Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CmguiDeformedSolutionsWriter.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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34*/
35
36#include "CmguiDeformedSolutionsWriter.hpp"
37#include "Exception.hpp"
38
39template<unsigned DIM>
41 std::string baseName,
43 CmguiMeshWriteType writeType)
44 : CmguiMeshWriter<DIM, DIM>(outputDirectory, baseName),
45 mpQuadraticMesh(&rQuadraticMesh),
46 mFinalCounter(0)
47{
48 QuadraticMesh<DIM>* p_quad_mesh = dynamic_cast<QuadraticMesh<DIM>* >(&rQuadraticMesh);
49
50 if (p_quad_mesh == nullptr)
51 {
52 EXCEPTION("CmguiDeformedSolutionsWriter only supports use of a QuadraticMesh");
53 }
54
56
57 if (writeType == WRITE_QUADRATIC_MESH)
58 {
60
61 switch (DIM)
62 {
63 //WriteCmguiScript Commented as CmguiDeformedSolutionsWriter is meant to correspond to
64 // output of nonlinear elasticity problems - 2d or 3d only, and there is
65 // no explicit instantiation of this class in 1d.
66 //case 1:
67 //{
68 // this->mElementFileHeader = CmguiElementFileHeader1DQuadratic;
69 // this->mCoordinatesFileHeader = CmguiCoordinatesFileHeader1DQuadratic;
70 // this->mAdditionalFieldHeader = CmguiAdditionalFieldHeader1DQuadratic;
71 // this->mNumNodesPerElement = 3;
72 // this->mReordering.resize(this->mNumNodesPerElement);
73 // unsigned reordering[6] = {0,2,1};
74 // for (unsigned i=0; i<3; i++)
75 // {
76 // this->mReordering[i] = reordering[i];
77 // }
78 // break;
79 //};
80
81 case 2:
82 {
83 this->mElementFileHeader = CmguiElementFileHeader2DQuadratic;
84 this->mCoordinatesFileHeader = CmguiCoordinatesFileHeader2DQuadratic;
85 this->mAdditionalFieldHeader = CmguiAdditionalFieldHeader2DQuadratic;
86 this->mNumNodesPerElement = 6;
87 this->mReordering.resize(this->mNumNodesPerElement);
88
89 // Go from Chaste(tetgen ordering) (see example comments in
90 // QuadraticBasisFunction::ComputeBasisFunction() to CMGUI ordering
91 // ("psi1 increasing, then psi1 increasing")
92 unsigned reordering[6] = {0,5,1,4,3,2};
93 for (unsigned i=0; i<6; i++)
94 {
95 this->mReordering[i] = reordering[i];
96 }
97 break;
98 }
99 case 3:
100 {
101 this->mElementFileHeader = CmguiElementFileHeader3DQuadratic;
102 this->mCoordinatesFileHeader = CmguiCoordinatesFileHeader3DQuadratic;
103 this->mAdditionalFieldHeader = CmguiAdditionalFieldHeader3DQuadratic;
104 this->mNumNodesPerElement = 10;
105 this->mReordering.resize(this->mNumNodesPerElement);
106
107 // Go from Chaste(tetgen ordering) (see example comments in
108 // QuadraticBasisFunction::ComputeBasisFunction() to CMGUI ordering
109 // ("psi1 increasing, then psi2 increasing, then psi3 increasing")
110 unsigned reordering[10] = {0,4,1,6,5,2,7,8,9,3};
111 for (unsigned i=0; i<10; i++)
112 {
113 this->mReordering[i] = reordering[i];
114 }
115 break;
116 }
117 default:
118 {
120 }
121 }
122 }
123}
124
125template<unsigned DIM>
127{
128 std::string saved_base_name = this->mBaseName;
129 if (fileName == "")
130 {
131 this->mBaseName = this->mBaseName + "_0";
132 }
133 else
134 {
135 this->mBaseName = fileName;
136 }
137 this->WriteFilesUsingMesh(*mpQuadraticMesh);
138 this->mBaseName = saved_base_name;
139}
140
141template<unsigned DIM>
142void CmguiDeformedSolutionsWriter<DIM>::WriteDeformationPositions(std::vector<c_vector<double,DIM> >& rDeformedPositions,
143 unsigned counter)
144{
145 if (mpQuadraticMesh->GetNumNodes() != rDeformedPositions.size() )
146 {
147 EXCEPTION("The size of rDeformedPositions does not match the number of nodes in the mesh");
148 }
149
150 mFinalCounter = counter;
151 std::stringstream node_file_name_stringstream;
152 node_file_name_stringstream << this->mBaseName << "_" << counter << ".exnode";
153
154 out_stream p_node_file = this->mpOutputFileHandler->OpenOutputFile(node_file_name_stringstream.str());
155
156 this->WriteNodeFileHeader(p_node_file);
157
158 // Write each node's data
159 for (unsigned index=0; index<this->GetNumNodes(); index++)
160 {
161 *p_node_file << "Node:\t" << index+1 << "\t";
162
163 for (unsigned i=0; i<DIM; i++)
164 {
165 *p_node_file << rDeformedPositions[index](i) << "\t";
166 }
167 *p_node_file << "\n";
168 }
169 p_node_file->close();
170}
171
172template<unsigned DIM>
173void CmguiDeformedSolutionsWriter<DIM>::WriteCmguiScript(std::string fieldBaseName, std::string undeformedBaseName)
174{
175 std::string field_string = "";
176 if (fieldBaseName != "")
177 {
178 field_string = " gfx read node " + fieldBaseName + "_$i time $i\n";
179 }
180
181 out_stream p_script_file = this->mpOutputFileHandler->OpenOutputFile("LoadSolutions.com");
182 *p_script_file << "#\n# Cmgui script automatically generated by Chaste\n#\n";
183
184 if (undeformedBaseName != "")
185 {
186 *p_script_file << "gfx read node " << undeformedBaseName << " time -1\n";
187 }
188
189 *p_script_file << "for ($i=0; $i<=" << mFinalCounter << "; $i++) { \n"
190 << " gfx read node " << this->mBaseName << "_$i time $i\n"
191 << field_string
192 << "}\n";
193
194 if (undeformedBaseName != "")
195 {
196 for (unsigned region_index=0; region_index<this->mRegionNames.size(); region_index++)
197 {
198 *p_script_file << "gfx read ele " << this->mRegionNames[region_index] << "\n";
199 }
200 }
201 else
202 {
203 *p_script_file << "gfx read ele " << this->mBaseName << "_0\n";
204 }
205 *p_script_file << "gfx define faces egroup "<<this->mBaseName<<"\n";
206 *p_script_file << "gfx modify g_element "<<this->mBaseName<<" lines select_on material default spectrum default selected_material default_selected;\n";
207 *p_script_file << "gfx cr win\n\n";
208 p_script_file->close();
209}
210
211template<unsigned DIM>
213 std::string inputFileBaseName,
214 unsigned finalCounter)
215{
216 // write the mesh to <inputFileBaseName>_0.exnode and <inputFileBaseName>_0.exelem
217 WriteInitialMesh();
218
219 std::vector<c_vector<double,DIM> > deformed_position(mpQuadraticMesh->GetNumNodes(), zero_vector<double>(DIM));
220
221 for (unsigned i=1; i<=finalCounter; i++) //not i=0
222 {
223 std::stringstream in_file_stream;
224 in_file_stream << inputDirectory << "/" << inputFileBaseName << "_" << i << ".nodes";
225
226 std::ifstream ifs(in_file_stream.str().c_str());
227 if (!ifs.is_open())
228 {
229 EXCEPTION("Could not open file: " + in_file_stream.str());
230 }
231
232 // the file into deformed_position
233 double data;
234 for (unsigned index=0; index<mpQuadraticMesh->GetNumNodes(); index++)
235 {
236 for (unsigned j=0; j<DIM; j++)
237 {
238 ifs >> data;
239 if (ifs.fail())
240 {
241 EXCEPTION("Error occurred when reading file " << in_file_stream.str()
242 << ". Expected " << mpQuadraticMesh->GetNumNodes() << " rows and "
243 << DIM << " columns");
244 }
245 deformed_position[index](j) = data;
246 }
247 }
248
249 ifs.close();
250
251 // convert
252 WriteDeformationPositions(deformed_position, i);
253 }
254
255 WriteCmguiScript();
256}
257
258
#define EXCEPTION(message)
#define NEVER_REACHED
virtual unsigned GetNumNodes() const
virtual unsigned GetNumVertices() const
AbstractTetrahedralMesh< DIM, DIM > * mpQuadraticMesh
void WriteCmguiScript(std::string fieldBaseName="", std::string undeformedBaseName="")
void ConvertOutput(std::string inputDirectory, std::string inputFileBaseName, unsigned finalCounter)
void WriteDeformationPositions(std::vector< c_vector< double, DIM > > &rDeformedPositions, unsigned counter)
void WriteInitialMesh(std::string fileName="")
CmguiDeformedSolutionsWriter(std::string outputDirectory, std::string baseName, AbstractTetrahedralMesh< DIM, DIM > &rQuadraticMesh, CmguiMeshWriteType writeType)
std::vector< unsigned > mReordering