REMS

% ---- File Names
%%
% project_name would be used as suffix for all files that are saved. For
% example data_project_name would have all the matlab workspace.
% struct_project_name would have the data that helps you visualize the
% structure or re-simulate the structure.

% ProjectDirectory is the full path to the root directory where you want
% project data files to be saved. Program would create Data, Figures,
% Log etc. directories under the ProjectDirectory location you specified.

% InputDirectory is the full path to the directory from where simulator
% would pick the required input files like refractive index data for
% various materials.

% GeometryDefDirectory is the full path to the directory from where
% simulator would pick the user defined geometry definition files.

% NVFDefDirectory is the full path to the directory from where
% simulator would pick the user defined geometry definition files.

% SimulatorRootPath is the full path to the directory inside which
% InternalFiles directory is installed.

REMS_PV.project_name='sim3_11';
REMS_PV.SimulatorRootPath='/opt/software/REMS/Version20/src';
REMS_PV.ProjectDirectory='/tmp/user1/job0';
REMS_PV.InputDirectory=[REMS_PV.ProjectDirectory '/InputFiles'];
REMS_PV.GeometryDefDirectory=[REMS_PV.ProjectDirectory '/GeometryDefinitions'];
REMS_PV.NVFDefDirectory=[REMS_PV.ProjectDirectory '/NVFDefinitions'];

% --- Various flags to choose the core simulation engine
%%

% REMS_flags.simulator_type:- 
% 1=MG RCWA 
% 2=LL RCWA without symmetry 
% 3=LL RCWA with symmetry 
% 4=NVF RCWA 
% 5=MA RCWA
REMS_flags.simulator_type=3;

% Only one of the following flags should be set to 1.
REMS_flags.only_abs_ref_trans_flag=1;
REMS_flags.layer_abs_identification_flag=0;
REMS_flags.material_region_identification_flag=0;
REMS_flags.field_profile_identification_flag=0;

% Following two parameters are needed only when
% material_region_identification_flag is switched ON.
% REMS_SP.type_of_integration= 1 , 2 and 3 are Newton-Cotes integration; 
% 4,5 and 6 are rectangular integration. 1, 4 keep all fields in memory; 
% 2, 5 keep fields within one layer in memory; 3, 6 keep fields at one Z 
% point in memory. 
% Its basically a memory versus computation time trade-off.
% REMS_SP.NCorder defines the order of Newton-Cotes integration. Orders 2 
% to 11 are programmed currently.

REMS_flags.type_of_integration=5;
REMS_flags.NCorder=5;

% Multiple of the following flags can be set to 1.
REMS_flags.save_files_flag=1;
% If this flag is switched ON, it would save the final data file, the
% strcuture definitions, the logs and the figures (see the next two flags
% as well).
REMS_flags.overwrite_files_flag=1;
% If this flag is switched ON, existing files would be overwritten.
REMS_flags.logging_option_flag=1;
% If this flag is switched ON, then program would output logs on screen.
% Logs are also saved in the log directory if save_files_flag is switched
% ON.
REMS_flags.generate_new_structure_flag=1;
% If this flag is OFF, then GeometryGenerator program is skipped, instead a
% saved strcuture data file is uploaded. Also
% material_region_identification_flag and field_profile_identification_flag
% and grid parameters would be uploaded. You can still analyze the same
% structure for different wavelengths, angles, polarizations or different
% number of harmonics but with same old grid.
REMS_flags.structure_visualization_flag=0;
% If this flag is ON then several plots would be plotted for
% structure visualization and debugging purposes. 
%%

% --- Following paramters control the geometry you want to simulate
%%
% First five of the following Structure Parameters (SP) are required.
% Rest, user can define any variable inside the structure variable REMS_SP 
% that would help user define geometry in the User Defined Script (*.uds) 
% file that is placed inside the REMS_PV.GeometryDefDirectory directory.
% Only the variables defined inside REMS_SP and inside Grid Prameters
% structure variable REMS_GP would be available for use inside the User 
% Defined Scripts placed under the REMS_PV.GeometryDefDirectory directory.


REMS_SP.Structure_Type='rect_rect';
REMS_SP.PeriodX=500.0e-9;              
% absolute period along X in m
REMS_SP.PeriodY=500.0e-9;              
% absolute period along Y in m
REMS_SP.Cover_material={'air'};        
% materials here can not be numbers -- have to have string name with a file associated
REMS_SP.Substrate_material={'air'};     
% materials here can not be numbers -- have to have string name with a file associated
REMS_SP.groove_materials={'air'};      
% materials here can not be numbers -- have to have string name with a file associated
REMS_SP.ridge_materials={'ag_sopra'};        
% materials here can not be numbers -- have to have string name with a file associated
REMS_SP.DispX=[0];                     
% displacement of center of ridges from origin along X axis given as fraction of period along X and its absolute value can not be greater than 1.0
REMS_SP.DispY=[0];                     
% displacement of center of ridges from origin along Y axis given as fraction of period along Y and its absolute value can not be greater than 1.0
REMS_SP.FilFacX=[0.5];   
% length of ridges along X axis given as fraction of period along X and it can not be less than 0 or greater than 1.0
REMS_SP.FilFacY=[0.5];                 
% length of ridges along Y axis given as fraction of period along Y and it can not be less than 0 or greater than 1.0
% a homegeneous layer of groove_material can be generated by specifyng the FilFacX=FilFacY=0
% a homegeneous layer of ridge_material can be generated by specifyng the FilFacX=FilFacY=1
REMS_SP.depth=[50].*1.0e-9;            
% absolute depth of grating layer in m
%%

% --- Following paramters control the grid in real and Fourier spaces 
%%
% Z grid (i.e. Zp) is needed only if material_region_identification_flag or
% field_profile_identification_flag is switched ON.
% Start_Z and End_Z is is needed only if material_region_identification_flag or
% field_profile_identification_flag or layer_abs_identification_flag is switched ON.
% Variables defined under REMS_GP would also be available for use inside 
% the User Defined Scripts placed under the 
% REMS_PV.GeometryDefDirectory directory.

REMS_GP.Xp=1001;
REMS_GP.Yp=1001;
REMS_GP.Zp=1;
REMS_GP.Start_Z=25.0e-9;%0;
REMS_GP.End_Z=25.0e-9;%sum(REMS_SP.depth);
%%

% --- Following two paramters selects spatial frequencies
%%
% Following two parameters are needed to select which spatial frequencies
% are retained in the problem analysis. 
% For REMS_flags.simulator_type=5, REMS_HP.total_no_of_harmonics most 
% important frequencies are selected by Fourier analyzing the layer 
% REMS_HP.representative_layer_no.
% For all other simulator types, lowest REMS_HP.MX spatial frequencies are 
% selected along X and lowest REMS_HP.NY spatial frequencies are selected 
% along Y.

REMS_HP.MX=11;
REMS_HP.NY=11;
REMS_HP.total_no_of_harmonics=101;
REMS_HP.representative_layer_no=1;

%%
% ---- Incident radiation
%%
% Polarization parameters

% psi is the polarization angle in degrees. psi=0 => TE polarization,
% psi=90 => TM polarization.Polarization angle is defined as the direction
% of incident E field with respect to plane of incidence (a uniquely
% defined entity even in case of non-symmetrical 2D diffraction).  For
% normal incidence, TE polarization is defined to mean incident E field
% oscillating along Y axis. 

% delta is the retardation phase angle from TE to TM in degrees. This
% parameter can be used to mix two polarizations (together with a non-TE
% and non-TM value of psi) differing in temporal phase of oscillations.


REMS_EV.psi	= 0;            
REMS_EV.delta	= 0; 		

% Wavelengths

% If wavelength becomes exactly equal to an integral multiple periodicity,
% end results may not be accurate. To avoid this, add a small irrational
% part on wavelength grid.

REMS_EV.start_lambda=(380.0+pi/100)*1.0e-9;
REMS_EV.end_lambda=(880.0+pi/100)*1.0e-9;
REMS_EV.no_of_lambda_points=51;      


% Polar angles

% Following parameters define the polar angles of incidence in cover medium
% in degree.

REMS_EV.start_angle_degree=0;
REMS_EV.end_angle_degree=0;
REMS_EV.no_of_angle_points=1;    


% Azimuthal angles

% Following parameters define the azimuth angles of incidence in cover
% medium in degree.

REMS_EV.start_azimuth_degree=0;
REMS_EV.end_azimuth_degree=0;
REMS_EV.no_of_azimuth_points=1; 

%%

% Following script when execute simulates the problem as defined by the user in the ProblemDefinitionFile (*.prb).
% This script helps in designing multitude of experiments and batch processing of such experiments.
% One can use entire Matlab scripting language in this script and make "for loops", "if-else" conditions etc.
% For example, one can change geometry variables, incidence conditions etc. and resimulate by repeating some of the commands below.


SimulatorInitializer;
% Needs to be called only once

GeometryProcessor;
% Needs to be called again whenever geometry variables (REMS_SP.* in *.prb file) or the grid variables (REMS_GP.* in *.prb file) are changed.

RefractiveIndexInterpolator;
% Needs to be called again whenever wavelength or materials in the geometry are changed.

IncidenceConditionProcessor;
% Needs to be called again whenever optical incidence conditions (REMS_EV.* in *.prb file) or the cover materials (REMS_SP.Cover_material in *.prb file) are changed.

StructureVisualization.uds;
% This is a UserDefinedScript (*.uds) and needs to be executed only when user wants.

Simulator;
% Needs to be called whenever a new simulation is required.

SimulatorFinisher;
% Needs to be called only once

PlotAndSave.uds; 
% This is a UserDefinedScript (*.uds) and needs to be executed only when user wants.

% Following script when execute simulates the problem as defined by the
% user in the ProblemDefinitionFile (*.prb). This script helps in designing
% multitude of experiments and batch processing of such experiments. One
% can use entire Matlab scripting language in this script and make "for
% loops", "if-else" conditions etc. For example, one can change geometry
% variables, incidence conditions etc. and resimulate by repeating some of
% the commands below.


SimulatorInitializer;
% Needs to be called only once

% thickness of first layer (closer to cover)
REMS_UDO.t1=10.0e-9:10.0e-9:100.0e-9;
% thickness of second layer (closer to substrate)
REMS_UDO.t2=10.0e-9:10.0e-9:160.0e-9;

for ii=1:1:length(REMS_UDO.t1)
    
    
    for jj=1:1:length(REMS_UDO.t2)
        
        REMS_SP.depth=[REMS_UDO.t1(ii),REMS_UDO.t2(jj)];
        
        GeometryProcessor;
        % Needs to be called again whenever geometry variables (REMS_SP.* in *.prb file) or the grid variables (REMS_GP.* in *.prb file) are changed.
        
        RefractiveIndexInterpolator;
        % Needs to be called again whenever wavelength or materials in the geometry are changed.
        
        IncidenceConditionProcessor;
        % Needs to be called again whenever optical incidence conditions (REMS_EV.* in *.prb file) or the cover materials (REMS_SP.Cover_material in *.prb file) are changed.
        
        %StructureVisualization.uds;
        % This is a UserDefinedScript (*.uds) and needs to be executed only when user wants.
        
        Simulator;
        % Needs to be called whenever a new simulation is required.
        
        
        
        cd(REMS_PV.InputDirectory);
        load('am15')
        cd(REMS_PV.ProjectDirectory);
        
        
        am15_wavelength=am15(:,1).*1.0e-9;                                                   % m
        am15_irradiance=am15(:,5).*1.0e6;                                                    % W/m^2/m; normalized to 1000 W/m^2
        input_irradiance=interp1(am15_wavelength,am15_irradiance,REMS_EV.wavelength,'cubic');            % W/m^2/m
        input_photon_count=abs(REMS_EV.wavelength(2)-REMS_EV.wavelength(1)).*input_irradiance.*REMS_EV.wavelength./REMS_PC.hbar./2./pi./REMS_PC.cc;            % number/s/m^2
        
        am15_weighted_reflected_current=sum(input_photon_count.*REMS_EV.reflectance_z_total.'./100)*REMS_PC.ee*1.0e3/1.0e4;          
        %mA/cm^2
        total_incident_current=sum(input_photon_count)*REMS_PC.ee*1.0e3/1.0e4; 
        %mA/cm^2
        REMS_UDO.am15_weighted_reflectivity(ii,jj)=am15_weighted_reflected_current*100/total_incident_current;      % in percentage
        
        
    end
    
    
end

SimulatorFinisher;
% Needs to be called only once

PlotAndSave.uds;
% This is a UserDefinedScript (*.uds) and needs to be executed only when user wants.