I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
Hi Nikhil,
it seems that your file is somehow corrupted - the actual number of cells probably does not agree with the number specified in the mesh at the beginning of the cells section (after Tetrahedra keyword, if you have a tetrahedral mesh).
r.
On 08/25/2016 10:36 AM, Nikhil Vaidya wrote:
I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
Hi Robert,
I had a look now and noticed that the node numbers start from 1. I created the mesh in Netgen and then converted to the medit format using gmsh. How can I solve this problem?
Best, Nikhil
On Monday, August 29, 2016 at 9:44:16 AM UTC+2, Robert Cimrman wrote:
Hi Nikhil,
it seems that your file is somehow corrupted - the actual number of cells probably does not agree with the number specified in the mesh at the beginning of the cells section (after Tetrahedra keyword, if you have a tetrahedral mesh).
r.
On 08/25/2016 10:36 AM, Nikhil Vaidya wrote:
I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
That is OK - medit uses numbering from 1 in its format.
r.
On 08/29/2016 09:52 AM, Nikhil Vaidya wrote:
Hi Robert,
I had a look now and noticed that the node numbers start from 1. I created the mesh in Netgen and then converted to the medit format using gmsh. How can I solve this problem?
Best, Nikhil
On Monday, August 29, 2016 at 9:44:16 AM UTC+2, Robert Cimrman wrote:
Hi Nikhil,
it seems that your file is somehow corrupted - the actual number of cells probably does not agree with the number specified in the mesh at the beginning of the cells section (after Tetrahedra keyword, if you have a tetrahedral mesh).
r.
On 08/25/2016 10:36 AM, Nikhil Vaidya wrote:
I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
The number of lines in the mesh file used to write all the elements is equal to the number written under tetrahedra. Is it still possible for the file to be corrupted?
On Monday, August 29, 2016 at 10:12:36 AM UTC+2, Robert Cimrman wrote:
That is OK - medit uses numbering from 1 in its format.
r.
On 08/29/2016 09:52 AM, Nikhil Vaidya wrote:
Hi Robert,
I had a look now and noticed that the node numbers start from 1. I created the mesh in Netgen and then converted to the medit format using gmsh. How can I solve this problem?
Best, Nikhil
On Monday, August 29, 2016 at 9:44:16 AM UTC+2, Robert Cimrman wrote:
Hi Nikhil,
it seems that your file is somehow corrupted - the actual number of
cells
probably does not agree with the number specified in the mesh at the beginning of the cells section (after Tetrahedra keyword, if you have a tetrahedral mesh).
r.
On 08/25/2016 10:36 AM, Nikhil Vaidya wrote:
I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
Probably yes - if it were correct you would be able to read it. I cannot say more without seeing the file.
r.
On 08/29/2016 10:33 AM, Nikhil Vaidya wrote:
The number of lines in the mesh file used to write all the elements is equal to the number written under tetrahedra. Is it still possible for the file to be corrupted?
On Monday, August 29, 2016 at 10:12:36 AM UTC+2, Robert Cimrman wrote:
That is OK - medit uses numbering from 1 in its format.
r.
On 08/29/2016 09:52 AM, Nikhil Vaidya wrote:
Hi Robert,
I had a look now and noticed that the node numbers start from 1. I created the mesh in Netgen and then converted to the medit format using gmsh. How can I solve this problem?
Best, Nikhil
On Monday, August 29, 2016 at 9:44:16 AM UTC+2, Robert Cimrman wrote:
Hi Nikhil,
it seems that your file is somehow corrupted - the actual number of
cells
probably does not agree with the number specified in the mesh at the beginning of the cells section (after Tetrahedra keyword, if you have a tetrahedral mesh).
r.
On 08/25/2016 10:36 AM, Nikhil Vaidya wrote:
I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
I made the mesh once more and sfepy was able to run the region definition part. I later saw some other strange behaviour. I noticed that my mesh was in the wrong units (mm). I therefore scaled it to metric units and the region definition was not successful. When I returned to the old units (mm), the region definition ran properly again. Is there a problem with small numbers? The following is the error when the mesh is scaled to meters.
sfepy: warning: bad element orientation, trying to correct... sfepy: warning: bad element orientation, trying to correct... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 89, in from_conf domain = FEDomain(mesh.name, mesh) File "C:\sfepy\sfepy\discrete\fem\domain.py", line 61, in __init__ self.fix_element_orientation() File "C:\sfepy\sfepy\discrete\fem\domain.py", line 146, in fix_element_orientation raise RuntimeError('elements cannot be oriented! (%s)' % key) RuntimeError: elements cannot be oriented! (3_4)
On Monday, August 29, 2016 at 1:15:17 PM UTC+2, Robert Cimrman wrote:
Probably yes - if it were correct you would be able to read it. I cannot say more without seeing the file.
r.
The number of lines in the mesh file used to write all the elements is equal to the number written under tetrahedra. Is it still possible for
On 08/29/2016 10:33 AM, Nikhil Vaidya wrote: the
file to be corrupted?
On Monday, August 29, 2016 at 10:12:36 AM UTC+2, Robert Cimrman wrote:
That is OK - medit uses numbering from 1 in its format.
r.
On 08/29/2016 09:52 AM, Nikhil Vaidya wrote:
Hi Robert,
I had a look now and noticed that the node numbers start from 1. I created the mesh in Netgen and then converted to the medit format using gmsh. How can I solve this problem?
Best, Nikhil
On Monday, August 29, 2016 at 9:44:16 AM UTC+2, Robert Cimrman wrote:
Hi Nikhil,
it seems that your file is somehow corrupted - the actual number of
cells
probably does not agree with the number specified in the mesh at the beginning of the cells section (after Tetrahedra keyword, if you have a tetrahedral mesh).
r.
On 08/25/2016 10:36 AM, Nikhil Vaidya wrote:
I am running a Navier stokes simulation. I observed the following output after I ran my file:
simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed!
I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong?
Best regards, Nikhil
On 08/29/2016 03:41 PM, Nikhil Vaidya wrote:
I made the mesh once more and sfepy was able to run the region definition part. I later saw some other strange behaviour. I noticed that my mesh was in the wrong units (mm). I therefore scaled it to metric units and the region definition was not successful. When I returned to the old units (mm), the region definition ran properly again. Is there a problem with small numbers? The following is the error when the mesh is scaled to meters.
It depends how you define the regions - if you select by coordinates, be aware of caveats of float comparisons.
sfepy: warning: bad element orientation, trying to correct... sfepy: warning: bad element orientation, trying to correct... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 89, in from_conf domain = FEDomain(mesh.name, mesh) File "C:\sfepy\sfepy\discrete\fem\domain.py", line 61, in __init__ self.fix_element_orientation() File "C:\sfepy\sfepy\discrete\fem\domain.py", line 146, in fix_element_orientation raise RuntimeError('elements cannot be oriented! (%s)' % key) RuntimeError: elements cannot be oriented! (3_4)
By scaling you mean multiplying the coordinates by a positive factor, while the connectivity remains the same, right? Then this should not happen. It is weird that it runs for another scaling. Can you send me the mesh?
r.
participants (2)
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Nikhil Vaidya -
Robert Cimrman