Sim1D.cpp

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/**
 * @file Sim1D.cpp
 */
 
// This file is part of Cantera. See License.txt in the top-level directory or
// at https://cantera.org/license.txt for license and copyright information.
 
#include "cantera/oneD/Sim1D.h"
#include "cantera/oneD/MultiJac.h"
#include "cantera/oneD/StFlow.h"
#include "cantera/oneD/MultiNewton.h"
#include "cantera/oneD/refine.h"
#include "cantera/numerics/funcs.h"
#include "cantera/base/xml.h"
#include "cantera/base/stringUtils.h"
#include "cantera/numerics/Func1.h"
#include <limits>
#include <fstream>
 
using namespace std;
 
namespace Cantera
{
 
Sim1D::Sim1D(vector<Domain1D*>& domains) :
    OneDim(domains),
    m_steady_callback(0)
{
    // resize the internal solution vector and the work array, and perform
    // domain-specific initialization of the solution vector.
    resize();
    for (size_t n = 0; n < nDomains(); n++) {
        domain(n)._getInitialSoln(&m_x[start(n)]);
    }
 
    // set some defaults
    m_tstep = 1.0e-5;
    m_steps = { 10 };
}
 
void Sim1D::setInitialGuess(const std::string& component, vector_fp& locs, vector_fp& vals)
{
    for (size_t dom=0; dom<nDomains(); dom++) {
        Domain1D& d = domain(dom);
        size_t ncomp = d.nComponents();
        for (size_t comp=0; comp<ncomp; comp++) {
            if (d.componentName(comp)==component) {
                setProfile(dom,comp,locs,vals);
            }
        }
    }
}
 
void Sim1D::setValue(size_t dom, size_t comp, size_t localPoint, doublereal value)
{
    size_t iloc = domain(dom).loc() + domain(dom).index(comp, localPoint);
    AssertThrowMsg(iloc < m_x.size(), "Sim1D::setValue",
                   "Index out of bounds: {} > {}", iloc, m_x.size());
    m_x[iloc] = value;
}
 
doublereal Sim1D::value(size_t dom, size_t comp, size_t localPoint) const
{
    size_t iloc = domain(dom).loc() + domain(dom).index(comp, localPoint);
    AssertThrowMsg(iloc < m_x.size(), "Sim1D::value",
                   "Index out of bounds: {} > {}", iloc, m_x.size());
    return m_x[iloc];
}
 
doublereal Sim1D::workValue(size_t dom, size_t comp, size_t localPoint) const
{
    size_t iloc = domain(dom).loc() + domain(dom).index(comp, localPoint);
    AssertThrowMsg(iloc < m_x.size(), "Sim1D::workValue",
                   "Index out of bounds: {} > {}", iloc, m_x.size());
    return m_xnew[iloc];
}
 
void Sim1D::setProfile(size_t dom, size_t comp,
                       const vector_fp& pos, const vector_fp& values)
{
    if (pos.front() != 0.0 || pos.back() != 1.0) {
        throw CanteraError("Sim1D::setProfile",
            "`pos` vector must span the range [0, 1]. Got a vector spanning "
            "[{}, {}] instead.", pos.front(), pos.back());
    }
    Domain1D& d = domain(dom);
    doublereal z0 = d.zmin();
    doublereal z1 = d.zmax();
    for (size_t n = 0; n < d.nPoints(); n++) {
        double zpt = d.z(n);
        double frac = (zpt - z0)/(z1 - z0);
        double v = linearInterp(frac, pos, values);
        setValue(dom, comp, n, v);
    }
}
 
void Sim1D::save(const std::string& fname, const std::string& id,
                 const std::string& desc, int loglevel)
{
    size_t dot = fname.find_last_of(".");
    string extension = (dot != npos) ? toLowerCopy(fname.substr(dot+1)) : "";
    if (extension != "yml" && extension != "yaml") {
        OneDim::save(fname, id, desc, m_x.data(), loglevel);
        return;
    }
 
    // Check for an existing file and load it if present
    AnyMap data;
    if (ifstream(fname).good()) {
        data = AnyMap::fromYamlFile(fname);
    }
    bool preexisting = data.hasKey(id);
 
    // Add this simulation to the YAML
    data[id] = serialize(m_x.data());
 
    // Add metadata
    data[id]["description"] = desc;
    data[id]["generator"] = "Cantera Sim1D";
    data[id]["cantera-version"] = CANTERA_VERSION;
    data[id]["git-commit"] = gitCommit();
 
    // Add a timestamp indicating the current time
    time_t aclock;
    ::time(&aclock); // Get time in seconds
    struct tm* newtime = localtime(&aclock); // Convert time to struct tm form
    data[id]["date"] = stripnonprint(asctime(newtime));
 
    // Force metadata fields to the top of the file
    data[id]["description"].setLoc(-6, 0);
    data[id]["generator"].setLoc(-5, 0);
    data[id]["cantera-version"].setLoc(-4, 0);
    data[id]["git-commit"].setLoc(-3, 0);
    data[id]["date"].setLoc(-2, 0);
 
    // If this is not replacing an existing solution, put it at the end
    if (!preexisting) {
        data[id].setLoc(INT_MAX, 0);
    }
 
    // Write the output file and remove the now-outdated cached file
    std::ofstream out(fname);
    out << data.toYamlString();
    AnyMap::clearCachedFile(fname);
    if (loglevel > 0) {
        writelog("Solution saved to file {} as solution '{}'.\n", fname, id);
    }
}
 
void Sim1D::saveResidual(const std::string& fname, const std::string& id,
                         const std::string& desc, int loglevel)
{
    vector_fp res(m_x.size(), -999);
    OneDim::eval(npos, &m_x[0], &res[0], 0.0);
    // Temporarily put the residual into m_x, since this is the vector that the save()
    // function reads.
    std::swap(res, m_x);
    save(fname, id, desc, loglevel);
    std::swap(res, m_x);
}
 
void Sim1D::restore(const std::string& fname, const std::string& id,
                    int loglevel)
{
    size_t dot = fname.find_last_of(".");
    string extension = (dot != npos) ? toLowerCopy(fname.substr(dot+1)) : "";
    if (extension == "yml" || extension == "yaml") {
        AnyMap root = AnyMap::fromYamlFile(fname);
        if (!root.hasKey(id)) {
            throw InputFileError("Sim1D::restore", root,
                                 "No solution with id '{}'", id);
        }
        const auto& state = root[id];
        for (auto dom : m_dom) {
            if (!state.hasKey(dom->id())) {
                throw InputFileError("Sim1D::restore", state,
                    "Saved state '{}' does not contain a domain named '{}'.",
                    id, dom->id());
            }
            dom->resize(dom->nComponents(), state[dom->id()]["points"].asInt());
        }
        resize();
        m_xlast_ts.clear();
        for (auto dom : m_dom) {
            dom->restore(state[dom->id()].as<AnyMap>(), m_x.data() + dom->loc(),
                         loglevel);
        }
    } else {
        XML_Node root;
        root.build(fname);
 
        XML_Node* f = root.findID(id);
        if (!f) {
            throw CanteraError("Sim1D::restore","No solution with id = "+id);
        }
 
        vector<XML_Node*> xd = f->getChildren("domain");
        if (xd.size() != nDomains()) {
            throw CanteraError("Sim1D::restore", "Solution does not contain the "
                " correct number of domains. Found {} expected {}.\n",
                xd.size(), nDomains());
        }
        for (size_t m = 0; m < nDomains(); m++) {
            Domain1D& dom = domain(m);
            if (loglevel > 0 && xd[m]->attrib("id") != dom.id()) {
                warn_user("Sim1D::restore", "Domain names do not match: "
                    "'{} and '{}'", (*xd[m])["id"], dom.id());
            }
            dom.resize(domain(m).nComponents(), intValue((*xd[m])["points"]));
        }
        resize();
        m_xlast_ts.clear();
        for (size_t m = 0; m < nDomains(); m++) {
            domain(m).restore(*xd[m], &m_x[start(m)], loglevel);
        }
    }
    finalize();
}
 
void Sim1D::setFlatProfile(size_t dom, size_t comp, doublereal v)
{
    size_t np = domain(dom).nPoints();
    for (size_t n = 0; n < np; n++) {
        setValue(dom, comp, n, v);
    }
}
 
void Sim1D::showSolution(ostream& s)
{
    for (size_t n = 0; n < nDomains(); n++) {
        if (domain(n).domainType() != cEmptyType) {
            domain(n).showSolution_s(s, &m_x[start(n)]);
        }
    }
}
 
void Sim1D::showSolution()
{
    for (size_t n = 0; n < nDomains(); n++) {
        if (domain(n).domainType() != cEmptyType) {
            writelog("\n\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "+domain(n).id()
                     +" <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n\n");
            domain(n).showSolution(&m_x[start(n)]);
        }
    }
}
 
void Sim1D::restoreTimeSteppingSolution()
{
    if (m_xlast_ts.empty()) {
        throw CanteraError("Sim1D::restoreTimeSteppingSolution",
                           "No successful time steps taken on this grid.");
    }
    m_x = m_xlast_ts;
}
 
void Sim1D::restoreSteadySolution()
{
    if (m_xlast_ss.empty()) {
        throw CanteraError("Sim1D::restoreSteadySolution",
                           "No successful steady state solution");
    }
    m_x = m_xlast_ss;
    for (size_t n = 0; n < nDomains(); n++) {
        vector_fp& z = m_grid_last_ss[n];
        domain(n).setupGrid(z.size(), z.data());
    }
}
 
void Sim1D::getInitialSoln()
{
    for (size_t n = 0; n < nDomains(); n++) {
        domain(n)._getInitialSoln(&m_x[start(n)]);
    }
}
 
void Sim1D::finalize()
{
    for (size_t n = 0; n < nDomains(); n++) {
        domain(n)._finalize(&m_x[start(n)]);
    }
}
 
void Sim1D::setTimeStep(double stepsize, size_t n, const int* tsteps)
{
    m_tstep = stepsize;
    m_steps.resize(n);
    for (size_t i = 0; i < n; i++) {
        m_steps[i] = tsteps[i];
    }
}
 
int Sim1D::newtonSolve(int loglevel)
{
    int m = OneDim::solve(m_x.data(), m_xnew.data(), loglevel);
    if (m >= 0) {
        m_x = m_xnew;
        return 0;
    } else if (m > -10) {
        return -1;
    } else {
        throw CanteraError("Sim1D::newtonSolve",
                           "ERROR: OneDim::solve returned m = {}", m);
    }
}
 
void Sim1D::solve(int loglevel, bool refine_grid)
{
    int new_points = 1;
    doublereal dt = m_tstep;
    m_nsteps = 0;
    int soln_number = -1;
    finalize();
 
    while (new_points > 0) {
        size_t istep = 0;
        int nsteps = m_steps[istep];
 
        bool ok = false;
        if (loglevel > 0) {
            writeline('.', 78, true, true);
        }
        while (!ok) {
            // Attempt to solve the steady problem
            setSteadyMode();
            newton().setOptions(m_ss_jac_age);
            debuglog("Attempt Newton solution of steady-state problem...", loglevel);
            int status = newtonSolve(loglevel-1);
 
            if (status == 0) {
                if (loglevel > 0) {
                    writelog("    success.\n\n");
                    writelog("Problem solved on [");
                    for (size_t mm = 1; mm < nDomains(); mm+=2) {
                        writelog("{}", domain(mm).nPoints());
                        if (mm + 2 < nDomains()) {
                            writelog(", ");
                        }
                    }
                    writelog("] point grid(s).\n");
                }
                if (m_steady_callback) {
                    m_steady_callback->eval(0);
                }
 
                if (loglevel > 6) {
                    save("debug_sim1d.yaml", "debug",
                         "After successful Newton solve");
                }
                if (loglevel > 7) {
                    saveResidual("debug_sim1d.yaml", "residual",
                                 "After successful Newton solve");
                }
                ok = true;
                soln_number++;
            } else {
                debuglog("    failure. \n", loglevel);
                if (loglevel > 6) {
                    save("debug_sim1d.yaml", "debug",
                         "After unsuccessful Newton solve");
                }
                if (loglevel > 7) {
                    saveResidual("debug_sim1d.yaml", "residual",
                                 "After unsuccessful Newton solve");
                }
                if (loglevel > 0) {
                    writelog("Take {} timesteps   ", nsteps);
                }
                dt = timeStep(nsteps, dt, m_x.data(), m_xnew.data(),
                              loglevel-1);
                m_xlast_ts = m_x;
                if (loglevel > 6) {
                    save("debug_sim1d.yaml", "debug", "After timestepping");
                }
                if (loglevel > 7) {
                    saveResidual("debug_sim1d.yaml", "residual",
                                 "After timestepping");
                }
 
                if (loglevel == 1) {
                    writelog(" {:10.4g} {:10.4g}\n", dt,
                             log10(ssnorm(m_x.data(), m_xnew.data())));
                }
                istep++;
                if (istep >= m_steps.size()) {
                    nsteps = m_steps.back();
                } else {
                    nsteps = m_steps[istep];
                }
                dt = std::min(dt, m_tmax);
            }
        }
        if (loglevel > 0) {
            writeline('.', 78, true, true);
        }
        if (loglevel > 2) {
            showSolution();
        }
 
        if (refine_grid) {
            new_points = refine(loglevel);
            if (new_points) {
                // If the grid has changed, preemptively reduce the timestep
                // to avoid multiple successive failed time steps.
                dt = m_tstep;
            }
            if (new_points && loglevel > 6) {
                save("debug_sim1d.yaml", "debug", "After regridding");
            }
            if (new_points && loglevel > 7) {
                saveResidual("debug_sim1d.yaml", "residual",
                             "After regridding");
            }
        } else {
            debuglog("grid refinement disabled.\n", loglevel);
            new_points = 0;
        }
    }
}
 
int Sim1D::refine(int loglevel)
{
    int ianalyze, np = 0;
    vector_fp znew, xnew;
    std::vector<size_t> dsize;
 
    m_xlast_ss = m_x;
    m_grid_last_ss.clear();
 
    for (size_t n = 0; n < nDomains(); n++) {
        Domain1D& d = domain(n);
        Refiner& r = d.refiner();
 
        // Save the old grid corresponding to the converged solution
        m_grid_last_ss.push_back(d.grid());
 
        // determine where new points are needed
        ianalyze = r.analyze(d.grid().size(), d.grid().data(), &m_x[start(n)]);
        if (ianalyze < 0) {
            return ianalyze;
        }
 
        if (loglevel > 0) {
            r.show();
        }
 
        np += r.nNewPoints();
        size_t comp = d.nComponents();
 
        // loop over points in the current grid
        size_t npnow = d.nPoints();
        size_t nstart = znew.size();
        for (size_t m = 0; m < npnow; m++) {
            if (r.keepPoint(m)) {
                // add the current grid point to the new grid
                znew.push_back(d.grid(m));
 
                // do the same for the solution at this point
                for (size_t i = 0; i < comp; i++) {
                    xnew.push_back(value(n, i, m));
                }
 
                // now check whether a new point is needed in the interval to
                // the right of point m, and if so, add entries to znew and xnew
                // for this new point
                if (r.newPointNeeded(m) && m + 1 < npnow) {
                    // add new point at midpoint
                    double zmid = 0.5*(d.grid(m) + d.grid(m+1));
                    znew.push_back(zmid);
                    np++;
 
                    // for each component, linearly interpolate
                    // the solution to this point
                    for (size_t i = 0; i < comp; i++) {
                        double xmid = 0.5*(value(n, i, m) + value(n, i, m+1));
                        xnew.push_back(xmid);
                    }
                }
            } else {
                if (loglevel > 0) {
                    writelog("refine: discarding point at {}\n", d.grid(m));
                }
            }
        }
        dsize.push_back(znew.size() - nstart);
    }
 
    // At this point, the new grid znew and the new solution vector xnew have
    // been constructed, but the domains themselves have not yet been modified.
    // Now update each domain with the new grid.
 
    size_t gridstart = 0, gridsize;
    for (size_t n = 0; n < nDomains(); n++) {
        Domain1D& d = domain(n);
        gridsize = dsize[n];
        d.setupGrid(gridsize, &znew[gridstart]);
        gridstart += gridsize;
    }
 
    // Replace the current solution vector with the new one
    m_x = xnew;
    resize();
    finalize();
    return np;
}
 
int Sim1D::setFixedTemperature(double t)
{
    int np = 0;
    vector_fp znew, xnew;
    double zfixed = 0.0;
    double z1 = 0.0, z2 = 0.0;
    std::vector<size_t> dsize;
 
    for (size_t n = 0; n < nDomains(); n++) {
        Domain1D& d = domain(n);
        size_t comp = d.nComponents();
        size_t mfixed = npos;
 
        // loop over current grid to determine where new point is needed
        StFlow* d_free = dynamic_cast<StFlow*>(&domain(n));
        size_t npnow = d.nPoints();
        size_t nstart = znew.size();
        if (d_free && d_free->domainType() == cFreeFlow) {
            for (size_t m = 0; m < npnow - 1; m++) {
                bool fixedpt = false;
                double t1 = value(n, 2, m);
                double t2 = value(n, 2, m + 1);
                // threshold to avoid adding new point too close to existing point
                double thresh = min(1., 1.e-1 * (t2 - t1));
                z1 = d.grid(m);
                z2 = d.grid(m + 1);
                if (fabs(t - t1) <= thresh) {
                    zfixed = z1;
                    fixedpt = true;
                } else if (fabs(t2 - t) <= thresh) {
                    zfixed = z2;
                    fixedpt = true;
                } else if ((t1 < t) && (t < t2)) {
                    mfixed = m;
                    zfixed = (z1 - z2) / (t1 - t2) * (t - t2) + z2;
                    fixedpt = true;
                }
 
                if (fixedpt) {
                    d_free->m_zfixed = zfixed;
                    d_free->m_tfixed = t;
                    break;
                }
            }
        }
 
        // copy solution domain and push back values
        for (size_t m = 0; m < npnow; m++) {
            // add the current grid point to the new grid
            znew.push_back(d.grid(m));
 
            // do the same for the solution at this point
            for (size_t i = 0; i < comp; i++) {
                xnew.push_back(value(n, i, m));
            }
            if (m == mfixed) {
                // add new point at zfixed (mfixed is not npos)
                znew.push_back(zfixed);
                np++;
                double interp_factor = (zfixed - z2) / (z1 - z2);
                // for each component, linearly interpolate
                // the solution to this point
                for (size_t i = 0; i < comp; i++) {
                    double xmid = interp_factor*(value(n, i, m) - value(n, i, m+1)) + value(n,i,m+1);
                    xnew.push_back(xmid);
                }
            }
        }
        dsize.push_back(znew.size() - nstart);
    }
 
    // At this point, the new grid znew and the new solution vector xnew have
    // been constructed, but the domains themselves have not yet been modified.
    // Now update each domain with the new grid.
    size_t gridstart = 0;
    for (size_t n = 0; n < nDomains(); n++) {
        Domain1D& d = domain(n);
        size_t gridsize = dsize[n];
        d.setupGrid(gridsize, &znew[gridstart]);
        gridstart += gridsize;
    }
 
    // Replace the current solution vector with the new one
    m_x = xnew;
 
    resize();
    finalize();
    return np;
}
 
double Sim1D::fixedTemperature()
{
    double t_fixed = std::numeric_limits<double>::quiet_NaN();
    for (size_t n = 0; n < nDomains(); n++) {
        StFlow* d = dynamic_cast<StFlow*>(&domain(n));
        if (d && d->domainType() == cFreeFlow && d->m_tfixed > 0) {
            t_fixed = d->m_tfixed;
            break;
        }
    }
    return t_fixed;
}
 
double Sim1D::fixedTemperatureLocation()
{
    double z_fixed = std::numeric_limits<double>::quiet_NaN();
    for (size_t n = 0; n < nDomains(); n++) {
        StFlow* d = dynamic_cast<StFlow*>(&domain(n));
        if (d && d->domainType() == cFreeFlow && d->m_tfixed > 0) {
            z_fixed = d->m_zfixed;
            break;
        }
    }
    return z_fixed;
}
 
void Sim1D::setRefineCriteria(int dom, double ratio,
                              double slope, double curve, double prune)
{
    if (dom >= 0) {
        Refiner& r = domain(dom).refiner();
        r.setCriteria(ratio, slope, curve, prune);
    } else {
        for (size_t n = 0; n < nDomains(); n++) {
            Refiner& r = domain(n).refiner();
            r.setCriteria(ratio, slope, curve, prune);
        }
    }
}
 
vector_fp Sim1D::getRefineCriteria(int dom)
{
   if (dom >= 0) {
       Refiner& r = domain(dom).refiner();
       return r.getCriteria();
   } else {
       throw CanteraError("Sim1D::getRefineCriteria",
           "Must specify domain to get criteria from");
   }
}
 
void Sim1D::setGridMin(int dom, double gridmin)
{
    if (dom >= 0) {
        Refiner& r = domain(dom).refiner();
        r.setGridMin(gridmin);
    } else {
        for (size_t n = 0; n < nDomains(); n++) {
            Refiner& r = domain(n).refiner();
            r.setGridMin(gridmin);
        }
    }
}
 
void Sim1D::setMaxGridPoints(int dom, int npoints)
{
    if (dom >= 0) {
        Refiner& r = domain(dom).refiner();
        r.setMaxPoints(npoints);
    } else {
        for (size_t n = 0; n < nDomains(); n++) {
            Refiner& r = domain(n).refiner();
            r.setMaxPoints(npoints);
        }
    }
}
 
size_t Sim1D::maxGridPoints(size_t dom)
{
    Refiner& r = domain(dom).refiner();
    return r.maxPoints();
}
 
doublereal Sim1D::jacobian(int i, int j)
{
    return OneDim::jacobian().value(i,j);
}
 
void Sim1D::evalSSJacobian()
{
    OneDim::evalSSJacobian(m_x.data(), m_xnew.data());
}
 
void Sim1D::solveAdjoint(const double* b, double* lambda)
{
    for (auto& D : m_dom) {
        D->forceFullUpdate(true);
    }
    evalSSJacobian();
    for (auto& D : m_dom) {
        D->forceFullUpdate(false);
    }
 
    // Form J^T
    size_t bw = bandwidth();
    BandMatrix Jt(size(), bw, bw);
    for (size_t i = 0; i < size(); i++) {
        size_t j1 = (i > bw) ? i - bw : 0;
        size_t j2 = (i + bw >= size()) ? size() - 1: i + bw;
        for (size_t j = j1; j <= j2; j++) {
            Jt(j,i) = m_jac->value(i,j);
        }
    }
 
    Jt.solve(b, lambda);
}
 
void Sim1D::resize()
{
    OneDim::resize();
    m_x.resize(size(), 0.0);
    m_xnew.resize(size(), 0.0);
}
 
}