#include "voz.h"
#include <cstdio>
#include <stdlib.h>
#include <math.h>
#include <vector>

#include "voro++.hh"
using namespace voro;

#define DL for (d=0;d<3;d++)
#define BF 1e30

#define MAX(a,b) ( ((a) < (b)) ? (a) : (b) )

int posread(char *posfile, float ***p, float fact);

int main(int argc, char *argv[]) {
  int exitcode;
  int i, j, np;
  float **r;
  double rtemp[3], *parts;
  double deladjs[3*MAXVERVER], points[3*MAXVERVER];
  FILE *pos, *out, *testFile;
  char *posfile, outfile[200], *suffix, *outDir;
  PARTADJ *adjs;
  float *vols;
  float predict, xmin,xmax,ymin,ymax,zmin,zmax;
  int *orig;
  
  int isitinbuf;
  char isitinmain, d;
  int numdiv;
  int nvp, nvpall, nvpbuf;
  float width, width2, totwidth, totwidth2, bf, s, g;
  float border, boxsize;
  float c[3];
  int b[3];
  double totalvol;
  int isObs = 0;

  printf("Routine: voz1b1\n");

  if (argc != 11) {
    printf("Wrong number of arguments.\n");
    printf("arg1: position file\n");
    printf("arg2: border size\n");
    printf("arg3: boxsize\n");
    printf("arg4: suffix\n");
    printf("arg5: number of divisions\n");
    printf("arg6-8: b[0-2]\n\n");
    printf("arg9: output directory\n");
    printf("arg10: observation flag\n");
    exit(0);
  }
  posfile = argv[1];
  if (sscanf(argv[2],"%f",&border) != 1) {
    printf("That's no border size; try again.\n");
    exit(0);
  }
  if (sscanf(argv[3],"%f",&boxsize) != 1) {
    printf("That's no boxsize; try again.\n");
    exit(0);
  }
  suffix = argv[4];
  if (sscanf(argv[5],"%d",&numdiv) != 1) {
    printf("%s is no number of divisions; try again.\n",argv[5]);
    exit(0);
  }
  if (numdiv == 1) {
    printf("Only using one division; should only use for an isolated segment.\n");
  }
  if (numdiv < 1) {
    printf("Cannot have a number of divisions less than 1.  Resetting to 1.\n");
    numdiv = 1;
  }
  if (sscanf(argv[6],"%d",&b[0]) != 1) {
    printf("That's no b index; try again.\n");
    exit(0);
  }
  if (sscanf(argv[7],"%d",&b[1]) != 1) {
    printf("That's no b index; try again.\n");
    exit(0);
  }
  if (sscanf(argv[8],"%d",&b[2]) != 1) {
    printf("That's no b index; try again.\n");
    exit(0);
  }
  outDir = argv[9];
  if (sscanf(argv[10],"%d",&isObs) != 1) {
    printf("That's no observation mode; try again.\n");
    exit(0);
  }
 
  printf("Working with subdomain b=[%d,%d,%d]\n", b[0], b[1], b[2]);

  /* Boxsize should be the range in r, yielding a range 0-1 */
  printf("Reading particle file...\n");
  np = posread(posfile,&r,1./boxsize);
  printf("%d particles\n",np);fflush(stdout);

  xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
  for (i=0; i<np;i++) {
    if (r[i][0]<xmin) xmin = r[i][0]; if (r[i][0]>xmax) xmax = r[i][0];
    if (r[i][1]<ymin) ymin = r[i][1]; if (r[i][1]>ymax) ymax = r[i][1];
    if (r[i][2]<zmin) zmin = r[i][2]; if (r[i][2]>zmax) zmax = r[i][2];
  }
  printf("Full box particle stats: np: %d, x: %f,%f; y: %f,%f; z: %f,%f\n",np,
         xmin,xmax, ymin,ymax, zmin,zmax); fflush(stdout);

  width = 1./(float)numdiv;
  width2 = 0.5*width;
  if (border > 0.) bf = border;
  else bf = 0.1;
      /* In units of 0-1, the thickness of each subregion's buffer*/
  totwidth = width+2.*bf;
  totwidth2 = width2 + bf;
  
  s = width/(float)NGUARD;
  if ((bf*bf - 2.*s*s) < 0.) {
    printf("bf = %f, s = %f.\n",bf,s);
    printf("Not enough guard points for given border.\nIncrease guards to >= %f\n.",
	   sqrt(2.)*width/bf);
    exit(0);
  }
  g = (bf / 2.)*(1. + sqrt(1 - 2.*s*s/(bf*bf)));
  printf("Guard particle information: s = %f, bf = %f, g = %f.\n",s,bf,g);

  fflush(stdout);

  adjs = (PARTADJ *)malloc(np*sizeof(PARTADJ));
  if (adjs == NULL) {
    printf("Unable to allocate adjs\n");
    exit(1);
  }
  
  DL c[d] = ((float)b[d]+0.5)*width;
  printf("Counting particles in subdomain...\n");
  /* Assign temporary array*/
  nvpbuf = 0; /* Number of particles to tesselate, includng buffer and guards */
  nvp = 0; /* Without the buffer */
  for (i=0; i<np; i++) {
    isitinbuf = 1;
    isitinmain = 1;
    DL {
      rtemp[d] = (double)r[i][d] - (double)c[d];
      if (rtemp[d] > 0.5) rtemp[d] --;
      if (rtemp[d] < -0.5) rtemp[d] ++;
      isitinbuf = isitinbuf && (fabs(rtemp[d]) < totwidth2);
      isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
    }
  
    if (isitinbuf) nvpbuf++;
    if (isitinmain) nvp++;
  }

  nvpbuf += 6*(NGUARD+1)*(NGUARD+1); /* number of guard points */

  parts = (double *)malloc(3*nvpbuf*sizeof(double));
  orig = (pid_t *)malloc(nvpbuf*sizeof(pid_t));

  if (parts == NULL) {
    printf("Unable to allocate parts\n");
    fflush(stdout);
    exit(1);
  }
  if (orig == NULL) {
    printf("Unable to allocate orig\n");
    fflush(stdout);
    exit(1);
  }

  printf("Placing particles in subdomain...\n");
  nvp = 0; nvpall = 0; /* nvp = number of particles without buffer */
  xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
  for (i=0; i<np; i++) {
    isitinmain = 1;
    DL {
      rtemp[d] = (float)r[i][d] - (float)c[d];
      if (rtemp[d] > 0.5) rtemp[d] --;
      if (rtemp[d] < -0.5) rtemp[d] ++;
      isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
    }
    if (isitinmain) {
      parts[3*nvp] = rtemp[0];
      parts[3*nvp+1] = rtemp[1];
      parts[3*nvp+2] = rtemp[2];
      orig[nvp] = i;
      nvp++;
      if (rtemp[0] < xmin) xmin = rtemp[0];
      if (rtemp[0] > xmax) xmax = rtemp[0];
      if (rtemp[1] < ymin) ymin = rtemp[1];
      if (rtemp[1] > ymax) ymax = rtemp[1];
      if (rtemp[2] < zmin) zmin = rtemp[2];
      if (rtemp[2] > zmax) zmax = rtemp[2];
    }
  }
  printf("Subdomain: b=(%d,%d,%d), c=(%f,%f,%f)\n",
         b[0],b[1],b[2],c[0],c[1],c[2]);
  printf("  nvp=%d, nvpbuf=%d\n", nvp,nvpbuf);
  printf("  Particle ranges: x: %f,%f; y: %f,%f; z:%f,%f\n",
         xmin,xmax,ymin,ymax,zmin,zmax);

  printf("Adding particles to buffer regions...\n");
  nvpbuf = nvp;
  for (i=0; i<np; i++) {
    isitinbuf = 1;
    isitinmain = 1;

    DL {
      rtemp[d] = (float)r[i][d] - (float)c[d];
      if (rtemp[d] > 0.5) rtemp[d] --;
      if (rtemp[d] < -0.5) rtemp[d] ++;
      isitinbuf = isitinbuf && (fabs(rtemp[d])<totwidth2);
      isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
    }
    if (isitinbuf && !isitinmain) {
      parts[3*nvpbuf] = rtemp[0];
      parts[3*nvpbuf+1] = rtemp[1];
      parts[3*nvpbuf+2] = rtemp[2];
      orig[nvpbuf] = i;

      nvpbuf++;
      if (rtemp[0] < xmin) xmin = rtemp[0];
      if (rtemp[0] > xmax) xmax = rtemp[0];
      if (rtemp[1] < ymin) ymin = rtemp[1];
      if (rtemp[1] > ymax) ymax = rtemp[1];
      if (rtemp[2] < zmin) zmin = rtemp[2];
      if (rtemp[2] > zmax) zmax = rtemp[2];
    }
  }
  nvpall = nvpbuf;
  predict = pow(width+2.*bf,3)*(float)np;
  printf("Total particles including buffer = %d (predicted ~%f)\n",
         nvpbuf, predict);
  printf(" Particle ranges including buffer: x: %f,%f; y: %f,%f; z:%f,%f\n",
         xmin,xmax,ymin,ymax,zmin,zmax);

  for (i=0;i<np;i++) free(r[i]);
  free(r);


  /* Add guard points */
  // first the internal boundaries between subdomains
  printf("Adding guard points to internal subdomain faces...\n");
  for (i=0; i<NGUARD+1; i++) {
  for (j=0; j<NGUARD+1; j++) {
      /* Bottom */
      if (b[2] != 0) { // we will do the outer edges next
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = -width2 + (float)j * s;
        parts[3*nvpall+2] = -width2 - g;
        nvpall++;
      }
      /* Top */
      if (b[2] != numdiv-1) {
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = -width2 + (float)j * s;
        parts[3*nvpall+2] = width2 + g;
        nvpall++;
      }
  }
  }
  for (i=0; i<NGUARD+1; i++) { /* Don't want to overdo the corners*/
  for (j=0; j<NGUARD+1; j++) {
      if (b[1] != 0) { // we will do the outer edges next
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = -width2 - g;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }

      if (b[1] != numdiv-1) {
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = width2 + g;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }
  }
  }
  for (i=0; i<NGUARD+1; i++) {
  for (j=0; j<NGUARD+1; j++) {
      if (b[0] != 0) { // we will do the outer edges next
        parts[3*nvpall]   = -width2 - g;
        parts[3*nvpall+1] = -width2 + (float)i * s;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }
      
      if (b[0] != numdiv-1) {
        parts[3*nvpall]   = width2 + g;
        parts[3*nvpall+1] = -width2 + (float)i * s;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }
  }
  }
 
  // now the external faces of the domain
  // (i'm tired and can't think of a better way to do this)
  isObs = 0;
  if (isObs != 1) {
    printf("Adding guard points to external domain faces...\n");
    for (i=0; i<NGUARD+1; i++) {
    for (j=0; j<NGUARD+1; j++) {
      /* Bottom */
      if (b[2] == 0) {
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = -width2 + (float)j * s;
        parts[3*nvpall+2] = -width2 - g;
        nvpall++;
      }
      /* Top */
      if (b[2] == numdiv-1) {
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = -width2 + (float)j * s;
        parts[3*nvpall+2] = width2 + g;
        nvpall++;
      }
    }
    }
    for (i=0; i<NGUARD+1; i++) { /* Don't want to overdo the corners*/
    for (j=0; j<NGUARD+1; j++) {
      if (b[1] == 0) {
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = -width2 - g;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }

      if (b[1] == numdiv-1) {
        parts[3*nvpall]   = -width2 + (float)i * s;
        parts[3*nvpall+1] = width2 + g;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }
    }
    }
    for (i=0; i<NGUARD+1; i++) {
    for (j=0; j<NGUARD+1; j++) {
      if (b[0] == 0) {
        parts[3*nvpall]   = -width2 - g;
        parts[3*nvpall+1] = -width2 + (float)i * s;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }
      
      if (b[0] == numdiv-1) {
        parts[3*nvpall]   = width2 + g;
        parts[3*nvpall+1] = -width2 + (float)i * s;
        parts[3*nvpall+2] = -width2 + (float)j * s;
        nvpall++;
      }
    }
    }
  } // end if isObs != -1
  

  // TEST TEMP
  testFile = fopen("test.txt", "a");
  for (i=0; i<nvpall; i++){
    int itype = 0;
    if (i > nvp) itype = 1;    // it's a buffer particle
    if (i > nvpbuf) itype = 2; // it's a guard particle
    fprintf(testFile, "%f %f %f %d %f %f %f\n", c[0], c[1], c[2], 
                                                itype,
                                                parts[3*i],
                                                parts[3*i+1],
                                                parts[3*i+2]);
  }
  fclose(testFile);

  xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
  for (i=nvpbuf;i<nvpall;i++) {
    if (parts[3*i] < xmin) xmin = parts[3*i];
    if (parts[3*i] > xmax) xmax = parts[3*i];
    if (parts[3*i+1] < ymin) ymin = parts[3*i+1];
    if (parts[3*i+1] > ymax) ymax = parts[3*i+1];
    if (parts[3*i+2] < zmin) zmin = parts[3*i+2];
    if (parts[3*i+2] > zmax) zmax = parts[3*i+2];
  }
  
  printf("Added guard points to total %d points (should be %d)\n",nvpall,
	 nvpbuf + 6*(NGUARD+1)*(NGUARD+1));
  printf("New particle ranges including guards: x: %f,%f; y: %f,%f; z:%f,%f\n",
          xmin,xmax,ymin,ymax,zmin,zmax);
  
  /* Do tesselation*/
  printf("File read.  Tessellating ...\n"); fflush(stdout);

  // initialize a voro++ container with non-periodic boundaries
  // per voro++ documentaiton, max efficiency is achieved with ~8 particles per subdomain block
  int nblocks = floor(pow(nvpall, 1/3.)/8);
  container con(xmin,xmax,ymin,ymax,zmin,zmax, nblocks,nblocks,nblocks, false,false,false, 8);

  particle_order po; // this will keep track of only original particles

  // initialize storage arrays
  vols = (float *)malloc(nvp*sizeof(float));

  // place our particles in the container
  for (i=0; i<nvpall; i++) {
    if (i < nvp) con.put(po, i, parts[3*i], parts[3*i+1], parts[3*i+2]);
    else con.put(i, parts[3*i], parts[3*i+1], parts[3*i+2]);
  }

  // loop over main particles and compute tesselation
  voronoicell_neighbor cell;
  c_loop_order vl(con,po);
  int p = 0;
  if(vl.start()) do if(con.compute_cell(cell,vl)) {
    // grab neighbor information and store in internal arrays
    std::vector<int> adjsv;
    cell.neighbors(adjsv);

    // copy adjacencies to old-school data format
    adjs[p].nadj = adjsv.size();
    adjs[p].adj = (int *)malloc(adjsv.size() * sizeof(int));

    for (int iAdj; iAdj < adjsv.size(); ++iAdj) {
      adjs[p].adj[iAdj] = adjsv[iAdj];
    }

    // grab volume and store
    vols[p] = cell.volume()*(float)np;
    p++;
  } while(vl.inc());

    //if (i % 1000 == 0)
    //  printf("%d: %d, %f\n",i,adjs[i].nadj,vols[i]);

// PMS - reset number of adjancies to not include links to border guards
/*
  for (i=0; i<nvp; i++) {
    int nActual = 0;
    for (j = 0; j < adjs[i].nadj; j++)
      if (adjs[i].adj[j] < nvp) nActual++;
    adjs[i].nadj = nActual;
  }
*/

  /* Get the adjacencies back to their original values */

  for (i=0; i<nvp; i++)
    for (j = 0; j < adjs[i].nadj; j++)
      adjs[i].adj[j] = orig[adjs[i].adj[j]];

  totalvol = 0.;
  for (i=0;i<nvp; i++) {
    totalvol += (double)vols[i];
  }
  printf("Average volume = %g\n",totalvol/(float)nvp);
 
  /* Now the output!
     First number of particles */
  sprintf(outfile,"%s/part.%s.%02d.%02d.%02d",outDir,suffix,b[0],b[1],b[2]);

  printf("Output to %s\n\n",outfile);
  out = fopen(outfile,"w");
  if (out == NULL) {
    printf("Unable to open %s\n",outfile);
    exit(1);
  }
  fwrite(&np,1, sizeof(int),out);
  fwrite(&nvp,1, sizeof(int),out);
  printf("nvp = %d\n",nvp);

  /* Tell us where the original particles were */
  fwrite(orig,sizeof(pid_t),nvp,out);
  /* Volumes*/
  fwrite(vols,sizeof(float),nvp,out);
  /* Adjacencies */
  for (i=0;i<nvp;i++) {
    fwrite(&(adjs[i].nadj),1,sizeof(pid_t),out);
    if (adjs[i].nadj > 0)
      fwrite(adjs[i].adj,adjs[i].nadj,sizeof(pid_t),out);
    else printf("0");
  }
  fclose(out);
  
  return(0);
}