Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
OffLatticeRandomFieldGenerator.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
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7University of Oxford, having an administrative office at Wellington
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10This file is part of Chaste.
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15 this list of conditions and the following disclaimer.
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19 * Neither the name of the University of Oxford nor the names of its
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21 software without specific prior written permission.
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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33
34*/
35
36#include "OffLatticeRandomFieldGenerator.hpp"
37
38#include <algorithm>
39#include <iomanip>
40#include <fstream>
41#include <memory>
42#include <numeric>
43
44#include "Exception.hpp"
45#include "RandomNumberGenerator.hpp"
46#include "RandomFieldUtilityFunctions.hpp"
47
48template <unsigned SPACE_DIM>
50 std::array<double, SPACE_DIM> lowerCorner,
51 std::array<double, SPACE_DIM> upperCorner,
52 std::array<bool, SPACE_DIM> periodicity,
53 double lengthScale,
54 double boxWidth)
55 : mLowerCorner(lowerCorner),
56 mUpperCorner(upperCorner),
57 mPeriodicity(periodicity),
58 mLengthScale(lengthScale),
59 mpBoxCollection(nullptr)
60{
61 // Reset the box width if the default value is being used
62 if (boxWidth == DOUBLE_UNSET)
63 {
64 const double max_box_width = 4.0 * lengthScale;
65 boxWidth = std::min(max_box_width, upperCorner[0] - lowerCorner[0]);
66 }
67
68 // Set up the box collection
69 c_vector<double, 2 * SPACE_DIM> domain_size;
70 for (unsigned dim = 0; dim < SPACE_DIM; ++dim)
71 {
72 domain_size[2 * dim] = lowerCorner[dim];
73 domain_size[2 * dim + 1] = upperCorner[dim];
74 }
75
77 bool periodic_x = periodicity[0];
78 bool periodic_y = SPACE_DIM > 1 ? periodicity[1] : false;
79 bool periodic_z = SPACE_DIM > 2 ? periodicity[2] : false;
80
81 mpBoxCollection = std::make_unique<ObsoleteBoxCollection<SPACE_DIM>>(
82 boxWidth,
83 domain_size,
84 periodic_x,
85 periodic_y,
86 periodic_z
87 );
88
89 mpBoxCollection->SetupLocalBoxesHalfOnly();
91}
92
93template <unsigned SPACE_DIM>
95 const unsigned seed)
96{
97 mOpenSimplex = OpenSimplex2S(seed);
98}
99
100template <unsigned SPACE_DIM>
102 const std::vector<Node<SPACE_DIM>*>& rNodes)
103{
104 return this->SampleRandomFieldAtTime(rNodes, 100.0 * mLengthScale * RandomNumberGenerator::Instance()->ranf());
105}
106
107template <unsigned SPACE_DIM>
109 const std::vector<Node<SPACE_DIM>*>& rNodes,
110 const double time)
111{
112 std::vector<double> samples(rNodes.size());
113 for (unsigned i = 0; i < samples.size(); ++i)
114 {
115 const c_vector<double, SPACE_DIM> node_location = rNodes[i]->rGetLocation();
116 switch (SPACE_DIM)
117 {
118 case 1:
119 {
120 samples[i] = random_field::Reshape(mOpenSimplex.noise2_XBeforeY(node_location[0] * mLengthScale, time + 0.5));
121 break;
122 }
123 case 2:
124 {
125 samples[i] = random_field::Reshape(mOpenSimplex.noise3_XYBeforeZ(node_location[0] * mLengthScale, node_location[1] * mLengthScale, time));
126 break;
127 }
128 case 3:
129 {
130 samples[i] = random_field::Reshape(mOpenSimplex.noise4_XYBeforeZW(node_location[0] * mLengthScale, node_location[1] * mLengthScale, node_location[2] * mLengthScale, time));
131 break;
132 }
133 default:
134 // This can't happen
136 }
137 }
138
139 return samples;
140}
141// Explicit instantiation
const double DOUBLE_UNSET
Definition Exception.hpp:57
#define NEVER_REACHED
Definition Node.hpp:59
std::vector< double > SampleRandomField(const std::vector< Node< SPACE_DIM > * > &rNodes)
std::unique_ptr< ObsoleteBoxCollection< SPACE_DIM > > mpBoxCollection
std::vector< double > SampleRandomFieldAtTime(const std::vector< Node< SPACE_DIM > * > &rNodes, double time)
OffLatticeRandomFieldGenerator(std::array< double, SPACE_DIM > lowerCorner, std::array< double, SPACE_DIM > upperCorner, std::array< bool, SPACE_DIM > periodicity, double lengthScale, double boxWidth=DOUBLE_UNSET)
static RandomNumberGenerator * Instance()