diff --git a/doc/src/Eqs/ptm_rmsd.jpg b/doc/src/Eqs/ptm_rmsd.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..2d20da706ef61194305123d5673042d2318aec23
Binary files /dev/null and b/doc/src/Eqs/ptm_rmsd.jpg differ
diff --git a/doc/src/Eqs/ptm_rmsd.tex b/doc/src/Eqs/ptm_rmsd.tex
new file mode 100644
index 0000000000000000000000000000000000000000..a9c29ce18970fa7c2e9f7c62bdf1423e2b7968a4
--- /dev/null
+++ b/doc/src/Eqs/ptm_rmsd.tex
@@ -0,0 +1,21 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
+\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
+\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
+
+\begin{document}
+
+\begin{equation*}
+\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+\norm{
+s[\vec{u_i} - \mean{\set{u}}]
+-
+\set{Q} \vec{v_i}
+}^2}
+\end{equation*}
+
+\end{document}
diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c668eb772614f237f54516fab6be48b89c86285b
--- /dev/null
+++ b/doc/src/compute_ptm_atom.txt
@@ -0,0 +1,117 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute ptm/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID ptm/atom structures threshold :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+ptm/atom = style name of this compute command
+structures = structure types to search for
+threshold = lattice distortion threshold (RMSD) :ul
+
+[Examples:]
+
+compute 1 all ptm/atom default 0.1
+compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
+compute 1 all ptm/atom all 0 :pre
+
+[Description:]
+
+Define a computation that determines the local lattice structure
+around an atom using the PTM (Polyhedral Template Matching) method.
+The PTM method is described in "(Larsen)"_#Larsen.
+
+Currently, there are seven lattice structures PTM recognizes:
+
+fcc = 1
+hcp = 2
+bcc = 3
+ico (icosahedral) = 4
+sc (simple cubic) = 5
+dcub (diamond cubic) = 6
+dhex (diamond hexagonal) = 7
+other = 8 :ul
+
+The value of the PTM structure will be 0 for atoms not in the specified
+compute group. The choice of structures to search for can be specified using the "structures"
+argument, which is a hyphen-separated list of structure keywords.
+Two convenient pre-set options are provided:
+
+default: fcc-hcp-bcc-ico
+all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
+
+The 'default' setting detects the same structures as the Common Neighbor Analysis method.
+The 'all' setting searches for all structure types. A small performance penalty is
+incurred for the diamond structures, so it is not recommended to use this option if
+it is known that the simulation does not contain diamond structures.
+
+
+PTM identifies structures using two steps. First, a graph isomorphism test is used
+to identify potential structure matches. Next, the deviation is computed between the
+local structure (in the simulation) and a template of the ideal lattice structure.
+The deviation is calculated as:
+
+:c,image(Eqs/ptm_rmsd.jpg)
+
+Here, u and v contain the coordinates of the local and ideal structures respectively,
+s is a scale factor, and Q is a rotation. The best match is identified by the
+lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
+points.
+
+The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
+a local structure is identified as disordered. Typical values are in the range 0.1-0.15,
+but larger values may be desirable at higher temperatures.
+A value of 0 is equivalent to infinity and can be used if no threshold is desired.
+
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+{ptm/atom} style.
+
+[Output info:]
+
+This compute calculates a per-atom array, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+Results are stored in the per-atom array in the following order:
+
+type
+rmsd
+interatomic distance
+qw
+qx
+qy
+qw :ul
+
+The type is a number from 0 to 8. The rmsd is a positive real number.
+The interatomic distance is computed from the scale factor in the RMSD equation.
+The (qw,qx,qy,qz) parameters represent the orientation of the local structure
+in quaternion form. The reference coordinates for each template (from which the
+orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute centro/atom"_compute_centro_atom.html
+"compute cna/atom"_compute_cna_atom.html
+
+[Default:] none
+
+:line
+
+:link(Larsen)
+[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
+
diff --git a/src/USER-PTM/LICENSE b/src/USER-PTM/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..dc1e0a5e7edd510aa8aaa9865ce08f5874fb8224
--- /dev/null
+++ b/src/USER-PTM/LICENSE
@@ -0,0 +1,7 @@
+Copyright (c) 2016 PM Larsen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/src/USER-PTM/alloy_types.cpp b/src/USER-PTM/alloy_types.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..bde51c19b1afa3568d69db0865f93f7b3ce63c74
--- /dev/null
+++ b/src/USER-PTM/alloy_types.cpp
@@ -0,0 +1,101 @@
+#include <algorithm>
+#include "ptm_constants.h"
+#include "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/USER-PTM/alloy_types.h b/src/USER-PTM/alloy_types.h
new file mode 100644
index 0000000000000000000000000000000000000000..1f2980593a8e7b84781ab1cf998b1023e30d31cf
--- /dev/null
+++ b/src/USER-PTM/alloy_types.h
@@ -0,0 +1,9 @@
+#ifndef ALLOY_TYPES_H
+#define ALLOY_TYPES_H
+
+#include "initialize_data.h"
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
+
+#endif
+
diff --git a/src/USER-PTM/canonical_coloured.cpp b/src/USER-PTM/canonical_coloured.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..af446e1a958bee79b361c512c170d68e9b0a315c
--- /dev/null
+++ b/src/USER-PTM/canonical_coloured.cpp
@@ -0,0 +1,167 @@
+#include <string.h>
+#include <climits>
+#include <algorithm>
+#include "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/USER-PTM/canonical_coloured.h b/src/USER-PTM/canonical_coloured.h
new file mode 100644
index 0000000000000000000000000000000000000000..4a7b5f5a4a6a1cd2b85687ac1a96ad63097812c8
--- /dev/null
+++ b/src/USER-PTM/canonical_coloured.h
@@ -0,0 +1,9 @@
+#ifndef CANONICAL_COLOURED_H
+#define 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/USER-PTM/cell.cpp b/src/USER-PTM/cell.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f88e310b748bc2fc65d860f6e9e6393256281235
--- /dev/null
+++ b/src/USER-PTM/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 "config.h"
+#include "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/USER-PTM/cell.h b/src/USER-PTM/cell.h
new file mode 100644
index 0000000000000000000000000000000000000000..51a0cbb9ef3129628ab7de00edfe86004b02a488
--- /dev/null
+++ b/src/USER-PTM/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 VOROPP_CELL_HH
+#define VOROPP_CELL_HH
+
+#include <vector>
+#include <cstdio>
+
+#include "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/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b6b4a9786c1175450f772c45227b4b1441c411b6
--- /dev/null
+++ b/src/USER-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/USER-PTM/compute_ptm_atom.h b/src/USER-PTM/compute_ptm_atom.h
new file mode 100644
index 0000000000000000000000000000000000000000..5c10e0c44322776e1486f10d2376dafca26e715d
--- /dev/null
+++ b/src/USER-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/USER-PTM/config.h b/src/USER-PTM/config.h
new file mode 100644
index 0000000000000000000000000000000000000000..eba69b337334b9e2982c696ca52c82f183680775
--- /dev/null
+++ b/src/USER-PTM/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 VOROPP_CONFIG_HH
+#define 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
diff --git a/src/USER-PTM/convex_hull_incremental.cpp b/src/USER-PTM/convex_hull_incremental.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..bfe173cc025746bdf6a23d75a6887e25bb0343fb
--- /dev/null
+++ b/src/USER-PTM/convex_hull_incremental.cpp
@@ -0,0 +1,363 @@
+#include <cmath>
+#include <cfloat>
+#include <string.h>
+#include <cassert>
+#include <algorithm>
+#include "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/USER-PTM/convex_hull_incremental.h b/src/USER-PTM/convex_hull_incremental.h
new file mode 100644
index 0000000000000000000000000000000000000000..d384a0457ecf71552c2da05fa243af11ef08a8dc
--- /dev/null
+++ b/src/USER-PTM/convex_hull_incremental.h
@@ -0,0 +1,27 @@
+#ifndef CONVEX_HULL_INCREMENTAL_H
+#define 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/USER-PTM/deformation_gradient.cpp b/src/USER-PTM/deformation_gradient.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..9a86dff6a31a18d1f6e8606dc9bc56962c276e3c
--- /dev/null
+++ b/src/USER-PTM/deformation_gradient.cpp
@@ -0,0 +1,37 @@
+#include "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/USER-PTM/deformation_gradient.h b/src/USER-PTM/deformation_gradient.h
new file mode 100644
index 0000000000000000000000000000000000000000..059a06fdec974e93d3fc2a0d35ddcb69feae3c91
--- /dev/null
+++ b/src/USER-PTM/deformation_gradient.h
@@ -0,0 +1,142 @@
+#ifndef DEFORMATION_GRADIENT_H
+#define 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/USER-PTM/fundamental_mappings.h b/src/USER-PTM/fundamental_mappings.h
new file mode 100644
index 0000000000000000000000000000000000000000..9030d3a2b2aba7d51089ca75523bc9c830b19dc3
--- /dev/null
+++ b/src/USER-PTM/fundamental_mappings.h
@@ -0,0 +1,180 @@
+#ifndef FUNDAMENTAL_MAPPINGS_H
+#define 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/USER-PTM/graph_data.cpp b/src/USER-PTM/graph_data.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..aea2e59eac34c10a42ccb62c49e3a69787a08061
--- /dev/null
+++ b/src/USER-PTM/graph_data.cpp
@@ -0,0 +1,2059 @@
+#include "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},
+{{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},{4,6,7},{2,4,7}}},
+
+{10,
+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},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{11,
+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},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{12,
+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},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{13,
+0,
+10,
+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},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{14,
+0,
+12,
+10,
+{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},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{15,
+0,
+22,
+10,
+{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},{5,10,11},{1,5,11},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+};
+
+graph_t graphs_bcc[NUM_BCC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{4,
+0,
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+graph_t graphs_dcub[NUM_DCUB_GRAPHS] = {
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+
+};
+
+graph_t graphs_dhex[NUM_DHEX_GRAPHS] = {
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+{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/USER-PTM/graph_data.h b/src/USER-PTM/graph_data.h
new file mode 100644
index 0000000000000000000000000000000000000000..3a8a5c7ae72ba201010c4d27a0dc8ec04aa03698
--- /dev/null
+++ b/src/USER-PTM/graph_data.h
@@ -0,0 +1,37 @@
+#ifndef GRAPH_DATA_H
+#define 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/USER-PTM/graph_tools.cpp b/src/USER-PTM/graph_tools.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..864e921b518709f1b5aeddfaa328243281cc4953
--- /dev/null
+++ b/src/USER-PTM/graph_tools.cpp
@@ -0,0 +1,52 @@
+#include <string.h>
+#include <algorithm>
+#include "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/USER-PTM/graph_tools.h b/src/USER-PTM/graph_tools.h
new file mode 100644
index 0000000000000000000000000000000000000000..791a44f9a670aa9309ce548fa5416e03aa1e4c59
--- /dev/null
+++ b/src/USER-PTM/graph_tools.h
@@ -0,0 +1,11 @@
+#ifndef GRAPH_TOOLS_H
+#define 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/USER-PTM/index_ptm.cpp b/src/USER-PTM/index_ptm.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..2683323ac564860cd531b4d65009ddc64265806a
--- /dev/null
+++ b/src/USER-PTM/index_ptm.cpp
@@ -0,0 +1,218 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "convex_hull_incremental.h"
+#include "graph_data.h"
+#include "deformation_gradient.h"
+#include "alloy_types.h"
+#include "neighbour_ordering.h"
+#include "normalize_vertices.h"
+#include "quat.h"
+#include "polar.h"
+#include "initialize_data.h"
+#include "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/USER-PTM/initialize_data.cpp b/src/USER-PTM/initialize_data.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6c177bfb70f08efcd412e4bab3e0b784412d71f0
--- /dev/null
+++ b/src/USER-PTM/initialize_data.cpp
@@ -0,0 +1,71 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "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/USER-PTM/initialize_data.h b/src/USER-PTM/initialize_data.h
new file mode 100644
index 0000000000000000000000000000000000000000..644dfea8c4309dd9790b2893a341c102925b0cd6
--- /dev/null
+++ b/src/USER-PTM/initialize_data.h
@@ -0,0 +1,61 @@
+#ifndef INITIALIZE_DATA_H
+#define INITIALIZE_DATA_H
+
+
+#include "graph_data.h"
+#include "graph_tools.h"
+#include "deformation_gradient.h"
+#include "fundamental_mappings.h"
+#include "neighbour_ordering.h"
+#include "canonical_coloured.h"
+#include "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/USER-PTM/neighbour_ordering.cpp b/src/USER-PTM/neighbour_ordering.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..8e8b016cfcdf1f7764d9e148004dd8c41883bd2f
--- /dev/null
+++ b/src/USER-PTM/neighbour_ordering.cpp
@@ -0,0 +1,203 @@
+#include <cstdlib>
+#include <cmath>
+#include <cstring>
+#include <cassert>
+#include <algorithm>
+#include "ptm_constants.h"
+#include "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/USER-PTM/neighbour_ordering.h b/src/USER-PTM/neighbour_ordering.h
new file mode 100644
index 0000000000000000000000000000000000000000..33160caa4f3c03add1084e28249229f72e2c0181
--- /dev/null
+++ b/src/USER-PTM/neighbour_ordering.h
@@ -0,0 +1,13 @@
+#ifndef NEIGHBOUR_ORDERING_H
+#define 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/USER-PTM/normalize_vertices.cpp b/src/USER-PTM/normalize_vertices.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..61dca5006f6d8c8a47f96cc65e8e541d89fafe5e
--- /dev/null
+++ b/src/USER-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/USER-PTM/normalize_vertices.h b/src/USER-PTM/normalize_vertices.h
new file mode 100644
index 0000000000000000000000000000000000000000..e18990cd9bdbb091db96b8de51181e92816aeaac
--- /dev/null
+++ b/src/USER-PTM/normalize_vertices.h
@@ -0,0 +1,8 @@
+#ifndef NORMALIZE_VERTICES_H
+#define 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/USER-PTM/polar.cpp b/src/USER-PTM/polar.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..fdb759a1f321057208f99e1261677c4b7693537c
--- /dev/null
+++ b/src/USER-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 "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/USER-PTM/polar.h b/src/USER-PTM/polar.h
new file mode 100644
index 0000000000000000000000000000000000000000..3ec025b8068b3b315cb2b125d2881c1bebfbbe66
--- /dev/null
+++ b/src/USER-PTM/polar.h
@@ -0,0 +1,12 @@
+#ifndef POLAR_H
+#define 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/USER-PTM/ptm_constants.h b/src/USER-PTM/ptm_constants.h
new file mode 100644
index 0000000000000000000000000000000000000000..f868f51e843baf604f3f034fb3e447560bd4ac49
--- /dev/null
+++ b/src/USER-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/USER-PTM/ptm_functions.h b/src/USER-PTM/ptm_functions.h
new file mode 100644
index 0000000000000000000000000000000000000000..69141a37c47c8e8903ef3e8678dab62ce18ccad6
--- /dev/null
+++ b/src/USER-PTM/ptm_functions.h
@@ -0,0 +1,27 @@
+#ifndef PTM_FUNCTIONS_H
+#define PTM_FUNCTIONS_H
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "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/USER-PTM/quat.cpp b/src/USER-PTM/quat.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f55aff3d2b923d7ced41a49ee46140a13ce8613d
--- /dev/null
+++ b/src/USER-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/USER-PTM/quat.h b/src/USER-PTM/quat.h
new file mode 100644
index 0000000000000000000000000000000000000000..725086322cb2170d0d1ea262ff7f44d95ef84198
--- /dev/null
+++ b/src/USER-PTM/quat.h
@@ -0,0 +1,32 @@
+#ifndef QUAT_H
+#define 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/USER-PTM/structure_matcher.cpp b/src/USER-PTM/structure_matcher.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..dad8e3599a0daab6466dc50f64e365e31180d5ab
--- /dev/null
+++ b/src/USER-PTM/structure_matcher.cpp
@@ -0,0 +1,294 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "convex_hull_incremental.h"
+#include "canonical_coloured.h"
+#include "graph_data.h"
+#include "graph_tools.h"
+#include "normalize_vertices.h"
+#include "polar.h"
+#include "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/USER-PTM/structure_matcher.h b/src/USER-PTM/structure_matcher.h
new file mode 100644
index 0000000000000000000000000000000000000000..25e80a94e1a2f3e695129ca5c1efa8e599a45b3b
--- /dev/null
+++ b/src/USER-PTM/structure_matcher.h
@@ -0,0 +1,21 @@
+#ifndef STRUCTURE_MATCHER_H
+#define STRUCTURE_MATCHER_H
+
+#include "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
+