init.c File Reference

contains initialization functions More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "global.h"
#include "inline.h"

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Functions
void	defaultValues ()
void	checkParameters ()
void	simulationInit (int argc, char **argv)

Detailed Description

contains initialization functions

Definition in file init.c.

Function Documentation

void checkParameters

(

)

This functions checks the consistence of key simulation parameters.

Definition at line 61 of file init.c.

References cOutType, fOutType, and stopRun().

{
  /* under construction */
  if (strcmp(cOutType, "VTK") && strcmp(cOutType, "POV")
      && strcmp(cOutType, "NON"))
    stopRun(116, "COUTTYPE", __FILE__, __LINE__);
  if (strcmp(fOutType, "VNF") && strcmp(fOutType, "NON"))
    stopRun(116, "FOUTTYPE", __FILE__, __LINE__);
}

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void defaultValues

(

)

This function sets default values for the simulation.

Definition at line 38 of file init.c.

References cellVolume, csizeInUnits, nhs, povout, rst, rstOutStep, rstReset, statOutStep, tgs, vnfout, vtkout, and vtkOutStep.

{
  rst = 0;
  rstReset = 0;
  nhs = -1;
  tgs = 0;

  statOutStep = 1;
  rstOutStep = 1;
  vtkOutStep = 1;

  povout = 0;
  vtkout = 0;
  vnfout = 0;

  csizeInUnits = 10.0;      /* eukaryotic cell size is usually between 10-30 micrometers */
  cellVolume = (4.0 / 3.0) * M_PI * pow(csizeInUnits * 0.0001, 3.0);

}

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void simulationInit	(	int	argc,
		char **	argv
	)

This function intializes the simulation by setting all most important simulation parameters.

Definition at line 74 of file init.c.

References allocateGrid(), cellsAllocate(), cellsCycleInit(), cellsRandomInit(), checkEndiannes(), checkParameters(), computeGridSize(), cOutType, csize, decompositionInit(), defaultValues(), defineColormaps(), densityCriticalLevel1, densityCriticalLevel2, fieldsInit(), fOutType, getLocalRankAndSize(), getMemoryPerProcess(), gfDt, gfIterPerStep, h2, h3, initParams(), lnc, maxSpeed, maxSpeedInUnits, memPerProc, MPI_CART_COMM, MPIcoords, MPIdim, MPINodeRank, MPINodeSize, MPIrank, MPIsize, nc, povout, POWER_OF_TWO, printBasicInfo(), printExecInfo(), printHelp(), randomStreamInit(), readParams(), rst, sdim, secondsPerStep, simStart, stopRun(), tlnc, vnfout, and vtkout.

{
  int i;
  int periods[3];
  int reorder;

  /* print basic informations */
  printBasicInfo();

  /* check necessary arguments */
  //if( (argc<3 || (strcmp(argv[1],"-p"))) || (argc<2 || (strcmp(argv[1],"-h"))) )
  //  stopRun(102,NULL,__FILE__,__LINE__);

  if (argc < 2)
    stopRun(102, NULL, __FILE__, __LINE__);
  else if ((argc < 3 && strcmp(argv[1], "-p") == 0)
       || (strcmp(argv[1], "-p") && strcmp(argv[1], "-h")))
    stopRun(102, NULL, __FILE__, __LINE__);

  initParams();

  if (strcmp(argv[1], "-h") == 0)
    printHelp();

  /* check number of processes */
  if (!POWER_OF_TWO(MPIsize))
    stopRun(101, NULL, __FILE__, __LINE__);

  /* checking system and runtime configuration */
  checkEndiannes();
  getLocalRankAndSize(MPIrank, MPIsize, &MPINodeRank, &MPINodeSize);
  memPerProc = getMemoryPerProcess(MPINodeSize);

  /* print execution informations */
  printExecInfo();

  /* set default values */
  defaultValues();

  /* initialize random number generator */
  randomStreamInit();

  /* read parameters file and restart file (if present) */
  readParams(argc, argv);

  /* generate random cells if not a restart simulation */
  if (!rst) {
    simStart = 0;
    /* calculating number of cells per process */
    lnc = nc / MPIsize;
    if (MPIrank < nc % MPIsize)
      lnc++;
    /* allocating tables */
    cellsAllocate();
    /* total number of cells - initialization */
    for (i = 0; i < MPIsize; i++)
      tlnc[i] = lnc;        //ZLE!!!!!
    /* cell cycle init */
    cellsCycleInit();
    /* random cell placement */
    cellsRandomInit();
    /* decomposition - initialization */
    decompositionInit(argc, argv, MPI_COMM_WORLD);
  }

  /* maximum distance cell can travel in 1 sec */
  maxSpeedInUnits = (maxSpeed * csize) / (24.0 * 60.0 * 60.0);
  /* at least one global fields iteration per step */
  gfDt = (gfDt > secondsPerStep ? secondsPerStep : gfDt);
  /* global fields iterations per step */
  gfIterPerStep = (int) (secondsPerStep / gfDt);

  /* density critical levels (very important parameters) */
  if (sdim == 3) {
    densityCriticalLevel1 = 6 * h3 * sph_kernel(1.5 * csize);   //1.8  //1.4 //1.75
    densityCriticalLevel2 = 6 * h3 * sph_kernel(1.1 * csize);   //1.1 //1.4
  }
  if (sdim == 2) {
    densityCriticalLevel1 = 4 * h2 * sph_kernel(1.4 * csize);   //1.4 //1.75
    densityCriticalLevel2 = 4 * h2 * sph_kernel(1.15 * csize);  //1.1 //1.4
  }

  /* checking the consistency */
  checkParameters();

  if (!strcmp(cOutType, "POV"))
    povout = 1;
  if (!strcmp(cOutType, "VTK"))
    vtkout = 1;
  if (!strcmp(fOutType, "VNF"))
    vnfout = 1;

  /* organizing processes in a Cartesian grid for global fields computations */
  MPI_Dims_create(MPIsize, sdim, MPIdim);
  periods[0] = 0;
  periods[1] = 0;
  periods[2] = 0;
  reorder = 0;
  MPI_Cart_create(MPI_COMM_WORLD, sdim, MPIdim, periods, reorder,
          &MPI_CART_COMM);
  MPIcoords = (int **) malloc(MPIsize * sizeof(int *));
  for (i = 0; i < MPIsize; i++) {
    MPIcoords[i] = (int *) malloc(3 * sizeof(int));
    MPI_Cart_coords(MPI_CART_COMM, i, sdim, MPIcoords[i]);
  }
  /* compute grid size */
  computeGridSize();

  /* allocate grid data */
  allocateGrid();
  /* initialize global fields (might take some time) */
  fieldsInit();

  /* define colormaps for PovRay outputs */
  defineColormaps();

  /* define vessels - TBD */
  //initVessel();
}

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