From c705e8d0e6a3b1a739f2ddf6cd1ee40a3241d40a Mon Sep 17 00:00:00 2001
From: pmla <pete.mahler.larsen@gmail.com>
Date: Wed, 19 Sep 2018 20:46:48 -0400
Subject: [PATCH] renamed files for LAMMPS build system compatibility
---
src/PTM/compute_ptm_atom.cpp | 307 ++++
src/PTM/compute_ptm_atom.h | 48 +
src/PTM/ptm_alloy_types.cpp | 101 ++
src/PTM/ptm_alloy_types.h | 9 +
src/PTM/ptm_canonical_coloured.cpp | 167 ++
src/PTM/ptm_canonical_coloured.h | 9 +
src/PTM/ptm_constants.h | 174 ++
src/PTM/ptm_convex_hull_incremental.cpp | 363 ++++
src/PTM/ptm_convex_hull_incremental.h | 27 +
src/PTM/ptm_deformation_gradient.cpp | 37 +
src/PTM/ptm_deformation_gradient.h | 142 ++
src/PTM/ptm_functions.h | 27 +
src/PTM/ptm_fundamental_mappings.h | 180 ++
src/PTM/ptm_graph_data.cpp | 2059 +++++++++++++++++++++++
src/PTM/ptm_graph_data.h | 37 +
src/PTM/ptm_graph_tools.cpp | 52 +
src/PTM/ptm_graph_tools.h | 11 +
src/PTM/ptm_index.cpp | 218 +++
src/PTM/ptm_initialize_data.cpp | 71 +
src/PTM/ptm_initialize_data.h | 61 +
src/PTM/ptm_neighbour_ordering.cpp | 203 +++
src/PTM/ptm_neighbour_ordering.h | 13 +
src/PTM/ptm_normalize_vertices.cpp | 55 +
src/PTM/ptm_normalize_vertices.h | 8 +
src/PTM/ptm_polar.cpp | 337 ++++
src/PTM/ptm_polar.h | 12 +
src/PTM/ptm_quat.cpp | 396 +++++
src/PTM/ptm_quat.h | 32 +
src/PTM/ptm_structure_matcher.cpp | 294 ++++
src/PTM/ptm_structure_matcher.h | 21 +
src/PTM/ptm_voronoi_cell.cpp | 1368 +++++++++++++++
src/PTM/ptm_voronoi_cell.h | 324 ++++
src/PTM/ptm_voronoi_config.h | 129 ++
33 files changed, 7292 insertions(+)
create mode 100644 src/PTM/compute_ptm_atom.cpp
create mode 100644 src/PTM/compute_ptm_atom.h
create mode 100644 src/PTM/ptm_alloy_types.cpp
create mode 100644 src/PTM/ptm_alloy_types.h
create mode 100644 src/PTM/ptm_canonical_coloured.cpp
create mode 100644 src/PTM/ptm_canonical_coloured.h
create mode 100644 src/PTM/ptm_constants.h
create mode 100644 src/PTM/ptm_convex_hull_incremental.cpp
create mode 100644 src/PTM/ptm_convex_hull_incremental.h
create mode 100644 src/PTM/ptm_deformation_gradient.cpp
create mode 100644 src/PTM/ptm_deformation_gradient.h
create mode 100644 src/PTM/ptm_functions.h
create mode 100644 src/PTM/ptm_fundamental_mappings.h
create mode 100644 src/PTM/ptm_graph_data.cpp
create mode 100644 src/PTM/ptm_graph_data.h
create mode 100644 src/PTM/ptm_graph_tools.cpp
create mode 100644 src/PTM/ptm_graph_tools.h
create mode 100644 src/PTM/ptm_index.cpp
create mode 100644 src/PTM/ptm_initialize_data.cpp
create mode 100644 src/PTM/ptm_initialize_data.h
create mode 100644 src/PTM/ptm_neighbour_ordering.cpp
create mode 100644 src/PTM/ptm_neighbour_ordering.h
create mode 100644 src/PTM/ptm_normalize_vertices.cpp
create mode 100644 src/PTM/ptm_normalize_vertices.h
create mode 100644 src/PTM/ptm_polar.cpp
create mode 100644 src/PTM/ptm_polar.h
create mode 100644 src/PTM/ptm_quat.cpp
create mode 100644 src/PTM/ptm_quat.h
create mode 100644 src/PTM/ptm_structure_matcher.cpp
create mode 100644 src/PTM/ptm_structure_matcher.h
create mode 100644 src/PTM/ptm_voronoi_cell.cpp
create mode 100644 src/PTM/ptm_voronoi_cell.h
create mode 100644 src/PTM/ptm_voronoi_config.h
diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp
new file mode 100644
index 0000000000..b6b4a9786c
--- /dev/null
+++ b/src/PTM/compute_ptm_atom.cpp
@@ -0,0 +1,307 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed
+under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: PM Larsen (MIT)
+------------------------------------------------------------------------- */
+
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+
+#include "atom.h"
+#include "comm.h"
+#include "compute_ptm_atom.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
+
+#include "ptm_functions.h"
+
+#define MAX_NEIGHBORS 30
+#define NUM_COLUMNS 7
+#define UNKNOWN 0
+#define OTHER 8
+
+using namespace LAMMPS_NS;
+
+static const char cite_user_ptm_package[] =
+ "USER-PTM package:\n\n"
+ "@Article{larsen2016ptm,\n"
+ " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, "
+ "Jakob},\n"
+ " title={Robust structural identification via polyhedral template "
+ "matching},\n"
+ " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n"
+ " year={2016},\n"
+ " number={5},\n"
+ " volume={24},\n"
+ " pages={055007},\n"
+ " DOI = {10.1088/0965-0393/24/5/055007}"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
+ : Compute(lmp, narg, arg), list(NULL), output(NULL) {
+ if (narg != 5)
+ error->all(FLERR, "Illegal compute ptm/atom command");
+
+ char *structures = arg[3];
+ char *ptr = structures;
+
+ const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc",
+ "dcub", "dhex", "all", "default"};
+ int32_t flags[] = {
+ PTM_CHECK_FCC,
+ PTM_CHECK_HCP,
+ PTM_CHECK_BCC,
+ PTM_CHECK_ICO,
+ PTM_CHECK_SC,
+ PTM_CHECK_DCUB,
+ PTM_CHECK_DHEX,
+ PTM_CHECK_ALL,
+ PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
+
+ input_flags = 0;
+ while (*ptr != '\0') {
+
+ bool found = false;
+ for (int i = 0; i < 9; i++) {
+ int len = strlen(strings[i]);
+ if (strncmp(ptr, strings[i], len) == 0) {
+ input_flags |= flags[i];
+ ptr += len;
+ found = true;
+ break;
+ }
+ }
+
+ if (!found)
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (invalid structure type)");
+
+ if (*ptr == '\0')
+ break;
+
+ if (*ptr != '-')
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (invalid structure type)");
+
+ ptr++;
+ }
+
+ double threshold = force->numeric(FLERR, arg[4]);
+ if (threshold < 0.0)
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (threshold is negative)");
+ rmsd_threshold = threshold;
+ if (rmsd_threshold == 0)
+ rmsd_threshold = INFINITY;
+
+ peratom_flag = 1;
+ size_peratom_cols = NUM_COLUMNS;
+ create_attribute = 1;
+ nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); }
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePTMAtom::init() {
+ if (force->pair == NULL)
+ error->all(FLERR, "Compute ptm/atom requires a pair style be defined");
+
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "ptm/atom") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute ptm/atom defined");
+
+ // need an occasional full neighbor list
+
+ int irequest = neighbor->request(this, instance_me);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; }
+
+/* ---------------------------------------------------------------------- */
+
+typedef struct {
+ int index;
+ double d;
+} ptmnbr_t;
+
+static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) {
+ return a.d < b.d;
+}
+
+static int get_neighbors(double *pos, int jnum, int *jlist, double **x,
+ double (*nbr)[3]) {
+
+ ptmnbr_t *nbr_order = new ptmnbr_t[jnum];
+
+ for (int jj = 0; jj < jnum; jj++) {
+ int j = jlist[jj];
+ j &= NEIGHMASK;
+
+ double dx = pos[0] - x[j][0];
+ double dy = pos[1] - x[j][1];
+ double dz = pos[2] - x[j][2];
+ double rsq = dx * dx + dy * dy + dz * dz;
+
+ nbr_order[jj].index = j;
+ nbr_order[jj].d = rsq;
+ }
+
+ std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare);
+ int num_nbrs = std::min(MAX_NEIGHBORS, jnum);
+
+ nbr[0][0] = nbr[0][1] = nbr[0][2] = 0;
+ for (int jj = 0; jj < num_nbrs; jj++) {
+
+ int j = nbr_order[jj].index;
+ nbr[jj + 1][0] = x[j][0] - pos[0];
+ nbr[jj + 1][1] = x[j][1] - pos[1];
+ nbr[jj + 1][2] = x[j][2] - pos[2];
+ }
+
+ delete[] nbr_order;
+ return num_nbrs;
+}
+
+void ComputePTMAtom::compute_peratom() {
+ // PTM global initialization. If already initialized this function does
+ // nothing.
+ ptm_initialize_global();
+
+ // initialize PTM local storage
+ ptm_local_handle_t local_handle = ptm_initialize_local();
+
+ invoked_peratom = update->ntimestep;
+
+ // grow arrays if necessary
+ if (atom->nmax > nmax) {
+ memory->destroy(output);
+ nmax = atom->nmax;
+
+ memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output");
+ array_atom = output;
+ }
+
+ // invoke full neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ int inum = list->inum;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int ii = 0; ii < inum; ii++) {
+
+ int i = ilist[ii];
+ output[i][0] = UNKNOWN;
+ if (!(mask[i] & groupbit))
+ continue;
+
+ double *pos = x[i];
+
+ int *jlist = firstneigh[i];
+ int jnum = numneigh[i];
+ if (jnum <= 0)
+ continue;
+
+ // get neighbours ordered by increasing distance
+ double nbr[MAX_NEIGHBORS + 1][3];
+ int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr);
+
+ // check that we have enough neighbours for the desired structure types
+ int32_t flags = 0;
+ if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC))
+ flags |= PTM_CHECK_SC;
+ if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC))
+ flags |= PTM_CHECK_FCC;
+ if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP))
+ flags |= PTM_CHECK_HCP;
+ if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO))
+ flags |= PTM_CHECK_ICO;
+ if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC))
+ flags |= PTM_CHECK_BCC;
+ if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB))
+ flags |= PTM_CHECK_DCUB;
+ if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX))
+ flags |= PTM_CHECK_DHEX;
+
+ // now run PTM
+ int8_t mapping[MAX_NEIGHBORS + 1];
+ int32_t type, alloy_type;
+ double scale, rmsd, interatomic_distance, lattice_constant;
+ double q[4], F[9], F_res[3], U[9], P[9];
+ ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type,
+ &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping,
+ &interatomic_distance, &lattice_constant);
+
+ if (rmsd > rmsd_threshold) {
+ type = PTM_MATCH_NONE;
+ }
+
+ // printf("%d type=%d rmsd=%f\n", i, type, rmsd);
+
+ if (type == PTM_MATCH_NONE)
+ type = OTHER;
+
+ output[i][0] = type;
+ output[i][1] = rmsd;
+ output[i][2] = interatomic_distance;
+ output[i][3] = q[0];
+ output[i][4] = q[1];
+ output[i][5] = q[2];
+ output[i][6] = q[3];
+ }
+
+ // printf("finished ptm analysis\n");
+ ptm_uninitialize_local(local_handle);
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputePTMAtom::memory_usage() {
+ double bytes = nmax * NUM_COLUMNS * sizeof(double);
+ bytes += nmax * sizeof(double);
+ return bytes;
+}
diff --git a/src/PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h
new file mode 100644
index 0000000000..5c10e0c443
--- /dev/null
+++ b/src/PTM/compute_ptm_atom.h
@@ -0,0 +1,48 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(ptm/atom,ComputePTMAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_PTM_ATOM_H
+#define LMP_COMPUTE_PTM_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputePTMAtom : public Compute {
+ public:
+ ComputePTMAtom(class LAMMPS *, int, char **);
+ ~ComputePTMAtom();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_peratom();
+ double memory_usage();
+
+ private:
+ int nmax;
+ int32_t input_flags;
+ double rmsd_threshold;
+ class NeighList *list;
+ double **output;
+};
+
+}
+
+#endif
+#endif
+
diff --git a/src/PTM/ptm_alloy_types.cpp b/src/PTM/ptm_alloy_types.cpp
new file mode 100644
index 0000000000..e14d06db99
--- /dev/null
+++ b/src/PTM/ptm_alloy_types.cpp
@@ -0,0 +1,101 @@
+#include <algorithm>
+#include "ptm_constants.h"
+#include "ptm_initialize_data.h"
+
+
+#define NUM_ALLOY_TYPES 3
+static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
+ {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe},
+ {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e},
+ {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe},
+};
+
+static bool test_pure(int num_nbrs, int32_t* numbers)
+{
+ for (int i=1;i<num_nbrs + 1;i++)
+ if (numbers[i] != numbers[0])
+ return false;
+ return true;
+}
+
+static bool test_binary(int num_nbrs, int32_t* numbers)
+{
+ int a = numbers[0], b = -1;
+ for (int i=1;i<num_nbrs + 1;i++)
+ {
+ if (numbers[i] != a)
+ {
+ if (b == -1)
+ b = numbers[i];
+ else if (numbers[i] != b)
+ return false;
+ }
+ }
+
+ return true;
+}
+
+static bool test_shell_structure(const refdata_t* ref, int8_t* mapping, int32_t* numbers, int num_inner)
+{
+ int8_t binary[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
+
+ for (int i=1;i<num_inner + 1;i++)
+ if (binary[i] == binary[0])
+ return false;
+
+ for (int i=num_inner+1;i<ref->num_nbrs+1;i++)
+ if (binary[i] != binary[0])
+ return false;
+
+ return true;
+}
+
+static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
+{
+ int8_t binary[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
+
+ int8_t temp[PTM_MAX_POINTS];
+ uint32_t best = 0xFFFFFFFF;
+ for (int j=0;j<ref->num_mappings;j++)
+ {
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ temp[ref->mapping[j][i]] = binary[i];
+
+ uint32_t code = 0;
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ code |= (temp[i] << i);
+
+ best = std::min(best, code);
+ }
+
+ return best;
+}
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
+{
+ if (test_pure(ref->num_nbrs, numbers))
+ return PTM_ALLOY_PURE;
+
+ if (!test_binary(ref->num_nbrs, numbers))
+ return PTM_ALLOY_NONE;
+
+ uint32_t code = canonical_alloy_representation(ref, mapping, numbers);
+ for (int i=0;i<NUM_ALLOY_TYPES;i++)
+ if ((uint32_t)ref->type == typedata[i][0] && code == typedata[i][2])
+ return typedata[i][1];
+
+ if (ref->type == PTM_MATCH_BCC)
+ if (test_shell_structure(ref, mapping, numbers, 8))
+ return PTM_ALLOY_B2;
+
+ if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)
+ if (test_shell_structure(ref, mapping, numbers, 4))
+ return PTM_ALLOY_SIC;
+
+ return PTM_ALLOY_NONE;
+}
+
diff --git a/src/PTM/ptm_alloy_types.h b/src/PTM/ptm_alloy_types.h
new file mode 100644
index 0000000000..6ea6ed1b8a
--- /dev/null
+++ b/src/PTM/ptm_alloy_types.h
@@ -0,0 +1,9 @@
+#ifndef PTM_ALLOY_TYPES_H
+#define PTM_ALLOY_TYPES_H
+
+#include "ptm_initialize_data.h"
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
+
+#endif
+
diff --git a/src/PTM/ptm_canonical_coloured.cpp b/src/PTM/ptm_canonical_coloured.cpp
new file mode 100644
index 0000000000..551f52d7e4
--- /dev/null
+++ b/src/PTM/ptm_canonical_coloured.cpp
@@ -0,0 +1,167 @@
+#include <string.h>
+#include <climits>
+#include <algorithm>
+#include "ptm_graph_tools.h"
+#include "ptm_constants.h"
+
+
+static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b)
+{
+ bool m[PTM_MAX_NBRS][PTM_MAX_NBRS];
+ memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS);
+
+ int8_t index[PTM_MAX_NBRS];
+ memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS);
+
+
+ int n = 0;
+ index[a] = colours[a] * num_nodes + n++;
+ if (index[a] > best_code[0])
+ return false;
+
+ bool winning = false;
+ if (index[a] < best_code[0])
+ {
+ best_code[0] = index[a];
+ winning = true;
+ }
+
+ int c = -1;
+ for (int it=1;it<2*num_edges;it++)
+ {
+ bool newvertex = index[b] == -1;
+
+ if (newvertex)
+ index[b] = colours[b] * num_nodes + n++;
+
+ if (!winning && index[b] > best_code[it])
+ return false;
+
+ if (winning || index[b] < best_code[it])
+ {
+ winning = true;
+ best_code[it] = index[b];
+ }
+
+ if (newvertex)
+ {
+ //When a new vertex is reached, take the right-most edge
+ //relative to the edge on which the vertex is reached.
+
+ c = common[a][b];
+ }
+ else if (m[b][a] == false)
+ {
+ //When an old vertex is reached on a new path, go back
+ //in the opposite direction.
+
+ c = a;
+ }
+ else
+ {
+ //When an old vertex is reached on an old path, leave the
+ //vertex on the right-most edge that has not previously
+ //been traversed in that direction.
+
+ c = common[a][b];
+ while (m[b][c] == true)
+ c = common[c][b];
+ }
+
+ m[a][b] = true;
+ a = b;
+ b = c;
+ }
+
+ if (winning)
+ {
+ memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes);
+ return true;
+ }
+
+ return false;
+}
+
+int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash)
+{
+ int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}};
+ int num_edges = 3 * num_facets / 2;
+ if (!build_facet_map(num_facets, facets, common))
+ return -1;
+
+ memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES);
+
+ bool equal = true;
+ for (int i = 1;i<num_nodes;i++)
+ if (degree[i] != degree[0] || colours[i] != colours[0])
+ equal = false;
+
+ if (equal)
+ {
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, facets[0][0], facets[0][1]);
+ }
+ else
+ {
+ uint32_t best_degree = 0;
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //int da = colours[a] * num_nodes + degree[a];
+ //int db = colours[b] * num_nodes + degree[b];
+ //int dc = colours[c] * num_nodes + degree[c];
+
+ int da = degree[a];
+ int db = degree[b];
+ int dc = degree[c];
+
+ best_degree = std::max(best_degree, ((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0));
+ best_degree = std::max(best_degree, ((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8));
+ best_degree = std::max(best_degree, ((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16));
+ }
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //int da = colours[a] * num_nodes + degree[a];
+ //int db = colours[b] * num_nodes + degree[b];
+ //int dc = colours[c] * num_nodes + degree[c];
+
+ int da = degree[a];
+ int db = degree[b];
+ int dc = degree[c];
+
+ if (best_degree == (((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, a, b);
+
+ if (best_degree == (((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, b, c);
+
+ if (best_degree == (((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, c, a);
+ }
+ }
+
+ for (int i = num_nodes-1;i>=0;i--)
+ canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1;
+ canonical_labelling[0] = 0;
+
+ uint64_t hash = 0;
+ for (int i = 0;i<2 * num_edges;i++)
+ {
+ uint64_t e = best_code[i];
+ e += i % 8;
+ e &= 0xF;
+ e <<= (4 * i) % 64;
+ hash ^= e;
+ }
+
+ *p_hash = hash;
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/PTM/ptm_canonical_coloured.h b/src/PTM/ptm_canonical_coloured.h
new file mode 100644
index 0000000000..e71bb08bfc
--- /dev/null
+++ b/src/PTM/ptm_canonical_coloured.h
@@ -0,0 +1,9 @@
+#ifndef PTM_CANONICAL_COLOURED_H
+#define PTM_CANONICAL_COLOURED_H
+
+#include <stdint.h>
+
+int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash);
+
+#endif
+
diff --git a/src/PTM/ptm_constants.h b/src/PTM/ptm_constants.h
new file mode 100644
index 0000000000..f868f51e84
--- /dev/null
+++ b/src/PTM/ptm_constants.h
@@ -0,0 +1,174 @@
+#ifndef PTM_CONSTANTS_H
+#define PTM_CONSTANTS_H
+
+//------------------------------------
+// definitions
+//------------------------------------
+#define PTM_NO_ERROR 0
+
+
+#define PTM_CHECK_FCC (1 << 0)
+#define PTM_CHECK_HCP (1 << 1)
+#define PTM_CHECK_BCC (1 << 2)
+#define PTM_CHECK_ICO (1 << 3)
+#define PTM_CHECK_SC (1 << 4)
+#define PTM_CHECK_DCUB (1 << 5)
+#define PTM_CHECK_DHEX (1 << 6)
+#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)
+#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX)
+
+#define PTM_MATCH_NONE 0
+#define PTM_MATCH_FCC 1
+#define PTM_MATCH_HCP 2
+#define PTM_MATCH_BCC 3
+#define PTM_MATCH_ICO 4
+#define PTM_MATCH_SC 5
+#define PTM_MATCH_DCUB 6
+#define PTM_MATCH_DHEX 7
+
+#define PTM_ALLOY_NONE 0
+#define PTM_ALLOY_PURE 1
+#define PTM_ALLOY_L10 2
+#define PTM_ALLOY_L12_CU 3
+#define PTM_ALLOY_L12_AU 4
+#define PTM_ALLOY_B2 5
+#define PTM_ALLOY_SIC 6
+
+
+#define PTM_MAX_INPUT_POINTS 35
+#define PTM_MAX_NBRS 16
+#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1)
+#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4
+#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6
+
+
+//------------------------------------
+// number of neighbours
+//------------------------------------
+#define PTM_NUM_NBRS_FCC 12
+#define PTM_NUM_NBRS_HCP 12
+#define PTM_NUM_NBRS_BCC 14
+#define PTM_NUM_NBRS_ICO 12
+#define PTM_NUM_NBRS_SC 6
+#define PTM_NUM_NBRS_DCUB 16
+#define PTM_NUM_NBRS_DHEX 16
+
+#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1)
+#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1)
+#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1)
+#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1)
+#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1)
+#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1)
+#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1)
+
+const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX};
+
+//------------------------------------
+// template structures
+//------------------------------------
+
+//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1
+
+const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. },
+ { 0. , 0.707106781187, 0.707106781187 },
+ { 0. , -0.707106781187, -0.707106781187 },
+ { 0. , 0.707106781187, -0.707106781187 },
+ { 0. , -0.707106781187, 0.707106781187 },
+ { 0.707106781187, 0. , 0.707106781187 },
+ { -0.707106781187, 0. , -0.707106781187 },
+ { 0.707106781187, 0. , -0.707106781187 },
+ { -0.707106781187, 0. , 0.707106781187 },
+ { 0.707106781187, 0.707106781187, 0. },
+ { -0.707106781187, -0.707106781187, 0. },
+ { 0.707106781187, -0.707106781187, 0. },
+ { -0.707106781187, 0.707106781187, 0. } };
+
+const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. },
+ { 0.707106781186, 0. , 0.707106781186 },
+ { -0.235702260395, -0.942809041583, -0.235702260395 },
+ { 0.707106781186, 0.707106781186, 0. },
+ { -0.235702260395, -0.235702260395, -0.942809041583 },
+ { 0. , 0.707106781186, 0.707106781186 },
+ { -0.942809041583, -0.235702260395, -0.235702260395 },
+ { -0.707106781186, 0.707106781186, 0. },
+ { 0. , 0.707106781186, -0.707106781186 },
+ { 0.707106781186, 0. , -0.707106781186 },
+ { 0.707106781186, -0.707106781186, 0. },
+ { -0.707106781186, 0. , 0.707106781186 },
+ { 0. , -0.707106781186, 0.707106781186 } };
+
+const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. },
+ { -0.541451884327, -0.541451884327, -0.541451884327 },
+ { 0.541451884327, 0.541451884327, 0.541451884327 },
+ { 0.541451884327, -0.541451884327, -0.541451884327 },
+ { -0.541451884327, 0.541451884327, 0.541451884327 },
+ { -0.541451884327, 0.541451884327, -0.541451884327 },
+ { 0.541451884327, -0.541451884327, 0.541451884327 },
+ { -0.541451884327, -0.541451884327, 0.541451884327 },
+ { 0.541451884327, 0.541451884327, -0.541451884327 },
+ { 0. , 0. , -1.082903768655 },
+ { 0. , 0. , 1.082903768655 },
+ { 0. , -1.082903768655, 0. },
+ { 0. , 1.082903768655, 0. },
+ { -1.082903768655, 0. , 0. },
+ { 1.082903768655, 0. , 0. } };
+
+const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. },
+ { 0. , 0.525731112119, 0.850650808352 },
+ { 0. , -0.525731112119, -0.850650808352 },
+ { 0. , 0.525731112119, -0.850650808352 },
+ { 0. , -0.525731112119, 0.850650808352 },
+ { -0.525731112119, -0.850650808352, 0. },
+ { 0.525731112119, 0.850650808352, 0. },
+ { 0.525731112119, -0.850650808352, 0. },
+ { -0.525731112119, 0.850650808352, 0. },
+ { -0.850650808352, 0. , -0.525731112119 },
+ { 0.850650808352, 0. , 0.525731112119 },
+ { 0.850650808352, 0. , -0.525731112119 },
+ { -0.850650808352, 0. , 0.525731112119 } };
+
+const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. },
+ { 0. , 0. , -1. },
+ { 0. , 0. , 1. },
+ { 0. , -1. , 0. },
+ { 0. , 1. , 0. },
+ { -1. , 0. , 0. },
+ { 1. , 0. , 0. } };
+
+const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. },
+ { -0.391491627053, 0.391491627053, 0.391491627053 },
+ { -0.391491627053, -0.391491627053, -0.391491627053 },
+ { 0.391491627053, -0.391491627053, 0.391491627053 },
+ { 0.391491627053, 0.391491627053, -0.391491627053 },
+ { -0.782983254107, 0. , 0.782983254107 },
+ { -0.782983254107, 0.782983254107, 0. },
+ { 0. , 0.782983254107, 0.782983254107 },
+ { -0.782983254107, -0.782983254107, 0. },
+ { -0.782983254107, 0. , -0.782983254107 },
+ { 0. , -0.782983254107, -0.782983254107 },
+ { 0. , -0.782983254107, 0.782983254107 },
+ { 0.782983254107, -0.782983254107, 0. },
+ { 0.782983254107, 0. , 0.782983254107 },
+ { 0. , 0.782983254107, -0.782983254107 },
+ { 0.782983254107, 0. , -0.782983254107 },
+ { 0.782983254107, 0.782983254107, 0. } };
+
+const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. },
+ { -0.391491627053, -0.391491627053, -0.391491627053 },
+ { 0.391491627053, -0.391491627053, 0.391491627053 },
+ { -0.391491627053, 0.391491627053, 0.391491627053 },
+ { 0.391491627053, 0.391491627053, -0.391491627053 },
+ { -0.260994418036, -1.043977672142, -0.260994418036 },
+ { -1.043977672142, -0.260994418036, -0.260994418036 },
+ { -0.260994418036, -0.260994418036, -1.043977672142 },
+ { 0.782983254107, 0. , 0.782983254107 },
+ { 0.782983254107, -0.782983254107, 0. },
+ { 0. , -0.782983254107, 0.782983254107 },
+ { 0. , 0.782983254107, 0.782983254107 },
+ { -0.782983254107, 0.782983254107, 0. },
+ { -0.782983254107, 0. , 0.782983254107 },
+ { 0.782983254107, 0.782983254107, 0. },
+ { 0. , 0.782983254107, -0.782983254107 },
+ { 0.782983254107, 0. , -0.782983254107 } };
+#endif
+
diff --git a/src/PTM/ptm_convex_hull_incremental.cpp b/src/PTM/ptm_convex_hull_incremental.cpp
new file mode 100644
index 0000000000..c996b17b58
--- /dev/null
+++ b/src/PTM/ptm_convex_hull_incremental.cpp
@@ -0,0 +1,363 @@
+#include <cmath>
+#include <cfloat>
+#include <string.h>
+#include <cassert>
+#include <algorithm>
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_constants.h"
+
+
+#define VISIBLE 1
+#define INVISIBLE 2
+#define BOTH 3
+#define TOLERANCE 1E-8
+
+static double norm_squared(double* p)
+{
+ double x = p[0];
+ double y = p[1];
+ double z = p[2];
+
+ return x*x + y*y + z*z;
+}
+
+static double dot_product(const double* a, const double* b)
+{
+ return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
+}
+
+static void cross_product(double* a, double* b, double* c)
+{
+ c[0] = a[1] * b[2] - a[2] * b[1];
+ c[1] = a[2] * b[0] - a[0] * b[2];
+ c[2] = a[0] * b[1] - a[1] * b[0];
+}
+
+static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal)
+{
+ double u[3] = { points[b][0] - points[a][0],
+ points[b][1] - points[a][1],
+ points[b][2] - points[a][2] };
+
+ double v[3] = { points[c][0] - points[a][0],
+ points[c][1] - points[a][1],
+ points[c][2] - points[a][2] };
+
+ cross_product(u, v, plane_normal);
+ double norm = sqrt(norm_squared(plane_normal));
+ plane_normal[0] /= norm;
+ plane_normal[1] /= norm;
+ plane_normal[2] /= norm;
+}
+
+static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross)
+{
+ return plane_cross[0] * (plane_point[0] - w[0])
+ + plane_cross[1] * (plane_point[1] - w[1])
+ + plane_cross[2] * (plane_point[2] - w[2]);
+}
+
+static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index)
+{
+ for (int j=0;j<3;j++)
+ {
+ double dmin = DBL_MAX, dmax = -DBL_MAX;
+ int imin = 0, imax = 0;
+
+ for (int i = 0;i<num_points;i++)
+ {
+ double d = points[i][j];
+ if (d < dmin)
+ {
+ dmin = d;
+ imin = i;
+ }
+ if (d > dmax)
+ {
+ dmax = d;
+ imax = i;
+ }
+ }
+
+ if (imin == imax)
+ return false; //degenerate point set
+
+ min_index[j] = imin;
+ max_index[j] = imax;
+ }
+
+ return true;
+}
+
+static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c)
+{
+ const double* x1 = points[a];
+ const double* x2 = points[b];
+
+ double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]};
+ double ns_x2x1 = norm_squared(x2x1);
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<num_points;i++)
+ {
+ if (i == a || i == b)
+ continue;
+
+ const double* x0 = points[i];
+
+ double x1x0[3] = {x1[0] - x0[0], x1[1] - x0[1], x1[2] - x0[2]};
+ double dot = dot_product(x1x0, x2x1);
+ double dist = (norm_squared(x1x0) * ns_x2x1 - dot*dot) / ns_x2x1;
+
+ if (dist > max_dist)
+ {
+ max_dist = dist;
+ bi = i;
+ }
+ }
+
+ *p_c = bi;
+ return max_dist > TOLERANCE;
+}
+
+static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d)
+{
+ double plane_normal[3];
+ calculate_plane_normal(points, a, b, c, plane_normal);
+
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<num_points;i++)
+ {
+ if (i == a || i == b || i == c)
+ continue;
+
+ const double* x0 = points[i];
+ double dist = fabs(point_plane_distance(x0, points[a], plane_normal));
+ if (dist > max_dist)
+ {
+ max_dist = dist;
+ bi = i;
+ }
+ }
+
+ *p_d = bi;
+ return max_dist > TOLERANCE;
+}
+
+static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices)
+{
+ int min_index[3] = {0};
+ int max_index[3] = {0};
+ if (!calc_max_extent(num_points, points, min_index, max_index))
+ return -1;
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<3;i++)
+ {
+ int a = min_index[i], b = max_index[i];
+ double delta[3] = { points[a][0] - points[b][0],
+ points[a][1] - points[b][1],
+ points[a][2] - points[b][2] };
+ double dist = norm_squared(delta);
+ if (dist > max_dist)
+ {
+ bi = i;
+ max_dist = dist;
+ }
+ }
+
+ //first two points are (a, b)
+ int a = min_index[bi], b = max_index[bi], c = -1, d = -1;
+
+ if (!find_third_point(num_points, points, a, b, &c))
+ return -2;
+
+ if (!find_fourth_point(num_points, points, a, b, c, &d))
+ return -3;
+
+ initial_vertices[0] = a;
+ initial_vertices[1] = b;
+ initial_vertices[2] = c;
+ initial_vertices[3] = d;
+ return 0;
+}
+
+static bool visible(const double* w, const double* plane_point, const double* plane_normal)
+{
+ return point_plane_distance(w, plane_point, plane_normal) > 0;
+}
+
+void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre)
+{
+ calculate_plane_normal(points, a, b, c, plane_normal);
+ if (visible(barycentre, points[a], plane_normal))
+ {
+ plane_normal[0] = -plane_normal[0];
+ plane_normal[1] = -plane_normal[1];
+ plane_normal[2] = -plane_normal[2];
+
+ facet[0] = b;
+ facet[1] = a;
+ facet[2] = c;
+ }
+ else
+ {
+ facet[0] = a;
+ facet[1] = b;
+ facet[2] = c;
+ }
+}
+
+static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre)
+{
+ memset(processed, 0, PTM_MAX_POINTS * sizeof(bool));
+ memset(barycentre, 0, 3 * sizeof(double));
+ int ret = initial_simplex(num_points, points, initial_vertices);
+ if (ret != 0)
+ return ret;
+
+ for (int i = 0;i<4;i++)
+ {
+ int a = initial_vertices[i];
+ processed[a] = true;
+
+ barycentre[0] += points[a][0];
+ barycentre[1] += points[a][1];
+ barycentre[2] += points[a][2];
+ }
+ barycentre[0] /= 4;
+ barycentre[1] /= 4;
+ barycentre[2] /= 4;
+
+ add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre);
+ add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre);
+ add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre);
+ add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre);
+ return 0;
+}
+
+int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3])
+{
+ assert( num_points == PTM_NUM_POINTS_FCC
+ || num_points == PTM_NUM_POINTS_HCP
+ || num_points == PTM_NUM_POINTS_BCC
+ || num_points == PTM_NUM_POINTS_ICO
+ || num_points == PTM_NUM_POINTS_SC
+ || num_points == PTM_NUM_POINTS_DCUB
+ || num_points == PTM_NUM_POINTS_DHEX);
+
+ int ret = 0;
+ int num_prev = ch->num_prev;
+ ch->num_prev = num_points;
+ if (!ch->ok || 0)
+ {
+ ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre);
+ if (ret != 0)
+ return ret;
+
+ ch->num_facets = 4;
+ num_prev = 0;
+ }
+
+ for (int i = num_prev;i<num_points;i++)
+ {
+ if (ch->processed[i])
+ continue;
+ ch->processed[i] = true;
+
+ int num_to_add = 0;
+ int8_t to_add[PTM_MAX_FACETS][3];
+ int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS];
+ memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS);
+ for (int j = 0;j<ch->num_facets;j++)
+ {
+ int a = ch->facets[j][0];
+ int b = ch->facets[j][1];
+ int c = ch->facets[j][2];
+
+ int u = 0, v = 0, w = 0;
+
+ double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]);
+ bool vis = distance > TOLERANCE;
+ if (vis)
+ {
+ u = edge_visible[a][b] |= VISIBLE;
+ edge_visible[b][a] |= VISIBLE;
+
+ v = edge_visible[b][c] |= VISIBLE;
+ edge_visible[c][b] |= VISIBLE;
+
+ w = edge_visible[c][a] |= VISIBLE;
+ edge_visible[a][c] |= VISIBLE;
+
+ memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t));
+ memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double));
+ ch->num_facets--;
+ j--;
+ }
+ else
+ {
+ u = edge_visible[a][b] |= INVISIBLE;
+ edge_visible[b][a] |= INVISIBLE;
+
+ v = edge_visible[b][c] |= INVISIBLE;
+ edge_visible[c][b] |= INVISIBLE;
+
+ w = edge_visible[c][a] |= INVISIBLE;
+ edge_visible[a][c] |= INVISIBLE;
+ }
+
+ if (u == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = a;
+ to_add[num_to_add][2] = b;
+ num_to_add++;
+ }
+
+ if (v == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = b;
+ to_add[num_to_add][2] = c;
+ num_to_add++;
+ }
+
+ if (w == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = c;
+ to_add[num_to_add][2] = a;
+ num_to_add++;
+ }
+ }
+
+ for (int j = 0;j<num_to_add;j++)
+ {
+ if (ch->num_facets >= PTM_MAX_FACETS)
+ return -4;
+
+ add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++;
+ }
+ }
+
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int a = ch->facets[i][0];
+ int b = ch->facets[i][1];
+ int c = ch->facets[i][2];
+ if (a == 0 || b == 0 || c == 0)
+ return 1; //central atom contained in convex hull
+
+ simplex[i][0] = a - 1;
+ simplex[i][1] = b - 1;
+ simplex[i][2] = c - 1;
+ }
+
+ return ret;
+}
+
diff --git a/src/PTM/ptm_convex_hull_incremental.h b/src/PTM/ptm_convex_hull_incremental.h
new file mode 100644
index 0000000000..563a0c436a
--- /dev/null
+++ b/src/PTM/ptm_convex_hull_incremental.h
@@ -0,0 +1,27 @@
+#ifndef PTM_CONVEX_HULL_INCREMENTAL_H
+#define PTM_CONVEX_HULL_INCREMENTAL_H
+
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "ptm_constants.h"
+
+
+typedef struct
+{
+ int8_t facets[PTM_MAX_FACETS][3];
+ double plane_normal[PTM_MAX_FACETS][3];
+ bool processed[PTM_MAX_POINTS];
+ int initial_vertices[4];
+ double barycentre[3];
+ int num_facets;
+ int num_prev;
+ bool ok;
+
+} convexhull_t;
+
+void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre);
+int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]);
+
+#endif
+
diff --git a/src/PTM/ptm_deformation_gradient.cpp b/src/PTM/ptm_deformation_gradient.cpp
new file mode 100644
index 0000000000..d566d5ca11
--- /dev/null
+++ b/src/PTM/ptm_deformation_gradient.cpp
@@ -0,0 +1,37 @@
+#include "ptm_deformation_gradient.h"
+
+
+void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res)
+{
+ for (int i = 0;i<3;i++)
+ {
+ for (int j = 0;j<3;j++)
+ {
+ double acc = 0.0;
+ for (int k = 0;k<num_points;k++)
+ acc += penrose[k][j] * normalized[mapping[k]][i];
+
+ F[i*3 + j] = acc;
+ }
+ }
+
+ res[0] = 0;
+ res[1] = 0;
+ res[2] = 0;
+
+ for (int k = 0;k<num_points;k++)
+ {
+ for (int i = 0;i<3;i++)
+ {
+ double acc = 0.0;
+ for (int j = 0;j<3;j++)
+ {
+ acc += F[i*3 + j] * ideal_points[k][j];
+ }
+
+ double delta = acc - normalized[mapping[k]][i];
+ res[i] += delta * delta;
+ }
+ }
+}
+
diff --git a/src/PTM/ptm_deformation_gradient.h b/src/PTM/ptm_deformation_gradient.h
new file mode 100644
index 0000000000..7decab4b76
--- /dev/null
+++ b/src/PTM/ptm_deformation_gradient.h
@@ -0,0 +1,142 @@
+#ifndef PTM_DEFORMATION_GRADIENT_H
+#define PTM_DEFORMATION_GRADIENT_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res);
+
+//sc
+#define k_sc 0.5
+const double penrose_sc[PTM_NUM_POINTS_SC][3] = {
+ {0, 0, 0},
+ {0, 0, -k_sc},
+ {0, 0, k_sc},
+ {0, -k_sc, 0},
+ {0, k_sc, 0},
+ {-k_sc, 0, 0},
+ {k_sc, 0, 0},
+ };
+
+//fcc
+#define k_fcc 0.17677669529663678216
+const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = {
+ {0, 0, 0},
+ {0, k_fcc, k_fcc},
+ {0, -k_fcc, -k_fcc},
+ {0, k_fcc, -k_fcc},
+ {0, -k_fcc, k_fcc},
+ {k_fcc, 0, k_fcc},
+ {-k_fcc, 0, -k_fcc},
+ {k_fcc, 0, -k_fcc},
+ {-k_fcc, 0, k_fcc},
+ {k_fcc, k_fcc, -0},
+ {-k_fcc, -k_fcc, 0},
+ {k_fcc, -k_fcc, 0},
+ {-k_fcc, k_fcc, -0},
+ };
+
+//hcp
+#define k_hcp 0.17677669529663678216
+const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = {
+ {0, 0, 0},
+ {k_hcp, 0, k_hcp},
+ {-k_hcp/3, -4*k_hcp/3, -k_hcp/3},
+ {k_hcp, k_hcp, 0},
+ {-k_hcp/3, -k_hcp/3, -4*k_hcp/3},
+ {0, k_hcp, k_hcp},
+ {-4*k_hcp/3, -k_hcp/3, -k_hcp/3},
+ {-k_hcp, k_hcp, -0},
+ {0, k_hcp, -k_hcp},
+ {k_hcp, 0, -k_hcp},
+ {k_hcp, -k_hcp, 0},
+ {-k_hcp, 0, k_hcp},
+ {0, -k_hcp, k_hcp},
+ };
+
+//ico
+#define k_ico 0.13143277802974323576
+#define phi 1.61803398874989490253
+//((1.0 + sqrt(5)) / 2)
+const double penrose_ico[PTM_NUM_POINTS_ICO][3] = {
+ {0, 0, 0},
+ {0, k_ico, phi*k_ico},
+ {0, -k_ico, -phi*k_ico},
+ {0, k_ico, -phi*k_ico},
+ {0, -k_ico, phi*k_ico},
+ {-k_ico, -phi*k_ico, -0},
+ {k_ico, phi*k_ico, 0},
+ {k_ico, -phi*k_ico, 0},
+ {-k_ico, phi*k_ico, -0},
+ {-phi*k_ico, 0, -k_ico},
+ {phi*k_ico, 0, k_ico},
+ {phi*k_ico, 0, -k_ico},
+ {-phi*k_ico, 0, k_ico},
+ };
+
+//bcc
+#define k_bcc 0.11543038598460284017
+const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = {
+ {0, 0, 0},
+ {-k_bcc, -k_bcc, -k_bcc},
+ {k_bcc, k_bcc, k_bcc},
+ {k_bcc, -k_bcc, -k_bcc},
+ {-k_bcc, k_bcc, k_bcc},
+ {-k_bcc, k_bcc, -k_bcc},
+ {k_bcc, -k_bcc, k_bcc},
+ {-k_bcc, -k_bcc, k_bcc},
+ {k_bcc, k_bcc, -k_bcc},
+ {0, 0, -2*k_bcc},
+ {0, 0, 2*k_bcc},
+ {0, -2*k_bcc, 0},
+ {0, 2*k_bcc, 0},
+ {-2*k_bcc, 0, 0},
+ {2*k_bcc, 0, -0},
+ };
+
+//dcub
+#define kdcub 0.07095369570691034689
+const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = {
+ { 0, 0, 0 },
+ { -kdcub, kdcub, kdcub },
+ { -kdcub, -kdcub, -kdcub },
+ { kdcub, -kdcub, kdcub },
+ { kdcub, kdcub, -kdcub },
+ { -2 * kdcub, 0, 2 * kdcub },
+ { -2 * kdcub, 2 * kdcub, 0 },
+ { 0, 2 * kdcub, 2 * kdcub },
+ { -2 * kdcub, -2 * kdcub, 0 },
+ { -2 * kdcub, 0, -2 * kdcub },
+ { 0, -2 * kdcub, -2 * kdcub },
+ { 0, -2 * kdcub, 2 * kdcub },
+ { 2 * kdcub, -2 * kdcub, 0 },
+ { 2 * kdcub, 0, 2 * kdcub },
+ { 0, 2 * kdcub, -2 * kdcub },
+ { 2 * kdcub, 0, -2 * kdcub },
+ { 2 * kdcub, 2 * kdcub, 0 },
+ };
+
+
+#define kdhex 0.04730246380471011397
+const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
+ { 0, 0, 0 },
+ { -kdcub, -kdcub, -kdcub },
+ { kdcub, -kdcub, kdcub },
+ { -kdcub, kdcub, kdcub },
+ { kdcub, kdcub, -kdcub },
+ { -kdhex, -4 * kdhex, -kdhex },
+ { -4 * kdhex, -kdhex, -kdhex },
+ { -kdhex, -kdhex, -4 * kdhex },
+ { 2 * kdcub, 0, 2 * kdcub },
+ { 2 * kdcub, -2 * kdcub, 0 },
+ { 0, -2 * kdcub, 2 * kdcub },
+ { 0, 2 * kdcub, 2 * kdcub },
+ { -2 * kdcub, 2 * kdcub, 0 },
+ { -2 * kdcub, 0, 2 * kdcub },
+ { 2 * kdcub, 2 * kdcub, 0 },
+ { 0, 2 * kdcub, -2 * kdcub },
+ { 2 * kdcub, 0, -2 * kdcub },
+ };
+#endif
+
+
diff --git a/src/PTM/ptm_functions.h b/src/PTM/ptm_functions.h
new file mode 100644
index 0000000000..cd67d4940d
--- /dev/null
+++ b/src/PTM/ptm_functions.h
@@ -0,0 +1,27 @@
+#ifndef PTM_FUNCTIONS_H
+#define PTM_FUNCTIONS_H
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "ptm_initialize_data.h"
+#include "ptm_constants.h"
+
+
+//------------------------------------
+// function declarations
+//------------------------------------
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
diff --git a/src/PTM/ptm_fundamental_mappings.h b/src/PTM/ptm_fundamental_mappings.h
new file mode 100644
index 0000000000..3dd7c39cbb
--- /dev/null
+++ b/src/PTM/ptm_fundamental_mappings.h
@@ -0,0 +1,180 @@
+#ifndef PTM_FUNDAMENTAL_MAPPINGS_H
+#define PTM_FUNDAMENTAL_MAPPINGS_H
+
+#include <stdint.h>
+
+#define NUM_CUBIC_MAPPINGS 24
+#define NUM_ICO_MAPPINGS 60
+#define NUM_HEX_MAPPINGS 6
+#define NUM_DCUB_MAPPINGS 12
+#define NUM_DHEX_MAPPINGS 3
+
+const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6},
+ {0, 2, 1, 4, 3, 5, 6},
+ {0, 2, 1, 3, 4, 6, 5},
+ {0, 1, 2, 4, 3, 6, 5},
+ {0, 3, 4, 5, 6, 1, 2},
+ {0, 5, 6, 2, 1, 4, 3},
+ {0, 6, 5, 1, 2, 4, 3},
+ {0, 4, 3, 5, 6, 2, 1},
+ {0, 5, 6, 1, 2, 3, 4},
+ {0, 4, 3, 6, 5, 1, 2},
+ {0, 3, 4, 6, 5, 2, 1},
+ {0, 6, 5, 2, 1, 3, 4},
+ {0, 3, 4, 2, 1, 5, 6},
+ {0, 6, 5, 3, 4, 1, 2},
+ {0, 1, 2, 5, 6, 4, 3},
+ {0, 4, 3, 1, 2, 5, 6},
+ {0, 5, 6, 3, 4, 2, 1},
+ {0, 1, 2, 6, 5, 3, 4},
+ {0, 2, 1, 5, 6, 3, 4},
+ {0, 5, 6, 4, 3, 1, 2},
+ {0, 3, 4, 1, 2, 6, 5},
+ {0, 2, 1, 6, 5, 4, 3},
+ {0, 6, 5, 4, 3, 2, 1},
+ {0, 4, 3, 2, 1, 6, 5} };
+
+const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10},
+ {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9},
+ {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11},
+ {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7},
+ {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3},
+ {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
+ {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5},
+ {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4},
+ {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6},
+ {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
+ {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2},
+ {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6},
+ {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3},
+ {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9},
+ {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8},
+ {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1},
+ {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10},
+ {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11},
+ {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2},
+ {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5},
+ {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12},
+ {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4},
+ {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} };
+
+const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14},
+ {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14},
+ {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13},
+ {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13},
+ {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10},
+ {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11},
+ {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11},
+ {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9},
+ {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12},
+ {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10},
+ {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9},
+ {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12},
+ {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14},
+ {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10},
+ {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11},
+ {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14},
+ {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9},
+ {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12},
+ {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12},
+ {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10},
+ {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13},
+ {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11},
+ {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9},
+ {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} };
+
+const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4},
+ {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4},
+ {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5},
+ {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1},
+ {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5},
+ {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12},
+ {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12},
+ {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1},
+ {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9},
+ {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8},
+ {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9},
+ {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8},
+ {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8},
+ {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9},
+ {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3},
+ {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5},
+ {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6},
+ {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
+ {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6},
+ {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4},
+ {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2},
+ {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3},
+ {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10},
+ {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10},
+ {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1},
+ {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7},
+ {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
+ {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2},
+ {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4},
+ {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7},
+ {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5},
+ {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9},
+ {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2},
+ {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10},
+ {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7},
+ {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7},
+ {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12},
+ {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6},
+ {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12},
+ {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3},
+ {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10},
+ {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3},
+ {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6},
+ {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2},
+ {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9},
+ {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3},
+ {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8},
+ {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2},
+ {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5},
+ {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4},
+ {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11},
+ {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1},
+ {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11},
+ {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11},
+ {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6},
+ {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11},
+ {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7},
+ {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11},
+ {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} };
+
+const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7},
+ {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9},
+ {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8},
+ {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10},
+ {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} };
+
+const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12},
+ {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6},
+ {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8},
+ {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13},
+ {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10},
+ {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11},
+ {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15},
+ {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7},
+ {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5},
+ {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9},
+ {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} };
+
+const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10},
+ {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} };
+
+#endif
+
diff --git a/src/PTM/ptm_graph_data.cpp b/src/PTM/ptm_graph_data.cpp
new file mode 100644
index 0000000000..a591dbf993
--- /dev/null
+++ b/src/PTM/ptm_graph_data.cpp
@@ -0,0 +1,2059 @@
+#include "ptm_graph_data.h"
+
+
+int8_t automorphisms[65][17] = {
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1},
+ { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1},
+ { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1},
+ { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1},
+ { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1},
+ { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1},
+ { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1},
+ { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1},
+ { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1},
+ { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1},
+ { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1},
+ { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1},
+ { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1},
+ { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1},
+ { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1},
+ { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1},
+ { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1},
+ { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1},
+ { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1},
+ { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1},
+ { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1},
+ { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1},
+ { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9},
+ { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11},
+ { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9},
+ { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11},
+ { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
+};
+
+graph_t graphs_sc[NUM_SC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}},
+
+};
+
+graph_t graphs_ico[NUM_ICO_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}},
+
+};
+
+graph_t graphs_fcc[NUM_FCC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
+
+{6,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
+
+{7,
+0,
+1,
+5,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+};
+
+graph_t graphs_hcp[NUM_HCP_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{6,
+0,
+6,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{7,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{8,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{9,
+0,
+8,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}},
+
+{8,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}},
+
+{9,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
+
+{10,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{4,10,12},{4,6,12},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
+
+{11,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{4,7,8},{4,5,8},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}},
+
+};
+
+graph_t graphs_dhex[NUM_DHEX_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{7,13,15},{7,8,15}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{6,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{7,
+0,
+53,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{8,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{9,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{10,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{11,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{12,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{13,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{14,
+0,
+55,
+4,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{15,
+0,
+59,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{16,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{17,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{18,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{19,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{20,
+0,
+61,
+4,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{21,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{22,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{23,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+};
+
diff --git a/src/PTM/ptm_graph_data.h b/src/PTM/ptm_graph_data.h
new file mode 100644
index 0000000000..11f46a471f
--- /dev/null
+++ b/src/PTM/ptm_graph_data.h
@@ -0,0 +1,37 @@
+#ifndef PTM_GRAPH_DATA_H
+#define PTM_GRAPH_DATA_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+
+typedef struct
+{
+ int id;
+ uint64_t hash;
+ int automorphism_index;
+ int num_automorphisms;
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ int8_t facets[PTM_MAX_FACETS][3];
+} graph_t;
+
+#define NUM_SC_GRAPHS 1
+#define NUM_ICO_GRAPHS 1
+#define NUM_FCC_GRAPHS 8
+#define NUM_HCP_GRAPHS 16
+#define NUM_BCC_GRAPHS 218
+#define NUM_DCUB_GRAPHS 12
+#define NUM_DHEX_GRAPHS 24
+
+extern int8_t automorphisms[][PTM_MAX_POINTS];
+
+extern graph_t graphs_sc[NUM_SC_GRAPHS];
+extern graph_t graphs_fcc[NUM_FCC_GRAPHS];
+extern graph_t graphs_hcp[NUM_HCP_GRAPHS];
+extern graph_t graphs_ico[NUM_ICO_GRAPHS];
+extern graph_t graphs_bcc[NUM_BCC_GRAPHS];
+extern graph_t graphs_dcub[NUM_DCUB_GRAPHS];
+extern graph_t graphs_dhex[NUM_DHEX_GRAPHS];
+
+#endif
+
diff --git a/src/PTM/ptm_graph_tools.cpp b/src/PTM/ptm_graph_tools.cpp
new file mode 100644
index 0000000000..89d07fc87a
--- /dev/null
+++ b/src/PTM/ptm_graph_tools.cpp
@@ -0,0 +1,52 @@
+#include <string.h>
+#include <algorithm>
+#include "ptm_graph_tools.h"
+#include "ptm_constants.h"
+
+
+bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS])
+{
+ memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //assert(common[a][b] == -1);
+ //assert(common[b][c] == -1);
+ //assert(common[c][a] == -1);
+ if (common[a][b] != -1 || common[b][c] != -1 || common[c][a] != -1)
+ return false;
+
+ common[a][b] = c;
+ common[b][c] = a;
+ common[c][a] = b;
+ }
+
+ return true;
+}
+
+int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree)
+{
+ memset(degree, 0, sizeof(int8_t) * num_nodes);
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ degree[a]++;
+ degree[b]++;
+ degree[c]++;
+ }
+
+ int8_t max_degree = 0;
+ for (int i = 0;i<num_nodes;i++)
+ max_degree = std::max(max_degree, degree[i]);
+
+ return max_degree;
+}
+
diff --git a/src/PTM/ptm_graph_tools.h b/src/PTM/ptm_graph_tools.h
new file mode 100644
index 0000000000..78934e87c1
--- /dev/null
+++ b/src/PTM/ptm_graph_tools.h
@@ -0,0 +1,11 @@
+#ifndef PTM_GRAPH_TOOLS_H
+#define PTM_GRAPH_TOOLS_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]);
+int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree);
+
+#endif
+
diff --git a/src/PTM/ptm_index.cpp b/src/PTM/ptm_index.cpp
new file mode 100644
index 0000000000..7b6618848e
--- /dev/null
+++ b/src/PTM/ptm_index.cpp
@@ -0,0 +1,218 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_graph_data.h"
+#include "ptm_deformation_gradient.h"
+#include "ptm_alloy_types.h"
+#include "ptm_neighbour_ordering.h"
+#include "ptm_normalize_vertices.h"
+#include "ptm_quat.h"
+#include "ptm_polar.h"
+#include "ptm_initialize_data.h"
+#include "ptm_structure_matcher.h"
+#include "ptm_functions.h"
+#include "ptm_constants.h"
+
+
+//todo: verify that c == norm(template[1])
+static double calculate_interatomic_distance(int type, double scale)
+{
+ assert(type >= 1 && type <= 7);
+ double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))};
+ return c[type] / scale;
+}
+
+static double calculate_lattice_constant(int type, double interatomic_distance)
+{
+ assert(type >= 1 && type <= 7);
+ double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)};
+ return c[type] * interatomic_distance;
+}
+
+static int rotate_into_fundamental_zone(int type, double* q)
+{
+ if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q);
+ if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q);
+ if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
+ return -1;
+}
+
+static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
+ int8_t* ordering, double (*points)[3], int32_t* numbers)
+{
+ if (topological_ordering)
+ {
+ double normalized_points[PTM_MAX_INPUT_POINTS][3];
+ normalize_vertices(num_points, unpermuted_points, normalized_points);
+ int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
+ if (ret != 0)
+ topological_ordering = false;
+ }
+
+ if (!topological_ordering)
+ for (int i=0;i<num_points;i++)
+ ordering[i] = i;
+
+ for (int i=0;i<num_points;i++)
+ {
+ memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
+
+ if (unpermuted_numbers != NULL)
+ numbers[i] = unpermuted_numbers[ordering[i]];
+ }
+}
+
+static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
+ double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
+{
+ *p_type = PTM_MATCH_NONE;
+ if (p_alloy_type != NULL)
+ *p_alloy_type = PTM_ALLOY_NONE;
+
+ if (mapping != NULL)
+ memset(mapping, -1, num_points * sizeof(int8_t));
+
+ const refdata_t* ref = res->ref_struct;
+ if (ref == NULL)
+ return;
+
+ *p_type = ref->type;
+ if (p_alloy_type != NULL && unpermuted_numbers != NULL)
+ *p_alloy_type = find_alloy_type(ref, res->mapping, numbers);
+
+ int bi = rotate_into_fundamental_zone(ref->type, res->q);
+ int8_t temp[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ temp[ref->mapping[bi][i]] = res->mapping[i];
+
+ memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t));
+
+ if (F != NULL && F_res != NULL)
+ {
+ double scaled_points[PTM_MAX_INPUT_POINTS][3];
+
+ subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
+ for (int i = 0;i<ref->num_nbrs + 1;i++)
+ {
+ scaled_points[i][0] *= res->scale;
+ scaled_points[i][1] *= res->scale;
+ scaled_points[i][2] *= res->scale;
+ }
+ calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
+
+ if (P != NULL && U != NULL)
+ polar_decomposition_3x3(F, false, U, P);
+ }
+
+ if (mapping != NULL)
+ for (int i=0;i<ref->num_nbrs + 1;i++)
+ mapping[i] = ordering[res->mapping[i]];
+
+ double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale);
+ double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance);
+
+ if (p_interatomic_distance != NULL)
+ *p_interatomic_distance = interatomic_distance;
+
+ if (p_lattice_constant != NULL)
+ *p_lattice_constant = lattice_constant;
+
+ *p_rmsd = res->rmsd;
+ *p_scale = res->scale;
+ memcpy(q, res->q, 4 * sizeof(double));
+}
+
+
+extern bool ptm_initialized;
+
+int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
+ int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
+ double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
+{
+ assert(ptm_initialized);
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ if (flags & PTM_CHECK_SC)
+ assert(num_points >= PTM_NUM_POINTS_SC);
+
+ if (flags & PTM_CHECK_BCC)
+ assert(num_points >= PTM_NUM_POINTS_BCC);
+
+ if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
+ assert(num_points >= PTM_NUM_POINTS_FCC);
+
+ if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
+ assert(num_points >= PTM_NUM_POINTS_DCUB);
+
+ int ret = 0;
+ result_t res;
+ res.ref_struct = NULL;
+ res.rmsd = INFINITY;
+
+ int8_t ordering[PTM_MAX_INPUT_POINTS];
+ double points[PTM_MAX_POINTS][3];
+ int32_t numbers[PTM_MAX_POINTS];
+
+ int8_t dordering[PTM_MAX_INPUT_POINTS];
+ double dpoints[PTM_MAX_POINTS][3];
+ int32_t dnumbers[PTM_MAX_POINTS];
+
+ convexhull_t ch;
+ double ch_points[PTM_MAX_INPUT_POINTS][3];
+
+ if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC))
+ {
+ int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points);
+ order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers);
+ normalize_vertices(num_lpoints, points, ch_points);
+ ch.ok = false;
+
+ if (flags & PTM_CHECK_SC)
+ ret = match_general(&structure_sc, ch_points, points, &ch, &res);
+
+ if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
+ ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);
+
+ if (flags & PTM_CHECK_BCC)
+ ret = match_general(&structure_bcc, ch_points, points, &ch, &res);
+ }
+
+ if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
+ {
+ ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
+ if (ret == 0)
+ {
+ normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
+ ch.ok = false;
+
+ ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
+ }
+ }
+
+ if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX))
+ {
+ output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering,
+ p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
+ U, P, mapping, p_interatomic_distance, p_lattice_constant);
+ }
+ else
+ {
+ output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering,
+ p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
+ U, P, mapping, p_interatomic_distance, p_lattice_constant);
+ }
+
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/PTM/ptm_initialize_data.cpp b/src/PTM/ptm_initialize_data.cpp
new file mode 100644
index 0000000000..6157ff862f
--- /dev/null
+++ b/src/PTM/ptm_initialize_data.cpp
@@ -0,0 +1,71 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "ptm_initialize_data.h"
+
+
+static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
+{
+ double plane_normal[3];
+ double origin[3] = {0, 0, 0};
+
+ for (int i = 0;i<num_facets;i++)
+ add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
+}
+
+static int initialize_graphs(const refdata_t* s, int8_t* colours)
+{
+ for (int i = 0;i<s->num_graphs;i++)
+ {
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t degree[PTM_MAX_NBRS];
+ int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
+ assert(_max_degree <= s->max_degree);
+
+ make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
+ int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
+ if (ret != 0)
+ return ret;
+ }
+
+ return PTM_NO_ERROR;
+}
+
+bool ptm_initialized = false;
+int ptm_initialize_global()
+{
+ if (ptm_initialized)
+ return PTM_NO_ERROR;
+
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+
+ int ret = initialize_graphs(&structure_sc, colours);
+ ret |= initialize_graphs(&structure_fcc, colours);
+ ret |= initialize_graphs(&structure_hcp, colours);
+ ret |= initialize_graphs(&structure_ico, colours);
+ ret |= initialize_graphs(&structure_bcc, colours);
+ ret |= initialize_graphs(&structure_dcub, dcolours);
+ ret |= initialize_graphs(&structure_dhex, dcolours);
+
+ if (ret == PTM_NO_ERROR)
+ ptm_initialized = true;
+
+ return ret;
+}
+
+ptm_local_handle_t ptm_initialize_local()
+{
+ assert(ptm_initialized);
+ return (ptm_local_handle_t)voronoi_initialize_local();
+}
+
+void ptm_uninitialize_local(ptm_local_handle_t ptr)
+{
+ voronoi_uninitialize_local(ptr);
+}
+
diff --git a/src/PTM/ptm_initialize_data.h b/src/PTM/ptm_initialize_data.h
new file mode 100644
index 0000000000..f381dd864b
--- /dev/null
+++ b/src/PTM/ptm_initialize_data.h
@@ -0,0 +1,61 @@
+#ifndef PTM_INITIALIZE_DATA_H
+#define PTM_INITIALIZE_DATA_H
+
+
+#include "ptm_graph_data.h"
+#include "ptm_graph_tools.h"
+#include "ptm_deformation_gradient.h"
+#include "ptm_fundamental_mappings.h"
+#include "ptm_neighbour_ordering.h"
+#include "ptm_canonical_coloured.h"
+#include "ptm_convex_hull_incremental.h"
+
+
+typedef struct
+{
+ int type;
+ int num_nbrs;
+ int num_facets;
+ int max_degree;
+ int num_graphs;
+ int num_mappings;
+ graph_t* graphs;
+ const double (*points)[3];
+ const double (*penrose)[3];
+ const int8_t (*mapping)[PTM_MAX_POINTS];
+} refdata_t;
+
+
+//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc };
+const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc };
+const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc };
+const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp };
+const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico };
+const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc };
+const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub };
+const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex };
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct ptm_local_handle* ptm_local_handle_t;
+ptm_local_handle_t ptm_initialize_local();
+void ptm_uninitialize_local(ptm_local_handle_t ptr);
+
+int ptm_initialize_global();
+
+//------------------------------------
+// global initialization switch
+//------------------------------------
+extern bool ptm_initialized;
+
+
+#ifdef __cplusplus
+}
+#endif
+
+
+#endif
+
diff --git a/src/PTM/ptm_neighbour_ordering.cpp b/src/PTM/ptm_neighbour_ordering.cpp
new file mode 100644
index 0000000000..6b5ac9601a
--- /dev/null
+++ b/src/PTM/ptm_neighbour_ordering.cpp
@@ -0,0 +1,203 @@
+#include <cstdlib>
+#include <cmath>
+#include <cstring>
+#include <cassert>
+#include <algorithm>
+#include "ptm_constants.h"
+#include "ptm_voronoi_cell.h"
+using namespace voro;
+
+
+
+typedef struct
+{
+ double area;
+ double dist;
+ int index;
+} sorthelper_t;
+
+static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
+{
+ if (a.area > b.area)
+ return true;
+
+ if (a.area < b.area)
+ return false;
+
+ if (a.dist < b.dist)
+ return true;
+
+ return false;
+}
+
+//todo: change voronoi code to return errors rather than exiting
+static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
+{
+ const double k = 1000 * max_norm; //todo: reduce this constant
+ v->init(-k,k,-k,k,-k,k);
+
+ for (int i=1;i<num_points;i++)
+ {
+ double x = _points[i][0] - _points[0][0];
+ double y = _points[i][1] - _points[0][1];
+ double z = _points[i][2] - _points[0][2];
+ v->nplane(x,y,z,normsq[i],i);
+ }
+
+ v->neighbors(nbr_indices);
+ v->face_areas(face_areas);
+ return 0;
+}
+
+int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering)
+{
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle;
+
+ double max_norm = 0;
+ double points[PTM_MAX_INPUT_POINTS][3];
+ double normsq[PTM_MAX_INPUT_POINTS];
+ for (int i = 0;i<num_points;i++)
+ {
+ double x = _points[i][0] - _points[0][0];
+ double y = _points[i][1] - _points[0][1];
+ double z = _points[i][2] - _points[0][2];
+ points[i][0] = x;
+ points[i][1] = y;
+ points[i][2] = z;
+
+ normsq[i] = x*x + y*y + z*z;
+ max_norm = std::max(max_norm, normsq[i]);
+#ifdef DEBUG
+ printf("point %d: %f\t%f\t%f\t%f\n", i, x, y, z, x*x + y*y + z*z);
+#endif
+ }
+
+ max_norm = sqrt(max_norm);
+
+ std::vector<int> nbr_indices(num_points + 6);
+ std::vector<double> face_areas(num_points + 6);
+ int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas);
+ if (ret != 0)
+ return ret;
+
+ double areas[PTM_MAX_INPUT_POINTS];
+ memset(areas, 0, num_points * sizeof(double));
+ areas[0] = INFINITY;
+ for (size_t i=0;i<nbr_indices.size();i++)
+ {
+ int index = nbr_indices[i];
+ if (index > 0)
+ areas[index] = face_areas[i];
+ }
+
+ sorthelper_t data[PTM_MAX_INPUT_POINTS];
+ for (int i=0;i<num_points;i++)
+ {
+ assert(areas[i] == areas[i]);
+ data[i].area = areas[i];
+ data[i].dist = normsq[i];
+ data[i].index = i;
+ }
+
+ std::sort(data, data + num_points, &sorthelper_compare);
+
+#ifdef DEBUG
+ for (int i=0;i<num_points;i++)
+ printf("%d %f\n", data[i].index, data[i].area);
+#endif
+
+ for (int i=0;i<num_points;i++)
+ ordering[i] = data[i].index;
+
+ return ret;
+}
+
+void* voronoi_initialize_local()
+{
+ voronoicell_neighbor* ptr = new voronoicell_neighbor;
+ return (void*)ptr;
+}
+
+void voronoi_uninitialize_local(void* _ptr)
+{
+ voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr;
+ delete ptr;
+}
+
+
+typedef struct
+{
+ double dist;
+ int p;
+ int index;
+} diamond_t;
+
+static bool diamond_compare(diamond_t const& a, diamond_t const& b)
+{
+ return a.dist < b.dist;
+}
+
+int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
+ int8_t* ordering, double (*points)[3], int32_t* numbers)
+{
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ diamond_t data[4 * (PTM_MAX_INPUT_POINTS - 5)];
+ int index = 0;
+ for (int i=5;i<num_points;i++)
+ {
+ for (int j=1;j<5;j++)
+ {
+ double dx = unpermuted_points[i][0] - unpermuted_points[j][0];
+ double dy = unpermuted_points[i][1] - unpermuted_points[j][1];
+ double dz = unpermuted_points[i][2] - unpermuted_points[j][2];
+
+ double d = dx*dx + dy*dy + dz*dz;
+
+ data[index].p = j - 1;
+ data[index].index = i;
+ data[index].dist = d;
+ index++;
+ }
+ }
+ int n = index;
+
+ std::sort(data, data + n, &diamond_compare);
+
+ for (index=0;index<5;index++)
+ ordering[index] = index;
+
+ int num_found = 0;
+ bool hit[PTM_MAX_INPUT_POINTS] = {0};
+ int counts[4] = {0};
+ for (int i=0;i<n;i++)
+ {
+ int p = data[i].p;
+ int q = data[i].index;
+ if (hit[q] || counts[p] >= 3)
+ continue;
+
+ ordering[1 + 4 + 3 * p + counts[p]] = q;
+ counts[p]++;
+ index++;
+ num_found++;
+ if (num_found >= 12)
+ break;
+ }
+
+ if (num_found != 12)
+ return -1;
+
+ for (int i=0;i<PTM_NUM_NBRS_DCUB+1;i++)
+ {
+ memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
+
+ if (unpermuted_numbers != NULL)
+ numbers[i] = unpermuted_numbers[ordering[i]];
+ }
+
+ return 0;
+}
+
diff --git a/src/PTM/ptm_neighbour_ordering.h b/src/PTM/ptm_neighbour_ordering.h
new file mode 100644
index 0000000000..ce4dfca2c0
--- /dev/null
+++ b/src/PTM/ptm_neighbour_ordering.h
@@ -0,0 +1,13 @@
+#ifndef PTM_NEIGHBOUR_ORDERING_H
+#define PTM_NEIGHBOUR_ORDERING_H
+
+int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering);
+
+int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
+ int8_t* ordering, double (*points)[3], int32_t* numbers);
+
+void* voronoi_initialize_local();
+void voronoi_uninitialize_local(void* ptr);
+
+#endif
+
diff --git a/src/PTM/ptm_normalize_vertices.cpp b/src/PTM/ptm_normalize_vertices.cpp
new file mode 100644
index 0000000000..61dca5006f
--- /dev/null
+++ b/src/PTM/ptm_normalize_vertices.cpp
@@ -0,0 +1,55 @@
+#include <cmath>
+
+
+void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
+{
+ //calculate barycentre
+ double sum[3] = {0, 0, 0};
+ for (int i=0;i<num;i++)
+ {
+ sum[0] += points[i][0];
+ sum[1] += points[i][1];
+ sum[2] += points[i][2];
+ }
+
+ sum[0] /= num;
+ sum[1] /= num;
+ sum[2] /= num;
+
+ //subtract barycentre
+ for (int i=0;i<num;i++)
+ {
+ normalized[i][0] = points[i][0] - sum[0];
+ normalized[i][1] = points[i][1] - sum[1];
+ normalized[i][2] = points[i][2] - sum[2];
+ }
+}
+
+double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
+{
+ subtract_barycentre(num, points, normalized);
+
+ //calculate mean length
+ double scale = 0.0;
+ for (int i=1;i<num;i++)
+ {
+ double x = normalized[i][0];
+ double y = normalized[i][1];
+ double z = normalized[i][2];
+
+ double norm = sqrt(x*x + y*y + z*z);
+ scale += norm;
+ }
+ scale /= num;
+
+ //scale vertices such that mean length is 1
+ for (int i=0;i<num;i++)
+ {
+ normalized[i][0] /= scale;
+ normalized[i][1] /= scale;
+ normalized[i][2] /= scale;
+ }
+
+ return scale;
+}
+
diff --git a/src/PTM/ptm_normalize_vertices.h b/src/PTM/ptm_normalize_vertices.h
new file mode 100644
index 0000000000..2c7b722752
--- /dev/null
+++ b/src/PTM/ptm_normalize_vertices.h
@@ -0,0 +1,8 @@
+#ifndef PTM_NORMALIZE_VERTICES_H
+#define PTM_NORMALIZE_VERTICES_H
+
+void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]);
+double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]);
+
+#endif
+
diff --git a/src/PTM/ptm_polar.cpp b/src/PTM/ptm_polar.cpp
new file mode 100644
index 0000000000..9089b327b9
--- /dev/null
+++ b/src/PTM/ptm_polar.cpp
@@ -0,0 +1,337 @@
+/*******************************************************************************
+ * -/_|:|_|_\-
+ *
+ * This code is a modification of D.L. Theobald's QCP rotation code.
+ * It has been adapted to calculate the polar decomposition of a 3x3 matrix
+ * Adaption by P.M. Larsen
+ *
+ * Original Author(s): Douglas L. Theobald
+ * Department of Biochemistry
+ * MS 009
+ * Brandeis University
+ * 415 South St
+ * Waltham, MA 02453
+ * USA
+ *
+ * dtheobald@brandeis.edu
+ *
+ * Pu Liu
+ * Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
+ * 665 Stockton Drive
+ * Exton, PA 19341
+ * USA
+ *
+ * pliu24@its.jnj.com
+ *
+ *
+ * If you use this QCP rotation calculation method in a publication, please
+ * reference:
+ *
+ * Douglas L. Theobald (2005)
+ * "Rapid calculation of RMSD using a quaternion-based characteristic
+ * polynomial."
+ * Acta Crystallographica A 61(4):478-480.
+ *
+ * Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009)
+ * "Fast determination of the optimal rotational matrix for macromolecular
+ * superpositions."
+ * Journal of Computational Chemistry 31(7):1561-1563.
+ *
+ *
+ * Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without modification, are permitted
+ * provided that the following conditions are met:
+ *
+ * * Redistributions of source code must retain the above copyright notice, this list of
+ * conditions and the following disclaimer.
+ * * Redistributions in binary form must reproduce the above copyright notice, this list
+ * of conditions and the following disclaimer in the documentation and/or other materials
+ * provided with the distribution.
+ * * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to
+ * endorse or promote products derived from this software without specific prior written
+ * permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * Source: started anew.
+ *
+ * Change History:
+ * 2009/04/13 Started source
+ * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr
+ * If trying all rows of the adjoint still gives too small
+ * qsqr, then just return identity matrix. (DLT)
+ * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct()
+ * invalid mem access
+ * 2011/02/21 Made CenterCoords use weights
+ * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h
+ * Also changed some functions to static
+ * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error
+ * 2012/07/26 minor changes to comments and main.c, more info (v.1.4)
+ *
+ * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix,
+ * for use in Polyhedral Template Matching.
+ *
+ ******************************************************************************/
+
+#include <cmath>
+#include <algorithm>
+#include <string.h>
+#include "ptm_quat.h"
+
+
+static void matmul_3x3(double* A, double* x, double* b)
+{
+ b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6];
+ b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6];
+ b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6];
+
+ b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7];
+ b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7];
+ b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7];
+
+ b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8];
+ b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8];
+ b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8];
+}
+
+static double matrix_determinant_3x3(double* A)
+{
+ return A[0] * (A[4]*A[8] - A[5]*A[7])
+ - A[1] * (A[3]*A[8] - A[5]*A[6])
+ + A[2] * (A[3]*A[7] - A[4]*A[6]);
+}
+
+static void flip_matrix(double* A)
+{
+ for (int i=0;i<9;i++)
+ A[i] = -A[i];
+}
+
+static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt)
+{
+ const double evecprec = 1e-6;
+ const double evalprec = 1e-11;
+
+ double Sxx = A[0], Sxy = A[1], Sxz = A[2],
+ Syx = A[3], Syy = A[4], Syz = A[5],
+ Szx = A[6], Szy = A[7], Szz = A[8];
+
+ double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz,
+ Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz,
+ Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx;
+
+ double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2;
+
+ double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz);
+ double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2;
+ double SxzpSzx = Sxz + Szx;
+ double SyzpSzy = Syz + Szy;
+ double SxypSyx = Sxy + Syx;
+ double SyzmSzy = Syz - Szy;
+ double SxzmSzx = Sxz - Szx;
+ double SxymSyx = Sxy - Syx;
+ double SxxpSyy = Sxx + Syy;
+ double SxxmSyy = Sxx - Syy;
+ double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2;
+
+ double C[3];
+ C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2
+ + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2)
+ + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz))
+ + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz))
+ + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz))
+ + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz));
+
+ C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz);
+ C[2] = -2.0 * fnorm_squared;
+
+ //Newton-Raphson
+ double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0;
+ if (mxEigenV > evalprec)
+ {
+ for (int i=0;i<50;i++)
+ {
+ double oldg = mxEigenV;
+ double x2 = mxEigenV*mxEigenV;
+ double b = (x2 + C[2])*mxEigenV;
+ double a = b + C[1];
+ double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a));
+ mxEigenV -= delta;
+ if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV))
+ break;
+ }
+ }
+ else
+ {
+ mxEigenV = 0.0;
+ }
+
+ (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV));
+
+ double a11 = SxxpSyy + Szz - mxEigenV;
+ double a12 = SyzmSzy;
+ double a13 = -SxzmSzx;
+ double a14 = SxymSyx;
+
+ double a21 = SyzmSzy;
+ double a22 = SxxmSyy - Szz -mxEigenV;
+ double a23 = SxypSyx;
+ double a24 = SxzpSzx;
+
+ double a31 = a13;
+ double a32 = a23;
+ double a33 = Syy - Sxx - Szz - mxEigenV;
+ double a34 = SyzpSzy;
+
+ double a41 = a14;
+ double a42 = a24;
+ double a43 = a34;
+ double a44 = Szz - SxxpSyy - mxEigenV;
+
+ double a3344_4334 = a33 * a44 - a43 * a34;
+ double a3244_4234 = a32 * a44 - a42 * a34;
+ double a3243_4233 = a32 * a43 - a42 * a33;
+ double a3143_4133 = a31 * a43 - a41 * a33;
+ double a3144_4134 = a31 * a44 - a41 * a34;
+ double a3142_4132 = a31 * a42 - a41 * a32;
+ double a1324_1423 = a13 * a24 - a14 * a23;
+ double a1224_1422 = a12 * a24 - a14 * a22;
+ double a1223_1322 = a12 * a23 - a13 * a22;
+ double a1124_1421 = a11 * a24 - a14 * a21;
+ double a1123_1321 = a11 * a23 - a13 * a21;
+ double a1122_1221 = a11 * a22 - a12 * a21;
+
+ double q[4][4];
+ q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233;
+ q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133;
+ q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132;
+ q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132;
+
+ q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233;
+ q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133;
+ q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132;
+ q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132;
+
+ q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322;
+ q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321;
+ q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221;
+ q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221;
+
+ q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322;
+ q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321;
+ q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221;
+ q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221;
+
+ double qsqr[4];
+ for (int i=0;i<4;i++)
+ qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3];
+
+ int bi = 0;
+ double max = 0;
+ for (int i=0;i<4;i++)
+ {
+ if (qsqr[i] > max)
+ {
+ bi = i;
+ max = qsqr[i];
+ }
+ }
+
+ bool too_small = false;
+ if (qsqr[bi] < evecprec)
+ {
+ //if qsqr is still too small, return the identity rotation.
+ q[bi][0] = 1;
+ q[bi][1] = 0;
+ q[bi][2] = 0;
+ q[bi][3] = 0;
+ too_small = true;
+ }
+ else
+ {
+ double normq = sqrt(qsqr[bi]);
+ q[bi][0] /= normq;
+ q[bi][1] /= normq;
+ q[bi][2] /= normq;
+ q[bi][3] /= normq;
+ }
+
+ memcpy(qopt, q[bi], 4 * sizeof(double));
+ return !too_small;
+}
+
+int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P)
+{
+ double A[9];
+ memcpy(A, _A, 9 * sizeof(double));
+
+ double det = matrix_determinant_3x3(A);
+ if (det < 0)
+ flip_matrix(A);
+
+ double q[4];
+ double nrmsdsq = 0;
+ optimal_quaternion(A, true, -1, &nrmsdsq, q);
+ q[0] = -q[0];
+ quaternion_to_rotation_matrix(q, U);
+
+ if (det < 0)
+ flip_matrix(U);
+
+ double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]};
+
+ if (right_sided)
+ matmul_3x3(UT, _A, P);
+ else
+ matmul_3x3(_A, UT, P);
+
+ return 0;
+}
+
+void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation)
+{
+ A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0;
+
+ for (int i = 0; i < num; ++i)
+ {
+ double x1 = coords1[i][0];
+ double y1 = coords1[i][1];
+ double z1 = coords1[i][2];
+
+ double x2 = coords2[permutation[i]][0];
+ double y2 = coords2[permutation[i]][1];
+ double z2 = coords2[permutation[i]][2];
+
+ A[0] += x1 * x2;
+ A[1] += x1 * y2;
+ A[2] += x1 * z2;
+
+ A[3] += y1 * x2;
+ A[4] += y1 * y2;
+ A[5] += y1 * z2;
+
+ A[6] += z1 * x2;
+ A[7] += z1 * y2;
+ A[8] += z1 * z2;
+ }
+}
+
+int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U)
+{
+ optimal_quaternion(A, false, E0, p_nrmsdsq, q);
+ quaternion_to_rotation_matrix(q, U);
+ return 0;
+}
+
diff --git a/src/PTM/ptm_polar.h b/src/PTM/ptm_polar.h
new file mode 100644
index 0000000000..d5aa3d9540
--- /dev/null
+++ b/src/PTM/ptm_polar.h
@@ -0,0 +1,12 @@
+#ifndef PTM_POLAR_H
+#define PTM_POLAR_H
+
+#include <stdint.h>
+#include <stdbool.h>
+
+int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P);
+void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation);
+int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U);
+
+#endif
+
diff --git a/src/PTM/ptm_quat.cpp b/src/PTM/ptm_quat.cpp
new file mode 100644
index 0000000000..f55aff3d2b
--- /dev/null
+++ b/src/PTM/ptm_quat.cpp
@@ -0,0 +1,396 @@
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+
+
+#define SIGN(x) (x >= 0 ? 1 : -1)
+#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
+#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y))
+
+
+#define SQRT_2 1.4142135623730951454746218587388284504414
+#define HALF_SQRT_2 0.7071067811865474617150084668537601828575
+
+#define PHI 1.6180339887498949025257388711906969547272
+#define HALF_PHI 0.8090169943749474512628694355953484773636
+
+#define INV_PHI 0.6180339887498947915034364086750429123640
+#define HALF_INV_PHI 0.3090169943749473957517182043375214561820
+
+#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089
+#define SQRT_2_3 0.8164965809277260344600790631375275552273
+#define SQRT_1_6 0.4082482904638630172300395315687637776136
+
+
+double generator_cubic[24][4] = { {1, 0, 0, 0 },
+ {0, 1, 0, 0 },
+ {0, 0, 1, 0 },
+ {0, 0, 0, 1 },
+ {0.5, 0.5, 0.5, 0.5 },
+ {0.5, 0.5, -0.5, 0.5 },
+ {0.5, -0.5, 0.5, 0.5 },
+ {0.5, -0.5, -0.5, 0.5 },
+ {-0.5, 0.5, 0.5, 0.5 },
+ {-0.5, 0.5, -0.5, 0.5 },
+ {-0.5, -0.5, 0.5, 0.5 },
+ {-0.5, -0.5, -0.5, 0.5 },
+ {HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
+ {HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
+ {HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
+ {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
+ {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
+ {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
+ {0, HALF_SQRT_2, HALF_SQRT_2, 0 },
+ {0, HALF_SQRT_2, 0, HALF_SQRT_2 },
+ {0, 0, HALF_SQRT_2, HALF_SQRT_2 },
+ {0, -HALF_SQRT_2, HALF_SQRT_2, 0 },
+ {0, -HALF_SQRT_2, 0, HALF_SQRT_2 },
+ {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } };
+
+double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 },
+ {0, 1, 0, 0 },
+ {0, 0, 1, 0 },
+ {0, 0, 0, 1 },
+ {0.5, 0.5, 0.5, 0.5 },
+ {0.5, 0.5, -0.5, 0.5 },
+ {0.5, -0.5, 0.5, 0.5 },
+ {0.5, -0.5, -0.5, 0.5 },
+ {-0.5, 0.5, 0.5, 0.5 },
+ {-0.5, 0.5, -0.5, 0.5 },
+ {-0.5, -0.5, 0.5, 0.5 },
+ {-0.5, -0.5, -0.5, 0.5 } };
+
+double generator_hcp[6][4] = { {1, 0, 0, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5},
+ {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6},
+ {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6},
+ {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} };
+
+double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5} };
+
+double generator_icosahedral[60][4] = { {1, 0, 0, 0},
+ {HALF_PHI, -HALF_INV_PHI, -0.5, 0},
+ {HALF_PHI, 0, -HALF_INV_PHI, -0.5},
+ {HALF_PHI, -0.5, 0, -HALF_INV_PHI},
+ {HALF_PHI, HALF_INV_PHI, -0.5, 0},
+ {HALF_PHI, 0, HALF_INV_PHI, -0.5},
+ {HALF_PHI, -0.5, 0, HALF_INV_PHI},
+ {HALF_PHI, 0.5, 0, -HALF_INV_PHI},
+ {HALF_PHI, 0, -HALF_INV_PHI, 0.5},
+ {HALF_PHI, -HALF_INV_PHI, 0.5, 0},
+ {HALF_PHI, 0, HALF_INV_PHI, 0.5},
+ {HALF_PHI, HALF_INV_PHI, 0.5, 0},
+ {HALF_PHI, 0.5, 0, HALF_INV_PHI},
+ {0.5, HALF_PHI, -HALF_INV_PHI, 0},
+ {0.5, HALF_PHI, HALF_INV_PHI, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, 0.5, 0.5, -0.5},
+ {0.5, 0.5, -0.5, 0.5},
+ {0.5, 0.5, -0.5, -0.5},
+ {0.5, HALF_INV_PHI, 0, HALF_PHI},
+ {0.5, HALF_INV_PHI, 0, -HALF_PHI},
+ {0.5, 0, HALF_PHI, -HALF_INV_PHI},
+ {0.5, 0, HALF_PHI, HALF_INV_PHI},
+ {0.5, 0, -HALF_PHI, -HALF_INV_PHI},
+ {0.5, 0, -HALF_PHI, HALF_INV_PHI},
+ {0.5, -HALF_INV_PHI, 0, HALF_PHI},
+ {0.5, -HALF_INV_PHI, 0, -HALF_PHI},
+ {0.5, -0.5, 0.5, 0.5},
+ {0.5, -0.5, 0.5, -0.5},
+ {0.5, -0.5, -0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5},
+ {0.5, -HALF_PHI, -HALF_INV_PHI, 0},
+ {0.5, -HALF_PHI, HALF_INV_PHI, 0},
+ {HALF_INV_PHI, -HALF_PHI, 0, -0.5},
+ {HALF_INV_PHI, 0, -0.5, -HALF_PHI},
+ {HALF_INV_PHI, -0.5, -HALF_PHI, 0},
+ {HALF_INV_PHI, 0, 0.5, -HALF_PHI},
+ {HALF_INV_PHI, -HALF_PHI, 0, 0.5},
+ {HALF_INV_PHI, 0.5, -HALF_PHI, 0},
+ {HALF_INV_PHI, HALF_PHI, 0, -0.5},
+ {HALF_INV_PHI, -0.5, HALF_PHI, 0},
+ {HALF_INV_PHI, 0, -0.5, HALF_PHI},
+ {HALF_INV_PHI, HALF_PHI, 0, 0.5},
+ {HALF_INV_PHI, 0, 0.5, HALF_PHI},
+ {HALF_INV_PHI, 0.5, HALF_PHI, 0},
+ {0, 1, 0, 0},
+ {0, HALF_PHI, -0.5, HALF_INV_PHI},
+ {0, HALF_PHI, -0.5, -HALF_INV_PHI},
+ {0, HALF_PHI, 0.5, HALF_INV_PHI},
+ {0, HALF_PHI, 0.5, -HALF_INV_PHI},
+ {0, 0.5, HALF_INV_PHI, -HALF_PHI},
+ {0, 0.5, HALF_INV_PHI, HALF_PHI},
+ {0, 0.5, -HALF_INV_PHI, -HALF_PHI},
+ {0, 0.5, -HALF_INV_PHI, HALF_PHI},
+ {0, HALF_INV_PHI, -HALF_PHI, 0.5},
+ {0, HALF_INV_PHI, -HALF_PHI, -0.5},
+ {0, HALF_INV_PHI, HALF_PHI, 0.5},
+ {0, HALF_INV_PHI, HALF_PHI, -0.5},
+ {0, 0, 1, 0},
+ {0, 0, 0, 1} };
+
+static void quat_rot(double* r, double* a, double* b)
+{
+ b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]);
+ b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]);
+ b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]);
+ b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]);
+}
+
+static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q)
+{
+ double max = 0.0;
+ int i = 0, bi = -1;
+ for (i=0;i<num_generators;i++)
+ {
+ double* g = generator[i];
+ double t = fabs(q[0] * g[0] - q[1] * g[1] - q[2] * g[2] - q[3] * g[3]);
+ if (t > max)
+ {
+ max = t;
+ bi = i;
+ }
+ }
+
+ double f[4];
+ quat_rot(q, generator[bi], f);
+ memcpy(q, &f, 4 * sizeof(double));
+ if (q[0] < 0)
+ {
+ q[0] = -q[0];
+ q[1] = -q[1];
+ q[2] = -q[2];
+ q[3] = -q[3];
+ }
+
+ return bi;
+}
+
+int rotate_quaternion_into_cubic_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q);
+}
+
+int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q);
+}
+
+int rotate_quaternion_into_icosahedral_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q);
+}
+
+int rotate_quaternion_into_hcp_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q);
+}
+
+int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q);
+}
+
+double quat_dot(double* a, double* b)
+{
+ return a[0] * b[0]
+ + a[1] * b[1]
+ + a[2] * b[2]
+ + a[3] * b[3];
+}
+
+double quat_size(double* q)
+{
+ return sqrt(quat_dot(q, q));
+}
+
+void normalize_quaternion(double* q)
+{
+ double size = quat_size(q);
+
+ q[0] /= size;
+ q[1] /= size;
+ q[2] /= size;
+ q[3] /= size;
+}
+
+void rotation_matrix_to_quaternion(double* u, double* q)
+{
+ double r11 = u[0];
+ double r12 = u[1];
+ double r13 = u[2];
+ double r21 = u[3];
+ double r22 = u[4];
+ double r23 = u[5];
+ double r31 = u[6];
+ double r32 = u[7];
+ double r33 = u[8];
+
+ q[0] = (1.0 + r11 + r22 + r33) / 4.0;
+ q[1] = (1.0 + r11 - r22 - r33) / 4.0;
+ q[2] = (1.0 - r11 + r22 - r33) / 4.0;
+ q[3] = (1.0 - r11 - r22 + r33) / 4.0;
+
+ q[0] = sqrt(MAX(0, q[0]));
+ q[1] = sqrt(MAX(0, q[1]));
+ q[2] = sqrt(MAX(0, q[2]));
+ q[3] = sqrt(MAX(0, q[3]));
+
+ double m0 = MAX(q[0], q[1]);
+ double m1 = MAX(q[2], q[3]);
+ double max = MAX(m0, m1);
+
+ int i = 0;
+ for (i=0;i<4;i++)
+ if (q[i] == max)
+ break;
+
+ if (i == 0)
+ {
+ q[1] *= SIGN(r32 - r23);
+ q[2] *= SIGN(r13 - r31);
+ q[3] *= SIGN(r21 - r12);
+ }
+ else if (i == 1)
+ {
+ q[0] *= SIGN(r32 - r23);
+ q[2] *= SIGN(r21 + r12);
+ q[3] *= SIGN(r13 + r31);
+ }
+ else if (i == 2)
+ {
+ q[0] *= SIGN(r13 - r31);
+ q[1] *= SIGN(r21 + r12);
+ q[3] *= SIGN(r32 + r23);
+ }
+ else if (i == 3)
+ {
+ q[0] *= SIGN(r21 - r12);
+ q[1] *= SIGN(r31 + r13);
+ q[2] *= SIGN(r32 + r23);
+ }
+
+ normalize_quaternion(q);
+}
+
+void quaternion_to_rotation_matrix(double* q, double* u)
+{
+ double a = q[0];
+ double b = q[1];
+ double c = q[2];
+ double d = q[3];
+
+ u[0] = a*a + b*b - c*c - d*d;
+ u[1] = 2*b*c - 2*a*d;
+ u[2] = 2*b*d + 2*a*c;
+
+ u[3] = 2*b*c + 2*a*d;
+ u[4] = a*a - b*b + c*c - d*d;
+ u[5] = 2*c*d - 2*a*b;
+
+ u[6] = 2*b*d - 2*a*c;
+ u[7] = 2*c*d + 2*a*b;
+ u[8] = a*a - b*b - c*c + d*d;
+}
+
+double quat_quick_misorientation(double* q1, double* q2)
+{
+ double t = quat_dot(q1, q2);
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_misorientation(double* q1, double* q2)
+{
+ return acos(quat_quick_misorientation(q1, q2));
+}
+
+
+double quat_quick_disorientation_cubic(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_cubic_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_cubic(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_cubic(q0, q1));
+}
+
+double quat_quick_disorientation_diamond_cubic(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_diamond_cubic(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_diamond_cubic(q0, q1));
+}
+
+double quat_quick_disorientation_hcp(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_hcp_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_hcp(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_hcp(q0, q1));
+}
+
+double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_diamond_hexagonal(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1));
+}
+
+double quat_quick_disorientation_icosahedral(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_icosahedral_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_icosahedral(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_icosahedral(q0, q1));
+}
+
diff --git a/src/PTM/ptm_quat.h b/src/PTM/ptm_quat.h
new file mode 100644
index 0000000000..381c3ce876
--- /dev/null
+++ b/src/PTM/ptm_quat.h
@@ -0,0 +1,32 @@
+#ifndef PTM_QUAT_H
+#define PTM_QUAT_H
+
+int rotate_quaternion_into_cubic_fundamental_zone(double* q);
+int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q);
+int rotate_quaternion_into_icosahedral_fundamental_zone(double* q);
+int rotate_quaternion_into_hcp_fundamental_zone(double* q);
+int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q);
+
+void normalize_quaternion(double* q);
+void quaternion_to_rotation_matrix(double* q, double* U);
+void rotation_matrix_to_quaternion(double* u, double* q);
+double quat_dot(double* a, double* b);
+double quat_quick_misorientation(double* q1, double* q2);
+double quat_misorientation(double* q1, double* q2);
+
+double quat_quick_disorientation_cubic(double* q0, double* q1);
+double quat_disorientation_cubic(double* q0, double* q1);
+double quat_quick_disorientation_diamond_cubic(double* q0, double* q1);
+double quat_disorientation_diamond_cubic(double* q0, double* q1);
+double quat_quick_disorientation_hcp(double* q0, double* q1);
+double quat_disorientation_hcp(double* q0, double* q1);
+double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1);
+double quat_disorientation_diamond_hexagonal(double* q0, double* q1);
+double quat_quick_disorientation_icosahedral(double* q0, double* q1);
+double quat_disorientation_icosahedral(double* q0, double* q1);
+
+#endif
+
+
+
+
diff --git a/src/PTM/ptm_structure_matcher.cpp b/src/PTM/ptm_structure_matcher.cpp
new file mode 100644
index 0000000000..7eb0a44143
--- /dev/null
+++ b/src/PTM/ptm_structure_matcher.cpp
@@ -0,0 +1,294 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_canonical_coloured.h"
+#include "ptm_graph_data.h"
+#include "ptm_graph_tools.h"
+#include "ptm_normalize_vertices.h"
+#include "ptm_polar.h"
+#include "ptm_structure_matcher.h"
+#include "ptm_constants.h"
+
+
+static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping,
+ double G1, double G2, double E0, double* q, double* p_scale)
+{
+ double A0[9];
+ InnerProduct(A0, num_points, ideal_points, normalized, mapping);
+
+ double nrmsdsq, rot[9];
+ FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot);
+
+ double k0 = 0;
+ for (int i=0;i<num_points;i++)
+ {
+ for (int j=0;j<3;j++)
+ {
+ double v = 0.0;
+ for (int k=0;k<3;k++)
+ v += rot[j*3+k] * ideal_points[i][k];
+
+ k0 += v * normalized[mapping[i]][j];
+ }
+ }
+
+ double scale = k0 / G2;
+ *p_scale = scale;
+ return sqrt(fabs(G1 - scale*k0) / num_points);
+}
+
+static void check_graphs( const refdata_t* s,
+ uint64_t hash,
+ int8_t* canonical_labelling,
+ double (*normalized)[3],
+ result_t* res)
+{
+ int num_points = s->num_nbrs + 1;
+ const double (*ideal_points)[3] = s->points;
+ int8_t inverse_labelling[PTM_MAX_POINTS];
+ int8_t mapping[PTM_MAX_POINTS];
+
+ for (int i=0; i<num_points; i++)
+ inverse_labelling[ canonical_labelling[i] ] = i;
+
+ double G1 = 0, G2 = 0;
+ for (int i=0;i<num_points;i++)
+ {
+ double x1 = ideal_points[i][0];
+ double y1 = ideal_points[i][1];
+ double z1 = ideal_points[i][2];
+
+ double x2 = normalized[i][0];
+ double y2 = normalized[i][1];
+ double z2 = normalized[i][2];
+
+ G1 += x1 * x1 + y1 * y1 + z1 * z1;
+ G2 += x2 * x2 + y2 * y2 + z2 * z2;
+ }
+ double E0 = (G1 + G2) / 2;
+
+ for (int i = 0;i<s->num_graphs;i++)
+ {
+ if (hash != s->graphs[i].hash)
+ continue;
+
+ graph_t* gref = &s->graphs[i];
+ for (int j = 0;j<gref->num_automorphisms;j++)
+ {
+ for (int k=0;k<num_points;k++)
+ mapping[automorphisms[gref->automorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ];
+
+ double q[4], scale = 0;
+ double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale);
+ if (rmsd < res->rmsd)
+ {
+ res->rmsd = rmsd;
+ res->scale = scale;
+ res->ref_struct = s;
+ memcpy(res->q, q, 4 * sizeof(double));
+ memcpy(res->mapping, mapping, sizeof(int8_t) * num_points);
+ }
+ }
+ }
+}
+
+int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res)
+{
+ int8_t degree[PTM_MAX_NBRS];
+ int8_t facets[PTM_MAX_FACETS][3];
+
+ int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ if (ch->num_facets != s->num_facets)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree);
+ if (max_degree > s->max_degree)
+ return PTM_NO_ERROR;
+
+ if (s->type == PTM_MATCH_SC)
+ for (int i = 0;i<s->num_nbrs;i++)
+ if (degree[i] != 4)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(s->num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ check_graphs(s, hash, canonical_labelling, normalized, res);
+ return PTM_NO_ERROR;
+}
+
+int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
+{
+ int num_nbrs = structure_fcc.num_nbrs;
+ int num_facets = structure_fcc.num_facets;
+ int max_degree = structure_fcc.max_degree;
+
+ int8_t degree[PTM_MAX_NBRS];
+ int8_t facets[PTM_MAX_FACETS][3];
+
+ int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ if (ch->num_facets != num_facets)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res);
+ return PTM_NO_ERROR;
+}
+
+int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
+{
+ int num_nbrs = structure_dcub.num_nbrs;
+ int num_facets = structure_fcc.num_facets;
+ int max_degree = structure_dcub.max_degree;
+
+
+ int8_t facets[PTM_MAX_FACETS][3];
+ int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ //check for facets with multiple inner atoms
+ bool inverted[4] = {false, false, false, false};
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int n = 0;
+ for (int j=0;j<3;j++)
+ {
+ if (facets[i][j] <= 3)
+ {
+ inverted[facets[i][j]] = true;
+ n++;
+ }
+ }
+ if (n > 1)
+ return PTM_NO_ERROR;
+ }
+
+ int num_inverted = 0;
+ for (int i=0;i<4;i++)
+ num_inverted += inverted[i] ? 1 : 0;
+
+ if (ch->num_facets != num_facets + 2 * num_inverted)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int8_t degree[PTM_MAX_NBRS];
+ int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ int num_found = 0;
+ int8_t toadd[4][3];
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+ if (a <= 3 || b <= 3 || c <= 3)
+ continue;
+
+ int i0 = (a - 4) / 3;
+ int i1 = (b - 4) / 3;
+ int i2 = (c - 4) / 3;
+
+ if (i0 == i1 && i0 == i2)
+ {
+ if (num_found + num_inverted >= 4)
+ return PTM_NO_ERROR;
+
+ toadd[num_found][0] = a;
+ toadd[num_found][1] = b;
+ toadd[num_found][2] = c;
+ num_found++;
+
+ memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t));
+ ch->num_facets--;
+ i--;
+ }
+ }
+
+ if (num_found + num_inverted != 4)
+ return PTM_NO_ERROR;
+
+ for (int i=0;i<num_found;i++)
+ {
+ int a = toadd[i][0];
+ int b = toadd[i][1];
+ int c = toadd[i][2];
+
+ int i0 = (a - 4) / 3;
+
+ facets[ch->num_facets][0] = i0;
+ facets[ch->num_facets][1] = b;
+ facets[ch->num_facets][2] = c;
+ ch->num_facets++;
+
+ facets[ch->num_facets][0] = a;
+ facets[ch->num_facets][1] = i0;
+ facets[ch->num_facets][2] = c;
+ ch->num_facets++;
+
+ facets[ch->num_facets][0] = a;
+ facets[ch->num_facets][1] = b;
+ facets[ch->num_facets][2] = i0;
+ ch->num_facets++;
+ }
+
+ _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res);
+
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/PTM/ptm_structure_matcher.h b/src/PTM/ptm_structure_matcher.h
new file mode 100644
index 0000000000..4b6f969597
--- /dev/null
+++ b/src/PTM/ptm_structure_matcher.h
@@ -0,0 +1,21 @@
+#ifndef PTM_STRUCTURE_MATCHER_H
+#define PTM_STRUCTURE_MATCHER_H
+
+#include "ptm_initialize_data.h"
+#include "ptm_constants.h"
+
+typedef struct
+{
+ double rmsd;
+ double scale;
+ double q[4]; //rotation in quaternion form (rigid body transformation)
+ int8_t mapping[PTM_MAX_POINTS];
+ const refdata_t* ref_struct;
+} result_t;
+
+int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res);
+int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+
+#endif
+
diff --git a/src/PTM/ptm_voronoi_cell.cpp b/src/PTM/ptm_voronoi_cell.cpp
new file mode 100644
index 0000000000..6503ea16c6
--- /dev/null
+++ b/src/PTM/ptm_voronoi_cell.cpp
@@ -0,0 +1,1368 @@
+// 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 <cstring>
+#include <cstdlib>
+#include "ptm_voronoi_config.h"
+#include "ptm_voronoi_cell.h"
+
+namespace 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) {
+ 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();
+}
+
+// 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*);
+
+}
+
diff --git a/src/PTM/ptm_voronoi_cell.h b/src/PTM/ptm_voronoi_cell.h
new file mode 100644
index 0000000000..80a0501b3c
--- /dev/null
+++ b/src/PTM/ptm_voronoi_cell.h
@@ -0,0 +1,324 @@
+// 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.hh
+ * \brief Header file for the voronoicell and related classes. */
+
+#ifndef PTM_VOROPP_CELL_HH
+#define PTM_VOROPP_CELL_HH
+
+#include <vector>
+#include <cstdio>
+
+#include "ptm_voronoi_config.h"
+
+namespace voro {
+
+/** \brief A class representing a single Voronoi cell.
+ *
+ * This class represents a single Voronoi cell, as a collection of vertices
+ * that are connected by edges. The class contains routines for initializing
+ * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron.
+ * It the contains routines for recomputing the cell based on cutting it
+ * by a plane, which forms the key routine for the Voronoi cell computation.
+ * It contains numerous routine for computing statistics about the Voronoi cell,
+ * and it can output the cell in several formats.
+ *
+ * This class is not intended for direct use, but forms the base of the
+ * voronoicell and voronoicell_neighbor classes, which extend it based on
+ * whether neighboring particle ID information needs to be tracked. */
+class voronoicell_base {
+ public:
+ /** This holds the current size of the arrays ed and nu, which
+ * hold the vertex information. If more vertices are created
+ * than can fit in this array, then it is dynamically extended
+ * using the add_memory_vertices routine. */
+ int current_vertices;
+ /** This holds the current maximum allowed order of a vertex,
+ * which sets the size of the mem, mep, and mec arrays. If a
+ * vertex is created with more vertices than this, the arrays
+ * are dynamically extended using the add_memory_vorder routine.
+ */
+ int current_vertex_order;
+ /** This sets the size of the main delete stack. */
+ int current_delete_size;
+ /** This sets the size of the auxiliary delete stack. */
+ int current_delete2_size;
+ /** This sets the total number of vertices in the current cell.
+ */
+ int p;
+ /** This is the index of particular point in the cell, which is
+ * used to start the tracing routines for plane intersection
+ * and cutting. These routines will work starting from any
+ * point, but it's often most efficient to start from the last
+ * point considered, since in many cases, the cell construction
+ * algorithm may consider many planes with similar vectors
+ * concurrently. */
+ int up;
+ /** This is a two dimensional array that holds information
+ * about the edge connections of the vertices that make up the
+ * cell. The two dimensional array is not allocated in the
+ * usual method. To account for the fact the different vertices
+ * have different orders, and thus require different amounts of
+ * storage, the elements of ed[i] point to one-dimensional
+ * arrays in the mep[] array of different sizes.
+ *
+ * More specifically, if vertex i has order m, then ed[i]
+ * points to a one-dimensional array in mep[m] that has 2*m+1
+ * entries. The first m elements hold the neighboring edges, so
+ * that the jth edge of vertex i is held in ed[i][j]. The next
+ * m elements hold a table of relations which is redundant but
+ * helps speed up the computation. It satisfies the relation
+ * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back
+ * pointer, so that ed[i+2*m]=i. The back pointers are used
+ * when rearranging the memory. */
+ int **ed;
+ /** This array holds the order of the vertices in the Voronoi
+ * cell. This array is dynamically allocated, with its current
+ * size held by current_vertices. */
+ int *nu;
+ /** This in an array with size 3*current_vertices for holding
+ * the positions of the vertices. */
+ double *pts;
+ voronoicell_base();
+ virtual ~voronoicell_base();
+ void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
+ void init_octahedron_base(double l);
+ void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
+ void translate(double x,double y,double z);
+ double volume();
+ double max_radius_squared();
+ double total_edge_distance();
+ double surface_area();
+ void centroid(double &cx,double &cy,double &cz);
+ int number_of_faces();
+ int number_of_edges();
+ void vertex_orders(std::vector<int> &v);
+ void vertices(std::vector<double> &v);
+ void vertices(double x,double y,double z,std::vector<double> &v);
+ void face_areas(std::vector<double> &v);
+ void face_orders(std::vector<int> &v);
+ void face_freq_table(std::vector<int> &v);
+ void face_vertices(std::vector<int> &v);
+ void face_perimeters(std::vector<double> &v);
+ void normals(std::vector<double> &v);
+ template<class vc_class>
+ bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id);
+ bool plane_intersects(double x,double y,double z,double rsq);
+ bool plane_intersects_guess(double x,double y,double z,double rsq);
+ void construct_relations();
+ void check_relations();
+ void check_duplicates();
+ /** Returns a list of IDs of neighboring particles
+ * corresponding to each face.
+ * \param[out] v a reference to a vector in which to return the
+ * results. If no neighbor information is
+ * available, a blank vector is returned. */
+ virtual void neighbors(std::vector<int> &v) {v.clear();}
+ /** This a virtual function that is overridden by a routine to
+ * print the neighboring particle IDs for a given vertex. By
+ * default, when no neighbor information is available, the
+ * routine does nothing.
+ * \param[in] i the vertex to consider. */
+ /** This is a simple inline function for picking out the index
+ * of the next edge counterclockwise at the current vertex.
+ * \param[in] a the index of an edge of the current vertex.
+ * \param[in] p the number of the vertex.
+ * \return 0 if a=nu[p]-1, or a+1 otherwise. */
+ inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;}
+ /** This is a simple inline function for picking out the index
+ * of the next edge clockwise from the current vertex.
+ * \param[in] a the index of an edge of the current vertex.
+ * \param[in] p the number of the vertex.
+ * \return nu[p]-1 if a=0, or a-1 otherwise. */
+ inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
+ protected:
+ /** This a one dimensional array that holds the current sizes
+ * of the memory allocations for them mep array.*/
+ int *mem;
+ /** This is a one dimensional array that holds the current
+ * number of vertices of order p that are stored in the mep[p]
+ * array. */
+ int *mec;
+ /** This is a two dimensional array for holding the information
+ * about the edges of the Voronoi cell. mep[p] is a
+ * one-dimensional array for holding the edge information about
+ * all vertices of order p, with each vertex holding 2*p+1
+ * integers of information. The total number of vertices held
+ * on mep[p] is stored in mem[p]. If the space runs out, the
+ * code allocates more using the add_memory() routine. */
+ int **mep;
+ inline void reset_edges();
+ template<class vc_class>
+ void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
+ void copy(voronoicell_base* vb);
+ private:
+ /** This is the delete stack, used to store the vertices which
+ * are going to be deleted during the plane cutting procedure.
+ */
+ int *ds,*stacke;
+ /** This is the auxiliary delete stack, which has size set by
+ * current_delete2_size. */
+ int *ds2,*stacke2;
+ /** This stores the current memory allocation for the marginal
+ * cases. */
+ int current_marginal;
+ /** This stores the total number of marginal points which are
+ * currently in the buffer. */
+ int n_marg;
+ /** This array contains a list of the marginal points, and also
+ * the outcomes of the marginal tests. */
+ int *marg;
+ /** The x coordinate of the normal vector to the test plane. */
+ double px;
+ /** The y coordinate of the normal vector to the test plane. */
+ double py;
+ /** The z coordinate of the normal vector to the test plane. */
+ double pz;
+ /** The magnitude of the normal vector to the test plane. */
+ double prsq;
+ template<class vc_class>
+ void add_memory(vc_class &vc,int i,int *stackp2);
+ template<class vc_class>
+ void add_memory_vertices(vc_class &vc);
+ template<class vc_class>
+ void add_memory_vorder(vc_class &vc);
+ void add_memory_ds(int *&stackp);
+ void add_memory_ds2(int *&stackp2);
+ template<class vc_class>
+ inline bool collapse_order1(vc_class &vc);
+ template<class vc_class>
+ inline bool collapse_order2(vc_class &vc);
+ template<class vc_class>
+ inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
+ template<class vc_class>
+ inline bool search_for_outside_edge(vc_class &vc,int &up);
+ template<class vc_class>
+ inline void add_to_stack(vc_class &vc,int lp,int *&stackp2);
+ inline bool plane_intersects_track(double x,double y,double z,double rs,double g);
+ inline void normals_search(std::vector<double> &v,int i,int j,int k);
+ inline bool search_edge(int l,int &m,int &k);
+ inline int m_test(int n,double &ans);
+ int check_marginal(int n,double &ans);
+ friend class voronoicell;
+ friend class voronoicell_neighbor;
+};
+
+/** \brief Extension of the voronoicell_base class to represent a Voronoi cell
+ * with neighbor information.
+ *
+ * This class is an extension of the voronoicell_base class, in cases when the
+ * IDs of neighboring particles associated with each face of the Voronoi cell.
+ * It contains additional data structures mne and ne for storing this
+ * information. */
+class voronoicell_neighbor : public voronoicell_base {
+ public:
+ using voronoicell_base::nplane;
+ /** This two dimensional array holds the neighbor information
+ * associated with each vertex. mne[p] is a one dimensional
+ * array which holds all of the neighbor information for
+ * vertices of order p. */
+ int **mne;
+ /** This is a two dimensional array that holds the neighbor
+ * information associated with each vertex. ne[i] points to a
+ * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
+ * neighbor information associated with the jth edge of vertex
+ * i. It is set to the ID number of the plane that made the
+ * face that is clockwise from the jth edge. */
+ int **ne;
+ voronoicell_neighbor();
+ ~voronoicell_neighbor();
+ void operator=(voronoicell_neighbor &c);
+ /** 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] (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. */
+ inline bool nplane(double x,double y,double z,double rsq,int p_id) {
+ return nplane(*this,x,y,z,rsq,p_id);
+ }
+ /** This routine calculates the modulus squared of the vector
+ * before passing it to the main nplane() routine with full
+ * arguments.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool nplane(double x,double y,double z,int p_id) {
+ double rsq=x*x+y*y+z*z;
+ return nplane(*this,x,y,z,rsq,p_id);
+ }
+ /** This version of the plane routine just makes up the plane
+ * ID to be zero. It will only be referenced if neighbor
+ * tracking is enabled.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \param[in] rsq the modulus squared of the vector.
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool plane(double x,double y,double z,double rsq) {
+ return nplane(*this,x,y,z,rsq,0);
+ }
+ /** Cuts a Voronoi cell using the influence of a particle at
+ * (x,y,z), first calculating the modulus squared of this
+ * vector before passing it to the main nplane() routine. Zero
+ * is supplied as the plane ID, which will be ignored unless
+ * neighbor tracking is enabled.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool plane(double x,double y,double z) {
+ double rsq=x*x+y*y+z*z;
+ return nplane(*this,x,y,z,rsq,0);
+ }
+ void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
+ void check_facets();
+ virtual void neighbors(std::vector<int> &v);
+
+ private:
+ int *paux1;
+ int *paux2;
+ inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
+ inline void n_add_memory_vertices(int i) {
+ int **pp=new int*[i];
+ for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
+ delete [] ne;ne=pp;
+ }
+ inline void n_add_memory_vorder(int i) {
+ int **p2=new int*[i];
+ for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
+ delete [] mne;mne=p2;
+ }
+ inline void n_set_pointer(int p,int n) {
+ ne[p]=mne[n]+n*mec[n];
+ }
+ inline void n_copy(int a,int b,int c,int d) {ne[a][b]=ne[c][d];}
+ inline void n_set(int a,int b,int c) {ne[a][b]=c;}
+ inline void n_set_aux1(int k) {paux1=mne[k]+k*mec[k];}
+ inline void n_copy_aux1(int a,int b) {paux1[b]=ne[a][b];}
+ inline void n_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
+ inline void n_set_aux2_copy(int a,int b) {
+ paux2=mne[b]+b*mec[b];
+ for(int i=0;i<b;i++) ne[a][i]=paux2[i];
+ }
+ inline void n_copy_pointer(int a,int b) {ne[a]=ne[b];}
+ inline void n_set_to_aux1(int j) {ne[j]=paux1;}
+ inline void n_set_to_aux2(int j) {ne[j]=paux2;}
+ inline void n_allocate_aux1(int i) {paux1=new int[i*mem[i]];}
+ inline void n_switch_to_aux1(int i) {delete [] mne[i];mne[i]=paux1;}
+ inline void n_copy_to_aux1(int i,int m) {paux1[m]=mne[i][m];}
+ inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
+ friend class voronoicell_base;
+};
+
+}
+
+#endif
+
diff --git a/src/PTM/ptm_voronoi_config.h b/src/PTM/ptm_voronoi_config.h
new file mode 100644
index 0000000000..86257e60cc
--- /dev/null
+++ b/src/PTM/ptm_voronoi_config.h
@@ -0,0 +1,129 @@
+// 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 config.hh
+ * \brief Master configuration file for setting various compile-time options. */
+
+#ifndef PTM_VOROPP_CONFIG_HH
+#define PTM_VOROPP_CONFIG_HH
+
+namespace voro {
+
+// These constants set the initial memory allocation for the Voronoi cell
+/** The initial memory allocation for the number of vertices. */
+const int init_vertices=256;
+/** The initial memory allocation for the maximum vertex order. */
+const int init_vertex_order=64;
+/** The initial memory allocation for the number of regular vertices of order
+ * 3. */
+const int init_3_vertices=256;
+/** The initial memory allocation for the number of vertices of higher order.
+ */
+const int init_n_vertices=8;
+/** The initial buffer size for marginal cases used by the suretest class. */
+const int init_marginal=64;
+/** The initial size for the delete stack. */
+const int init_delete_size=256;
+/** The initial size for the auxiliary delete stack. */
+const int init_delete2_size=256;
+/** The initial size for the wall pointer array. */
+const int init_wall_size=32;
+/** The default initial size for the ordering class. */
+const int init_ordering_size=4096;
+/** The initial size of the pre_container chunk index. */
+const int init_chunk_size=256;
+
+// If the initial memory is too small, the program dynamically allocates more.
+// However, if the limits below are reached, then the program bails out.
+/** The maximum memory allocation for the number of vertices. */
+const int max_vertices=16777216;
+/** The maximum memory allocation for the maximum vertex order. */
+const int max_vertex_order=2048;
+/** The maximum memory allocation for the any particular order of vertex. */
+const int max_n_vertices=16777216;
+/** The maximum buffer size for marginal cases used by the suretest class. */
+const int max_marginal=16777216;
+/** The maximum size for the delete stack. */
+const int max_delete_size=16777216;
+/** The maximum size for the auxiliary delete stack. */
+const int max_delete2_size=16777216;
+/** The maximum amount of particle memory allocated for a single region. */
+const int max_particle_memory=16777216;
+/** The maximum size for the wall pointer array. */
+const int max_wall_size=2048;
+/** The maximum size for the ordering class. */
+const int max_ordering_size=67108864;
+/** The maximum size for the pre_container chunk index. */
+const int max_chunk_size=65536;
+
+/** The chunk size in the pre_container classes. */
+const int pre_container_chunk_size=1024;
+
+#ifndef VOROPP_VERBOSE
+/** Voro++ can print a number of different status and debugging messages to
+ * notify the user of special behavior, and this macro sets the amount which
+ * are displayed. At level 0, no messages are printed. At level 1, messages
+ * about unusual cases during cell construction are printed, such as when the
+ * plane routine bails out due to floating point problems. At level 2, general
+ * messages about memory expansion are printed. At level 3, technical details
+ * about memory management are printed. */
+#define VOROPP_VERBOSE 0
+#endif
+
+/** If a point is within this distance of a cutting plane, then the code
+ * assumes that point exactly lies on the plane. */
+const double tolerance=1e-11;
+
+/** If a point is within this distance of a cutting plane, then the code stores
+ * whether this point is inside, outside, or exactly on the cutting plane in
+ * the marginal cases buffer, to prevent the test giving a different result on
+ * a subsequent evaluation due to floating point rounding errors. */
+const double tolerance2=2e-11;
+
+/** The square of the tolerance, used when deciding whether some squared
+ * quantities are large enough to be used. */
+const double tolerance_sq=tolerance*tolerance;
+
+/** A large number that is used in the computation. */
+const double large_number=1e30;
+
+/** A radius to use as a placeholder when no other information is available. */
+const double default_radius=0.5;
+
+/** The maximum number of shells of periodic images to test over. */
+const int max_unit_voro_shells=10;
+
+/** A guess for the optimal number of particles per block, used to set up the
+ * container grid. */
+const double optimal_particles=5.6;
+
+/** If this is set to 1, then the code reports any instances of particles being
+ * put outside of the container geometry. */
+#define VOROPP_REPORT_OUT_OF_BOUNDS 0
+
+/** Voro++ returns this status code if there is a file-related error, such as
+ * not being able to open file. */
+#define VOROPP_FILE_ERROR 1
+
+/** Voro++ returns this status code if there is a memory allocation error, if
+ * one of the safe memory limits is exceeded. */
+#define VOROPP_MEMORY_ERROR 2
+
+/** Voro++ returns this status code if there is any type of internal error, if
+ * it detects that representation of the Voronoi cell is inconsistent. This
+ * status code will generally indicate a bug, and the developer should be
+ * contacted. */
+#define VOROPP_INTERNAL_ERROR 3
+
+/** Voro++ returns this status code if it could not interpret the command line
+ * arguments passed to the command line utility. */
+#define VOROPP_CMD_LINE_ERROR 4
+
+}
+
+#endif
--
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