// clang-format off
/*
Voro++ Copyright (c) 2008, The Regents of the University of California, through
Lawrence Berkeley National Laboratory (subject to receipt of any required
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*/

// Voro++, a 3D cell-based Voronoi library
//
// Author   : Chris H. Rycroft (LBL / UC Berkeley)
// Email    : chr@alum.mit.edu
// Date     : August 30th 2011
//
// Modified by PM Larsen for use in Polyhedral Template Matching

/** \file cell.cc
 * \brief Function implementations for the voronoicell and related classes. */

#include <cmath>
#include <cstdio>
#include <cstdlib>
#include "ptm_voronoi_config.h"
#include "ptm_voronoi_cell.h"

namespace ptm_voro {

inline void voro_fatal_error(const char *p,int status) {
        fprintf(stderr,"voro++: %s\n",p);
        exit(status);
        //return -1;//status;
}

/** Constructs a Voronoi cell and sets up the initial memory. */
voronoicell_base::voronoicell_base() :
        current_vertices(init_vertices), current_vertex_order(init_vertex_order),
        current_delete_size(init_delete_size), current_delete2_size(init_delete2_size),
        ed(new int*[current_vertices]), nu(new int[current_vertices]),
        pts(new double[3*current_vertices]), mem(new int[current_vertex_order]),
        mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]),
        ds(new int[current_delete_size]), stacke(ds+current_delete_size),
        ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size),
        current_marginal(init_marginal), marg(new int[current_marginal]) {
        int i;
        for (i=0;i<3;i++) {
                mem[i]=init_n_vertices;mec[i]=0;
                mep[i]=new int[init_n_vertices*((i<<1)+1)];
        }
        mem[3]=init_3_vertices;mec[3]=0;
        mep[3]=new int[init_3_vertices*7];
        for (i=4;i<current_vertex_order;i++) {
                mem[i]=init_n_vertices;mec[i]=0;
                mep[i]=new int[init_n_vertices*((i<<1)+1)];
        }
}

/** The voronoicell destructor deallocates all the dynamic memory. */
voronoicell_base::~voronoicell_base() {
        for (int i=current_vertex_order-1;i>=0;i--) if (mem[i]>0) delete [] mep[i];
        delete [] marg;
        delete [] ds2;delete [] ds;
        delete [] mep;delete [] mec;
        delete [] mem;delete [] pts;
        delete [] nu;delete [] ed;
}

/** Ensures that enough memory is allocated prior to carrying out a copy.
 * \param[in] vc a reference to the specialized version of the calling class.
 * \param[in] vb a pointered to the class to be copied. */
template<class vc_class>
void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) {
        while (current_vertex_order<vb->current_vertex_order) add_memory_vorder(vc);
        for (int i=0;i<current_vertex_order;i++) while (mem[i]<vb->mec[i]) add_memory(vc,i,ds2);
        while (current_vertices<vb->p) add_memory_vertices(vc);
}

/** Increases the memory storage for a particular vertex order, by increasing
 * the size of the of the corresponding mep array. If the arrays already exist,
 * their size is doubled; if they don't exist, then new ones of size
 * init_n_vertices are allocated. The routine also ensures that the pointers in
 * the ed array are updated, by making use of the back pointers. For the cases
 * where the back pointer has been temporarily overwritten in the marginal
 * vertex code, the auxiliary delete stack is scanned to find out how to update
 * the ed value. If the template has been instantiated with the neighbor
 * tracking turned on, then the routine also reallocates the corresponding mne
 * array.
 * \param[in] i the order of the vertex memory to be increased. */
template<class vc_class>
void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) {
        int s=(i<<1)+1;
        if (mem[i]==0) {
                vc.n_allocate(i,init_n_vertices);
                mep[i]=new int[init_n_vertices*s];
                mem[i]=init_n_vertices;
#if VOROPP_VERBOSE >=2
                fprintf(stderr,"Order %d vertex memory created\n",i);
#endif
        } else {
                int j=0,k,*l;
                mem[i]<<=1;
                if (mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
                fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]);
#endif
                l=new int[s*mem[i]];
                int m=0;
                vc.n_allocate_aux1(i);
                while (j<s*mec[i]) {
                        k=mep[i][j+(i<<1)];
                        if (k>=0) {
                                ed[k]=l+j;
                                vc.n_set_to_aux1_offset(k,m);
                        } else {
                                int *dsp;
                                for (dsp=ds2;dsp<stackp2;dsp++) {
                                        if (ed[*dsp]==mep[i]+j) {
                                                ed[*dsp]=l+j;
                                                vc.n_set_to_aux1_offset(*dsp,m);
                                                break;
                                        }
                                }
                                if (dsp==stackp2) voro_fatal_error("Couldn't relocate dangling pointer",VOROPP_INTERNAL_ERROR);
#if VOROPP_VERBOSE >=3
                                fputs("Relocated dangling pointer",stderr);
#endif
                        }
                        for (k=0;k<s;k++,j++) l[j]=mep[i][j];
                        for (k=0;k<i;k++,m++) vc.n_copy_to_aux1(i,m);
                }
                delete [] mep[i];
                mep[i]=l;
                vc.n_switch_to_aux1(i);
        }
}

/** Doubles the maximum number of vertices allowed, by reallocating the ed, nu,
 * and pts arrays. If the allocation exceeds the absolute maximum set in
 * max_vertices, then the routine exits with a fatal error. If the template has
 * been instantiated with the neighbor tracking turned on, then the routine
 * also reallocates the ne array. */
template<class vc_class>
void voronoicell_base::add_memory_vertices(vc_class &vc) {

printf("nope: %d\n", current_vertices);
exit(3);

        int i=(current_vertices<<1),j,**pp,*pnu;
        if (i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
        fprintf(stderr,"Vertex memory scaled up to %d\n",i);
#endif
        double *ppts;
        pp=new int*[i];
        for (j=0;j<current_vertices;j++) pp[j]=ed[j];
        delete [] ed;ed=pp;
        vc.n_add_memory_vertices(i);
        pnu=new int[i];
        for (j=0;j<current_vertices;j++) pnu[j]=nu[j];
        delete [] nu;nu=pnu;
        ppts=new double[3*i];
        for (j=0;j<3*current_vertices;j++) ppts[j]=pts[j];
        delete [] pts;pts=ppts;
        current_vertices=i;
}

/** Doubles the maximum allowed vertex order, by reallocating mem, mep, and mec
 * arrays. If the allocation exceeds the absolute maximum set in
 * max_vertex_order, then the routine causes a fatal error. If the template has
 * been instantiated with the neighbor tracking turned on, then the routine
 * also reallocates the mne array. */
template<class vc_class>
void voronoicell_base::add_memory_vorder(vc_class &vc) {
        int i=(current_vertex_order<<1),j,*p1,**p2;
        if (i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
        fprintf(stderr,"Vertex order memory scaled up to %d\n",i);
#endif
        p1=new int[i];
        for (j=0;j<current_vertex_order;j++) p1[j]=mem[j];
        while (j<i) p1[j++]=0;
        delete [] mem;mem=p1;
        p2=new int*[i];
        for (j=0;j<current_vertex_order;j++) p2[j]=mep[j];
        delete [] mep;mep=p2;
        p1=new int[i];
        for (j=0;j<current_vertex_order;j++) p1[j]=mec[j];
        while (j<i) p1[j++]=0;
        delete [] mec;mec=p1;
        vc.n_add_memory_vorder(i);
        current_vertex_order=i;
}

/** Doubles the size allocation of the main delete stack. If the allocation
 * exceeds the absolute maximum set in max_delete_size, then routine causes a
 * fatal error. */
void voronoicell_base::add_memory_ds(int *&stackp) {
        current_delete_size<<=1;
        if (current_delete_size>max_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
        fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size);
#endif
        int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds;
        while (dsp<stackp) *(dsnp++)=*(dsp++);
        delete [] ds;ds=dsn;stackp=dsnp;
        stacke=ds+current_delete_size;
}

/** Doubles the size allocation of the auxiliary delete stack. If the
 * allocation exceeds the absolute maximum set in max_delete2_size, then the
 * routine causes a fatal error. */
void voronoicell_base::add_memory_ds2(int *&stackp2) {
        current_delete2_size<<=1;
        if (current_delete2_size>max_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
        fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size);
#endif
        int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2;
        while (dsp<stackp2) *(dsnp++)=*(dsp++);
        delete [] ds2;ds2=dsn;stackp2=dsnp;
        stacke2=ds2+current_delete2_size;
}

/** Initializes a Voronoi cell as a rectangular box with the given dimensions.
 * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
 * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
 * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
void voronoicell_base::init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
        for (int i=0;i<current_vertex_order;i++) mec[i]=0;
        up=0;mec[3]=p=8;xmin*=2;xmax*=2;ymin*=2;ymax*=2;zmin*=2;zmax*=2;
        *pts=xmin;pts[1]=ymin;pts[2]=zmin;
        pts[3]=xmax;pts[4]=ymin;pts[5]=zmin;
        pts[6]=xmin;pts[7]=ymax;pts[8]=zmin;
        pts[9]=xmax;pts[10]=ymax;pts[11]=zmin;
        pts[12]=xmin;pts[13]=ymin;pts[14]=zmax;
        pts[15]=xmax;pts[16]=ymin;pts[17]=zmax;
        pts[18]=xmin;pts[19]=ymax;pts[20]=zmax;
        pts[21]=xmax;pts[22]=ymax;pts[23]=zmax;
        int *q=mep[3];
        *q=1;q[1]=4;q[2]=2;q[3]=2;q[4]=1;q[5]=0;q[6]=0;
        q[7]=3;q[8]=5;q[9]=0;q[10]=2;q[11]=1;q[12]=0;q[13]=1;
        q[14]=0;q[15]=6;q[16]=3;q[17]=2;q[18]=1;q[19]=0;q[20]=2;
        q[21]=2;q[22]=7;q[23]=1;q[24]=2;q[25]=1;q[26]=0;q[27]=3;
        q[28]=6;q[29]=0;q[30]=5;q[31]=2;q[32]=1;q[33]=0;q[34]=4;
        q[35]=4;q[36]=1;q[37]=7;q[38]=2;q[39]=1;q[40]=0;q[41]=5;
        q[42]=7;q[43]=2;q[44]=4;q[45]=2;q[46]=1;q[47]=0;q[48]=6;
        q[49]=5;q[50]=3;q[51]=6;q[52]=2;q[53]=1;q[54]=0;q[55]=7;
        *ed=q;ed[1]=q+7;ed[2]=q+14;ed[3]=q+21;
        ed[4]=q+28;ed[5]=q+35;ed[6]=q+42;ed[7]=q+49;
        *nu=nu[1]=nu[2]=nu[3]=nu[4]=nu[5]=nu[6]=nu[7]=3;
}

/** Starting from a point within the current cutting plane, this routine attempts
 * to find an edge to a point outside the cutting plane. This prevents the plane
 * routine from .
 * \param[in] vc a reference to the specialized version of the calling class.
 * \param[in,out] up */
template<class vc_class>
inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) {
        int i,lp,lw,*j(ds2),*stackp2(ds2);
        double l;
        *(stackp2++)=up;
        while (j<stackp2) {
                up=*(j++);
                for (i=0;i<nu[up];i++) {
                        lp=ed[up][i];
                        lw=m_test(lp,l);
                        if (lw==-1) return true;
                        else if (lw==0) add_to_stack(vc,lp,stackp2);
                }
        }
        return false;
}

/** Adds a point to the auxiliary delete stack if it is not already there.
 * \param[in] vc a reference to the specialized version of the calling class.
 * \param[in] lp the index of the point to add.
 * \param[in,out] stackp2 a pointer to the end of the stack entries. */
template<class vc_class>
inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) {
(void)vc;
        for (int *k(ds2);k<stackp2;k++) if (*k==lp) return;
        if (stackp2==stacke2) add_memory_ds2(stackp2);
        *(stackp2++)=lp;
}

/** Cuts the Voronoi cell by a particle whose center is at a separation of
 * (x,y,z) from the cell center. The value of rsq should be initially set to
 * \f$x^2+y^2+z^2\f$.
 * \param[in] vc a reference to the specialized version of the calling class.
 * \param[in] (x,y,z) the normal vector to the plane.
 * \param[in] rsq the distance along this vector of the plane.
 * \param[in] p_id the plane ID (for neighbor tracking only).
 * \return False if the plane cut deleted the cell entirely, true otherwise. */
template<class vc_class>
bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) {
        int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp;
        int us=0,ls=0,qs,iqs,cs,uw,qw,lw;
        int *edp,*edd;
        double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false;

        // Initialize the safe testing routine
        n_marg=0;px=x;py=y;pz=z;prsq=rsq;

        // Test approximately sqrt(n)/4 points for their proximity to the plane
        // and keep the one which is closest
        uw=m_test(up,u);

        // Starting from an initial guess, we now move from vertex to vertex,
        // to try and find an edge which intersects the cutting plane,
        // or a vertex which is on the plane
        try {
                if (uw==1) {

                        // The test point is inside the cutting plane.
                        us=0;
                        do {
                                lp=ed[up][us];
                                lw=m_test(lp,l);
                                if (l<u) break;
                                us++;
                        } while (us<nu[up]);

                        if (us==nu[up]) {
                                return false;
                        }

                        ls=ed[up][nu[up]+us];
                        while (lw==1) {
                                if (++count>=p) throw true;
                                u=l;up=lp;
                                for (us=0;us<ls;us++) {
                                        lp=ed[up][us];
                                        lw=m_test(lp,l);
                                        if (l<u) break;
                                }
                                if (us==ls) {
                                        us++;
                                        while (us<nu[up]) {
                                                lp=ed[up][us];
                                                lw=m_test(lp,l);
                                                if (l<u) break;
                                                us++;
                                        }
                                        if (us==nu[up]) {
                                                return false;
                                        }
                                }
                                ls=ed[up][nu[up]+us];
                        }

                        // If the last point in the iteration is within the
                        // plane, we need to do the complicated setup
                        // routine. Otherwise, we use the regular iteration.
                        if (lw==0) {
                                up=lp;
                                complicated_setup=true;
                        } else complicated_setup=false;
                } else if (uw==-1) {
                        us=0;
                        do {
                                qp=ed[up][us];
                                qw=m_test(qp,q);
                                if (u<q) break;
                                us++;
                        } while (us<nu[up]);
                        if (us==nu[up]) return true;

                        while (qw==-1) {
                                qs=ed[up][nu[up]+us];
                                if (++count>=p) throw true;
                                u=q;up=qp;
                                for (us=0;us<qs;us++) {
                                        qp=ed[up][us];
                                        qw=m_test(qp,q);
                                        if (u<q) break;
                                }
                                if (us==qs) {
                                        us++;
                                        while (us<nu[up]) {
                                                qp=ed[up][us];
                                                qw=m_test(qp,q);
                                                if (u<q) break;
                                                us++;
                                        }
                                        if (us==nu[up]) return true;
                                }
                        }
                        if (qw==1) {
                                lp=up;ls=us;l=u;
                                up=qp;us=ed[lp][nu[lp]+ls];u=q;
                                complicated_setup=false;
                        } else {
                                up=qp;
                                complicated_setup=true;
                        }
                } else {

                        // Our original test point was on the plane, so we
                        // automatically head for the complicated setup
                        // routine
                        complicated_setup=true;
                }
        }
        catch(bool except) {
                // This routine is a fall-back, in case floating point errors
                // cause the usual search routine to fail. In the fall-back
                // routine, we just test every edge to find one straddling
                // the plane.
#if VOROPP_VERBOSE >=1
                fputs("Bailed out of convex calculation\n",stderr);
#endif
                qw=1;lw=0;
                for (qp=0;qp<p;qp++) {
                        qw=m_test(qp,q);
                        if (qw==1) {

                                // The point is inside the cutting space. Now
                                // see if we can find a neighbor which isn't.
                                for (us=0;us<nu[qp];us++) {
                                        lp=ed[qp][us];
                                        if (lp<qp) {
                                                lw=m_test(lp,l);
                                                if (lw!=1) break;
                                        }
                                }
                                if (us<nu[qp]) {
                                        up=qp;
                                        if (lw==0) {
                                                complicated_setup=true;
                                        } else {
                                                complicated_setup=false;
                                                u=q;
                                                ls=ed[up][nu[up]+us];
                                        }
                                        break;
                                }
                        } else if (qw==-1) {

                                // The point is outside the cutting space. See
                                // if we can find a neighbor which isn't.
                                for (ls=0;ls<nu[qp];ls++) {
                                        up=ed[qp][ls];
                                        if (up<qp) {
                                                uw=m_test(up,u);
                                                if (uw!=-1) break;
                                        }
                                }
                                if (ls<nu[qp]) {
                                        if (uw==0) {
                                                up=qp;
                                                complicated_setup=true;
                                        } else {
                                                complicated_setup=false;
                                                lp=qp;l=q;
                                                us=ed[lp][nu[lp]+ls];
                                        }
                                        break;
                                }
                        } else {

                                // The point is in the plane, so we just
                                // proceed with the complicated setup routine
                                up=qp;
                                complicated_setup=true;
                                break;
                        }
                }
                if (qp==p) return qw==-1;
        }

        // We're about to add the first point of the new facet. In either
        // routine, we have to add a point, so first check there's space for
        // it.
        if (p==current_vertices) add_memory_vertices(vc);

        if (complicated_setup) {

                // We want to be strict about reaching the conclusion that the
                // cell is entirely within the cutting plane. It's not enough
                // to find a vertex that has edges which are all inside or on
                // the plane. If the vertex has neighbors that are also on the
                // plane, we should check those too.
                if (!search_for_outside_edge(vc,up)) return false;

                // The search algorithm found a point which is on the cutting
                // plane. We leave that point in place, and create a new one at
                // the same location.
                pts[3*p]=pts[3*up];
                pts[3*p+1]=pts[3*up+1];
                pts[3*p+2]=pts[3*up+2];

                // Search for a collection of edges of the test vertex which
                // are outside of the cutting space. Begin by testing the
                // zeroth edge.
                i=0;
                lp=*ed[up];
                lw=m_test(lp,l);
                if (lw!=-1) {

                        // The first edge is either inside the cutting space,
                        // or lies within the cutting plane. Test the edges
                        // sequentially until we find one that is outside.
                        rp=lw;
                        do {
                                i++;

                                // If we reached the last edge with no luck
                                // then all of the vertices are inside
                                // or on the plane, so the cell is completely
                                // deleted
                                if (i==nu[up]) return false;
                                lp=ed[up][i];
                                lw=m_test(lp,l);
                        } while (lw!=-1);
                        j=i+1;

                        // We found an edge outside the cutting space. Keep
                        // moving through these edges until we find one that's
                        // inside or on the plane.
                        while (j<nu[up]) {
                                lp=ed[up][j];
                                lw=m_test(lp,l);
                                if (lw!=-1) break;
                                j++;
                        }

                        // Compute the number of edges for the new vertex. In
                        // general it will be the number of outside edges
                        // found, plus two. But we need to recognize the
                        // special case when all but one edge is outside, and
                        // the remaining one is on the plane. For that case we
                        // have to reduce the edge count by one to prevent
                        // doubling up.
                        if (j==nu[up]&&i==1&&rp==0) {
                                nu[p]=nu[up];
                                double_edge=true;
                        } else nu[p]=j-i+2;
                        k=1;

                        // Add memory for the new vertex if needed, and
                        // initialize
                        while (nu[p]>=current_vertex_order) add_memory_vorder(vc);
                        if (mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
                        vc.n_set_pointer(p,nu[p]);
                        ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
                        ed[p][nu[p]<<1]=p;

                        // Copy the edges of the original vertex into the new
                        // one. Delete the edges of the original vertex, and
                        // update the relational table.
                        us=cycle_down(i,up);
                        while (i<j) {
                                qp=ed[up][i];
                                qs=ed[up][nu[up]+i];
                                vc.n_copy(p,k,up,i);
                                ed[p][k]=qp;
                                ed[p][nu[p]+k]=qs;
                                ed[qp][qs]=p;
                                ed[qp][nu[qp]+qs]=k;
                                ed[up][i]=-1;
                                i++;k++;
                        }
                        qs=i==nu[up]?0:i;
                } else {

                        // In this case, the zeroth edge is outside the cutting
                        // plane. Begin by searching backwards from the last
                        // edge until we find an edge which isn't outside.
                        i=nu[up]-1;
                        lp=ed[up][i];
                        lw=m_test(lp,l);
                        while (lw==-1) {
                                i--;

                                // If i reaches zero, then we have a point in
                                // the plane all of whose edges are outside
                                // the cutting space, so we just exit
                                if (i==0) return true;
                                lp=ed[up][i];
                                lw=m_test(lp,l);
                        }

                        // Now search forwards from zero
                        j=1;
                        qp=ed[up][j];
                        qw=m_test(qp,q);
                        while (qw==-1) {
                                j++;
                                qp=ed[up][j];
                                qw=m_test(qp,l);
                        }

                        // Compute the number of edges for the new vertex. In
                        // general it will be the number of outside edges
                        // found, plus two. But we need to recognize the
                        // special case when all but one edge is outside, and
                        // the remaining one is on the plane. For that case we
                        // have to reduce the edge count by one to prevent
                        // doubling up.
                        if (i==j&&qw==0) {
                                double_edge=true;
                                nu[p]=nu[up];
                        } else {
                                nu[p]=nu[up]-i+j+1;
                        }

                        // Add memory to store the vertex if it doesn't exist
                        // already
                        k=1;
                        while (nu[p]>=current_vertex_order) add_memory_vorder(vc);
                        if (mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);

                        // Copy the edges of the original vertex into the new
                        // one. Delete the edges of the original vertex, and
                        // update the relational table.
                        vc.n_set_pointer(p,nu[p]);
                        ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
                        ed[p][nu[p]<<1]=p;
                        us=i++;
                        while (i<nu[up]) {
                                qp=ed[up][i];
                                qs=ed[up][nu[up]+i];
                                vc.n_copy(p,k,up,i);
                                ed[p][k]=qp;
                                ed[p][nu[p]+k]=qs;
                                ed[qp][qs]=p;
                                ed[qp][nu[qp]+qs]=k;
                                ed[up][i]=-1;
                                i++;k++;
                        }
                        i=0;
                        while (i<j) {
                                qp=ed[up][i];
                                qs=ed[up][nu[up]+i];
                                vc.n_copy(p,k,up,i);
                                ed[p][k]=qp;
                                ed[p][nu[p]+k]=qs;
                                ed[qp][qs]=p;
                                ed[qp][nu[qp]+qs]=k;
                                ed[up][i]=-1;
                                i++;k++;
                        }
                        qs=j;
                }
                if (!double_edge) {
                        vc.n_copy(p,k,up,qs);
                        vc.n_set(p,0,p_id);
                } else vc.n_copy(p,0,up,qs);

                // Add this point to the auxiliary delete stack
                if (stackp2==stacke2) add_memory_ds2(stackp2);
                *(stackp2++)=up;

                // Look at the edges on either side of the group that was
                // detected. We're going to commence facet computation by
                // moving along one of them. We are going to end up coming back
                // along the other one.
                cs=k;
                qp=up;q=u;
                i=ed[up][us];
                us=ed[up][nu[up]+us];
                up=i;
                ed[qp][nu[qp]<<1]=-p;

        } else {

                // The search algorithm found an intersected edge between the
                // points lp and up. Create a new vertex between them which
                // lies on the cutting plane. Since u and l differ by at least
                // the tolerance, this division should never screw up.
                if (stackp==stacke) add_memory_ds(stackp);
                *(stackp++)=up;
                r=u/(u-l);l=1-r;
                pts[3*p]=pts[3*lp]*r+pts[3*up]*l;
                pts[3*p+1]=pts[3*lp+1]*r+pts[3*up+1]*l;
                pts[3*p+2]=pts[3*lp+2]*r+pts[3*up+2]*l;

                // This point will always have three edges. Connect one of them
                // to lp.
                nu[p]=3;
                if (mec[3]==mem[3]) add_memory(vc,3,stackp2);
                vc.n_set_pointer(p,3);
                vc.n_set(p,0,p_id);
                vc.n_copy(p,1,up,us);
                vc.n_copy(p,2,lp,ls);
                ed[p]=mep[3]+7*mec[3]++;
                ed[p][6]=p;
                ed[up][us]=-1;
                ed[lp][ls]=p;
                ed[lp][nu[lp]+ls]=1;
                ed[p][1]=lp;
                ed[p][nu[p]+1]=ls;
                cs=2;

                // Set the direction to move in
                qs=cycle_up(us,up);
                qp=up;q=u;
        }

        // When the code reaches here, we have initialized the first point, and
        // we have a direction for moving it to construct the rest of the facet
        cp=p;rp=p;p++;
        while (qp!=up||qs!=us) {

                // We're currently tracing round an intersected facet. Keep
                // moving around it until we find a point or edge which
                // intersects the plane.
                lp=ed[qp][qs];
                lw=m_test(lp,l);

                if (lw==1) {

                        // The point is still in the cutting space. Just add it
                        // to the delete stack and keep moving.
                        qs=cycle_up(ed[qp][nu[qp]+qs],lp);
                        qp=lp;
                        q=l;
                        if (stackp==stacke) add_memory_ds(stackp);
                        *(stackp++)=qp;

                } else if (lw==-1) {

                        // The point is outside of the cutting space, so we've
                        // found an intersected edge. Introduce a regular point
                        // at the point of intersection. Connect it to the
                        // point we just tested. Also connect it to the previous
                        // new point in the facet we're constructing.
                        if (p==current_vertices) add_memory_vertices(vc);
                        r=q/(q-l);l=1-r;
                        pts[3*p]=pts[3*lp]*r+pts[3*qp]*l;
                        pts[3*p+1]=pts[3*lp+1]*r+pts[3*qp+1]*l;
                        pts[3*p+2]=pts[3*lp+2]*r+pts[3*qp+2]*l;
                        nu[p]=3;
                        if (mec[3]==mem[3]) add_memory(vc,3,stackp2);
                        ls=ed[qp][qs+nu[qp]];
                        vc.n_set_pointer(p,3);
                        vc.n_set(p,0,p_id);
                        vc.n_copy(p,1,qp,qs);
                        vc.n_copy(p,2,lp,ls);
                        ed[p]=mep[3]+7*mec[3]++;
                        *ed[p]=cp;
                        ed[p][1]=lp;
                        ed[p][3]=cs;
                        ed[p][4]=ls;
                        ed[p][6]=p;
                        ed[lp][ls]=p;
                        ed[lp][nu[lp]+ls]=1;
                        ed[cp][cs]=p;
                        ed[cp][nu[cp]+cs]=0;
                        ed[qp][qs]=-1;
                        qs=cycle_up(qs,qp);
                        cp=p++;
                        cs=2;
                } else {

                        // We've found a point which is on the cutting plane.
                        // We're going to introduce a new point right here, but
                        // first we need to figure out the number of edges it
                        // has.
                        if (p==current_vertices) add_memory_vertices(vc);

                        // If the previous vertex detected a double edge, our
                        // new vertex will have one less edge.
                        k=double_edge?0:1;
                        qs=ed[qp][nu[qp]+qs];
                        qp=lp;
                        iqs=qs;

                        // Start testing the edges of the current point until
                        // we find one which isn't outside the cutting space
                        do {
                                k++;
                                qs=cycle_up(qs,qp);
                                lp=ed[qp][qs];
                                lw=m_test(lp,l);
                        } while (lw==-1);

                        // Now we need to find out whether this marginal vertex
                        // we are on has been visited before, because if that's
                        // the case, we need to add vertices to the existing
                        // new vertex, rather than creating a fresh one. We also
                        // need to figure out whether we're in a case where we
                        // might be creating a duplicate edge.
                        j=-ed[qp][nu[qp]<<1];
                         if (qp==up&&qs==us) {

                                // If we're heading into the final part of the
                                // new facet, then we never worry about the
                                // duplicate edge calculation.
                                new_double_edge=false;
                                if (j>0) k+=nu[j];
                        } else {
                                if (j>0) {

                                        // This vertex was visited before, so
                                        // count those vertices to the ones we
                                        // already have.
                                        k+=nu[j];

                                        // The only time when we might make a
                                        // duplicate edge is if the point we're
                                        // going to move to next is also a
                                        // marginal point, so test for that
                                        // first.
                                        if (lw==0) {

                                                // Now see whether this marginal point
                                                // has been visited before.
                                                i=-ed[lp][nu[lp]<<1];
                                                if (i>0) {

                                                        // Now see if the last edge of that other
                                                        // marginal point actually ends up here.
                                                        if (ed[i][nu[i]-1]==j) {
                                                                new_double_edge=true;
                                                                k-=1;
                                                        } else new_double_edge=false;
                                                } else {

                                                        // That marginal point hasn't been visited
                                                        // before, so we probably don't have to worry
                                                        // about duplicate edges, except in the
                                                        // case when that's the way into the end
                                                        // of the facet, because that way always creates
                                                        // an edge.
                                                        if (j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) {
                                                                new_double_edge=true;
                                                                k-=1;
                                                        } else new_double_edge=false;
                                                }
                                        } else new_double_edge=false;
                                } else {

                                        // The vertex hasn't been visited
                                        // before, but let's see if it's
                                        // marginal
                                        if (lw==0) {

                                                // If it is, we need to check
                                                // for the case that it's a
                                                // small branch, and that we're
                                                // heading right back to where
                                                // we came from
                                                i=-ed[lp][nu[lp]<<1];
                                                if (i==cp) {
                                                        new_double_edge=true;
                                                        k-=1;
                                                } else new_double_edge=false;
                                        } else new_double_edge=false;
                                }
                        }

                        // k now holds the number of edges of the new vertex
                        // we are forming. Add memory for it if it doesn't exist
                        // already.
                        while (k>=current_vertex_order) add_memory_vorder(vc);
                        if (mec[k]==mem[k]) add_memory(vc,k,stackp2);

                        // Now create a new vertex with order k, or augment
                        // the existing one
                        if (j>0) {

                                // If we're augmenting a vertex but we don't
                                // actually need any more edges, just skip this
                                // routine to avoid memory confusion
                                if (nu[j]!=k) {
                                        // Allocate memory and copy the edges
                                        // of the previous instance into it
                                        vc.n_set_aux1(k);
                                        edp=mep[k]+((k<<1)+1)*mec[k]++;
                                        i=0;
                                        while (i<nu[j]) {
                                                vc.n_copy_aux1(j,i);
                                                edp[i]=ed[j][i];
                                                edp[k+i]=ed[j][nu[j]+i];
                                                i++;
                                        }
                                        edp[k<<1]=j;

                                        // Remove the previous instance with
                                        // fewer vertices from the memory
                                        // structure
                                        edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
                                        if (edd!=ed[j]) {
                                                for (lw=0;lw<=(nu[j]<<1);lw++) ed[j][lw]=edd[lw];
                                                vc.n_set_aux2_copy(j,nu[j]);
                                                vc.n_copy_pointer(edd[nu[j]<<1],j);
                                                ed[edd[nu[j]<<1]]=ed[j];
                                        }
                                        vc.n_set_to_aux1(j);
                                        ed[j]=edp;
                                } else i=nu[j];
                        } else {

                                // Allocate a new vertex of order k
                                vc.n_set_pointer(p,k);
                                ed[p]=mep[k]+((k<<1)+1)*mec[k]++;
                                ed[p][k<<1]=p;
                                if (stackp2==stacke2) add_memory_ds2(stackp2);
                                *(stackp2++)=qp;
                                pts[3*p]=pts[3*qp];
                                pts[3*p+1]=pts[3*qp+1];
                                pts[3*p+2]=pts[3*qp+2];
                                ed[qp][nu[qp]<<1]=-p;
                                j=p++;
                                i=0;
                        }
                        nu[j]=k;

                        // Unless the previous case was a double edge, connect
                        // the first available edge of the new vertex to the
                        // last one in the facet
                        if (!double_edge) {
                                ed[j][i]=cp;
                                ed[j][nu[j]+i]=cs;
                                vc.n_set(j,i,p_id);
                                ed[cp][cs]=j;
                                ed[cp][nu[cp]+cs]=i;
                                i++;
                        }

                        // Copy in the edges of the underlying vertex,
                        // and do one less if this was a double edge
                        qs=iqs;
                        while (i<(new_double_edge?k:k-1)) {
                                qs=cycle_up(qs,qp);
                                lp=ed[qp][qs];ls=ed[qp][nu[qp]+qs];
                                vc.n_copy(j,i,qp,qs);
                                ed[j][i]=lp;
                                ed[j][nu[j]+i]=ls;
                                ed[lp][ls]=j;
                                ed[lp][nu[lp]+ls]=i;
                                ed[qp][qs]=-1;
                                i++;
                        }
                        qs=cycle_up(qs,qp);
                        cs=i;
                        cp=j;
                        vc.n_copy(j,new_double_edge?0:cs,qp,qs);

                        // Update the double_edge flag, to pass it
                        // to the next instance of this routine
                        double_edge=new_double_edge;
                }
        }

        // Connect the final created vertex to the initial one
        ed[cp][cs]=rp;
        *ed[rp]=cp;
        ed[cp][nu[cp]+cs]=0;
        ed[rp][nu[rp]]=cs;

        // Delete points: first, remove any duplicates
        dsp=ds;
        while (dsp<stackp) {
                j=*dsp;
                if (ed[j][nu[j]]!=-1) {
                        ed[j][nu[j]]=-1;
                        dsp++;
                } else *dsp=*(--stackp);
        }

        // Add the points in the auxiliary delete stack,
        // and reset their back pointers
        for (dsp=ds2;dsp<stackp2;dsp++) {
                j=*dsp;
                ed[j][nu[j]<<1]=j;
                if (ed[j][nu[j]]!=-1) {
                        ed[j][nu[j]]=-1;
                        if (stackp==stacke) add_memory_ds(stackp);
                        *(stackp++)=j;
                }
        }

        // Scan connections and add in extras
        for (dsp=ds;dsp<stackp;dsp++) {
                cp=*dsp;
                for (edp=ed[cp];edp<ed[cp]+nu[cp];edp++) {
                        qp=*edp;
                        if (qp!=-1&&ed[qp][nu[qp]]!=-1) {
                                if (stackp==stacke) {
                                        int dis=stackp-dsp;
                                        add_memory_ds(stackp);
                                        dsp=ds+dis;
                                }
                                *(stackp++)=qp;
                                ed[qp][nu[qp]]=-1;
                        }
                }
        }
        up=0;

        // Delete them from the array structure
        while (stackp>ds) {
                --p;
                while (ed[p][nu[p]]==-1) {
                        j=nu[p];
                        edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]);
                        while (edp<ed[p]+(j<<1)+1) *(edp++)=*(edd++);
                        vc.n_set_aux2_copy(p,j);
                        vc.n_copy_pointer(ed[p][(j<<1)],p);
                        ed[ed[p][(j<<1)]]=ed[p];
                        --p;
                }
                up=*(--stackp);
                if (up<p) {

                        // Vertex management
                        pts[3*up]=pts[3*p];
                        pts[3*up+1]=pts[3*p+1];
                        pts[3*up+2]=pts[3*p+2];

                        // Memory management
                        j=nu[up];
                        edp=ed[up];edd=(mep[j]+((j<<1)+1)*--mec[j]);
                        while (edp<ed[up]+(j<<1)+1) *(edp++)=*(edd++);
                        vc.n_set_aux2_copy(up,j);
                        vc.n_copy_pointer(ed[up][j<<1],up);
                        vc.n_copy_pointer(up,p);
                        ed[ed[up][j<<1]]=ed[up];

                        // Edge management
                        ed[up]=ed[p];
                        nu[up]=nu[p];
                        for (i=0;i<nu[up];i++) ed[ed[up][i]][ed[up][nu[up]+i]]=up;
                        ed[up][nu[up]<<1]=up;
                } else up=p++;
        }

        // Check for any vertices of zero order
        if (*mec>0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR);

        // Collapse any order 2 vertices and exit
        return collapse_order2(vc);
}

/** During the creation of a new facet in the plane routine, it is possible
 * that some order two vertices may arise. This routine removes them.
 * Suppose an order two vertex joins c and d. If there's a edge between
 * c and d already, then the order two vertex is just removed; otherwise,
 * the order two vertex is removed and c and d are joined together directly.
 * It is possible this process will create order two or order one vertices,
 * and the routine is continually run until all of them are removed.
 * \return False if the vertex removal was unsuccessful, indicative of the cell
 *         reducing to zero volume and disappearing; true if the vertex removal
 *         was successful. */
template<class vc_class>
inline bool voronoicell_base::collapse_order2(vc_class &vc) {
        if (!collapse_order1(vc)) return false;
        int a,b,i,j,k,l;
        while (mec[2]>0) {

                // Pick a order 2 vertex and read in its edges
                i=--mec[2];
                j=mep[2][5*i];k=mep[2][5*i+1];
                if (j==k) {
#if VOROPP_VERBOSE >=1
                        fputs("Order two vertex joins itself",stderr);
#endif
                        return false;
                }

                // Scan the edges of j to see if joins k
                for (l=0;l<nu[j];l++) {
                        if (ed[j][l]==k) break;
                }

                // If j doesn't already join k, join them together.
                // Otherwise delete the connection to the current
                // vertex from j and k.
                a=mep[2][5*i+2];b=mep[2][5*i+3];i=mep[2][5*i+4];
                if (l==nu[j]) {
                        ed[j][a]=k;
                        ed[k][b]=j;
                        ed[j][nu[j]+a]=b;
                        ed[k][nu[k]+b]=a;
                } else {
                        if (!delete_connection(vc,j,a,false)) return false;
                        if (!delete_connection(vc,k,b,true)) return false;
                }

                // Compact the memory
                --p;
                if (up==i) up=0;
                if (p!=i) {
                        if (up==p) up=i;
                        pts[3*i]=pts[3*p];
                        pts[3*i+1]=pts[3*p+1];
                        pts[3*i+2]=pts[3*p+2];
                        for (k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
                        vc.n_copy_pointer(i,p);
                        ed[i]=ed[p];
                        nu[i]=nu[p];
                        ed[i][nu[i]<<1]=i;
                }

                // Collapse any order 1 vertices if they were created
                if (!collapse_order1(vc)) return false;
        }
        return true;
}

/** Order one vertices can potentially be created during the order two collapse
 * routine. This routine keeps removing them until there are none left.
 * \return False if the vertex removal was unsuccessful, indicative of the cell
 *         having zero volume and disappearing; true if the vertex removal was
 *         successful. */
template<class vc_class>
inline bool voronoicell_base::collapse_order1(vc_class &vc) {
        int i,j,k;
        while (mec[1]>0) {
                up=0;
#if VOROPP_VERBOSE >=1
                fputs("Order one collapse\n",stderr);
#endif
                i=--mec[1];
                j=mep[1][3*i];k=mep[1][3*i+1];
                i=mep[1][3*i+2];
                if (!delete_connection(vc,j,k,false)) return false;
                --p;
                if (up==i) up=0;
                if (p!=i) {
                        if (up==p) up=i;
                        pts[3*i]=pts[3*p];
                        pts[3*i+1]=pts[3*p+1];
                        pts[3*i+2]=pts[3*p+2];
                        for (k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
                        vc.n_copy_pointer(i,p);
                        ed[i]=ed[p];
                        nu[i]=nu[p];
                        ed[i][nu[i]<<1]=i;
                }
        }
        return true;
}

/** This routine deletes the kth edge of vertex j and reorganizes the memory.
 * If the neighbor computation is enabled, we also have to supply an handedness
 * flag to decide whether to preserve the plane on the left or right of the
 * connection.
 * \return False if a zero order vertex was formed, indicative of the cell
 *         disappearing; true if the vertex removal was successful. */
template<class vc_class>
inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) {
        int q=hand?k:cycle_up(k,j);
        int i=nu[j]-1,l,*edp,*edd,m;
#if VOROPP_VERBOSE >=1
        if (i<1) {
                fputs("Zero order vertex formed\n",stderr);
                return false;
        }
#endif
        if (mec[i]==mem[i]) add_memory(vc,i,ds2);
        vc.n_set_aux1(i);
        for (l=0;l<q;l++) vc.n_copy_aux1(j,l);
        while (l<i) {
                vc.n_copy_aux1_shift(j,l);
                l++;
        }
        edp=mep[i]+((i<<1)+1)*mec[i]++;
        edp[i<<1]=j;
        for (l=0;l<k;l++) {
                edp[l]=ed[j][l];
                edp[l+i]=ed[j][l+nu[j]];
        }
        while (l<i) {
                m=ed[j][l+1];
                edp[l]=m;
                k=ed[j][l+nu[j]+1];
                edp[l+i]=k;
                ed[m][nu[m]+k]--;
                l++;
        }

        edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
        for (l=0;l<=(nu[j]<<1);l++) ed[j][l]=edd[l];
        vc.n_set_aux2_copy(j,nu[j]);
        vc.n_set_to_aux2(edd[nu[j]<<1]);
        vc.n_set_to_aux1(j);
        ed[edd[nu[j]<<1]]=edd;
        ed[j]=edp;
        nu[j]=i;
        return true;
}

/** Calculates the areas of each face of the Voronoi cell and prints the
 * results to an output stream.
 * \param[out] v the vector to store the results in. */
void voronoicell_base::face_areas(std::vector<double> &v) {
        double area;
        v.clear();
        int i,j,k,l,m,n;
        double ux,uy,uz,vx,vy,vz,wx,wy,wz;
        for (i=1;i<p;i++) for(j=0;j<nu[i];j++) {
                k=ed[i][j];
                if (k>=0) {
                        area=0;
                        ed[i][j]=-1-k;
                        l=cycle_up(ed[i][nu[i]+j],k);
                        m=ed[k][l];ed[k][l]=-1-m;
                        while (m!=i) {
                                n=cycle_up(ed[k][nu[k]+l],m);
                                ux=pts[3*k]-pts[3*i];
                                uy=pts[3*k+1]-pts[3*i+1];
                                uz=pts[3*k+2]-pts[3*i+2];
                                vx=pts[3*m]-pts[3*i];
                                vy=pts[3*m+1]-pts[3*i+1];
                                vz=pts[3*m+2]-pts[3*i+2];
                                wx=uy*vz-uz*vy;
                                wy=uz*vx-ux*vz;
                                wz=ux*vy-uy*vx;
                                area+=sqrt(wx*wx+wy*wy+wz*wz);
                                k=m;l=n;
                                m=ed[k][l];ed[k][l]=-1-m;
                        }
                        v.push_back(0.125*area);
                }
        }
        reset_edges();
}

/** Several routines in the class that gather cell-based statistics internally
 * track their progress by flipping edges to negative so that they know what
 * parts of the cell have already been tested. This function resets them back
 * to positive. When it is called, it assumes that every edge in the routine
 * should have already been flipped to negative, and it bails out with an
 * internal error if it encounters a positive edge. */
inline void voronoicell_base::reset_edges() {
        int i,j;
        for (i=0;i<p;i++) for(j=0;j<nu[i];j++) {
                if (ed[i][j]>=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR);
                ed[i][j]=-1-ed[i][j];
        }
}

/** Checks to see if a given vertex is inside, outside or within the test
 * plane. If the point is far away from the test plane, the routine immediately
 * returns whether it is inside or outside. If the routine is close the the
 * plane and within the specified tolerance, then the special check_marginal()
 * routine is called.
 * \param[in] n the vertex to test.
 * \param[out] ans the result of the scalar product used in evaluating the
 *                 location of the point.
 * \return -1 if the point is inside the plane, 1 if the point is outside the
 *         plane, or 0 if the point is within the plane. */
inline int voronoicell_base::m_test(int n,double &ans) {
        double *pp=pts+n+(n<<1);
        ans=*(pp++)*px;
        ans+=*(pp++)*py;
        ans+=*pp*pz-prsq;
        if (ans<-tolerance2) {
                return -1;
        } else if (ans>tolerance2) {
                return 1;
        }
        return check_marginal(n,ans);
}

/** Checks to see if a given vertex is inside, outside or within the test
 * plane, for the case when the point has been detected to be very close to the
 * plane. The routine ensures that the returned results are always consistent
 * with previous tests, by keeping a table of any marginal results. The routine
 * first sees if the vertex is in the table, and if it finds a previously
 * computed result it uses that. Otherwise, it computes a result for this
 * vertex and adds it the table.
 * \param[in] n the vertex to test.
 * \param[in] ans the result of the scalar product used in evaluating
 *                the location of the point.
 * \return -1 if the point is inside the plane, 1 if the point is outside the
 *         plane, or 0 if the point is within the plane. */
int voronoicell_base::check_marginal(int n,double &ans) {
        int i;
        for (i=0;i<n_marg;i+=2) if (marg[i]==n) return marg[i+1];
        if (n_marg==current_marginal) {
                current_marginal<<=1;
                if (current_marginal>max_marginal)
                        voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
#if VOROPP_VERBOSE >=2
                fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i);
#endif
                int *pmarg=new int[current_marginal];
                for (int j=0;j<n_marg;j++) pmarg[j]=marg[j];
                delete [] marg;
                marg=pmarg;
        }
        marg[n_marg++]=n;
        marg[n_marg++]=ans>tolerance?1:(ans<-tolerance?-1:0);
        return marg[n_marg-1];
}

/** This initializes the class to be a rectangular box. It calls the base class
 * initialization routine to set up the edge and vertex information, and then
 * sets up the neighbor information, with initial faces being assigned ID
 * numbers from -1 to -6.
 * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
 * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
 * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
        init_base(xmin,xmax,ymin,ymax,zmin,zmax);
        int *q=mne[3];
        *q=-5;q[1]=-3;q[2]=-1;
        q[3]=-5;q[4]=-2;q[5]=-3;
        q[6]=-5;q[7]=-1;q[8]=-4;
        q[9]=-5;q[10]=-4;q[11]=-2;
        q[12]=-6;q[13]=-1;q[14]=-3;
        q[15]=-6;q[16]=-3;q[17]=-2;
        q[18]=-6;q[19]=-4;q[20]=-1;
        q[21]=-6;q[22]=-2;q[23]=-4;
        *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9;
        ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21;
}

/** This routine checks to make sure the neighbor information of each face is
 * consistent. */
void voronoicell_neighbor::check_facets() {
        int i,j,k,l,m,q;
        for (i=1;i<p;i++) for(j=0;j<nu[i];j++) {
                k=ed[i][j];
                if (k>=0) {
                        ed[i][j]=-1-k;
                        q=ne[i][j];
                        l=cycle_up(ed[i][nu[i]+j],k);
                        do {
                                m=ed[k][l];
                                ed[k][l]=-1-m;
                                if (ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q);
                                l=cycle_up(ed[k][nu[k]+l],m);
                                k=m;
                        } while (k!=i);
                }
        }
        reset_edges();
}

/** The class constructor allocates memory for storing neighbor information. */
voronoicell_neighbor::voronoicell_neighbor() {
        int i;
        mne=new int*[current_vertex_order];
        ne=new int*[current_vertices];
        for (i=0;i<3;i++) mne[i]=new int[init_n_vertices*i];
        mne[3]=new int[init_3_vertices*3];
        for (i=4;i<current_vertex_order;i++) mne[i]=new int[init_n_vertices*i];
}

/** The class destructor frees the dynamically allocated memory for storing
 * neighbor information. */
voronoicell_neighbor::~voronoicell_neighbor() {
        for (int i=current_vertex_order-1;i>=0;i--) if (mem[i]>0) delete [] mne[i];
        delete [] mne;
        delete [] ne;
}

/** Computes a vector list of neighbors. */
void voronoicell_neighbor::neighbors(std::vector<int> &v) {
        v.clear();
        int i,j,k,l,m;
        for (i=1;i<p;i++) for(j=0;j<nu[i];j++) {
                k=ed[i][j];
                if (k>=0) {
                        v.push_back(ne[i][j]);
                        ed[i][j]=-1-k;
                        l=cycle_up(ed[i][nu[i]+j],k);
                        do {
                                m=ed[k][l];
                                ed[k][l]=-1-m;
                                l=cycle_up(ed[k][nu[k]+l],m);
                                k=m;
                        } while (k!=i);
                }
        }
        reset_edges();
}

/** Returns the number of faces of a computed Voronoi cell.
 * \return The number of faces. */
int voronoicell_base::number_of_faces() {
        int i,j,k,l,m,s=0;
        for (i=1;i<p;i++) for(j=0;j<nu[i];j++) {
                k=ed[i][j];
                if (k>=0) {
                        s++;
                        ed[i][j]=-1-k;
                        l=cycle_up(ed[i][nu[i]+j],k);
                        do {
                                m=ed[k][l];
                                ed[k][l]=-1-m;
                                l=cycle_up(ed[k][nu[k]+l],m);
                                k=m;
                        } while (k!=i);

                }
        }
        reset_edges();
        return s;
}

/** Returns a vector of the vertex vectors in the global coordinate system.
 * \param[out] v the vector to store the results in.
 * \param[in] (x,y,z) the position vector of the particle in the global
 *                    coordinate system. */
void voronoicell_base::vertices(double x,double y,double z,std::vector<double> &v) {
        v.resize(3*p);
        double *ptsp=pts;
        for (int i=0;i<3*p;i+=3) {
                v[i]=x+*(ptsp++)*0.5;
                v[i+1]=y+*(ptsp++)*0.5;
                v[i+2]=z+*(ptsp++)*0.5;
        }
}

/** For each face, this routine outputs a bracketed sequence of numbers
 * containing a list of all the vertices that make up that face.
 * \param[out] v the vector to store the results in. */
void voronoicell_base::face_vertices(std::vector<int> &v) {
        int i,j,k,l,m,vp(0),vn;
        v.clear();
        for (i=1;i<p;i++) for(j=0;j<nu[i];j++) {
                k=ed[i][j];
                if (k>=0) {
                        v.push_back(0);
                        v.push_back(i);
                        ed[i][j]=-1-k;
                        l=cycle_up(ed[i][nu[i]+j],k);
                        do {
                                v.push_back(k);
                                m=ed[k][l];
                                ed[k][l]=-1-m;
                                l=cycle_up(ed[k][nu[k]+l],m);
                                k=m;
                        } while (k!=i);
                        vn=v.size();
                        v[vp]=vn-vp-1;
                        vp=vn;
                }
        }
        reset_edges();
}

// Explicit instantiation
template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int);
template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*);

}