newproject;

##
## Materials
##

addmodelmaterial;
set("name","dielectric_1_45");
addemmaterialproperty("Dielectric");
set("name","dielectric_1_45");
set("refractive index",1.45);

addmodelmaterial;
set("name","Au (Gold) - CRC");
addmaterialproperties("EM","Au (Gold) - CRC");
setnamed("::model::materials::Au (Gold) - CRC","color",getnamed("::model::materials::Au (Gold) - CRC::Au (Gold) - CRC","color"));

addmodelmaterial;
set("name","dielectric_analyte");
addemmaterialproperty("Dielectric");
set("name","analyte");
set("refractive index",1);
setnamed("::model::materials::dielectric_analyte","color",getnamed("::model::materials::dielectric_analyte::analyte","color"));


##
## Geometry
##

addrect;
set("name","substrate");
set("x",0);
set("x span",1e-6);
set("y",0);
set("y span",1e-6);
set("z",-0.525e-6);
set("z span",0.96e-6);
set("material","dielectric_1_45");

addrect;
set("name","film");
set("x",0);
set("x span",1e-6);
set("y",0);
set("y span",1e-6);
set("z",0);
set("z span",0.1e-6);
set("material","Au (Gold) - CRC");
set("mesh order",2);

xC = [-0.4e-6;0.;0.4e-6];
yC = [-0.4e-6;0.;0.4e-6];
for(xI=1:3) {
    for(yI=1:3) {
        addcircle;
        set("name","hole");
        set("x",xC(xI));
        set("y",yC(yI));
        set("z",0);
        set("z span",0.1e-6);
        set("radius",0.1e-6);
        set("material","dielectric_analyte");
        set("mesh order",1);
    }
}
clear(xC);
clear(yC);

##
## Simulation
##

select("::model::simulation region");
set("dimension","3D");
set("background material","dielectric_analyte");
set("x",0);
set("x span",0.4e-6);
set("y",0);
set("y span",0.4e-6);
set("z min",-0.3e-6);
set("z max",0.3e-6);
set("z min boundary","shell");
set("z min shell thickness",0.3e-6);
set("z max boundary","shell");
set("z max shell thickness",0.3e-6);

adddgtdsolver;
set("simulation time",500e-15);
addperiodic;
set("x periodic",1);
set("y periodic",1);
addpml;

##
## Source
##

add2drect;
set("name","source plane");
set("surface normal","z");
set("x",0);
set("x span",0.8e-6);
set("y",0);
set("y span",0.8e-6);
set("z",-0.2e-6);

addplane;
set("surface type","solid");
set("solid","source plane");
set("wavelength start",0.4e-6);
set("wavelength stop",1e-6);

##
## Transmission/Reflection Monitors
##

add2drect;
set("name","reflection plane");
set("surface normal","z");
set("x span",1e-6);
set("y",0);
set("y span",1e-6);
set("z",-0.3e-6);

addemfieldmonitor;
set("name","R");
set("use linear wavelength spacing",1);
set("frequency points",200);
set("geometry type","surface");
set("surface type","solid");
set("solid","reflection plane");

add2drect;
set("name","transmission plane");
set("surface normal","z");
set("x span",1e-6);
set("y",0);
set("y span",1e-6);
set("z",0.3e-6);

addemfieldmonitor;
set("name","T");
set("use linear wavelength spacing",1);
set("frequency points",200);
set("geometry type","surface");
set("surface type","solid");
set("solid","transmission plane");

##
## Field Snapshot Monitor
##

addemfieldmonitor;
set("name","profile_at_700nm");
set("use source limits",0);
set("frequency points",1);
set("minimum wavelength",0.7e-6);
set("maximum wavelength",0.7e-6);
set("geometry type","volume");
set("volume type","all domains");

##
## Create Sweep
##

sweepName = "analyte_index_sweep";

addsweep;
setsweep("sweep","name",sweepName);
setsweep(sweepName,"type","Ranges");
setsweep(sweepName,"number of points",20);

indexParam = struct;
indexParam.Name = "analyte_index";
indexParam.Parameter = "::model::materials::dielectric_analyte::analyte::refractive index";
indexParam.Start = 1.0;
indexParam.Stop = 1.5;
addsweepparameter(sweepName, indexParam);

transResult = struct;
transResult.Name = "T";
transResult.Result = "::model::DGTD::T::flux";
addsweepresult(sweepName, transResult);

reflecResult = struct;
reflecResult.Name = "R";
reflecResult.Result = "::model::DGTD::R::flux";
addsweepresult(sweepName, reflecResult);