{yz}], [t_{zx}, t_{zy}, 1+t_{zz}]] \, \textbf{v}_0,</math>		<math>\textbf{v} (i_\text{step}) = \frac{i_\text{step}}{N_\text{steps}} [[1+t_{xx}, t_{xy}, t_{xz}], [t_{yx}, 1+t_{yy}, t_{yz}], [t_{zx}, t_{zy}, 1+t_{zz}]] \, \textbf{v}_0,</math>

Box scaling factor - Revision history

Miguel Caro: /* Example */

Miguel Caro at 11:37, 30 July 2021

Miguel Caro: Created page with "box_scaling_factor determines the change in lattice vectors taking place throughout a molecular dynamics simulation. It needs to be used in combination with sc..."

Miguel Caro: Created page with "box_scaling_factor determines the change in lattice vectors taking place throughout a molecular dynamics simulation. It needs to be used in combination with `sc..."`