Gullom2说明书.pdf

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【核心代码】

1 CONTENTS
1 Contents.........................................................................................................................................................0
2 Introduction ...................................................................................................................................................4
2.1 Updates and new functionalities: IMPORTANT CHANGES....................................................................4
2.2 The Advisory Board: ..............................................................................................................................4
2.3 Citing Gollum.........................................................................................................................................4
2.4 Gollum Units .........................................................................................................................................4
2.5 Distributed Folder Structure .................................................................................................................5
3 The scope of the Gollum project....................................................................................................................6
4 Installation and Running. ...............................................................................................................................7
4.1 MATLAB version....................................................................................................................................7
4.1.1 Installing the MCR and running in Windows ....................................................................................7
4.1.2 Installing the MCR and running LINUX..............................................................................................7
4.1.3 Installing the MCR and running MAC................................................................................................8
5 Test Examples and TUTORIALS. ...................................................................................................................10
5.1 The Gollum INPUT FILE GENERATOR...................................................................................................10
Table 5.1.......................................................................................................................................................11
5.2 Overview .............................................................................................................................................12
Summary of the examples: TABLE 5.2..............................................................................................................14
5.3 Step by step Tight-binding-based EXAMPLE: 1. single-atom_chain.spin ............................................16
5.4 Step by step siesta-based example: 1.au_linear_chain ......................................................................17
5.5 AiiDA plugin for GOLLUM....................................................................................................................18
5.5.1 installing the plugin.........................................................................................................................18
5.5.2 Standard GOLLUM plugin ...............................................................................................................19
5.5.3 GOLLUM-Siesta workflow...............................................................................................................19
6 Hamiltonian generation...............................................................................................................................20
7 Theoretical Approach...................................................................................................................................21
7.1 Nomenclature. ....................................................................................................................................21
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7.2 The surface Green’s function for the current carrying leads. .............................................................23
7.3 The extended scattering region Hamiltonian......................................................................................24
7.4 Hamiltonian Assembly ........................................................................................................................25
7.5 Scattering matrix and transmission in multi-terminal devices............................................................25
7.6 Functionalities delivered by gollum2 ..................................................................................................28
7.7 Input files format and notation...........................................................................................................28
8 the file ‘input’...............................................................................................................................................30
8.1 Mandatory Variable: Mode.................................................................................................................30
8.2 A summary of the Mode function.......................................................................................................31
8.3 Mandatory Variable: Leadp.................................................................................................................31
8.4 Mandatory Variable: atom..................................................................................................................32
8.5 Mandatory Variable: HamiltonianProvider.........................................................................................32
8.6 Partial mandatory variable variable: Path_EM ...................................................................................33
8.7 Mandatory Variable: PATH_LEADs......................................................................................................33
8.8 Partial Mandatory variable for modes 0, 1 and 3: ERange..................................................................33
8.9 Partial mandatory variable for modes 3 and 5: ThermoTRange. ........................................................33
8.10 Partial mandatory variable for mode 3: Thermosweep......................................................................33
8.11 Partial mandatory variable for modes: Thermoefrange. ....................................................................34
8.12 Partial mandatory variable for mode 3: Thermotemp........................................................................34
8.13 Partial mandatory variable for mode-3: ThermoSpinmethod. ...........................................................34
8.14 Partial mandatory variable for Mode=4: Bias.....................................................................................34
8.15 Partial mandatory variable for mode 5: WRange ...............................................................................35
8.16 Optional variable for all Modes: variable: EFshift...............................................................................35
8.17 Optional variable for Mode=4: variable: Bias_accuracy .....................................................................35
8.18 Optional variable for Modes 1,2,3,4: variable: scissors......................................................................35
8.19 Optional variable for all Modes: User defined Gate PoTENTIAL .........................................................35
8.20 Optional variable for all Modes: VgateFACTOR ..................................................................................36
8.21 Optional variable for mode-4: User defined bias potential ................................................................36
8.22 Optional variable for mode-3: thermousesavetrm.............................................................................36
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8.23 Example input file. ..............................................................................................................................36
9 The ‘Extended Molecule’ file. ......................................................................................................................38
9.1 An Example ‘Extended_Molecule’ file.................................................................................................38
9.2 Variable: nspin ....................................................................................................................................38
9.3 Variable: Fermie..................................................................................................................................38
9.4 Variable: iorb.......................................................................................................................................39
9.5 Variable: kpoints .................................................................................................................................39
9.6 Variable: HSM......................................................................................................................................39
10 THE ‘Lead_i’ input file. .................................................................................................................................40
10.1 Example ‘Lead_i’ file. ..........................................................................................................................40
10.2 Variable: kpoints_lead ........................................................................................................................40
10.3 Variable: HSL .......................................................................................................................................40
11 Output file format and notation. .................................................................................................................41
11.1 The Universal files. ..............................................................................................................................41
11.1.1 The Universal output at a glance: TABLE 10.1.1.........................................................................41
11.1.2 Transmission (reflection) coefficients. .......................................................................................41
11.1.3 The number of open channels....................................................................................................42
11.1.4 Shot noise...................................................................................................................................42
11.2 Additional Mode generated files.........................................................................................................42
11.2.1 Mode generated files at a glance: Table 10.2.1. ........................................................................42
11.2.2 Mode-2 generated files. .............................................................................................................42
11.2.3 Mode-3 generated files. .............................................................................................................43
11.2.4 Mode-4 generated files. .............................................................................................................44
11.2.5 Mode-5 generated files. .............................................................................................................44
12 References ...................................................................................................................................................45
13 Index ............................................................................................................................................................46