lammps-sys 0.6.0

/*
Voro++ Copyright (c) 2008, The Regents of the University of California, through
Lawrence Berkeley National Laboratory (subject to receipt of any required
approvals from the U.S. Dept. of Energy). All rights reserved.

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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?true:false;
        }

        // 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*);

}