WIP:MaterialGrid #1242

smartalecH · 2020-06-09T21:02:03Z

Initial stab. The current iteration has memory leaks and struggles with dense meshes near the border of the object containing the material grid.

As of now, the user can create a MaterialGrid (in python). The routine accepts as arguments the number of design parameters, an optional initialization array, and the two Mediums that are to be interpolated. The user can then assign this new MaterialGrid object to a geometry's (e.g. a block) material.

Example waveguides:

Swig and C++ routines are also in place. It also uses the existing libctl TO routines, so it's pretty efficient.

Todo:

src/meepgeom.cpp

src/fields.cpp

src/meepgeom.cpp

smartalecH · 2020-06-12T16:56:49Z

The overlap and add/multiply method works great for rotational symmetries:

Is there an easy way to do mirror symmetries using the same machinery?

stevengj · 2020-06-12T19:38:34Z

Is there an easy way to do mirror symmetries using the same machinery?

Yes, you just mirror the block object by flipping one or more of its basis vectors.

smartalecH · 2020-06-17T01:20:36Z

The gradients are slightly less accurate than our previous approach:

Old method:

New method:

(plots taken from the bend jupyter notebook).

stevengj · 2020-06-17T02:09:04Z

To compare errors, it might be more reliable to look at the convergence with resolution rather than the numbers at a particular resolution.

smartalecH · 2020-06-19T18:13:36Z

I've fixed most of the gradient errors. If the two mediums in the grid are dispersionless, then the results look great:

Dispersive media aren't as straightforward. If I strictly interpolate the Lorentzians (silicon and silicon dioxide in this case) without adding the conductivity damping term, the results also look good (note, I dropped the Courant factor to prevent aliasing/field instabilities):

But as discussed, the conductivity factor is important to prevent instabilities as well. If I also try to interpolate the conductivity then the gradients start to fall apart:

Here is a write-up that describes my implementation. I'll highlight important code pieces below.

I still need to figure out why mpb.py and simulation.py are failing. It has something to do with the default_material interpolating from a NumPy array.

smartalecH · 2020-06-19T18:15:42Z

src/meepgeom.cpp

+void epsilon_material_grid(material_data *md, meep::realnum u) {
+  // NOTE: assume p lies on normalized grid within (0,1)
+
+  if (!(md->design_parameters)) meep::abort("material params were not initialized!");
+
+  medium_struct *mm = &(md->medium);
+  medium_struct *m1 = &(md->medium_1);
+  medium_struct *m2 = &(md->medium_2);
+
+  // Linearly interpolate dc epsilon values
+  cinterp_tensors(m1->epsilon_diag, m1->epsilon_offdiag, m2->epsilon_diag, m2->epsilon_offdiag, &mm->epsilon_diag, &mm->epsilon_offdiag, u);
+
+  //Interpolate resonant strength from d.p.
+  vector3 zero_vec;
+  zero_vec.x = zero_vec.y = zero_vec.z = 0;
+  for (int i = 0; i < m1->E_susceptibilities.num_items; i++) {
+    // iterate through medium1 sus list first
+    interp_tensors(zero_vec, zero_vec, m1->E_susceptibilities.items[i].sigma_diag, m1->E_susceptibilities.items[i].sigma_offdiag, 
+    &mm->E_susceptibilities.items[i].sigma_diag, &mm->E_susceptibilities.items[i].sigma_offdiag, (1-u));
+  }
+  for (int i = 0; i < m2->E_susceptibilities.num_items; i++) {
+    // iterate through medium2 sus list next
+    int j = i + m1->E_susceptibilities.num_items;
+    interp_tensors(zero_vec, zero_vec, m2->E_susceptibilities.items[i].sigma_diag, m2->E_susceptibilities.items[i].sigma_offdiag, 
+    &mm->E_susceptibilities.items[j].sigma_diag, &mm->E_susceptibilities.items[j].sigma_offdiag, u);  
+  }
+
+  //Linearly interpolate electric conductivity from d.p.
+  //This prevents instabilities when interpolating between sus. profiles.
+  //We assume that the material doesn't have any underlying conductance....
+  if ((m1->E_susceptibilities.num_items + m2->E_susceptibilities.num_items) > 0.0) {
+    // calculate mean harmonic frequency
+    double omega_mean = 0;
+    for (int i = 0; i < m1->E_susceptibilities.num_items; i++) { omega_mean += m1->E_susceptibilities.items[i].frequency;}
+    for (int i = 0; i < m2->E_susceptibilities.num_items; i++) { omega_mean += m2->E_susceptibilities.items[i].frequency;}
+    omega_mean = omega_mean / (m1->E_susceptibilities.num_items + m2->E_susceptibilities.num_items);
+
+    // assign interpolated, nondimensionalized conductivity term
+    mm->D_conductivity_diag.x = mm->D_conductivity_diag.y = mm->D_conductivity_diag.z = u*(1-u) * omega_mean;
+  }
+}


Materials are interpolated in this function.

smartalecH · 2020-06-19T18:16:35Z

src/meepgeom.cpp

+     master_printf("r %g \n",temp);
+   return 2 * (md->medium_2.epsilon_diag.x - md->medium_1.epsilon_diag.x) * (
+     (fields_a[0]*fields_f[0]).real() + (fields_a[1]*fields_f[1]).real() + (fields_a[2]*fields_f[2]).real());
+  }*/
+
+  // nontrivial case 
+  std::complex<double> a[9] = {std::complex<double>(0, 0)};
+  std::complex<double> dadu[9] = {std::complex<double>(0, 0)};
+  std::complex<double> b[9] = {std::complex<double>(0, 0)};
+  std::complex<double> dbdu[9] = {std::complex<double>(0, 0)};
+
+  const medium_struct *mm = &(md->medium);
+  const medium_struct *m1 = &(md->medium_1);
+  const medium_struct *m2 = &(md->medium_2);
+
+  a[0] = a[4] = a[8] = std::complex<double>(1, 0);
+  for (int i = 0; i < 9; i++) {
+    // compute first part containing conductivity
+    // NOTE: Current implementation assumes thatmaterials being interpolated
+    // don't have their own conductivities! Just the synthetic conductivity
+    // used to dampen the interpolated lorentzians
+    vector3 dummy; dummy.x = dummy.y = dummy.z = 0.0;
+    double conductivityCur = vec_to_value(mm->D_conductivity_diag, dummy, i);
+    a[i] += std::complex<double>(0.0, conductivityCur / freq);
+
+    // compute derivative of conductivity component wrt u
+    if ((m1->E_susceptibilities.num_items + m2->E_susceptibilities.num_items) > 0.0) {
+      // calculate mean harmonic frequency
+      double omega_mean = 0;
+      for (int i = 0; i < m1->E_susceptibilities.num_items; i++) { omega_mean += m1->E_susceptibilities.items[i].frequency;}
+      for (int i = 0; i < m2->E_susceptibilities.num_items; i++) { omega_mean += m2->E_susceptibilities.items[i].frequency;}
+      omega_mean = omega_mean / (m1->E_susceptibilities.num_items + m2->E_susceptibilities.num_items);
+
+      // assign interpolated, nondimensionalized conductivity term to diag comps
+      if ((i == 0) || (i == 4) || (i==8)) dadu[i] += std::complex<double>(0.0,(1-2*u)*omega_mean/freq);
+    }
+
+    // compute lorentzian component
+    b[i] = cvec_to_value(mm->epsilon_diag, mm->epsilon_offdiag, i);
+    for (int nl = 0; nl < mm->E_susceptibilities.num_items; ++nl){
+      meep::lorentzian_susceptibility sus = meep::lorentzian_susceptibility(mm->E_susceptibilities.items[nl].frequency, mm->E_susceptibilities.items[nl].gamma, mm->E_susceptibilities.items[nl].drude);
+      double sigma = vec_to_value(mm->E_susceptibilities.items[nl].sigma_diag, mm->E_susceptibilities.items[nl].sigma_offdiag, i);
+      b[i]+= sus.chi1(freq, sigma);
+    }
+
+    // compute derivative of lorentzian component wrt u
+    dbdu[i] = (cvec_to_value(m2->epsilon_diag, m2->epsilon_offdiag, i) - cvec_to_value(m1->epsilon_diag, m1->epsilon_offdiag, i));
+    for (int nl = 0; nl < m1->E_susceptibilities.num_items; ++nl){
+      meep::lorentzian_susceptibility sus = meep::lorentzian_susceptibility(m1->E_susceptibilities.items[nl].frequency, m1->E_susceptibilities.items[nl].gamma, m1->E_susceptibilities.items[nl].drude);
+      double sigma = vec_to_value(m1->E_susceptibilities.items[nl].sigma_diag, m1->E_susceptibilities.items[nl].sigma_offdiag, i);
+      dbdu[i]-= sus.chi1(freq, sigma); // subtract these ones
+    }
+    for (int nl = 0; nl < m2->E_susceptibilities.num_items; ++nl){
+      meep::lorentzian_susceptibility sus = meep::lorentzian_susceptibility(m2->E_susceptibilities.items[nl].frequency, m2->E_susceptibilities.items[nl].gamma, m2->E_susceptibilities.items[nl].drude);
+      double sigma = vec_to_value(m2->E_susceptibilities.items[nl].sigma_diag, m2->E_susceptibilities.items[nl].sigma_offdiag, i);
+      dbdu[i]+= sus.chi1(freq, sigma);
+    }
+  }
+
+  std::complex<double> left[9] = {std::complex<double>(0,0)};
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < 3; j++) {
+      for (int u = 0; u < 3; u++) {
+        int idxo = i * 3 + j; int idx1 = i * 3 + u; int idx2 = u * 3 + j;
+        left[idxo] += a[idx1] * dbdu[idx2];
+      }
+    }
+  }
+
+  std::complex<double> right[9] = {std::complex<double>(0,0)};
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < 3; j++) {
+      for (int u = 0; u < 3; u++) {
+        int idxo = i * 3 + j; int idx1 = i * 3 + u; int idx2 = u * 3 + j;
+        right[idxo] += b[idx1] * dadu[idx2];
+      }
+    }
+  }
+
+  std::complex<double> dA_du[9] = {std::complex<double>(0,0)};
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < 3; j++) {
+      int idx = i * 3 + j;
+      dA_du[idx] = left[idx] + right[idx];
+    }
+  }
+
+  /*Calculate the vector-matrix-vector product conj(v1) A v2.*/
+  std::complex<double> dummy[3] = {std::complex<double>(0,0)};
+  // first matrix-vector product
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < 3; j++) {
+      int idx = i * 3 + j;
+      dummy[i] += dA_du[idx] * fields_f[j];
+    }
+  }
+
+  // inner product
+  std::complex<double> result = dummy[0] * fields_a[0] + dummy[1] * fields_a[1]  + dummy[2] * fields_a[2] ;
+  return 2*result.real();


Gradient considering material interpolation is computed here.

stevengj · 2020-06-19T19:08:43Z

Maybe try to debug the conductivity term by itself, with no Lorentzians.

smartalecH · 2020-06-23T18:20:35Z

All tests are passing now.

After testing just the conductivity (i.e. no dispersion), I was unable to produce an accurate gradient. Consequently, I think the issue is with lossy materials in general.

For now, lossy support is disabled. The user can still interpolate Lorentzians, but they better choose profiles that won't cross zero when being turned on and off (Si in the materials library should be fine, for example). Once we can figure out how to calculate the gradients with lossy materials, we can add the Lorentzian damping parameter.

Note: I think this is a math issue, rather than a code issue.

smartalecH · 2020-07-01T00:29:43Z

Ready to merge once checks pass.

Note that gradients of FOM with lossy materials still don't converge. Everything else works well, however. I think the next step is to use a simpler objective function to debug (i.e. just a DFT component).

The current test only checks that the material_grid object initializes properly. Once we work out the lossy materials bug, we can think of some more comprehensive tests.

You can view the updated notebooks to see how the material grid works.

* init * basic functionality with bugs * fix boundary issues and memory leak * remove print statements * add function to update design parameters * add material sus to interpolation * add support for u_add, u_prod, etc. * init stab at gradient * fix most gradients * fix failing tests and disable conductivity * add test and update notebooks * add test to makefile * Update material_grid.py * rm matplotlib from test Co-authored-by: Alec Hammond <[email protected]> Co-authored-by: Steven G. Johnson <[email protected]>

stevengj · 2021-10-13T15:42:54Z

src/meepgeom.cpp

+
+    // assign interpolated, nondimensionalized conductivity term
+    // TODO: dampen the lorentzians to improve stability
+    //mm->D_conductivity_diag.x = mm->D_conductivity_diag.y = mm->D_conductivity_diag.z = u*(1-u) * omega_mean;


@smartalecH, I thought this had been enabled? We mention it in the paper…

Alec Hammond added 2 commits June 3, 2020 13:27

init

1098721

basic functionality with bugs

255204f

stevengj reviewed Jun 10, 2020

View reviewed changes

src/meepgeom.cpp Outdated Show resolved Hide resolved

Alec Hammond added 2 commits June 10, 2020 11:26

fix boundary issues and memory leak

220c9b2

remove print statements

1559e79

smartalecH commented Jun 10, 2020

View reviewed changes

src/fields.cpp Outdated Show resolved Hide resolved

Alec Hammond added 3 commits June 10, 2020 16:57

add function to update design parameters

32d6636

add material sus to interpolation

bfa21ad

add support for u_add, u_prod, etc.

5ab44f4

smartalecH commented Jun 12, 2020

View reviewed changes

src/meepgeom.cpp Show resolved Hide resolved

init stab at gradient

63f2848

fix most gradients

da3dad6

smartalecH commented Jun 19, 2020

View reviewed changes

fix failing tests and disable conductivity

bf38a13

smartalecH mentioned this pull request Jun 25, 2020

Non-reproducible outputs from adjoint solver (memory leak?) #1262

Closed

add test and update notebooks

7ce12c9

smartalecH mentioned this pull request Jul 1, 2020

Fix dft fields memory leak #1264

Closed

Alec Hammond and others added 3 commits June 30, 2020 21:48

add test to makefile

4546eb5

Update material_grid.py

0516304

rm matplotlib from test

af6ccd9

stevengj merged commit 4befdef into NanoComp:master Jul 4, 2020

This was referenced Feb 15, 2021

enabling support for subpixel smoothing of MaterialGrid #1500

Closed

unit test and documentation for MaterialGrid #1508

Merged

oskooi mentioned this pull request May 1, 2021

computing the normal vector to an interface for a MaterialGrid using analytic gradient #1539

Merged

stevengj reviewed Oct 13, 2021

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

WIP:MaterialGrid #1242

WIP:MaterialGrid #1242

smartalecH commented Jun 9, 2020 •

edited

Loading

smartalecH commented Jun 12, 2020

stevengj commented Jun 12, 2020

smartalecH commented Jun 17, 2020

stevengj commented Jun 17, 2020

smartalecH commented Jun 19, 2020

smartalecH Jun 19, 2020

smartalecH Jun 19, 2020

stevengj commented Jun 19, 2020

smartalecH commented Jun 23, 2020 •

edited

Loading

smartalecH commented Jul 1, 2020

stevengj Oct 13, 2021

WIP:MaterialGrid #1242

WIP:MaterialGrid #1242

Conversation

smartalecH commented Jun 9, 2020 • edited Loading

smartalecH commented Jun 12, 2020

stevengj commented Jun 12, 2020

smartalecH commented Jun 17, 2020

stevengj commented Jun 17, 2020

smartalecH commented Jun 19, 2020

smartalecH Jun 19, 2020

Choose a reason for hiding this comment

smartalecH Jun 19, 2020

Choose a reason for hiding this comment

stevengj commented Jun 19, 2020

smartalecH commented Jun 23, 2020 • edited Loading

smartalecH commented Jul 1, 2020

stevengj Oct 13, 2021

Choose a reason for hiding this comment

smartalecH commented Jun 9, 2020 •

edited

Loading

smartalecH commented Jun 23, 2020 •

edited

Loading