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malamastmalamast
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6f_landau: Minor formatting changes.
1 parent f160bd3 commit 1ba8c85

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Lines changed: 86 additions & 82 deletions

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‎examples/6f_landau/6f_landau.cxx‎

Lines changed: 86 additions & 82 deletions
Original file line numberDiff line numberDiff line change
@@ -1239,7 +1239,6 @@ class Elm_6f : public PhysicsModel {
12391239
diffusion_coef_Hmode0 = options["diffusion_coef_Hmode0"].withDefault(1.0); // default value of radial diffusion coefficient
12401240
diffusion_coef_Hmode1 = options["diffusion_coef_Hmode1"].withDefault(10.0); // upper limit of radial diffusion coefficient
12411241

1242-
//path = options["path"].withDefault("./"); // The path of the original Vexb data
12431242
pos_filter = options["pos_filter"].withDefault(false); // switch to turn on the filter of the negative value of zonal background
12441243
pos_filter2 = options["pos_filter2"].withDefault(false); // switch to turn on the filter inside certain position
12451244
pos_filter_zf = options["pos_filter_zf"].withDefault(false); // switch to turn on the filter of the dc profiles inside certain postion with tanh function
@@ -1716,6 +1715,7 @@ class Elm_6f : public PhysicsModel {
17161715
if (mesh->get(Bbar, "bmag")) { // Typical magnetic field
17171716
Bbar = 1.0;
17181717
}
1718+
17191719
// Lbar = options["Lbar"].doc("Reference length scale [m]").withDefault(1.0);
17201720
if (mesh->get(Lbar, "rmag")) { // Typical length scale
17211721
Lbar = 1.0;
@@ -1742,7 +1742,8 @@ class Elm_6f : public PhysicsModel {
17421742

17431743
Tbar = Lbar / Va;
17441744

1745-
output.write("Normalisations: Bbar = {:e} T Lbar = {:e} m\n", Bbar, Lbar);
1745+
output.write("Normalisations:\n");
1746+
output.write("\t Bbar = {:e} T Lbar = {:e} m\n", Bbar, Lbar);
17461747
output.write("\t Va = {:e} m/s Tbar = {:e} s\n", Va, Tbar);
17471748
output.write("\t Nbar = {:e} * {:e} m^-3\n", Nbar, density);
17481749
output.write("\t Pibar = {:e} Pa Pebar = {:e} Pa\n", ee * Tibar * Nbar * density, ee * Tebar * Nbar * density);
@@ -1965,6 +1966,7 @@ class Elm_6f : public PhysicsModel {
19651966
P00 = P00 / (ee * Tebar * Nbar * density);
19661967
N0 = n0_height * (pow(P0 / P00, 0.3));
19671968
} else {
1969+
// N0 = N0tanh(n0_height, n0_ave, n0_width, n0_center, n0_bottom_x);
19681970
N0 = N0tanh(n0_height * Nbar, n0_ave * Nbar, n0_width, n0_center, n0_bottom_x); // Do we need Nbar here?
19691971
}
19701972
Ti0 = P0 / N0 / (1.0 + Zi);
@@ -2512,11 +2514,12 @@ class Elm_6f : public PhysicsModel {
25122514
// kappa_par_i_lin = B0; // It was B0 in older version of v3
25132515
// kappa_par_e_lin = B0; // It was B0 in older version of v3
25142516

2515-
for (jx = 0; jx < mesh->LocalNx; jx++)
2517+
for (jx = 0; jx < mesh->LocalNx; jx++) {
25162518
for (jy = 0; jy < mesh->LocalNy; jy++) {
25172519
kappa_par_i_lin(jx,jy) = kappa_par_i(jx,jy,0);
25182520
kappa_par_e_lin(jx,jy) = kappa_par_e(jx,jy,0);
25192521
}
2522+
}
25202523
}
25212524

25222525
if (diffusion_perp > 0.0) {
@@ -4563,6 +4566,9 @@ class Elm_6f : public PhysicsModel {
45634566

45644567
if (nonlinear) {
45654568
ddt(U) -= bracket(phi, U, bm_exb); // Advection
4569+
/*if (compress0)
4570+
// ddt(U) -= Vipar*Grad_par(U);
4571+
ddt(U) -= Vpar_Grad_par(Vipar, U);*/
45664572

45674573
if (compress0 && include_vipar) {
45684574
ddt(U) -= Vpar_Grad_par(Vipar, U);
@@ -4808,7 +4814,7 @@ class Elm_6f : public PhysicsModel {
48084814
}
48094815

48104816
if (compress0) {
4811-
// ddt(Ni) -= Vipar * Grad_parP(N0, CELL_YLOW);
4817+
// ddt(Ni) -= Vipar * Grad_parP(N0);
48124818
// ddt(Ni) -= Vpar_Grad_par(Vipar, N0);
48134819
if (include_vipar) {
48144820
ddt(Ni) -= Vipar * Grad_parP(N0);
@@ -4835,7 +4841,7 @@ class Elm_6f : public PhysicsModel {
48354841
}
48364842

48374843
if (nonlinear) {
4838-
// ddt(Ni) -= Vipar * Grad_par(Ni, CELL_YLOW);
4844+
// ddt(Ni) -= Vipar * Grad_par(Ni);
48394845

48404846
// ddt(Ni) -= Vpar_Grad_par(Vipar, Ni);
48414847
// ddt(Ni) += Vipar * bracket(Psi, N0, bm_mag)*B0;
@@ -4964,7 +4970,7 @@ class Elm_6f : public PhysicsModel {
49644970
}
49654971

49664972
if (nonlinear) {
4967-
// ddt(Ti) -= Vipar * Grad_par(Ti, CELL_YLOW);
4973+
// ddt(Ti) -= Vipar * Grad_par(Ti);
49684974

49694975
// ddt(Ti) -= Vpar_Grad_par(Vipar, Ti);
49704976
// ddt(Ti) += Vipar * bracket(Psi, Ti0, bm_mag)*B0;
@@ -4990,48 +4996,47 @@ class Elm_6f : public PhysicsModel {
49904996

49914997
if (diffusion_par > 0.0) {
49924998

4993-
ddt(Ti) += kappa_par_i * Grad2_par2(Ti) / N0; // Parallel diffusion
4994-
ddt(Ti) += Grad_par(kappa_par_i) * Grad_par(Ti) / N0;
4999+
ddt(Ti) += kappa_par_i * Grad2_par2(Ti) / N0; // Parallel diffusion
5000+
ddt(Ti) += Grad_par(kappa_par_i) * Grad_par(Ti) / N0;
49955001

4996-
if (diff_par_flutter) {
4997-
if (nonlinear) {
4998-
if (evolve_psi)
4999-
bracket1i = -bracket(Psi, Ti + Ti0, bm_mag) * B0;
5000-
else
5001-
bracket1i = -bracket(Apar, Ti + Ti0, bm_mag);
5002+
if (diff_par_flutter) {
5003+
if (nonlinear) {
5004+
if (evolve_psi)
5005+
bracket1i = -bracket(Psi, Ti + Ti0, bm_mag) * B0;
5006+
else
5007+
bracket1i = -bracket(Apar, Ti + Ti0, bm_mag);
5008+
} else {
5009+
if (evolve_psi)
5010+
bracket1i = -bracket(Psi, Ti0, bm_mag) * B0;
5011+
else
5012+
bracket1i = -bracket(Apar, Ti0, bm_mag);
5013+
}
5014+
mesh->communicate(bracket1i);
5015+
bracket1i.applyBoundary();
5016+
gradpar_ti = Grad_par(Ti); //NOTE(malamast): Do I need to add Ti0 here?
5017+
mesh->communicate(gradpar_ti);
5018+
gradpar_ti.applyBoundary();
5019+
5020+
ddt(Ti) += Grad_par(kappa_par_i) * bracket1i / N0;
5021+
ddt(Ti) += kappa_par_i * Grad_par(bracket1i) / N0;
5022+
if (nonlinear) {
5023+
if (evolve_psi) {
5024+
ddt(Ti) -= bracket(Psi, kappa_par_i, bm_mag) * B0 * gradpar_ti / N0;
5025+
ddt(Ti) -= kappa_par_i * bracket(Psi, gradpar_ti, bm_mag) * B0 / N0;
5026+
ddt(Ti) -= bracket(Psi, kappa_par_i, bm_mag) * B0 * bracket1i / N0;
5027+
ddt(Ti) -= kappa_par_i * bracket(Psi, bracket1i, bm_mag) * B0 / N0;
50025028
} else {
5003-
if (evolve_psi)
5004-
bracket1i = -bracket(Psi, Ti0, bm_mag) * B0;
5005-
else
5006-
bracket1i = -bracket(Apar, Ti0, bm_mag);
5007-
}
5008-
mesh->communicate(bracket1i);
5009-
bracket1i.applyBoundary();
5010-
gradpar_ti = Grad_par(Ti); //NOTE(malamast): Do I need to add Ti0 here?
5011-
mesh->communicate(gradpar_ti);
5012-
gradpar_ti.applyBoundary();
5013-
5014-
ddt(Ti) += Grad_par(kappa_par_i) * bracket1i / N0;
5015-
ddt(Ti) += kappa_par_i * Grad_par(bracket1i) / N0;
5016-
if (nonlinear) {
5017-
if (evolve_psi) {
5018-
ddt(Ti) -= bracket(Psi, kappa_par_i, bm_mag) * B0 * gradpar_ti / N0;
5019-
ddt(Ti) -= kappa_par_i * bracket(Psi, gradpar_ti, bm_mag) * B0 / N0;
5020-
ddt(Ti) -= bracket(Psi, kappa_par_i, bm_mag) * B0 * bracket1i / N0;
5021-
ddt(Ti) -= kappa_par_i * bracket(Psi, bracket1i, bm_mag) * B0 / N0;
5022-
} else {
5023-
ddt(Ti) -= bracket(Apar, kappa_par_i, bm_mag) * gradpar_ti / N0;
5024-
ddt(Ti) -= kappa_par_i * bracket(Apar, gradpar_ti, bm_mag) / N0;
5025-
ddt(Ti) -= bracket(Apar, kappa_par_i, bm_mag) * bracket1i / N0;
5026-
ddt(Ti) -= kappa_par_i * bracket(Apar, bracket1i, bm_mag) / N0;
5027-
}
5029+
ddt(Ti) -= bracket(Apar, kappa_par_i, bm_mag) * gradpar_ti / N0;
5030+
ddt(Ti) -= kappa_par_i * bracket(Apar, gradpar_ti, bm_mag) / N0;
5031+
ddt(Ti) -= bracket(Apar, kappa_par_i, bm_mag) * bracket1i / N0;
5032+
ddt(Ti) -= kappa_par_i * bracket(Apar, bracket1i, bm_mag) / N0;
50285033
}
5034+
}
50295035

5030-
if (output_flux_par) {
5031-
heatf_par_flutter_i = -kappa_par_i * bracket1i;
5032-
}
5036+
if (output_flux_par) {
5037+
heatf_par_flutter_i = -kappa_par_i * bracket1i;
50335038
}
5034-
// }
5039+
}
50355040
}
50365041

50375042
if (diffusion_perp > 0.0) {
@@ -5216,49 +5221,48 @@ class Elm_6f : public PhysicsModel {
52165221
}
52175222

52185223
if (diffusion_par > 0.0) {
5219-
ddt(Te) += kappa_par_e * Grad2_par2(Te) / Ne0; // Parallel diffusion
5220-
ddt(Te) += Grad_par(kappa_par_e) * Grad_par(Te) / Ne0;
5221-
5222-
if (diff_par_flutter) {
5223-
if (nonlinear) {
5224-
if (evolve_psi)
5225-
bracket1e = -bracket(Psi, Te + Te0, bm_mag) * B0;
5226-
else
5227-
bracket1e = -bracket(Apar, Te + Te0, bm_mag);
5224+
ddt(Te) += kappa_par_e * Grad2_par2(Te) / Ne0; // Parallel diffusion
5225+
ddt(Te) += Grad_par(kappa_par_e) * Grad_par(Te) / Ne0;
5226+
5227+
if (diff_par_flutter) {
5228+
if (nonlinear) {
5229+
if (evolve_psi)
5230+
bracket1e = -bracket(Psi, Te + Te0, bm_mag) * B0;
5231+
else
5232+
bracket1e = -bracket(Apar, Te + Te0, bm_mag);
5233+
} else {
5234+
if (evolve_psi)
5235+
bracket1e = -bracket(Psi, Te0, bm_mag) * B0;
5236+
else
5237+
bracket1e = -bracket(Apar, Te0, bm_mag);
5238+
}
5239+
mesh->communicate(bracket1e);
5240+
bracket1e.applyBoundary();
5241+
gradpar_te = Grad_par(Te); //NOTE(malamast): Should we add Te0 here?
5242+
mesh->communicate(gradpar_te);
5243+
gradpar_te.applyBoundary();
5244+
5245+
ddt(Te) += Grad_par(kappa_par_e) * bracket1e / Ne0;
5246+
ddt(Te) += kappa_par_e * Grad_par(bracket1e) / Ne0;
5247+
5248+
if (nonlinear) {
5249+
if (evolve_psi) {
5250+
ddt(Te) -= bracket(Psi, kappa_par_e, bm_mag) * B0 * gradpar_te / Ne0;
5251+
ddt(Te) -= kappa_par_e * bracket(Psi, gradpar_te, bm_mag) * B0 / Ne0;
5252+
ddt(Te) -= bracket(Psi, kappa_par_e, bm_mag) * B0 * bracket1e / Ne0;
5253+
ddt(Te) -= kappa_par_e * bracket(Psi, bracket1e, bm_mag) * B0 / Ne0;
52285254
} else {
5229-
if (evolve_psi)
5230-
bracket1e = -bracket(Psi, Te0, bm_mag) * B0;
5231-
else
5232-
bracket1e = -bracket(Apar, Te0, bm_mag);
5233-
}
5234-
mesh->communicate(bracket1e);
5235-
bracket1e.applyBoundary();
5236-
gradpar_te = Grad_par(Te); //NOTE(malamast): Should we add Te0 here?
5237-
mesh->communicate(gradpar_te);
5238-
gradpar_te.applyBoundary();
5239-
5240-
ddt(Te) += Grad_par(kappa_par_e) * bracket1e / Ne0;
5241-
ddt(Te) += kappa_par_e * Grad_par(bracket1e) / Ne0;
5242-
5243-
if (nonlinear) {
5244-
if (evolve_psi) {
5245-
ddt(Te) -= bracket(Psi, kappa_par_e, bm_mag) * B0 * gradpar_te / Ne0;
5246-
ddt(Te) -= kappa_par_e * bracket(Psi, gradpar_te, bm_mag) * B0 / Ne0;
5247-
ddt(Te) -= bracket(Psi, kappa_par_e, bm_mag) * B0 * bracket1e / Ne0;
5248-
ddt(Te) -= kappa_par_e * bracket(Psi, bracket1e, bm_mag) * B0 / Ne0;
5249-
} else {
5250-
ddt(Te) -= bracket(Apar, kappa_par_e, bm_mag) * gradpar_te / Ne0;
5251-
ddt(Te) -= kappa_par_e * bracket(Apar, gradpar_te, bm_mag) / Ne0;
5252-
ddt(Te) -= bracket(Apar, kappa_par_e, bm_mag) * bracket1e / Ne0;
5253-
ddt(Te) -= kappa_par_e * bracket(Apar, bracket1e, bm_mag) / Ne0;
5254-
}
5255+
ddt(Te) -= bracket(Apar, kappa_par_e, bm_mag) * gradpar_te / Ne0;
5256+
ddt(Te) -= kappa_par_e * bracket(Apar, gradpar_te, bm_mag) / Ne0;
5257+
ddt(Te) -= bracket(Apar, kappa_par_e, bm_mag) * bracket1e / Ne0;
5258+
ddt(Te) -= kappa_par_e * bracket(Apar, bracket1e, bm_mag) / Ne0;
52555259
}
5260+
}
52565261

5257-
if (output_flux_par) {
5258-
heatf_par_flutter_e = -kappa_par_e * bracket1e;
5259-
}
5262+
if (output_flux_par) {
5263+
heatf_par_flutter_e = -kappa_par_e * bracket1e;
52605264
}
5261-
// }
5265+
}
52625266
}
52635267

52645268
if (diffusion_perp > 0.0) {

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