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jwwildjwwild
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included new TAU-NetCDF wrapper
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+317
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3 files changed

+317
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‎FileWrapper.cxx

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,9 @@ using std::endl;
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#include "GMGW_FileWrapper.hxx"
4040
#include "GMGW_UGridFileWrapper.hxx"
4141
#include "GMGW_VTKFileWrapper.hxx"
42-
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#ifdef HAVE_TAU
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#include "GMGW_TAUFileWrapper.hxx"
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#endif
4345
FileWrapper::FileWrapper() :
4446
input(nullptr), coordsStart(-1), connectStart(-1), nVerts(0), nCells(0), nBdryTris(
4547
0), nBdryQuads(0), nTets(0), nPyrs(0), nPrisms(0), nHexes(0), nBdryVerts(
@@ -108,6 +110,11 @@ FileWrapper::factory(const char baseName[], const char type[],
108110
else if (strstr(type, "ugrid")) {
109111
return new UGridFileWrapper(baseName, ugridInfix);
110112
}
113+
#ifdef HAVE_TAU
114+
else if (strstr(type, "tau")) {
115+
return new TAUFileWrapper(baseName);
116+
}
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#endif
111118
else {
112119
fprintf(stderr, "Missing or invalid file type: %s\n", type);
113120
exit(1);

‎GMGW_TAUFileWrapper.hxx

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
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/*
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* GMGW_TAUFileWrapper.hxx
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*
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* Created on: Jan 07, 2019
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* Author: jww
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*/
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/*
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Copyright (C) The University of British Columbia, 2018.
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This file is part of UnstructuredMeshAnalyzer.
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UnstructuredMeshAnalyzer is free software: you can redistribute it
14+
and/or modify it under the terms of the GNU General Public License
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as published by the Free Software Foundation, either version 3 of
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the License, or (at your option) any later version.
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UnstructuredMeshAnalyzer is distributed in the hope that it will be
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useful, but WITHOUT ANY WARRANTY; without even the implied warranty
20+
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
21+
General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with UnstructuredMeshAnalyzer. If not, see
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<https://www.gnu.org/licenses/>.
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*/
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#ifndef GMGW_TAUFILEWRAPPER_HXX_
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#define GMGW_TAUFILEWRAPPER_HXX_
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#include "GMGW_FileWrapper.hxx"
32+
#include "primgrid.h"
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34+
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class TAUFileWrapper : public FileWrapper {
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public:
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TAUFileWrapper(const char fileNameBase[]);
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virtual ~TAUFileWrapper();
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virtual void scanFile();
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virtual void getNextCellConnectivity(GMGW_int& nConn, GMGW_int connect[]) const;
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virtual void getNextVertexCoords(double& x, double& y, double &z) const ;
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virtual void
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seekStartOfCoords() const;
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virtual void
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seekStartOfConnectivity() const;
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private:
49+
// TauPrimGrid *m_pg;
50+
mutable long int m_point_idx=0;
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mutable long int m_cell_idx=0;
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};
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#endif /* GMGW_TAUFILEWRAPPER_HXX_ */

‎TAUFileWrapper.cxx

Lines changed: 255 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,255 @@
1+
/*
2+
* TAUFileWrapper.cxx
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*
4+
* Created on: Jan 07, 2019
5+
* Author: jww
6+
*/
7+
8+
/*
9+
Copyright (C) The University of British Columbia, 2018.
10+
11+
This file is part of UnstructuredMeshAnalyzer.
12+
13+
UnstructuredMeshAnalyzer is free software: you can redistribute it
14+
and/or modify it under the terms of the GNU General Public License
15+
as published by the Free Software Foundation, either version 3 of
16+
the License, or (at your option) any later version.
17+
18+
UnstructuredMeshAnalyzer is distributed in the hope that it will be
19+
useful, but WITHOUT ANY WARRANTY; without even the implied warranty
20+
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
21+
General Public License for more details.
22+
23+
You should have received a copy of the GNU General Public License
24+
along with UnstructuredMeshAnalyzer. If not, see
25+
<https://www.gnu.org/licenses/>.
26+
*/
27+
28+
#include <stdlib.h>
29+
#include <stdio.h>
30+
31+
#include <GMGW_unstr.hxx>
32+
#include <GMGW_TAUFileWrapper.hxx>
33+
#include "check_malloc.h"
34+
#include "stream_interface.h"
35+
#include "tau_io_names.h"
36+
#include "primgrid_io_pdat.h"
37+
#include <cstring>
38+
39+
static long int m_point_idx=0;
40+
static long int m_cell_idx=0;
41+
42+
43+
TAUFileWrapper::TAUFileWrapper(const char fileNameBase[]) :
44+
FileWrapper()//, m_pg(nullptr) , m_point_idx(0), m_cell_idx(0)
45+
{
46+
char fileNameIn[1000];
47+
char *stream = "primgrid_read";
48+
// m_pg = init_primgrid();
49+
snprintf(fileNameIn, 1000, "%s", fileNameBase);
50+
stream_open(stream, STREAM_BUFFER_ATTS);
51+
52+
stream_open_file(stream, STREAM_NETCDF, fileNameIn, STREAM_READ_ONLY);
53+
}
54+
55+
TAUFileWrapper::~TAUFileWrapper(void)
56+
{
57+
char *stream = "primgrid_read";
58+
stream_close(stream);
59+
// free_primgrid(&m_pg);
60+
}
61+
62+
void TAUFileWrapper::scanFile()
63+
{
64+
char *stream = "primgrid_read";
65+
66+
coordsStart = 0;
67+
nVerts = stream_get_dim(stream, NO_OF_POINTS);
68+
69+
connectStart = 0;
70+
nTets = stream_get_dim(stream, NO_OF_TETRAS);
71+
nPrisms = stream_get_dim(stream, NO_OF_PRISMS);
72+
nHexes = stream_get_dim(stream, NO_OF_HEXAS);
73+
nPyrs = stream_get_dim(stream, NO_OF_PYRAS);
74+
nBdryTris = stream_get_dim(stream, NO_OF_SURFACETRIANGLES);
75+
nBdryQuads = stream_get_dim(stream, NO_OF_SURFACEQUADRILATERALS);
76+
nCells = nTets + nPrisms + nHexes + nPyrs + nBdryTris + nBdryQuads;
77+
78+
m_cellTypes = new char[nCells];
79+
m_isBdryFace = new bool[nCells];
80+
81+
unsigned int i_cell = 0;
82+
for (unsigned int ii = 0; ii < nTets; ii++,i_cell++) {
83+
m_isBdryFace[i_cell] = false;
84+
m_cellTypes[i_cell] = TET;
85+
}
86+
for (unsigned int ii = 0; ii < nPrisms; ii++,i_cell++) {
87+
m_isBdryFace[i_cell] = false;
88+
m_cellTypes[i_cell] = PRISM;
89+
}
90+
for (unsigned int ii = 0; ii < nHexes; ii++,i_cell++) {
91+
m_isBdryFace[i_cell] = false;
92+
m_cellTypes[i_cell] = HEX;
93+
}
94+
for (unsigned int ii = 0; ii < nPyrs; ii++,i_cell++) {
95+
m_isBdryFace[i_cell] = false;
96+
m_cellTypes[i_cell] = PYRAMID;
97+
}
98+
for (unsigned int ii = 0; ii < nBdryTris; ii++,i_cell++) {
99+
m_isBdryFace[i_cell] = true;
100+
m_cellTypes[i_cell] = BDRY_TRI;
101+
}
102+
for (unsigned int ii = 0; ii < nBdryQuads; ii++,i_cell++) {
103+
m_isBdryFace[i_cell] = true;
104+
m_cellTypes[i_cell] = BDRY_QUAD;
105+
}
106+
107+
identifyBdryVerts();
108+
109+
printf("Scanned mesh and found:\n");
110+
printf("%'13lu verts\n", nVerts);
111+
printf("%'13lu bdry verts\n", nBdryVerts);
112+
printf("%'13lu bdry tris\n", nBdryTris);
113+
printf("%'13lu bdry quads\n", nBdryQuads);
114+
printf("%'13lu tets\n", nTets);
115+
printf("%'13lu pyramids\n", nPyrs);
116+
printf("%'13lu prisms\n", nPrisms);
117+
printf("%'13lu hexes\n", nHexes);
118+
printf("%'13lu total cells\n", nCells);
119+
}
120+
121+
void TAUFileWrapper::getNextVertexCoords(double& x, double& y, double& z) const
122+
{
123+
char *st = "primgrid_read";
124+
size_t tmp_offset = m_point_idx;
125+
size_t tmp_pnts = 1;
126+
127+
QueVarFormat format = stream_array_format(&tmp_offset, &tmp_pnts);
128+
TauDouble (*xx)[3] = NULL;
129+
xx = stream_get_double3_format_var(st, POINT_COORDINATES,
130+
&format);
131+
132+
if(xx == NULL) /* if coordinates are stored with old names */
133+
{
134+
char *xyzname[3] = { POINT_X_COORDINATES,
135+
POINT_Y_COORDINATES,
136+
POINT_Z_COORDINATES };
137+
int n_points = static_cast<int> (nVerts);
138+
read_xyz(st, &xx, &n_points, xyzname, &format);
139+
}
140+
141+
x = xx[0][0];
142+
y = xx[0][1];
143+
z = xx[0][2];
144+
check_free(xx);
145+
m_point_idx++;
146+
}
147+
148+
void TAUFileWrapper::getNextCellConnectivity(GMGW_int& nConn, GMGW_int connect[]) const
149+
{
150+
char *stream = "primgrid_read";
151+
assert (m_cell_idx < nCells);
152+
153+
long int cell_offset = m_cell_idx;
154+
if (cell_offset >= nTets) {
155+
cell_offset-= nTets;
156+
if (cell_offset >= nPrisms) {
157+
cell_offset-= nPrisms;
158+
if (cell_offset >= nHexes) {
159+
cell_offset-= nHexes;
160+
if (cell_offset >= nPyrs) {
161+
cell_offset-= nPyrs;
162+
if (cell_offset >= nBdryTris) {
163+
cell_offset-= nBdryTris;
164+
assert (cell_offset < nBdryQuads);
165+
}
166+
}
167+
}
168+
}
169+
}
170+
171+
size_t start[2], tmp_offset[2];
172+
start[0] = cell_offset;
173+
start[1] = 0;
174+
tmp_offset[0] = 1;
175+
176+
TauIndex act[8];
177+
QueVarFormat format;
178+
179+
int j;
180+
switch(m_cellTypes[m_cell_idx])
181+
{
182+
case TET:
183+
nConn = tmp_offset[1] = 4;
184+
format = stream_array_format(start, tmp_offset);
185+
186+
TauIndex (*act_tet)[4];
187+
act_tet = stream_get_index4_format_var(stream, TETRA_POINTS, &format);
188+
memcpy(act,act_tet[0],tmp_offset[1]*sizeof(TauIndex));
189+
check_free(act_tet);
190+
191+
break;
192+
case PRISM:
193+
nConn = tmp_offset[1] = 6;
194+
format = stream_array_format(start, tmp_offset);
195+
196+
// act = stream_get_index6_format_var(stream, PRISM_POINTS, &format);
197+
TauIndex (*act_prism)[6];
198+
act_prism = stream_get_index6_format_var(stream, PRISM_POINTS, &format);
199+
memcpy(act,act_prism[0],tmp_offset[1]*sizeof(TauIndex));
200+
check_free(act_prism);
201+
202+
break;
203+
case HEX:
204+
nConn = tmp_offset[1] = 8;
205+
format = stream_array_format(start, tmp_offset);
206+
207+
// act = stream_get_index8_format_var(stream, HEXA_POINTS, &format);
208+
TauIndex (*act_hexa)[8];
209+
act_hexa = stream_get_index8_format_var(stream, HEXA_POINTS, &format);
210+
memcpy(act,act_hexa[0],tmp_offset[1]*sizeof(TauIndex));
211+
check_free(act_hexa);
212+
213+
break;
214+
case PYRAMID:
215+
nConn = tmp_offset[1] = 5;
216+
format = stream_array_format(start, tmp_offset);
217+
218+
// act = stream_get_index5_format_var(stream, PYRA_POINTS, &format);
219+
TauIndex (*act_pyra)[5];
220+
act_pyra = stream_get_index5_format_var(stream, PYRA_POINTS, &format);
221+
memcpy(act,act_pyra[0],tmp_offset[1]*sizeof(TauIndex));
222+
check_free(act_pyra);
223+
224+
break;
225+
case BDRY_TRI:
226+
nConn = tmp_offset[1] = 3;
227+
format = stream_array_format(start, tmp_offset);
228+
229+
// act = stream_get_index3_format_var(stream, SURFTRI_POINTS, &format);
230+
TauIndex (*act_stri)[3];
231+
act_stri = stream_get_index3_format_var(stream, SURFTRI_POINTS, &format);
232+
memcpy(act,act_stri[0],tmp_offset[1]*sizeof(TauIndex));
233+
check_free(act_stri);
234+
235+
break;
236+
case BDRY_QUAD:
237+
nConn = tmp_offset[1] = 4;
238+
format = stream_array_format(start, tmp_offset);
239+
240+
// act = stream_get_index4_format_var(stream, SURFQUAD_POINTS, &format);
241+
TauIndex (*act_squad)[4];
242+
act_squad = stream_get_index4_format_var(stream, SURFQUAD_POINTS, &format);
243+
memcpy(act,act_squad[0],tmp_offset[1]*sizeof(TauIndex));
244+
check_free(act_squad);
245+
246+
break;
247+
}
248+
for (j=0; j<nConn; j++)
249+
connect[j] = act[j];
250+
// check_free(act);
251+
m_cell_idx++;
252+
}
253+
254+
void TAUFileWrapper::seekStartOfCoords() const {m_point_idx = 0;}
255+
void TAUFileWrapper::seekStartOfConnectivity() const {m_cell_idx = 0;}

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