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Merge pull request #1339 from pmla/ptm-update

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USER-PTM package update
This commit is contained in:
Axel Kohlmeyer
2019-02-18 19:43:31 +01:00
committed by GitHub
parent 9207b8814e f0a410aa96
commit 12bec9cbad
36 changed files with 5412 additions and 4083 deletions
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16
doc/src/compute_ptm_atom.txt
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@ -38,20 +38,20 @@ ico (icosahedral) = 4
sc (simple cubic) = 5 sc (simple cubic) = 5
dcub (diamond cubic) = 6 dcub (diamond cubic) = 6
dhex (diamond hexagonal) = 7 dhex (diamond hexagonal) = 7
other = 8 :ul graphene = 8 :ul
The value of the PTM structure will be 0 for atoms not in the specified The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
compute group. The choice of structures to search for can be specified using the "structures" 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. argument, which is a hyphen-separated list of structure keywords.
Two convenient pre-set options are provided: Two convenient pre-set options are provided:
default: fcc-hcp-bcc-ico default: fcc-hcp-bcc-ico
all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul
The 'default' setting detects the same structures as the Common Neighbor Analysis method. 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 The 'all' setting searches for all structure types. A performance penalty is
incurred for the diamond structures, so it is not recommended to use this option if incurred for the diamond and graphene structures, so it is not recommended to use this option if
it is known that the simulation does not contain diamond structures. it is known that the simulation does not contain these structures.
PTM identifies structures using two steps. First, a graph isomorphism test is used PTM identifies structures using two steps. First, a graph isomorphism test is used
@ -93,9 +93,9 @@ interatomic distance
qw qw
qx qx
qy qy
qw :ul qz :ul
The type is a number from 0 to 8. The rmsd is a positive real number. The type is a number from -1 to 8. The rmsd is a positive real number.
The interatomic distance is computed from the scale factor in the RMSD equation. 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 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 in quaternion form. The reference coordinates for each template (from which the

47
examples/USER/ptm/ptm_example.in Normal file
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@ -0,0 +1,47 @@
# LAMMPS Input File for Grain Boundaries
# Mark Tschopp, Dec2009
# Modified by PM Larsen to demonstrate the use of PTM in LAMMPS
# This file will generate a single Sigma5(310) STGB and run PTM
# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic
# ---------- Create Sigma5(310) Structure ---------
lattice fcc 4.05
region whole block 0.000000 12.807225 -64.0361225 64.0361225 0.000000 4.050000 units box
create_box 2 whole
region upper block INF INF 0.000000 64.0361225 INF INF units box
lattice fcc 4.05 orient x 0 3 1 orient y 0 -1 3 orient z 1 0 0
create_atoms 1 region upper
region lower block INF INF -64.0361225 0.000000 INF INF units box
lattice fcc 4.05 orient x 0 3 -1 orient y 0 1 3 orient z 1 0 0
create_atoms 2 region lower
group upper type 1
group lower type 2
mass 1 1.0
mass 2 1.0
# ---------- Define Interatomic Potential ---------------------
pair_style lj/cut 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
# ---------- Displace atoms and delete overlapping atoms ---------------------
displace_atoms upper move 0 0 0 units lattice
delete_atoms overlap 0.35 lower upper
# ---------- Define PTM settings (default structures, RMSD threshold of 0.1) -------------------
compute ptm all ptm/atom default 0.1
# ---------- Dump data into Data file -------------
reset_timestep 0
dump 1 all cfg 10000 dump.ptm_example_*.cfg mass type xs ys zs c_ptm[1] c_ptm[2] c_ptm[3] c_ptm[4] c_ptm[5] c_ptm[6] c_ptm[7]
dump_modify 1 element Al Al
run 1
print "All done"

1
src/USER-PTM/README
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@ -24,3 +24,4 @@ Preprint available at:
http://arxiv.org/abs/1603.05143 http://arxiv.org/abs/1603.05143
Contact email: pmla@mit.edu

123
src/USER-PTM/compute_ptm_atom.cpp
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@ -3,9 +3,9 @@
http://lammps.sandia.gov, Sandia National Laboratories http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed certain rights in this software. This software is distributed
under under
the GNU General Public License. the GNU General Public License.
@ -20,6 +20,7 @@ under
#include <cmath> #include <cmath>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include <vector>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
@ -36,10 +37,9 @@ under
#include "ptm_functions.h" #include "ptm_functions.h"
#define MAX_NEIGHBORS 30
#define NUM_COLUMNS 7 #define NUM_COLUMNS 7
#define UNKNOWN 0 #define PTM_LAMMPS_UNKNOWN -1
#define OTHER 8 #define PTM_LAMMPS_OTHER 0
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -69,7 +69,9 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
char *ptr = structures; char *ptr = structures;
const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc", const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc",
"dcub", "dhex", "all", "default"}; "dcub", "dhex", "graphene", "all", "default"};
int num_strings = sizeof(strings) / sizeof(const char*);
int32_t flags[] = { int32_t flags[] = {
PTM_CHECK_FCC, PTM_CHECK_FCC,
PTM_CHECK_HCP, PTM_CHECK_HCP,
@ -78,6 +80,7 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
PTM_CHECK_SC, PTM_CHECK_SC,
PTM_CHECK_DCUB, PTM_CHECK_DCUB,
PTM_CHECK_DHEX, PTM_CHECK_DHEX,
PTM_CHECK_GRAPHENE,
PTM_CHECK_ALL, PTM_CHECK_ALL,
PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
@ -85,7 +88,7 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
while (*ptr != '\0') { while (*ptr != '\0') {
bool found = false; bool found = false;
for (int i = 0; i < 9; i++) { for (int i = 0; i < num_strings; i++) {
int len = strlen(strings[i]); int len = strlen(strings[i]);
if (strncmp(ptr, strings[i], len) == 0) { if (strncmp(ptr, strings[i], len) == 0) {
input_flags |= flags[i]; input_flags |= flags[i];
@ -152,10 +155,21 @@ void ComputePTMAtom::init() {
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; } void ComputePTMAtom::init_list(int /* id */, NeighList *ptr) { list = ptr; }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
typedef struct
{
double **x;
int *numneigh;
int **firstneigh;
int *ilist;
int nlocal;
} ptmnbrdata_t;
typedef struct { typedef struct {
int index; int index;
double d; double d;
@ -165,38 +179,59 @@ static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) {
return a.d < b.d; return a.d < b.d;
} }
static int get_neighbors(double *pos, int jnum, int *jlist, double **x, static int get_neighbours(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3])
double (*nbr)[3]) { {
ptmnbrdata_t* data = (ptmnbrdata_t*)vdata;
ptmnbr_t *nbr_order = new ptmnbr_t[jnum]; double **x = data->x;
double *pos = x[atom_index];
int *jlist = NULL;
int jnum = 0;
if (atom_index < data->nlocal) {
jlist = data->firstneigh[atom_index];
jnum = data->numneigh[atom_index];
}
else {
jlist = data->firstneigh[central_index];
jnum = data->numneigh[central_index];
}
std::vector<ptmnbr_t> nbr_order;
for (int jj = 0; jj < jnum; jj++) { for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj]; int j = jlist[jj];
j &= NEIGHMASK; j &= NEIGHMASK;
if (j == atom_index)
continue;
double dx = pos[0] - x[j][0]; double dx = pos[0] - x[j][0];
double dy = pos[1] - x[j][1]; double dy = pos[1] - x[j][1];
double dz = pos[2] - x[j][2]; double dz = pos[2] - x[j][2];
double rsq = dx * dx + dy * dy + dz * dz; double rsq = dx * dx + dy * dy + dz * dz;
nbr_order[jj].index = j; ptmnbr_t nbr = {j, rsq};
nbr_order[jj].d = rsq; nbr_order.push_back(nbr);
} }
std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare); std::sort(nbr_order.begin(), nbr_order.end(), &sorthelper_compare);
int num_nbrs = std::min(MAX_NEIGHBORS, jnum); int num_nbrs = std::min(num - 1, (int)nbr_order.size());
nbr[0][0] = nbr[0][1] = nbr[0][2] = 0; nbr_pos[0][0] = nbr_pos[0][1] = nbr_pos[0][2] = 0;
nbr_indices[0] = atom_index;
numbers[0] = 0;
for (int jj = 0; jj < num_nbrs; jj++) { for (int jj = 0; jj < num_nbrs; jj++) {
int j = nbr_order[jj].index; int j = nbr_order[jj].index;
nbr[jj + 1][0] = x[j][0] - pos[0]; nbr_pos[jj + 1][0] = x[j][0] - pos[0];
nbr[jj + 1][1] = x[j][1] - pos[1]; nbr_pos[jj + 1][1] = x[j][1] - pos[1];
nbr[jj + 1][2] = x[j][2] - pos[2]; nbr_pos[jj + 1][2] = x[j][2] - pos[2];
nbr_indices[jj + 1] = j;
numbers[jj + 1] = 0;
} }
delete[] nbr_order; return num_nbrs + 1;
return num_nbrs;
} }
void ComputePTMAtom::compute_peratom() { void ComputePTMAtom::compute_peratom() {
@ -228,51 +263,29 @@ void ComputePTMAtom::compute_peratom() {
double **x = atom->x; double **x = atom->x;
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; ptmnbrdata_t nbrlist = {x, numneigh, firstneigh, ilist, atom->nlocal};
for (int ii = 0; ii < inum; ii++) { for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii]; int i = ilist[ii];
output[i][0] = UNKNOWN; output[i][0] = PTM_LAMMPS_UNKNOWN;
if (!(mask[i] & groupbit)) if (!(mask[i] & groupbit))
continue; continue;
double *pos = x[i];
int *jlist = firstneigh[i];
int jnum = numneigh[i]; int jnum = numneigh[i];
if (jnum <= 0) if (jnum <= 0)
continue; 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 // now run PTM
int8_t mapping[MAX_NEIGHBORS + 1];
int32_t type, alloy_type; int32_t type, alloy_type;
double scale, rmsd, interatomic_distance, lattice_constant; double scale, rmsd, interatomic_distance;
double q[4], F[9], F_res[3], U[9], P[9]; double q[4];
ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type, bool standard_orientations = false;
&alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping, ptm_index(local_handle, i, get_neighbours, (void*)&nbrlist,
&interatomic_distance, &lattice_constant); input_flags, standard_orientations,
&type, &alloy_type, &scale, &rmsd, q,
NULL, NULL, NULL, NULL, &interatomic_distance, NULL, NULL);
if (rmsd > rmsd_threshold) { if (rmsd > rmsd_threshold) {
type = PTM_MATCH_NONE; type = PTM_MATCH_NONE;
@ -280,8 +293,10 @@ void ComputePTMAtom::compute_peratom() {
// printf("%d type=%d rmsd=%f\n", i, type, rmsd); // printf("%d type=%d rmsd=%f\n", i, type, rmsd);
if (type == PTM_MATCH_NONE) if (type == PTM_MATCH_NONE) {
type = OTHER; type = PTM_LAMMPS_OTHER;
rmsd = INFINITY;
}
output[i][0] = type; output[i][0] = type;
output[i][1] = rmsd; output[i][1] = rmsd;

136
src/USER-PTM/ptm_alloy_types.cpp
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@ -1,3 +1,12 @@
/*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.
*/
#include <algorithm> #include <algorithm>
#include "ptm_constants.h" #include "ptm_constants.h"
#include "ptm_initialize_data.h" #include "ptm_initialize_data.h"
@ -6,98 +15,107 @@ namespace ptm {
#define NUM_ALLOY_TYPES 3 #define NUM_ALLOY_TYPES 3
static uint32_t typedata[NUM_ALLOY_TYPES][3] = { static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
{PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe}, {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x00000db6},
{PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e}, {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x00000492},
{PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe}, {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe},
}; };
static bool test_pure(int num_nbrs, int32_t* numbers) static bool test_pure(int num_nbrs, int32_t* numbers)
{ {
for (int i=1;i<num_nbrs + 1;i++) for (int i=1;i<num_nbrs + 1;i++)
if (numbers[i] != numbers[0]) if (numbers[i] != numbers[0])
return false; return false;
return true; return true;
} }
static bool test_binary(int num_nbrs, int32_t* numbers) static bool test_binary(int num_nbrs, int32_t* numbers)
{ {
int a = numbers[0], b = -1; int a = numbers[0], b = -1;
for (int i=1;i<num_nbrs + 1;i++) for (int i=1;i<num_nbrs + 1;i++)
{ {
if (numbers[i] != a) if (numbers[i] != a)
{ {
if (b == -1) if (b == -1)
b = numbers[i]; b = numbers[i];
else if (numbers[i] != b) else if (numbers[i] != b)
return false; return false;
} }
} }
return true; return true;
} }
static bool test_shell_structure(const refdata_t* ref, int8_t* mapping, int32_t* numbers, int num_inner) static bool test_shell_structure(const refdata_t* ref, int8_t* mapping, int32_t* numbers, int num_inner)
{ {
int8_t binary[PTM_MAX_POINTS]; int8_t binary[PTM_MAX_POINTS];
for (int i=0;i<ref->num_nbrs+1;i++) for (int i=0;i<ref->num_nbrs+1;i++)
binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
for (int i=1;i<num_inner + 1;i++) for (int i=1;i<num_inner + 1;i++)
if (binary[i] == binary[0]) if (binary[i] == binary[0])
return false; return false;
for (int i=num_inner+1;i<ref->num_nbrs+1;i++) for (int i=num_inner+1;i<ref->num_nbrs+1;i++)
if (binary[i] != binary[0]) if (binary[i] != binary[0])
return false; return false;
return true; return true;
} }
static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers) static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
{ {
int8_t binary[PTM_MAX_POINTS]; int8_t binary[PTM_MAX_POINTS];
for (int i=0;i<ref->num_nbrs+1;i++) for (int i=0;i<ref->num_nbrs+1;i++)
binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
int8_t temp[PTM_MAX_POINTS]; int8_t temp[PTM_MAX_POINTS];
uint32_t best = 0xFFFFFFFF; uint32_t best = 0xFFFFFFFF;
for (int j=0;j<ref->num_mappings;j++) for (int j=0;j<ref->num_mappings;j++)
{ {
for (int i=0;i<ref->num_nbrs+1;i++) for (int i=0;i<ref->num_nbrs+1;i++)
temp[ref->mapping[j][i]] = binary[i]; temp[ref->mapping[j][i]] = binary[i];
uint32_t code = 0; uint32_t code = 0;
for (int i=0;i<ref->num_nbrs+1;i++) for (int i=0;i<ref->num_nbrs+1;i++)
code |= (temp[i] << i); code |= (temp[i] << i);
best = std::min(best, code); best = std::min(best, code);
} }
return best; return best;
} }
int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers) int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
{ {
if (test_pure(ref->num_nbrs, numbers)) for (int i=0;i<ref->num_nbrs+1;i++)
return PTM_ALLOY_PURE; if (numbers[i] == -1)
return PTM_ALLOY_NONE;
if (!test_binary(ref->num_nbrs, numbers)) if (test_pure(ref->num_nbrs, numbers))
return PTM_ALLOY_NONE; return PTM_ALLOY_PURE;
uint32_t code = canonical_alloy_representation(ref, mapping, numbers); if (!test_binary(ref->num_nbrs, numbers))
for (int i=0;i<NUM_ALLOY_TYPES;i++) return PTM_ALLOY_NONE;
if ((uint32_t)ref->type == typedata[i][0] && code == typedata[i][2])
return typedata[i][1];
if (ref->type == PTM_MATCH_BCC) uint32_t code = canonical_alloy_representation(ref, mapping, numbers);
if (test_shell_structure(ref, mapping, numbers, 8)) for (int i=0;i<NUM_ALLOY_TYPES;i++)
return PTM_ALLOY_B2; if ((uint32_t)ref->type == typedata[i][0] && code == typedata[i][2])
return typedata[i][1];
if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX) if (ref->type == PTM_MATCH_BCC)
if (test_shell_structure(ref, mapping, numbers, 4)) if (test_shell_structure(ref, mapping, numbers, 8))
return PTM_ALLOY_SIC; return PTM_ALLOY_B2;
return PTM_ALLOY_NONE; if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)
if (test_shell_structure(ref, mapping, numbers, 4))
return PTM_ALLOY_SIC;
if (ref->type == PTM_MATCH_GRAPHENE)
if (test_shell_structure(ref, mapping, numbers, 3))
return PTM_ALLOY_BN;
return PTM_ALLOY_NONE;
} }
} }

9
src/USER-PTM/ptm_alloy_types.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_ALLOY_TYPES_H #ifndef PTM_ALLOY_TYPES_H
#define PTM_ALLOY_TYPES_H #define PTM_ALLOY_TYPES_H

127
src/USER-PTM/ptm_alt_templates.h Normal file
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@ -0,0 +1,127 @@
/*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.
*/
#ifndef PTM_ALT_TEMPLATES_H
#define PTM_ALT_TEMPLATES_H
#include <cmath>
const double ptm_template_hcp_alt1[PTM_NUM_POINTS_HCP][3] = {
{ 0, 0, 0 },
{ 1, 0, 0 },
{ -0.5, -sqrt(3)/2, 0 },
{ -0.5, -sqrt(3)/6, -sqrt(6)/3 },
{ 0, sqrt(3)/3, -sqrt(6)/3 },
{ 0.5, -sqrt(3)/6, -sqrt(6)/3 },
{ -1, 0, 0 },
{ -0.5, sqrt(3)/2, 0 },
{ 0.5, sqrt(3)/2, 0 },
{ 0.5, -sqrt(3)/2, 0 },
{ 0.5, -sqrt(3)/6, sqrt(6)/3 },
{ 0, sqrt(3)/3, sqrt(6)/3 },
{ -0.5, -sqrt(3)/6, sqrt(6)/3 },
};
const double ptm_template_dcub_alt1[PTM_NUM_POINTS_DCUB][3] = {
{ 0, 0, 0 },
{ 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) },
{ 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) },
{ -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) },
{ -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) },
{ 8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) },
{ 0, -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) },
{ 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 },
{ 0, 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) },
{ 8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) },
{ 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 },
{ -8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) },
{ 0, -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) },
{ -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 },
{ -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 },
{ -8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) },
{ 0, 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) },
};
const double ptm_template_dhex_alt1[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, 0, 4*sqrt(3)/(sqrt(3)+6*sqrt(2)) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
};
const double ptm_template_dhex_alt2[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, 0, -4*sqrt(3)/(sqrt(3)+6*sqrt(2)) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
};
const double ptm_template_dhex_alt3[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, 0, -4*sqrt(3)/(sqrt(3)+6*sqrt(2)) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
};
const double ptm_template_graphene_alt1[PTM_NUM_POINTS_GRAPHENE][3] = {
{ 0, 0, 0 },
{ 3*sqrt(3)/22-9./11, -3./22+3*sqrt(3)/11, 0 },
{ 9./11-3*sqrt(3)/22, -3./22+3*sqrt(3)/11, 0 },
{ 0, -6*sqrt(3)/11+3./11, 0 },
{ -18./11+3*sqrt(3)/11, 0, 0 },
{ 3*sqrt(3)/22-9./11, -9./22+9*sqrt(3)/11, 0 },
{ 9./11-3*sqrt(3)/22, -9./22+9*sqrt(3)/11, 0 },
{ -3*sqrt(3)/11+18./11, 0, 0 },
{ 9./11-3*sqrt(3)/22, -9*sqrt(3)/11+9./22, 0 },
{ 3*sqrt(3)/22-9./11, -9*sqrt(3)/11+9./22, 0 },
};
#endif

253
src/USER-PTM/ptm_canonical_coloured.cpp
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@ -1,3 +1,12 @@
/*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.
*/
#include <cstring> #include <cstring>
#include <climits> #include <climits>
#include <algorithm> #include <algorithm>
@ -8,162 +17,162 @@ namespace ptm {
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) 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]; bool m[PTM_MAX_NBRS][PTM_MAX_NBRS];
memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS); memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS);
int8_t index[PTM_MAX_NBRS]; int8_t index[PTM_MAX_NBRS];
memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS); memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS);
int n = 0; int n = 0;
index[a] = colours[a] * num_nodes + n++; index[a] = colours[a] * num_nodes + n++;
if (index[a] > best_code[0]) if (index[a] > best_code[0])
return false; return false;
bool winning = false; bool winning = false;
if (index[a] < best_code[0]) if (index[a] < best_code[0])
{ {
best_code[0] = index[a]; best_code[0] = index[a];
winning = true; winning = true;
} }
int c = -1; int c = -1;
for (int it=1;it<2*num_edges;it++) for (int it=1;it<2*num_edges;it++)
{ {
bool newvertex = index[b] == -1; bool newvertex = index[b] == -1;
if (newvertex) if (newvertex)
index[b] = colours[b] * num_nodes + n++; index[b] = colours[b] * num_nodes + n++;
if (!winning && index[b] > best_code[it]) if (!winning && index[b] > best_code[it])
return false; return false;
if (winning || index[b] < best_code[it]) if (winning || index[b] < best_code[it])
{ {
winning = true; winning = true;
best_code[it] = index[b]; best_code[it] = index[b];
} }
if (newvertex) if (newvertex)
{ {
//When a new vertex is reached, take the right-most edge //When a new vertex is reached, take the right-most edge
//relative to the edge on which the vertex is reached. //relative to the edge on which the vertex is reached.
c = common[a][b]; c = common[a][b];
} }
else if (m[b][a] == false) else if (m[b][a] == false)
{ {
//When an old vertex is reached on a new path, go back //When an old vertex is reached on a new path, go back
//in the opposite direction. //in the opposite direction.
c = a; c = a;
} }
else else
{ {
//When an old vertex is reached on an old path, leave the //When an old vertex is reached on an old path, leave the
//vertex on the right-most edge that has not previously //vertex on the right-most edge that has not previously
//been traversed in that direction. //been traversed in that direction.
c = common[a][b]; c = common[a][b];
while (m[b][c] == true) while (m[b][c] == true)
c = common[c][b]; c = common[c][b];
} }
m[a][b] = true; m[a][b] = true;
a = b; a = b;
b = c; b = c;
} }
if (winning) if (winning)
{ {
memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes); memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes);
return true; return true;
} }
return false; 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) 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}}; int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}};
int num_edges = 3 * num_facets / 2; int num_edges = 3 * num_facets / 2;
if (!build_facet_map(num_facets, facets, common)) if (!build_facet_map(num_facets, facets, common))
return -1; return -1;
memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES); memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES);
bool equal = true; bool equal = true;
for (int i = 1;i<num_nodes;i++) for (int i = 1;i<num_nodes;i++)
if (degree[i] != degree[0] || colours[i] != colours[0]) if (degree[i] != degree[0] || colours[i] != colours[0])
equal = false; equal = false;
if (equal) if (equal)
{ {
weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, facets[0][0], facets[0][1]); weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, facets[0][0], facets[0][1]);
} }
else else
{ {
uint32_t best_degree = 0; uint32_t best_degree = 0;
for (int i = 0;i<num_facets;i++) for (int i = 0;i<num_facets;i++)
{ {
int a = facets[i][0]; int a = facets[i][0];
int b = facets[i][1]; int b = facets[i][1];
int c = facets[i][2]; int c = facets[i][2];
//int da = colours[a] * num_nodes + degree[a]; //int da = colours[a] * num_nodes + degree[a];
//int db = colours[b] * num_nodes + degree[b]; //int db = colours[b] * num_nodes + degree[b];
//int dc = colours[c] * num_nodes + degree[c]; //int dc = colours[c] * num_nodes + degree[c];
int da = degree[a]; int da = degree[a];
int db = degree[b]; int db = degree[b];
int dc = degree[c]; 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 << 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 << 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)); 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++) for (int i = 0;i<num_facets;i++)
{ {
int a = facets[i][0]; int a = facets[i][0];
int b = facets[i][1]; int b = facets[i][1];
int c = facets[i][2]; int c = facets[i][2];
//int da = colours[a] * num_nodes + degree[a]; //int da = colours[a] * num_nodes + degree[a];
//int db = colours[b] * num_nodes + degree[b]; //int db = colours[b] * num_nodes + degree[b];
//int dc = colours[c] * num_nodes + degree[c]; //int dc = colours[c] * num_nodes + degree[c];
int da = degree[a]; int da = degree[a];
int db = degree[b]; int db = degree[b];
int dc = degree[c]; int dc = degree[c];
if (best_degree == (((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0))) 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); 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))) 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); 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))) 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); weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, c, a);
} }
} }
for (int i = num_nodes-1;i>=0;i--) for (int i = num_nodes-1;i>=0;i--)
canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1; canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1;
canonical_labelling[0] = 0; canonical_labelling[0] = 0;
uint64_t hash = 0; uint64_t hash = 0;
for (int i = 0;i<2 * num_edges;i++) for (int i = 0;i<2 * num_edges;i++)
{ {
uint64_t e = best_code[i]; uint64_t e = best_code[i];
e += i % 8; e += i % 8;
e &= 0xF; e &= 0xF;
e <<= (4 * i) % 64; e <<= (4 * i) % 64;
hash ^= e; hash ^= e;
} }
*p_hash = hash; *p_hash = hash;
return PTM_NO_ERROR; return PTM_NO_ERROR;
} }
} }

9
src/USER-PTM/ptm_canonical_coloured.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_CANONICAL_COLOURED_H #ifndef PTM_CANONICAL_COLOURED_H
#define PTM_CANONICAL_COLOURED_H #define PTM_CANONICAL_COLOURED_H

300
src/USER-PTM/ptm_constants.h
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@ -1,45 +1,59 @@
/*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.
*/
#ifndef PTM_CONSTANTS_H #ifndef PTM_CONSTANTS_H
#define PTM_CONSTANTS_H #define PTM_CONSTANTS_H
#include <cmath>
//------------------------------------ //------------------------------------
// definitions // definitions
//------------------------------------ //------------------------------------
#define PTM_NO_ERROR 0 #define PTM_NO_ERROR 0
#define PTM_CHECK_FCC (1 << 0) #define PTM_CHECK_FCC (1 << 0)
#define PTM_CHECK_HCP (1 << 1) #define PTM_CHECK_HCP (1 << 1)
#define PTM_CHECK_BCC (1 << 2) #define PTM_CHECK_BCC (1 << 2)
#define PTM_CHECK_ICO (1 << 3) #define PTM_CHECK_ICO (1 << 3)
#define PTM_CHECK_SC (1 << 4) #define PTM_CHECK_SC (1 << 4)
#define PTM_CHECK_DCUB (1 << 5) #define PTM_CHECK_DCUB (1 << 5)
#define PTM_CHECK_DHEX (1 << 6) #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_GRAPHENE (1 << 7)
#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_CHECK_DEFAULT (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 | PTM_CHECK_GRAPHENE)
#define PTM_MATCH_NONE 0 #define PTM_MATCH_NONE 0
#define PTM_MATCH_FCC 1 #define PTM_MATCH_FCC 1
#define PTM_MATCH_HCP 2 #define PTM_MATCH_HCP 2
#define PTM_MATCH_BCC 3 #define PTM_MATCH_BCC 3
#define PTM_MATCH_ICO 4 #define PTM_MATCH_ICO 4
#define PTM_MATCH_SC 5 #define PTM_MATCH_SC 5
#define PTM_MATCH_DCUB 6 #define PTM_MATCH_DCUB 6
#define PTM_MATCH_DHEX 7 #define PTM_MATCH_DHEX 7
#define PTM_MATCH_GRAPHENE 8
#define PTM_ALLOY_NONE 0 #define PTM_ALLOY_NONE 0
#define PTM_ALLOY_PURE 1 #define PTM_ALLOY_PURE 1
#define PTM_ALLOY_L10 2 #define PTM_ALLOY_L10 2
#define PTM_ALLOY_L12_CU 3 #define PTM_ALLOY_L12_CU 3
#define PTM_ALLOY_L12_AU 4 #define PTM_ALLOY_L12_AU 4
#define PTM_ALLOY_B2 5 #define PTM_ALLOY_B2 5
#define PTM_ALLOY_SIC 6 #define PTM_ALLOY_SIC 6
#define PTM_ALLOY_BN 7
#define PTM_MAX_INPUT_POINTS 35 #define PTM_MAX_INPUT_POINTS 19
#define PTM_MAX_NBRS 16 #define PTM_MAX_NBRS 16
#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) #define PTM_MAX_POINTS (PTM_MAX_NBRS + 1)
#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 #define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4
#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 #define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6
//------------------------------------ //------------------------------------
@ -52,16 +66,18 @@
#define PTM_NUM_NBRS_SC 6 #define PTM_NUM_NBRS_SC 6
#define PTM_NUM_NBRS_DCUB 16 #define PTM_NUM_NBRS_DCUB 16
#define PTM_NUM_NBRS_DHEX 16 #define PTM_NUM_NBRS_DHEX 16
#define PTM_NUM_NBRS_GRAPHENE 9
#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1) #define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1)
#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 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_BCC (PTM_NUM_NBRS_BCC + 1)
#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 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_SC (PTM_NUM_NBRS_SC + 1)
#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1) #define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1)
#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) #define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1)
#define PTM_NUM_POINTS_GRAPHENE (PTM_NUM_NBRS_GRAPHENE + 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}; const int ptm_num_nbrs[9] = {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, PTM_NUM_NBRS_GRAPHENE};
//------------------------------------ //------------------------------------
// template structures // template structures
@ -69,106 +85,134 @@ const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS
//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 //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. }, const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = {
{ 0. , 0.707106781187, 0.707106781187 }, { 0, 0, 0 },
{ 0. , -0.707106781187, -0.707106781187 }, { sqrt(2)/2, sqrt(2)/2, 0 },
{ 0. , 0.707106781187, -0.707106781187 }, { 0, sqrt(2)/2, sqrt(2)/2 },
{ 0. , -0.707106781187, 0.707106781187 }, { sqrt(2)/2, 0, sqrt(2)/2 },
{ 0.707106781187, 0. , 0.707106781187 }, { -sqrt(2)/2, -sqrt(2)/2, 0 },
{ -0.707106781187, 0. , -0.707106781187 }, { 0, -sqrt(2)/2, -sqrt(2)/2 },
{ 0.707106781187, 0. , -0.707106781187 }, { -sqrt(2)/2, 0, -sqrt(2)/2 },
{ -0.707106781187, 0. , 0.707106781187 }, { -sqrt(2)/2, sqrt(2)/2, 0 },
{ 0.707106781187, 0.707106781187, 0. }, { 0, -sqrt(2)/2, sqrt(2)/2 },
{ -0.707106781187, -0.707106781187, 0. }, { -sqrt(2)/2, 0, sqrt(2)/2 },
{ 0.707106781187, -0.707106781187, 0. }, { sqrt(2)/2, -sqrt(2)/2, 0 },
{ -0.707106781187, 0.707106781187, 0. } }; { 0, sqrt(2)/2, -sqrt(2)/2 },
{ sqrt(2)/2, 0, -sqrt(2)/2 },
};
const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. }, const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = {
{ 0.707106781186, 0. , 0.707106781186 }, { 0, 0, 0 },
{ -0.235702260395, -0.942809041583, -0.235702260395 }, { 0.5, -sqrt(3)/2, 0 },
{ 0.707106781186, 0.707106781186, 0. }, { -1, 0, 0 },
{ -0.235702260395, -0.235702260395, -0.942809041583 }, { -0.5, sqrt(3)/6, -sqrt(6)/3 },
{ 0. , 0.707106781186, 0.707106781186 }, { 0.5, sqrt(3)/6, -sqrt(6)/3 },
{ -0.942809041583, -0.235702260395, -0.235702260395 }, { 0, -sqrt(3)/3, -sqrt(6)/3 },
{ -0.707106781186, 0.707106781186, 0. }, { -0.5, sqrt(3)/2, 0 },
{ 0. , 0.707106781186, -0.707106781186 }, { 0.5, sqrt(3)/2, 0 },
{ 0.707106781186, 0. , -0.707106781186 }, { 1, 0, 0 },
{ 0.707106781186, -0.707106781186, 0. }, { -0.5, -sqrt(3)/2, 0 },
{ -0.707106781186, 0. , 0.707106781186 }, { 0, -sqrt(3)/3, sqrt(6)/3 },
{ 0. , -0.707106781186, 0.707106781186 } }; { 0.5, sqrt(3)/6, sqrt(6)/3 },
{ -0.5, sqrt(3)/6, sqrt(6)/3 },
};
const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. }, const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = {
{ -0.541451884327, -0.541451884327, -0.541451884327 }, { 0, 0, 0 },
{ 0.541451884327, 0.541451884327, 0.541451884327 }, { 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2 },
{ 0.541451884327, -0.541451884327, -0.541451884327 }, { 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2 },
{ -0.541451884327, 0.541451884327, 0.541451884327 }, { 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3 },
{ -0.541451884327, 0.541451884327, -0.541451884327 }, { 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2 },
{ 0.541451884327, -0.541451884327, 0.541451884327 }, { 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2 },
{ -0.541451884327, -0.541451884327, 0.541451884327 }, { 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3 },
{ 0.541451884327, 0.541451884327, -0.541451884327 }, { 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3 },
{ 0. , 0. , -1.082903768655 }, { 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3 },
{ 0. , 0. , 1.082903768655 }, { 14*sqrt(3)/3-7, 0, 0 },
{ 0. , -1.082903768655, 0. }, { 7-14*sqrt(3)/3, 0, 0 },
{ 0. , 1.082903768655, 0. }, { 0, 14*sqrt(3)/3-7, 0 },
{ -1.082903768655, 0. , 0. }, { 0, 7-14*sqrt(3)/3, 0 },
{ 1.082903768655, 0. , 0. } }; { 0, 0, 14*sqrt(3)/3-7 },
{ 0, 0, 7-14*sqrt(3)/3 },
};
const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. }, const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = {
{ 0. , 0.525731112119, 0.850650808352 }, { 0, 0, 0 },
{ 0. , -0.525731112119, -0.850650808352 }, { 0, 0, 1 },
{ 0. , 0.525731112119, -0.850650808352 }, { 0, 0, -1 },
{ 0. , -0.525731112119, 0.850650808352 }, { -sqrt((5-sqrt(5))/10), (5+sqrt(5))/10, -sqrt(5)/5 },
{ -0.525731112119, -0.850650808352, 0. }, { sqrt((5-sqrt(5))/10), -(5+sqrt(5))/10, sqrt(5)/5 },
{ 0.525731112119, 0.850650808352, 0. }, { 0, -2*sqrt(5)/5, -sqrt(5)/5 },
{ 0.525731112119, -0.850650808352, 0. }, { 0, 2*sqrt(5)/5, sqrt(5)/5 },
{ -0.525731112119, 0.850650808352, 0. }, { sqrt((5+sqrt(5))/10), -(5-sqrt(5))/10, -sqrt(5)/5 },
{ -0.850650808352, 0. , -0.525731112119 }, { -sqrt((5+sqrt(5))/10), (5-sqrt(5))/10, sqrt(5)/5 },
{ 0.850650808352, 0. , 0.525731112119 }, { -sqrt((5+sqrt(5))/10), -(5-sqrt(5))/10, -sqrt(5)/5 },
{ 0.850650808352, 0. , -0.525731112119 }, { sqrt((5+sqrt(5))/10), (5-sqrt(5))/10, sqrt(5)/5 },
{ -0.850650808352, 0. , 0.525731112119 } }; { sqrt((5-sqrt(5))/10), (5+sqrt(5))/10, -sqrt(5)/5 },
{ -sqrt((5-sqrt(5))/10), -(5+sqrt(5))/10, sqrt(5)/5 },
};
const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. }, const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = {
{ 0. , 0. , -1. }, { 0, 0, 0 },
{ 0. , 0. , 1. }, { 0, 0, -1 },
{ 0. , -1. , 0. }, { 0, 0, 1 },
{ 0. , 1. , 0. }, { 0, -1, 0 },
{ -1. , 0. , 0. }, { 0, 1, 0 },
{ 1. , 0. , 0. } }; { -1, 0, 0 },
{ 1, 0, 0 },
};
const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. }, const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = {
{ -0.391491627053, 0.391491627053, 0.391491627053 }, { 0, 0, 0 },
{ -0.391491627053, -0.391491627053, -0.391491627053 }, { 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) },
{ 0.391491627053, -0.391491627053, 0.391491627053 }, { 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) },
{ 0.391491627053, 0.391491627053, -0.391491627053 }, { -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) },
{ -0.782983254107, 0. , 0.782983254107 }, { -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) },
{ -0.782983254107, 0.782983254107, 0. }, { 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 },
{ 0. , 0.782983254107, 0.782983254107 }, { 0, 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) },
{ -0.782983254107, -0.782983254107, 0. }, { 8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) },
{ -0.782983254107, 0. , -0.782983254107 }, { 0, -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) },
{ 0. , -0.782983254107, -0.782983254107 }, { 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 },
{ 0. , -0.782983254107, 0.782983254107 }, { 8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) },
{ 0.782983254107, -0.782983254107, 0. }, { -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 },
{ 0.782983254107, 0. , 0.782983254107 }, { 0, -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) },
{ 0. , 0.782983254107, -0.782983254107 }, { -8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) },
{ 0.782983254107, 0. , -0.782983254107 }, { -8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) },
{ 0.782983254107, 0.782983254107, 0. } }; { -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 },
{ 0, 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) },
};
const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) },
{ 0, 0, 4*sqrt(3)/(sqrt(3)+6*sqrt(2)) },
{ -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 },
{ 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 },
{ 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
{ -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) },
};
const double ptm_template_graphene[PTM_NUM_POINTS_GRAPHENE][3] = {
{ 0, 0, 0 },
{ 0, -3./11+6*sqrt(3)/11, 0 },
{ -3*sqrt(3)/22+9./11, -3*sqrt(3)/11+3./22, 0 },
{ -9./11+3*sqrt(3)/22, -3*sqrt(3)/11+3./22, 0 },
{ -9./11+3*sqrt(3)/22, -9./22+9*sqrt(3)/11, 0 },
{ -3*sqrt(3)/22+9./11, -9./22+9*sqrt(3)/11, 0 },
{ -3*sqrt(3)/11+18./11, 0, 0 },
{ -3*sqrt(3)/22+9./11, -9*sqrt(3)/11+9./22, 0 },
{ -9./11+3*sqrt(3)/22, -9*sqrt(3)/11+9./22, 0 },
{ -18./11+3*sqrt(3)/11, 0, 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 #endif

513
src/USER-PTM/ptm_convex_hull_incremental.cpp
View File

@ -1,3 +1,12 @@
/*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.
*/
#include <cmath> #include <cmath>
#include <cfloat> #include <cfloat>
#include <cstring> #include <cstring>
@ -15,351 +24,351 @@ namespace ptm {
static double norm_squared(double* p) static double norm_squared(double* p)
{ {
double x = p[0]; double x = p[0];
double y = p[1]; double y = p[1];
double z = p[2]; double z = p[2];
return x*x + y*y + z*z; return x*x + y*y + z*z;
} }
static double dot_product(const double* a, const double* b) static double dot_product(const double* a, const double* b)
{ {
return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
} }
static void cross_product(double* a, double* b, double* c) static void cross_product(double* a, double* b, double* c)
{ {
c[0] = a[1] * b[2] - a[2] * b[1]; c[0] = a[1] * b[2] - a[2] * b[1];
c[1] = a[2] * b[0] - a[0] * b[2]; c[1] = a[2] * b[0] - a[0] * b[2];
c[2] = a[0] * b[1] - a[1] * b[0]; 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) 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], double u[3] = { points[b][0] - points[a][0],
points[b][1] - points[a][1], points[b][1] - points[a][1],
points[b][2] - points[a][2] }; points[b][2] - points[a][2] };
double v[3] = { points[c][0] - points[a][0], double v[3] = { points[c][0] - points[a][0],
points[c][1] - points[a][1], points[c][1] - points[a][1],
points[c][2] - points[a][2] }; points[c][2] - points[a][2] };
cross_product(u, v, plane_normal); cross_product(u, v, plane_normal);
double norm = sqrt(norm_squared(plane_normal)); double norm = sqrt(norm_squared(plane_normal));
plane_normal[0] /= norm; plane_normal[0] /= norm;
plane_normal[1] /= norm; plane_normal[1] /= norm;
plane_normal[2] /= norm; plane_normal[2] /= norm;
} }
static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross) 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]) return plane_cross[0] * (plane_point[0] - w[0])
+ plane_cross[1] * (plane_point[1] - w[1]) + plane_cross[1] * (plane_point[1] - w[1])
+ plane_cross[2] * (plane_point[2] - w[2]); + 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) 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++) for (int j=0;j<3;j++)
{ {
double dmin = DBL_MAX, dmax = -DBL_MAX; double dmin = DBL_MAX, dmax = -DBL_MAX;
int imin = 0, imax = 0; int imin = 0, imax = 0;
for (int i = 0;i<num_points;i++) for (int i = 0;i<num_points;i++)
{ {
double d = points[i][j]; double d = points[i][j];
if (d < dmin) if (d < dmin)
{ {
dmin = d; dmin = d;
imin = i; imin = i;
} }
if (d > dmax) if (d > dmax)
{ {
dmax = d; dmax = d;
imax = i; imax = i;
} }
} }
if (imin == imax) if (imin == imax)
return false; //degenerate point set return false; //degenerate point set
min_index[j] = imin; min_index[j] = imin;
max_index[j] = imax; max_index[j] = imax;
} }
return true; return true;
} }
static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c) 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* x1 = points[a];
const double* x2 = points[b]; const double* x2 = points[b];
double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]}; double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]};
double ns_x2x1 = norm_squared(x2x1); double ns_x2x1 = norm_squared(x2x1);
int bi = -1; int bi = -1;
double max_dist = 0.0; double max_dist = 0.0;
for (int i = 0;i<num_points;i++) for (int i = 0;i<num_points;i++)
{ {
if (i == a || i == b) if (i == a || i == b)
continue; continue;
const double* x0 = points[i]; const double* x0 = points[i];
double x1x0[3] = {x1[0] - x0[0], x1[1] - x0[1], x1[2] - x0[2]}; double x1x0[3] = {x1[0] - x0[0], x1[1] - x0[1], x1[2] - x0[2]};
double dot = dot_product(x1x0, x2x1); double dot = dot_product(x1x0, x2x1);
double dist = (norm_squared(x1x0) * ns_x2x1 - dot*dot) / ns_x2x1; double dist = (norm_squared(x1x0) * ns_x2x1 - dot*dot) / ns_x2x1;
if (dist > max_dist) if (dist > max_dist)
{ {
max_dist = dist; max_dist = dist;
bi = i; bi = i;
} }
} }
*p_c = bi; *p_c = bi;
return max_dist > TOLERANCE; 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) 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]; double plane_normal[3];
calculate_plane_normal(points, a, b, c, plane_normal); calculate_plane_normal(points, a, b, c, plane_normal);
int bi = -1; int bi = -1;
double max_dist = 0.0; double max_dist = 0.0;
for (int i = 0;i<num_points;i++) for (int i = 0;i<num_points;i++)
{ {
if (i == a || i == b || i == c) if (i == a || i == b || i == c)
continue; continue;
const double* x0 = points[i]; const double* x0 = points[i];
double dist = fabs(point_plane_distance(x0, points[a], plane_normal)); double dist = fabs(point_plane_distance(x0, points[a], plane_normal));
if (dist > max_dist) if (dist > max_dist)
{ {
max_dist = dist; max_dist = dist;
bi = i; bi = i;
} }
} }
*p_d = bi; *p_d = bi;
return max_dist > TOLERANCE; return max_dist > TOLERANCE;
} }
static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices) static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices)
{ {
int min_index[3] = {0}; int min_index[3] = {0};
int max_index[3] = {0}; int max_index[3] = {0};
if (!calc_max_extent(num_points, points, min_index, max_index)) if (!calc_max_extent(num_points, points, min_index, max_index))
return -1; return -1;
int bi = -1; int bi = -1;
double max_dist = 0.0; double max_dist = 0.0;
for (int i = 0;i<3;i++) for (int i = 0;i<3;i++)
{ {
int a = min_index[i], b = max_index[i]; int a = min_index[i], b = max_index[i];
double delta[3] = { points[a][0] - points[b][0], double delta[3] = { points[a][0] - points[b][0],
points[a][1] - points[b][1], points[a][1] - points[b][1],
points[a][2] - points[b][2] }; points[a][2] - points[b][2] };
double dist = norm_squared(delta); double dist = norm_squared(delta);
if (dist > max_dist) if (dist > max_dist)
{ {
bi = i; bi = i;
max_dist = dist; max_dist = dist;
} }
} }
//first two points are (a, b) //first two points are (a, b)
int a = min_index[bi], b = max_index[bi], c = -1, d = -1; int a = min_index[bi], b = max_index[bi], c = -1, d = -1;
if (!find_third_point(num_points, points, a, b, &c)) if (!find_third_point(num_points, points, a, b, &c))
return -2; return -2;
if (!find_fourth_point(num_points, points, a, b, c, &d)) if (!find_fourth_point(num_points, points, a, b, c, &d))
return -3; return -3;
initial_vertices[0] = a; initial_vertices[0] = a;
initial_vertices[1] = b; initial_vertices[1] = b;
initial_vertices[2] = c; initial_vertices[2] = c;
initial_vertices[3] = d; initial_vertices[3] = d;
return 0; return 0;
} }
static bool visible(const double* w, const double* plane_point, const double* plane_normal) static bool visible(const double* w, const double* plane_point, const double* plane_normal)
{ {
return point_plane_distance(w, plane_point, plane_normal) > 0; 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) 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); calculate_plane_normal(points, a, b, c, plane_normal);
if (visible(barycentre, points[a], plane_normal)) if (visible(barycentre, points[a], plane_normal))
{ {
plane_normal[0] = -plane_normal[0]; plane_normal[0] = -plane_normal[0];
plane_normal[1] = -plane_normal[1]; plane_normal[1] = -plane_normal[1];
plane_normal[2] = -plane_normal[2]; plane_normal[2] = -plane_normal[2];
facet[0] = b; facet[0] = b;
facet[1] = a; facet[1] = a;
facet[2] = c; facet[2] = c;
} }
else else
{ {
facet[0] = a; facet[0] = a;
facet[1] = b; facet[1] = b;
facet[2] = c; 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) 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(processed, 0, PTM_MAX_POINTS * sizeof(bool));
memset(barycentre, 0, 3 * sizeof(double)); memset(barycentre, 0, 3 * sizeof(double));
int ret = initial_simplex(num_points, points, initial_vertices); int ret = initial_simplex(num_points, points, initial_vertices);
if (ret != 0) if (ret != 0)
return ret; return ret;
for (int i = 0;i<4;i++) for (int i = 0;i<4;i++)
{ {
int a = initial_vertices[i]; int a = initial_vertices[i];
processed[a] = true; processed[a] = true;
barycentre[0] += points[a][0]; barycentre[0] += points[a][0];
barycentre[1] += points[a][1]; barycentre[1] += points[a][1];
barycentre[2] += points[a][2]; barycentre[2] += points[a][2];
} }
barycentre[0] /= 4; barycentre[0] /= 4;
barycentre[1] /= 4; barycentre[1] /= 4;
barycentre[2] /= 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[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[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[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); add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre);
return 0; return 0;
} }
int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]) 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 assert( num_points == PTM_NUM_POINTS_FCC
|| num_points == PTM_NUM_POINTS_HCP || num_points == PTM_NUM_POINTS_HCP
|| num_points == PTM_NUM_POINTS_BCC || num_points == PTM_NUM_POINTS_BCC
|| num_points == PTM_NUM_POINTS_ICO || num_points == PTM_NUM_POINTS_ICO
|| num_points == PTM_NUM_POINTS_SC || num_points == PTM_NUM_POINTS_SC
|| num_points == PTM_NUM_POINTS_DCUB || num_points == PTM_NUM_POINTS_DCUB
|| num_points == PTM_NUM_POINTS_DHEX); || num_points == PTM_NUM_POINTS_DHEX);
int ret = 0; int ret = 0;
int num_prev = ch->num_prev; int num_prev = ch->num_prev;
ch->num_prev = num_points; ch->num_prev = num_points;
if (!ch->ok || 0) if (!ch->ok || 0)
{ {
ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre); ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre);
if (ret != 0) if (ret != 0)
return ret; return ret;
ch->num_facets = 4; ch->num_facets = 4;
num_prev = 0; num_prev = 0;
} }
for (int i = num_prev;i<num_points;i++) for (int i = num_prev;i<num_points;i++)
{ {
if (ch->processed[i]) if (ch->processed[i])
continue; continue;
ch->processed[i] = true; ch->processed[i] = true;
int num_to_add = 0; int num_to_add = 0;
int8_t to_add[PTM_MAX_FACETS][3]; int8_t to_add[PTM_MAX_FACETS][3];
int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS]; int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS];
memset(edge_visible, 0, sizeof(int8_t) * 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++) for (int j = 0;j<ch->num_facets;j++)
{ {
int a = ch->facets[j][0]; int a = ch->facets[j][0];
int b = ch->facets[j][1]; int b = ch->facets[j][1];
int c = ch->facets[j][2]; int c = ch->facets[j][2];
int u = 0, v = 0, w = 0; int u = 0, v = 0, w = 0;
double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]); double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]);
bool vis = distance > TOLERANCE; bool vis = distance > TOLERANCE;
if (vis) if (vis)
{ {
u = edge_visible[a][b] |= VISIBLE; u = edge_visible[a][b] |= VISIBLE;
edge_visible[b][a] |= VISIBLE; edge_visible[b][a] |= VISIBLE;
v = edge_visible[b][c] |= VISIBLE; v = edge_visible[b][c] |= VISIBLE;
edge_visible[c][b] |= VISIBLE; edge_visible[c][b] |= VISIBLE;
w = edge_visible[c][a] |= VISIBLE; w = edge_visible[c][a] |= VISIBLE;
edge_visible[a][c] |= VISIBLE; edge_visible[a][c] |= VISIBLE;
memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t)); 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)); memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double));
ch->num_facets--; ch->num_facets--;
j--; j--;
} }
else else
{ {
u = edge_visible[a][b] |= INVISIBLE; u = edge_visible[a][b] |= INVISIBLE;
edge_visible[b][a] |= INVISIBLE; edge_visible[b][a] |= INVISIBLE;
v = edge_visible[b][c] |= INVISIBLE; v = edge_visible[b][c] |= INVISIBLE;
edge_visible[c][b] |= INVISIBLE; edge_visible[c][b] |= INVISIBLE;
w = edge_visible[c][a] |= INVISIBLE; w = edge_visible[c][a] |= INVISIBLE;
edge_visible[a][c] |= INVISIBLE; edge_visible[a][c] |= INVISIBLE;
} }
if (u == BOTH) if (u == BOTH)
{ {
to_add[num_to_add][0] = i; to_add[num_to_add][0] = i;
to_add[num_to_add][1] = a; to_add[num_to_add][1] = a;
to_add[num_to_add][2] = b; to_add[num_to_add][2] = b;
num_to_add++; num_to_add++;
} }
if (v == BOTH) if (v == BOTH)
{ {
to_add[num_to_add][0] = i; to_add[num_to_add][0] = i;
to_add[num_to_add][1] = b; to_add[num_to_add][1] = b;
to_add[num_to_add][2] = c; to_add[num_to_add][2] = c;
num_to_add++; num_to_add++;
} }
if (w == BOTH) if (w == BOTH)
{ {
to_add[num_to_add][0] = i; to_add[num_to_add][0] = i;
to_add[num_to_add][1] = c; to_add[num_to_add][1] = c;
to_add[num_to_add][2] = a; to_add[num_to_add][2] = a;
num_to_add++; num_to_add++;
} }
} }
for (int j = 0;j<num_to_add;j++) for (int j = 0;j<num_to_add;j++)
{ {
if (ch->num_facets >= PTM_MAX_FACETS) if (ch->num_facets >= PTM_MAX_FACETS)
return -4; 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++; 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++) for (int i=0;i<ch->num_facets;i++)
{ {
int a = ch->facets[i][0]; int a = ch->facets[i][0];
int b = ch->facets[i][1]; int b = ch->facets[i][1];
int c = ch->facets[i][2]; int c = ch->facets[i][2];
if (a == 0 || b == 0 || c == 0) if (a == 0 || b == 0 || c == 0)
return 1; //central atom contained in convex hull return 1; //central atom contained in convex hull
simplex[i][0] = a - 1; simplex[i][0] = a - 1;
simplex[i][1] = b - 1; simplex[i][1] = b - 1;
simplex[i][2] = c - 1; simplex[i][2] = c - 1;
} }
return ret; return ret;
} }
} }

25
src/USER-PTM/ptm_convex_hull_incremental.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_CONVEX_HULL_INCREMENTAL_H #ifndef PTM_CONVEX_HULL_INCREMENTAL_H
#define PTM_CONVEX_HULL_INCREMENTAL_H #define PTM_CONVEX_HULL_INCREMENTAL_H
@ -10,14 +19,14 @@ namespace ptm {
typedef struct typedef struct
{ {
int8_t facets[PTM_MAX_FACETS][3]; int8_t facets[PTM_MAX_FACETS][3];
double plane_normal[PTM_MAX_FACETS][3]; double plane_normal[PTM_MAX_FACETS][3];
bool processed[PTM_MAX_POINTS]; bool processed[PTM_MAX_POINTS];
int initial_vertices[4]; int initial_vertices[4];
double barycentre[3]; double barycentre[3];
int num_facets; int num_facets;
int num_prev; int num_prev;
bool ok; bool ok;
} convexhull_t; } convexhull_t;

61
src/USER-PTM/ptm_deformation_gradient.cpp
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@ -1,39 +1,48 @@
/*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.
*/
#include "ptm_deformation_gradient.h" #include "ptm_deformation_gradient.h"
namespace ptm { namespace ptm {
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) 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 i = 0;i<3;i++)
{ {
for (int j = 0;j<3;j++) for (int j = 0;j<3;j++)
{ {
double acc = 0.0; double acc = 0.0;
for (int k = 0;k<num_points;k++) for (int k = 0;k<num_points;k++)
acc += penrose[k][j] * normalized[mapping[k]][i]; acc += penrose[k][j] * normalized[mapping[k]][i];
F[i*3 + j] = acc; F[i*3 + j] = acc;
} }
} }
res[0] = 0; res[0] = 0;
res[1] = 0; res[1] = 0;
res[2] = 0; res[2] = 0;
for (int k = 0;k<num_points;k++) for (int k = 0;k<num_points;k++)
{ {
for (int i = 0;i<3;i++) for (int i = 0;i<3;i++)
{ {
double acc = 0.0; double acc = 0.0;
for (int j = 0;j<3;j++) for (int j = 0;j<3;j++)
{ {
acc += F[i*3 + j] * ideal_points[k][j]; acc += F[i*3 + j] * ideal_points[k][j];
} }
double delta = acc - normalized[mapping[k]][i]; double delta = acc - normalized[mapping[k]][i];
res[i] += delta * delta; res[i] += delta * delta;
} }
} }
} }
} }

353
src/USER-PTM/ptm_deformation_gradient.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_DEFORMATION_GRADIENT_H #ifndef PTM_DEFORMATION_GRADIENT_H
#define PTM_DEFORMATION_GRADIENT_H #define PTM_DEFORMATION_GRADIENT_H
@ -8,139 +17,247 @@ namespace ptm {
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); 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] = { const double penrose_sc[PTM_NUM_POINTS_SC][3] = {
{0, 0, 0}, { 0, 0, 0 },
{0, 0, -k_sc}, { 0, 0, -0.5 },
{0, 0, k_sc}, { 0, 0, 0.5 },
{0, -k_sc, 0}, { 0, -0.5, 0 },
{0, k_sc, 0}, { 0, 0.5, 0 },
{-k_sc, 0, 0}, { -0.5, 0, 0 },
{k_sc, 0, 0}, { 0.5, 0, 0 },
}; };
//fcc
#define k_fcc 0.17677669529663678216
const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = { const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = {
{0, 0, 0}, { 0, 0, 0 },
{0, k_fcc, k_fcc}, { sqrt(2)/8, sqrt(2)/8, 0 },
{0, -k_fcc, -k_fcc}, { 0, sqrt(2)/8, sqrt(2)/8 },
{0, k_fcc, -k_fcc}, { sqrt(2)/8, 0, sqrt(2)/8 },
{0, -k_fcc, k_fcc}, { -sqrt(2)/8, -sqrt(2)/8, 0 },
{k_fcc, 0, k_fcc}, { 0, -sqrt(2)/8, -sqrt(2)/8 },
{-k_fcc, 0, -k_fcc}, { -sqrt(2)/8, 0, -sqrt(2)/8 },
{k_fcc, 0, -k_fcc}, { -sqrt(2)/8, sqrt(2)/8, 0 },
{-k_fcc, 0, k_fcc}, { 0, -sqrt(2)/8, sqrt(2)/8 },
{k_fcc, k_fcc, -0}, { -sqrt(2)/8, 0, sqrt(2)/8 },
{-k_fcc, -k_fcc, 0}, { sqrt(2)/8, -sqrt(2)/8, 0 },
{k_fcc, -k_fcc, 0}, { 0, sqrt(2)/8, -sqrt(2)/8 },
{-k_fcc, k_fcc, -0}, { sqrt(2)/8, 0, -sqrt(2)/8 },
}; };
//hcp
#define k_hcp 0.17677669529663678216
const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = { const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = {
{0, 0, 0}, { 0, 0, 0 },
{k_hcp, 0, k_hcp}, { 1./8, -sqrt(3)/8, 0 },
{-k_hcp/3, -4*k_hcp/3, -k_hcp/3}, { -1./4, 0, 0 },
{k_hcp, k_hcp, 0}, { -1./8, sqrt(3)/24, -sqrt(6)/12 },
{-k_hcp/3, -k_hcp/3, -4*k_hcp/3}, { 1./8, sqrt(3)/24, -sqrt(6)/12 },
{0, k_hcp, k_hcp}, { 0, -sqrt(3)/12, -sqrt(6)/12 },
{-4*k_hcp/3, -k_hcp/3, -k_hcp/3}, { -1./8, sqrt(3)/8, 0 },
{-k_hcp, k_hcp, -0}, { 1./8, sqrt(3)/8, 0 },
{0, k_hcp, -k_hcp}, { 1./4, 0, 0 },
{k_hcp, 0, -k_hcp}, { -1./8, -sqrt(3)/8, 0 },
{k_hcp, -k_hcp, 0}, { 0, -sqrt(3)/12, sqrt(6)/12 },
{-k_hcp, 0, k_hcp}, { 1./8, sqrt(3)/24, sqrt(6)/12 },
{0, -k_hcp, k_hcp}, { -1./8, sqrt(3)/24, sqrt(6)/12 },
}; };
const double penrose_hcp_alt1[PTM_NUM_POINTS_HCP][3] = {
{ 0, 0, 0 },
{ 1./4, 0, 0 },
{ -1./8, -sqrt(3)/8, 0 },
{ -1./8, -sqrt(3)/24, -sqrt(6)/12 },
{ 0, sqrt(3)/12, -sqrt(6)/12 },
{ 1./8, -sqrt(3)/24, -sqrt(6)/12 },
{ -1./4, 0, 0 },
{ -1./8, sqrt(3)/8, 0 },
{ 1./8, sqrt(3)/8, 0 },
{ 1./8, -sqrt(3)/8, 0 },
{ 1./8, -sqrt(3)/24, sqrt(6)/12 },
{ 0, sqrt(3)/12, sqrt(6)/12 },
{ -1./8, -sqrt(3)/24, sqrt(6)/12 },
};
//ico
#define k_ico 0.13143277802974323576
#define phi 1.61803398874989490253
//((1.0 + sqrt(5)) / 2)
const double penrose_ico[PTM_NUM_POINTS_ICO][3] = { const double penrose_ico[PTM_NUM_POINTS_ICO][3] = {
{0, 0, 0}, { 0, 0, 0 },
{0, k_ico, phi*k_ico}, { 0, 0, 0.25 },
{0, -k_ico, -phi*k_ico}, { 0, 0, -0.25 },
{0, k_ico, -phi*k_ico}, { -sqrt(-10*sqrt(5) + 50)/40, sqrt(5)/40 + 1./8, -sqrt(5)/20 },
{0, -k_ico, phi*k_ico}, { sqrt(-10*sqrt(5) + 50)/40, -1./8 - sqrt(5)/40, sqrt(5)/20 },
{-k_ico, -phi*k_ico, -0}, { 0, -sqrt(5)/10, -sqrt(5)/20 },
{k_ico, phi*k_ico, 0}, { 0, sqrt(5)/10, sqrt(5)/20 },
{k_ico, -phi*k_ico, 0}, { sqrt(10*sqrt(5) + 50)/40, -1./8 + sqrt(5)/40, -sqrt(5)/20 },
{-k_ico, phi*k_ico, -0}, { -sqrt(10*sqrt(5) + 50)/40, -sqrt(5)/40 + 1./8, sqrt(5)/20 },
{-phi*k_ico, 0, -k_ico}, { -sqrt(10*sqrt(5) + 50)/40, -1./8 + sqrt(5)/40, -sqrt(5)/20 },
{phi*k_ico, 0, k_ico}, { sqrt(10*sqrt(5) + 50)/40, -sqrt(5)/40 + 1./8, sqrt(5)/20 },
{phi*k_ico, 0, -k_ico}, { sqrt(-10*sqrt(5) + 50)/40, sqrt(5)/40 + 1./8, -sqrt(5)/20 },
{-phi*k_ico, 0, k_ico}, { -sqrt(-10*sqrt(5) + 50)/40, -1./8 - sqrt(5)/40, sqrt(5)/20 },
}; };
//bcc
#define k_bcc 0.11543038598460284017
const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = { const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = {
{0, 0, 0}, { 0, 0, 0 },
{-k_bcc, -k_bcc, -k_bcc}, { 3./56 + sqrt(3)/28, 3./56 + sqrt(3)/28, 3./56 + sqrt(3)/28 },
{k_bcc, k_bcc, k_bcc}, { -sqrt(3)/28 - 3./56, 3./56 + sqrt(3)/28, 3./56 + sqrt(3)/28 },
{k_bcc, -k_bcc, -k_bcc}, { 3./56 + sqrt(3)/28, 3./56 + sqrt(3)/28, -sqrt(3)/28 - 3./56 },
{-k_bcc, k_bcc, k_bcc}, { -sqrt(3)/28 - 3./56, -sqrt(3)/28 - 3./56, 3./56 + sqrt(3)/28 },
{-k_bcc, k_bcc, -k_bcc}, { 3./56 + sqrt(3)/28, -sqrt(3)/28 - 3./56, 3./56 + sqrt(3)/28 },
{k_bcc, -k_bcc, k_bcc}, { -sqrt(3)/28 - 3./56, 3./56 + sqrt(3)/28, -sqrt(3)/28 - 3./56 },
{-k_bcc, -k_bcc, k_bcc}, { -sqrt(3)/28 - 3./56, -sqrt(3)/28 - 3./56, -sqrt(3)/28 - 3./56 },
{k_bcc, k_bcc, -k_bcc}, { 3./56 + sqrt(3)/28, -sqrt(3)/28 - 3./56, -sqrt(3)/28 - 3./56 },
{0, 0, -2*k_bcc}, { 3./28 + sqrt(3)/14, 0, 0 },
{0, 0, 2*k_bcc}, { -sqrt(3)/14 - 3./28, 0, 0 },
{0, -2*k_bcc, 0}, { 0, 3./28 + sqrt(3)/14, 0 },
{0, 2*k_bcc, 0}, { 0, -sqrt(3)/14 - 3./28, 0 },
{-2*k_bcc, 0, 0}, { 0, 0, 3./28 + sqrt(3)/14 },
{2*k_bcc, 0, -0}, { 0, 0, -sqrt(3)/14 - 3./28 },
}; };
//dcub
#define kdcub 0.07095369570691034689
const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = { const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = {
{ 0, 0, 0 }, { 0, 0, 0 },
{ -kdcub, kdcub, kdcub }, { 23./(48*(-sqrt(3) + 6*sqrt(2))), 23./(48*(-sqrt(3) + 6*sqrt(2))), 23./(48*(-sqrt(3) + 6*sqrt(2))) },
{ -kdcub, -kdcub, -kdcub }, { 23./(48*(-sqrt(3) + 6*sqrt(2))), -23./(-48*sqrt(3) + 288*sqrt(2)), -23./(-48*sqrt(3) + 288*sqrt(2)) },
{ kdcub, -kdcub, kdcub }, { -23./(-48*sqrt(3) + 288*sqrt(2)), -23./(-48*sqrt(3) + 288*sqrt(2)), 23./(48*(-sqrt(3) + 6*sqrt(2))) },
{ kdcub, kdcub, -kdcub }, { -23./(-48*sqrt(3) + 288*sqrt(2)), 23./(48*(-sqrt(3) + 6*sqrt(2))), -23./(-48*sqrt(3) + 288*sqrt(2)) },
{ -2 * kdcub, 0, 2 * kdcub }, { 23./(24*(-sqrt(3) + 6*sqrt(2))), 23./(24*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -2 * kdcub, 2 * kdcub, 0 }, { 0, 23./(24*(-sqrt(3) + 6*sqrt(2))), 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 2 * kdcub, 2 * kdcub }, { 23./(24*(-sqrt(3) + 6*sqrt(2))), 0, 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ -2 * kdcub, -2 * kdcub, 0 }, { 0, -23./(-24*sqrt(3) + 144*sqrt(2)), -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ -2 * kdcub, 0, -2 * kdcub }, { 23./(24*(-sqrt(3) + 6*sqrt(2))), -23./(-24*sqrt(3) + 144*sqrt(2)), 0 },
{ 0, -2 * kdcub, -2 * kdcub }, { 23./(24*(-sqrt(3) + 6*sqrt(2))), 0, -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ 0, -2 * kdcub, 2 * kdcub }, { -23./(-24*sqrt(3) + 144*sqrt(2)), -23./(-24*sqrt(3) + 144*sqrt(2)), 0 },
{ 2 * kdcub, -2 * kdcub, 0 }, { 0, -23./(-24*sqrt(3) + 144*sqrt(2)), 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ 2 * kdcub, 0, 2 * kdcub }, { -23./(-24*sqrt(3) + 144*sqrt(2)), 0, 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 2 * kdcub, -2 * kdcub }, { -23./(-24*sqrt(3) + 144*sqrt(2)), 0, -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ 2 * kdcub, 0, -2 * kdcub }, { -23./(-24*sqrt(3) + 144*sqrt(2)), 23./(24*(-sqrt(3) + 6*sqrt(2))), 0 },
{ 2 * kdcub, 2 * kdcub, 0 }, { 0, 23./(24*(-sqrt(3) + 6*sqrt(2))), -23./(-24*sqrt(3) + 144*sqrt(2)) },
}; };
const double penrose_dcub_alt1[PTM_NUM_POINTS_DCUB][3] = {
{ 0, 0, 0 },
{ 23./(48*(-sqrt(3) + 6*sqrt(2))), -23./(-48*sqrt(3) + 288*sqrt(2)), 23./(48*(-sqrt(3) + 6*sqrt(2))) },
{ 23./(48*(-sqrt(3) + 6*sqrt(2))), 23./(48*(-sqrt(3) + 6*sqrt(2))), -23./(-48*sqrt(3) + 288*sqrt(2)) },
{ -23./(-48*sqrt(3) + 288*sqrt(2)), -23./(-48*sqrt(3) + 288*sqrt(2)), -23./(-48*sqrt(3) + 288*sqrt(2)) },
{ -23./(-48*sqrt(3) + 288*sqrt(2)), 23./(48*(-sqrt(3) + 6*sqrt(2))), 23./(48*(-sqrt(3) + 6*sqrt(2))) },
{ 23./(24*(-sqrt(3) + 6*sqrt(2))), 0, 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ 0, -23./(-24*sqrt(3) + 144*sqrt(2)), 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ 23./(24*(-sqrt(3) + 6*sqrt(2))), -23./(-24*sqrt(3) + 144*sqrt(2)), 0 },
{ 0, 23./(24*(-sqrt(3) + 6*sqrt(2))), -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ 23./(24*(-sqrt(3) + 6*sqrt(2))), 0, -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ 23./(24*(-sqrt(3) + 6*sqrt(2))), 23./(24*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -23./(-24*sqrt(3) + 144*sqrt(2)), 0, -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ 0, -23./(-24*sqrt(3) + 144*sqrt(2)), -23./(-24*sqrt(3) + 144*sqrt(2)) },
{ -23./(-24*sqrt(3) + 144*sqrt(2)), -23./(-24*sqrt(3) + 144*sqrt(2)), 0 },
{ -23./(-24*sqrt(3) + 144*sqrt(2)), 23./(24*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -23./(-24*sqrt(3) + 144*sqrt(2)), 0, 23./(24*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 23./(24*(-sqrt(3) + 6*sqrt(2))), 23./(24*(-sqrt(3) + 6*sqrt(2))) },
};
#define kdhex 0.04730246380471011397
const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = { const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 }, { 0, 0, 0 },
{ -kdcub, -kdcub, -kdcub }, { -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-144*sqrt(3) + 864*sqrt(2)) },
{ kdcub, -kdcub, kdcub }, { 0, -23*sqrt(6)/(-72*sqrt(3) + 432*sqrt(2)), -23*sqrt(3)/(-144*sqrt(3) + 864*sqrt(2)) },
{ -kdcub, kdcub, kdcub }, { 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-144*sqrt(3) + 864*sqrt(2)) },
{ kdcub, kdcub, -kdcub }, { 0, 0, 23*sqrt(3)/(48*(-sqrt(3) + 6*sqrt(2))) },
{ -kdhex, -4 * kdhex, -kdhex }, { -23*sqrt(2)/(-24*sqrt(3) + 144*sqrt(2)), 0, 0 },
{ -4 * kdhex, -kdhex, -kdhex }, { -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ -kdhex, -kdhex, -4 * kdhex }, { -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ 2 * kdcub, 0, 2 * kdcub }, { 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ 2 * kdcub, -2 * kdcub, 0 }, { 0, -23*sqrt(6)/(-72*sqrt(3) + 432*sqrt(2)), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ 0, -2 * kdcub, 2 * kdcub }, { -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ 0, 2 * kdcub, 2 * kdcub }, { 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ -2 * kdcub, 2 * kdcub, 0 }, { 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -2 * kdcub, 0, 2 * kdcub }, { 23*sqrt(2)/(24*(-sqrt(3) + 6*sqrt(2))), 0, 0 },
{ 2 * kdcub, 2 * kdcub, 0 }, { 0, -23*sqrt(6)/(-72*sqrt(3) + 432*sqrt(2)), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 2 * kdcub, -2 * kdcub }, { 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 2 * kdcub, 0, -2 * kdcub }, { -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
}; };
const double penrose_dhex_alt1[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), -23*sqrt(3)/(-144*sqrt(3) + 864*sqrt(2)) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), -23*sqrt(3)/(-144*sqrt(3) + 864*sqrt(2)) },
{ 0, 23*sqrt(6)/(72*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-144*sqrt(3) + 864*sqrt(2)) },
{ 0, 0, 23*sqrt(3)/(48*(-sqrt(3) + 6*sqrt(2))) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ -23*sqrt(2)/(-24*sqrt(3) + 144*sqrt(2)), 0, 0 },
{ 23*sqrt(2)/(24*(-sqrt(3) + 6*sqrt(2))), 0, 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ 0, 23*sqrt(6)/(72*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 23*sqrt(6)/(72*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
};
const double penrose_dhex_alt2[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ 0, -23*sqrt(6)/(-72*sqrt(3) + 432*sqrt(2)), 23*sqrt(3)/(144*(-sqrt(3) + 6*sqrt(2))) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(144*(-sqrt(3) + 6*sqrt(2))) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(144*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 0, -23*sqrt(3)/(-48*sqrt(3) + 288*sqrt(2)) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ 0, -23*sqrt(6)/(-72*sqrt(3) + 432*sqrt(2)), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ -23*sqrt(2)/(-24*sqrt(3) + 144*sqrt(2)), 0, 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 23*sqrt(2)/(24*(-sqrt(3) + 6*sqrt(2))), 0, 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(144*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ 0, -23*sqrt(6)/(-72*sqrt(3) + 432*sqrt(2)), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
};
const double penrose_dhex_alt3[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 0, 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), 23*sqrt(3)/(144*(-sqrt(3) + 6*sqrt(2))) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), 23*sqrt(3)/(144*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 23*sqrt(6)/(72*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(144*(-sqrt(3) + 6*sqrt(2))) },
{ 0, 0, -23*sqrt(3)/(-48*sqrt(3) + 288*sqrt(2)) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 23*sqrt(2)/(24*(-sqrt(3) + 6*sqrt(2))), 0, 0 },
{ -23*sqrt(2)/(-24*sqrt(3) + 144*sqrt(2)), 0, 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-48*sqrt(3) + 288*sqrt(2)), 0 },
{ 0, 23*sqrt(6)/(72*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(3)/(36*(-sqrt(3) + 6*sqrt(2))) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), 23*sqrt(6)/(48*(-sqrt(3) + 6*sqrt(2))), 0 },
{ -23*sqrt(2)/(-48*sqrt(3) + 288*sqrt(2)), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ 0, 23*sqrt(6)/(72*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
{ 23*sqrt(2)/(48*(-sqrt(3) + 6*sqrt(2))), -23*sqrt(6)/(-144*sqrt(3) + 864*sqrt(2)), -23*sqrt(3)/(-36*sqrt(3) + 216*sqrt(2)) },
};
const double penrose_graphene[PTM_NUM_POINTS_GRAPHENE][3] = {
{ 0, 0, 0 },
{ 0, 2./63 + 4*sqrt(3)/63, 0 },
{ sqrt(3)/63 + 2./21, -2*sqrt(3)/63 - 1./63, 0 },
{ -2./21 - sqrt(3)/63, -2*sqrt(3)/63 - 1./63, 0 },
{ -2./21 - sqrt(3)/63, 1./21 + 2*sqrt(3)/21, 0 },
{ sqrt(3)/63 + 2./21, 1./21 + 2*sqrt(3)/21, 0 },
{ 2*sqrt(3)/63 + 4./21, 0, 0 },
{ sqrt(3)/63 + 2./21, -2*sqrt(3)/21 - 1./21, 0 },
{ -2./21 - sqrt(3)/63, -2*sqrt(3)/21 - 1./21, 0 },
{ -4./21 - 2*sqrt(3)/63, 0, 0 },
};
const double penrose_graphene_alt1[PTM_NUM_POINTS_GRAPHENE][3] = {
{ 0, 0, 0 },
{ -2./21 - sqrt(3)/63, 1./63 + 2*sqrt(3)/63, 0 },
{ sqrt(3)/63 + 2./21, 1./63 + 2*sqrt(3)/63, 0 },
{ 0, -4*sqrt(3)/63 - 2./63, 0 },
{ -4./21 - 2*sqrt(3)/63, 0, 0 },
{ -2./21 - sqrt(3)/63, 1./21 + 2*sqrt(3)/21, 0 },
{ sqrt(3)/63 + 2./21, 1./21 + 2*sqrt(3)/21, 0 },
{ 2*sqrt(3)/63 + 4./21, 0, 0 },
{ sqrt(3)/63 + 2./21, -2*sqrt(3)/21 - 1./21, 0 },
{ -2./21 - sqrt(3)/63, -2*sqrt(3)/21 - 1./21, 0 },
};
} }
#endif #endif

16
src/USER-PTM/ptm_functions.h
View File

@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_FUNCTIONS_H #ifndef PTM_FUNCTIONS_H
#define PTM_FUNCTIONS_H #define PTM_FUNCTIONS_H
@ -15,8 +24,11 @@ extern "C" {
#endif #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 int ptm_index( ptm_local_handle_t local_handle,
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 size_t atom_index, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3]), void* nbrlist,
int32_t flags, bool output_conventional_orientation, //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, double* p_interatomic_distance, double* p_lattice_constant,
size_t* output_indices); //outputs
#ifdef __cplusplus #ifdef __cplusplus

452
src/USER-PTM/ptm_fundamental_mappings.h
View File

@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_FUNDAMENTAL_MAPPINGS_H #ifndef PTM_FUNDAMENTAL_MAPPINGS_H
#define PTM_FUNDAMENTAL_MAPPINGS_H #define PTM_FUNDAMENTAL_MAPPINGS_H
@ -11,172 +20,309 @@ namespace ptm {
#define NUM_DCUB_MAPPINGS 12 #define NUM_DCUB_MAPPINGS 12
#define NUM_DHEX_MAPPINGS 3 #define NUM_DHEX_MAPPINGS 3
#define NUM_GRAPHENE_MAPPINGS 6
#define NUM_CONVENTIONAL_GRAPHENE_MAPPINGS 12
#define NUM_CONVENTIONAL_HEX_MAPPINGS 12
#define NUM_CONVENTIONAL_DCUB_MAPPINGS 24
#define NUM_CONVENTIONAL_DHEX_MAPPINGS 12
//-----------------------------------------------------------------------------
// sc
//-----------------------------------------------------------------------------
const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
{0, 1, 2, 3, 4, 5, 6}, { 0, 1, 2, 3, 4, 5, 6},
{0, 2, 1, 4, 3, 5, 6}, { 0, 3, 4, 2, 1, 5, 6},
{0, 2, 1, 3, 4, 6, 5}, { 0, 6, 5, 3, 4, 1, 2},
{0, 1, 2, 4, 3, 6, 5}, { 0, 1, 2, 5, 6, 4, 3},
{0, 3, 4, 5, 6, 1, 2}, { 0, 1, 2, 6, 5, 3, 4},
{0, 5, 6, 2, 1, 4, 3}, { 0, 5, 6, 3, 4, 2, 1},
{0, 6, 5, 1, 2, 4, 3}, { 0, 4, 3, 1, 2, 5, 6},
{0, 4, 3, 5, 6, 2, 1}, { 0, 3, 4, 5, 6, 1, 2},
{0, 5, 6, 1, 2, 3, 4}, { 0, 6, 5, 2, 1, 3, 4},
{0, 4, 3, 6, 5, 1, 2}, { 0, 5, 6, 2, 1, 4, 3},
{0, 3, 4, 6, 5, 2, 1}, { 0, 3, 4, 6, 5, 2, 1},
{0, 6, 5, 2, 1, 3, 4}, { 0, 6, 5, 1, 2, 4, 3},
{0, 3, 4, 2, 1, 5, 6}, { 0, 4, 3, 6, 5, 1, 2},
{0, 6, 5, 3, 4, 1, 2}, { 0, 4, 3, 5, 6, 2, 1},
{0, 1, 2, 5, 6, 4, 3}, { 0, 5, 6, 1, 2, 3, 4},
{0, 4, 3, 1, 2, 5, 6}, { 0, 2, 1, 4, 3, 5, 6},
{0, 5, 6, 3, 4, 2, 1}, { 0, 2, 1, 5, 6, 3, 4},
{0, 1, 2, 6, 5, 3, 4}, { 0, 5, 6, 4, 3, 1, 2},
{0, 2, 1, 5, 6, 3, 4}, { 0, 6, 5, 4, 3, 2, 1},
{0, 5, 6, 4, 3, 1, 2}, { 0, 2, 1, 6, 5, 4, 3},
{0, 3, 4, 1, 2, 6, 5}, { 0, 2, 1, 3, 4, 6, 5},
{0, 2, 1, 6, 5, 4, 3}, { 0, 3, 4, 1, 2, 6, 5},
{0, 6, 5, 4, 3, 2, 1}, { 0, 4, 3, 2, 1, 6, 5},
{0, 4, 3, 2, 1, 6, 5} }; { 0, 1, 2, 4, 3, 6, 5},
};
//-----------------------------------------------------------------------------
// fcc
//-----------------------------------------------------------------------------
const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { 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, 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, 12, 11, 1, 9, 8, 4, 6, 2, 7, 3, 5, 10},
{0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9}, { 0, 2, 7, 9, 5, 10, 12, 11, 4, 6, 8, 1, 3},
{0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11}, { 0, 10, 3, 8, 7, 6, 11, 1, 9, 2, 4, 12, 5},
{0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7}, { 0, 7, 9, 2, 10, 12, 5, 4, 3, 8, 1, 6, 11},
{0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3}, { 0, 11, 1, 12, 8, 4, 9, 2, 10, 3, 5, 7, 6},
{0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, { 0, 3, 8, 10, 6, 11, 7, 9, 5, 4, 12, 2, 1},
{0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5}, { 0, 3, 1, 2, 6, 4, 5, 12, 7, 11, 9, 10, 8},
{0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4}, { 0, 11, 6, 7, 8, 3, 10, 5, 9, 4, 2, 12, 1},
{0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6}, { 0, 5, 12, 10, 2, 9, 7, 11, 3, 1, 8, 6, 4},
{0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, { 0, 6, 7, 11, 3, 10, 8, 9, 1, 2, 12, 4, 5},
{0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2}, { 0, 8, 9, 4, 11, 12, 1, 2, 6, 7, 5, 3, 10},
{0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6}, { 0, 9, 4, 8, 12, 1, 11, 6, 10, 5, 3, 7, 2},
{0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3}, { 0, 12, 10, 5, 9, 7, 2, 3, 4, 8, 6, 1, 11},
{0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9}, { 0, 2, 3, 1, 5, 6, 4, 8, 12, 10, 11, 9, 7},
{0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8}, { 0, 10, 5, 12, 7, 2, 9, 4, 11, 6, 1, 8, 3},
{0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1}, { 0, 1, 12, 11, 4, 9, 8, 10, 6, 5, 7, 3, 2},
{0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10}, { 0, 8, 10, 3, 11, 7, 6, 5, 1, 12, 2, 4, 9},
{0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11}, { 0, 5, 4, 6, 2, 1, 3, 8, 7, 9, 11, 10, 12},
{0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2}, { 0, 4, 6, 5, 1, 3, 2, 7, 12, 11, 10, 9, 8},
{0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5}, { 0, 7, 11, 6, 10, 8, 3, 1, 5, 12, 4, 2, 9},
{0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12}, { 0, 9, 2, 7, 12, 5, 10, 3, 11, 1, 6, 8, 4},
{0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4}, { 0, 6, 5, 4, 3, 2, 1, 12, 8, 10, 9, 11, 7},
{0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} }; { 0, 4, 8, 9, 1, 11, 12, 10, 2, 3, 7, 5, 6},
};
//-----------------------------------------------------------------------------
// bcc
//-----------------------------------------------------------------------------
const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { 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, 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, 3, 6, 8, 2, 1, 7, 4, 5, 9, 10, 14, 13, 11, 12},
{0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13}, { 0, 2, 6, 1, 7, 4, 3, 8, 5, 13, 14, 11, 12, 10, 9},
{0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13}, { 0, 5, 1, 8, 2, 4, 3, 6, 7, 12, 11, 9, 10, 13, 14},
{0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10}, { 0, 2, 4, 6, 5, 1, 7, 8, 3, 11, 12, 10, 9, 13, 14},
{0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11}, { 0, 3, 1, 6, 5, 8, 2, 4, 7, 14, 13, 11, 12, 9, 10},
{0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11}, { 0, 5, 4, 1, 7, 8, 2, 6, 3, 9, 10, 13, 14, 12, 11},
{0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9}, { 0, 1, 3, 5, 6, 2, 8, 7, 4, 13, 14, 9, 10, 11, 12},
{0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12}, { 0, 6, 7, 3, 4, 2, 8, 5, 1, 11, 12, 14, 13, 10, 9},
{0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10}, { 0, 8, 3, 7, 1, 5, 6, 2, 4, 12, 11, 14, 13, 9, 10},
{0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9}, { 0, 6, 2, 7, 1, 3, 4, 5, 8, 14, 13, 10, 9, 11, 12},
{0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12}, { 0, 4, 2, 5, 6, 7, 1, 3, 8, 12, 11, 13, 14, 10, 9},
{0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14}, { 0, 4, 7, 2, 8, 5, 6, 3, 1, 13, 14, 10, 9, 12, 11},
{0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10}, { 0, 8, 5, 3, 4, 7, 1, 2, 6, 14, 13, 9, 10, 12, 11},
{0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11}, { 0, 1, 5, 2, 8, 3, 4, 7, 6, 11, 12, 13, 14, 9, 10},
{0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14}, { 0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13},
{0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9}, { 0, 3, 8, 1, 7, 6, 5, 4, 2, 11, 12, 9, 10, 14, 13},
{0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12}, { 0, 5, 8, 4, 3, 1, 7, 6, 2, 13, 14, 12, 11, 9, 10},
{0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12}, { 0, 7, 4, 8, 2, 6, 5, 1, 3, 14, 13, 12, 11, 10, 9},
{0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10}, { 0, 7, 6, 4, 3, 8, 2, 1, 5, 12, 11, 10, 9, 14, 13},
{0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13}, { 0, 6, 3, 2, 8, 7, 1, 5, 4, 10, 9, 11, 12, 14, 13},
{0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11}, { 0, 2, 1, 4, 3, 6, 5, 8, 7, 10, 9, 13, 14, 11, 12},
{0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9}, { 0, 7, 8, 6, 5, 4, 3, 1, 2, 10, 9, 14, 13, 12, 11},
{0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} }; { 0, 4, 5, 7, 1, 2, 8, 3, 6, 10, 9, 12, 11, 13, 14},
};
//-----------------------------------------------------------------------------
// ico
//-----------------------------------------------------------------------------
const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = { 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, 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, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8},
{0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4}, { 0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1},
{0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5}, { 0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12},
{0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1}, { 0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1},
{0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5}, { 0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9},
{0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12}, { 0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8},
{0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12}, { 0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4},
{0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1}, { 0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4},
{0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9}, { 0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5},
{0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8}, { 0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12},
{0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9}, { 0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9},
{0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8}, { 0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5},
{0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 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, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6},
{0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3}, { 0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9},
{0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5}, { 0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
{0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6}, { 0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6},
{0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, { 0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10},
{0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6}, { 0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3},
{0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4}, { 0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10},
{0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2}, { 0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5},
{0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3}, { 0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4},
{0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10}, { 0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1},
{0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10}, { 0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4},
{0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1}, { 0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3},
{0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7}, { 0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7},
{0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, { 0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2},
{0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2}, { 0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7},
{0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4}, { 0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
{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, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5}, { 0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2},
{0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9}, { 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, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3},
{0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10}, { 0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6},
{0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7}, { 0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12},
{0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7}, { 0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10},
{0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12}, { 0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2},
{0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6}, { 0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6},
{0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12}, { 0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10},
{0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3}, { 0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7},
{0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10}, { 0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7},
{0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3}, { 0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12},
{0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6}, { 0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3},
{0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2}, { 0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 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, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3}, { 0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9},
{0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8}, { 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, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11},
{0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5}, { 0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11},
{0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4}, { 0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2},
{0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11}, { 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, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6},
{0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11}, { 0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11},
{0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11}, { 0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5},
{0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6}, { 0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1},
{0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11}, { 0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10},
{0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7}, { 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, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4},
{0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} }; { 0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11},
};
//-----------------------------------------------------------------------------
// hcp
//-----------------------------------------------------------------------------
const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = { 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, 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, 2, 7, 4, 5, 3, 8, 1, 9, 6, 12, 10, 11},
{0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9}, { 0, 7, 1, 5, 3, 4, 9, 2, 6, 8, 11, 12, 10},
{0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8}, { 0, 6, 9, 10, 11, 12, 1, 8, 7, 2, 3, 4, 5},
{0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10}, { 0, 8, 6, 12, 10, 11, 2, 9, 1, 7, 4, 5, 3},
{0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} }; { 0, 9, 8, 11, 12, 10, 7, 6, 2, 1, 5, 3, 4},
};
const int8_t template_indices_hcp[NUM_CONVENTIONAL_HEX_MAPPINGS] = {0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1};
const int8_t mapping_hcp_conventional[NUM_CONVENTIONAL_HEX_MAPPINGS][PTM_MAX_POINTS] = {
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
{ 0, 2, 7, 4, 5, 3, 8, 1, 9, 6, 12, 10, 11},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
{ 0, 2, 7, 4, 5, 3, 8, 1, 9, 6, 12, 10, 11},
{ 0, 7, 1, 5, 3, 4, 9, 2, 6, 8, 11, 12, 10},
{ 0, 8, 6, 12, 10, 11, 2, 9, 1, 7, 4, 5, 3},
{ 0, 6, 9, 10, 11, 12, 1, 8, 7, 2, 3, 4, 5},
{ 0, 8, 6, 12, 10, 11, 2, 9, 1, 7, 4, 5, 3},
{ 0, 6, 9, 10, 11, 12, 1, 8, 7, 2, 3, 4, 5},
{ 0, 9, 8, 11, 12, 10, 7, 6, 2, 1, 5, 3, 4},
{ 0, 9, 8, 11, 12, 10, 7, 6, 2, 1, 5, 3, 4},
{ 0, 7, 1, 5, 3, 4, 9, 2, 6, 8, 11, 12, 10},
};
//-----------------------------------------------------------------------------
// dcub
//-----------------------------------------------------------------------------
const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = { 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, 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, 1, 3, 4, 2, 7, 5, 6, 11, 13, 12, 14, 15, 16, 8, 10, 9},
{0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6}, { 0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 12, 13, 11, 9, 8, 10},
{0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8}, { 0, 2, 3, 1, 4, 8, 10, 9, 13, 12, 11, 6, 7, 5, 15, 16, 14},
{0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13}, { 0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 7, 5, 6, 12, 13, 11},
{0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10}, { 0, 3, 2, 4, 1, 12, 13, 11, 10, 8, 9, 16, 14, 15, 5, 6, 7},
{0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11}, { 0, 3, 1, 2, 4, 13, 11, 12, 5, 7, 6, 10, 9, 8, 16, 14, 15},
{0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15}, { 0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 13, 11, 12, 6, 7, 5},
{0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7}, { 0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 8, 10, 9, 11, 12, 13},
{0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5}, { 0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 15, 16, 14, 13, 11, 12},
{0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9}, { 0, 4, 3, 2, 1, 15, 16, 14, 12, 11, 13, 9, 8, 10, 7, 5, 6},
{0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} }; { 0, 3, 4, 1, 2, 11, 12, 13, 16, 15, 14, 5, 6, 7, 10, 9, 8},
};
const int8_t template_indices_dcub[NUM_CONVENTIONAL_DCUB_MAPPINGS] = {0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0};
const int8_t mapping_dcub_conventional[NUM_CONVENTIONAL_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, 15, 16, 14, 13, 11, 12},
{ 0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 12, 13, 11, 9, 8, 10},
{ 0, 1, 3, 4, 2, 7, 5, 6, 11, 13, 12, 14, 15, 16, 8, 10, 9},
{ 0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 7, 5, 6, 12, 13, 11},
{ 0, 2, 3, 1, 4, 8, 10, 9, 13, 12, 11, 6, 7, 5, 15, 16, 14},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 1, 3, 4, 2, 7, 5, 6, 11, 13, 12, 14, 15, 16, 8, 10, 9},
{ 0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 12, 13, 11, 9, 8, 10},
{ 0, 2, 3, 1, 4, 8, 10, 9, 13, 12, 11, 6, 7, 5, 15, 16, 14},
{ 0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 7, 5, 6, 12, 13, 11},
{ 0, 3, 2, 4, 1, 12, 13, 11, 10, 8, 9, 16, 14, 15, 5, 6, 7},
{ 0, 3, 1, 2, 4, 13, 11, 12, 5, 7, 6, 10, 9, 8, 16, 14, 15},
{ 0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 13, 11, 12, 6, 7, 5},
{ 0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 8, 10, 9, 11, 12, 13},
{ 0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 15, 16, 14, 13, 11, 12},
{ 0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 13, 11, 12, 6, 7, 5},
{ 0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 8, 10, 9, 11, 12, 13},
{ 0, 3, 2, 4, 1, 12, 13, 11, 10, 8, 9, 16, 14, 15, 5, 6, 7},
{ 0, 3, 1, 2, 4, 13, 11, 12, 5, 7, 6, 10, 9, 8, 16, 14, 15},
{ 0, 4, 3, 2, 1, 15, 16, 14, 12, 11, 13, 9, 8, 10, 7, 5, 6},
{ 0, 4, 3, 2, 1, 15, 16, 14, 12, 11, 13, 9, 8, 10, 7, 5, 6},
{ 0, 3, 4, 1, 2, 11, 12, 13, 16, 15, 14, 5, 6, 7, 10, 9, 8},
{ 0, 3, 4, 1, 2, 11, 12, 13, 16, 15, 14, 5, 6, 7, 10, 9, 8},
};
//-----------------------------------------------------------------------------
// dhex
//-----------------------------------------------------------------------------
const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = { 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, 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, 3, 1, 2, 4, 12, 11, 13, 5, 6, 7, 9, 8, 10, 16, 14, 15},
{0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} }; { 0, 2, 3, 1, 4, 8, 9, 10, 12, 11, 13, 6, 5, 7, 15, 16, 14},
};
const int8_t template_indices_dhex[NUM_CONVENTIONAL_DHEX_MAPPINGS] = {0, 1, 1, 0, 0, 3, 2, 2, 3, 3, 2, 1};
const int8_t mapping_dhex_conventional[NUM_CONVENTIONAL_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 3, 1, 2, 4, 12, 11, 13, 5, 6, 7, 9, 8, 10, 16, 14, 15},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 3, 1, 2, 4, 12, 11, 13, 5, 6, 7, 9, 8, 10, 16, 14, 15},
{ 0, 2, 3, 1, 4, 8, 9, 10, 12, 11, 13, 6, 5, 7, 15, 16, 14},
{ 0, 2, 3, 1, 4, 8, 9, 10, 12, 11, 13, 6, 5, 7, 15, 16, 14},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 2, 3, 1, 4, 8, 9, 10, 12, 11, 13, 6, 5, 7, 15, 16, 14},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 3, 1, 2, 4, 12, 11, 13, 5, 6, 7, 9, 8, 10, 16, 14, 15},
{ 0, 3, 1, 2, 4, 12, 11, 13, 5, 6, 7, 9, 8, 10, 16, 14, 15},
{ 0, 2, 3, 1, 4, 8, 9, 10, 12, 11, 13, 6, 5, 7, 15, 16, 14},
};
//-----------------------------------------------------------------------------
// graphene
//-----------------------------------------------------------------------------
const int8_t mapping_graphene[NUM_GRAPHENE_MAPPINGS][PTM_MAX_POINTS] = {
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9},
{ 0, 2, 3, 1, 6, 7, 8, 9, 4, 5},
{ 0, 3, 1, 2, 8, 9, 4, 5, 6, 7},
{ 0, 2, 1, 3, 7, 6, 5, 4, 9, 8},
{ 0, 3, 2, 1, 9, 8, 7, 6, 5, 4},
{ 0, 1, 3, 2, 5, 4, 9, 8, 7, 6},
};
const int8_t template_indices_graphene[NUM_CONVENTIONAL_GRAPHENE_MAPPINGS] = {0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1};
const int8_t mapping_graphene_conventional[NUM_CONVENTIONAL_GRAPHENE_MAPPINGS][PTM_MAX_POINTS] = {
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9},
{ 0, 2, 3, 1, 6, 7, 8, 9, 4, 5},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9},
{ 0, 2, 3, 1, 6, 7, 8, 9, 4, 5},
{ 0, 3, 1, 2, 8, 9, 4, 5, 6, 7},
{ 0, 3, 2, 1, 9, 8, 7, 6, 5, 4},
{ 0, 2, 1, 3, 7, 6, 5, 4, 9, 8},
{ 0, 3, 2, 1, 9, 8, 7, 6, 5, 4},
{ 0, 2, 1, 3, 7, 6, 5, 4, 9, 8},
{ 0, 1, 3, 2, 5, 4, 9, 8, 7, 6},
{ 0, 1, 3, 2, 5, 4, 9, 8, 7, 6},
{ 0, 3, 1, 2, 8, 9, 4, 5, 6, 7},
};
} }
#endif #endif

1247
src/USER-PTM/ptm_graph_data.cpp
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21
src/USER-PTM/ptm_graph_data.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_GRAPH_DATA_H #ifndef PTM_GRAPH_DATA_H
#define PTM_GRAPH_DATA_H #define PTM_GRAPH_DATA_H
@ -8,12 +17,12 @@ namespace ptm {
typedef struct typedef struct
{ {
int id; int id;
uint64_t hash; uint64_t hash;
int automorphism_index; int automorphism_index;
int num_automorphisms; int num_automorphisms;
int8_t canonical_labelling[PTM_MAX_POINTS]; int8_t canonical_labelling[PTM_MAX_POINTS];
int8_t facets[PTM_MAX_FACETS][3]; int8_t facets[PTM_MAX_FACETS][3];
} graph_t; } graph_t;
#define NUM_SC_GRAPHS 1 #define NUM_SC_GRAPHS 1

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src/USER-PTM/ptm_graph_tools.cpp
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@ -1,3 +1,12 @@
/*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.
*/
#include <cstring> #include <cstring>
#include <algorithm> #include <algorithm>
#include "ptm_graph_tools.h" #include "ptm_graph_tools.h"
@ -8,48 +17,48 @@ namespace ptm {
bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]) 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); memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
for (int i = 0;i<num_facets;i++) for (int i = 0;i<num_facets;i++)
{ {
int a = facets[i][0]; int a = facets[i][0];
int b = facets[i][1]; int b = facets[i][1];
int c = facets[i][2]; int c = facets[i][2];
//assert(common[a][b] == -1); //assert(common[a][b] == -1);
//assert(common[b][c] == -1); //assert(common[b][c] == -1);
//assert(common[c][a] == -1); //assert(common[c][a] == -1);
if (common[a][b] != -1 || common[b][c] != -1 || common[c][a] != -1) if (common[a][b] != -1 || common[b][c] != -1 || common[c][a] != -1)
return false; return false;
common[a][b] = c; common[a][b] = c;
common[b][c] = a; common[b][c] = a;
common[c][a] = b; common[c][a] = b;
} }
return true; return true;
} }
int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree) int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree)
{ {
memset(degree, 0, sizeof(int8_t) * num_nodes); memset(degree, 0, sizeof(int8_t) * num_nodes);
for (int i = 0;i<num_facets;i++) for (int i = 0;i<num_facets;i++)
{ {
int a = facets[i][0]; int a = facets[i][0];
int b = facets[i][1]; int b = facets[i][1];
int c = facets[i][2]; int c = facets[i][2];
degree[a]++; degree[a]++;
degree[b]++; degree[b]++;
degree[c]++; degree[c]++;
} }
int8_t max_degree = 0; int8_t max_degree = 0;
for (int i = 0;i<num_nodes;i++) for (int i = 0;i<num_nodes;i++)
max_degree = std::max(max_degree, degree[i]); max_degree = std::max(max_degree, degree[i]);
return max_degree; return max_degree;
} }
} }

9
src/USER-PTM/ptm_graph_tools.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_GRAPH_TOOLS_H #ifndef PTM_GRAPH_TOOLS_H
#define PTM_GRAPH_TOOLS_H #define PTM_GRAPH_TOOLS_H

450
src/USER-PTM/ptm_index.cpp
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@ -1,218 +1,302 @@
/*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.
*/
#include "ptm_alloy_types.h"
#include "ptm_constants.h"
#include "ptm_convex_hull_incremental.h"
#include "ptm_deformation_gradient.h"
#include "ptm_functions.h"
#include "ptm_graph_data.h"
#include "ptm_initialize_data.h"
#include "ptm_neighbour_ordering.h"
#include "ptm_normalize_vertices.h"
#include "ptm_polar.h"
#include "ptm_quat.h"
#include "ptm_structure_matcher.h"
#include <algorithm>
#include <cassert>
#include <cfloat>
#include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include <cmath>
#include <cfloat>
#include <cassert>
#include <algorithm>
#include "ptm_convex_hull_incremental.h"
#include "ptm_graph_data.h"
#include "ptm_deformation_gradient.h"
#include "ptm_alloy_types.h"
#include "ptm_neighbour_ordering.h"
#include "ptm_normalize_vertices.h"
#include "ptm_quat.h"
#include "ptm_polar.h"
#include "ptm_initialize_data.h"
#include "ptm_structure_matcher.h"
#include "ptm_functions.h"
#include "ptm_constants.h"
static double calculate_interatomic_distance(int type, double scale) {
assert(type >= 1 && type <= 8);
//todo: verify that c == norm(template[1]) // these values should be equal to norm(template[1])
static double calculate_interatomic_distance(int type, double scale) double c[9] = {0,
{ 1,
assert(type >= 1 && type <= 7); 1,
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))}; (7. - 3.5 * sqrt(3)),
return c[type] / scale; 1,
1,
sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)),
sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)),
-3. / 11 + 6 * sqrt(3) / 11};
return c[type] / scale;
} }
static double calculate_lattice_constant(int type, double interatomic_distance) static double calculate_lattice_constant(int type,
{ double interatomic_distance) {
assert(type >= 1 && type <= 7); assert(type >= 1 && type <= 8);
double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)}; double c[9] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2),
return c[type] * interatomic_distance; 1, 4 / sqrt(3), 4 / sqrt(3), sqrt(3)};
return c[type] * interatomic_distance;
} }
static int rotate_into_fundamental_zone(int type, double* q) static int rotate_into_fundamental_zone(int type,
{ bool output_conventional_orientation,
if (type == PTM_MATCH_SC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); double *q) {
if (type == PTM_MATCH_FCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); if (type == PTM_MATCH_SC)
if (type == PTM_MATCH_BCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
if (type == PTM_MATCH_ICO) return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q); if (type == PTM_MATCH_FCC)
if (type == PTM_MATCH_HCP) return ptm::rotate_quaternion_into_hcp_fundamental_zone(q); return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
if (type == PTM_MATCH_DCUB) return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q); if (type == PTM_MATCH_BCC)
if (type == PTM_MATCH_DHEX) return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
return -1; if (type == PTM_MATCH_ICO)
return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q);
if (type == PTM_MATCH_HCP || type == PTM_MATCH_GRAPHENE) {
if (output_conventional_orientation) {
return ptm::rotate_quaternion_into_hcp_conventional_fundamental_zone(q);
} else {
return ptm::rotate_quaternion_into_hcp_fundamental_zone(q);
}
}
if (type == PTM_MATCH_DCUB) {
if (output_conventional_orientation) {
return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
} else {
return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
}
}
if (type == PTM_MATCH_DHEX) {
if (output_conventional_orientation) {
return ptm::rotate_quaternion_into_hcp_conventional_fundamental_zone(q);
} else {
return ptm::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, static void output_data(ptm::result_t *res, double (*points)[3],
int8_t* ordering, double (*points)[3], int32_t* numbers) int32_t *numbers, size_t *ordering,
{ bool output_conventional_orientation, int32_t *p_type,
if (topological_ordering) int32_t *p_alloy_type, double *p_scale, double *p_rmsd,
{ double *q, double *F, double *F_res, double *U,
double normalized_points[PTM_MAX_INPUT_POINTS][3]; double *P, double *p_interatomic_distance,
ptm::normalize_vertices(num_points, unpermuted_points, normalized_points); double *p_lattice_constant, size_t *output_indices) {
int ret = ptm::calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); const ptm::refdata_t *ref = res->ref_struct;
if (ret != 0) if (ref == NULL)
topological_ordering = false; return;
}
if (!topological_ordering) *p_type = ref->type;
for (int i=0;i<num_points;i++) if (p_alloy_type != NULL)
ordering[i] = i; *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers);
for (int i=0;i<num_points;i++) int8_t temp[PTM_MAX_POINTS];
{ memset(temp, -1, PTM_MAX_POINTS * sizeof(int8_t));
memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double)); int bi = rotate_into_fundamental_zone(ref->type,
output_conventional_orientation, res->q);
//todo: return if bi == -1
if (bi != -1)
{
if (output_conventional_orientation & (ref->type == PTM_MATCH_HCP || ref->type == PTM_MATCH_GRAPHENE || ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX))
{
for (int i = 0; i < ref->num_nbrs + 1; i++)
temp[ref->mapping_conventional[bi][i]] = res->mapping[i];
}
else
{
for (int i = 0; i < ref->num_nbrs + 1; i++)
temp[ref->mapping[bi][i]] = res->mapping[i];
}
}
if (unpermuted_numbers != NULL) memcpy(res->mapping, temp, (ref->num_nbrs + 1) * sizeof(int8_t));
numbers[i] = unpermuted_numbers[ordering[i]];
} if (F != NULL && F_res != NULL) {
double scaled_points[PTM_MAX_INPUT_POINTS][3];
ptm::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;
}
const double (*ref_template)[3] = ref->points;
const double (*ref_penrose)[3] = ref->penrose;
if (output_conventional_orientation & (ref->type == PTM_MATCH_HCP || ref->type == PTM_MATCH_GRAPHENE || ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX))
{
if (ref->template_indices[bi] == 1)
{
ref_template = ref->points_alt1;
ref_penrose = ref->penrose_alt1;
}
else if (ref->template_indices[bi] == 2)
{
ref_template = ref->points_alt2;
ref_penrose = ref->penrose_alt2;
}
else if (ref->template_indices[bi] == 3)
{
ref_template = ref->points_alt3;
ref_penrose = ref->penrose_alt3;
}
}
ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref_template,
res->mapping, scaled_points, ref_penrose,
F, F_res);
if (ref->type == PTM_MATCH_GRAPHENE) // hack for pseudo-2d structures
F[8] = 1;
if (P != NULL && U != NULL)
ptm::polar_decomposition_3x3(F, false, U, P);
}
if (output_indices != NULL)
for (int i = 0; i < ref->num_nbrs + 1; i++)
output_indices[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));
} }
static void output_data(ptm::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 ptm::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 = ptm::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];
ptm::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;
}
ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
if (P != NULL && U != NULL)
ptm::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; extern bool ptm_initialized;
int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int ptm_index(ptm_local_handle_t local_handle, size_t atom_index,
int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, int(get_neighbours)(void *vdata, size_t central_index, size_t atom_index, int num,
int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, size_t *nbr_indices, int32_t *numbers,
double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) double (*nbr_pos)[3]),
{ void *nbrlist, int32_t flags,
assert(ptm_initialized); bool output_conventional_orientation, int32_t *p_type,
assert(num_points <= PTM_MAX_INPUT_POINTS); int32_t *p_alloy_type, double *p_scale, double *p_rmsd, double *q,
double *F, double *F_res, double *U, double *P,
double *p_interatomic_distance, double *p_lattice_constant,
size_t *output_indices) {
assert(ptm_initialized);
if (flags & PTM_CHECK_SC) int ret = 0;
assert(num_points >= PTM_NUM_POINTS_SC); ptm::result_t res;
res.ref_struct = NULL;
res.rmsd = INFINITY;
if (flags & PTM_CHECK_BCC) size_t ordering[PTM_MAX_INPUT_POINTS];
assert(num_points >= PTM_NUM_POINTS_BCC); int32_t numbers[PTM_MAX_INPUT_POINTS];
double points[PTM_MAX_INPUT_POINTS][3];
if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) size_t dordering[PTM_MAX_INPUT_POINTS];
assert(num_points >= PTM_NUM_POINTS_FCC); int32_t dnumbers[PTM_MAX_INPUT_POINTS];
double dpoints[PTM_MAX_INPUT_POINTS][3];
if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) size_t gordering[PTM_MAX_INPUT_POINTS];
assert(num_points >= PTM_NUM_POINTS_DCUB); int32_t gnumbers[PTM_MAX_INPUT_POINTS];
double gpoints[PTM_MAX_INPUT_POINTS][3];
int ret = 0; ptm::convexhull_t ch;
ptm::result_t res; double ch_points[PTM_MAX_INPUT_POINTS][3];
res.ref_struct = NULL; int num_lpoints = 0;
res.rmsd = INFINITY;
int8_t ordering[PTM_MAX_INPUT_POINTS]; if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO |
double points[PTM_MAX_POINTS][3]; PTM_CHECK_BCC)) {
int32_t numbers[PTM_MAX_POINTS]; int min_points = PTM_NUM_POINTS_SC;
if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
min_points = PTM_NUM_POINTS_FCC;
if (flags & PTM_CHECK_BCC)
min_points = PTM_NUM_POINTS_BCC;
int8_t dordering[PTM_MAX_INPUT_POINTS]; num_lpoints = ptm::calculate_neighbour_ordering(
double dpoints[PTM_MAX_POINTS][3]; local_handle, atom_index, min_points, get_neighbours, nbrlist, false,
int32_t dnumbers[PTM_MAX_POINTS]; ordering, points, numbers);
if (num_lpoints >= min_points) {
ptm::normalize_vertices(num_lpoints, points, ch_points);
ch.ok = false;
ptm::convexhull_t ch; if (flags & PTM_CHECK_SC)
double ch_points[PTM_MAX_INPUT_POINTS][3]; ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res);
if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)) if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
{ ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);
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);
ptm::normalize_vertices(num_lpoints, points, ch_points);
ch.ok = false;
if (flags & PTM_CHECK_SC) if (flags & PTM_CHECK_BCC)
ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res); ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res);
}
}
if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) {
ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); const int num_inner = 4, num_outer = 3, max_snbrs = 12;
ret = ptm::calculate_two_shell_neighbour_ordering(
(void *)local_handle, atom_index, get_neighbours, nbrlist, num_inner,
num_outer, max_snbrs, false, dordering, dpoints, dnumbers);
if (ret == 0) {
ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
ch.ok = false;
if (flags & PTM_CHECK_BCC) ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res); }
} }
if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) if (flags & PTM_CHECK_GRAPHENE) {
{ const int num_inner = 3, num_outer = 2, max_snbrs = 12;
ret = ptm::calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); ret = ptm::calculate_two_shell_neighbour_ordering(
if (ret == 0) (void *)local_handle, atom_index, get_neighbours, nbrlist, num_inner,
{ num_outer, max_snbrs, true, gordering, gpoints, gnumbers);
ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); if (ret == 0) {
ch.ok = false; ret = match_graphene(gpoints, &res);
}
}
ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); *p_type = PTM_MATCH_NONE;
} if (p_alloy_type != NULL)
} *p_alloy_type = PTM_ALLOY_NONE;
if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX)) if (output_indices != NULL)
{ memset(output_indices, -1, PTM_MAX_INPUT_POINTS * sizeof(size_t));
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; if (res.ref_struct == NULL)
return PTM_NO_ERROR;
if (res.ref_struct->type == PTM_MATCH_DCUB ||
res.ref_struct->type == PTM_MATCH_DHEX) {
output_data(&res, dpoints, dnumbers, dordering,
output_conventional_orientation, p_type, p_alloy_type, p_scale,
p_rmsd, q, F, F_res, U, P, p_interatomic_distance,
p_lattice_constant, output_indices);
} else if (res.ref_struct->type == PTM_MATCH_GRAPHENE) {
output_data(&res, gpoints, gnumbers, gordering,
output_conventional_orientation, p_type, p_alloy_type, p_scale,
p_rmsd, q, F, F_res, U, P, p_interatomic_distance,
p_lattice_constant, output_indices);
} else {
output_data(&res, points, numbers, ordering, output_conventional_orientation,
p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, U, P,
p_interatomic_distance, p_lattice_constant, output_indices);
}
return PTM_NO_ERROR;
} }

75
src/USER-PTM/ptm_initialize_data.cpp
View File

@ -1,3 +1,12 @@
/*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.
*/
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
@ -10,62 +19,62 @@
static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
{ {
double plane_normal[3]; double plane_normal[3];
double origin[3] = {0, 0, 0}; double origin[3] = {0, 0, 0};
for (int i = 0;i<num_facets;i++) for (int i = 0;i<num_facets;i++)
ptm::add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin); ptm::add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
} }
static int initialize_graphs(const ptm::refdata_t* s, int8_t* colours) static int initialize_graphs(const ptm::refdata_t* s, int8_t* colours)
{ {
for (int i = 0;i<s->num_graphs;i++) for (int i = 0;i<s->num_graphs;i++)
{ {
int8_t code[2 * PTM_MAX_EDGES]; int8_t code[2 * PTM_MAX_EDGES];
int8_t degree[PTM_MAX_NBRS]; int8_t degree[PTM_MAX_NBRS];
int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
assert(_max_degree <= s->max_degree); assert(_max_degree <= s->max_degree);
make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
int ret = ptm::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); int ret = ptm::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) if (ret != 0)
return ret; return ret;
} }
return PTM_NO_ERROR; return PTM_NO_ERROR;
} }
bool ptm_initialized = false; bool ptm_initialized = false;
int ptm_initialize_global() int ptm_initialize_global()
{ {
if (ptm_initialized) if (ptm_initialized)
return PTM_NO_ERROR; return PTM_NO_ERROR;
int8_t colours[PTM_MAX_POINTS] = {0}; 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}; 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(&ptm::structure_sc, colours); int ret = initialize_graphs(&ptm::structure_sc, colours);
ret |= initialize_graphs(&ptm::structure_fcc, colours); ret |= initialize_graphs(&ptm::structure_fcc, colours);
ret |= initialize_graphs(&ptm::structure_hcp, colours); ret |= initialize_graphs(&ptm::structure_hcp, colours);
ret |= initialize_graphs(&ptm::structure_ico, colours); ret |= initialize_graphs(&ptm::structure_ico, colours);
ret |= initialize_graphs(&ptm::structure_bcc, colours); ret |= initialize_graphs(&ptm::structure_bcc, colours);
ret |= initialize_graphs(&ptm::structure_dcub, dcolours); ret |= initialize_graphs(&ptm::structure_dcub, dcolours);
ret |= initialize_graphs(&ptm::structure_dhex, dcolours); ret |= initialize_graphs(&ptm::structure_dhex, dcolours);
if (ret == PTM_NO_ERROR) if (ret == PTM_NO_ERROR)
ptm_initialized = true; ptm_initialized = true;
return ret; return ret;
} }
ptm_local_handle_t ptm_initialize_local() ptm_local_handle_t ptm_initialize_local()
{ {
assert(ptm_initialized); assert(ptm_initialized);
return (ptm_local_handle_t)ptm::voronoi_initialize_local(); return (ptm_local_handle_t)ptm::voronoi_initialize_local();
} }
void ptm_uninitialize_local(ptm_local_handle_t ptr) void ptm_uninitialize_local(ptm_local_handle_t ptr)
{ {
ptm::voronoi_uninitialize_local(ptr); ptm::voronoi_uninitialize_local(ptr);
} }

204
src/USER-PTM/ptm_initialize_data.h
View File

@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_INITIALIZE_DATA_H #ifndef PTM_INITIALIZE_DATA_H
#define PTM_INITIALIZE_DATA_H #define PTM_INITIALIZE_DATA_H
@ -9,34 +18,193 @@
#include "ptm_neighbour_ordering.h" #include "ptm_neighbour_ordering.h"
#include "ptm_canonical_coloured.h" #include "ptm_canonical_coloured.h"
#include "ptm_convex_hull_incremental.h" #include "ptm_convex_hull_incremental.h"
#include "ptm_alt_templates.h"
namespace ptm { namespace ptm {
typedef struct typedef struct
{ {
int type; int type;
int num_nbrs; int num_nbrs;
int num_facets; int num_facets;
int max_degree; int max_degree;
int num_graphs; int num_graphs;
int num_mappings; graph_t* graphs;
graph_t* graphs; const double (*points)[3];
const double (*points)[3]; const double (*points_alt1)[3];
const double (*penrose)[3]; const double (*points_alt2)[3];
const int8_t (*mapping)[PTM_MAX_POINTS]; const double (*points_alt3)[3];
const double (*penrose)[3];
const double (*penrose_alt1)[3];
const double (*penrose_alt2)[3];
const double (*penrose_alt3)[3];
int num_mappings;
const int8_t (*mapping)[PTM_MAX_POINTS];
const int8_t (*mapping_conventional)[PTM_MAX_POINTS];
const int8_t *template_indices;
} refdata_t; } 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, //.type
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 }; 6, //.num_nbrs
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 }; 8, //.num_facets
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 }; 4, //.max_degree
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 }; NUM_SC_GRAPHS, //.num_graphs
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 }; graphs_sc, //.graphs
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 }; ptm_template_sc, //.points
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 }; NULL, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_sc, //.penrose
NULL, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
NUM_CUBIC_MAPPINGS, //.num_mappings
mapping_sc, //.mapping
NULL, //.mapping_conventional
NULL, //.template_indices
};
const refdata_t structure_fcc = { PTM_MATCH_FCC, //.type
12, //.num_nbrs
20, //.num_facets
6, //.max_degree
NUM_FCC_GRAPHS, //.num_graphs
graphs_fcc, //.graphs
ptm_template_fcc, //.points
NULL, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_fcc, //.penrose
NULL, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
NUM_CUBIC_MAPPINGS, //.num_mappings
mapping_fcc, //.mapping
NULL, //.mapping_conventional
NULL, //.template_indices
};
const refdata_t structure_hcp = { PTM_MATCH_HCP, //.type
12, //.num_nbrs
20, //.num_facets
6, //.max_degree
NUM_HCP_GRAPHS, //.num_graphs
graphs_hcp, //.graphs
ptm_template_hcp, //.points
ptm_template_hcp_alt1, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_hcp, //.penrose
penrose_hcp_alt1, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
NUM_HEX_MAPPINGS, //.num_mappings
mapping_hcp, //.mapping
mapping_hcp_conventional, //.mapping_conventional
template_indices_hcp, //.template_indices
};
const refdata_t structure_ico = { PTM_MATCH_ICO, //.type
12, //.num_nbrs
20, //.num_facets
6, //.max_degree
NUM_ICO_GRAPHS, //.num_graphs
graphs_ico, //.graphs
ptm_template_ico, //.points
NULL, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_ico, //.penrose
NULL, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
NUM_ICO_MAPPINGS, //.num_mappings
mapping_ico, //.mapping
NULL, //.mapping_conventional
NULL, //.template_indices
};
const refdata_t structure_bcc = { PTM_MATCH_BCC, //.type
14, //.num_nbrs
24, //.num_facets
8, //.max_degree
NUM_BCC_GRAPHS, //.num_graphs
graphs_bcc, //.graphs
ptm_template_bcc, //.points
NULL, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_bcc, //.penrose
NULL, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
NUM_CUBIC_MAPPINGS, //.num_mappings
mapping_bcc, //.mapping
NULL, //.mapping_conventional
NULL, //.template_indices
};
const refdata_t structure_dcub = { PTM_MATCH_DCUB, //.type
16, //.num_nbrs
28, //.num_facets
8, //.max_degree
NUM_DCUB_GRAPHS, //.num_graphs
graphs_dcub, //.graphs
ptm_template_dcub, //.points
ptm_template_dcub_alt1, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_dcub, //.penrose
penrose_dcub_alt1, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
NUM_DCUB_MAPPINGS, //.num_mappings
mapping_dcub, //.mapping
mapping_dcub_conventional, //.mapping_conventional
template_indices_dcub, //.template_indices
};
const refdata_t structure_dhex = { PTM_MATCH_DHEX, //.type
16, //.num_nbrs
28, //.num_facets
8, //.max_degree
NUM_DHEX_GRAPHS, //.num_graphs
graphs_dhex, //.graphs
ptm_template_dhex, //.points
ptm_template_dhex_alt1, //.points_alt1
ptm_template_dhex_alt2, //.points_alt2
ptm_template_dhex_alt3, //.points_alt3
penrose_dhex, //.penrose
penrose_dhex_alt1, //.penrose_alt1
penrose_dhex_alt2, //.penrose_alt2
penrose_dhex_alt3, //.penrose_alt3
NUM_DHEX_MAPPINGS, //.num_mappings
mapping_dhex, //.mapping
mapping_dhex_conventional, //.mapping_conventional
template_indices_dhex, //.template_indices
};
const refdata_t structure_graphene = { PTM_MATCH_GRAPHENE, //.type
9, //.num_nbrs
-1, //.num_facets
-1, //.max_degree
-1, //.num_graphs
NULL, //.graphs
ptm_template_graphene, //.points
ptm_template_graphene_alt1, //.points_alt1
NULL, //.points_alt2
NULL, //.points_alt3
penrose_graphene, //.penrose
penrose_graphene_alt1, //.penrose_alt1
NULL, //.penrose_alt2
NULL, //.penrose_alt3
-1, //.num_mappings
mapping_graphene, //.mapping
mapping_graphene_conventional, //.mapping_conventional
template_indices_graphene, //.template_indices
};
} }
#ifdef __cplusplus #ifdef __cplusplus

466
src/USER-PTM/ptm_neighbour_ordering.cpp
View File

@ -1,205 +1,399 @@
/*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.
*/
//todo: normalize vertices
#include <cstdlib> #include <cstdlib>
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
#include <cassert> #include <cassert>
#include <algorithm> #include <algorithm>
#include <set>
#include "ptm_constants.h" #include "ptm_constants.h"
#include "ptm_voronoi_cell.h" #include "ptm_voronoi_cell.h"
#include "ptm_neighbour_ordering.h" #include "ptm_neighbour_ordering.h"
#include "ptm_normalize_vertices.h"
namespace ptm { namespace ptm {
typedef struct typedef struct
{ {
double area; double area;
double dist; double dist;
int index; int index;
int inner;
int32_t number;
double offset[3];
} sorthelper_t; } sorthelper_t;
typedef struct
{
size_t index;
int32_t number;
double area;
double offset[3];
} solidnbr_t;
static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b) static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
{ {
if (a.area > b.area) if (a.area > b.area)
return true; return true;
if (a.area < b.area) if (a.area < b.area)
return false; return false;
if (a.dist < b.dist) if (a.dist < b.dist)
return true; return true;
return false; return false;
}
static double dot_product(double* a, 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 double calculate_solid_angle(double* R1, double* R2, double* R3) //norms of R1-R3 must be 1
{
double R2R3[3];
cross_product(R2, R3, R2R3);
double numerator = dot_product(R1, R2R3);
double r1r2 = dot_product(R1, R2);
double r2r3 = dot_product(R2, R3);
double r3r1 = dot_product(R3, R1);
double denominator = 1 + r1r2 + r3r1 + r2r3;
return fabs(2 * atan2(numerator, denominator));
} }
//todo: change voronoi code to return errors rather than exiting //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, ptm_voro::voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas) static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, ptm_voro::voronoicell_neighbor* v, bool calc_solid_angles,
std::vector<int>& nbr_indices, std::vector<double>& face_areas)
{ {
const double k = 1000 * max_norm; //todo: reduce this constant const double k = 10 * max_norm;
v->init(-k,k,-k,k,-k,k); v->init(-k,k,-k,k,-k,k);
for (int i=1;i<num_points;i++) for (int i=1;i<num_points;i++)
{ {
double x = _points[i][0] - _points[0][0]; double x = _points[i][0] - _points[0][0];
double y = _points[i][1] - _points[0][1]; double y = _points[i][1] - _points[0][1];
double z = _points[i][2] - _points[0][2]; double z = _points[i][2] - _points[0][2];
v->nplane(x,y,z,normsq[i],i); v->nplane(x,y,z,normsq[i],i);
} }
v->neighbors(nbr_indices); v->neighbors(nbr_indices);
v->face_areas(face_areas);
return 0; //v->face_areas(face_areas);
if (!calc_solid_angles)
{
v->face_areas(face_areas);
return 0;
}
else
{
std::vector<int> face_vertices;
std::vector<double> vertices;
v->face_vertices(face_vertices);
v->vertices(0, 0, 0, vertices);
size_t num_vertices = vertices.size() / 3;
for (size_t i=0;i<num_vertices;i++)
{
double x = vertices[i * 3 + 0];
double y = vertices[i * 3 + 1];
double z = vertices[i * 3 + 2];
double s = sqrt(x*x + y*y + z*z);
vertices[i * 3 + 0] /= s;
vertices[i * 3 + 1] /= s;
vertices[i * 3 + 2] /= s;
}
int num_faces = v->number_of_faces();
#ifdef DEBUG
printf("number of voronoi faces: %d\n", num_faces);
#endif
//std::vector<double> solids(face_areas.size()+1);
size_t c = 0;
for (int current_face=0;current_face<num_faces;current_face++)
{
int num = face_vertices[c++];
int point_index = nbr_indices[current_face];
if (point_index > 0)
{
double solid_angle = 0;
int u = face_vertices[c];
int v = face_vertices[c+1];
for (int i=2;i<num;i++)
{
int w = face_vertices[c+i];
double omega = calculate_solid_angle(&vertices[u*3], &vertices[v*3], &vertices[w*3]);
solid_angle += omega;
v = w;
}
face_areas[current_face] = solid_angle;
//solids[current_face] = solid_angle;
//face_areas[point_index] = solid_angle;
}
c += num;
}
#ifdef DEBUG
printf("\n");
for (int i=0;i<solids.size();i++)
{
printf("%d\t%f\t%f\n", i, solids[i], face_areas[i]);
}
#endif
assert(c == face_vertices.size());
return 0;
}
} }
int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering) static int _calculate_neighbour_ordering(void* _voronoi_handle, int num_points, double (*_points)[3], bool calc_solid_angles, sorthelper_t* data)
{ {
assert(num_points <= PTM_MAX_INPUT_POINTS); assert(num_points <= PTM_MAX_INPUT_POINTS);
ptm_voro::voronoicell_neighbor* voronoi_handle = (ptm_voro::voronoicell_neighbor*)_voronoi_handle; ptm_voro::voronoicell_neighbor* voronoi_handle = (ptm_voro::voronoicell_neighbor*)_voronoi_handle;
double max_norm = 0; double max_norm = 0;
double points[PTM_MAX_INPUT_POINTS][3]; double points[PTM_MAX_INPUT_POINTS][3];
double normsq[PTM_MAX_INPUT_POINTS]; 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; for (int i=0;i<num_points;i++)
max_norm = std::max(max_norm, normsq[i]); {
#ifdef DEBUG double x = _points[i][0] - _points[0][0];
printf("point %d: %f\t%f\t%f\t%f\n", i, x, y, z, x*x + y*y + z*z); double y = _points[i][1] - _points[0][1];
#endif double z = _points[i][2] - _points[0][2];
} points[i][0] = x;
points[i][1] = y;
points[i][2] = z;
max_norm = sqrt(max_norm); normsq[i] = x*x + y*y + z*z;
max_norm = std::max(max_norm, normsq[i]);
}
std::vector<int> nbr_indices(num_points + 6); max_norm = sqrt(max_norm);
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]; std::vector<int> nbr_indices(num_points + 6);
memset(areas, 0, num_points * sizeof(double)); std::vector<double> face_areas(num_points + 6);
areas[0] = INFINITY; int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, calc_solid_angles, nbr_indices, face_areas);
for (size_t i=0;i<nbr_indices.size();i++) if (ret != 0)
{ return ret;
int index = nbr_indices[i];
if (index > 0)
areas[index] = face_areas[i];
}
sorthelper_t data[PTM_MAX_INPUT_POINTS]; double areas[PTM_MAX_INPUT_POINTS];
for (int i=0;i<num_points;i++) memset(areas, 0, num_points * sizeof(double));
{ areas[0] = INFINITY;
assert(areas[i] == areas[i]); for (size_t i=0;i<nbr_indices.size();i++)
data[i].area = areas[i]; {
data[i].dist = normsq[i]; int index = nbr_indices[i];
data[i].index = i; if (index > 0)
} areas[index] = face_areas[i];
}
std::sort(data, data + num_points, &sorthelper_compare); 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;
memcpy(data[i].offset, points[i], 3 * sizeof(double));
}
#ifdef DEBUG std::sort(data, data + num_points, &sorthelper_compare);
for (int i=0;i<num_points;i++) return ret;
printf("%d %f\n", data[i].index, data[i].area); }
#endif
for (int i=0;i<num_points;i++) int calculate_neighbour_ordering( void* _voronoi_handle, size_t atom_index, int min_points, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers,
ordering[i] = data[i].index; double (*nbr_pos)[3]), void* nbrlist, bool calc_solid_angles,
size_t* indices, double (*points)[3], int32_t* numbers)
{
size_t nbr_indices[PTM_MAX_INPUT_POINTS];
int32_t nbr_numbers[PTM_MAX_INPUT_POINTS];
double nbr_pos[PTM_MAX_INPUT_POINTS][3];
int num_points = get_neighbours(nbrlist, atom_index, atom_index, PTM_MAX_INPUT_POINTS, nbr_indices, nbr_numbers, nbr_pos);
if (num_points < min_points)
return -1;
return ret; sorthelper_t data[PTM_MAX_INPUT_POINTS];
int ret = _calculate_neighbour_ordering(_voronoi_handle, num_points, nbr_pos, calc_solid_angles, data);
if (ret != 0)
return ret;
for (int i=0;i<num_points;i++)
{
int index = data[i].index;
indices[i] = nbr_indices[index];
numbers[i] = nbr_numbers[index];
memcpy(&points[i], nbr_pos[index], 3 * sizeof(double));
}
return num_points;
}
static int find_diamond_neighbours(void* _voronoi_handle, int num_points, double (*_points)[3], size_t* nbr_indices, int32_t* nbr_numbers, int num_solid_nbrs, bool calc_solid_angles, solidnbr_t* nbrlist)
{
sorthelper_t data[PTM_MAX_INPUT_POINTS];
int ret = _calculate_neighbour_ordering(_voronoi_handle, num_points, _points, calc_solid_angles, data);
if (ret != 0)
return ret;
int n = std::min(num_solid_nbrs, num_points - 1);
for (int i=0;i<n;i++)
{
nbrlist[i].index = nbr_indices[data[i+1].index];
nbrlist[i].area = data[i+1].area;
nbrlist[i].number = nbr_numbers[data[i+1].index];
memcpy(nbrlist[i].offset, data[i+1].offset, 3 * sizeof(double));
}
return ret;
} }
void* voronoi_initialize_local() void* voronoi_initialize_local()
{ {
ptm_voro::voronoicell_neighbor* ptr = new ptm_voro::voronoicell_neighbor; ptm_voro::voronoicell_neighbor* ptr = new ptm_voro::voronoicell_neighbor;
return (void*)ptr; return (void*)ptr;
} }
void voronoi_uninitialize_local(void* _ptr) void voronoi_uninitialize_local(void* _ptr)
{ {
ptm_voro::voronoicell_neighbor* ptr = (ptm_voro::voronoicell_neighbor*)_ptr; ptm_voro::voronoicell_neighbor* ptr = (ptm_voro::voronoicell_neighbor*)_ptr;
delete ptr; delete ptr;
} }
#define MAX_INNER 4
#define MAX_SNBRS 12
typedef struct int calculate_two_shell_neighbour_ordering( void* _voronoi_handle, size_t atom_index, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3]), void* nbrlist,
int num_inner, int num_outer, int max_snbrs, bool calc_solid_angles,
size_t* nbr_indices, double (*points)[3], int32_t* numbers)
{ {
double dist; assert(num_inner <= MAX_INNER);
int p;
int index;
} diamond_t;
static bool diamond_compare(diamond_t const& a, diamond_t const& b) size_t central_nbr_indices[MAX_SNBRS + 1];
{ int32_t central_nbr_numbers[MAX_SNBRS + 1];
return a.dist < b.dist; double central_nbr_pos[MAX_SNBRS + 1][3];
} int num_points = get_neighbours(nbrlist, atom_index, atom_index, max_snbrs + 1, central_nbr_indices, central_nbr_numbers, central_nbr_pos);
if (num_points < num_inner + 1)
return -1;
int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, solidnbr_t central_solid[MAX_SNBRS];
int8_t* ordering, double (*points)[3], int32_t* numbers) int ret = find_diamond_neighbours(_voronoi_handle, num_points, central_nbr_pos, central_nbr_indices, central_nbr_numbers, max_snbrs, calc_solid_angles, central_solid);
{ if (ret != 0)
assert(num_points <= PTM_MAX_INPUT_POINTS); return ret;
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; sorthelper_t data[MAX_INNER * 6];
nbr_indices[0] = atom_index;
numbers[0] = central_nbr_numbers[0];
memset(&points[0], 0, 3 * sizeof(double));
data[index].p = j - 1; std::set<size_t> claimed;
data[index].index = i; claimed.insert(atom_index);
data[index].dist = d; for (int i=0;i<num_inner;i++)
index++; {
} nbr_indices[i+1] = central_solid[i].index;
} numbers[i+1] = central_solid[i].number;
int n = index; memcpy(&points[i+1], central_solid[i].offset, 3 * sizeof(double));
std::sort(data, data + n, &diamond_compare); claimed.insert(central_solid[i].index);
}
for (index=0;index<5;index++) int index = 0;
ordering[index] = index; for (int i=0;i<num_inner;i++)
{
size_t inner_index = central_solid[i].index;
int num_found = 0; //----------------------------------------------
bool hit[PTM_MAX_INPUT_POINTS] = {0}; size_t inner_nbr_indices[MAX_SNBRS + 1];
int counts[4] = {0}; int32_t inner_nbr_numbers[MAX_SNBRS + 1];
for (int i=0;i<n;i++) double inner_nbr_pos[MAX_SNBRS + 1][3];
{ int num_points = get_neighbours(nbrlist, atom_index, inner_index, max_snbrs + 1, inner_nbr_indices, inner_nbr_numbers, inner_nbr_pos);
int p = data[i].p; if (num_points < num_inner + 1)
int q = data[i].index; return -1;
if (hit[q] || counts[p] >= 3)
continue;
ordering[1 + 4 + 3 * p + counts[p]] = q; solidnbr_t inner_solid[MAX_SNBRS];
counts[p]++; ret = find_diamond_neighbours(_voronoi_handle, num_points, inner_nbr_pos, inner_nbr_indices, inner_nbr_numbers, max_snbrs, calc_solid_angles, inner_solid);
index++; if (ret != 0)
num_found++; return ret;
if (num_found >= 12) //----------------------------------------------
break;
}
if (num_found != 12) int n = std::min(6, num_points);
return -1; for (int j=0;j<n;j++)
{
bool already_claimed = claimed.find(inner_solid[j].index) != claimed.end();
if (already_claimed)
continue;
for (int i=0;i<PTM_NUM_NBRS_DCUB+1;i++) data[index].inner = i;
{ data[index].index = inner_solid[j].index;
memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double)); data[index].area = inner_solid[j].area;
data[index].dist = 0;
data[index].number = inner_solid[j].number;
if (unpermuted_numbers != NULL) memcpy(data[index].offset, inner_solid[j].offset, 3 * sizeof(double));
numbers[i] = unpermuted_numbers[ordering[i]]; for (int k=0;k<3;k++)
} data[index].offset[k] += central_solid[i].offset[k];
return 0; index++;
}
}
int n = index;
std::sort(data, data + n, &sorthelper_compare);
int num_found = 0;
int counts[MAX_INNER] = {0};
for (int i=0;i<n;i++)
{
int inner = data[i].inner;
int nbr_atom_index = data[i].index;
bool already_claimed = claimed.find(nbr_atom_index) != claimed.end();
if (counts[inner] >= num_outer || already_claimed)
continue;
nbr_indices[1 + num_inner + num_outer * inner + counts[inner]] = nbr_atom_index;
numbers[1 + num_inner + num_outer * inner + counts[inner]] = data[i].number;
memcpy(points[1 + num_inner + num_outer * inner + counts[inner]], &data[i].offset, 3 * sizeof(double));
claimed.insert(nbr_atom_index);
counts[inner]++;
num_found++;
if (num_found >= num_inner * num_outer)
break;
}
if (num_found != num_inner * num_outer)
return -1;
return 0;
} }
} }

20
src/USER-PTM/ptm_neighbour_ordering.h
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@ -1,14 +1,26 @@
/*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.
*/
#ifndef PTM_NEIGHBOUR_ORDERING_H #ifndef PTM_NEIGHBOUR_ORDERING_H
#define PTM_NEIGHBOUR_ORDERING_H #define PTM_NEIGHBOUR_ORDERING_H
#include <inttypes.h> #include <cstddef>
namespace ptm { namespace ptm {
int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering); int calculate_neighbour_ordering( void* _voronoi_handle, size_t atom_index, int min_points, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers,
double (*nbr_pos)[3]), void* nbrlist, bool calc_solid_angles,
size_t* nbr_indices, double (*points)[3], int32_t* numbers);
int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, int calculate_two_shell_neighbour_ordering( void* _voronoi_handle, size_t atom_index, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3]), void* nbrlist,
int8_t* ordering, double (*points)[3], int32_t* numbers); int num_inner, int num_outer, int max_snbrs, bool calc_solid_angles,
size_t* nbr_indices, double (*points)[3], int32_t* numbers);
void* voronoi_initialize_local(); void* voronoi_initialize_local();
void voronoi_uninitialize_local(void* ptr); void voronoi_uninitialize_local(void* ptr);

85
src/USER-PTM/ptm_normalize_vertices.cpp
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@ -1,57 +1,66 @@
/*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.
*/
#include <cmath> #include <cmath>
namespace ptm { namespace ptm {
void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]) void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
{ {
//calculate barycentre //calculate barycentre
double sum[3] = {0, 0, 0}; double sum[3] = {0, 0, 0};
for (int i=0;i<num;i++) for (int i=0;i<num;i++)
{ {
sum[0] += points[i][0]; sum[0] += points[i][0];
sum[1] += points[i][1]; sum[1] += points[i][1];
sum[2] += points[i][2]; sum[2] += points[i][2];
} }
sum[0] /= num; sum[0] /= num;
sum[1] /= num; sum[1] /= num;
sum[2] /= num; sum[2] /= num;
//subtract barycentre //subtract barycentre
for (int i=0;i<num;i++) for (int i=0;i<num;i++)
{ {
normalized[i][0] = points[i][0] - sum[0]; normalized[i][0] = points[i][0] - sum[0];
normalized[i][1] = points[i][1] - sum[1]; normalized[i][1] = points[i][1] - sum[1];
normalized[i][2] = points[i][2] - sum[2]; normalized[i][2] = points[i][2] - sum[2];
} }
} }
double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]) double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
{ {
subtract_barycentre(num, points, normalized); subtract_barycentre(num, points, normalized);
//calculate mean length //calculate mean length
double scale = 0.0; double scale = 0.0;
for (int i=1;i<num;i++) for (int i=1;i<num;i++)
{ {
double x = normalized[i][0]; double x = normalized[i][0];
double y = normalized[i][1]; double y = normalized[i][1];
double z = normalized[i][2]; double z = normalized[i][2];
double norm = sqrt(x*x + y*y + z*z); double norm = sqrt(x*x + y*y + z*z);
scale += norm; scale += norm;
} }
scale /= num; scale /= num;
//scale vertices such that mean length is 1 //scale vertices such that mean length is 1
for (int i=0;i<num;i++) for (int i=0;i<num;i++)
{ {
normalized[i][0] /= scale; normalized[i][0] /= scale;
normalized[i][1] /= scale; normalized[i][1] /= scale;
normalized[i][2] /= scale; normalized[i][2] /= scale;
} }
return scale; return scale;
} }
} }

9
src/USER-PTM/ptm_normalize_vertices.h
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@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_NORMALIZE_VERTICES_H #ifndef PTM_NORMALIZE_VERTICES_H
#define PTM_NORMALIZE_VERTICES_H #define PTM_NORMALIZE_VERTICES_H

449
src/USER-PTM/ptm_polar.cpp
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@ -5,37 +5,37 @@
* It has been adapted to calculate the polar decomposition of a 3x3 matrix * It has been adapted to calculate the polar decomposition of a 3x3 matrix
* Adaption by P.M. Larsen * Adaption by P.M. Larsen
* *
* Original Author(s): Douglas L. Theobald * Original Author(s): Douglas L. Theobald
* Department of Biochemistry * Department of Biochemistry
* MS 009 * MS 009
* Brandeis University * Brandeis University
* 415 South St * 415 South St
* Waltham, MA 02453 * Waltham, MA 02453
* USA * USA
* *
* dtheobald@brandeis.edu * dtheobald@brandeis.edu
* *
* Pu Liu * Pu Liu
* Johnson & Johnson Pharmaceutical Research and Development, L.L.C. * Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
* 665 Stockton Drive * 665 Stockton Drive
* Exton, PA 19341 * Exton, PA 19341
* USA * USA
* *
* pliu24@its.jnj.com * pliu24@its.jnj.com
* *
* *
* If you use this QCP rotation calculation method in a publication, please * If you use this QCP rotation calculation method in a publication, please
* reference: * reference:
* *
* Douglas L. Theobald (2005) * Douglas L. Theobald (2005)
* "Rapid calculation of RMSD using a quaternion-based characteristic * "Rapid calculation of RMSD using a quaternion-based characteristic
* polynomial." * polynomial."
* Acta Crystallographica A 61(4):478-480. * Acta Crystallographica A 61(4):478-480.
* *
* Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009) * Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009)
* "Fast determination of the optimal rotational matrix for macromolecular * "Fast determination of the optimal rotational matrix for macromolecular
* superpositions." * superpositions."
* Journal of Computational Chemistry 31(7):1561-1563. * Journal of Computational Chemistry 31(7):1561-1563.
* *
* *
* Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald * Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald
@ -45,13 +45,13 @@
* provided that the following conditions are met: * provided that the following conditions are met:
* *
* * Redistributions of source code must retain the above copyright notice, this list of * * Redistributions of source code must retain the above copyright notice, this list of
* conditions and the following disclaimer. * conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright notice, this list * * 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 * of conditions and the following disclaimer in the documentation and/or other materials
* provided with the distribution. * provided with the distribution.
* * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to * * 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 * endorse or promote products derived from this software without specific prior written
* permission. * permission.
* *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
@ -65,23 +65,23 @@
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
* *
* Source: started anew. * Source: started anew.
* *
* Change History: * Change History:
* 2009/04/13 Started source * 2009/04/13 Started source
* 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr
* If trying all rows of the adjoint still gives too small * If trying all rows of the adjoint still gives too small
* qsqr, then just return identity matrix. (DLT) * qsqr, then just return identity matrix. (DLT)
* 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct() * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct()
* invalid mem access * invalid mem access
* 2011/02/21 Made CenterCoords use weights * 2011/02/21 Made CenterCoords use weights
* 2011/05/02 Finally changed CenterCoords declaration in qcprot.h * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h
* Also changed some functions to static * Also changed some functions to static
* 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error * 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) * 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, * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix,
* for use in Polyhedral Template Matching. * for use in Polyhedral Template Matching.
* *
******************************************************************************/ ******************************************************************************/
@ -89,253 +89,252 @@
#include <algorithm> #include <algorithm>
#include <cstring> #include <cstring>
#include "ptm_quat.h" #include "ptm_quat.h"
#include "ptm_polar.h"
namespace ptm { namespace ptm {
static void matmul_3x3(double* A, double* x, double* b) 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[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[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[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[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[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[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[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[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]; b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8];
} }
static double matrix_determinant_3x3(double* A) static double matrix_determinant_3x3(double* A)
{ {
return A[0] * (A[4]*A[8] - A[5]*A[7]) return A[0] * (A[4]*A[8] - A[5]*A[7])
- A[1] * (A[3]*A[8] - A[5]*A[6]) - A[1] * (A[3]*A[8] - A[5]*A[6])
+ A[2] * (A[3]*A[7] - A[4]*A[6]); + A[2] * (A[3]*A[7] - A[4]*A[6]);
} }
static void flip_matrix(double* A) static void flip_matrix(double* A)
{ {
for (int i=0;i<9;i++) for (int i=0;i<9;i++)
A[i] = -A[i]; A[i] = -A[i];
} }
static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt) static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt)
{ {
const double evecprec = 1e-6; const double evecprec = 1e-6;
const double evalprec = 1e-11; const double evalprec = 1e-11;
double Sxx = A[0], Sxy = A[1], Sxz = A[2], double Sxx = A[0], Sxy = A[1], Sxz = A[2],
Syx = A[3], Syy = A[4], Syz = A[5], Syx = A[3], Syy = A[4], Syz = A[5],
Szx = A[6], Szy = A[7], Szz = A[8]; Szx = A[6], Szy = A[7], Szz = A[8];
double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz, double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz,
Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz, Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz,
Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx; Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx;
double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2; double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2;
double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz); double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz);
double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2; double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2;
double SxzpSzx = Sxz + Szx; double SxzpSzx = Sxz + Szx;
double SyzpSzy = Syz + Szy; double SyzpSzy = Syz + Szy;
double SxypSyx = Sxy + Syx; double SxypSyx = Sxy + Syx;
double SyzmSzy = Syz - Szy; double SyzmSzy = Syz - Szy;
double SxzmSzx = Sxz - Szx; double SxzmSzx = Sxz - Szx;
double SxymSyx = Sxy - Syx; double SxymSyx = Sxy - Syx;
double SxxpSyy = Sxx + Syy; double SxxpSyy = Sxx + Syy;
double SxxmSyy = Sxx - Syy; double SxxmSyy = Sxx - Syy;
double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2; double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2;
double C[3]; double C[3];
C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2
+ (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2) + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2)
+ (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz)) + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz))
+ (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz)) + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz))
+ (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz)) + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz))
+ (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(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[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; C[2] = -2.0 * fnorm_squared;
//Newton-Raphson //Newton-Raphson
double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0; double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0;
if (mxEigenV > evalprec) if (mxEigenV > evalprec)
{ {
for (int i=0;i<50;i++) for (int i=0;i<50;i++)
{ {
double oldg = mxEigenV; double oldg = mxEigenV;
double x2 = mxEigenV*mxEigenV; double x2 = mxEigenV*mxEigenV;
double b = (x2 + C[2])*mxEigenV; double b = (x2 + C[2])*mxEigenV;
double a = b + C[1]; double a = b + C[1];
double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a)); double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a));
mxEigenV -= delta; mxEigenV -= delta;
if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV)) if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV))
break; break;
} }
} }
else else
{ {
mxEigenV = 0.0; mxEigenV = 0.0;
} }
(*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV)); (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV));
double a11 = SxxpSyy + Szz - mxEigenV; double a11 = SxxpSyy + Szz - mxEigenV;
double a12 = SyzmSzy; double a12 = SyzmSzy;
double a13 = -SxzmSzx; double a13 = -SxzmSzx;
double a14 = SxymSyx; double a14 = SxymSyx;
double a21 = SyzmSzy; double a21 = SyzmSzy;
double a22 = SxxmSyy - Szz -mxEigenV; double a22 = SxxmSyy - Szz -mxEigenV;
double a23 = SxypSyx; double a23 = SxypSyx;
double a24 = SxzpSzx; double a24 = SxzpSzx;
double a31 = a13; double a31 = a13;
double a32 = a23; double a32 = a23;
double a33 = Syy - Sxx - Szz - mxEigenV; double a33 = Syy - Sxx - Szz - mxEigenV;
double a34 = SyzpSzy; double a34 = SyzpSzy;
double a41 = a14; double a41 = a14;
double a42 = a24; double a42 = a24;
double a43 = a34; double a43 = a34;
double a44 = Szz - SxxpSyy - mxEigenV; double a44 = Szz - SxxpSyy - mxEigenV;
double a3344_4334 = a33 * a44 - a43 * a34; double a3344_4334 = a33 * a44 - a43 * a34;
double a3244_4234 = a32 * a44 - a42 * a34; double a3244_4234 = a32 * a44 - a42 * a34;
double a3243_4233 = a32 * a43 - a42 * a33; double a3243_4233 = a32 * a43 - a42 * a33;
double a3143_4133 = a31 * a43 - a41 * a33; double a3143_4133 = a31 * a43 - a41 * a33;
double a3144_4134 = a31 * a44 - a41 * a34; double a3144_4134 = a31 * a44 - a41 * a34;
double a3142_4132 = a31 * a42 - a41 * a32; double a3142_4132 = a31 * a42 - a41 * a32;
double a1324_1423 = a13 * a24 - a14 * a23; double a1324_1423 = a13 * a24 - a14 * a23;
double a1224_1422 = a12 * a24 - a14 * a22; double a1224_1422 = a12 * a24 - a14 * a22;
double a1223_1322 = a12 * a23 - a13 * a22; double a1223_1322 = a12 * a23 - a13 * a22;
double a1124_1421 = a11 * a24 - a14 * a21; double a1124_1421 = a11 * a24 - a14 * a21;
double a1123_1321 = a11 * a23 - a13 * a21; double a1123_1321 = a11 * a23 - a13 * a21;
double a1122_1221 = a11 * a22 - a12 * a21; double a1122_1221 = a11 * a22 - a12 * a21;
double q[4][4]; double q[4][4];
q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233; 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][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133;
q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132; 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[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][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233;
q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133; 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][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132;
q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * 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][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322;
q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321; 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][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221;
q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * 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][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322;
q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321; 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][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221;
q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221; q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221;
double qsqr[4]; double qsqr[4];
for (int i=0;i<4;i++) 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]; 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; int bi = 0;
double max = 0; double max = 0;
for (int i=0;i<4;i++) for (int i=0;i<4;i++)
{ {
if (qsqr[i] > max) if (qsqr[i] > max)
{ {
bi = i; bi = i;
max = qsqr[i]; max = qsqr[i];
} }
} }
bool too_small = false; bool too_small = false;
if (qsqr[bi] < evecprec) if (qsqr[bi] < evecprec)
{ {
//if qsqr is still too small, return the identity rotation. //if qsqr is still too small, return the identity rotation.
q[bi][0] = 1; q[bi][0] = 1;
q[bi][1] = 0; q[bi][1] = 0;
q[bi][2] = 0; q[bi][2] = 0;
q[bi][3] = 0; q[bi][3] = 0;
too_small = true; too_small = true;
} }
else else
{ {
double normq = sqrt(qsqr[bi]); double normq = sqrt(qsqr[bi]);
q[bi][0] /= normq; q[bi][0] /= normq;
q[bi][1] /= normq; q[bi][1] /= normq;
q[bi][2] /= normq; q[bi][2] /= normq;
q[bi][3] /= normq; q[bi][3] /= normq;
} }
memcpy(qopt, q[bi], 4 * sizeof(double)); memcpy(qopt, q[bi], 4 * sizeof(double));
return !too_small; return !too_small;
} }
int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P) int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P)
{ {
double A[9]; double A[9];
memcpy(A, _A, 9 * sizeof(double)); memcpy(A, _A, 9 * sizeof(double));
double det = matrix_determinant_3x3(A); double det = matrix_determinant_3x3(A);
if (det < 0) if (det < 0)
flip_matrix(A); flip_matrix(A);
double q[4]; double q[4];
double nrmsdsq = 0; double nrmsdsq = 0;
optimal_quaternion(A, true, -1, &nrmsdsq, q); optimal_quaternion(A, true, -1, &nrmsdsq, q);
q[0] = -q[0]; q[0] = -q[0];
quaternion_to_rotation_matrix(q, U); quaternion_to_rotation_matrix(q, U);
if (det < 0) if (det < 0)
flip_matrix(U); flip_matrix(U);
double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]}; double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]};
if (right_sided) if (right_sided)
matmul_3x3(UT, _A, P); matmul_3x3(UT, _A, P);
else else
matmul_3x3(_A, UT, P); matmul_3x3(_A, UT, P);
return 0; return 0;
} }
void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation) 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; 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) for (int i = 0; i < num; ++i)
{ {
double x1 = coords1[i][0]; double x1 = coords1[i][0];
double y1 = coords1[i][1]; double y1 = coords1[i][1];
double z1 = coords1[i][2]; double z1 = coords1[i][2];
double x2 = coords2[permutation[i]][0]; double x2 = coords2[permutation[i]][0];
double y2 = coords2[permutation[i]][1]; double y2 = coords2[permutation[i]][1];
double z2 = coords2[permutation[i]][2]; double z2 = coords2[permutation[i]][2];
A[0] += x1 * x2; A[0] += x1 * x2;
A[1] += x1 * y2; A[1] += x1 * y2;
A[2] += x1 * z2; A[2] += x1 * z2;
A[3] += y1 * x2; A[3] += y1 * x2;
A[4] += y1 * y2; A[4] += y1 * y2;
A[5] += y1 * z2; A[5] += y1 * z2;
A[6] += z1 * x2; A[6] += z1 * x2;
A[7] += z1 * y2; A[7] += z1 * y2;
A[8] += z1 * z2; A[8] += z1 * z2;
} }
} }
int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U) int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U)
{ {
optimal_quaternion(A, false, E0, p_nrmsdsq, q); optimal_quaternion(A, false, E0, p_nrmsdsq, q);
quaternion_to_rotation_matrix(q, U); quaternion_to_rotation_matrix(q, U);
return 0; return 0;
} }
} }

10
src/USER-PTM/ptm_polar.h
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@ -1,9 +1,17 @@
/*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.
*/
#ifndef PTM_POLAR_H #ifndef PTM_POLAR_H
#define PTM_POLAR_H #define PTM_POLAR_H
#include <stdint.h> #include <stdint.h>
#include <stdbool.h> #include <stdbool.h>
#include <inttypes.h>
namespace ptm { namespace ptm {

586
src/USER-PTM/ptm_quat.cpp
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@ -1,399 +1,339 @@
/*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.
*/
#include <cstring> #include <cstring>
#include <cmath> #include <cmath>
#include <cfloat> #include <cfloat>
#include <algorithm>
namespace ptm { namespace ptm {
#define SIGN(x) (x >= 0 ? 1 : -1) #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 const double generator_cubic[24][4] = {
#define HALF_SQRT_2 0.7071067811865474617150084668537601828575 { 1, 0, 0, 0 },
{ sqrt(2)/2, sqrt(2)/2, 0, 0 },
{ sqrt(2)/2, 0, sqrt(2)/2, 0 },
{ sqrt(2)/2, 0, 0, sqrt(2)/2 },
{ sqrt(2)/2, 0, 0, -sqrt(2)/2 },
{ sqrt(2)/2, 0, -sqrt(2)/2, 0 },
{ sqrt(2)/2, -sqrt(2)/2, -0, -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, -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, 1, 0, 0 },
{ 0, sqrt(2)/2, sqrt(2)/2, 0 },
{ 0, sqrt(2)/2, 0, sqrt(2)/2 },
{ 0, sqrt(2)/2, 0, -sqrt(2)/2 },
{ 0, sqrt(2)/2, -sqrt(2)/2, 0 },
{ 0, 0, 1, 0 },
{ 0, 0, sqrt(2)/2, sqrt(2)/2 },
{ 0, 0, sqrt(2)/2, -sqrt(2)/2 },
{ 0, 0, 0, 1 },
};
#define PHI 1.6180339887498949025257388711906969547272 const double generator_diamond_cubic[12][4] = {
#define HALF_PHI 0.8090169943749474512628694355953484773636 { 1, 0, 0, 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, -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, 1, 0, 0 },
{ 0, 0, 1, 0 },
{ 0, 0, 0, 1 },
};
#define INV_PHI 0.6180339887498947915034364086750429123640 const double generator_hcp[6][4] = {
#define HALF_INV_PHI 0.3090169943749473957517182043375214561820 { 1, 0, 0, 0 },
{ 0.5, 0, 0, sqrt(3)/2 },
#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089 { 0.5, 0, 0, -sqrt(3)/2 },
#define SQRT_2_3 0.8164965809277260344600790631375275552273 { 0, sqrt(3)/2, 0.5, 0 },
#define SQRT_1_6 0.4082482904638630172300395315687637776136 { 0, sqrt(3)/2, -0.5, 0 },
{ 0, 0, 1, 0 },
};
double generator_cubic[24][4] = { {1, 0, 0, 0 }, const double generator_hcp_conventional[12][4] = {
{0, 1, 0, 0 }, { 1, 0, 0, 0 },
{0, 0, 1, 0 }, { sqrt(3)/2, 0, 0, 0.5 },
{0, 0, 0, 1 }, { sqrt(3)/2, 0, 0, -0.5 },
{0.5, 0.5, 0.5, 0.5 }, { 0.5, 0, 0, sqrt(3)/2 },
{0.5, 0.5, -0.5, 0.5 }, { 0.5, 0, 0, -sqrt(3)/2 },
{0.5, -0.5, 0.5, 0.5 }, { 0, 1, 0, 0 },
{0.5, -0.5, -0.5, 0.5 }, { 0, sqrt(3)/2, 0.5, 0 },
{-0.5, 0.5, 0.5, 0.5 }, { 0, sqrt(3)/2, -0.5, 0 },
{-0.5, 0.5, -0.5, 0.5 }, { 0, 0.5, sqrt(3)/2, 0 },
{-0.5, -0.5, 0.5, 0.5 }, { 0, 0.5, -sqrt(3)/2, 0 },
{-0.5, -0.5, -0.5, 0.5 }, { 0, 0, 1, 0 },
{HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, { 0, 0, 0, 1 },
{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 }, const double generator_diamond_hexagonal[3][4] = {
{0, 1, 0, 0 }, { 1, 0, 0, 0 },
{0, 0, 1, 0 }, { 0.5, 0, 0, sqrt(3)/2 },
{0, 0, 0, 1 }, { 0.5, 0, 0, -sqrt(3)/2 },
{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}, const double generator_icosahedral[60][4] = {
{0.5, 0.5, 0.5, 0.5}, { 1, 0, 0, 0 },
{0.5, -0.5, -0.5, -0.5}, { (1+sqrt(5))/4, 0.5, sqrt(25-10*sqrt(5))/10, sqrt(50-10*sqrt(5))/20 },
{0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6}, { (1+sqrt(5))/4, 0.5, -sqrt(25-10*sqrt(5))/10, -sqrt(50-10*sqrt(5))/20 },
{0, SQRT_1_6, -SQRT_2_3, SQRT_1_6}, { (1+sqrt(5))/4, 1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, -sqrt(50-10*sqrt(5))/20 },
{0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} }; { (1+sqrt(5))/4, 1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, sqrt(50-10*sqrt(5))/20 },
{ (1+sqrt(5))/4, 0, sqrt(50-10*sqrt(5))/10, sqrt(50-10*sqrt(5))/20 },
{ (1+sqrt(5))/4, 0, 0, sqrt(5./8-sqrt(5)/8) },
{ (1+sqrt(5))/4, 0, 0, -sqrt(5./8-sqrt(5)/8) },
{ (1+sqrt(5))/4, 0, -sqrt(50-10*sqrt(5))/10, -sqrt(50-10*sqrt(5))/20 },
{ (1+sqrt(5))/4, -1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, -sqrt(50-10*sqrt(5))/20 },
{ (1+sqrt(5))/4, -1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, sqrt(50-10*sqrt(5))/20 },
{ (1+sqrt(5))/4, -0.5, sqrt(25-10*sqrt(5))/10, sqrt(50-10*sqrt(5))/20 },
{ (1+sqrt(5))/4, -0.5, -sqrt(25-10*sqrt(5))/10, -sqrt(50-10*sqrt(5))/20 },
{ 0.5, (1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, -sqrt(25-10*sqrt(5))/10 },
{ 0.5, (1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, sqrt(25-10*sqrt(5))/10 },
{ 0.5, 0.5, sqrt((5+2*sqrt(5))/20), sqrt(25-10*sqrt(5))/10 },
{ 0.5, 0.5, sqrt(25-10*sqrt(5))/10, -sqrt((5+2*sqrt(5))/20) },
{ 0.5, 0.5, -sqrt(25-10*sqrt(5))/10, sqrt((5+2*sqrt(5))/20) },
{ 0.5, 0.5, -sqrt((5+2*sqrt(5))/20), -sqrt(25-10*sqrt(5))/10 },
{ 0.5, 1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, sqrt((5+2*sqrt(5))/20) },
{ 0.5, 1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, -sqrt((5+2*sqrt(5))/20) },
{ 0.5, 0, sqrt((5+sqrt(5))/10), -sqrt(25-10*sqrt(5))/10 },
{ 0.5, 0, sqrt(50-10*sqrt(5))/10, -sqrt((5+2*sqrt(5))/20) },
{ 0.5, 0, -sqrt(50-10*sqrt(5))/10, sqrt((5+2*sqrt(5))/20) },
{ 0.5, 0, -sqrt((5+sqrt(5))/10), sqrt(25-10*sqrt(5))/10 },
{ 0.5, -1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, sqrt((5+2*sqrt(5))/20) },
{ 0.5, -1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, -sqrt((5+2*sqrt(5))/20) },
{ 0.5, -0.5, sqrt((5+2*sqrt(5))/20), sqrt(25-10*sqrt(5))/10 },
{ 0.5, -0.5, sqrt(25-10*sqrt(5))/10, -sqrt((5+2*sqrt(5))/20) },
{ 0.5, -0.5, -sqrt(25-10*sqrt(5))/10, sqrt((5+2*sqrt(5))/20) },
{ 0.5, -0.5, -sqrt((5+2*sqrt(5))/20), -sqrt(25-10*sqrt(5))/10 },
{ 0.5, -(1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, -sqrt(25-10*sqrt(5))/10 },
{ 0.5, -(1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, sqrt(25-10*sqrt(5))/10 },
{ 1/(1+sqrt(5)), (1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), (1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, -sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), 0.5, sqrt((5+2*sqrt(5))/20), -sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), 0.5, -sqrt((5+2*sqrt(5))/20), sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), 0, sqrt((5+sqrt(5))/10), sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), 0, 0, sqrt(1-1/(2*sqrt(5)+6)) },
{ 1/(1+sqrt(5)), 0, 0, -sqrt(1-1/(2*sqrt(5)+6)) },
{ 1/(1+sqrt(5)), 0, -sqrt((5+sqrt(5))/10), -sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), -0.5, sqrt((5+2*sqrt(5))/20), -sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), -0.5, -sqrt((5+2*sqrt(5))/20), sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), -(1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, sqrt(10*sqrt(5)+50)/20 },
{ 1/(1+sqrt(5)), -(1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, -sqrt(10*sqrt(5)+50)/20 },
{ 0, 1, 0, 0 },
{ 0, (1+sqrt(5))/4, sqrt(5./8-sqrt(5)/8), 0 },
{ 0, (1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, -sqrt(50-10*sqrt(5))/10 },
{ 0, (1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, sqrt(50-10*sqrt(5))/10 },
{ 0, (1+sqrt(5))/4, -sqrt(5./8-sqrt(5)/8), 0 },
{ 0, 0.5, sqrt((5+2*sqrt(5))/20), sqrt(50-10*sqrt(5))/10 },
{ 0, 0.5, sqrt(25-10*sqrt(5))/10, sqrt((5+sqrt(5))/10) },
{ 0, 0.5, -sqrt(25-10*sqrt(5))/10, -sqrt((5+sqrt(5))/10) },
{ 0, 0.5, -sqrt((5+2*sqrt(5))/20), -sqrt(50-10*sqrt(5))/10 },
{ 0, 1/(1+sqrt(5)), sqrt(1-1/(2*sqrt(5)+6)), 0 },
{ 0, 1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, -sqrt((5+sqrt(5))/10) },
{ 0, 1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, sqrt((5+sqrt(5))/10) },
{ 0, 1/(1+sqrt(5)), -sqrt(1-1/(2*sqrt(5)+6)), 0 },
{ 0, 0, sqrt((5+sqrt(5))/10), -sqrt(50-10*sqrt(5))/10 },
{ 0, 0, sqrt(50-10*sqrt(5))/10, sqrt((5+sqrt(5))/10) },
};
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) 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[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[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[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]); 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) static int rotate_quaternion_into_fundamental_zone(int num_generators, const double (*generator)[4], double* q)
{ {
double max = 0.0; double max = 0.0;
int i = 0, bi = -1; int i = 0, bi = -1;
for (i=0;i<num_generators;i++) for (i=0;i<num_generators;i++)
{ {
double* g = generator[i]; const double* g = generator[i];
double t = fabs(q[0] * g[0] - q[1] * g[1] - q[2] * g[2] - q[3] * g[3]); double t = fabs(q[0] * g[0] - q[1] * g[1] - q[2] * g[2] - q[3] * g[3]);
if (t > max) if (t > max)
{ {
max = t; max = t;
bi = i; bi = i;
} }
} }
double f[4]; double f[4];
quat_rot(q, generator[bi], f); quat_rot(q, (double*)generator[bi], f);
memcpy(q, &f, 4 * sizeof(double)); memcpy(q, &f, 4 * sizeof(double));
if (q[0] < 0) if (q[0] < 0)
{ {
q[0] = -q[0]; q[0] = -q[0];
q[1] = -q[1]; q[1] = -q[1];
q[2] = -q[2]; q[2] = -q[2];
q[3] = -q[3]; q[3] = -q[3];
} }
return bi; return bi;
} }
int rotate_quaternion_into_cubic_fundamental_zone(double* q) int rotate_quaternion_into_cubic_fundamental_zone(double* q)
{ {
return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q); return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q);
} }
int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q) int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q)
{ {
return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q); return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q);
} }
int rotate_quaternion_into_icosahedral_fundamental_zone(double* q) int rotate_quaternion_into_icosahedral_fundamental_zone(double* q)
{ {
return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q); return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q);
} }
int rotate_quaternion_into_hcp_fundamental_zone(double* q) int rotate_quaternion_into_hcp_fundamental_zone(double* q)
{ {
return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q); return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q);
}
int rotate_quaternion_into_hcp_conventional_fundamental_zone(double* q)
{
return rotate_quaternion_into_fundamental_zone(12, generator_hcp_conventional, q);
} }
int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q) int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q)
{ {
return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q); return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q);
} }
double quat_dot(double* a, double* b) double quat_dot(double* a, double* b)
{ {
return a[0] * b[0] return a[0] * b[0]
+ a[1] * b[1] + a[1] * b[1]
+ a[2] * b[2] + a[2] * b[2]
+ a[3] * b[3]; + a[3] * b[3];
} }
double quat_size(double* q) double quat_size(double* q)
{ {
return sqrt(quat_dot(q, q)); return sqrt(quat_dot(q, q));
} }
void normalize_quaternion(double* q) void normalize_quaternion(double* q)
{ {
double size = quat_size(q); double size = quat_size(q);
q[0] /= size; q[0] /= size;
q[1] /= size; q[1] /= size;
q[2] /= size; q[2] /= size;
q[3] /= 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) void quaternion_to_rotation_matrix(double* q, double* u)
{ {
double a = q[0]; double a = q[0];
double b = q[1]; double b = q[1];
double c = q[2]; double c = q[2];
double d = q[3]; double d = q[3];
u[0] = a*a + b*b - c*c - d*d; u[0] = a*a + b*b - c*c - d*d;
u[1] = 2*b*c - 2*a*d; u[1] = 2*b*c - 2*a*d;
u[2] = 2*b*d + 2*a*c; u[2] = 2*b*d + 2*a*c;
u[3] = 2*b*c + 2*a*d; u[3] = 2*b*c + 2*a*d;
u[4] = a*a - b*b + c*c - d*d; u[4] = a*a - b*b + c*c - d*d;
u[5] = 2*c*d - 2*a*b; u[5] = 2*c*d - 2*a*b;
u[6] = 2*b*d - 2*a*c; u[6] = 2*b*d - 2*a*c;
u[7] = 2*c*d + 2*a*b; u[7] = 2*c*d + 2*a*b;
u[8] = a*a - b*b - c*c + d*d; u[8] = a*a - b*b - c*c + d*d;
}
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(std::max(0., q[0]));
q[1] = sqrt(std::max(0., q[1]));
q[2] = sqrt(std::max(0., q[2]));
q[3] = sqrt(std::max(0., q[3]));
double m0 = std::max(q[0], q[1]);
double m1 = std::max(q[2], q[3]);
double max = std::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);
} }
double quat_quick_misorientation(double* q1, double* q2) double quat_quick_misorientation(double* q1, double* q2)
{ {
double t = quat_dot(q1, q2); double t = quat_dot(q1, q2);
t = MIN(1, MAX(-1, t)); t = std::min(1., std::max(-1., t));
return 2 * t * t - 1; return 2 * t * t - 1;
} }
double quat_misorientation(double* q1, double* q2) double quat_misorientation(double* q1, double* q2)
{ {
return acos(quat_quick_misorientation(q1, 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));
} }
} }

22
src/USER-PTM/ptm_quat.h
View File

@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_QUAT_H #ifndef PTM_QUAT_H
#define PTM_QUAT_H #define PTM_QUAT_H
@ -7,26 +16,15 @@ int rotate_quaternion_into_cubic_fundamental_zone(double* q);
int rotate_quaternion_into_diamond_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_icosahedral_fundamental_zone(double* q);
int rotate_quaternion_into_hcp_fundamental_zone(double* q); int rotate_quaternion_into_hcp_fundamental_zone(double* q);
int rotate_quaternion_into_hcp_conventional_fundamental_zone(double* q);
int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q); int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q);
void normalize_quaternion(double* q); void normalize_quaternion(double* q);
void quaternion_to_rotation_matrix(double* q, double* U); void quaternion_to_rotation_matrix(double* q, double* U);
void rotation_matrix_to_quaternion(double* u, double* q); void rotation_matrix_to_quaternion(double* u, double* q);
double quat_dot(double* a, double* b); double quat_dot(double* a, double* b);
double quat_quick_misorientation(double* q1, double* q2);
double quat_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 #endif

500
src/USER-PTM/ptm_structure_matcher.cpp
View File

@ -1,3 +1,12 @@
/*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.
*/
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
@ -18,280 +27,349 @@
namespace ptm { namespace ptm {
static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping, 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 G1, double G2, double E0, double* q, double* p_scale)
{ {
double A0[9]; double A0[9];
InnerProduct(A0, num_points, ideal_points, normalized, mapping); InnerProduct(A0, num_points, ideal_points, normalized, mapping);
double nrmsdsq, rot[9]; double nrmsdsq, rot[9];
FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot); FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot);
double k0 = 0; double k0 = 0;
for (int i=0;i<num_points;i++) for (int i=0;i<num_points;i++)
{ {
for (int j=0;j<3;j++) for (int j=0;j<3;j++)
{ {
double v = 0.0; double v = 0.0;
for (int k=0;k<3;k++) for (int k=0;k<3;k++)
v += rot[j*3+k] * ideal_points[i][k]; v += rot[j*3+k] * ideal_points[i][k];
k0 += v * normalized[mapping[i]][j]; k0 += v * normalized[mapping[i]][j];
} }
} }
double scale = k0 / G2; double scale = k0 / G2;
*p_scale = scale; *p_scale = scale;
return sqrt(fabs(G1 - scale*k0) / num_points); return sqrt(fabs(G1 - scale*k0) / num_points);
} }
static void check_graphs( const refdata_t* s, static void check_graphs( const refdata_t* s,
uint64_t hash, uint64_t hash,
int8_t* canonical_labelling, int8_t* canonical_labelling,
double (*normalized)[3], double (*normalized)[3],
result_t* res) result_t* res)
{ {
int num_points = s->num_nbrs + 1; int num_points = s->num_nbrs + 1;
const double (*ideal_points)[3] = s->points; const double (*ideal_points)[3] = s->points;
int8_t inverse_labelling[PTM_MAX_POINTS]; int8_t inverse_labelling[PTM_MAX_POINTS];
int8_t mapping[PTM_MAX_POINTS]; int8_t mapping[PTM_MAX_POINTS];
for (int i=0; i<num_points; i++) for (int i=0; i<num_points; i++)
inverse_labelling[ canonical_labelling[i] ] = i; inverse_labelling[ canonical_labelling[i] ] = i;
double G1 = 0, G2 = 0; double G1 = 0, G2 = 0;
for (int i=0;i<num_points;i++) for (int i=0;i<num_points;i++)
{ {
double x1 = ideal_points[i][0]; double x1 = ideal_points[i][0];
double y1 = ideal_points[i][1]; double y1 = ideal_points[i][1];
double z1 = ideal_points[i][2]; double z1 = ideal_points[i][2];
double x2 = normalized[i][0]; double x2 = normalized[i][0];
double y2 = normalized[i][1]; double y2 = normalized[i][1];
double z2 = normalized[i][2]; double z2 = normalized[i][2];
G1 += x1 * x1 + y1 * y1 + z1 * z1; G1 += x1 * x1 + y1 * y1 + z1 * z1;
G2 += x2 * x2 + y2 * y2 + z2 * z2; G2 += x2 * x2 + y2 * y2 + z2 * z2;
} }
double E0 = (G1 + G2) / 2; double E0 = (G1 + G2) / 2;
for (int i = 0;i<s->num_graphs;i++) for (int i = 0;i<s->num_graphs;i++)
{ {
if (hash != s->graphs[i].hash) if (hash != s->graphs[i].hash)
continue; continue;
graph_t* gref = &s->graphs[i]; graph_t* gref = &s->graphs[i];
for (int j = 0;j<gref->num_automorphisms;j++) for (int j = 0;j<gref->num_automorphisms;j++)
{ {
for (int k=0;k<num_points;k++) for (int k=0;k<num_points;k++)
mapping[automorphisms[gref->automorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ]; mapping[automorphisms[gref->automorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ];
double q[4], scale = 0; double q[4], scale = 0;
double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale); double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale);
if (rmsd < res->rmsd) if (rmsd < res->rmsd)
{ {
res->rmsd = rmsd; res->rmsd = rmsd;
res->scale = scale; res->scale = scale;
res->ref_struct = s; res->ref_struct = s;
memcpy(res->q, q, 4 * sizeof(double)); memcpy(res->q, q, 4 * sizeof(double));
memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); 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) 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 degree[PTM_MAX_NBRS];
int8_t facets[PTM_MAX_FACETS][3]; int8_t facets[PTM_MAX_FACETS][3];
int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
ch->ok = ret >= 0; ch->ok = ret >= 0;
if (ret != 0) if (ret != 0)
return PTM_NO_ERROR; return PTM_NO_ERROR;
if (ch->num_facets != s->num_facets) if (ch->num_facets != s->num_facets)
return PTM_NO_ERROR; //incorrect number of facets in convex hull return PTM_NO_ERROR; //incorrect number of facets in convex hull
int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree); int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree);
if (max_degree > s->max_degree) if (max_degree > s->max_degree)
return PTM_NO_ERROR; return PTM_NO_ERROR;
if (s->type == PTM_MATCH_SC) if (s->type == PTM_MATCH_SC)
for (int i = 0;i<s->num_nbrs;i++) for (int i = 0;i<s->num_nbrs;i++)
if (degree[i] != 4) if (degree[i] != 4)
return PTM_NO_ERROR; return PTM_NO_ERROR;
double normalized[PTM_MAX_POINTS][3]; double normalized[PTM_MAX_POINTS][3];
subtract_barycentre(s->num_nbrs + 1, points, normalized); subtract_barycentre(s->num_nbrs + 1, points, normalized);
int8_t code[2 * PTM_MAX_EDGES]; int8_t code[2 * PTM_MAX_EDGES];
int8_t colours[PTM_MAX_POINTS] = {0}; int8_t colours[PTM_MAX_POINTS] = {0};
int8_t canonical_labelling[PTM_MAX_POINTS]; int8_t canonical_labelling[PTM_MAX_POINTS];
uint64_t hash = 0; uint64_t hash = 0;
ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
if (ret != PTM_NO_ERROR) if (ret != PTM_NO_ERROR)
return ret; return ret;
check_graphs(s, hash, canonical_labelling, normalized, res); check_graphs(s, hash, canonical_labelling, normalized, res);
return PTM_NO_ERROR; 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 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_nbrs = structure_fcc.num_nbrs;
int num_facets = structure_fcc.num_facets; int num_facets = structure_fcc.num_facets;
int max_degree = structure_fcc.max_degree; int max_degree = structure_fcc.max_degree;
int8_t degree[PTM_MAX_NBRS]; int8_t degree[PTM_MAX_NBRS];
int8_t facets[PTM_MAX_FACETS][3]; int8_t facets[PTM_MAX_FACETS][3];
int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
ch->ok = ret >= 0; ch->ok = ret >= 0;
if (ret != 0) if (ret != 0)
return PTM_NO_ERROR; return PTM_NO_ERROR;
if (ch->num_facets != num_facets) if (ch->num_facets != num_facets)
return PTM_NO_ERROR; //incorrect number of facets in convex hull return PTM_NO_ERROR; //incorrect number of facets in convex hull
int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
if (_max_degree > max_degree) if (_max_degree > max_degree)
return PTM_NO_ERROR; return PTM_NO_ERROR;
double normalized[PTM_MAX_POINTS][3]; double normalized[PTM_MAX_POINTS][3];
subtract_barycentre(num_nbrs + 1, points, normalized); subtract_barycentre(num_nbrs + 1, points, normalized);
int8_t code[2 * PTM_MAX_EDGES]; int8_t code[2 * PTM_MAX_EDGES];
int8_t colours[PTM_MAX_POINTS] = {0}; int8_t colours[PTM_MAX_POINTS] = {0};
int8_t canonical_labelling[PTM_MAX_POINTS]; int8_t canonical_labelling[PTM_MAX_POINTS];
uint64_t hash = 0; uint64_t hash = 0;
ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
if (ret != PTM_NO_ERROR) if (ret != PTM_NO_ERROR)
return ret; return ret;
if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res); 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_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res);
if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res); if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res);
return PTM_NO_ERROR; 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 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_nbrs = structure_dcub.num_nbrs;
int num_facets = structure_fcc.num_facets; int num_facets = structure_fcc.num_facets;
int max_degree = structure_dcub.max_degree; int max_degree = structure_dcub.max_degree;
int8_t facets[PTM_MAX_FACETS][3]; int8_t facets[PTM_MAX_FACETS][3];
int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
ch->ok = ret >= 0; ch->ok = ret >= 0;
if (ret != 0) if (ret != 0)
return PTM_NO_ERROR; return PTM_NO_ERROR;
//check for facets with multiple inner atoms //check for facets with multiple inner atoms
bool inverted[4] = {false, false, false, false}; bool inverted[4] = {false, false, false, false};
for (int i=0;i<ch->num_facets;i++) for (int i=0;i<ch->num_facets;i++)
{ {
int n = 0; int n = 0;
for (int j=0;j<3;j++) for (int j=0;j<3;j++)
{ {
if (facets[i][j] <= 3) if (facets[i][j] <= 3)
{ {
inverted[facets[i][j]] = true; inverted[facets[i][j]] = true;
n++; n++;
} }
} }
if (n > 1) if (n > 1)
return PTM_NO_ERROR; return PTM_NO_ERROR;
} }
int num_inverted = 0; int num_inverted = 0;
for (int i=0;i<4;i++) for (int i=0;i<4;i++)
num_inverted += inverted[i] ? 1 : 0; num_inverted += inverted[i] ? 1 : 0;
if (ch->num_facets != num_facets + 2 * num_inverted) if (ch->num_facets != num_facets + 2 * num_inverted)
return PTM_NO_ERROR; //incorrect number of facets in convex hull return PTM_NO_ERROR; //incorrect number of facets in convex hull
int8_t degree[PTM_MAX_NBRS]; int8_t degree[PTM_MAX_NBRS];
int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
if (_max_degree > max_degree) if (_max_degree > max_degree)
return PTM_NO_ERROR; return PTM_NO_ERROR;
int num_found = 0; int num_found = 0;
int8_t toadd[4][3]; int8_t toadd[4][3];
for (int i=0;i<ch->num_facets;i++) for (int i=0;i<ch->num_facets;i++)
{ {
int a = facets[i][0]; int a = facets[i][0];
int b = facets[i][1]; int b = facets[i][1];
int c = facets[i][2]; int c = facets[i][2];
if (a <= 3 || b <= 3 || c <= 3) if (a <= 3 || b <= 3 || c <= 3)
continue; continue;
int i0 = (a - 4) / 3; int i0 = (a - 4) / 3;
int i1 = (b - 4) / 3; int i1 = (b - 4) / 3;
int i2 = (c - 4) / 3; int i2 = (c - 4) / 3;
if (i0 == i1 && i0 == i2) if (i0 == i1 && i0 == i2)
{ {
if (num_found + num_inverted >= 4) if (num_found + num_inverted >= 4)
return PTM_NO_ERROR; return PTM_NO_ERROR;
toadd[num_found][0] = a; toadd[num_found][0] = a;
toadd[num_found][1] = b; toadd[num_found][1] = b;
toadd[num_found][2] = c; toadd[num_found][2] = c;
num_found++; num_found++;
memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t)); memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t));
ch->num_facets--; ch->num_facets--;
i--; i--;
} }
} }
if (num_found + num_inverted != 4) if (num_found + num_inverted != 4)
return PTM_NO_ERROR; return PTM_NO_ERROR;
for (int i=0;i<num_found;i++) for (int i=0;i<num_found;i++)
{ {
int a = toadd[i][0]; int a = toadd[i][0];
int b = toadd[i][1]; int b = toadd[i][1];
int c = toadd[i][2]; int c = toadd[i][2];
int i0 = (a - 4) / 3; int i0 = (a - 4) / 3;
facets[ch->num_facets][0] = i0; facets[ch->num_facets][0] = i0;
facets[ch->num_facets][1] = b; facets[ch->num_facets][1] = b;
facets[ch->num_facets][2] = c; facets[ch->num_facets][2] = c;
ch->num_facets++; ch->num_facets++;
facets[ch->num_facets][0] = a; facets[ch->num_facets][0] = a;
facets[ch->num_facets][1] = i0; facets[ch->num_facets][1] = i0;
facets[ch->num_facets][2] = c; facets[ch->num_facets][2] = c;
ch->num_facets++; ch->num_facets++;
facets[ch->num_facets][0] = a; facets[ch->num_facets][0] = a;
facets[ch->num_facets][1] = b; facets[ch->num_facets][1] = b;
facets[ch->num_facets][2] = i0; facets[ch->num_facets][2] = i0;
ch->num_facets++; ch->num_facets++;
} }
_max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree); _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree);
if (_max_degree > max_degree) if (_max_degree > max_degree)
return PTM_NO_ERROR; return PTM_NO_ERROR;
double normalized[PTM_MAX_POINTS][3]; double normalized[PTM_MAX_POINTS][3];
subtract_barycentre(num_nbrs + 1, points, normalized); subtract_barycentre(num_nbrs + 1, points, normalized);
int8_t code[2 * PTM_MAX_EDGES]; 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 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]; int8_t canonical_labelling[PTM_MAX_POINTS];
uint64_t hash = 0; uint64_t hash = 0;
ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
if (ret != PTM_NO_ERROR) if (ret != PTM_NO_ERROR)
return ret; return ret;
if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res); 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); if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res);
return PTM_NO_ERROR; return PTM_NO_ERROR;
}
static void check_graphs_graphene( const refdata_t* s,
int num_points,
const double (*ideal_points)[3],
double (*normalized)[3],
int8_t* mapping,
result_t* res)
{
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;
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_graphene(double (*points)[3], result_t* res)
{
int num_nbrs = structure_graphene.num_nbrs;
int num_points = num_nbrs + 1;
const double (*ideal_points)[3] = structure_graphene.points;
double normalized[PTM_MAX_POINTS][3];
subtract_barycentre(num_points, points, normalized);
int8_t mapping[PTM_MAX_POINTS];
for (int i=0;i<num_points;i++)
mapping[i] = i;
for (int i=0;i<2;i++)
{
std::swap(mapping[4], mapping[5]);
for (int j=0;j<2;j++)
{
std::swap(mapping[6], mapping[7]);
for (int k=0;k<2;k++)
{
std::swap(mapping[8], mapping[9]);
check_graphs_graphene(&structure_graphene, num_points, ideal_points, normalized, mapping, res);
}
}
}
return PTM_NO_ERROR;
} }
} }

20
src/USER-PTM/ptm_structure_matcher.h
View File

@ -1,3 +1,12 @@
/*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.
*/
#ifndef PTM_STRUCTURE_MATCHER_H #ifndef PTM_STRUCTURE_MATCHER_H
#define PTM_STRUCTURE_MATCHER_H #define PTM_STRUCTURE_MATCHER_H
@ -9,16 +18,17 @@ namespace ptm {
typedef struct typedef struct
{ {
double rmsd; double rmsd;
double scale; double scale;
double q[4]; //rotation in quaternion form (rigid body transformation) double q[4]; //rotation in quaternion form (rigid body transformation)
int8_t mapping[PTM_MAX_POINTS]; int8_t mapping[PTM_MAX_POINTS];
const refdata_t* ref_struct; const refdata_t* ref_struct;
} result_t; } result_t;
int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res); 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_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); int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
int match_graphene(double (*points)[3], result_t* res);
} }

2178
src/USER-PTM/ptm_voronoi_cell.cpp
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587
src/USER-PTM/ptm_voronoi_cell.h
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@ -1,3 +1,46 @@
/*
Voro++ Copyright (c) 2008, The Regents of the University of California, through
Lawrence Berkeley National Laboratory (subject to receipt of any required
approvals from the U.S. Dept. of Energy). All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
(1) Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
(2) 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.
(3) Neither the name of the University of California, Lawrence Berkeley
National Laboratory, U.S. Dept. of Energy 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 OWNER 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.
You are under no obligation whatsoever to provide any bug fixes, patches, or
upgrades to the features, functionality or performance of the source code
("Enhancements") to anyone; however, if you choose to make your Enhancements
available either publicly, or directly to Lawrence Berkeley National
Laboratory, without imposing a separate written license agreement for such
Enhancements, then you hereby grant the following license: a non-exclusive,
royalty-free perpetual license to install, use, modify, prepare derivative
works, incorporate into other computer software, distribute, and sublicense
such enhancements or derivative works thereof, in binary and source code form.
*/
// Voro++, a 3D cell-based Voronoi library // Voro++, a 3D cell-based Voronoi library
// //
// Author : Chris H. Rycroft (LBL / UC Berkeley) // Author : Chris H. Rycroft (LBL / UC Berkeley)
@ -33,180 +76,180 @@ namespace ptm_voro {
* voronoicell and voronoicell_neighbor classes, which extend it based on * voronoicell and voronoicell_neighbor classes, which extend it based on
* whether neighboring particle ID information needs to be tracked. */ * whether neighboring particle ID information needs to be tracked. */
class voronoicell_base { class voronoicell_base {
public: public:
/** This holds the current size of the arrays ed and nu, which /** This holds the current size of the arrays ed and nu, which
* hold the vertex information. If more vertices are created * hold the vertex information. If more vertices are created
* than can fit in this array, then it is dynamically extended * than can fit in this array, then it is dynamically extended
* using the add_memory_vertices routine. */ * using the add_memory_vertices routine. */
int current_vertices; int current_vertices;
/** This holds the current maximum allowed order of a vertex, /** This holds the current maximum allowed order of a vertex,
* which sets the size of the mem, mep, and mec arrays. If a * which sets the size of the mem, mep, and mec arrays. If a
* vertex is created with more vertices than this, the arrays * vertex is created with more vertices than this, the arrays
* are dynamically extended using the add_memory_vorder routine. * are dynamically extended using the add_memory_vorder routine.
*/ */
int current_vertex_order; int current_vertex_order;
/** This sets the size of the main delete stack. */ /** This sets the size of the main delete stack. */
int current_delete_size; int current_delete_size;
/** This sets the size of the auxiliary delete stack. */ /** This sets the size of the auxiliary delete stack. */
int current_delete2_size; int current_delete2_size;
/** This sets the total number of vertices in the current cell. /** This sets the total number of vertices in the current cell.
*/ */
int p; int p;
/** This is the index of particular point in the cell, which is /** This is the index of particular point in the cell, which is
* used to start the tracing routines for plane intersection * used to start the tracing routines for plane intersection
* and cutting. These routines will work starting from any * and cutting. These routines will work starting from any
* point, but it's often most efficient to start from the last * point, but it's often most efficient to start from the last
* point considered, since in many cases, the cell construction * point considered, since in many cases, the cell construction
* algorithm may consider many planes with similar vectors * algorithm may consider many planes with similar vectors
* concurrently. */ * concurrently. */
int up; int up;
/** This is a two dimensional array that holds information /** This is a two dimensional array that holds information
* about the edge connections of the vertices that make up the * about the edge connections of the vertices that make up the
* cell. The two dimensional array is not allocated in the * cell. The two dimensional array is not allocated in the
* usual method. To account for the fact the different vertices * usual method. To account for the fact the different vertices
* have different orders, and thus require different amounts of * have different orders, and thus require different amounts of
* storage, the elements of ed[i] point to one-dimensional * storage, the elements of ed[i] point to one-dimensional
* arrays in the mep[] array of different sizes. * arrays in the mep[] array of different sizes.
* *
* More specifically, if vertex i has order m, then ed[i] * 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 * points to a one-dimensional array in mep[m] that has 2*m+1
* entries. The first m elements hold the neighboring edges, so * 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 * 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 * m elements hold a table of relations which is redundant but
* helps speed up the computation. It satisfies the relation * helps speed up the computation. It satisfies the relation
* ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back * 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 * pointer, so that ed[i+2*m]=i. The back pointers are used
* when rearranging the memory. */ * when rearranging the memory. */
int **ed; int **ed;
/** This array holds the order of the vertices in the Voronoi /** This array holds the order of the vertices in the Voronoi
* cell. This array is dynamically allocated, with its current * cell. This array is dynamically allocated, with its current
* size held by current_vertices. */ * size held by current_vertices. */
int *nu; int *nu;
/** This in an array with size 3*current_vertices for holding /** This in an array with size 3*current_vertices for holding
* the positions of the vertices. */ * the positions of the vertices. */
double *pts; double *pts;
voronoicell_base(); voronoicell_base();
virtual ~voronoicell_base(); virtual ~voronoicell_base();
void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
void init_octahedron_base(double l); 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 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); void translate(double x,double y,double z);
double volume(); double volume();
double max_radius_squared(); double max_radius_squared();
double total_edge_distance(); double total_edge_distance();
double surface_area(); double surface_area();
void centroid(double &cx,double &cy,double &cz); void centroid(double &cx,double &cy,double &cz);
int number_of_faces(); int number_of_faces();
int number_of_edges(); int number_of_edges();
void vertex_orders(std::vector<int> &v); void vertex_orders(std::vector<int> &v);
void vertices(std::vector<double> &v); void vertices(std::vector<double> &v);
void vertices(double x,double y,double z,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_areas(std::vector<double> &v);
void face_orders(std::vector<int> &v); void face_orders(std::vector<int> &v);
void face_freq_table(std::vector<int> &v); void face_freq_table(std::vector<int> &v);
void face_vertices(std::vector<int> &v); void face_vertices(std::vector<int> &v);
void face_perimeters(std::vector<double> &v); void face_perimeters(std::vector<double> &v);
void normals(std::vector<double> &v); void normals(std::vector<double> &v);
template<class vc_class> template<class vc_class>
bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id); 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(double x,double y,double z,double rsq);
bool plane_intersects_guess(double x,double y,double z,double rsq); bool plane_intersects_guess(double x,double y,double z,double rsq);
void construct_relations(); void construct_relations();
void check_relations(); void check_relations();
void check_duplicates(); void check_duplicates();
/** Returns a list of IDs of neighboring particles /** Returns a list of IDs of neighboring particles
* corresponding to each face. * corresponding to each face.
* \param[out] v a reference to a vector in which to return the * \param[out] v a reference to a vector in which to return the
* results. If no neighbor information is * results. If no neighbor information is
* available, a blank vector is returned. */ * available, a blank vector is returned. */
virtual void neighbors(std::vector<int> &v) {v.clear();} virtual void neighbors(std::vector<int> &v) {v.clear();}
/** This a virtual function that is overridden by a routine to /** This a virtual function that is overridden by a routine to
* print the neighboring particle IDs for a given vertex. By * print the neighboring particle IDs for a given vertex. By
* default, when no neighbor information is available, the * default, when no neighbor information is available, the
* routine does nothing. * routine does nothing.
* \param[in] i the vertex to consider. */ * \param[in] i the vertex to consider. */
/** This is a simple inline function for picking out the index /** This is a simple inline function for picking out the index
* of the next edge counterclockwise at the current vertex. * of the next edge counterclockwise at the current vertex.
* \param[in] a the index of an edge of the current vertex. * \param[in] a the index of an edge of the current vertex.
* \param[in] p the number of the vertex. * \param[in] p the number of the vertex.
* \return 0 if a=nu[p]-1, or a+1 otherwise. */ * \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;} 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 /** This is a simple inline function for picking out the index
* of the next edge clockwise from the current vertex. * of the next edge clockwise from the current vertex.
* \param[in] a the index of an edge of the current vertex. * \param[in] a the index of an edge of the current vertex.
* \param[in] p the number of the vertex. * \param[in] p the number of the vertex.
* \return nu[p]-1 if a=0, or a-1 otherwise. */ * \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;} inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
protected: protected:
/** This a one dimensional array that holds the current sizes /** This a one dimensional array that holds the current sizes
* of the memory allocations for them mep array.*/ * of the memory allocations for them mep array.*/
int *mem; int *mem;
/** This is a one dimensional array that holds the current /** This is a one dimensional array that holds the current
* number of vertices of order p that are stored in the mep[p] * number of vertices of order p that are stored in the mep[p]
* array. */ * array. */
int *mec; int *mec;
/** This is a two dimensional array for holding the information /** This is a two dimensional array for holding the information
* about the edges of the Voronoi cell. mep[p] is a * about the edges of the Voronoi cell. mep[p] is a
* one-dimensional array for holding the edge information about * one-dimensional array for holding the edge information about
* all vertices of order p, with each vertex holding 2*p+1 * all vertices of order p, with each vertex holding 2*p+1
* integers of information. The total number of vertices held * integers of information. The total number of vertices held
* on mep[p] is stored in mem[p]. If the space runs out, the * on mep[p] is stored in mem[p]. If the space runs out, the
* code allocates more using the add_memory() routine. */ * code allocates more using the add_memory() routine. */
int **mep; int **mep;
inline void reset_edges(); inline void reset_edges();
template<class vc_class> template<class vc_class>
void check_memory_for_copy(vc_class &vc,voronoicell_base* vb); void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
void copy(voronoicell_base* vb); void copy(voronoicell_base* vb);
private: private:
/** This is the delete stack, used to store the vertices which /** This is the delete stack, used to store the vertices which
* are going to be deleted during the plane cutting procedure. * are going to be deleted during the plane cutting procedure.
*/ */
int *ds,*stacke; int *ds,*stacke;
/** This is the auxiliary delete stack, which has size set by /** This is the auxiliary delete stack, which has size set by
* current_delete2_size. */ * current_delete2_size. */
int *ds2,*stacke2; int *ds2,*stacke2;
/** This stores the current memory allocation for the marginal /** This stores the current memory allocation for the marginal
* cases. */ * cases. */
int current_marginal; int current_marginal;
/** This stores the total number of marginal points which are /** This stores the total number of marginal points which are
* currently in the buffer. */ * currently in the buffer. */
int n_marg; int n_marg;
/** This array contains a list of the marginal points, and also /** This array contains a list of the marginal points, and also
* the outcomes of the marginal tests. */ * the outcomes of the marginal tests. */
int *marg; int *marg;
/** The x coordinate of the normal vector to the test plane. */ /** The x coordinate of the normal vector to the test plane. */
double px; double px;
/** The y coordinate of the normal vector to the test plane. */ /** The y coordinate of the normal vector to the test plane. */
double py; double py;
/** The z coordinate of the normal vector to the test plane. */ /** The z coordinate of the normal vector to the test plane. */
double pz; double pz;
/** The magnitude of the normal vector to the test plane. */ /** The magnitude of the normal vector to the test plane. */
double prsq; double prsq;
template<class vc_class> template<class vc_class>
void add_memory(vc_class &vc,int i,int *stackp2); void add_memory(vc_class &vc,int i,int *stackp2);
template<class vc_class> template<class vc_class>
void add_memory_vertices(vc_class &vc); void add_memory_vertices(vc_class &vc);
template<class vc_class> template<class vc_class>
void add_memory_vorder(vc_class &vc); void add_memory_vorder(vc_class &vc);
void add_memory_ds(int *&stackp); void add_memory_ds(int *&stackp);
void add_memory_ds2(int *&stackp2); void add_memory_ds2(int *&stackp2);
template<class vc_class> template<class vc_class>
inline bool collapse_order1(vc_class &vc); inline bool collapse_order1(vc_class &vc);
template<class vc_class> template<class vc_class>
inline bool collapse_order2(vc_class &vc); inline bool collapse_order2(vc_class &vc);
template<class vc_class> template<class vc_class>
inline bool delete_connection(vc_class &vc,int j,int k,bool hand); inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
template<class vc_class> template<class vc_class>
inline bool search_for_outside_edge(vc_class &vc,int &up); inline bool search_for_outside_edge(vc_class &vc,int &up);
template<class vc_class> template<class vc_class>
inline void add_to_stack(vc_class &vc,int lp,int *&stackp2); 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 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 void normals_search(std::vector<double> &v,int i,int j,int k);
inline bool search_edge(int l,int &m,int &k); inline bool search_edge(int l,int &m,int &k);
inline int m_test(int n,double &ans); inline int m_test(int n,double &ans);
int check_marginal(int n,double &ans); int check_marginal(int n,double &ans);
friend class voronoicell; friend class voronoicell;
friend class voronoicell_neighbor; friend class voronoicell_neighbor;
}; };
/** \brief Extension of the voronoicell_base class to represent a Voronoi cell /** \brief Extension of the voronoicell_base class to represent a Voronoi cell
@ -217,105 +260,105 @@ class voronoicell_base {
* It contains additional data structures mne and ne for storing this * It contains additional data structures mne and ne for storing this
* information. */ * information. */
class voronoicell_neighbor : public voronoicell_base { class voronoicell_neighbor : public voronoicell_base {
public: public:
using voronoicell_base::nplane; using voronoicell_base::nplane;
/** This two dimensional array holds the neighbor information /** This two dimensional array holds the neighbor information
* associated with each vertex. mne[p] is a one dimensional * associated with each vertex. mne[p] is a one dimensional
* array which holds all of the neighbor information for * array which holds all of the neighbor information for
* vertices of order p. */ * vertices of order p. */
int **mne; int **mne;
/** This is a two dimensional array that holds the neighbor /** This is a two dimensional array that holds the neighbor
* information associated with each vertex. ne[i] points to a * information associated with each vertex. ne[i] points to a
* one-dimensional array in mne[nu[i]]. ne[i][j] holds the * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
* neighbor information associated with the jth edge of vertex * neighbor information associated with the jth edge of vertex
* i. It is set to the ID number of the plane that made the * i. It is set to the ID number of the plane that made the
* face that is clockwise from the jth edge. */ * face that is clockwise from the jth edge. */
int **ne; int **ne;
voronoicell_neighbor(); voronoicell_neighbor();
~voronoicell_neighbor(); ~voronoicell_neighbor();
void operator=(voronoicell_neighbor &c); void operator=(voronoicell_neighbor &c);
/** Cuts the Voronoi cell by a particle whose center is at a /** 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 * separation of (x,y,z) from the cell center. The value of rsq
* should be initially set to \f$x^2+y^2+z^2\f$. * 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] (x,y,z) the normal vector to the plane.
* \param[in] rsq the distance along this vector of the plane. * \param[in] rsq the distance along this vector of the plane.
* \param[in] p_id the plane ID (for neighbor tracking only). * \param[in] p_id the plane ID (for neighbor tracking only).
* \return False if the plane cut deleted the cell entirely, * \return False if the plane cut deleted the cell entirely,
* true otherwise. */ * true otherwise. */
inline bool nplane(double x,double y,double z,double rsq,int p_id) { inline bool nplane(double x,double y,double z,double rsq,int p_id) {
return nplane(*this,x,y,z,rsq,p_id); return nplane(*this,x,y,z,rsq,p_id);
} }
/** This routine calculates the modulus squared of the vector /** This routine calculates the modulus squared of the vector
* before passing it to the main nplane() routine with full * before passing it to the main nplane() routine with full
* arguments. * arguments.
* \param[in] (x,y,z) the vector to cut the cell by. * \param[in] (x,y,z) the vector to cut the cell by.
* \param[in] p_id the plane ID (for neighbor tracking only). * \param[in] p_id the plane ID (for neighbor tracking only).
* \return False if the plane cut deleted the cell entirely, * \return False if the plane cut deleted the cell entirely,
* true otherwise. */ * true otherwise. */
inline bool nplane(double x,double y,double z,int p_id) { inline bool nplane(double x,double y,double z,int p_id) {
double rsq=x*x+y*y+z*z; double rsq=x*x+y*y+z*z;
return nplane(*this,x,y,z,rsq,p_id); return nplane(*this,x,y,z,rsq,p_id);
} }
/** This version of the plane routine just makes up the plane /** This version of the plane routine just makes up the plane
* ID to be zero. It will only be referenced if neighbor * ID to be zero. It will only be referenced if neighbor
* tracking is enabled. * tracking is enabled.
* \param[in] (x,y,z) the vector to cut the cell by. * \param[in] (x,y,z) the vector to cut the cell by.
* \param[in] rsq the modulus squared of the vector. * \param[in] rsq the modulus squared of the vector.
* \return False if the plane cut deleted the cell entirely, * \return False if the plane cut deleted the cell entirely,
* true otherwise. */ * true otherwise. */
inline bool plane(double x,double y,double z,double rsq) { inline bool plane(double x,double y,double z,double rsq) {
return nplane(*this,x,y,z,rsq,0); return nplane(*this,x,y,z,rsq,0);
} }
/** Cuts a Voronoi cell using the influence of a particle at /** Cuts a Voronoi cell using the influence of a particle at
* (x,y,z), first calculating the modulus squared of this * (x,y,z), first calculating the modulus squared of this
* vector before passing it to the main nplane() routine. Zero * vector before passing it to the main nplane() routine. Zero
* is supplied as the plane ID, which will be ignored unless * is supplied as the plane ID, which will be ignored unless
* neighbor tracking is enabled. * neighbor tracking is enabled.
* \param[in] (x,y,z) the vector to cut the cell by. * \param[in] (x,y,z) the vector to cut the cell by.
* \return False if the plane cut deleted the cell entirely, * \return False if the plane cut deleted the cell entirely,
* true otherwise. */ * true otherwise. */
inline bool plane(double x,double y,double z) { inline bool plane(double x,double y,double z) {
double rsq=x*x+y*y+z*z; double rsq=x*x+y*y+z*z;
return nplane(*this,x,y,z,rsq,0); return nplane(*this,x,y,z,rsq,0);
} }
void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
void check_facets(); void check_facets();
virtual void neighbors(std::vector<int> &v); virtual void neighbors(std::vector<int> &v);
private: private:
int *paux1; int *paux1;
int *paux2; int *paux2;
inline void n_allocate(int i,int m) {mne[i]=new int[m*i];} inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
inline void n_add_memory_vertices(int i) { inline void n_add_memory_vertices(int i) {
int **pp=new int*[i]; int **pp=new int*[i];
for(int j=0;j<current_vertices;j++) pp[j]=ne[j]; for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
delete [] ne;ne=pp; delete [] ne;ne=pp;
} }
inline void n_add_memory_vorder(int i) { inline void n_add_memory_vorder(int i) {
int **p2=new int*[i]; int **p2=new int*[i];
for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j]; for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
delete [] mne;mne=p2; delete [] mne;mne=p2;
} }
inline void n_set_pointer(int p,int n) { inline void n_set_pointer(int p,int n) {
ne[p]=mne[n]+n*mec[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_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(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_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(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_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
inline void n_set_aux2_copy(int a,int b) { inline void n_set_aux2_copy(int a,int b) {
paux2=mne[b]+b*mec[b]; paux2=mne[b]+b*mec[b];
for(int i=0;i<b;i++) ne[a][i]=paux2[i]; 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_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_aux1(int j) {ne[j]=paux1;}
inline void n_set_to_aux2(int j) {ne[j]=paux2;} 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_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_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_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;} inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
friend class voronoicell_base; friend class voronoicell_base;
}; };
} }

43
src/USER-PTM/ptm_voronoi_config.h
View File

@ -1,3 +1,46 @@
/*
Voro++ Copyright (c) 2008, The Regents of the University of California, through
Lawrence Berkeley National Laboratory (subject to receipt of any required
approvals from the U.S. Dept. of Energy). All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
(1) Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
(2) 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.
(3) Neither the name of the University of California, Lawrence Berkeley
National Laboratory, U.S. Dept. of Energy 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 OWNER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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// Voro++, a 3D cell-based Voronoi library // Voro++, a 3D cell-based Voronoi library
// //
// Author : Chris H. Rycroft (LBL / UC Berkeley) // Author : Chris H. Rycroft (LBL / UC Berkeley)