test_C_chain_siesta_SZ.m

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%%   Eotvos Quantum Transport Utilities
%    Copyright (C) 2018 Peter Rakyta, Ph.D
%
%    This program is free software: you can redistribute it and/or modify
%    it under the terms of the GNU General Public License as published by
%    the Free Software Foundation, either version 3 of the License, or
%    (at your option) any later version.
%
%    This program is distributed in the hope that it will be useful,
%    but WITHOUT ANY WARRANTY; without even the implied warranty of
%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%    GNU General Public License for more details.
%
%    You should have received a copy of the GNU General Public License
%    along with this program.  If not, see http://www.gnu.org/licenses/.
%
%> @addtogroup unit_tests Unit Tests
%> @{
%> @file test_C_chain_siesta.m
%> @brief Testfile to check SIESTA (dft) interface on a carbon chain with
% two modified atoms
%> @Available
%> EQuUs v4.9.... or later
%> @}
function test_C_chain_siesta_SZ( filenum )

    filename = mfilename('fullpath');
    [directory, fncname] = fileparts( filename );

    Label = 'C_chain_siesta_SZ'
    % create input structures
    filenameIn  = ['Input_',Label,'.xml'];
    filenameOut = ['output-',Label,'.xml'];
    [Opt, param] = parseInput( filenameIn );

    Silent=1;
    Test = false;
    % calculated conductance (and number of open channels) at five different
    % energies

    Evec = [-3.2454];
    check_conductivity = [0.000001435198111];
    
    num = length(Evec);
    Conductivity = NaN(num,1); 
    Open_channels1 = NaN(num,1); 
    Open_channels2 = NaN(num,1);     
    format long;
    
    disp( '***** test of SIESTA interface, Transport of Carbon chain with Hamiltonian from Siesta *****' );    

    CalculateTransport();
 
    function CalculateTransport()           
        
        for idx = 1:length(Evec)
            cTwoTerminal = NTerminal('filenameIn', fullfile( pwd, filenameIn), 'filenameOut', fullfile( filenameOut), 'Silent',1);           
            DeltaC_tmp = 0;
            [Conductivity_tmp, ny_tmp, DeltaC_tmp] = cTwoTerminal.Transport( Evec(idx), 'constant_channels', false, 'SelfEnergy', 1);
      
            Conductivity(idx) = -Conductivity_tmp(1,1);
            Open_channels1(idx) = ny_tmp(1);
            Open_channels2(idx) = ny_tmp(2);
        end                      
    end

    % checking conductances
    checkpoint = max(Conductivity' - check_conductivity);
    if checkpoint > 1e-7
        warning(['EQuUs:Tests:', fncname, ':checkpoint failed with error ', num2str( checkpoint)]);
    end


end