CV:OPOS2: Difference between revisions

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{{CVS}}
{{CVS}}
===Definition===
===Definition===
The absolute position of the point along z-axis of re-oriented coordinate system along principal moments of the tensor inertia '''I'''.
The absolute position of the point along a selected axis of the superimposed coordinate system of a reference structure. Any axis of the superimposed coordinate system can be selected.


<center><math>\xi = A_{com,z}^'</math></center>
<center><math>\xi_{x} = A_{com,x}^'</math></center>
 
<center><math>\xi_{y} = A_{com,y}^'</math></center>
The z-axis can be reoriented to any axis of the re-oriented coordinate system.
<center><math>\xi_{z} = A_{com,z}^'</math></center>


The relation between re-oriented (') and native coordinate system is given by the transformation matrix '''T''':
The relation between re-oriented (') and native coordinate system is given by the transformation matrix '''T''':
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===Specification===
===Specification===
Section name: '''OPOS'''
Section name: '''OPOS2'''
{|
{|
| style="width: 5em;" | '''Key'''  
| style="width: 5em;" | '''Key'''  
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| atoms specifying the point '''A'''
| atoms specifying the point '''A'''
|-  style="vertical-align: top;"
|-  style="vertical-align: top;"
| '''z_direction'''
| '''reference_a'''
| string
|
| name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_a'''
|-
| '''group_b'''
| [[Mask format|mask]]
| [[Mask format|mask]]
|
|
| single atom specifying the end of approximate z-direction vector of the re-oriented coordinate system. The vector origin is in '''A'''<sub>com</sub>. The atom must be member of the group '''A'''.
| atoms specifying the point '''B'''
|-
|-
| '''direction'''
| '''direction'''
| x, y, z
| x, y, z
|
|
| determine direction of z-axis in the re-oriented coordinate system
| select axis in the superimposed coordinate system
|}
|}
''Keys in bold are mandatory.''
''Keys in bold are mandatory.''

Latest revision as of 09:19, 26 July 2021

Navigation: Documentation / Collective Variables / CV:OPOS2

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Definition

The absolute position of the point along a selected axis of the superimposed coordinate system of a reference structure. Any axis of the superimposed coordinate system can be selected.

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi_{x} = A_{com,x}^'}
Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi_{y} = A_{com,y}^'}
Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi_{z} = A_{com,z}^'}

The relation between re-oriented (') and native coordinate system is given by the transformation matrix T:

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \bold A_{com}^' = \bold T \bold A_{com}}


Specification

Section name: OPOS2

Key Type Default Description
name string unique CV name
group_a mask atoms specifying the point A
reference_a string name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a
group_b mask atoms specifying the point B
direction x, y, z select axis in the superimposed coordinate system

Keys in bold are mandatory.

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