- _ -

• __equus_c_MOD_deallocateelement() : EQuUs_MATLAB.h
• __fox_sax_equus_MOD_deallocatetargetnodes() : read_SiestaXML.cpp
• __fox_sax_equus_MOD_get_eq_structure() : read_SiestaXML.cpp
• __fox_sax_equus_MOD_read_xml() : read_SiestaXML.cpp
• __hsx_equus_MOD_read_hsx() : read_hsx.cpp

- a -

• appendAtomNodes() : XMLoutput.m
• automatic_test() : automatic_test.m
• automatic_test_MEX() : automatic_test_MEX.m

- c -

• calc_TBwavefnc() : Graphene_QAD_eig.m
• CalcHamiltonian_k() : TMDC_Monolayer_Spectrum.m , test_TMDC_Monolayer.m
• CalcHamiltonian_k_Bilayer() : test_TMDC_Bilayer_SOC.m
• CalcHamiltonian_k_Monolayer() : test_TMDC_Bilayer_SOC.m
• CalcSelfconsistentPotential() : Self_Consistent_Spectrum.m , Self_Consistent_Transport.m
• CalcSelfConsistentSpectrum() : Self_Consistent_Spectrum.m
• CalcSelfConsistentTransport() : Self_Consistent_Transport.m
• CalcSpectrum() : Graphene_antidot_transport.m
• CalcTransport() : Coulomb_Diamonds.m , Self_Consistent_Transport.m
• CalculateSpectralDensity() : SpectralDensity.m
• CalculateTranspor() : magnetic_ribbon.m
• CalculateTransporSpecq() : CalculateTransporSpecq.m
• CalculateTransport() : Differential_conductance.m , Graphene_antidot_transport.m , MinimalConductivity.m , magnetic_barrier.m , test_C_chain_siesta_SZ.m , test_graphene_kpoints_siesta_SZ.m , test_graphene_siesta_DZ.m , test_graphene_siesta_SZ.m
• checkinfo() : dggev.F , zggev.F
• convert2FortranString() : EQuUs_MATLAB.cpp , EQuUs_MATLAB.h
• ConvertParamLead() : ValidateStructures.m
• ConvertParamScatter() : ValidateStructures.m
• Coulomb_Diamonds() : Coulomb_Diamonds.m
• createAtom() : XMLinput.m
• CreateHandlesForMagneticField() : magnetic_barrier.m , magnetic_ribbon.m
• createLeadNode() : XMLinput.m
• createOutput() : createOutput.m
• CreatePlot() : Self_Consistent_Transport.m
• createRibbons() : SSH_transport.m , SSH_Josephson.m
• createShape() : XMLinput.m
• createVectorPotential() : magnetic_ribbon.m , magnetic_barrier.m
• createXMLnode() : XMLoutput.m
• currentVSDeltaPhi() : JosephsonCurrent.m , SSH_Josephson.m
• currentVSDeltaPhi_TwoTerminal() : JosephsonCurrent.m

- d -

• DensityCalc() : Self_Consistent_Spectrum.m , Self_Consistent_Transport.m
• dgetDiagInv_test() : dgetDiagInv_test.m
• dgetPartialInv_test() : dgetPartialInv_test.m
• dggev_test() : dggev_test.m
• Differential_conductance() : Differential_conductance.m

- e -

• EgeszAbra() : SSH_Josephson.m
• Egeszabra() : SSH_transport.m

- f -

• function() : Siesta_Interface.m

- g -

• gauge_field() : gauge_field.m
• Get_Atomic_Mass() : Get_Atomic_Mass.m
• getdiaginv_mp_dgetdiaginv_() : dgetDiagInv.c
• getdiaginv_mp_zgetdiaginv_() : zgetDiagInv.c
• getFieldnames() : EQuUs_MATLAB.h , EQuUs_MATLAB.cpp
• getFilenum() : automatic_test.m
• getpartialinv_mp_dgetpartialinv_() : dgetPartialInv.c
• getpartialinv_mp_zgetpartialinv_() : zgetPartialInv.c
• Graphene_antidot_transport() : Graphene_antidot_transport.m
• Graphene_Conductivity() : Graphene_Conductivity.m
• Graphene_QAD_eig() : Graphene_QAD_eig.m

- h -

• Hamiltonians() : JosephsonCurrent.m

- i -

• InterfaceModel() : Coulomb_Diamonds.m , Self_Consistent_Transport.m

- j -

• JosephsonCurrent() : JosephsonCurrent.m

- l -

• Landaux() : Landaux.m
• Landauy() : Landauy.m

- m -

• magnetic_barrier() : magnetic_barrier.m
• magnetic_ribbon() : magnetic_ribbon.m
• matrixio() : MatrixIO.F90
• mexfunction() : dggev.F
• mexFunction() : zggev.c , zgetPartialInv.c , zgetDiagInv.c , dggev.c , dgetPartialInv.c , dgetDiagInv.c
• mexfunction() : zggev.F , import_real_full.F , import_complex_full.F , export_real_sparse.F , export_complex_sparse.F
• mexFunction() : read_hsx.cpp
• mexfunction() : dgetSchur.F , dgetPartialInv.F
• mexFunction() : read_SiestaXML.cpp
• MinimalConductivity() : MinimalConductivity.m

- p -

• parseAttributes() : XMLinput.m
• parseInput() : parseInput.m
• parseXML() : XMLinput.m
• PlotFunction() : TMDC_Monolayer_Spectrum.m , Coulomb_Diamonds.m , JosephsonCurrent.m , Self_Consistent_Spectrum.m , magnetic_barrier.m , magnetic_ribbon.m , MinimalConductivity.m , SpectralDensity.m , Differential_conductance.m , Graphene_antidot_transport.m
• plotWavefnc() : Graphene_QAD_eig.m
• Pot_Self_Consistent() : Self_Consistent_Transport.m

- r -

• Read_Siesta_Scatter() : Read_Siesta_Scatter.m
• Read_Siesta_XML() : Read_Siesta_XML.m
• regularizeEQstruct() : EQuUs_MATLAB.cpp , EQuUs_MATLAB.h
• runTest() : automatic_test.m

- s -

• ScatterPot() : Self_Consistent_Spectrum.m
• ScatterPotential() : ScatterPotential.m
• ScatterPotQD() : Coulomb_Diamonds.m
• secular_H() : Graphene_antidot_transport.m
• Self_Consistent_Spectrum() : Self_Consistent_Spectrum.m
• Self_Consistent_Transport() : Self_Consistent_Transport.m
• setComputingParameters() : XMLoutput.m , XMLinput.m
• setDefaults() : XMLinput.m
• setField() : EQuUs_MATLAB.h , EQuUs_MATLAB.cpp
• setLead() : XMLoutput.m
• setLeadParameters() : XMLinput.m
• setLeads() : XMLoutput.m
• setOptValue() : XMLinput.m
• setOutputDir() : Self_Consistent_Transport.m , SpectralDensity.m , SSH_Josephson.m , SSH_transport.m , Graphene_QAD_eig.m , TMDC_Monolayer_Spectrum.m , Graphene_antidot_transport.m , Coulomb_Diamonds.m , magnetic_barrier.m , Differential_conductance.m , Self_Consistent_Spectrum.m , JosephsonCurrent.m , MinimalConductivity.m , magnetic_ribbon.m
• setParamValue() : XMLinput.m
• setRootElement() : XMLoutput.m
• setScatteringRegion() : XMLoutput.m
• setScatterParameters() : XMLinput.m
• setvectors() : SSH_Josephson.m
• setVectors() : SpectralDensity.m
• Siesta_Equus_Read_Lead() : Read_Siesta_Lead.m
• SpectralDensity() : SpectralDensity.m
• SpectrumCalc() : TMDC_Monolayer_Spectrum.m , test_LatticeTriangle.m
• Square_leads() : Coulomb_Diamonds.m , Self_Consistent_Transport.m
• SSH_Josephson() : SSH_Josephson.m
• SSH_transport() : SSH_transport.m
• structures() : structures.m
• SurfacePot() : SpectralDensity.m

- t -

• test() : documentationGuidelines.m
• test_C_chain_siesta_SZ() : test_C_chain_siesta_SZ.m
• test_CreateHamiltonians() : test_CreateHamiltonians.m
• test_graphene_kpoints_siesta_SZ() : test_graphene_kpoints_siesta_SZ.m
• test_graphene_siesta_DZ() : test_graphene_siesta_DZ.m
• test_graphene_siesta_SZ() : test_graphene_siesta_SZ.m
• test_Keldysh() : test_Keldysh.m
• test_LatticeTriangle() : test_LatticeTriangle.m
• test_Nambu() : test_Nambu.m
• test_TMDC_Bilayer_SOC() : test_TMDC_Bilayer_SOC.m
• test_TMDC_Monolayer() : test_TMDC_Monolayer.m
• ThreeTerminalHamiltonians() : ThreeTerminalHamiltonians.m
• TMDC_Monolayer_Spectrum() : TMDC_Monolayer_Spectrum.m
• Transport() : Self_Consistent_Transport.m , magnetic_ribbon.m , SSH_transport.m , magnetic_barrier.m
• traverseNodes() : XMLinput.m

- v -

• ValidateStructures() : ValidateStructures.m

- x -

• XMLinput() : XMLinput.m
• XMLnode2MatlabStruct() : read_SiestaXML.cpp
• XMLoutput() : XMLoutput.m

- z -

• zgetDiagInv_test() : zgetDiagInv_test.m
• zgetPartialInv_test() : zgetPartialInv_test.m
• zggev_test() : zggev_test.m