eonc::OHTSTJob Class Reference

#include <OHTSTJob.h>

Inheritance diagram for eonc::OHTSTJob:

Classes
struct	PlaneAverages

Public Member Functions
	OHTSTJob (std::unique_ptr< Parameters > parameters, Runtime &rt)
	~OHTSTJob (void)=default
std::vector< std::string >	run (void)
	Virtual run; used solely for dynamic dispatch.
Public Member Functions inherited from eonc::Job
void	adoptRuntime (std::unique_ptr< Runtime > rt)
	Take ownership of a Runtime previously passed as Runtime&.
	Job (std::unique_ptr< Parameters > parameters, Runtime &rt)
	Borrow: caller keeps Runtime alive (CLI stack / Python Session).
	Job (std::unique_ptr< Parameters > parameters, std::unique_ptr< Runtime > rt)
	Own a Runtime (one-shot makeJob / rvalue).
	Job (std::unique_ptr< Parameters > parameters)
	Own a default-constructed Runtime.
	Job (std::shared_ptr< Potential > potPassed, const Parameters &parameters)
virtual	~Job ()=default
JobType	getType ()
PotRegistry &	pots () noexcept
void	releasePotential ()
	Drop the Potential so on_destroyed is recorded before Runtime dies.

Private Member Functions
PlaneAverages	samplePlane (Matter &matter, VectorXd &x, const VectorXd &gamma, const VectorXd &normal)
double	reactantQRatio (Matter &matter, const VectorXd &gammaR, const VectorXd &normal)
void	drawThermalVelocities (VectorXd &vel, const VectorXd *normal)
bool	symmetryReflect (const VectorXd &xR, VectorXd &x, VectorXd &v, const VectorXd &xOld, const VectorXd *normal)
double	uniformDraw ()
	uniform (0,1)
double	gaussDraw ()
	standard normal (Box-Muller)

Private Attributes
std::vector< VectorXd >	m_symDirs
	p-hat_i, index 0 = primary
VectorXd	m_symXR
	reactant anchor R of the half-lines
VectorXd	m_masses3N
	per-DOF masses of the free atoms (amu)
double	m_dt {0.0}
	integration step, internal units
double	m_kbt {0.0}
	k_B T (eV)
double	m_andersenProb {0.0}
	per-step Andersen collision probability
long	m_seedState {12345}
	LCG state for the thermostat draws.
bool	m_gaussHave {false}
double	m_gaussSpare {0.0}

Friends
struct	::tests::OHTSTPlaneWrapTest
struct	OHTSTSymmetryTest

Additional Inherited Members
Protected Attributes inherited from eonc::Job
JobType	jtype
Parameters	params
std::unique_ptr< Runtime >	owned_runtime_
	Non-null when this Job owns the composition root (one-shot makeJob).
Runtime *	runtime_
	Always valid: either owned_runtime_.get() or a caller-owned Runtime.
std::shared_ptr< Potential >	pot

Detailed Description

Definition at line 51 of file OHTSTJob.h.

Constructor & Destructor Documentation

OHTSTJob()

eonc::OHTSTJob::OHTSTJob ( std::unique_ptr< Parameters > parameters, Runtime & rt )

inline

Definition at line 54 of file OHTSTJob.h.

      : Job(std::move(parameters), rt) {}

~OHTSTJob()

eonc::OHTSTJob::~OHTSTJob ( void )

default

Member Function Documentation

drawThermalVelocities()

void eonc::OHTSTJob::drawThermalVelocities ( VectorXd & vel, const VectorXd * normal )

private

Maxwell-Boltzmann draw on the free DOF, then projection onto the plane (n.v = 0) when a normal is supplied.

Definition at line 94 of file OHTSTJob.cpp.

                                                                          {
  for (long k = 0; k < vel.size(); ++k) {
    vel[k] = std::sqrt(m_kbt / m_masses3N[k]) * gaussDraw();
  }
  if (normal != nullptr) {
    vel -= (*normal) * normal->dot(vel);
  }
}

gaussDraw()

double eonc::OHTSTJob::gaussDraw ( )

private

standard normal (Box-Muller)

Definition at line 58 of file OHTSTJob.cpp.

                           {
  if (m_gaussHave) {
    m_gaussHave = false;
    return m_gaussSpare;
  }
  double u1 = std::max(uniformDraw(), 1e-12);
  double u2 = uniformDraw();
  double r = std::sqrt(-2.0 * std::log(u1));
  m_gaussSpare = r * std::sin(2.0 * helpers::pi * u2);
  m_gaussHave = true;
  return r * std::cos(2.0 * helpers::pi * u2);
}

reactantQRatio()

double eonc::OHTSTJob::reactantQRatio ( Matter & matter, const VectorXd & gammaR, const VectorXd & normal )

private

Eq 22: Q^ZR/Q^R from crossing statistics of an unconstrained reactant-basin trajectory through the plane (gammaR, normal).

Definition at line 247 of file OHTSTJob.cpp.

                                                        {
  // Eq 22: Q^ZR/Q^R = (dt / t_tot) * sum over plane crossings of
  // 1 / |(r_{i+1} - r_i).n|. The trajectory is unconstrained,
  // thermostatted, and stays in the reactant basin by construction
  // (it starts there and the barrier is >> kT).
  const long steps = params.oh_tst_options().reactant_md_steps;
  const long equilSteps = params.oh_tst_options().equil_steps;
  VectorXd x = matter.getPositionsFreeV();
  VectorXd v(x.size());
  drawThermalVelocities(v, nullptr);
  std::unique_ptr<GleThermostat> gle;
  if (params.oh_tst_options().thermostat == "gle") {
    const MatrixXd a =
        GleThermostat::loadDriftMatrix(params.oh_tst_options().gle_a_file);
    gle = std::make_unique<GleThermostat>(a, m_kbt, 0.5 * m_dt, x.size());
    if (!gle->valid()) {
      throw std::runtime_error("oh_tst: gle thermostat unusable");
    }
  }
  const auto gauss = [this]() { return gaussDraw(); };
  VectorXd f = matter.getForcesFreeV();
  double side = normal.dot(x - gammaR);
  double crossingSum = 0.0;
  long counted = 0;
  for (long step = 0; step < equilSteps + steps; ++step) {
    const VectorXd xOld = x;
    if (gle) {
      gle->apply(v, m_masses3N, gauss);
    }
    VectorXd a = f.cwiseQuotient(m_masses3N);
    x += m_dt * v + 0.5 * m_dt * m_dt * a;
    matter.setPositionsFreeV(x);
    f = matter.getForcesFreeV();
    VectorXd aNew = f.cwiseQuotient(m_masses3N);
    v += 0.5 * m_dt * (a + aNew);
    if (symmetryReflect(m_symXR, x, v, xOld, nullptr)) {
      matter.setPositionsFreeV(x);
      f = matter.getForcesFreeV();
    }
    if (gle) {
      gle->apply(v, m_masses3N, gauss);
    } else if (uniformDraw() < m_andersenProb) {
      drawThermalVelocities(v, nullptr);
    }
    const double sideNew = normal.dot(x - gammaR);
    if (step >= equilSteps) {
      if (side * sideNew < 0.0) {
        const double proj = std::fabs(normal.dot(x - xOld));
        if (proj > 1e-14) {
          crossingSum += 1.0 / proj;
        }
      }
      ++counted;
    }
    side = sideNew;
  }
  return counted > 0 ? crossingSum / static_cast<double>(counted) : 0.0;
}

run()

std::vector< std::string > eonc::OHTSTJob::run ( void )

virtual

Virtual run; used solely for dynamic dispatch.

Implements eonc::Job.

Definition at line 307 of file OHTSTJob.cpp.

                                       {
  auto reactant = std::make_shared<Matter>(pot, params);
  auto product = std::make_shared<Matter>(pot, params);
  if (!eonc::io::io_ok(
          reactant->con2matter(params.oh_tst_options().reactant_filename))) {
    EONC_LOG_CRITICAL("OH-TST failed to load {}",
                      params.oh_tst_options().reactant_filename);
    throw std::runtime_error("oh_tst: failed to load reactant");
  }
  if (!eonc::io::io_ok(
          product->con2matter(params.oh_tst_options().product_filename))) {
    EONC_LOG_CRITICAL("OH-TST failed to load {}",
                      params.oh_tst_options().product_filename);
    throw std::runtime_error("oh_tst: failed to load product");
  }
 
  const double temperature = params.main_options().temperature;
  EONC_LOG_INFO(
      "[oh_tst] thermostat = {}{}", params.oh_tst_options().thermostat,
      params.oh_tst_options().thermostat == "gle"
          ? std::string(" (drift: ") + params.oh_tst_options().gle_a_file + ")"
          : std::string());
  m_kbt = params.constants().kB * temperature;
  m_dt = params.oh_tst_options().time_step / params.constants().timeUnit;
  m_seedState = (params.main_options().randomSeed > 0)
                    ? params.main_options().randomSeed
                    : 12345;
  // Per-step collision probability from the Andersen collision period.
  const double tcol = params.thermostat_options().andersen_tcol_input /
                      params.constants().timeUnit;
  m_andersenProb = (tcol > 0.0) ? std::min(1.0, m_dt / tcol) : 0.1;
 
  // Free-DOF mass vector (amu per coordinate).
  const long nAtoms = reactant->numberOfAtoms();
  auto masses = reactant->getMasses();
  std::vector<double> m3;
  m3.reserve(3 * nAtoms);
  for (long i = 0; i < nAtoms; ++i) {
    if (!reactant->getFixed(i)) {
      for (int j = 0; j < 3; ++j)
        m3.push_back(masses[i]);
    }
  }
  m_masses3N = VectorXd::Map(m3.data(), static_cast<long>(m3.size()));
 
  // Straight guideline in 3N space, minimum-image on the endpoint
  // difference so the plane never strides a cell boundary.
  const VectorXd xR = reactant->getPositionsFreeV();
  VectorXd diff = product->getPositionsFreeV() - xR;
  {
    AtomMatrix d(AtomMatrix::Map(diff.data(), diff.size() / 3, 3));
    Eigen::RowVector3d total_drift = Eigen::RowVector3d::Zero();
    d = minImageRemoveRigidDrift(*reactant, std::move(d), &total_drift);
    EONC_LOG_INFO("[oh_tst] rigid drift removed: ({:.4f}, {:.4f}, "
                  "{:.4f}) A per atom",
                  total_drift[0], total_drift[1], total_drift[2]);
    diff = VectorXd::Map(d.data(), diff.size());
  }
  const double guideLen = diff.norm();
  EONC_LOG_INFO("[oh_tst] guideline length |P - R| = {:.4f} A over {} free "
                "DOF",
                guideLen, xR.size());
  // A sub-Angstrom guideline is an on-site shuffle (dumbbell rotation,
  // flicker partner): the plane progression has no room to climb and
  // the run would "converge" at s = 0 measuring nothing.
  if (guideLen < 0.5) {
    EONC_LOG_CRITICAL("[oh_tst] guideline too short ({:.4f} A) -- pick a "
                      "translation-class endpoint pair",
                      guideLen);
    throw std::runtime_error("oh_tst: degenerate guideline");
  }
  const VectorXd u = diff / guideLen;
 
  // Eqs 13-14: unit vectors to every symmetry-equivalent product;
  // index 0 is the primary product the guideline points to.
  m_symXR = xR;
  m_symDirs.clear();
  m_symDirs.push_back(u);
  if (!params.oh_tst_options().symmetry_products.empty()) {
    std::string rest = params.oh_tst_options().symmetry_products;
    while (!rest.empty()) {
      const auto comma = rest.find(',');
      std::string fname = rest.substr(0, comma);
      rest = (comma == std::string::npos) ? "" : rest.substr(comma + 1);
      if (fname.empty()) {
        continue;
      }
      Matter other(pot, params);
      if (!eonc::io::io_ok(other.con2matter(fname))) {
        EONC_LOG_CRITICAL("OH-TST failed to load symmetry product {}", fname);
        throw std::runtime_error("oh_tst: failed to load symmetry product");
      }
      VectorXd d = other.getPositionsFreeV() - xR;
      AtomMatrix dm(AtomMatrix::Map(d.data(), d.size() / 3, 3));
      dm = minImageRemoveRigidDrift(*reactant, std::move(dm), nullptr);
      d = VectorXd::Map(dm.data(), d.size());
      const double dn = d.norm();
      if (dn > 1e-8) {
        m_symDirs.push_back(d / dn);
      }
    }
    EONC_LOG_INFO("[oh_tst] symmetry restriction active over {} product "
                  "directions",
                  m_symDirs.size());
  }
 
  // Plane state: progression coordinate s, normal n, their conjugate
  // velocities, and the previous-iteration driving forces for the
  // two-force velocity Verlet updates (Eqs 6-7 and 9-10).
  double s = params.oh_tst_options().s_init * guideLen;
  double vS = 0.0;
  VectorXd n = u;
  VectorXd omega = VectorXd::Zero(n.size());
  const double mS = params.oh_tst_options().plane_mass;
  const double dtPlane = params.oh_tst_options().plane_time_step;
  const double dsMax = params.oh_tst_options().ds_max;
  const double dThetaMax = params.oh_tst_options().dtheta_max;
  const double fTol = params.oh_tst_options().force_tol;
 
  Matter walker(*reactant);
  // Carry the unwrapped free coordinates. The next plane must not reload
  // them after setPositionsFreeV has wrapped the configuration.
  VectorXd xFree = walker.getPositionsFreeV();
 
  // Reversible-work accumulators and the previous plane's averages
  // for the trapezoid rules of Eqs 18-19.
  double aTrans = 0.0, aRot = 0.0, aBest = 0.0, sBest = s;
  VectorXd nBest = n;
  bool havePrev = false;
  double fnPrev = 0.0;
  VectorXd rotRawPrev, posPrev, nPrev;
  double gSPrev = 0.0;
  VectorXd gRotPrev;
  int sideSign = 0; // sign of <F.n> at plane 1 (grooming, Sec IIE)
 
  // RAII: the divergence guard and samplePlane both throw out of the plane
  // loop below, so the handle has to close itself.
  std::ofstream prog("oh_tst_progression.dat");
  if (prog) {
    prog << "# plane  s/L  <F.n> (eV/A)  dA_trans (eV)  dA_rot (eV)  "
            "A (eV)  n.u\n";
  } else {
    EONC_LOG_ERROR("[oh_tst] cannot open oh_tst_progression.dat");
  }
 
  const bool scanMode = params.oh_tst_options().pmf_scan;
  const long nScan = std::max(2L, params.oh_tst_options().scan_planes);
  const long nPlanes = scanMode ? nScan : params.oh_tst_options().max_planes;
  // Adaptive runs start at s_init, off the force-free reactant. A PMF
  // scan is a uniform reactant->product grid, so plane 0 is s = 0.
  if (scanMode) {
    s = pmfScanS(0, nScan, guideLen);
    sBest = s;
  }
  long plane = 0;
  bool converged = false;
  // Sec IIC guideline refinement: after the translational force first
  // changes sign the guideline is re-anchored every step through the
  // previous plane's average position along the current normal, so a
  // small rotational force no longer demands a huge s move (the
  // failure mode that made small-inertia mechanism discovery diverge).
  bool guidelineMoving = false;
  VectorXd gOrigin = xR;
  VectorXd gDir = u;
  long rotOnlySteps = 0;
  for (; plane < nPlanes; ++plane) {
    if (scanMode) {
      s = pmfScanS(plane, nScan, guideLen);
    }
    const VectorXd gamma = gOrigin + s * gDir;
    PlaneAverages avg = samplePlane(walker, xFree, gamma, n);
 
    // Driving forces: translation climbs against <F.n> (Eq 5 with the
    // reversed-force convention); the normal is driven along
    // +<(n.F) R/(alpha |R|^2)> (Appendix A, Eq A1), projected onto
    // the tangent space of the unit sphere.
    const double gS = -avg.fn / mS;
    VectorXd gRot = avg.rotNorm - n * n.dot(avg.rotNorm);
 
    if (plane == 0) {
      sideSign = (avg.fn < 0.0) ? -1 : 1;
    } else if (!guidelineMoving && ((avg.fn < 0.0) ? -1 : 1) != sideSign) {
      guidelineMoving = true;
      EONC_LOG_DEBUG("[oh_tst] plane {}: translational force changed "
                     "sign; guideline now follows <r> along the normal",
                     plane);
    }
 
    // Reversible work (Eqs 18-19), trapezoid between consecutive
    // planes: the translational path is the piecewise-linear track of
    // the average configuration <r>, and the rotational work pairs
    // the unnormalized <(n.F) R> with the actual change of the
    // normal. Grooming (Sec IIE): only planes on the reactant side of
    // the ridge (same sign of <F.n> as plane 1) contribute.
    if (havePrev) {
      // Scan mode integrates the whole reactant->product path; the
      // adaptive run grooms to the reactant side of the ridge only.
      const bool sameSide = scanMode || ((fnPrev < 0.0 ? -1 : 1) == sideSign &&
                                         (avg.fn < 0.0 ? -1 : 1) == sideSign);
      if (sameSide) {
        const VectorXd fParMean = 0.5 * (fnPrev * nPrev + avg.fn * n);
        aTrans += -fParMean.dot(avg.pos - posPrev);
        const VectorXd rotMean = 0.5 * (rotRawPrev + avg.rotRaw);
        aRot += rotMean.dot(n - nPrev);
      }
    }
 
    const double aTotal = aTrans + aRot;
    if (aTotal > aBest) {
      aBest = aTotal;
      sBest = s;
      nBest = n;
    }
    if (prog) {
      prog << std::format("{:6} {:10.6f} {:14.6e} {:12.6f} {:12.6f} {:12.6f} "
                          "{:10.6f}\n",
                          plane, s / guideLen, avg.fn, aTrans, aRot, aTotal,
                          n.dot(u));
      prog.flush();
    }
    EONC_LOG_DEBUG("[oh_tst] plane {} s/L {:.4f} <F.n> {:.4e} A {:.4f} eV",
                   plane, s / guideLen, avg.fn, aTotal);
 
    // Divergence guard: reversible work beyond any physical barrier
    // means the endpoints were not minimized (static relaxation
    // forces leak into <F.n>) or the plane is chasing a drifting
    // ensemble; 300 planes of that is pure waste.
    if (aTotal > params.oh_tst_options().max_delta_a) {
      EONC_LOG_CRITICAL(
          "[oh_tst] accumulated work {:.2f} eV exceeds max_delta_a "
          "{:.2f} eV at plane {} -- endpoints likely unminimized",
          aTotal, params.oh_tst_options().max_delta_a, plane);
      throw std::runtime_error("oh_tst: diverging reversible work");
    }
    // A stationary plane only counts as the variational maximum
    // after the progression has actually climbed: the reactant basin
    // bottom is also force-free, and a short guideline puts the first
    // plane inside it. Two thermal energies of accumulated reversible
    // work is the cheapest evidence of a ridge.
    if (!scanMode && plane > 2 && aTotal > 2.0 * m_kbt &&
        std::fabs(avg.fn) < fTol &&
        gRot.norm() * params.oh_tst_options().alpha_rot < fTol) {
      converged = true;
      // The converged plane is the optimal one even if sampling noise
      // put an earlier plane marginally higher.
      aBest = aTotal;
      sBest = s;
      nBest = n;
      if (prog) {
        prog << std::format("# converged at plane {}\n", plane);
      }
      break;
    }
 
    if (scanMode) {
      // Fixed-increment PMF scan: normal stays along the guideline,
      // s advances uniformly, and the walker is projected onto the
      // next constraint plane for samplePlane to re-equilibrate. The
      // A(s) profile is the PMF; aBest already tracks its maximum.
      fnPrev = avg.fn;
      nPrev = n;
      rotRawPrev = avg.rotRaw;
      posPrev = avg.pos;
      gSPrev = gS;
      gRotPrev = gRot;
      havePrev = true;
      s = pmfScanS(plane + 1, nScan, guideLen);
      const VectorXd gammaNext = xR + s * u;
      xFree -= u * (u.dot(xFree - gammaNext));
      walker.setPositionsFreeV(xFree);
      continue;
    }
    // Damped two-force Verlet on s (Eqs 6-7): the velocity is zeroed
    // when it opposes the driving force, so the plane settles at the
    // free-energy maximum instead of oscillating over it ("the
    // velocity of the plane is zeroed if the plane has gone past the
    // maximum free energy position").
    // Pure-rotation step (Sec IIC): right after a guideline change a
    // spiked rotational force is relaxed at fixed s before the plane
    // translates again.
    const bool rotationOnly =
        guidelineMoving &&
        gRot.norm() * params.oh_tst_options().alpha_rot > 5.0 * fTol &&
        rotOnlySteps < 10;
    if (rotationOnly) {
      ++rotOnlySteps;
    } else {
      rotOnlySteps = 0;
    }
    if (havePrev) {
      vS += 0.5 * dtPlane * (gS + gSPrev);
    } else {
      vS += dtPlane * gS;
    }
    if (vS * gS < 0.0)
      vS = 0.0;
    double ds = dtPlane * vS + 0.5 * dtPlane * dtPlane * gS;
    ds = std::clamp(ds, -dsMax, dsMax);
    if (rotationOnly) {
      ds = 0.0;
      vS = 0.0;
    }
    const double sNew =
        guidelineMoving ? s + ds : std::clamp(s + ds, 0.0, guideLen);
 
    // Damped rotation (Eqs 9-10 with the Appendix A driving): the
    // angular velocity keeps only its projection along the current
    // driving force while aligned with it, and is zeroed otherwise.
    if (havePrev && gRotPrev.size() == gRot.size()) {
      omega += 0.5 * dtPlane * (gRot + gRotPrev);
    } else {
      omega += dtPlane * gRot;
    }
    omega -= n * n.dot(omega);
    const double gNorm = gRot.norm();
    if (gNorm > 1e-14) {
      const VectorXd gHat = gRot / gNorm;
      const double along = omega.dot(gHat);
      if (along > 0.0) {
        omega = gHat * along;
      } else {
        omega.setZero();
      }
    } else {
      omega.setZero();
    }
    VectorXd dn = dtPlane * omega + 0.5 * dtPlane * dtPlane * gRot;
    const double dTheta = dn.norm();
    if (dTheta > dThetaMax) {
      dn *= dThetaMax / dTheta;
    }
    const VectorXd nOld = n;
    n = (n + dn).normalized();
    if (n.dot(gDir) < 0.0) {
      // Keep the normal pointing towards increasing s.
      n = -n;
    }
 
    // Eq 11-12 restart: place the walker in the new plane at the
    // rotated image of the average arm, rescaled so rotation does not
    // change the arm length.
    VectorXd arm = avg.pos - gamma;
    VectorXd armNew = arm - nOld * arm.dot(n - nOld);
    const double armLen = arm.norm();
    const double armNewLen = armNew.norm();
    if (armLen > 1e-12 && armNewLen > 1e-12) {
      armNew *= armLen / armNewLen;
    }
    VectorXd gammaNew;
    if (guidelineMoving) {
      // Re-anchor: the guideline passes through the previous plane's
      // average position along the CURRENT normal, and the plane
      // ADVANCES by this iteration's ds along the fresh line. (A
      // dead re-assignment here used to pin the plane at <r> forever:
      // the walker drifted downhill and the trans-work integral ran
      // away by ~20 eV per plane on the Cu doorway.)
      gOrigin = avg.pos;
      gDir = n;
      s = ds;
      gammaNew = gOrigin + s * gDir;
    } else {
      gammaNew = gOrigin + sNew * gDir;
    }
    xFree = gammaNew + armNew;
    xFree -= n * n.dot(xFree - gammaNew);
    walker.setPositionsFreeV(xFree);
 
    fnPrev = avg.fn;
    nPrev = nOld;
    rotRawPrev = avg.rotRaw;
    posPrev = avg.pos;
    gSPrev = gS;
    gRotPrev = gRot;
    havePrev = true;
    if (!guidelineMoving) {
      s = sNew;
    }
  }
  bool progOk = prog.is_open();
  if (progOk) {
    prog.close();
    progOk = static_cast<bool>(prog);
    if (!progOk) {
      EONC_LOG_ERROR("[oh_tst] failed to write oh_tst_progression.dat");
    }
  }
  // A completed scan yields a valid PMF even with no interior
  // maximum; report it as converged so downstream tooling accepts
  // the profile (barrier = aBest, the max of A(s)).
  if (scanMode && plane >= nPlanes)
    converged = true;
 
  // `break` leaves `plane` at the 0-based index of the plane just
  // sampled. A finished loop leaves it at nPlanes. planes_used is
  // the number of planes sampled in either case.
  const long planesUsed = (plane < nPlanes) ? plane + 1 : plane;
 
  // Direction-dependent effective mass (Eq 24) and the one-sided
  // thermal flux factor sqrt(kBT / 2 pi mu) (Eq 23).
  const double mu = (m_masses3N.array() * nBest.array().square()).sum();
  const double vFlux = std::sqrt(m_kbt / (2.0 * helpers::pi * mu));
 
  // Q^ZR/Q^R at the FIRST plane of the progression (Z^R), whose
  // reversible work to the optimal plane is what aBest measures.
  Matter rWalker(*reactant);
  const double sFirst = scanMode ? pmfScanS(0, nScan, guideLen)
                                 : params.oh_tst_options().s_init * guideLen;
  const VectorXd gammaR = xR + sFirst * u;
  const double qRatio = reactantQRatio(rWalker, gammaR, u);
 
  // Rate in internal units (1/internal-time), then SI.
  const double kInternal = vFlux * qRatio * std::exp(-aBest / m_kbt);
  const double kSI = kInternal / (params.constants().timeUnit * 1.0e-15);
 
  std::vector<std::string> returnFiles;
  std::ofstream out("results.dat");
  if (!out) {
    EONC_LOG_ERROR("[oh_tst] cannot open results.dat");
    throw std::runtime_error("oh_tst: cannot open results.dat");
  }
  out << "oh_tst job_type\n";
  out << std::format("{} converged\n", converged ? 1 : 0);
  out << std::format("{} planes_used\n", planesUsed);
  out << std::format("{:.8f} free_energy_barrier_eV\n", aBest);
  out << std::format("{:.8f} delta_a_trans_eV\n", aTrans);
  out << std::format("{:.8f} delta_a_rot_eV\n", aRot);
  out << std::format("{:.8f} s_star_over_L\n", sBest / guideLen);
  out << std::format("{:.8f} guideline_length_A\n", guideLen);
  out << std::format("{:.8f} normal_overlap_with_guideline\n", nBest.dot(u));
  out << std::format("{:.8e} effective_mass_amu\n", mu);
  out << std::format("{:.8e} q_ratio_per_A\n", qRatio);
  out << std::format("{:.8e} rate_ohtst_per_s\n", kSI);
  out << std::format("{:.4f} temperature_K\n", temperature);
  out.close();
  if (!out) {
    EONC_LOG_ERROR("[oh_tst] failed to write results.dat");
    throw std::runtime_error("oh_tst: failed to write results.dat");
  }
  returnFiles.push_back("results.dat");
  if (progOk) {
    returnFiles.push_back("oh_tst_progression.dat");
  }
  EONC_LOG_INFO("[oh_tst] {} after {} planes: A = {:.4f} eV at s/L = {:.4f}, "
                "k = {:.4e} 1/s at {:.1f} K",
                converged ? "converged" : "max planes", planesUsed, aBest,
                sBest / guideLen, kSI, temperature);
  return returnFiles;
}

samplePlane()

OHTSTJob::PlaneAverages eonc::OHTSTJob::samplePlane ( Matter & matter, VectorXd & x, const VectorXd & gamma, const VectorXd & normal )

private

Definition at line 149 of file OHTSTJob.cpp.

                                                                      {
  const long equilSteps = params.oh_tst_options().equil_steps;
  const long sampleSteps = params.oh_tst_options().sample_steps;
  const double alphaRot = params.oh_tst_options().alpha_rot;
 
  // Constrain the unwrapped free coordinates onto the plane. Matter
  // stores the periodic image: a coordinate just outside the cell comes
  // back from getPositionsFreeV shifted by a lattice vector, and
  // projecting that image lands on a different 3N point.
  x -= normal * normal.dot(x - gamma);
  matter.setPositionsFreeV(x);
 
  VectorXd v(x.size());
  drawThermalVelocities(v, &normal);
 
  // Colored-noise option: an exact OU half-step before and after each
  // Verlet step (the auxiliary momenta start fresh per sampling
  // block); velocities re-project onto the plane after every kick.
  std::unique_ptr<GleThermostat> gle;
  if (params.oh_tst_options().thermostat == "gle") {
    const MatrixXd a =
        GleThermostat::loadDriftMatrix(params.oh_tst_options().gle_a_file);
    gle = std::make_unique<GleThermostat>(a, m_kbt, 0.5 * m_dt, x.size());
    if (!gle->valid()) {
      EONC_LOG_CRITICAL("OH-TST gle thermostat unusable (gle_a_file = {})",
                        params.oh_tst_options().gle_a_file);
      throw std::runtime_error("oh_tst: gle thermostat unusable");
    }
  }
  const auto gauss = [this]() { return gaussDraw(); };
 
  VectorXd f = matter.getForcesFreeV();
  VectorXd fPlane = f - normal * normal.dot(f);
 
  PlaneAverages avg;
  avg.rotNorm = VectorXd::Zero(x.size());
  avg.rotRaw = VectorXd::Zero(x.size());
  avg.pos = VectorXd::Zero(x.size());
  long nAccum = 0;
 
  VectorXd xPrev = x;
  for (long step = 0; step < equilSteps + sampleSteps; ++step) {
    // Velocity Verlet on the plane: forces and velocities projected,
    // positions corrected back onto the constraint (RATTLE for a
    // linear constraint is an exact projection).
    xPrev = x;
    if (gle) {
      gle->apply(v, m_masses3N, gauss);
      v -= normal * normal.dot(v);
    }
    VectorXd a = fPlane.cwiseQuotient(m_masses3N);
    x += m_dt * v + 0.5 * m_dt * m_dt * a;
    x -= normal * normal.dot(x - gamma);
    matter.setPositionsFreeV(x);
    f = matter.getForcesFreeV();
    fPlane = f - normal * normal.dot(f);
    VectorXd aNew = fPlane.cwiseQuotient(m_masses3N);
    v += 0.5 * m_dt * (a + aNew);
    v -= normal * normal.dot(v);
    // Eqs 14-17: keep the sampling in the primary product subregion.
    if (symmetryReflect(m_symXR, x, v, xPrev, &normal)) {
      x -= normal * normal.dot(x - gamma);
      matter.setPositionsFreeV(x);
      f = matter.getForcesFreeV();
      fPlane = f - normal * normal.dot(f);
    }
    if (gle) {
      gle->apply(v, m_masses3N, gauss);
      v -= normal * normal.dot(v);
    } else if (uniformDraw() < m_andersenProb) {
      // Andersen collisions keep the constrained ensemble canonical.
      drawThermalVelocities(v, &normal);
    }
    if (step >= equilSteps) {
      const double fn = normal.dot(f);
      const VectorXd arm = x - gamma;
      const double arm2 = arm.squaredNorm();
      avg.fn += fn;
      if (arm2 > 1e-16) {
        avg.rotNorm.noalias() += (fn / (alphaRot * arm2)) * arm;
      }
      avg.rotRaw.noalias() += fn * arm;
      avg.pos.noalias() += x;
      ++nAccum;
    }
  }
  if (nAccum > 0) {
    const double inv = 1.0 / static_cast<double>(nAccum);
    avg.fn *= inv;
    avg.rotNorm *= inv;
    avg.rotRaw *= inv;
    avg.pos *= inv;
  }
  return avg;
}

symmetryReflect()

bool eonc::OHTSTJob::symmetryReflect ( const VectorXd & xR, VectorXd & x, VectorXd & v, const VectorXd & xOld, const VectorXd * normal )

private

Eqs 14-17 symmetry restriction: if the configuration is closer to another equivalent product half-line than to the primary one, revert the position and reflect the velocity about the mirror that maps the primary direction onto the offending one. Returns true when a reflection was applied.

Definition at line 103 of file OHTSTJob.cpp.

                                                                             {
  if (m_symDirs.size() < 2) {
    return false;
  }
  // Eq 15: distance from the configuration to each half-line
  // l_i = { R + t p_i, t >= 0 }. For t < 0 the closest point is the
  // reactant endpoint, not the foot on the infinite line.
  const VectorXd rel = x - xR;
  const double rel2 = rel.squaredNorm();
  double dPrimary = 0.0;
  size_t closest = 0;
  double dMin = 0.0;
  for (size_t i = 0; i < m_symDirs.size(); ++i) {
    const double proj = rel.dot(m_symDirs[i]);
    const double d2 = (proj < 0.0) ? rel2 : std::max(0.0, rel2 - proj * proj);
    const double d = std::sqrt(d2);
    if (i == 0) {
      dPrimary = d;
      dMin = d;
    } else if (d < dMin) {
      dMin = d;
      closest = i;
    }
  }
  if (closest == 0 || dPrimary <= dMin) {
    return false;
  }
  // Eqs 16-17: step back and reflect the velocity about the mirror
  // that maps p_1 onto the offending p_i; the component of the mirror
  // normal along the hyperplane normal is removed so the reflected
  // velocity stays within the plane.
  VectorXd q = m_symDirs[0] - m_symDirs[closest];
  if (normal != nullptr) {
    q -= (*normal) * normal->dot(q);
  }
  const double qn = q.norm();
  if (qn < 1e-12) {
    return false;
  }
  q /= qn;
  x = xOld;
  v -= 2.0 * v.dot(q) * q;
  return true;
}

uniformDraw()

double eonc::OHTSTJob::uniformDraw ( )

private

uniform (0,1)

Definition at line 51 of file OHTSTJob.cpp.

                             {
  // Deterministic LCG: the job must be reproducible for a given
  // random_seed across MPI farm workers.
  m_seedState = (1664525L * m_seedState + 1013904223L) & 0x7fffffffL;
  return static_cast<double>(m_seedState) / 2147483648.0;
}

Friends And Related Symbol Documentation

::tests::OHTSTPlaneWrapTest

friend struct ::tests::OHTSTPlaneWrapTest

friend

Definition at line 75 of file OHTSTJob.h.

OHTSTSymmetryTest

friend struct OHTSTSymmetryTest

friend

Definition at line 93 of file OHTSTJob.h.

Member Data Documentation

m_andersenProb

double eonc::OHTSTJob::m_andersenProb {0.0}

private

per-step Andersen collision probability

Definition at line 101 of file OHTSTJob.h.

{0.0}; 

m_dt

double eonc::OHTSTJob::m_dt {0.0}

private

integration step, internal units

Definition at line 99 of file OHTSTJob.h.

{0.0};           

m_gaussHave

bool eonc::OHTSTJob::m_gaussHave {false}

private

Definition at line 105 of file OHTSTJob.h.

{false};

m_gaussSpare

double eonc::OHTSTJob::m_gaussSpare {0.0}

private

Definition at line 106 of file OHTSTJob.h.

{0.0};

m_kbt

double eonc::OHTSTJob::m_kbt {0.0}

private

k_B T (eV)

Definition at line 100 of file OHTSTJob.h.

{0.0};          

m_masses3N

VectorXd eonc::OHTSTJob::m_masses3N

private

per-DOF masses of the free atoms (amu)

Definition at line 98 of file OHTSTJob.h.

m_seedState

long eonc::OHTSTJob::m_seedState {12345}

private

LCG state for the thermostat draws.

Definition at line 102 of file OHTSTJob.h.

{12345};    

m_symDirs

std::vector<VectorXd> eonc::OHTSTJob::m_symDirs

private

p-hat_i, index 0 = primary

Definition at line 95 of file OHTSTJob.h.

m_symXR

VectorXd eonc::OHTSTJob::m_symXR

private

reactant anchor R of the half-lines

Definition at line 96 of file OHTSTJob.h.

---

The documentation for this class was generated from the following files:

• /home/runner/work/eOn/eOn/include/eon/OHTSTJob.h
• /home/runner/work/eOn/eOn/client/OHTSTJob.cpp