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Commit eb12c274 authored by Jonathan Lambrechts's avatar Jonathan Lambrechts
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Merge branch 'oneFluid' into weakBnd

parents 1ad4ac09 f7b61685
Pipeline #4584 passed with stage
in 1 minute and 48 seconds
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fluid/CMakeLists.txt
View file @ eb12c274
......@@ -27,7 +27,6 @@ set(SRC
hxt_linear_system.c
hxt_linear_system_lu.c
hxt_message.c
fluid_problem_io.c
)
if(PETSC_FOUND)
......
fluid/fluid_problem.c
View file @ eb12c274
......@@ -1141,6 +1141,7 @@ void fluid_problem_free(FluidProblem *problem)
free(problem->solution);
free(problem->porosity);
free(problem->oldporosity);
free(problem->node_volume);
hxtLinearSystemDelete(&problem->linear_system);
free(problem->particle_uvw);
free(problem->particle_element_id);
......@@ -1161,6 +1162,7 @@ void fluid_problem_free(FluidProblem *problem)
free(problem->strong_boundaries);
mesh_tree_free(problem->mesh_tree);
mesh_free(problem->mesh);
free(problem);
}
void fluid_problem_adapt_gen_mesh(FluidProblem *problem, double lcmax, double lcmin, double n_el, double cmax, double cmin)
......@@ -1594,3 +1596,81 @@ void fluid_problem_set_weak_boundary(FluidProblem *p, const char *tag, const cha
p->weak_boundaries[p->n_weak_boundaries-1].cb = f;
p->weak_boundaries[p->n_weak_boundaries-1].apply = apply;
}
int fluid_problem_n_elements(const FluidProblem *p)
{
return p->mesh->n_elements;
}
int *fluid_problem_elements(const FluidProblem *p)
{
return p->mesh->elements;
}
double *fluid_problem_porosity(const FluidProblem *p)
{
return p->porosity;
}
double *fluid_problem_old_porosity(const FluidProblem *p)
{
return p->oldporosity;
}
int fluid_problem_private_n_physical(const FluidProblem *p){
return p->mesh->n_phys;
}
void fluid_problem_private_physical(const FluidProblem *p, int i, char **phys_name, int *phys_dim, int *phys_id, int *phys_n_nodes, int **phys_nodes, int *phys_n_boundaries, int **phys_boundaries)
{
*phys_name = p->mesh->phys_name[i];
*phys_n_nodes = p->mesh->phys_n_nodes[i];
*phys_nodes = p->mesh->phys_nodes[i];
*phys_dim = p->mesh->phys_dimension[i];
*phys_id = p->mesh->phys_id[i];
*phys_n_boundaries = p->mesh->phys_n_boundaries[i];
*phys_boundaries = p->mesh->phys_boundaries[i];
}
void fluid_problem_private_set_elements(FluidProblem *p, int n_nodes, double *x, int n_elements, int *elements)
{
Mesh *m = malloc(sizeof(Mesh));
m->n_phys = 0;
m->phys_name = NULL;
m->phys_id = NULL;
m->phys_dimension = NULL;
m->phys_n_nodes = NULL;
m->phys_nodes = NULL;
m->phys_n_boundaries = NULL;
m->phys_boundaries = NULL;
m->n_nodes = n_nodes;
m->n_elements = n_elements;
m->x = malloc(n_nodes*3*sizeof(double));
memcpy(m->x,x,sizeof(double)*3*n_nodes);
m->elements = malloc(sizeof(int)*(DIMENSION+1)*n_elements);
memcpy(m->elements,elements,(DIMENSION+1)*sizeof(int)*n_elements);
fluid_problem_set_mesh(p,m);
}
void fluid_problem_private_add_physical(FluidProblem *p, int tag, int dim, const char *name, int n_nodes, int *nodes, int n_bnd, int *bnd)
{
Mesh *m = p->mesh;
int i = m->n_phys;
m->n_phys += 1;
m->phys_name = realloc(m->phys_name,m->n_phys*sizeof(char*));
m->phys_name[i] = strdup(name);
m->phys_id = realloc(m->phys_id,m->n_phys*sizeof(int));
m->phys_id[i] = tag;
m->phys_dimension = realloc(m->phys_dimension,m->n_phys*sizeof(int));
m->phys_dimension[i] = dim;
m->phys_n_nodes = realloc(m->phys_n_nodes,m->n_phys*sizeof(int));
m->phys_n_nodes[i] = n_nodes;
m->phys_nodes = realloc(m->phys_nodes,m->n_phys*sizeof(int*));
m->phys_nodes[i] = malloc(n_nodes*sizeof(int));
memcpy(m->phys_nodes[i],nodes,n_nodes*sizeof(int));
m->phys_n_boundaries = realloc(m->phys_n_boundaries,m->n_phys*sizeof(int));
m->phys_n_boundaries[i] = n_bnd;
m->phys_boundaries = realloc(m->phys_boundaries,m->n_phys*sizeof(int*));
m->phys_boundaries[i] = malloc(n_bnd*sizeof(int)*2);
memcpy(m->phys_boundaries[i],bnd,n_bnd*sizeof(int)*2);
}
fluid/fluid_problem.h
View file @ eb12c274
......@@ -85,9 +85,6 @@ struct FluidProblem {
int *particle_element_id;
};
int fluid_problem_export(const FluidProblem *problem, const char *output_dir, double t, int iter);
int fluid_problem_export_vtk(const FluidProblem *problem, const char *output_dir, double t, int iter);
int fluid_problem_import_vtk(FluidProblem *problem, const char *filename);
// complete force on the particle (including gravity)
void fluid_problem_compute_node_particle_force(FluidProblem *problem, double dt, double *particle_force);
int fluid_problem_implicit_euler(FluidProblem *problem, double dt, double newton_atol, double newton_rtol, int newton_max_it, int reduced_gravity, double stab_param);
......@@ -105,4 +102,13 @@ double *fluid_problem_coordinates(const FluidProblem *p);
int fluid_problem_n_nodes(const FluidProblem *p);
void fluid_problem_set_weak_boundary(FluidProblem *p, const char *tag, const char *bndtype, StrongBoundaryCallback *apply);
void fluid_problem_set_strong_boundary(FluidProblem *p, const char *tag, int field, int row, StrongBoundaryCallback *apply);
int fluid_problem_n_elements(const FluidProblem *p);
int *fluid_problem_elements(const FluidProblem *p);
double *fluid_problem_old_porosity(const FluidProblem *p);
double *fluid_problem_porosity(const FluidProblem *p);
int fluid_problem_private_n_physical(const FluidProblem *p);
void fluid_problem_private_physical(const FluidProblem *p, int i, char **phys_name, int *phys_dim, int *phys_id, int *phys_n_nodes, int **phys_nodes, int *phys_n_boundaries, int **phys_boundaries);
void fluid_problem_private_set_elements(FluidProblem *p, int n_nodes, double *x, int n_elements, int *elements);
void fluid_problem_private_add_physical(FluidProblem *p, int tag, int dim, const char *name, int n_nodes, int *nodes, int n_bnd, int *bnd);
#endif
fluid/fluid_problem_io.c deleted 100644 → 0
View file @ 1ad4ac09
/*
* MigFlow - Copyright (C) <2010-2018>
* <Universite catholique de Louvain (UCL), Belgium
* Universite de Montpellier, France>
*
* List of the contributors to the development of MigFlow: see AUTHORS file.
* Description and complete License: see LICENSE file.
*
* This program (MigFlow) is free software:
* you can redistribute it and/or modify it under the terms of the GNU Lesser General
* Public License as published by the Free Software Foundation, either version
* 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program (see COPYING and COPYING.LESSER files). If not,
* see <http://www.gnu.org/licenses/>.
*/
#include "fluid_problem.h"
#include "mbxml.h"
#include <string.h>
int fluid_problem_import_vtk(FluidProblem *problem, const char *filename)
{
const int n_fields = fluid_problem_n_fields(problem);
MbXmlReader *r = mb_xml_reader_create(filename);
MbXmlElement fileelement,gridelement,pieceelement;
mb_xml_read_element(r,&fileelement);
mb_xml_read_element(r,&gridelement);
mb_xml_read_element(r,&pieceelement);
if (problem->mesh)
mesh_free(problem->mesh);
problem->mesh = malloc(sizeof(Mesh));
Mesh *m = problem->mesh;
m->n_nodes = -1, m->n_elements = -1;
for(size_t i = 0; i < pieceelement.n_attr; ++i) {
if (!strcasecmp("NumberOfPoints",pieceelement.attr[i].name))
sscanf(pieceelement.attr[i].value,"%i",&m->n_nodes);
if (!strcasecmp("NumberOfCells",pieceelement.attr[i].name))
sscanf(pieceelement.attr[i].value,"%i",&m->n_elements);
}
if (m->n_nodes<0 || m->n_elements < 0){
printf("NumberOfPoints or NumberOfCells not specified in vtk piece");
}
MBVtkDataArray a;
MbXmlElement e;
while(mb_xml_read_element(r,&e)!=1) {
if (!strcasecmp(e.name,"Points")){
mb_read_vtk_data_array(r,&a);
m->x = mb_vtk_data_array_to_double(&a,m->n_nodes,3);
mb_vtk_data_array_destroy(&a);
}
else if (!strcasecmp(e.name,"Cells")) {
int ncon = -1;
while(mb_read_vtk_data_array(r,&a) != 0){
if(!strcasecmp(a.name,"Connectivity")) {
m->elements = mb_vtk_data_array_to_int(&a,m->n_elements,DIMENSION+1);
mb_vtk_data_array_destroy(&a);
}
else if(!strcasecmp(a.name,"Offsets")){
int *offsets = mb_vtk_data_array_to_int(&a,m->n_elements,1);
ncon = offsets[m->n_elements-1];
free(offsets);
mb_vtk_data_array_destroy(&a);
}
else if(!strcasecmp(a.name,"Types")){
mb_vtk_data_array_destroy(&a);
}
else {
printf("unknown data array \"%s\" in vtk piece\n", a.name);
exit(1);
}
}
}
else if (!strcasecmp(e.name,"PointData")) {
if (problem->solution){
free(problem->solution);
}
problem->solution = (double*)malloc(sizeof(double)*n_fields*m->n_nodes);
while(mb_read_vtk_data_array(r,&a) != 0){
if(!strcasecmp(a.name,"Porosity")) {
free(problem->porosity);
problem->porosity = mb_vtk_data_array_to_double(&a,m->n_nodes,1);
}else if(!strcasecmp(a.name,"OldPorosity")) {
free(problem->oldporosity);
problem->oldporosity = mb_vtk_data_array_to_double(&a,m->n_nodes,1);
}
else if(!strcasecmp(a.name,"Pressure")) {
double *p = mb_vtk_data_array_to_double(&a,m->n_nodes,1);
for (int i = 0; i < m->n_nodes; ++i)
problem->solution[n_fields*i+DIMENSION] = p[i];
free(p);
}
else if(!strcasecmp(a.name,"Velocity")) {
double *v = mb_vtk_data_array_to_double(&a,m->n_nodes,3);
for (int i = 0; i < m->n_nodes; ++i)
for (int d = 0; d < DIMENSION; ++d)
problem->solution[n_fields*i+d] = v[i*3+d];
free(v);
}else if(!strcasecmp(a.name,"Concentration")) {
double *c = mb_vtk_data_array_to_double(&a,m->n_nodes,1);
for (int i = 0; i < m->n_nodes; ++i)
problem->solution[n_fields*i+DIMENSION+1] = c[i];
free(c);
}
mb_vtk_data_array_destroy(&a);
}
}
else {
printf("unknown type in piece : \"%s\"\n", e.name);
exit(1);
}
mb_xml_end_element(r,&e);
}
mb_xml_end_element(r,&pieceelement);
MbXmlElement fielddataelement;
mb_xml_read_element(r,&fielddataelement);
int n_phys=0;
int n_phys_alloc = 10;
MBVtkDataArray *phys =(MBVtkDataArray*) malloc(sizeof(MBVtkDataArray)*10);
int n_boundaries = 0;
int n_boundaries_alloc = 10;
MBVtkDataArray *boundaries =(MBVtkDataArray*) malloc(sizeof(MBVtkDataArray)*10);
while(mb_read_vtk_data_array(r,&a) != 0){
if(!strncasecmp(a.name,"Physical ",9)) {
if (n_phys == n_phys_alloc) {
n_phys_alloc *= 2;
phys = (MBVtkDataArray*)realloc(phys,n_phys_alloc*sizeof(MBVtkDataArray));
}
phys[n_phys++] = a;
}
else if(!strncasecmp(a.name,"Boundary ",9)) {
if (n_boundaries == n_boundaries_alloc) {
n_boundaries_alloc *= 2;
boundaries = (MBVtkDataArray*)realloc(boundaries,n_boundaries_alloc*sizeof(MBVtkDataArray));
}
boundaries[n_boundaries++] = a;
}
else {
printf("unknown data array \"%s\" in vtk piece\n", a.name);
exit(1);
}
}
m->phys_id = malloc(n_phys*sizeof(int));
m->phys_dimension = (int*)malloc(n_phys*sizeof(int));
m->phys_n_nodes = (int*)malloc(n_phys*sizeof(int));
m->phys_name = (char**)malloc(n_phys*sizeof(char*));
m->phys_nodes = (int**)malloc(n_phys*sizeof(int*));
m->phys_n_boundaries = (int*)malloc(n_phys*sizeof(int));
m->phys_boundaries = (int**)malloc(n_phys*sizeof(int*));
if(n_phys != n_boundaries) {
printf("import vtk errors : number of physical and boundaries data does not match");
}
m->n_phys = n_phys;
for(int i = 0; i < n_phys; ++i) {
MBVtkDataArray a = phys[i];
int p, n;
sscanf(a.name+9,"%i %i%n",&m->phys_dimension[i],&m->phys_id[i],&p);
m->phys_nodes[i] = mb_vtk_data_array_to_int(&phys[i],-1,-1);
m->phys_n_nodes[i] = phys[i].number_of_tuples;
m->phys_name[i] = strdup(a.name+p+10);
mb_vtk_data_array_destroy(&phys[i]);
}
free(phys);
for(int i = 0; i < n_boundaries; ++i) {
MBVtkDataArray a = boundaries[i];
int p, n;
sscanf(a.name+9,"%i %i%n",&m->phys_dimension[i],&m->phys_id[i],&p);
m->phys_boundaries[i] = mb_vtk_data_array_to_int(&boundaries[i],-1,-1);
m->phys_n_boundaries[i] = boundaries[i].number_of_tuples;
mb_vtk_data_array_destroy(&boundaries[i]);
}
free(boundaries);
mb_xml_end_element(r,&fielddataelement);
mb_xml_end_element(r,&gridelement);
mb_xml_end_element(r,&fileelement);
mb_xml_reader_destroy(r);
fluid_problem_after_import(problem);
return 0;
}
int fluid_problem_export_vtk(const FluidProblem *problem, const char *output_dir, double t, int iter)
{
const int n_fields = fluid_problem_n_fields(problem);
Mesh *mesh = problem->mesh;
char file_name[1024];
sprintf(file_name,"%s/fluid_%05i.vtu",output_dir, iter);
FILE *f = fopen(file_name, "w");
if (!f){
printf("Cannot open file \"%s\" for writing.\n", file_name);
return -1;
}
fprintf(f,"<VTKFile type=\"UnstructuredGrid\" format=\"0.1\">\n");
fprintf(f,"<UnstructuredGrid>\n");
fprintf(f,"<Piece NumberOfPoints=\"%i\" NumberOfCells=\"%i\">\n", mesh->n_nodes, mesh->n_elements);
fprintf(f,"<Points>\n");
fprintf(f,"<DataArray NumberOfComponents=\"3\" type=\"Float64\" format=\"ascii\">\n");
for (int i = 0; i < 3*mesh->n_nodes; ++i) {
fprintf(f,"%.16e ", mesh->x[i]);
}
fprintf(f,"\n</DataArray>\n");
fprintf(f,"</Points>\n");
fprintf(f,"<Cells>\n");
fprintf(f,"<DataArray type=\"Int32\" Name=\"connectivity\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_elements*(DIMENSION+1); ++i) {
fprintf(f,"%i ", mesh->elements[i]);
}
fprintf(f,"\n</DataArray>\n");
fprintf(f,"<DataArray type=\"Int32\" Name=\"offsets\" format=\"ascii\">\n");
for(int i = 0; i < mesh->n_elements;++i) {
fprintf(f,"%i ", (i+1)*(DIMENSION+1));
}
#if DIMENSION == 2
fprintf(f,"\n</DataArray>\n");
fprintf(f,"<DataArray type=\"Int32\" Name=\"types\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_elements; ++i) {
fprintf(f,"%i ", 5); // 10 for 3d
}
#else
fprintf(f,"\n</DataArray>\n");
fprintf(f,"<DataArray type=\"Int32\" Name=\"types\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_elements; ++i) {
fprintf(f,"%i ", 10); // 10 for 3d
}
#endif
fprintf(f,"\n</DataArray>\n");
fprintf(f,"</Cells>\n");
fprintf(f,"<PointData Scalars=\"Porosity OldPorosity Pressure\" Vectors=\"Velocity\">\n");
fprintf(f,"<DataArray Name=\"Porosity\" NumberOfComponents = \"1\" type=\"Float64\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_nodes; ++i) {
fprintf(f, "%.16e ", problem->porosity[i]);
}
fprintf(f,"\n</DataArray>\n");
fprintf(f,"<DataArray Name=\"OldPorosity\" NumberOfComponents = \"1\" type=\"Float64\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_nodes; ++i) {
fprintf(f, "%.16e ", problem->oldporosity[i]);
}
fprintf(f,"\n</DataArray>\n");
fprintf(f,"<DataArray Name=\"Pressure\" NumberOfComponents = \"1\" type=\"Float64\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_nodes; ++i) {
fprintf(f, "%.16e ", problem->solution[i*n_fields+(DIMENSION)]);
}
fprintf(f,"\n</DataArray>\n");
if(problem->n_fluids == 2){
fprintf(f,"<DataArray Name=\"Concentration\" NumberOfComponents = \"1\" type=\"Float64\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_nodes; ++i) {
fprintf(f, "%.16e ", problem->solution[i*n_fields+(DIMENSION+1)]);
}
fprintf(f,"\n</DataArray>\n");
}
fprintf(f,"<DataArray Name=\"Velocity\" NumberOfComponents = \"3\" type=\"Float64\" format=\"ascii\">\n");
for (int i = 0; i < mesh->n_nodes; ++i) {
for (int j = 0; j < DIMENSION; ++j)
fprintf(f, "%.16e ", problem->solution[i*n_fields+j]);
if(DIMENSION==2)
fprintf(f, "0 ");
}
fprintf(f,"\n</DataArray>\n");
fprintf(f,"</PointData>\n");
fprintf(f,"</Piece>\n");
fprintf(f,"<FieldData>\n");
for(int i = 0; i < mesh->n_phys; ++i) {
fprintf(f,"<DataArray Name=\"Physical %i %i %s\" NumberOfTuples=\"%i\" NumberOfComponents=\"1\" type=\"Int32\" format=\"ascii\">\n",mesh->phys_dimension[i],mesh->phys_id[i],mesh->phys_name[i],mesh->phys_n_nodes[i]);
for (int j = 0; j < mesh->phys_n_nodes[i]; ++j) {
fprintf(f, "%i ", mesh->phys_nodes[i][j]);
}
fprintf(f,"\n</DataArray>\n");
fprintf(f,"<DataArray Name=\"Boundary %i %i %s\" NumberOfTuples=\"%i\" NumberOfComponents=\"2\" type=\"Int32\" format=\"ascii\">\n",mesh->phys_dimension[i],mesh->phys_id[i],mesh->phys_name[i],mesh->phys_n_boundaries[i]);
for (int j = 0; j < mesh->phys_n_boundaries[i]; ++j) {
fprintf(f, "%i %i ", mesh->phys_boundaries[i][j*2+0], mesh->phys_boundaries[i][j*2+1]);
}
fprintf(f,"\n</DataArray>\n");
}
fprintf(f,"</FieldData>\n");
fprintf(f,"</UnstructuredGrid>\n");
fprintf(f,"</VTKFile>\n");
fclose(f);
return 0;
}
fluid/mesh.h
View file @ eb12c274
......@@ -31,7 +31,7 @@ typedef struct {
int n_nodes;
double *x;
int n_elements;
uint32_t *elements;
int *elements;
int n_phys;
char **phys_name;
int *phys_n_nodes;
......
python/CMakeLists.txt
View file @ eb12c274
......@@ -26,6 +26,7 @@ set(SRC
lmgc90Interface.py
mesh.py
scontact.py
VTK.py
)
foreach(f ${SRC})
......
python/VTK.py 0 → 100644
View file @ eb12c274
import zlib
import struct
import os
import numpy as np
import re
from base64 import b64decode,b64encode
from xml.etree import ElementTree as ET
def _typename(a) :
if a.dtype == np.int32 :
return b"Int32"
elif a.dtype == np.int64 :
return b"Int64"
elif a.dtype == np.float64 :
return b"Float64"
elif a.dtype == np.float32 :
return b"Float32"
else :
raise(NameError("unown array type : " + str(a.dtype)))
def _write_array_ascii(f,a,attr) :
f.write(b'<DataArray %s type="%s" format="ascii">\n'%(attr,_typename(a)))
f.write((" ".join(map(str,a.flat))).encode("utf-8"))
f.write(b'\n</DataArray>\n')
def _write_array(f,appended,a,ds,attr) :
f.write(b'<DataArray %s type="%s" format="appended" offset="%i"/>\n'%(attr,_typename(a),len(appended)-1))
data = zlib.compress(a,2)
# return appended + struct.pack("iiii",1,a.size*ds,0,len(data)) + data
return appended + b64encode(struct.pack("iiii",1,a.size*ds,0,len(data))) + b64encode(data)
def write(basename,i,t,elements,x,data,field_data) :
appended = b"_"
filename = "%s_%05d.vtu"%(basename,i)
f = open(filename,"wb")
f.write(b'<?xml version="1.0"?>\n')
f.write(b'<VTKFile type="UnstructuredGrid" format="0.1" compressor="vtkZLibDataCompressor">\n')
f.write(b'<UnstructuredGrid>\n')
nel = elements.shape[0]
nptbyel = elements.shape[1]
npt = x.shape[0]
f.write(b'<Piece NumberOfPoints="%i" NumberOfCells="%i">\n'%(npt,nel))
f.write(b'<Points>\n')
appended = _write_array(f,appended,x,8,b'NumberOfComponents="3"')
f.write(b'</Points>\n')
f.write(b'<Cells>\n')
appended = _write_array(f,appended,elements,4,b'Name="connectivity"')
offsets = np.array(range(nptbyel,(nel+1)*nptbyel,nptbyel),np.int32)
appended = _write_array(f,appended,offsets,4,b'Name="offsets"')
types = np.ones(nel,np.int32)*(5 if elements.shape[1] == 3 else 13)
appended = _write_array(f,appended,types,4,b'Name="types"')
f.write(b'</Cells>\n')
f.write(b'<PointData>\n')
for name,v in data :
vc = np.ascontiguousarray(v)
appended = _write_array(f,appended,vc,8,b'Name="%s" NumberOfComponents="%i"' % (name.encode("utf8"),vc.shape[-1]))
f.write(b'</PointData>\n')
f.write(b'</Piece>\n')
f.write(b'<FieldData>\n');
for name,v in field_data :
vc = np.ascontiguousarray(v)
appended = _write_array(f,appended,vc,4,b'Name="%s" NumberOfTuples="%i" NumberOfComponents="%i"' % (name,vc.shape[0],vc.shape[1]))
f.write(b'</FieldData>\n');
f.write(b'</UnstructuredGrid>\n')
f.write(b'<AppendedData encoding="base64">\n')
f.write(appended)
f.write(b'</AppendedData>\n')
f.write(b'</VTKFile>\n')
f.close()
def _get_array_info(a) :
ncomp = int(a["NumberOfComponents"]) if "NumberOfComponents" in a else None
ntuples = int(a["NumberOfTuples"]) if "NumberOfTuples" in a else None
return (a["Name"],a["type"],int(a["offset"]),(ntuples,ncomp))
def _get_binary_array(appended,pos,dtype,shape) :
data = appended[pos:pos+24]
_,n,_,s = struct.unpack("iiii",b64decode(data))
data = appended[pos+24:pos+24-(-s//3)*4]
data = b64decode(data)
data = zlib.decompress(data)
return np.frombuffer(data,dtype).reshape(shape)
def read(fname) :
f = open(fname,"rb")
root = ET.parse(f).getroot()
grid = root.find("UnstructuredGrid")
piece = grid.find("Piece")
npoints = int(piece.attrib["NumberOfPoints"])
ncells = int(piece.attrib["NumberOfCells"])
appended = root.find("AppendedData").text
shift = appended.find("_")+1
dim = 2
pointsoffset = int(piece.find("Points/DataArray").attrib["offset"])
x = _get_binary_array(appended,shift+pointsoffset,np.float64,(npoints,3))
for f in piece.find("Cells") :
if f.attrib["Name"] == "connectivity" :
connectivityoffset = int(f.attrib["offset"])
el = _get_binary_array(appended,shift+connectivityoffset,np.int32,(ncells,dim+1))
fdata = []
for f in grid.find("FieldData") :
name,ntype,offset,shape = _get_array_info(f.attrib)
v = _get_binary_array(appended,shift+offset,np.int32,shape)
fdata.append((name,v))
data = []
for f in piece.find("PointData") :
name,ntype,offset,shape = _get_array_info(f.attrib)
v = _get_binary_array(appended,shift+offset,np.float64,(npoints,shape[1]))
data.append((name,v))
return x,el,data,fdata
python/fluid.py
View file @ eb12c274
......@@ -32,6 +32,7 @@ from ctypes import *
import numpy
import signal
import os
from . import VTK
dir_path = os.path.dirname(os.path.realpath(__file__))
lib2 = CDLL(os.path.join(dir_path,"libmbfluid2.so"))
......@@ -39,7 +40,6 @@ lib3 = CDLL(os.path.join(dir_path,"libmbfluid3.so"))
signal.signal(signal.SIGINT, signal.SIG_DFL)
BNDCB = CFUNCTYPE(None,c_int,POINTER(c_double),POINTER(c_double))
class FluidProblem :
......@@ -83,7 +83,7 @@ class FluidProblem :
def __del__(self):
"""Delete the fluid structure."""
if(self._fp != None) :