refineable_mixed_order_petrov_galerkin_space_time_navier_stokes_elements.cc
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26 // Non-inline functions for space-time Navier-Stokes elements
28 
29 /// //////////////////////////////////////////////////////////////////////
30 /// //////////////////////////////////////////////////////////////////////
31 /// //////////////////////////////////////////////////////////////////////
32 
33 namespace oomph
34 {
35  //===================================================================
36  /// Compute the diagonal of the velocity/pressure mass matrices.
37  /// If which one=0, both are computed, otherwise only the pressure
38  /// (which_one=1) or the velocity mass matrix (which_one=2 -- the
39  /// LSC version of the preconditioner only needs that one)
40  //===================================================================
41  template<unsigned DIM>
44  Vector<double>& press_mass_diag,
45  Vector<double>& veloc_mass_diag,
46  const unsigned& which_one)
47  {
48  // Resize and initialise
49  unsigned n_dof = ndof();
50 
51  // If the pressure mass matrix needs to be constructed
52  if ((which_one == 0) || (which_one == 1))
53  {
54  // Assign the appropriate amount of space
55  press_mass_diag.assign(n_dof, 0.0);
56  }
57 
58  // If the velocity mass matrix needs to be constructed
59  if ((which_one == 0) || (which_one == 2))
60  {
61  // Assign the appropriate amount of space
62  veloc_mass_diag.assign(n_dof, 0.0);
63  }
64 
65  // Pointer to hang info object
66  HangInfo* hang_info_pt = 0;
67 
68  // Number of master nodes
69  unsigned n_master = 1;
70 
71  // Hang weight for shape functions
72  double hang_weight = 1.0;
73 
74  // Find out how many nodes there are in the element
75  unsigned n_node = nnode();
76 
77  // Local coordinates
78  Vector<double> s(DIM + 1, 0.0);
79 
80  // Storage for the local velocity indices
81  Vector<unsigned> u_nodal_index(DIM, 0.0);
82 
83  // Find the indices at which the local velocities are stored
84  for (unsigned i = 0; i < DIM; i++)
85  {
86  // Calculate the i-th local velocity component
87  u_nodal_index[i] = this->u_index_nst(i);
88  }
89 
90  // Set up memory for velocity shape functions
91  Shape psi(n_node);
92 
93  // Find number of pressure dofs
94  unsigned n_pres = this->npres_nst();
95 
96  // Pressure shape function
97  Shape psi_p(n_pres);
98 
99  // Which nodal value represents the pressure? (Negative if pressure
100  // is not based on nodal interpolation).
101  int p_index = this->p_nodal_index_nst();
102 
103  // Local array of booleans that are true if the l-th pressure value is
104  // hanging (avoid repeated virtual function calls)
105  bool pressure_dof_is_hanging[n_pres];
106 
107  // If the pressure is stored at a node
108  if (p_index >= 0)
109  {
110  // Loop over the pressure nodes
111  for (unsigned l = 0; l < n_pres; l++)
112  {
113  // Read out the hang status of the pressure node
114  pressure_dof_is_hanging[l] =
115  this->pressure_node_pt(l)->is_hanging(p_index);
116  }
117  }
118  // Otherwise the pressure is not stored at a node and so cannot hang
119  else
120  {
121  // Loop over the pressures nodes
122  for (unsigned l = 0; l < n_pres; l++)
123  {
124  // Indicate that the pressure node is not hanging
125  pressure_dof_is_hanging[l] = false;
126  }
127  } // if (p_index>=0)
128 
129  // Number of integration points
130  unsigned n_intpt = integral_pt()->nweight();
131 
132  // Integer to store the local equations no
133  int local_eqn = 0;
134 
135  // Loop over the integration points
136  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
137  {
138  // Get the integral weight
139  double w = integral_pt()->weight(ipt);
140 
141  // Get determinant of Jacobian of the mapping
142  double J = J_eulerian_at_knot(ipt);
143 
144  // Assign values of s
145  for (unsigned i = 0; i < DIM + 1; i++)
146  {
147  // Calculate the i-th local coordinate at the ipt-th integration point
148  s[i] = integral_pt()->knot(ipt, i);
149  }
150 
151  // Premultiply weights and Jacobian
152  double W = w * J;
153 
154  // Do we want the velocity one?
155  if ((which_one == 0) || (which_one == 2))
156  {
157  // Get the velocity shape functions
158  shape_at_knot(ipt, psi);
159 
160  // Loop over the velocity shape functions
161  for (unsigned l = 0; l < n_node; l++)
162  {
163  // Local boolean to indicate whether or not the node is hanging
164  bool is_node_hanging = node_pt(l)->is_hanging();
165 
166  // If the node is hanging
167  if (is_node_hanging)
168  {
169  // Get the HangInfo pointer from the node
170  hang_info_pt = node_pt(l)->hanging_pt();
171 
172  // Read out number of master nodes from hanging data
173  n_master = hang_info_pt->nmaster();
174  }
175  // Otherwise the node is its own master
176  else
177  {
178  // There is only one node to consider; the node itself
179  n_master = 1;
180  }
181 
182  // Loop over the master nodes
183  for (unsigned m = 0; m < n_master; m++)
184  {
185  // Loop over velocity components for equations
186  for (unsigned i = 0; i < DIM; i++)
187  {
188  // If the node is hanging
189  if (is_node_hanging)
190  {
191  // Get the equation number from the master node
192  local_eqn = this->local_hang_eqn(
193  hang_info_pt->master_node_pt(m), u_nodal_index[i]);
194 
195  // Get the hang weight from the master node
196  hang_weight = hang_info_pt->master_weight(m);
197  }
198  // If the node is not hanging
199  else
200  {
201  // Local equation number
202  local_eqn = this->nodal_local_eqn(l, u_nodal_index[i]);
203 
204  // Node contributes with full weight
205  hang_weight = 1.0;
206  }
207 
208  // If it's not a boundary condition
209  if (local_eqn >= 0)
210  {
211  // Add the contribution
212  veloc_mass_diag[local_eqn] += pow(psi[l] * hang_weight, 2) * W;
213  }
214  } // for (unsigned i=0;i<DIM;i++)
215  } // for (unsigned m=0;m<n_master;m++)
216  } // if ((which_one==0)||(which_one==2))
217  } // for (unsigned ipt=0;ipt<n_intpt;ipt++)
218 
219  // Do we want the pressure one?
220  if ((which_one == 0) || (which_one == 1))
221  {
222  // Get the pressure shape functions
223  this->pshape_nst(s, psi_p);
224 
225  // Loop over the pressure shape functions
226  for (unsigned l = 0; l < n_pres; l++)
227  {
228  // If the pressure dof is hanging
229  if (pressure_dof_is_hanging[l])
230  {
231  // Get the HangInfo object
232  hang_info_pt = this->pressure_node_pt(l)->hanging_pt(p_index);
233 
234  // Get the number of master nodes from the pressure node
235  n_master = hang_info_pt->nmaster();
236  }
237  // Otherwise the node is its own master
238  else
239  {
240  // There is only one node to consider; the node itself
241  n_master = 1;
242  }
243 
244  // Loop over the master nodes
245  for (unsigned m = 0; m < n_master; m++)
246  {
247  // If the pressure dof is hanging
248  if (pressure_dof_is_hanging[l])
249  {
250  // Get the local equation from the master node
251  local_eqn =
252  this->local_hang_eqn(hang_info_pt->master_node_pt(m), p_index);
253 
254  // Get the weight for the node
255  hang_weight = hang_info_pt->master_weight(m);
256  }
257  // If the pressure dof is not hanging
258  else
259  {
260  // Get the local equation number of this pressure dof
261  local_eqn = this->p_local_eqn(l);
262 
263  // Get the hang weight associated with this pressure node
264  hang_weight = 1.0;
265  }
266 
267  // If the equation is not pinned
268  if (local_eqn >= 0)
269  {
270  // Add the contribution
271  press_mass_diag[local_eqn] += pow(psi_p[l] * hang_weight, 2) * W;
272  }
273  } // for (unsigned m=0;m<n_master;m++)
274  } // for (unsigned l=0;l<n_pres;l++)
275  } // if ((which_one==0)||(which_one==1))
276  } // for (unsigned ipt=0;ipt<n_intpt;ipt++)
277  } // End of get_pressure_and_velocity_mass_matrix_diagonal
278 
279 
280  //==============================================================
281  /// Compute the residuals for the associated pressure advection
282  /// diffusion problem. Used by the Fp preconditioner.
283  /// flag=1(or 0): do (or don't) compute the Jacobian as well.
284  //==============================================================
285  template<unsigned DIM>
288  Vector<double>& residuals,
289  DenseMatrix<double>& jacobian,
290  const unsigned& flag)
291  {
292  OomphLibWarning("I'm not sure this is correct yet...",
293  OOMPH_CURRENT_FUNCTION,
294  OOMPH_EXCEPTION_LOCATION);
295 
296  // Return immediately if there are no dofs
297  if (ndof() == 0) return;
298 
299  // Find out how many nodes there are
300  unsigned n_node = nnode();
301 
302  // Find out how many pressure dofs there are
303  unsigned n_pres = this->npres_nst();
304 
305  // Find the indices at which the local velocities are stored
306  unsigned u_nodal_index[DIM];
307  for (unsigned i = 0; i < DIM; i++)
308  {
309  u_nodal_index[i] = this->u_index_nst(i);
310  }
311 
312 
313  // Which nodal value represents the pressure? (Negative if pressure
314  // is not based on nodal interpolation).
315  int p_index = this->p_nodal_index_nst();
316 
317  // Local array of booleans that are true if the l-th pressure value is
318  // hanging (avoid repeated virtual function calls)
319  bool pressure_dof_is_hanging[n_pres];
320  // If the pressure is stored at a node
321  if (p_index >= 0)
322  {
323  // Read out whether the pressure is hanging
324  for (unsigned l = 0; l < n_pres; ++l)
325  {
326  pressure_dof_is_hanging[l] =
327  this->pressure_node_pt(l)->is_hanging(p_index);
328  }
329  }
330  // Otherwise the pressure is not stored at a node and so cannot hang
331  else
332  {
333  // pressure advection diffusion doesn't work for this one!
334  throw OomphLibError(
335  "Pressure advection diffusion does not work in this case\n",
336  OOMPH_CURRENT_FUNCTION,
337  OOMPH_EXCEPTION_LOCATION);
338 
339  for (unsigned l = 0; l < n_pres; ++l)
340  {
341  pressure_dof_is_hanging[l] = false;
342  }
343  }
344 
345  // Set up memory for the velocity shape fcts
346  Shape psif(n_node);
347  DShape dpsidx(n_node, DIM);
348 
349  // Set up memory for pressure shape and test functions
350  Shape psip(n_pres), testp(n_pres);
351  DShape dpsip(n_pres, DIM);
352  DShape dtestp(n_pres, DIM);
353 
354  // Number of integration points
355  unsigned n_intpt = integral_pt()->nweight();
356 
357  // Set the Vector to hold local coordinates
358  Vector<double> s(DIM);
359 
360  // Get Physical Variables from Element
361  // Reynolds number must be multiplied by the density ratio
362  double scaled_re = this->re() * this->density_ratio();
363 
364  // Integers to store the local equations and unknowns
365  int local_eqn = 0, local_unknown = 0;
366 
367  // Pointers to hang info objects
368  HangInfo *hang_info_pt = 0, *hang_info2_pt = 0;
369 
370  // Loop over the integration points
371  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
372  {
373  // Assign values of s
374  for (unsigned i = 0; i < DIM; i++) s[i] = integral_pt()->knot(ipt, i);
375 
376  // Get the integral weight
377  double w = integral_pt()->weight(ipt);
378 
379  // Call the derivatives of the veloc shape functions
380  // (Derivs not needed but they are free)
381  double J = this->dshape_eulerian_at_knot(ipt, psif, dpsidx);
382 
383  // Call the pressure shape and test functions
384  this->dpshape_and_dptest_eulerian_nst(s, psip, dpsip, testp, dtestp);
385 
386  // Premultiply the weights and the Jacobian
387  double W = w * J;
388 
389  // Calculate local values of the pressure and velocity components
390  // Allocate
391  Vector<double> interpolated_u(DIM, 0.0);
392  Vector<double> interpolated_x(DIM, 0.0);
393  Vector<double> interpolated_dpdx(DIM, 0.0);
394 
395  // Calculate pressure gradient
396  for (unsigned l = 0; l < n_pres; l++)
397  {
398  for (unsigned i = 0; i < DIM; i++)
399  {
400  interpolated_dpdx[i] += this->p_nst(l) * dpsip(l, i);
401  }
402  }
403 
404  // Calculate velocities
405 
406  // Loop over nodes
407  for (unsigned l = 0; l < n_node; l++)
408  {
409  // Loop over directions
410  for (unsigned i = 0; i < DIM; i++)
411  {
412  // Get the nodal value
413  double u_value = nodal_value(l, u_nodal_index[i]);
414  interpolated_u[i] += u_value * psif[l];
415  interpolated_x[i] += nodal_position(l, i) * psif[l];
416  }
417  }
418 
419  // Source function (for validaton only)
420  double source = 0.0;
421  if (this->Press_adv_diff_source_fct_pt != 0)
422  {
423  source = this->Press_adv_diff_source_fct_pt(interpolated_x);
424  }
425 
426 
427  // Number of master nodes and storage for the weight of the shape function
428  unsigned n_master = 1;
429  double hang_weight = 1.0;
430 
431 
432  // Loop over the pressure shape functions
433  for (unsigned l = 0; l < n_pres; l++)
434  {
435  // If the pressure dof is hanging
436  if (pressure_dof_is_hanging[l])
437  {
438  // Pressure dof is hanging so it must be nodal-based
439  // Get the hang info object
440  hang_info_pt = this->pressure_node_pt(l)->hanging_pt(p_index);
441 
442  // Get the number of master nodes from the pressure node
443  n_master = hang_info_pt->nmaster();
444  }
445  // Otherwise the node is its own master
446  else
447  {
448  n_master = 1;
449  }
450 
451  // Loop over the master nodes
452  for (unsigned m = 0; m < n_master; m++)
453  {
454  // Get the number of the unknown
455  // If the pressure dof is hanging
456  if (pressure_dof_is_hanging[l])
457  {
458  // Get the local equation from the master node
459  local_eqn =
460  this->local_hang_eqn(hang_info_pt->master_node_pt(m), p_index);
461  // Get the weight for the node
462  hang_weight = hang_info_pt->master_weight(m);
463  }
464  else
465  {
466  local_eqn = this->p_local_eqn(l);
467  hang_weight = 1.0;
468  }
469 
470  // If the equation is not pinned
471  if (local_eqn >= 0)
472  {
473  residuals[local_eqn] -= source * testp[l] * W * hang_weight;
474  for (unsigned k = 0; k < DIM; k++)
475  {
476  residuals[local_eqn] +=
477  interpolated_dpdx[k] *
478  (scaled_re * interpolated_u[k] * testp[l] + dtestp(l, k)) * W *
479  hang_weight;
480  }
481 
482  // Jacobian too?
483  if (flag)
484  {
485  // Number of master nodes and weights
486  unsigned n_master2 = 1;
487  double hang_weight2 = 1.0;
488 
489  // Loop over the pressure shape functions
490  for (unsigned l2 = 0; l2 < n_pres; l2++)
491  {
492  // If the pressure dof is hanging
493  if (pressure_dof_is_hanging[l2])
494  {
495  hang_info2_pt =
496  this->pressure_node_pt(l2)->hanging_pt(p_index);
497  // Pressure dof is hanging so it must be nodal-based
498  // Get the number of master nodes from the pressure node
499  n_master2 = hang_info2_pt->nmaster();
500  }
501  // Otherwise the node is its own master
502  else
503  {
504  n_master2 = 1;
505  }
506 
507  // Loop over the master nodes
508  for (unsigned m2 = 0; m2 < n_master2; m2++)
509  {
510  // Get the number of the unknown
511  // If the pressure dof is hanging
512  if (pressure_dof_is_hanging[l2])
513  {
514  // Get the unknown from the master node
515  local_unknown = this->local_hang_eqn(
516  hang_info2_pt->master_node_pt(m2), p_index);
517  // Get the weight from the hanging object
518  hang_weight2 = hang_info2_pt->master_weight(m2);
519  }
520  else
521  {
522  local_unknown = this->p_local_eqn(l2);
523  hang_weight2 = 1.0;
524  }
525 
526  // If the unknown is not pinned
527  if (local_unknown >= 0)
528  {
529  if ((int(eqn_number(local_eqn)) !=
530  this->Pinned_fp_pressure_eqn) &&
531  (int(eqn_number(local_unknown)) !=
532  this->Pinned_fp_pressure_eqn))
533  {
534  for (unsigned k = 0; k < DIM; k++)
535  {
536  jacobian(local_eqn, local_unknown) +=
537  dtestp(l2, k) *
538  (scaled_re * interpolated_u[k] * testp[l] +
539  dtestp(l, k)) *
540  W * hang_weight * hang_weight2;
541  }
542  }
543  else
544  {
545  if ((int(eqn_number(local_eqn)) ==
546  this->Pinned_fp_pressure_eqn) &&
547  (int(eqn_number(local_unknown)) ==
548  this->Pinned_fp_pressure_eqn))
549  {
550  jacobian(local_eqn, local_unknown) = 1.0;
551  }
552  }
553  }
554  }
555  }
556  } /*End of Jacobian calculation*/
557  } // End of if not boundary condition
558  } // End of loop over master nodes
559  } // End of loop over l
560  } // end of integration loop
561 
562  // Now add boundary contributions from Robin BCs
563  unsigned nrobin =
564  this->Pressure_advection_diffusion_robin_element_pt.size();
565  for (unsigned e = 0; e < nrobin; e++)
566  {
567  this->Pressure_advection_diffusion_robin_element_pt[e]
568  ->fill_in_generic_residual_contribution_fp_press_adv_diff_robin_bc(
569  residuals, jacobian, flag);
570  }
571  }
572 
573 
574  //========================================================================
575  /// Add element's contribution to the elemental
576  /// residual vector and/or Jacobian matrix.
577  /// flag=1: compute both
578  /// flag=0: compute only residual vector
579  //========================================================================
580  template<unsigned DIM>
583  DenseMatrix<double>& jacobian,
584  DenseMatrix<double>& mass_matrix,
585  const unsigned& flag)
586  {
587  // Return immediately if there are no dofs
588  if (ndof() == 0) return;
589 
590  // Find out how many nodes there are
591  unsigned n_node = nnode();
592 
593  // Find out how many pressure dofs there are
594  unsigned n_pres = this->npres_nst();
595 
596  // Allocate storage for the indices of the velocity components
597  unsigned u_nodal_index[DIM];
598 
599  // Loop over the velocity components
600  for (unsigned i = 0; i < DIM; i++)
601  {
602  // Find the index at which the i-th local velocity is stored
603  u_nodal_index[i] = this->u_index_nst(i);
604  }
605 
606  // Which nodal value represents the pressure? (Negative if pressure
607  // is not based on nodal interpolation).
608  int p_index = this->p_nodal_index_nst();
609 
610  // Local array of booleans that are true if the l-th pressure value is
611  // hanging (avoid repeated virtual function calls)
612  bool pressure_dof_is_hanging[n_pres];
613 
614  // If the pressure is stored at a node
615  if (p_index >= 0)
616  {
617  // Loop over the pressure nodes
618  for (unsigned l = 0; l < n_pres; ++l)
619  {
620  // Get the hang status of the l-th pressure node
621  pressure_dof_is_hanging[l] =
622  this->pressure_node_pt(l)->is_hanging(p_index);
623  }
624  }
625  // Otherwise the pressure is not stored at a node and so cannot hang
626  else
627  {
628  // Loop over the pressure nodes
629  for (unsigned l = 0; l < n_pres; ++l)
630  {
631  // Indicate that the l-th pressure node is not hangings
632  pressure_dof_is_hanging[l] = false;
633  }
634  } // if (p_index>=0)
635 
636  // Set up memory for the shape functions
637  Shape psif(n_node);
638 
639  // Set up memory for the test functions
640  Shape testf(n_node);
641 
642  // Allocate space for the derivatives of the shape functions
643  DShape dpsifdx(n_node, DIM + 1);
644 
645  // Allocate space for the derivatives of the test functions
646  DShape dtestfdx(n_node, DIM + 1);
647 
648  // Set up memory for pressure shape functions
649  Shape psip(n_pres);
650 
651  // Set up memory for pressure test functions
652  Shape testp(n_pres);
653 
654  // Number of integration points
655  unsigned n_intpt = integral_pt()->nweight();
656 
657  // Set the Vector to hold local coordinates
658  Vector<double> s(DIM + 1, 0.0);
659 
660  //-------------------------------------
661  // Get physical variables from element:
662  //-------------------------------------
663  // Reynolds number must be multiplied by the density ratio
664  double scaled_re = this->re() * this->density_ratio();
665 
666  // Get the scaled Womersley value
667  double scaled_re_st = this->re_st() * this->density_ratio();
668 
669  // Get the scaled Womersley value differentiated w.r.t. the Strouhal number
670  double scaled_dre_st_dre_st = this->density_ratio();
671 
672  // Get the scaled Reynolds / Froude number
673  double scaled_re_inv_fr = this->re_invfr() * this->density_ratio();
674 
675  // Get the viscosity ratio
676  double visc_ratio = this->viscosity_ratio();
677 
678  // Get the gravity vector
679  Vector<double> G = this->g();
680 
681  // Integer to store the local equation number
682  int local_eqn = 0;
683 
684  // Integer to store the local unknown number
685  int local_unknown = 0;
686 
687  // Pointers to first hang info object
688  HangInfo* hang_info_pt = 0;
689 
690  // Pointers to second hang info object
691  HangInfo* hang_info2_pt = 0;
692 
693  // Loop over the integration points
694  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
695  {
696  // Assign values of s
697  for (unsigned i = 0; i < DIM + 1; i++)
698  {
699  // Calculate the i-th local coordinate
700  s[i] = integral_pt()->knot(ipt, i);
701  }
702 
703  // Get the integral weight
704  double w = integral_pt()->weight(ipt);
705 
706  // Call the derivatives of the shape and test functions
707  double J = this->dshape_and_dtest_eulerian_at_knot_nst(
708  ipt, psif, dpsifdx, testf, dtestfdx);
709 
710  // Call the pressure shape and test functions
711  this->pshape_nst(s, psip, testp);
712 
713  // Pre-multiply the weights and the Jacobian
714  double W = w * J;
715 
716  // Storage for the interpolated time value
717  double interpolated_t = 0.0;
718 
719  // Storage for the interpolated pressure value
720  double interpolated_p = 0.0;
721 
722  // Storage for the spatial coordinates
723  Vector<double> interpolated_x(DIM, 0.0);
724 
725  // Storage for the interpolated velocity components
726  Vector<double> interpolated_u(DIM, 0.0);
727 
728  // Storage for the interpolated time-derivative of the velocities
729  Vector<double> interpolated_dudt(DIM, 0.0);
730 
731  // Storage for the mesh velocity
732  Vector<double> mesh_velocity(DIM, 0.0);
733 
734  // Storage for the spatial derivatives of the velocity components
735  DenseMatrix<double> interpolated_dudx(DIM, DIM, 0.0);
736 
737  // Calculate pressure
738  for (unsigned l = 0; l < n_pres; l++)
739  {
740  // Update the current approximation to the interpolated pressure
741  interpolated_p += this->p_nst(l) * psip[l];
742  }
743 
744  //-------------------------------------------------------------------
745  // Calculate velocities, derivatives, source function and body force:
746  //-------------------------------------------------------------------
747  // Loop over nodes
748  for (unsigned l = 0; l < n_node; l++)
749  {
750  // Update the interpolated time value
751  interpolated_t += this->nodal_position(l, DIM) * psif(l);
752 
753  // Loop over coordinate directions
754  for (unsigned i = 0; i < DIM; i++)
755  {
756  // Get the nodal value
757  double u_value = this->nodal_value(l, u_nodal_index[i]);
758 
759  // Update the i-th interpolated velocity component
760  interpolated_u[i] += u_value * psif[l];
761 
762  // Update the i-th interpolated coordinate value
763  interpolated_x[i] += this->nodal_position(l, i) * psif[l];
764 
765  // Update the interpolated du_i/dt value
766  interpolated_dudt[i] += u_value * dpsifdx(l, DIM);
767 
768  // Loop over derivative directions
769  for (unsigned j = 0; j < DIM; j++)
770  {
771  // Update the interpolated du_i/dx_j value
772  interpolated_dudx(i, j) += u_value * dpsifdx(l, j);
773  }
774  } // for (unsigned i=0;i<DIM;i++)
775  } // for (unsigned l=0;l<n_node;l++)
776 
777  // If ALE is enabled
778  if (!(this->ALE_is_disabled))
779  {
780  // Loop over nodes
781  for (unsigned l = 0; l < n_node; l++)
782  {
783  // Loop over directions
784  for (unsigned i = 0; i < DIM; i++)
785  {
786  // Update the i-th mesh velocity component
787  mesh_velocity[i] += this->nodal_position(l, i) * dpsifdx(l, DIM);
788  }
789  } // for (unsigned l=0;l<n_node;l++)
790  } // if (!(this->ALE_is_disabled))
791 
792  // Allocate space for the body force
793  Vector<double> body_force(DIM, 0.0);
794 
795  // Get the user-defined body force term
796  this->get_body_force_nst(
797  interpolated_t, ipt, s, interpolated_x, body_force);
798 
799  // Get the user-defined source function
800  double source = this->get_source_nst(interpolated_t, ipt, interpolated_x);
801 
802  //---------------------------------
803  // Assemble residuals and Jacobian:
804  //---------------------------------
805  //--------------------
806  // Momentum equations:
807  //--------------------
808  // Number of master nodes
809  unsigned n_master = 1;
810 
811  // Storage for the weight of the shape function
812  double hang_weight = 1.0;
813 
814  // Loop over the test functions
815  for (unsigned l = 0; l < n_node; l++)
816  {
817  // Local boolean to indicate whether the node is hanging
818  bool is_node_hanging = node_pt(l)->is_hanging();
819 
820  // If the node is hanging
821  if (is_node_hanging)
822  {
823  // Get the HangInfo object associated with the l-th node
824  hang_info_pt = node_pt(l)->hanging_pt();
825 
826  // Read out number of master nodes from hanging data
827  n_master = hang_info_pt->nmaster();
828  }
829  // Otherwise the node is its own master
830  else
831  {
832  // There is only one node to consider; the node itself
833  n_master = 1;
834  }
835 
836  // Loop over the master nodes
837  for (unsigned m = 0; m < n_master; m++)
838  {
839  // Loop over velocity components
840  for (unsigned i = 0; i < DIM; i++)
841  {
842  // Check if the node is hanging
843  if (is_node_hanging)
844  {
845  // Get the equation number from the master node
846  local_eqn = this->local_hang_eqn(hang_info_pt->master_node_pt(m),
847  u_nodal_index[i]);
848 
849  // Get the hang weight from the master node
850  hang_weight = hang_info_pt->master_weight(m);
851  }
852  // If the node is not hanging
853  else
854  {
855  // Local equation number
856  local_eqn = this->nodal_local_eqn(l, u_nodal_index[i]);
857 
858  // Node contributes with full weight
859  hang_weight = 1.0;
860  }
861 
862  // If it's not a boundary condition
863  if (local_eqn >= 0)
864  {
865  // Add the user-defined body force terms
866  residuals[local_eqn] +=
867  body_force[i] * testf[l] * W * hang_weight;
868 
869  // Add the gravitational body force term
870  residuals[local_eqn] +=
871  scaled_re_inv_fr * testf[l] * G[i] * W * hang_weight;
872 
873  // Add the pressure gradient term
874  residuals[local_eqn] +=
875  interpolated_p * dtestfdx(l, i) * W * hang_weight;
876 
877  // Add in the contribution from the time derivative
878  residuals[local_eqn] -= (scaled_re_st * interpolated_dudt[i] *
879  testf[l] * W * hang_weight);
880 
881  // If ALE is enabled
882  if (!(this->ALE_is_disabled))
883  {
884  // Loop over the coordinate directions
885  for (unsigned k = 0; k < DIM; k++)
886  {
887  // Add in the mesh velocity contribution
888  residuals[local_eqn] +=
889  (scaled_re_st * mesh_velocity[k] * interpolated_dudx(i, k) *
890  testf[l] * W * hang_weight);
891  }
892  } // if (!(this->ALE_is_disabled))
893 
894  // Loop over the coordinate directions
895  for (unsigned k = 0; k < DIM; k++)
896  {
897  // Add in the convective term contribution
898  residuals[local_eqn] -=
899  (scaled_re * interpolated_u[k] * interpolated_dudx(i, k) *
900  testf[l] * W * hang_weight);
901  }
902 
903  // Loop over the coordinate directions
904  for (unsigned k = 0; k < DIM; k++)
905  {
906  // Add in the stress tensor terms:
907  // NOTE: The viscosity ratio needs to go in here to ensure
908  // continuity of normal stress is satisfied even in flows
909  // with zero pressure gradient!
910  residuals[local_eqn] -=
911  ((interpolated_dudx(i, k) +
912  this->Gamma[i] * interpolated_dudx(k, i)) *
913  visc_ratio * dtestfdx(l, k) * W * hang_weight);
914  }
915 
916  //------------------------
917  // Calculate the Jacobian:
918  //------------------------
919  // If we also need to construct the Jacobian
920  if (flag)
921  {
922  // Number of master nodes
923  unsigned n_master2 = 1;
924 
925  // Storage for the weight of the shape function
926  double hang_weight2 = 1.0;
927 
928  // Loop over the velocity nodes for columns
929  for (unsigned l2 = 0; l2 < n_node; l2++)
930  {
931  // Local boolean to indicate whether the node is hanging
932  bool is_node2_hanging = node_pt(l2)->is_hanging();
933 
934  // If the node is hanging
935  if (is_node2_hanging)
936  {
937  // Get the HangInfo object associated with the l-th node
938  hang_info2_pt = node_pt(l2)->hanging_pt();
939 
940  // Read out number of master nodes from hanging data
941  n_master2 = hang_info2_pt->nmaster();
942  }
943  // Otherwise the node is its own master
944  else
945  {
946  // There is only one node to consider; the node itself
947  n_master2 = 1;
948  }
949 
950  // Loop over the master nodes
951  for (unsigned m2 = 0; m2 < n_master2; m2++)
952  {
953  // Loop over the velocity components
954  for (unsigned i2 = 0; i2 < DIM; i2++)
955  {
956  // Check if the node is hanging
957  if (is_node2_hanging)
958  {
959  // Get the equation number from the master node
960  local_unknown = this->local_hang_eqn(
961  hang_info2_pt->master_node_pt(m2), u_nodal_index[i2]);
962 
963  // Get the hang weight from the master node
964  hang_weight2 = hang_info2_pt->master_weight(m2);
965  }
966  // If the node is not hanging
967  else
968  {
969  // Get the local equation number
970  local_unknown =
971  this->nodal_local_eqn(l2, u_nodal_index[i2]);
972 
973  // Node contributes with full weight
974  hang_weight2 = 1.0;
975  }
976 
977  // If the unknown is non-zero
978  if (local_unknown >= 0)
979  {
980  // Add contribution to elemental matrix
981  jacobian(local_eqn, local_unknown) -=
982  (visc_ratio * this->Gamma[i] * dpsifdx(l2, i) *
983  dtestfdx(l, i2) * W * hang_weight * hang_weight2);
984 
985  // Now add in the inertial terms
986  jacobian(local_eqn, local_unknown) -=
987  (scaled_re * psif[l2] * interpolated_dudx(i, i2) *
988  testf[l] * W * hang_weight * hang_weight2);
989 
990  // Extra component if i2=i
991  if (i2 == i)
992  {
993  // If we also need to construct the mass matrix (only
994  // diagonal entries)
995  if (flag == 2)
996  {
997  // NOTE: This is positive because the mass matrix is
998  // taken to the other side of the equation when
999  // formulating the generalised eigenproblem.
1000  mass_matrix(local_eqn, local_unknown) +=
1001  (scaled_re_st * psif[l2] * testf[l] * W *
1002  hang_weight * hang_weight2);
1003  }
1004 
1005  // Add in the time-derivative contribution
1006  jacobian(local_eqn, local_unknown) -=
1007  (scaled_re_st * dpsifdx(l2, DIM) * testf[l] * W *
1008  hang_weight * hang_weight2);
1009 
1010  // Loop over the velocity components
1011  for (unsigned k = 0; k < DIM; k++)
1012  {
1013  // Add in the convective term contribution
1014  jacobian(local_eqn, local_unknown) -=
1015  (scaled_re * interpolated_u[k] * dpsifdx(l2, k) *
1016  testf[l] * W * hang_weight * hang_weight2);
1017  }
1018 
1019  // If ALE is enabled
1020  if (!(this->ALE_is_disabled))
1021  {
1022  // Loop over the velocity components
1023  for (unsigned k = 0; k < DIM; k++)
1024  {
1025  // Add in the mesh velocity contribution
1026  jacobian(local_eqn, local_unknown) +=
1027  (scaled_re_st * mesh_velocity[k] *
1028  dpsifdx(l2, k) * testf[l] * W * hang_weight *
1029  hang_weight2);
1030  }
1031  } // if (!(this->ALE_is_disabled))
1032 
1033  // Loop over velocity components
1034  for (unsigned k = 0; k < DIM; k++)
1035  {
1036  // Add in the velocity gradient terms
1037  jacobian(local_eqn, local_unknown) -=
1038  (visc_ratio * dpsifdx(l2, k) * dtestfdx(l, k) *
1039  W * hang_weight * hang_weight2);
1040  }
1041  } // if (i2==i)
1042  } // if (local_unknown>=0)
1043  } // for (unsigned i2=0;i2<DIM;i2++)
1044  } // for (unsigned m2=0;m2<n_master2;m2++)
1045  } // for (unsigned l2=0;l2<n_node;l2++)
1046 
1047  // Loop over the pressure shape functions
1048  for (unsigned l2 = 0; l2 < n_pres; l2++)
1049  {
1050  // If the pressure dof is hanging
1051  if (pressure_dof_is_hanging[l2])
1052  {
1053  // Get the HangInfo object associated with the l2-th
1054  // pressure node
1055  hang_info2_pt =
1056  this->pressure_node_pt(l2)->hanging_pt(p_index);
1057 
1058  // Get the number of master nodes from the pressure node
1059  n_master2 = hang_info2_pt->nmaster();
1060  }
1061  // Otherwise the node is its own master
1062  else
1063  {
1064  // There is only one node to consider; the node itself
1065  n_master2 = 1;
1066  }
1067 
1068  // Loop over the master nodes
1069  for (unsigned m2 = 0; m2 < n_master2; m2++)
1070  {
1071  // If the pressure dof is hanging
1072  if (pressure_dof_is_hanging[l2])
1073  {
1074  // Get the unknown from the master node
1075  local_unknown = this->local_hang_eqn(
1076  hang_info2_pt->master_node_pt(m2), p_index);
1077 
1078  // Get the weight from the HangInfo object
1079  hang_weight2 = hang_info2_pt->master_weight(m2);
1080  }
1081  // If the node is not hanging
1082  else
1083  {
1084  // Get the local equation number
1085  local_unknown = this->p_local_eqn(l2);
1086 
1087  // Node contributes with full weight
1088  hang_weight2 = 1.0;
1089  }
1090 
1091  // If the unknown is not pinned
1092  if (local_unknown >= 0)
1093  {
1094  jacobian(local_eqn, local_unknown) +=
1095  (psip[l2] * dtestfdx(l, i) * W * hang_weight *
1096  hang_weight2);
1097  }
1098  } // for (unsigned m2=0;m2<n_master2;m2++)
1099  } // for (unsigned l2=0;l2<n_pres;l2++)
1100 
1101  //------------------------------------
1102  // Calculate external data information
1103  //------------------------------------
1104  // If we're storing the Strouhal number as external data then we
1105  // need to calculate dr/d(St) in the elemental Jacobian
1106  if (this->ReynoldsStrouhal_is_stored_as_external_data)
1107  {
1108  // The index of the external data (there's only one!)
1109  unsigned data_index = 0;
1110 
1111  // The index of the unknown value stored in the external data
1112  unsigned value_index = 0;
1113 
1114  // Get the local equation number associated with the extra
1115  // unknown
1116  local_unknown =
1117  this->external_local_eqn(data_index, value_index);
1118 
1119  // If we're at a non-zero degree of freedom add in the entry
1120  if (local_unknown >= 0)
1121  {
1122  // Add in the contribution from the time derivative
1123  jacobian(local_eqn, local_unknown) -=
1124  (scaled_dre_st_dre_st * interpolated_dudt[i] * testf[l] *
1125  W * hang_weight);
1126 
1127  // If ALE is enabled
1128  if (!this->ALE_is_disabled)
1129  {
1130  // Loop over the coordinate directions
1131  for (unsigned k = 0; k < DIM; k++)
1132  {
1133  // Add in the mesh velocity contribution
1134  jacobian(local_eqn, local_unknown) +=
1135  (scaled_dre_st_dre_st * mesh_velocity[k] *
1136  interpolated_dudx(i, k) * testf[l] * W *
1137  hang_weight);
1138  }
1139  } // if (!ALE_is_disabled)
1140  } // if (local_unknown>=0)
1141  } // if (Strouhal_is_stored_as_external_data)
1142  } // if (flag)
1143  } // if (local_eqn>=0)
1144  } // for (unsigned i=0;i<DIM;i++)
1145  } // for (unsigned m=0;m<n_master;m++)
1146  } // for (unsigned l=0;l<n_node;l++)
1147 
1148  //---------------------
1149  // Continuity equation:
1150  //---------------------
1151  // Loop over the pressure shape functions
1152  for (unsigned l = 0; l < n_pres; l++)
1153  {
1154  // If the pressure dof is hanging
1155  if (pressure_dof_is_hanging[l])
1156  {
1157  // Get the HangInfo object associated with the l2-th pressure node
1158  hang_info_pt = this->pressure_node_pt(l)->hanging_pt(p_index);
1159 
1160  // Get the number of master nodes from the pressure node
1161  n_master = hang_info_pt->nmaster();
1162  }
1163  // Otherwise the node is its own master
1164  else
1165  {
1166  // There is only one node to consider; the node itself
1167  n_master = 1;
1168  }
1169 
1170  // Loop over the master nodes
1171  for (unsigned m = 0; m < n_master; m++)
1172  {
1173  // If the pressure dof is hanging
1174  if (pressure_dof_is_hanging[l])
1175  {
1176  // Get the unknown from the master node
1177  local_eqn =
1178  this->local_hang_eqn(hang_info_pt->master_node_pt(m), p_index);
1179 
1180  // Get the weight from the HangInfo object
1181  hang_weight = hang_info_pt->master_weight(m);
1182  }
1183  // If the node is not hanging
1184  else
1185  {
1186  // Get the local equation number
1187  local_eqn = this->p_local_eqn(l);
1188 
1189  // Node contributes with full weight
1190  hang_weight = 1.0;
1191  }
1192 
1193  // If the equation is not pinned
1194  if (local_eqn >= 0)
1195  {
1196  // Add in the source term contribution
1197  residuals[local_eqn] -= source * testp[l] * W * hang_weight;
1198 
1199  // Loop over velocity components
1200  for (unsigned k = 0; k < DIM; k++)
1201  {
1202  // Add in the velocity gradient terms
1203  residuals[local_eqn] +=
1204  interpolated_dudx(k, k) * testp[l] * W * hang_weight;
1205  }
1206 
1207  //------------------------
1208  // Calculate the Jacobian:
1209  //------------------------
1210  // If we also need to construct the Jacobian
1211  if (flag)
1212  {
1213  // Number of master nodes
1214  unsigned n_master2 = 1;
1215 
1216  // Storage for the weight of the shape function
1217  double hang_weight2 = 1.0;
1218 
1219  // Loop over the velocity nodes for columns
1220  for (unsigned l2 = 0; l2 < n_node; l2++)
1221  {
1222  // Local boolean to indicate whether the node is hanging
1223  bool is_node2_hanging = node_pt(l2)->is_hanging();
1224 
1225  // If the node is hanging
1226  if (is_node2_hanging)
1227  {
1228  // Get the HangInfo object associated with the l2-th node
1229  hang_info2_pt = node_pt(l2)->hanging_pt();
1230 
1231  // Read out number of master nodes from hanging data
1232  n_master2 = hang_info2_pt->nmaster();
1233  }
1234  // Otherwise the node is its own master
1235  else
1236  {
1237  // There is only one node to consider; the node itself
1238  n_master2 = 1;
1239  }
1240 
1241  // Loop over the master nodes
1242  for (unsigned m2 = 0; m2 < n_master2; m2++)
1243  {
1244  // Loop over the velocity components
1245  for (unsigned i2 = 0; i2 < DIM; i2++)
1246  {
1247  // If the node is hanging
1248  if (is_node2_hanging)
1249  {
1250  // Get the equation number from the master node
1251  local_unknown = this->local_hang_eqn(
1252  hang_info2_pt->master_node_pt(m2), u_nodal_index[i2]);
1253 
1254  // Get the weight from the HangInfo object
1255  hang_weight2 = hang_info2_pt->master_weight(m2);
1256  }
1257  // If the node is not hanging
1258  else
1259  {
1260  // Get the local equation number
1261  local_unknown =
1262  this->nodal_local_eqn(l2, u_nodal_index[i2]);
1263 
1264  // Node contributes with full weight
1265  hang_weight2 = 1.0;
1266  }
1267 
1268  // If the unknown is not pinned
1269  if (local_unknown >= 0)
1270  {
1271  // Add in the velocity gradient contribution
1272  jacobian(local_eqn, local_unknown) +=
1273  (dpsifdx(l2, i2) * testp[l] * W * hang_weight *
1274  hang_weight2);
1275  }
1276  } // for (unsigned i2=0;i2<DIM;i2++)s
1277  } // for (unsigned m2=0;m2<n_master2;m2++)
1278  } // for (unsigned l2=0;l2<n_node;l2++)
1279  } // if (flag)
1280  } // if (local_eqn>=0)
1281  } // for (unsigned m=0;m<n_master;m++)
1282  } // for (unsigned l=0;l<n_pres;l++)
1283  } // for (unsigned ipt=0;ipt<n_intpt;ipt++)
1284  } // End of fill_in_generic_residual_contribution_nst
1285 
1286 
1287  //======================================================================
1288  /// Compute derivatives of elemental residual vector with respect
1289  /// to nodal coordinates.
1290  /// dresidual_dnodal_coordinates(l,i,j) = d res(l) / dX_{ij}
1291  /// Overloads the FD-based version in the FE base class.
1292  //======================================================================
1293  template<unsigned DIM>
1295  DIM>::get_dresidual_dnodal_coordinates(RankThreeTensor<double>&
1296  dresidual_dnodal_coordinates)
1297  {
1298  // Throw an error
1299  throw OomphLibError("Space-time version has not been implemented yet!",
1300  OOMPH_CURRENT_FUNCTION,
1301  OOMPH_EXCEPTION_LOCATION);
1302  } // End of
1303 
1304 
1305  //====================================================================
1306  /// Force build of templates
1307  //====================================================================
1310 } // namespace oomph
e
Definition: cfortran.h:571
static char t char * s
Definition: cfortran.h:568
cstr elem_len * i
Definition: cfortran.h:603
A Class for the derivatives of shape functions The class design is essentially the same as Shape,...
Definition: shape.h:278
Class that contains data for hanging nodes.
Definition: nodes.h:742
double const & master_weight(const unsigned &i) const
Return weight for dofs on i-th master node.
Definition: nodes.h:808
Node *const & master_node_pt(const unsigned &i) const
Return a pointer to the i-th master node.
Definition: nodes.h:791
unsigned nmaster() const
Return the number of master nodes.
Definition: nodes.h:785
An OomphLibError object which should be thrown when an run-time error is encountered....
An OomphLibWarning object which should be created as a temporary object to issue a warning....
////////////////////////////////////////////////////////////////// //////////////////////////////////...
Definition: matrices.h:1370
Refineable version of Taylor Hood elements. These classes can be written in total generality.
//////////////////////////////////////////////////////////////////// ////////////////////////////////...
void get_pressure_and_velocity_mass_matrix_diagonal(Vector< double > &press_mass_diag, Vector< double > &veloc_mass_diag, const unsigned &which_one=0)
Compute the diagonal of the velocity/pressure mass matrices. If which one=0, both are computed,...
void fill_in_generic_residual_contribution_nst(Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix, const unsigned &compute_jacobian_flag)
Add the elements contribution to elemental residual vector and/or Jacobian matrix....
void fill_in_generic_pressure_advection_diffusion_contribution_nst(Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &compute_jacobian_flag)
Compute the residuals for the associated pressure advection diffusion problem. Used by the Fp precond...
A Class for shape functions. In simple cases, the shape functions have only one index that can be tho...
Definition: shape.h:76
//////////////////////////////////////////////////////////////////// ////////////////////////////////...