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hesel.cxx
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/*
* hesel.cxx
*
* This file holds the main codes for HESEL model based on Jen. Madsen's POP 2016
* paper. Two collisional model is included: standard simplified HESEL model
* and full model that contains higher order drifts. Plasma neutral interaction
* is also included based on Alexander's work. Drift wave dynamics is included
* according to Ander's PPCF 2017 paper.
*
* Created on: Sep 29, 2015
* Author: yolen
*
* Change Log
* 2017-01-10 by alexander:
* 1. Include neutral models.
* 2. Rearrange code structure.
* 2017-04-28 by Jens Madsen:
* 1. Upgrade to BOUT++ version 4
* 2. Rearrange code structure.
* 3. Separate HeselParameters to be a submodule.
* 2017-06-06 by alexander:
* 1. Add plasma neutral interaction model.
* 2018-02-05 by jeppe:
* 1. Correct mistakes in LFS of vorticity equation, add missing terms in
* RHS of ion pressure equation and correct mistakes in HeselParameters.
* 2018-07-24 by xiang liu:
* 1. Clean and restructure the code.
* 2. Correct bug in initialization of magnetic fields.
* 3. Solve problem that no boundary value for using bracket.
* 4. Check through and correct several mistakes according to Jens Madsen
* POP paper.
* 5. Add drift wave dynamics.
* 6. Revise initial profile functions, make pressure profile linear drops
* in the edge.
* 7. Adjust C() and Brackets() to suite for right-handed coordinate system
* 8. Rewrite full collisional model.
* 9. Separate the equations and add switches for different dynamics
* 10. Add invert_w_star
* 11. Reformulate and not using reciprocal explicitly, which might lead to
* sharp points near steep gradient and stop the time solver.
* 12. reorganize physical and derived fields, avoid using reciprocal.
* 2018-08-07 by xiang liu
* 1. find a solution for convergence error for full model and for low q or
* high Te in std model
* 2. add a bunch of controls for approximations
* 2018-08-20 by xiang liu
* 1. add feature: use experiment profiles stored in grid file
* 2018-09-03 by xiangl
* add feature: ramp up initial profiles
* 2018-09-07 by xiangl
* add hyper diffusion with 4th oder
* 2018-09-21 by xiangl
* reorganize hyper diffusion code with switches added and add 6th order
* 2018-09-27 by xiangl
* add parallel thermal energy diagnostics and reorganize parallel dynamics
* 2018-09-28 by xiangl
* add perpendicular thermal energy diagnostics
* 2018-12-04 by xiangl
* fix bugs in DriftWave and C(), adjust viscous heating \eta with full variation
*
* TO DO: neutral model cleanup and test
*/
#include "hesel.hxx"
/// ****** Constructor ******
hesel::hesel() : neutrals(solver,HeselPara,n,phi,pi,pe,B),
parallel(solver,HeselPara,n,phi,vort,pi,pe,B),
kinetic_neutrals(HeselPara, n, te, ti, phi, B)
{}
/// ****** Overwrite Initialization Function ******
int hesel::init(bool restart) {
InitMesh();
InitParameters();
InitMagneticField();
InitFieldGroups();
InitIntialProfiles();
InitRampInitProfiles();
InitEvolvingFields();
InitOtherFields();
InitPhiSolver();
InitDiagnostics();
InitNeutrals();
InitParallel();
InitKineticNeutrals(restart);
if (fast_output.enabled) {
// Add monitor if necessary
if (fast_output.enable_monitor) {
solver->addMonitor(&fast_output);
}
// Add points from the input file
int i = 0;
BoutReal xpos, ypos, zpos;
int ix, iy, iz;
Options* fast_output_options = Options::getRoot()->getSection("fast_output");
while (true) {
// Add more points if explicitly set in input file
fast_output_options->get("xpos"+std::to_string(i), xpos, -1.);
fast_output_options->get("ypos"+std::to_string(i), ypos, -1.);
fast_output_options->get("zpos"+std::to_string(i), zpos, -1.);
if (xpos<0. || ypos<0. || zpos<0.) {
output.write("\tAdded %i fast_output points\n", i);
break;
}
ix = int(xpos*mesh->GlobalNx);
iy = int(ypos*mesh->GlobalNy);
iz = int(zpos*mesh->GlobalNz);
// Add fields to be monitored
fast_output.add("n"+std::to_string(i), n, ix, iy, iz);
fast_output.add("phi"+std::to_string(i), phi, ix, iy, iz);
fast_output.add("te"+std::to_string(i), te, ix, iy, iz);
fast_output.add("ti"+std::to_string(i), ti, ix, iy, iz);
if (plasma_neutral_interactions){
fast_output.add("Ncold"+std::to_string(i), neutrals.Ncold, ix, iy, iz);
fast_output.add("Nwarm"+std::to_string(i), neutrals.Nwarm, ix, iy, iz);
fast_output.add("Nhot"+std::to_string(i), neutrals.Nhot, ix, iy, iz);
}
i++;
}
}
/*if (intercomm_monitor.enabled){
solver->addMonitor(&intercomm_monitor);
}*/
return 0;
}
/// ****** Overwrite Time Evolution Function ******
int hesel::rhs(BoutReal t) {
RhsEvolvingFieldsStart(); // Communicate evolving fields
RhsKineticPlasmaNeutralInteractionInit(t);
t1 = std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::system_clock::now().time_since_epoch()).count();
CalculateFieldGroupPhyd();// calculate derived physical fields
CalculatePhi(); // calculate phi from generalized vorticity
RhsTestBlob(); // blob testing code, must put just after CalculatePhi()
CalculateFieldGroupGradp();// calculate vector fields, only call after phi has been calculated
CalculateFieldGroupAvg(); // calculate average fields, only call after phi has been calculated
RhsInterchangeDynamics(); // non collisional part of equations
RhsPerpendicularDynamics(); // add collisional effects to the RHS's of the plasma fields e.g. diffusion to particle density field.
RhsParallelDynamics(); // parallel damping dynamics
RhsDiagnostics(t);
//RhsKineticPlasmaNeutralInteraction(t);
RhsPlasmaNeutralInteraction(t);
RhsRampInitProfiles(t);
RhsParallelTransport(t);
RhsPlasmaFieldsForce(); // force field towards fixed profiles in inner edge region
RhsPlasmaFieldsFloor(); // if required make sure that field stay above a minimum level (a floor)
RhsRampTiReference(t); // ramp up reference ion temperature
RhsPlasmaFieldsStatic(); // special case were plasma i static and neutral are evolved
t2 = std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::system_clock::now().time_since_epoch()).count();
rhs_wall_time_not_including_neutrals += t2 - t1;
RhsKineticPlasmaNeutralInteractionFinal();
RhsEvolvingFieldsEnd();
if (fast_output.enabled){
fast_output.monitor_method(t); // Store fast output in BOUT.fast.<processor_no.>
}
/*
std::cout << "############### ddt_lnn = " << SumField(ddt_lnn) << std::endl;
std::cout << "############### ddt_lnpe = " << SumField(ddt_lnpe) << std::endl;
std::cout << "############### ddt_lnpi = " << SumField(ddt_lnpi) << std::endl;
*/
return 0;
}
BoutReal hesel::SumField(Field3D f){
BoutReal sum = 0;
int loc_proc_nx = n.getNx()-2;
int loc_proc_ny = n.getNy();
int loc_proc_nz = n.getNz();
int N_per_proc = loc_proc_nx*loc_proc_ny*loc_proc_nz;
for(int i = 0; i < loc_proc_nx; i++){
for(int j = 0; j < loc_proc_ny; j++){
for(int k = 0; k < loc_proc_nz; k++){
//mxg guard cells are placed in the x-dimension. Dont read any data into these cells.
sum += abs(f(i+1, j, k))/(N_per_proc);
//std::cout << "My field at " << i << ", " << j << ", " << k << " is " << buffer_field(i, j, k) << std::endl;
}
}
}
return sum;
}
//******************************************************************************
int hesel::InitMesh(){
// TO DO: would it possible to set metric tensor to change to right-handed
// coordinate system?
TRACE("Updating geometry");
// Options *meshoptions = Options::getRoot()->getSection("mesh");
// set toroidal magnetic field
mesh->getCoordinates()->Bxy = 1. ;
// covariant metric tensor and magnetic field
mesh->getCoordinates()->g11 = 1.0 ;
mesh->getCoordinates()->g22 = 1.0 ;
mesh->getCoordinates()->g33 = 1.0 ;
mesh->getCoordinates()->g12 = 0.0 ;
mesh->getCoordinates()->g13 = 0.0 ;
mesh->getCoordinates()->g23 = 0.0 ;
//...contravariant
mesh->getCoordinates()->g_11 = 1.0 ;
mesh->getCoordinates()->g_22 = 1.0 ;
mesh->getCoordinates()->g_33 = 1.0 ;
mesh->getCoordinates()->g_12 = 0.0;
mesh->getCoordinates()->g_13 = 0.0;
mesh->getCoordinates()->g_23 = 0.0;
mesh->getCoordinates()->geometry();
if (mesh->sourceHasVar("init_n")){
use_grid_file = true;
output << ">>>>>>> Using Initial Profiles in Grid File <<<<<<<" << endl;
} else {
use_grid_file = false;
}
return 0;
}
int hesel::InitParameters(){
TRACE("Loading parameters");
Options *opt_hesel = Options::getRoot()->getSection("hesel");
// switches and options
OPTION(opt_hesel, compact_output, false);
OPTION(opt_hesel, test_blob, false);
OPTION(opt_hesel, test_laplace, false);
OPTION(opt_hesel, right_handed_coord, false);
OPTION(opt_hesel, interchange_dynamics, true);
OPTION(opt_hesel, parallel_dynamics, true);
OPTION(opt_hesel, perpendicular_dynamics, true);
OPTION(opt_hesel, invert_w_star, false);
OPTION(opt_hesel, plasma_neutral_interactions, 0);
OPTION(opt_hesel, kinetic_plasma_neutral_interactions, 0);
if (plasma_neutral_interactions && kinetic_plasma_neutral_interactions){
throw BoutException("ERROR: Kinetic AND fluid neutrals is switched on. Choose one or neither");
}
OPTION(opt_hesel, parallel_transport, false);
OPTION(opt_hesel, force_profiles, true);
OPTION(opt_hesel, floor_profiles, false);
OPTION(opt_hesel, rampup_ti0, false);
OPTION(opt_hesel, static_plasma, false);
OPTION(opt_hesel, rampup_init_prof, false);
OPTION(opt_hesel, diagnostics, false);
OPTION(opt_hesel, init_zero_potential, false);
// sub switches and options
OPTION(opt_hesel, test_blob_use_gen_vort, false);
OPTION(opt_hesel, test_vort_cross_term, false);
OPTION(opt_hesel, collisional_model, 1);
OPTION(opt_hesel, perpend_heat_exchange, true);
OPTION(opt_hesel, perpend_viscous_heating, true);
OPTION(opt_hesel, perpend_hyper_diffusion, false);
OPTION(opt_hesel, parallel_conduction, 1);
OPTION(opt_hesel, parallel_sheath_damping, 2);
OPTION(opt_hesel, parallel_advection_damping, 3);
OPTION(opt_hesel, parallel_drift_wave, 1);
OPTION(opt_hesel, ti_over_te, 3);
OPTION(opt_hesel, diffusion_coeff, 1);
OPTION(opt_hesel, reciprocal_approx, 3);
OPTION(opt_hesel, neoclass_correction_factor, -1); // use default value: R/a*q^2
OPTION(opt_hesel, qdelta_approx, 1);
OPTION(opt_hesel, diag_particle_flux, false);
OPTION(opt_hesel, diag_thermal, 0);
OPTION(opt_hesel, double_curvature_coeff, false);
OPTION(opt_hesel, Lc_from_grid, false);
OPTION(opt_hesel, Z_eff, 1);
// bracket method
OPTION(opt_hesel, bracket_method, 2);
// settings for modifying profiles
OPTION(opt_hesel, force_time, 50.);
OPTION(opt_hesel, floor_time, 0.);
OPTION(opt_hesel, floor_n, 0.);
OPTION(opt_hesel, floor_pe, 0.);
OPTION(opt_hesel, floor_pi, 0.);
OPTION(opt_hesel, rampup_init_time, 1000.);
SAVE_ONCE2(force_time, floor_time);
SAVE_ONCE3(floor_n, floor_pe, floor_pi);
SAVE_ONCE(rampup_init_time);
// settings for hyper diffusion
OPTION(opt_hesel, hyper_dc_n, 1);
OPTION(opt_hesel, hyper_dc_pe, 1);
OPTION(opt_hesel, hyper_dc_pi, 1);
OPTION(opt_hesel, hyper_dc_vort, 1);
OPTION(opt_hesel, hyper_order, 4);
SAVE_ONCE2(hyper_dc_n, hyper_dc_pe);
SAVE_ONCE2(hyper_dc_pi, hyper_dc_vort);
SAVE_ONCE(hyper_order);
// physical and engineering parameters
OPTION(opt_hesel, Rmajor, 1.90);
OPTION(opt_hesel, Rminor, 0.45);
OPTION(opt_hesel, Bt, 2.3);
OPTION(opt_hesel, q, 5);
OPTION(opt_hesel, Te0, 20.);
OPTION(opt_hesel, Ti0, 20.);
OPTION(opt_hesel, n0, 1.5E19);
OPTION(opt_hesel, A, 2.);
OPTION(opt_hesel, Z, 1.);
if (Lc_from_grid){
mesh->get(lconn, "lconn" );
}else{
OPTION(opt_hesel, lconn, 15.);
}
OPTION(opt_hesel, lblob, -1); // use default value: q*R
OPTION(opt_hesel, Mach, 1.);
B0 = Bt*Rmajor/(Rmajor+Rminor); // should use reference value at LCFS
HeselPara.R(Rmajor);
HeselPara.a(Rminor);
HeselPara.B(B0);
HeselPara.q(q);
HeselPara.Te(Te0);
HeselPara.Ti(Ti0);
HeselPara.n(n0);
HeselPara.A(A);
HeselPara.Z(Z);
HeselPara.lconn(lconn);
HeselPara.Mach(Mach);
HeselPara.lblob(lblob);
HeselPara.neocorr_factor(neoclass_correction_factor);
lconn = HeselPara.lconn();
lblob = HeselPara.lblob();
neoclass_correction_factor = HeselPara.neocorr_factor();
SAVE_ONCE4(Bt, Rmajor, Rminor, q);
SAVE_ONCE4(Te0, Ti0, n0, B0);
SAVE_ONCE2(A, Z)
SAVE_ONCE3(lconn, lblob, Mach);
SAVE_ONCE(neoclass_correction_factor);
// ramp up ion temperatures
OPTION(opt_hesel, rampup_ti0_timax, Ti0);
OPTION(opt_hesel, rampup_ti0_time, 0.);
SAVE_ONCE2(rampup_ti0_timax, rampup_ti0_time);
// regions separating parameters
OPTION(opt_hesel, x_lcfs, 0.33333);
OPTION(opt_hesel, x_wall, 0.66666);
lcfs_ind = (mesh->GlobalNx - 2*mesh->xstart) * x_lcfs + mesh->xstart;
SAVE_ONCE2(x_lcfs, x_wall);
// curvature operator
curvature_coeff = 1;
if (double_curvature_coeff){
curvature_coeff = 2;
}
// dump calculated parameters
oci = HeselPara.oci();
nuii = HeselPara.nuii();
nuei = HeselPara.nuei();
nuee = HeselPara.nuee();
rhoe = HeselPara.rhoe();
rhos = HeselPara.rhos();
SAVE_ONCE(oci);
SAVE_ONCE3(nuii, nuei, nuee);
SAVE_ONCE2(rhoe, rhos);
// *****************************************************************************
output << "+++++++++++++++++++++++++++++++++++++++++++++++++++++++" << endl;
// warning message for blob testing
if (test_blob){
output << ">>>>>>> [WARNING]: BLOB TESTING IS TURNED ON!" << endl;
}
// warning message for Laplace testing
if (test_laplace){
output << ">>>>>>> [WARNING]: LAPLACE TESTING IS TURNED ON!" << endl;
}
// output for switches part 1
output << ">>>>>>> Use right-handed coordinate: " << bool2str(right_handed_coord) << endl;
output << ">>>>>>> Invert Omega star: " << bool2str(invert_w_star) << endl;
output << ">>>>>>> Interchange dynamics: " << bool2str(interchange_dynamics) << endl;
if (interchange_dynamics && test_vort_cross_term){
output << ">>>>>>> [WARNING]: cross term of vorticity equation in interchange dynamics is turned off!" << endl;
}
// output for perpendicular dynamics
output << ">>>>>>> Perpendicular dynamics: " << bool2str(perpendicular_dynamics) << endl;
if (perpendicular_dynamics){
// output for collisional models
switch (collisional_model){
case 0:{
collisional_model_enum = off;
output << ">>>>>>> 1) collisional model: off" << endl;
break;
}
case 1:{
collisional_model_enum = simple;
output << ">>>>>>> 1) collisional model: simple" << endl;
break;
}
case 2:{
collisional_model_enum = standard;
output << ">>>>>>> 1) collisional model: standard" << endl;
break;
}
case 3:{
collisional_model_enum = full;
output << ">>>>>>> 1) collisional model: full" << endl;
break;
}
default:{
throw BoutException("ERROR: Collisional model not recognized!\n");
}
}
output << ">>>>>>> 2) heat exchange: " << bool2str(perpend_heat_exchange) << endl;
output << ">>>>>>> 3) viscous heating: " << bool2str(perpend_viscous_heating) << endl;
output << ">>>>>>> 4) hyper diffusion: " << bool2str(perpend_hyper_diffusion) << endl;
output << ">>>>>>> 5) approx of ti/te: " << ti_over_te << endl;
output << ">>>>>>> 6) diffusion coeff: " << diffusion_coeff << endl;
output << ">>>>>>> 7) Qdelta approx: " << qdelta_approx << endl;
}
// output for parallel dynamics
output << ">>>>>>> Parallel dynamics: " << bool2str(parallel_dynamics) << endl;
if (parallel_dynamics){
output << ">>>>>>> 1) sheath : " << parallel_sheath_damping << endl;
output << ">>>>>>> 2) advection : " << parallel_advection_damping << endl;
output << ">>>>>>> 3) conduction: " << parallel_conduction << endl;
output << ">>>>>>> 4) drift wave: " << parallel_drift_wave << endl;
output << ">>>>>>> 5) rcp approx: " << reciprocal_approx << endl;
}
// output for switches part 2
output << ">>>>>>> Plasma neutral interactions: " << bool2str(plasma_neutral_interactions) << endl;
output << ">>>>>>> Kinetic Plasma neutral interactions: " << bool2str(kinetic_plasma_neutral_interactions) << endl;
output << ">>>>>>> Plasma parallel transport: " << bool2str(parallel_transport) << endl;
output << ">>>>>>> Force profiles: " << bool2str(force_profiles) << endl;
output << ">>>>>>> Floor profiles: " << bool2str(floor_profiles) << endl;
output << ">>>>>>> Ramp up Ti0: " << bool2str(rampup_ti0) << endl;
// output for static plasma
static_n = static_plasma & 1;
static_pe = static_plasma & 2;
static_pi = static_plasma & 4;
static_vort = static_plasma & 8;
static_te = static_plasma & 16;
static_ti = static_plasma & 32;
if (static_plasma == 0){
output << ">>>>>>> Static plasma: " << bool2str(false) << endl;
}else{
if (static_pi && static_ti){
throw BoutException("ti and pi can not be both static, please set n and ti static instead!");
}
if (static_pe && static_te){
throw BoutException("te and pe can not be both static, please set n and ti static instead!");
}
output << ">>>>>>> Static plasma: | n | pe | pi | vort | te | ti |" << endl;
output << " | ";
output << static_n;
output << " | "<< static_pe;
output << " | "<< static_pi;
output << " | "<< static_vort;
output << " | " << static_te;
output << " | " << static_ti;
output << " |" << endl;
}
// output for ramping up init profiles
rampup_init_n = rampup_init_prof & 1;
rampup_init_pe = rampup_init_prof & 2;
rampup_init_pi = rampup_init_prof & 4;
if (rampup_init_prof == 0){
output << ">>>>>>> Ramp up Initial Profiles: " << bool2str(false) << endl;
}else{
output << ">>>>>>> Ramp up Initial Profiles: | n | pe | pi |" << endl;
output << " | ";
output << rampup_init_n;
output << " | "<< rampup_init_pe;
output << " | "<< rampup_init_pi;
output << " |" << endl;
}
// output for diagnostics
diag_thermal_para_ad = diag_thermal & 1;
diag_thermal_para_sh = diag_thermal & 2;
diag_thermal_perp_neo = diag_thermal & 4;
diag_thermal_perp_turb = diag_thermal & 8;
output << ">>>>>>> Diagnostics: " << bool2str(diagnostics) << endl;
if (diagnostics) {
output << ">>>>>>> 1) thermal energy (ad, sh, neo, turb): " <<
bool2int(diag_thermal_para_ad) <<
bool2int(diag_thermal_para_sh) <<
bool2int(diag_thermal_perp_neo) <<
bool2int(diag_thermal_perp_turb) << endl;
}
// output for bracket methods
switch(bracket_method) {
case 0: {
bracket_method_enum = BRACKET_STD;
output << ">>>>>>> Brackets for ExB: default differencing" << endl;
break;
}
case 1: {
bracket_method_enum = BRACKET_SIMPLE;
output << ">>>>>>> Brackets for ExB: simplified operator" << endl;
break;
}
case 2: {
bracket_method_enum = BRACKET_ARAKAWA;
output << ">>>>>>> Brackets for ExB: Arakawa scheme" << endl;
break;
}
case 3: {
bracket_method_enum = BRACKET_CTU;
output << ">>>>>>> Brackets for ExB: Corner Transport Upwind method" << endl;
break;
}
default:
throw BoutException("ERROR: Invalid choice of bracket method. Must be 0 - 3!\n");
}
// print parameters
output << endl;
HeselPara.printvalues(); //print to standard output
output << "+++++++++++++++++++++++++++++++++++++++++++++++++++++++" << endl;
return 0;
}
int hesel::InitMagneticField(){
//Calculate magnetic field - gyro-Bohm normalized
TRACE("Initialize magnetic field");
B.allocate();
invR.allocate();
for (auto i:B){
invR[i] = 1. / ( HeselPara.R() + HeselPara.a()
+ HeselPara.rhos() * mesh->getCoordinates()->dx[i]
* (mesh->GlobalNx * mesh->GlobalX(i.x()) - lcfs_ind) );
B[i] = (HeselPara.R()+HeselPara.a()) * invR[i];
}
SAVE_ONCE(B);
invB = 1./B;
return 0;
}
int hesel::InitFieldGroups(){
//parallel communication of fields
field_group_ln.add(lnn, lnpe, lnpi);
field_group_ddt.add(ddt_lnn, ddt_lnpe, ddt_lnpi, ddt_vort);
field_group_phyd.add(n, pe, pi, te, ti, lnte, lnti, csHot, tau);
field_group_gradp.add(gradp_phi, gradp_pi);
field_group_gradp.add(gradp_lnn, gradp_lnte, gradp_lnti);
field_group_avg.add(avg_n, avg_te, avg_phi, avg_csHot, avg_tau);
field_group_pert.add(pert_n, pert_te, pert_phi);
return 0;
}
int hesel::InitIntialProfiles(){
TRACE("Load initial profiles");
// read initial profiles
if (use_grid_file){
mesh->get(init_n, "init_n" );
mesh->get(init_pe, "init_pe");
mesh->get(init_pi, "init_pi");
} else {
initial_profile("init_n", init_n);
initial_profile("init_pe", init_pe);
initial_profile("init_pi", init_pi);
}
initial_profile("seed_n", seed_n);
initial_profile("seed_pe", seed_pe);
initial_profile("seed_pi", seed_pi);
// Check for negatives
if (min(init_n, true) < 0.0) {
throw BoutException("Starting density is negative");
}
if (min(init_pe, true) < 0.0) {
throw BoutException("Starting electron pressure is negative");
}
if (min(init_pi, true) < 0.0) {
throw BoutException("Starting ion pressure is negative");
}
if (min(seed_n, true) < 0.0) {
throw BoutException("Starting density perturbation is negative");
}
// save initial profiles
if (!rampup_init_prof){
SAVE_ONCE(init_n);
SAVE_ONCE(init_pe);
SAVE_ONCE(init_pi);
}
SAVE_ONCE3(seed_n, seed_pe, seed_pi);
// gather inner edge value
n_inner = init_n (0,0);
pe_inner = init_pe(0,0);
pi_inner = init_pi(0,0);
// derived initial variables
init_te = init_pe/init_n;
init_ti = init_pi/init_n;
return 0;
}
int hesel::InitRampInitProfiles(){
TRACE("Initialize process of ramping up initial profiles");
if (rampup_init_prof){
init_n0 = 0; init_pe0 = 0; init_pi0 = 0;
init_n_fake = 0; init_pe_fake = 0; init_pi_fake = 0;
for (auto i:init_n){
init_n0[i] = init_n[i];
init_pe0[i] = init_pe[i];
init_pi0[i] = init_pi[i];
init_n_fake[i] = init_n[i];
init_pe_fake[i] = init_pe[i];
init_pi_fake[i] = init_pi[i];
if (rampup_init_n && init_n_fake[i] > 1) {init_n_fake[i] = 1.;}
if (rampup_init_pe && init_pe_fake[i] > 1) {init_pe_fake[i] = 1.;}
if (rampup_init_pi && init_pi_fake[i] > 1) {init_pi_fake[i] = 1.;}
}
dump.add(init_n0, "init_n", 0);
dump.add(init_pe0, "init_pe", 0);
dump.add(init_pi0, "init_pi", 0);
RhsRampInitProfiles(0);
}
return 0;
}
int hesel::InitEvolvingFields(){
///Fields that are time-integrated.
///Time integrated fields are saved to datafile automatically
SOLVE_FOR3(lnn, lnpe, lnpi);
SOLVE_FOR(vort);
lnn = log(init_n + seed_n);
lnpe = log(init_pe + seed_pe);
lnpi = log(init_pi + seed_pi);
lnte = lnpe - lnn;
lnti = lnpi - lnn;
if(init_zero_potential){
vort = Laplace_perp(init_pi + seed_pi);
}
return 0;
}
int hesel::InitOtherFields(){
// initialize physical and derived fields
CalculateFieldGroupPhyd();
if(!compact_output){
SAVE_REPEAT5(n, pe, pi, te, ti);
}
//step functions for open and closed field lines and for forcing profiles
initial_profile("sigma_open", sigma_open);
initial_profile("sigma_closed", sigma_closed);
initial_profile("sigma_force", sigma_force);
SAVE_ONCE(sigma_open);
SAVE_ONCE(sigma_closed);
SAVE_ONCE(sigma_force);
return 0;
}
int hesel::InitPhiSolver(){
//INITIALIZE Laplace inversion
phiSolver = Laplacian::create();
phiSolver->setCoefA(0.);
// initialize phi related fields
phi = 0.; // Starting phi
if(!compact_output){
SAVE_REPEAT(phi);
}
if (invert_w_star){
phi_star = phi;
if(!compact_output){
SAVE_REPEAT(phi_star);
}
// }else{
// evort = Delp2(phi);
// delpi = Delp2(pi);
// mesh->communicate(evort, delpi);
// SAVE_REPEAT2(evort, delpi);
}
// vort = 0.;// has to be zero, now set by input file
// laplace testing
if(test_laplace){
vort_residual = 0.;
if(!compact_output){
SAVE_REPEAT(vort_residual);
}
}
return 0;
}
int hesel::InitDiagnostics(){
TRACE("Initialize diagnostics!");
if (diagnostics) {
// ExB drift velocity
Calculate_uExB();
if(!compact_output){
SAVE_REPEAT(uExB);
}
// thermal diagnostics
if (diag_thermal_para_ad){
qe_para_advection = 0.;
qi_para_advection = 0.;
//if(!compact_output){
// SAVE_REPEAT2(qe_para_advection, qi_para_advection);
//}
avg__qe_para_advection = 0.;
avg__qi_para_advection = 0.;
SAVE_REPEAT2(avg__qe_para_advection, avg__qi_para_advection);
}
if (diag_thermal_para_sh){
qe_para_conduction = 0.;
qi_para_conduction = 0.;
//if(!compact_output){
// SAVE_REPEAT2(qe_para_conduction, qi_para_conduction);
//}
avg__qe_para_conduction = 0.;
avg__qi_para_conduction = 0.;
SAVE_REPEAT2(avg__qe_para_conduction, avg__qi_para_conduction);
}
if (diag_thermal_perp_neo){
qe_perp_neoclassic = 0.;
qi_perp_neoclassic = 0.;
//if(!compact_output){
// SAVE_REPEAT2(qe_perp_neoclassic, qi_perp_neoclassic);
//}
avg__qe_perp_neoclassic = 0.;
avg__qi_perp_neoclassic = 0.;
SAVE_REPEAT2(avg__qe_perp_neoclassic, avg__qi_perp_neoclassic);
}
if (diag_thermal_perp_turb){
qe_perp_turbulence = 0.;
qi_perp_turbulence = 0.;
//if(!compact_output){
// SAVE_REPEAT2(qe_perp_turbulence, qi_perp_turbulence);
//}
avg__qe_perp_turbulence = 0.;
avg__qi_perp_turbulence = 0.;
SAVE_REPEAT2(avg__qe_perp_turbulence, avg__qi_perp_turbulence);
}
// particle flux diagnostics
if (diag_particle_flux){
part_turb_flux = 0.;
part_diff_flux = 0.;
avg__part_turb_flux = 0.;
avg__part_diff_flux = 0.;
SAVE_REPEAT2(avg__part_turb_flux, avg__part_diff_flux);
}
}
return 0;
}
int hesel::InitNeutrals(){
if (plasma_neutral_interactions){
SOLVE_FOR3(neutrals.lnNcold,neutrals.lnNwarm,neutrals.lnNhot);
SOLVE_FOR(neutrals.lnNhelium);
neutrals.InitNeutrals();
}
return 0;
}
int hesel::InitParallel(){
if (parallel_transport){
SOLVE_FOR2(parallel.ue_parl, parallel.ui_parl);
parallel.InitParallel();
}
return 0;
}
int hesel::InitKineticNeutrals(bool restart){
if (kinetic_plasma_neutral_interactions){
kinetic_neutrals.InitKineticNeutrals(restart);
}
return 0;
}
//******************************************************************************
int hesel::RhsEvolvingFieldsStart(){
ddt_lnn = 0.;
ddt_lnpe = 0.;
ddt_lnpi = 0.;
ddt_vort = 0.;
mesh->communicate(field_group_ln);
mesh->communicate(vort);
return 0;
}
int hesel::RhsInterchangeDynamics(){
TRACE("Interchange dynamics");
if (interchange_dynamics){
// particle density
ddt_lnn +=
- invB*Brackets(phi,lnn)
- C(phi)
+ C(te)
+ C(lnn)*te;
// electron pressure
ddt_lnpe +=
- invB*Brackets(phi,lnpe)
- 5./3.*C(phi)
+ 5./3.*C(te)
+ 5./3.*C(lnpe)*te;
// ion pressure
ddt_lnpi +=
- invB*Brackets(phi,lnpi)
- 5./3.*C(phi)
- 5./3.*C(ti)
- 5./3.*C(lnpi)*ti
+ 2./3.*C(pe+pi);
// vorticity
ddt_vort +=
- Brackets(phi, vort)
+ C(pe+pi);
// cross term of vorticity
if (!test_vort_cross_term){
ddt_vort +=
- Brackets(gradp_phi.x,gradp_pi.x)
- Brackets(gradp_phi.z,gradp_pi.z);
}
}
return 0;
}
int hesel::RhsPerpendicularDynamics(){
TRACE("Perpendicular dynamics");
if (perpendicular_dynamics){
// calculate ti_rcpte
switch (ti_over_te){
case 1:{
ti_rcpte = HeselPara.tau();
break;
}
case 2:{
ti_rcpte = avg_tau; // [approx]
break;
}
case 3:{
ti_rcpte = tau; // [approx]
break;
}
default:{
throw BoutException("no support settings for ti_over_te\n");
}
}
// neo-classical collisions
switch(collisional_model_enum){
case off:{
break;
}
case simple:{
RhsCollisionalSimple();
break;
}
case standard:{
CalculateDiffusionCoeff();
Calculate_uR(0);
RhsCollisionalStandard();
break;
}
case full:{
CalculateDiffusionCoeff();
Calculate_uR(1);
RhsCollisionalFull();
break;
}
default:{
throw BoutException("Collisional model not recognized\n");
}
}
// electron-ion heat exchanging
if (perpend_heat_exchange){
Qresist_Rcppi = uR*(gradp_lnn + gradp_lnti);// UR*gradp_pi/pi, heat exchange term due to resistivity, J. Madsen Equation 42
switch (qdelta_approx){
case 0:{
Qdelta_Rcppe = 0.;
break;
}
case 1:{
Qdelta_Rcppe = 3*HeselPara.me()/HeselPara.mi()*HeselPara.nnuei()*(1-ti_rcpte);// [approx], Qdelta/pe, heat exchange term due to elastic collisions, J. Madsen Equation 26
break;
}
case 2:{
Qdelta_Rcppe = 3*HeselPara.me()/HeselPara.mi()*HeselPara.nnuei()*(1-ti_rcpte) * avg_n / avg_te / sqrt(avg_te); // [approx]
break;
}
case 3:{
Qdelta_Rcppe = 3*HeselPara.me()/HeselPara.mi()*HeselPara.nnuei()*(1-ti_rcpte) * n / te / sqrt(te); // [division]
break;
}
case 4:{
Qdelta_Rcppe = 3*HeselPara.me()/HeselPara.mi()*HeselPara.nnuei()*(1-ti_rcpte) * n / avg_te / sqrt(avg_te); // [approx]
break;
}
default:{
throw BoutException("Qdelta approximation is not recognized\n");
}
}
ddt_lnpe +=
- 2./3. * Qresist_Rcppi* ti_rcpte
- 2./3. * Qdelta_Rcppe;
ddt_lnpi +=
+ 2./3. * Qresist_Rcppi
+ 2./3. * Qdelta_Rcppe / ti_rcpte; // [division]
}
// ion viscous heating
if (perpend_viscous_heating){
Qviscous = 3./10. * Di*( pow(D2DX2(phi+pi)-D2DZ2(phi+pi),2)+4*pow(D2DXDZ(phi+pi),2) )/ti; // [division]
// Qviscous = HeselPara.normEta()*( pow(D2DX2(phi+pi)-D2DZ2(phi+pi),2)+4*pow(D2DXDZ(phi+pi),2) ); // [approx], not approximate n*Ti in eta, approximate nuii
mesh->communicate(Qviscous);
ddt_lnpi += 2./3. * Qviscous;
}
// hyper diffusion
if (perpend_hyper_diffusion){
if (hyper_order == 4) {
ddt_lnn +=
- hyper_dc_n * Dn * Delp4(n)/avg_n;
ddt_lnpe +=
- 2./3. * hyper_dc_pe * Dn * Delp4(pe)/avg_n/avg_te;
ddt_lnpi +=
- 2./3. * hyper_dc_pi * 5./2.*Dn * Delp4(pi)/avg_n/avg_ti;
ddt_vort +=
- hyper_dc_vort * HeselPara.normEta() * Delp4(vort);
} else if (hyper_order == 6) {
ddt_lnn +=
+ hyper_dc_n * Dn * Delp6(n)/avg_n;
ddt_lnpe +=
+ 2./3. * hyper_dc_pe * Dn * Delp6(pe)/avg_n/avg_te;
ddt_lnpi +=
+ 2./3. * hyper_dc_pi * 5./2.*Dn * Delp6(pi)/avg_n/avg_ti;
ddt_vort +=