File: Pos_Formulation.cpp

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// GetDP - Copyright (C) 1997-2016 P. Dular and C. Geuzaine, University of Liege
//
// See the LICENSE.txt file for license information. Please report all
// bugs and problems to the public mailing list <getdp@onelab.info>.

#include <string.h>
#include <math.h>
#include "ProData.h"
#include "DofData.h"
#include "GeoData.h"
#include "Get_DofOfElement.h"
#include "Cal_Quantity.h"
#include "Pos_Print.h"
#include "Pos_Format.h"
#include "ListUtils.h"
#include "Message.h"
#include "OS.h"
#if defined(HAVE_GMSH)
#include <gmsh/Gmsh.h>
#include <gmsh/MVertex.h>
#include <gmsh/GModel.h>
#include <gmsh/PView.h>
#include <gmsh/PViewData.h>
#endif
#include "MallocUtils.h"
#include "SolvingAnalyse.h"
#if defined(HAVE_GSL)
#include <gsl/gsl_errno.h>
#include <gsl/gsl_spline.h>
#endif

#define TWO_PI             6.2831853071795865

extern struct Problem Problem_S ;
extern struct CurrentData Current ;
extern int    Flag_BIN, Flag_GMSH_VERSION ;
extern char   *Name_Path ;

FILE *PostStream = stdout;
char PostFileName[256];

/* ------------------------------------------------------------------------ */
/*  P o s _ F e m F o r m u l a t i o n                                     */
/* ------------------------------------------------------------------------ */

void  Pos_FemFormulation(struct Formulation       *Formulation_P,
			 struct PostQuantity      *NCPQ_P,
			 struct PostQuantity      *CPQ_P,
			 int                       Order,
			 struct PostSubOperation  *PostSubOperation_P)
{
  struct Element           Element ;
  struct DefineQuantity   *DefineQuantity_P0 ;
  struct QuantityStorage  *QuantityStorage_P0, QuantityStorage ;

  List_T   *QuantityStorage_L ;
  int       i ;

  Get_InitDofOfElement(&Element) ;

  DefineQuantity_P0 = (struct DefineQuantity*)
    List_Pointer(Formulation_P->DefineQuantity, 0) ;
  QuantityStorage_L = List_Create(List_Nbr(Formulation_P->DefineQuantity),  1,
				  sizeof (struct QuantityStorage) ) ;

  for(i = 0 ; i < List_Nbr(Formulation_P->DefineQuantity) ; i++) {
    QuantityStorage.DefineQuantity = DefineQuantity_P0 + i ;

    if(QuantityStorage.DefineQuantity->Type == INTEGRALQUANTITY &&
       QuantityStorage.DefineQuantity->IntegralQuantity.DefineQuantityIndexDof < 0){
      QuantityStorage.TypeQuantity = VECTOR ; /* on ne sait pas... */
    }
    else{
      QuantityStorage.TypeQuantity =
	((struct FunctionSpace *)
	 List_Pointer(Problem_S.FunctionSpace,
		      (DefineQuantity_P0+i)->FunctionSpaceIndex))->Type ;
    }

    QuantityStorage.NumLastElementForFunctionSpace = 0 ;
    List_Add(QuantityStorage_L, &QuantityStorage) ;
  }

  QuantityStorage_P0 = (struct QuantityStorage*)List_Pointer(QuantityStorage_L, 0) ;

  switch (PostSubOperation_P->Type) {

  case POP_PRINT :
    switch (PostSubOperation_P->SubType) {
    case PRINT_ONREGION :
      Pos_PrintOnRegion(NCPQ_P, CPQ_P, Order, DefineQuantity_P0,
			QuantityStorage_P0, PostSubOperation_P) ;
      break ;
    case PRINT_ONELEMENTSOF :
    case PRINT_ONGRID   :
      Pos_PrintOnElementsOf(NCPQ_P, CPQ_P, Order, DefineQuantity_P0,
			    QuantityStorage_P0, PostSubOperation_P) ;
      break ;
    case PRINT_ONSECTION_1D :
    case PRINT_ONSECTION_2D :
      Pos_PrintOnSection(NCPQ_P, CPQ_P, Order, DefineQuantity_P0,
			 QuantityStorage_P0, PostSubOperation_P) ;
      break ;
    case PRINT_ONGRID_0D    :
    case PRINT_ONGRID_1D    :
    case PRINT_ONGRID_2D    :
    case PRINT_ONGRID_3D    :
    case PRINT_ONGRID_PARAM :
      Pos_PrintOnGrid(NCPQ_P, CPQ_P, Order, DefineQuantity_P0,
		      QuantityStorage_P0, PostSubOperation_P) ;
      break ;
    case PRINT_WITHARGUMENT :
      Pos_PrintWithArgument(NCPQ_P, CPQ_P, Order, DefineQuantity_P0,
			    QuantityStorage_P0, PostSubOperation_P) ;
      break ;
    default :
      Message::Error("Unknown Operation type for Print");
      break;
    }
    break ;

  case POP_EXPRESSION :
    Pos_PrintExpression(PostSubOperation_P);
    break;

  case POP_GROUP :
    Pos_PrintGroup(PostSubOperation_P);
    break;

  default :
    Message::Error("Unknown PostSubOperation type") ;
    break;
  }

  List_Delete(QuantityStorage_L);
}

/* ------------------------------------------------------------------------ */
/*  P o s _ I n i t T i m e S t e p s                                       */
/* ------------------------------------------------------------------------ */

int Pos_InitTimeSteps(struct PostSubOperation *PostSubOperation_P)
{
  int iTime, NbTimeStep;
  double TOL = 1.e-15;

  // last time step only
  if(PostSubOperation_P->LastTimeStepOnly ||
     PostSubOperation_P->AppendTimeStepToFileName){
    iTime = List_Nbr(Current.DofData->Solutions) - 1;
    List_Reset(PostSubOperation_P->TimeStep_L);
    List_Add(PostSubOperation_P->TimeStep_L, &iTime);
    return 1;
  }

  // specific time values or time interval
  if(PostSubOperation_P->TimeInterval_Flag ||
     List_Nbr(PostSubOperation_P->TimeValue_L) ||
     List_Nbr(PostSubOperation_P->TimeImagValue_L)){
    List_Reset(PostSubOperation_P->TimeStep_L);
    for(int i = 0; i < List_Nbr(Current.DofData->Solutions); i++){
      Solution *s = (struct Solution*)List_Pointer(Current.DofData->Solutions, i);
      int step = s->TimeStep;
      double time = s->Time, timeImag = s->TimeImag;
      if(PostSubOperation_P->TimeInterval_Flag){
        if((time >= PostSubOperation_P->TimeInterval[0]-TOL) &&
           (time <= PostSubOperation_P->TimeInterval[1]+TOL)){
          List_Insert(PostSubOperation_P->TimeStep_L, &step, fcmp_int);
        }
      }
      else{
        for(int j = 0; j < List_Nbr(PostSubOperation_P->TimeValue_L); j++){
          double t;
          List_Read(PostSubOperation_P->TimeValue_L, j, &t);
          if(fabs(t - time) < TOL){
            List_Insert(PostSubOperation_P->TimeStep_L, &step, fcmp_int);
          }
        }
        for(int j = 0; j < List_Nbr(PostSubOperation_P->TimeImagValue_L); j++){
          double t;
          List_Read(PostSubOperation_P->TimeImagValue_L, j, &t);
          if(fabs(t - timeImag) < TOL)
            List_Insert(PostSubOperation_P->TimeStep_L, &step, fcmp_int);
        }
      }
    }
    NbTimeStep = List_Nbr(PostSubOperation_P->TimeStep_L);
    if(NbTimeStep) return NbTimeStep;
  }

  // specific time steps
  NbTimeStep = List_Nbr(PostSubOperation_P->TimeStep_L);

  if(!NbTimeStep || !PostSubOperation_P->FrozenTimeStepList){
    NbTimeStep = List_Nbr(Current.DofData->Solutions);
    List_Reset(PostSubOperation_P->TimeStep_L);
    for(iTime = 0 ; iTime < NbTimeStep ; iTime++)
      List_Add(PostSubOperation_P->TimeStep_L, &iTime);
  }

  return NbTimeStep;
}

/* ------------------------------------------------------------------------ */
/*  P o s _ I n i t A l l S o l u t i o n s                                 */
/* ------------------------------------------------------------------------ */

void Pos_InitAllSolutions(List_T * TimeStep_L, int Index_TimeStep)
{
  int  TimeStepIndex, k, Num_Solution ;

  List_Read(TimeStep_L, Index_TimeStep, &TimeStepIndex) ;

  for(k = 0 ; k < Current.NbrSystem ; k++)
    if( (Num_Solution = std::min(List_Nbr((Current.DofData_P0+k)->Solutions)-1,
				 TimeStepIndex)) >=0 )
      (Current.DofData_P0+k)->CurrentSolution = (struct Solution*)
	List_Pointer((Current.DofData_P0+k)->Solutions, Num_Solution) ;

  if(TimeStepIndex >= 0 && TimeStepIndex < List_Nbr(Current.DofData->Solutions)){
    Solution *Solution_P = ((struct Solution*)List_Pointer
                            (Current.DofData->Solutions, TimeStepIndex));
    Current.TimeStep = Solution_P->TimeStep ;
    Current.Time = Solution_P->Time ;
    Current.TimeImag = Solution_P->TimeImag ;
  }
  else{ // Warning: this can be wrong
    Current.TimeStep = TimeStepIndex;
    if(Current.DofData->CurrentSolution){
      Current.Time = Current.DofData->CurrentSolution->Time;
      Current.TimeImag = Current.DofData->CurrentSolution->TimeImag;
    }
  }
}

/* ------------------------------------------------------------------------ */
/*  P o s _ R e s a m p l e T i m e                                         */
/* ------------------------------------------------------------------------ */

#if !defined(HAVE_GSL)

void Pos_ResampleTime(struct PostOperation *PostOperation_P)
{
  Message::Error("ResampleTime requires the GSL");
}

#else

void Pos_ResampleTime(struct PostOperation *PostOperation_P)
{
  double   ResampleTimeStart, ResampleTimeStop, ResampleTimeStep;
  double   OriginalStopTime, *OriginalTime_P, *OriginalValueR_P, *OriginalValueI_P;
  double   InterpValueRe, InterpValueIm;
  int      OriginalNbrOfSolutions, NewNbrOfSolutions, xLength;
  Solution *Solution_P, Solution_S;
  List_T   *NewSolutions_L;

  ResampleTimeStart = PostOperation_P->ResampleTimeStart;
  ResampleTimeStop = PostOperation_P->ResampleTimeStop;
  ResampleTimeStep = PostOperation_P->ResampleTimeStep;
  OriginalNbrOfSolutions = List_Nbr(Current.DofData->Solutions);

  OriginalTime_P  = (double *)Malloc(OriginalNbrOfSolutions * sizeof(double));
  OriginalValueR_P = (double *)Malloc(OriginalNbrOfSolutions * sizeof(double));
  if (gSCALAR_SIZE == 2)
    OriginalValueI_P = (double *)Malloc(OriginalNbrOfSolutions * sizeof(double));
  else
    OriginalValueI_P = NULL;

  Solution_P = (struct Solution*)List_Pointer(Current.DofData->Solutions,
                                              OriginalNbrOfSolutions-1);
  OriginalStopTime = Solution_P->Time;
  ResampleTimeStop = (OriginalStopTime < ResampleTimeStop) ? OriginalStopTime :
                                                             ResampleTimeStop;
  for (int i=0; i<OriginalNbrOfSolutions; i++) {
    Solution_P = (struct Solution*)List_Pointer(Current.DofData->Solutions, i);
    if (!Solution_P->SolutionExist)
      Message::Error("Empty solution(s) found");
    OriginalTime_P[i] = Solution_P->Time;
  }

  LinAlg_GetVectorSize(&Solution_P->x, &xLength);

  NewNbrOfSolutions = floor((ResampleTimeStop-ResampleTimeStart) /
                            ResampleTimeStep) + 1;
  if (NewNbrOfSolutions < 1)
    Message::Error("Invalid ResampleTime settings - t_start: %.6g  t_stop: %.6g  "
                   "t_sample: %.6g", ResampleTimeStart, ResampleTimeStop,
                   ResampleTimeStep);
  NewSolutions_L = List_Create(NewNbrOfSolutions, 1, sizeof(Solution));
  for (int i=0; i<NewNbrOfSolutions; i++) {
    // Create new Solutions list
    Solution_S.TimeStep = i ;
    Solution_S.Time = ResampleTimeStart + i * ResampleTimeStep;
    Solution_S.TimeImag = 0.0;
    Solution_S.SolutionExist = 1 ;
    LinAlg_CreateVector(&Solution_S.x, &Current.DofData->Solver, xLength);
    List_Add(NewSolutions_L, &Solution_S);
  }

  for (int i=0; i<xLength; i++) {
    if (gSCALAR_SIZE == 1) {
      for (int j=0; j<OriginalNbrOfSolutions; j++) {
        Solution_P = (struct Solution*)List_Pointer(Current.DofData->Solutions, j);
        LinAlg_GetDoubleInVector(&OriginalValueR_P[j], &Solution_P->x, i);
      }
      gsl_interp_accel *acc = gsl_interp_accel_alloc ();
      gsl_spline *spline = gsl_spline_alloc (gsl_interp_cspline, OriginalNbrOfSolutions);
      gsl_spline_init (spline, OriginalTime_P, OriginalValueR_P, OriginalNbrOfSolutions);

      for (int j=0; j<NewNbrOfSolutions; j++) {
        Solution_P = (struct Solution*)List_Pointer(NewSolutions_L, j);
        InterpValueRe = gsl_spline_eval (spline, Solution_P->Time, acc);
        LinAlg_SetDoubleInVector(InterpValueRe, &Solution_P->x, i);
      }

      gsl_spline_free (spline);
      gsl_interp_accel_free (acc);
    }
    if (gSCALAR_SIZE == 2) {
      for (int j=0; j<OriginalNbrOfSolutions; j++) {
        Solution_P = (struct Solution*)List_Pointer(Current.DofData->Solutions, j);
        LinAlg_GetComplexInVector(&OriginalValueR_P[j], &OriginalValueI_P[j], &Solution_P->x, i, -1);
      }
      gsl_interp_accel *accRe = gsl_interp_accel_alloc ();
      gsl_interp_accel *accIm = gsl_interp_accel_alloc ();
      gsl_spline *splineRe = gsl_spline_alloc (gsl_interp_cspline, OriginalNbrOfSolutions);
      gsl_spline *splineIm = gsl_spline_alloc (gsl_interp_cspline, OriginalNbrOfSolutions);
      gsl_spline_init (splineRe, OriginalTime_P, OriginalValueR_P, OriginalNbrOfSolutions);
      gsl_spline_init (splineIm, OriginalTime_P, OriginalValueI_P, OriginalNbrOfSolutions);

      for (int j=0; j<NewNbrOfSolutions; j++) {
        Solution_P = (struct Solution*)List_Pointer(NewSolutions_L, j);
        InterpValueRe = gsl_spline_eval (splineRe, Solution_P->Time, accRe);
        InterpValueIm = gsl_spline_eval (splineIm, Solution_P->Time, accIm);
        LinAlg_SetComplexInVector(InterpValueRe, InterpValueIm, &Solution_P->x, i, -1);
      }

      gsl_spline_free (splineRe);
      gsl_spline_free (splineIm);
      gsl_interp_accel_free (accRe);
      gsl_interp_accel_free (accIm);
    }
  }
  Current.DofData->Solutions = NewSolutions_L;
  Current.DofData->CurrentSolution = (struct Solution*)
          List_Pointer(NewSolutions_L, List_Nbr(NewSolutions_L)-1) ;
  for (int j=0; j<NewNbrOfSolutions; j++) {
    Solution_P = (struct Solution*)List_Pointer(Current.DofData->Solutions, j);
    Solution_P->TimeFunctionValues = Get_TimeFunctionValues(Current.DofData) ;
  }

  Free(OriginalTime_P);
  Free(OriginalValueR_P);
  Free(OriginalValueI_P);
}
#endif

/* ------------------------------------------------------------------------ */
/*  P o s _ F o r m u l a t i o n                                           */
/* ------------------------------------------------------------------------ */

void  Pos_Formulation(struct Formulation       *Formulation_P,
		      struct PostProcessing    *PostProcessing_P,
		      struct PostSubOperation  *PostSubOperation_P)
{
  struct PostQuantity   *NCPQ_P = NULL, *CPQ_P = NULL ;
  double                 Pulsation ;
  int                    i, Order = 0 ;

  if(PostSubOperation_P->Type == POP_MERGE){
    Message::SendMergeFileRequest(PostSubOperation_P->FileOut);
    return;
  }

  if(PostSubOperation_P->FileOut){
    strcpy(PostFileName, Fix_RelativePath(PostSubOperation_P->FileOut,
                                          Name_Path).c_str());

    if(PostSubOperation_P->AppendExpressionToFileName >= 0) {
      struct Value Value ;
      Get_ValueOfExpressionByIndex(PostSubOperation_P->AppendExpressionToFileName,
                                   NULL, 0., 0., 0., &Value) ;
      char AddExt[100];
      if(PostSubOperation_P->AppendExpressionFormat)
        sprintf(AddExt, PostSubOperation_P->AppendExpressionFormat, Value.Val[0]);
      else
        sprintf(AddExt, "%.16g", Value.Val[0]);
      strcat(PostFileName, AddExt);
    }

    if(PostSubOperation_P->AppendTimeStepToFileName) {
      char AddExt[100] ;
      sprintf(AddExt, "_%03d", (PostSubOperation_P->OverrideTimeStepValue >= 0) ?
              PostSubOperation_P->OverrideTimeStepValue : (int)Current.TimeStep) ;
      strcat(PostFileName, AddExt);
    }

    if(PostSubOperation_P->AppendStringToFileName) {
      strcat(PostFileName, PostSubOperation_P->AppendStringToFileName);
    }

    if(!strlen(PostFileName) ||
       (Message::GetIsCommWorld() && Message::GetCommRank())){
      // in parallel mode (SetCommWorld), only rank 0 prints output
      PostStream = NULL ;
    }
    else if(!PostSubOperation_P->CatFile) {
      if((PostStream = FOpen(PostFileName, Flag_BIN ? "wb" : "w")))
	Message::Direct(4, "          > '%s'", PostFileName) ;
      else{
	Message::Error("Unable to open file '%s'", PostFileName) ;
        PostStream = stdout ;
      }
    }
    else {
      if((PostStream = FOpen(PostFileName, Flag_BIN ? "ab" : "a")))
	Message::Direct(4, "          >> '%s'", PostFileName) ;
      else{
	Message::Error("Unable to open file '%s'", PostFileName) ;
        PostStream = stdout ;
      }
    }
  }
  else{
    PostStream = stdout ;
  }

  // force Gmsh version 1 for anything else than OnElementsOf, or if we store in
  // memory (which requires old-style list ordering)
  int oldVersion = Flag_GMSH_VERSION;
  if(PostSubOperation_P->SubType != PRINT_ONELEMENTSOF ||
     PostSubOperation_P->Depth != 1 ||
     PostSubOperation_P->StoreInField >= 0)
    Flag_GMSH_VERSION = 1;

  if(PostSubOperation_P->StoreInField >= 0 &&
     PostSubOperation_P->Format != FORMAT_GMSH)
    Message::Warning("StoreInField only available with Gmsh output format");

  if(PostSubOperation_P->StoreInMeshBasedField >= 0){
    Flag_GMSH_VERSION = 2;
    if(PostSubOperation_P->SubType != PRINT_ONELEMENTSOF ||
       PostSubOperation_P->Depth != 1)
      Message::Error("StoreInMeshBasedField not compatible with selected options");
  }

  if(PostStream && PostSubOperation_P->CatFile == 2)  fprintf(PostStream, "\n\n") ;
  /*  two blanks lines for -index in gnuplot  */

  Format_PostFormat(PostSubOperation_P) ;

  if(PostSubOperation_P->PostQuantityIndex[0] >= 0) {
    if(PostSubOperation_P->PostQuantitySupport[0] < 0) { /* Noncumulative */
      NCPQ_P =
	(struct PostQuantity *) List_Pointer(PostProcessing_P->PostQuantity,
					     PostSubOperation_P->PostQuantityIndex[0]) ;
      CPQ_P =
	(PostSubOperation_P->PostQuantityIndex[1] >= 0) ?
	(struct PostQuantity *)List_Pointer(PostProcessing_P->PostQuantity,
					    PostSubOperation_P->PostQuantityIndex[1]) :
	NULL ;
      Order = 1 ;
    }
    else {
      CPQ_P =
	(struct PostQuantity *) List_Pointer(PostProcessing_P->PostQuantity,
					     PostSubOperation_P->PostQuantityIndex[0]) ;
      NCPQ_P =
	(PostSubOperation_P->PostQuantityIndex[1] >= 0) ?
	(struct PostQuantity *)List_Pointer(PostProcessing_P->PostQuantity,
					    PostSubOperation_P->PostQuantityIndex[1]) :
	NULL ;
      Order = 0 ;
    }
  }

  if(List_Nbr(PostSubOperation_P->Frequency_L)){
    if(List_Nbr(PostSubOperation_P->Frequency_L) > List_Nbr(Current.DofData->Pulsation))
      Message::Error("Too many frequencies specified in PostOperation");
    else{
      for(i = 0 ; i < List_Nbr(PostSubOperation_P->Frequency_L) ; i++){
        Pulsation = *((double *)List_Pointer(PostSubOperation_P->Frequency_L, i)) * TWO_PI ;
        List_Write(Current.DofData->Pulsation, i, &Pulsation) ;
      }
    }
  }

  switch (Formulation_P->Type) {

  case FEMEQUATION :
    Pos_FemFormulation(Formulation_P, NCPQ_P, CPQ_P, Order, PostSubOperation_P) ;
    break ;

  case GLOBALEQUATION :
    break ;

  default :
    Message::Error("Unknown Type for Formulation (%s)", Formulation_P->Name) ;
    break;

  }

  Flag_GMSH_VERSION = oldVersion;

  if(PostStream && PostSubOperation_P->FileOut){
    fclose(PostStream) ;

    if(PostSubOperation_P->SendToServer == NULL ||
       strcmp(PostSubOperation_P->SendToServer, "No")){
      if(PostSubOperation_P->Format == FORMAT_GMSH_PARSED ||
         PostSubOperation_P->Format == FORMAT_GMSH){
        // send merge request
        Message::SendMergeFileRequest(PostFileName);
      }
      // Add link to file
      Message::AddOnelabStringChoice(Message::GetOnelabClientName() + "/9Output files",
                                     "file", PostFileName);
    }

    /* NewCoordinates print option: write a new mesh */
    if(PostSubOperation_P->NewCoordinates){

#if defined(HAVE_GMSH)

      GmshMergeFile(std::string(PostFileName));
      int iview = PView::list.size() - 1;
      PViewData *data = PView::list[iview]->getData();

      GModel* m = new GModel();
      m->readMSH(std::string(Current.GeoData->Name));

      std::vector<GEntity*> entities;
      m->getEntities(entities);
      std::map<MVertex*, std::vector<double>, MVertexLessThanNum> newcoords;
      for(unsigned int i = 0; i < entities.size(); i++) {
        for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++) {
          MVertex* v = entities[i]->mesh_vertices[j];
          std::vector<double> xyz(3);
          if(!data->searchVector(v->x(), v->y(), v->z(), &xyz[0]))
            Message::Error("Did not find new coordinate Vector at point (%g,%g,%g) "
                           "from file %s", v->x(), v->y(), v->z(), PostFileName);
          newcoords[v] = xyz;
        }
      }

      for(std::map<MVertex*, std::vector<double>, MVertexLessThanNum>::iterator
            it = newcoords.begin(); it != newcoords.end(); it++) {
        it->first->x() = it->second[0];
        it->first->y() = it->second[1];
        it->first->z() = it->second[2];
      }

      char NewCoordsFileName[256];
      strcpy(NewCoordsFileName, Fix_RelativePath(PostSubOperation_P->NewCoordinatesFile,
                                                 Name_Path).c_str());
      m->writeMSH(NewCoordsFileName);
      Message::Info("Wrote new coordinates in file %s", NewCoordsFileName);
      delete m;
      delete PView::list[iview];
      PView::list.pop_back();

#else
    Message::Error("You need to compile GetDP with Gmsh support to use 'NewCoordinates'");
#endif

    }

  }

}