Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CompareHdf5ResultsFiles.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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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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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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33
34*/
35
36#include "CompareHdf5ResultsFiles.hpp"
37
38#include <iostream>
39#include <vector>
40#include "DistributedVectorFactory.hpp"
41#include "Hdf5DataReader.hpp"
42#include "petscvec.h"
43
44bool CompareFilesViaHdf5DataReader(std::string pathname1, std::string filename1, bool makeAbsolute1,
45 std::string pathname2, std::string filename2, bool makeAbsolute2,
46 double tol, std::string datasetName)
47{
48 Hdf5DataReader reader1(pathname1, filename1, makeAbsolute1, datasetName);
49 Hdf5DataReader reader2(pathname2, filename2, makeAbsolute2, datasetName);
50
51 unsigned number_nodes1 = reader1.GetNumberOfRows();
52 unsigned number_nodes2 = reader2.GetNumberOfRows();
53 if (number_nodes1 != number_nodes2)
54 {
55 std::cout << "Number of nodes " << number_nodes1 << " and " << number_nodes2 << " don't match\n";
56 return false;
57 }
58
59 // Check the variable names and units
60 std::vector<std::string> variable_names1 = reader1.GetVariableNames();
61 std::vector<std::string> variable_names2 = reader2.GetVariableNames();
62 std::string unlimited_variable1 = reader1.GetUnlimitedDimensionName();
63 std::string unlimited_variable2 = reader2.GetUnlimitedDimensionName();
64 std::string unlimited_variable_unit1 = reader1.GetUnlimitedDimensionUnit();
65 std::string unlimited_variable_unit2 = reader2.GetUnlimitedDimensionUnit();
66
67 unsigned num_vars = variable_names1.size();
68 if (num_vars != variable_names2.size())
69 {
70 std::cout << "Number of variables " << variable_names1.size()
71 << " and " << variable_names2.size() << " don't match\n";
72 return false;
73 }
74 if (unlimited_variable1 != unlimited_variable2)
75 {
76 std::cout << "Unlimited variable names " << unlimited_variable1 << " and "
77 << unlimited_variable2 << " don't match\n";
78 return false;
79 }
80 if (unlimited_variable_unit1 != unlimited_variable_unit2)
81 {
82 std::cout << "Unlimited variable units " << unlimited_variable_unit1 << " and "
83 << unlimited_variable_unit2 << " don't match\n";
84 return false;
85 }
86 for (unsigned var = 0; var < num_vars; var++)
87 {
88 std::string var_name = variable_names1[var];
89 if (var_name != variable_names2[var])
90 {
91 std::cout << "Variable names " << var_name << " and "
92 << variable_names2[var] << " don't match\n";
93 return false;
94 }
95 if (reader1.GetUnit(var_name) != reader2.GetUnit(var_name))
96 {
97 std::cout << "Units names " << reader1.GetUnit(var_name)
98 << " and " << reader2.GetUnit(var_name) << " don't match\n";
99 return false;
100 }
101 }
102
103 // Check the timestep vectors
104 std::vector<double> times1 = reader1.GetUnlimitedDimensionValues();
105 std::vector<double> times2 = reader2.GetUnlimitedDimensionValues();
106
107 if (times1.size() != times2.size())
108 {
109 std::cout << "Number of time steps " << times1.size()
110 << " and " << times2.size() << " don't match\n";
111 return false;
112 }
113
114 for (unsigned timestep = 0; timestep < times1.size(); timestep++)
115 {
117 if (fabs(times1[timestep] - times2[timestep]) > 1e-8)
118 {
119 std::cout << "Time step " << timestep << " doesn't match. First file says " << times1[timestep]
120 << " and second says " << times2[timestep] << std::endl;
121 return false;
122 }
123 }
124
125 bool is_complete1 = reader1.IsDataComplete();
126 bool is_complete2 = reader2.IsDataComplete();
127
128 if (is_complete1 != is_complete2)
129 {
130 std::cout << "One of the readers has incomplete data and the other doesn't\n";
131 return false;
132 }
133
134 if (is_complete1)
135 {
136 DistributedVectorFactory factory(number_nodes1);
137
138 Vec data1 = factory.CreateVec();
139 Vec data2 = factory.CreateVec();
140
141 for (unsigned timestep = 0; timestep < times1.size(); timestep++)
142 {
143 for (unsigned var = 0; var < num_vars; var++)
144 {
145 reader1.GetVariableOverNodes(data1, variable_names1[var], timestep);
146 reader2.GetVariableOverNodes(data2, variable_names2[var], timestep);
147
148#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
149 double minus_one = -1.0;
150 VecAXPY(&minus_one, data2, data1);
151#else
152 //[note: VecAXPY(y,a,x) computes y = ax+y]
153 VecAXPY(data1, -1.0, data2);
154#endif
155
156 PetscReal difference_norm;
157 VecNorm(data1, NORM_2, &difference_norm);
158
159 if (difference_norm > tol)
160 {
161 std::cout << "Time " << times1[timestep] << ": vectors differ in NORM_2 by " << difference_norm << std::endl;
162 return false;
163 }
164 }
165 }
166 PetscTools::Destroy(data1);
167 PetscTools::Destroy(data2);
168 }
169 else
170 {
171 // Incomplete data
172
173 // Check the index vectors
174 std::vector<unsigned> indices1 = reader1.GetIncompleteNodeMap();
175 std::vector<unsigned> indices2 = reader2.GetIncompleteNodeMap();
176
177 if (indices1.size() != indices2.size())
178 {
179 std::cout << "Index map sizes " << indices1.size() << " and " << indices2.size() << " don't match\n";
180 return false;
181 }
182
183 for (unsigned index = 0; index < indices1.size(); index++)
184 {
185 if (indices1[index] != indices2[index])
186 {
187 std::cout << "Node indices " << indices1[index] << " and " << indices2[index] << " don't match\n";
188 return false;
189 }
190 }
191
192 // Check all the data
193 for (unsigned index = 0; index < indices1.size(); index++)
194 {
195 unsigned node_index = indices1[index];
196 for (unsigned var = 0; var < num_vars; var++)
197 {
198 std::vector<double> var_over_time1 = reader1.GetVariableOverTime(variable_names1[var], node_index);
199 std::vector<double> var_over_time2 = reader2.GetVariableOverTime(variable_names1[var], node_index);
200 for (unsigned time_step = 0; time_step < var_over_time1.size(); time_step++)
201 {
202 if (fabs(var_over_time1[time_step] - var_over_time2[time_step]) > tol)
203 {
204 std::cout << "Node " << node_index << " at time step " << time_step << " variable " << variable_names1[var]
205 << " differs (" << var_over_time1[time_step] << " != " << var_over_time2[time_step] << ")" << std::endl;
206 return false;
207 }
208 }
209 }
210 }
211 }
212 return true;
213}
214
215bool CompareFilesViaHdf5DataReaderGlobalNorm(std::string pathname1, std::string filename1, bool makeAbsolute1,
216 std::string pathname2, std::string filename2, bool makeAbsolute2,
217 double tol, std::string datasetName)
218{
219 Hdf5DataReader reader1(pathname1, filename1, makeAbsolute1, datasetName);
220 Hdf5DataReader reader2(pathname2, filename2, makeAbsolute2, datasetName);
221
222 unsigned number_nodes1 = reader1.GetNumberOfRows();
223 bool is_the_same = true;
224 std::vector<std::string> variable_names1 = reader1.GetVariableNames();
225 std::vector<std::string> variable_names2 = reader2.GetVariableNames();
226 std::vector<double> times1 = reader1.GetUnlimitedDimensionValues();
227 unsigned num_vars = variable_names1.size();
228 DistributedVectorFactory factory(number_nodes1);
229
230 Vec data1 = factory.CreateVec();
231 Vec data2 = factory.CreateVec();
232
233 for (unsigned timestep = 0; timestep < times1.size(); timestep++)
234 {
235 for (unsigned var = 0; var < num_vars; var++)
236 {
237 reader1.GetVariableOverNodes(data1, variable_names1[var], timestep);
238 reader2.GetVariableOverNodes(data2, variable_names2[var], timestep);
239
240 PetscReal data1_norm;
241 PetscReal data2_norm;
242 VecNorm(data1, NORM_2, &data1_norm);
243 VecNorm(data2, NORM_2, &data2_norm);
244 PetscReal norm = fabs(data1_norm - data2_norm);
245 if (norm > tol)
246 {
247 is_the_same = false;
248 std::cout << "Vectors differ in global NORM_2 by " << norm << std::endl;
249 }
250 }
251 }
252
253 PetscTools::Destroy(data1);
254 PetscTools::Destroy(data2);
255
256 return is_the_same;
257}
static void Destroy(Vec &rVec)