Create a function to perform baseline correction on acceleration time…

… histories (refs idaholab#296)

include/functions/BaselineCorrection.h

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+/*************************************************/
+/*           DO NOT MODIFY THIS HEADER           */
+/*                                               */
+/*                     MASTODON                  */
+/*                                               */
+/*    (c) 2015 Battelle Energy Alliance, LLC     */
+/*            ALL RIGHTS RESERVED                */
+/*                                               */
+/*   Prepared by Battelle Energy Alliance, LLC   */
+/*     With the U. S. Department of Energy       */
+/*                                               */
+/*     See COPYRIGHT for full restrictions       */
+/*************************************************/
+
+// This code was implemented in collaboration with Christopher J. Wong
+// (chris.wong@utah.edu) from the University of Utah.
+
+#pragma once
+
+// MOOSE includes
+#include "Function.h"
+#include "LinearInterpolation.h"
+
+// Forward Declarations
+class BaselineCorrection;
+
+/**
+ * Applies a baseline correction to an accceleration time history using least
+ * squares polynomial fits and outputs the adjusted acceleration
+ */
+class BaselineCorrection : public Function
+{
+public:
+  static InputParameters validParams();
+
+  BaselineCorrection(const InputParameters & parameters);
+
+  virtual Real value(Real t, const Point & /*P*/) const override;
+
+protected:
+  /// Newmark integration parameters
+  const Real & _gamma;
+  const Real & _beta;
+
+  /// set which kinematic variables a polynomial fit will be applied to
+  const bool _fit_accel;
+  const bool _fit_vel;
+  const bool _fit_disp;
+
+  /// order used for the least squares polynomial fit
+  const unsigned int _order;
+
+  /// acceleration time history variables from input
+  std::vector<Real> _time;
+  std::vector<Real> _accel;
+
+  /// adjusted (corrected) acceleration ordinates
+  std::vector<Real> _adj_accel;
+
+  /// object to output linearly interpolated corrected acceleration ordinates
+  std::unique_ptr<LinearInterpolation> _linear_interp;
+
+  /// function value scale factor
+  const Real & _scale_factor;
+
+private:
+  /// Applies baseline correction to raw acceleration time history
+  void applyCorrection();
+
+  /// Reads and builds data from supplied CSV file
+  void buildFromFile();
+
+  /// Builds data from pairs of `time_values` and `acceleration_values'
+  void buildFromXandY();
+};

include/utils/BaselineCorrectionUtils.h

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+/*************************************************/
+/*           DO NOT MODIFY THIS HEADER           */
+/*                                               */
+/*                     MASTODON                  */
+/*                                               */
+/*    (c) 2015 Battelle Energy Alliance, LLC     */
+/*            ALL RIGHTS RESERVED                */
+/*                                               */
+/*   Prepared by Battelle Energy Alliance, LLC   */
+/*     With the U. S. Department of Energy       */
+/*                                               */
+/*     See COPYRIGHT for full restrictions       */
+/*************************************************/
+
+// This code was implemented in collaboration with Christopher J. Wong
+// (chris.wong@utah.edu) from the University of Utah.
+
+#pragma once
+
+// LIBMESH includes
+#include "DenseMatrix.h"
+#include "libmesh/dense_vector.h"
+
+/**
+ * This namespace contains the functions used for the calculations corresponding
+ * to the time history adjustment procedure in BaselineCorrection
+ **/
+namespace BaselineCorrectionUtils
+{
+/// Evaluates an integral over a single time step with Newmark-beta method
+/// Also is used as simple trapezoidal rule when gamma = 0.5.
+Real newmarkGammaIntegrate(const Real & u_ddot_old,
+                           const Real & u_ddot,
+                           const Real & u_dot_old,
+                           const Real & gamma,
+                           const Real & dt);
+
+/// Evaluates a double integral over a single time step with Newmark-beta method
+Real newmarkBetaIntegrate(const Real & u_ddot_old,
+                          const Real & u_ddot,
+                          const Real & u_dot_old,
+                          const Real & u_old,
+                          const Real & beta,
+                          const Real & dt);
+
+/// Solves linear normal equation for minimum acceleration square error
+DenseVector<Real> getAccelerationFitCoeffs(unsigned int order,
+                                           const std::vector<Real> & accel,
+                                           const std::vector<Real> & t,
+                                           const unsigned int & num_steps,
+                                           const Real & gamma);
+
+/// Solves linear normal equation for minimum velocity square error
+DenseVector<Real> getVelocityFitCoeffs(unsigned int order,
+                                       const std::vector<Real> & accel,
+                                       const std::vector<Real> & vel,
+                                       const std::vector<Real> & t,
+                                       const unsigned int & num_steps,
+                                       const Real & beta);
+
+/// Solves linear normal equation for minimum displacement square error
+DenseVector<Real> getDisplacementFitCoeffs(unsigned int order,
+                                           const std::vector<Real> & disp,
+                                           const std::vector<Real> & t,
+                                           const unsigned int & num_steps);
+
+/// Evaluates the least squares polynomials over at a single time step
+std::vector<Real> computePolynomials(unsigned int order,
+                                     const DenseVector<Real> & coeffs,
+                                     const Real & t);
+
+} // namespace BaselineCorrectionUtils

src/functions/BaselineCorrection.C

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+/*************************************************/
+/*           DO NOT MODIFY THIS HEADER           */
+/*                                               */
+/*                     MASTODON                  */
+/*                                               */
+/*    (c) 2015 Battelle Energy Alliance, LLC     */
+/*            ALL RIGHTS RESERVED                */
+/*                                               */
+/*   Prepared by Battelle Energy Alliance, LLC   */
+/*     With the U. S. Department of Energy       */
+/*                                               */
+/*     See COPYRIGHT for full restrictions       */
+/*************************************************/
+
+// This code was implemented in collaboration with Christopher J. Wong
+// (chris.wong@utah.edu) from the University of Utah.
+
+// MASTODON includes
+#include "BaselineCorrection.h"
+#include "BaselineCorrectionUtils.h"
+
+// MOOSE includes
+#include "DelimitedFileReader.h"
+
+registerMooseObject("MastodonApp", BaselineCorrection);
+
+InputParameters
+BaselineCorrection::validParams()
+{
+  InputParameters params = Function::validParams();
+
+  params.addParam<FileName>("data_file",
+      "The name of a CSV file containing raw acceleration time history data.");
+  params.addParam<std::string>("time_name",
+      "The header name of the column which contains the time values in the data file. If not "
+      "specified, they are assumed to be in the first column index.");
+  params.addParam<std::string>("acceleration_name",
+      "The header name for the column which contains the acceleration values in the data file. If "
+      "not specified, they are assumed to be in the second column index.");
+  params.addParam<std::vector<Real>>("time_values", "The time abscissa values.");
+  params.addParam<std::vector<Real>>("acceleration_values", "The acceleration ordinate values.");
+
+  params.addRequiredParam<Real>("gamma", "The gamma parameter for Newmark time integration.");
+  params.addRequiredParam<Real>("beta", "The beta parameter for Newmark time integration.");
+
+  params.addParam<bool>("fit_acceleration", true,
+      "If set to \"true\", the acceleration time history will be adjusted using a polynomial fit "
+      "of the acceleration data.");
+  params.addParam<bool>("fit_velocity", false,
+      "If set to \"true\", the acceleration time history will be adjusted using a polynomial fit "
+      "of the velocity data obtained by integration.");
+  params.addParam<bool>("fit_displacement", false,
+      "If set to \"true\", the acceleration time history will be adjusted using a polynomial fit "
+      "of the displacement data obtained by double-integration.");
+  params.addRequiredRangeCheckedParam<unsigned int>("order", "(0 < order) & (order < 10)",
+      "The order of the polynomial fit(s) used to adjust the nominal time histories (coefficients "
+      "of higher order polynomials can be difficult to compute and the method generally becomes "
+      "unstable when order >= 10).");
+
+  params.addParam<Real>("scale_factor", 1.0,
+      "A scale factor to be applied to the adjusted acceleration time history.");
+  params.declareControllable("scale_factor");
+
+  return params;
+}
+
+BaselineCorrection::BaselineCorrection(const InputParameters & parameters)
+  : Function(parameters),
+    _gamma(getParam<Real>("gamma")),
+    _beta(getParam<Real>("beta")),
+    _fit_accel(getParam<bool>("fit_acceleration")),
+    _fit_vel(getParam<bool>("fit_velocity")),
+    _fit_disp(getParam<bool>("fit_displacement")),
+    _order(getParam<unsigned int>("order")),
+    _scale_factor(getParam<Real>("scale_factor"))
+{
+  // determine data source and check parameter consistency
+  if (isParamValid("data_file") && !isParamValid("time_values") &&
+      !isParamValid("acceleration_values"))
+    buildFromFile();
+  else if (!isParamValid("data_file") && isParamValid("time_values") &&
+           isParamValid("acceleration_values"))
+    buildFromXandY();
+  else
+    mooseError("In BaselineCorrection ",
+               _name,
+               ": Either `data_file` or `time_values` and `acceleration_values` must be specified "
+               "exclusively.");
+
+  // size checks
+  if (_time.size() != _accel.size())
+    mooseError("In BaselineCorrection ",
+               _name,
+               ": The length of time and acceleration data must be equal.");
+  if (_time.size() == 0 || _accel.size() == 0)
+    mooseError("In BaselineCorrection ",
+               _name,
+               ": The length of time and acceleration data must be > 0.");
+
+  // ensure that at least one best-fit will be created
+  if (!_fit_accel && !_fit_vel && !_fit_disp)
+    mooseWarning("Warning in " + name() +
+                 ". Computation of a polynomial fit is set to \"false\" for all three "
+                 "kinematic variables. No adjustments will occur and the output will be the "
+                 "raw acceleration time history.");
+
+  // apply baseline correction to raw acceleration time history
+  applyCorrection();
+
+  // try building a linear interpolation object
+  try
+  {
+    _linear_interp = libmesh_make_unique<LinearInterpolation>(_time, _adj_accel);
+  }
+  catch (std::domain_error & e)
+  {
+    mooseError("In BaselineCorrection ", _name, ": ", e.what());
+  }
+}
+
+Real
+BaselineCorrection::value(Real t, const Point & /*P*/) const
+{
+  return _scale_factor * _linear_interp->sample(t);
+}
+
+void
+BaselineCorrection::applyCorrection()
+{
+  // store a reference to final array index
+  unsigned int index_end = _accel.size() - 1;
+
+  // Compute unadjusted velocity and displacment time histories
+  Real dt;
+  std::vector<Real> vel, disp;
+  vel.push_back(0); disp.push_back(0);
+  for (unsigned int i = 0; i < index_end; ++i)
+  {
+    dt = _time[i+1] - _time[i];
+
+    vel.push_back(BaselineCorrectionUtils::newmarkGammaIntegrate(
+        _accel[i], _accel[i+1], vel[i], _gamma, dt));
+    disp.push_back(BaselineCorrectionUtils::newmarkBetaIntegrate(
+        _accel[i], _accel[i+1], vel[i], disp[i], _beta, dt));
+  }
+
+  // initialize polyfits and adjusted time history arrays as the nominal ones
+  DenseVector<Real> coeffs;
+  _adj_accel = _accel;
+  std::vector<Real> p_fit, adj_vel = vel, adj_disp = disp;
+
+  // adjust time histories with acceleration fit if desired
+  if (_fit_accel)
+  {
+    coeffs = BaselineCorrectionUtils::getAccelerationFitCoeffs(
+      _order, _adj_accel, _time, index_end, _gamma);
+
+    for (unsigned int i = 0; i <= index_end; ++i)
+    {
+      p_fit = BaselineCorrectionUtils::computePolynomials(_order, coeffs, _time[i]);
+      _adj_accel[i] -= p_fit[0];
+      adj_vel[i] -= p_fit[1];
+      adj_disp[i] -= p_fit[2];
+    }
+  }
+
+  // adjust with velocity fit
+  if (_fit_vel)
+  {
+    coeffs = BaselineCorrectionUtils::getVelocityFitCoeffs(
+      _order, _adj_accel, adj_vel, _time, index_end, _beta);
+
+    for (unsigned int i = 0; i <= index_end; ++i)
+    {
+      p_fit = BaselineCorrectionUtils::computePolynomials(_order, coeffs, _time[i]);
+      _adj_accel[i] -= p_fit[0];
+      adj_disp[i] -= p_fit[2];
+    }
+  }
+
+  // adjust with displacement fit
+  if (_fit_disp)
+  {
+    coeffs = BaselineCorrectionUtils::getDisplacementFitCoeffs(_order, adj_disp, _time, index_end);
+
+    for (unsigned int i = 0; i <= index_end; ++i)
+    {
+      p_fit = BaselineCorrectionUtils::computePolynomials(_order, coeffs, _time[i]);
+      _adj_accel[i] -= p_fit[0];
+    }
+  }
+}
+
+void
+BaselineCorrection::buildFromFile()
+{
+  // Read data from CSV file
+  MooseUtils::DelimitedFileReader reader(getParam<FileName>("data_file"), &_communicator);
+  reader.read();
+
+  // Check if specific column headers were input
+  const bool time_header = isParamValid("time_name"),
+             accel_header = isParamValid("acceleration_name");
+
+  if (time_header && !accel_header)
+    mooseError("In BaselineCorrection ",
+               _name,
+               ": A column header name was specified for the for the time data. Please specify a ",
+               "header for the acceleration data using the 'accelertation_name' parameter.");
+  else if (!time_header && accel_header)
+    mooseError("In BaselineCorrection ",
+               _name,
+               ": A column header name was specified for the for the acceleration data. Please "
+               "specify a header for the time data using the 'time_name' parameter.");
+
+  // Obtain acceleration time history from file data
+  if (time_header && accel_header)
+  {
+    _time = reader.getData(getParam<std::string>("time_name"));
+    _accel = reader.getData(getParam<std::string>("acceleration_name"));
+  }
+  else
+  {
+    _time = reader.getData(0);
+    _accel = reader.getData(1);
+  }
+}
+
+void
+BaselineCorrection::buildFromXandY()
+{
+  _time = getParam<std::vector<Real>>("time_values");
+  _accel = getParam<std::vector<Real>>("acceleration_values");
+}