Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
Thank you for your answer.
I understand well the reason why coneSize begins with faces of cells and
vertices first.
However, I am not sure to understand how cone points are numbered in the
definition of start.
For example, in CreateSimplex2D in ex5.c (two triangles sharing an edge), we
have:
PetscInt numPoints[3] = {4, 5, 2};
PetscInt coneSize[11] = {3, 3, 0, 0, 0, 0, 2, 2, 2, 2, 2};
PetscInt cones[16] = {6, 7, 8, 9, 7, 10, 2, 3, 3, 4, 4, 2, 5, 4, 3, 5};
PetscInt coneOrientations[16] = {0, 0, 0, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
The fact that coneOrientations[4] equals -2 means that edge cones[4]=7 must be
oriented in reverse order starting at vertex 1.
However, edge 7 is defined by vertices (3,4). Does it mean that a local
numbering is used here: (3,4)~(v0,v1)?
In algebraic topology, a convenient way to orient simplices is to number their
vertices in ascendant order.
For example, an edge (i,j) is oriented so that ij, a face (i,j,k) is oriented
so that ijk, etc.
Can we adopt the same convention here and does it simplify something?
Best regards,
Cédric Doucet
- Mail original -
De: Matthew Knepley knep...@gmail.com
À: Cedric Doucet cedric.dou...@inria.fr
Cc: petsc-users@mcs.anl.gov
Envoyé: Jeudi 30 Janvier 2014 19:26:36
Objet: Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Thu, Jan 30, 2014 at 12:19 PM, Cedric Doucet
cedric.dou...@inria.fr wrote:
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM
structure
from a hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not understand.
1. Why does coneSize lists faces of cells first, then faces of
vertices and finally faces of edges (in 2D)? Listing faces of
vertices, then faces of edges and finally faces of cells is not
simpler?
This is really about what order you number points. I wanted to
support meshes with just cells and vertices, as well as
those with face and edges. I also wanted to be able to convert
between them. Thus it made sense to leave the cell
and vertex numbers invariant under this change. I still think this is
the best pragmatic alternative.
2 What does coneOrientations contain? For two counterclockwise
oriented triangles sharing an edge e={v0,v1}, I understand that
{v0,v1} is the right oriented edge for the second triangle (and e
for the first one) but what is the meaning of value -2? I read that
it is -(o+1) with o=1 but why does o equal 1 in this case?
Right now, orientation o = signstart means:
sign: + means traverse in cone order
- means traverse in the reverse of cone order
start: cone point to start iteration on
if sign is -, then start on point -(start+1)
Thus -2 means start on point 1 and go in reverse order, so
for an edge that would be {1, 0} which is what you want.
What we should really have is start identify a group element from
the symmetry
group of the point, and sign indicate inversion. However, that will
be a big rewrite
and needs to be motivated by applications.
Matt
Thank you very much for your help!
Best regards,
Cédric Doucet
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener
Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Fri, Jan 31, 2014 at 3:23 AM, Cedric Doucet cedric.dou...@inria.frwrote:
Thank you for your answer.
I understand well the reason why coneSize begins with faces of cells and
vertices first.
However, I am not sure to understand how cone points are numbered in the
definition of start.
For example, in CreateSimplex2D in ex5.c (two triangles sharing an edge),
we have:
PetscIntnumPoints[3] = {4, 5, 2};
PetscIntconeSize[11] = {3, 3, 0, 0, 0, 0, 2, 2, 2, 2, 2};
PetscIntcones[16] = {6, 7, 8, 9, 7, 10, 2, 3, 3,
4, 4, 2, 5, 4, 3, 5};
PetscIntconeOrientations[16] = {0, 0, 0, 0, -2, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5,
0.5};
The fact that coneOrientations[4] equals -2 means that edge cones[4]=7
must be oriented in reverse order starting at vertex 1.
However, edge 7 is defined by vertices (3,4). Does it mean that a local
numbering is used here: (3,4)~(v0,v1)?
Yes, exactly the numbering from cones[8-9].
In algebraic topology, a convenient way to orient simplices is to number
their vertices in ascendant order.
For example, an edge (i,j) is oriented so that ij, a face (i,j,k) is
oriented so that ijk, etc.
Can we adopt the same convention here and does it simplify something?
No, because we do not have exclusively simplices.
You can simplify by only specifying cells and vertices, which need no
orientations, and then calling DMPlexInterpolate().
Matt
Best regards,
Cédric Doucet
--
*De: *Matthew Knepley knep...@gmail.com
*À: *Cedric Doucet cedric.dou...@inria.fr
*Cc: *petsc-users@mcs.anl.gov
*Envoyé: *Jeudi 30 Janvier 2014 19:26:36
*Objet: *Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Thu, Jan 30, 2014 at 12:19 PM, Cedric Doucet cedric.dou...@inria.frwrote:
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM structure from
a hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not understand.
1. Why does coneSize lists faces of cells first, then faces of vertices
and finally faces of edges (in 2D)? Listing faces of vertices, then faces
of edges and finally faces of cells is not simpler?
This is really about what order you number points. I wanted to support
meshes with just cells and vertices, as well as
those with face and edges. I also wanted to be able to convert between
them. Thus it made sense to leave the cell
and vertex numbers invariant under this change. I still think this is the
best pragmatic alternative.
2 What does coneOrientations contain? For two counterclockwise oriented
triangles sharing an edge e={v0,v1}, I understand that {v0,v1} is the right
oriented edge for the second triangle (and e for the first one) but what
is the meaning of value -2? I read that it is -(o+1) with o=1 but why does
o equal 1 in this case?
Right now, orientation o = signstart means:
sign: + means traverse in cone order
- means traverse in the reverse of cone order
start: cone point to start iteration on
if sign is -, then start on point -(start+1)
Thus -2 means start on point 1 and go in reverse order, so
for an edge that would be {1, 0} which is what you want.
What we should really have is start identify a group element from the
symmetry
group of the point, and sign indicate inversion. However, that will be a
big rewrite
and needs to be motivated by applications.
Matt
Thank you very much for your help!
Best regards,
Cédric Doucet
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
Hello,
DMPlexInterpolate is very interesting!
Is it slow?
If I want to call DMplexInterpolate, just after DMPlexCreateFromDAG call, for
the example of two triangles sharing an edge, I only have to specify cells and
vertices like this in DMPlexCreateFromDAG:
PetscInt numPoints[3] = {4, 0, 2};
PetscInt coneSize[11] = {3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
and let cones and coneOrientations be empty?
Cédric
- Mail original -
De: Matthew Knepley knep...@gmail.com
À: Cedric Doucet cedric.dou...@inria.fr
Cc: petsc-users@mcs.anl.gov
Envoyé: Vendredi 31 Janvier 2014 12:21:40
Objet: Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Fri, Jan 31, 2014 at 3:23 AM, Cedric Doucet
cedric.dou...@inria.fr wrote:
Thank you for your answer.
I understand well the reason why coneSize begins with faces of
cells
and vertices first.
However, I am not sure to understand how cone points are numbered
in
the definition of start.
For example, in CreateSimplex2D in ex5.c (two triangles sharing an
edge), we have:
PetscInt numPoints[3] = {4, 5, 2};
PetscInt coneSize[11] = {3, 3, 0, 0, 0, 0, 2, 2, 2, 2, 2};
PetscInt cones[16] = {6, 7, 8, 9, 7, 10, 2, 3, 3, 4, 4, 2, 5, 4, 3,
5};
PetscInt coneOrientations[16] = {0, 0, 0, 0, -2, 0, 0, 0, 0, 0, 0,
0,
0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5,
0.5};
The fact that coneOrientations[4] equals -2 means that edge
cones[4]=7 must be oriented in reverse order starting at vertex 1.
However, edge 7 is defined by vertices (3,4). Does it mean that a
local numbering is used here: (3,4)~(v0,v1)?
Yes, exactly the numbering from cones[8-9].
In algebraic topology, a convenient way to orient simplices is to
number their vertices in ascendant order.
For example, an edge (i,j) is oriented so that ij, a face (i,j,k)
is
oriented so that ijk, etc.
Can we adopt the same convention here and does it simplify
something?
No, because we do not have exclusively simplices.
You can simplify by only specifying cells and vertices, which need no
orientations, and then calling DMPlexInterpolate().
Matt
Best regards,
Cédric Doucet
De: Matthew Knepley knep...@gmail.com
À: Cedric Doucet cedric.dou...@inria.fr
Cc: petsc-users@mcs.anl.gov
Envoyé: Jeudi 30 Janvier 2014 19:26:36
Objet: Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Thu, Jan 30, 2014 at 12:19 PM, Cedric Doucet
cedric.dou...@inria.fr wrote:
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM
structure
from a hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not understand.
1. Why does coneSize lists faces of cells first, then faces of
vertices and finally faces of edges (in 2D)? Listing faces of
vertices, then faces of edges and finally faces of cells is not
simpler?
This is really about what order you number points. I wanted to
support meshes with just cells and vertices, as well as
those with face and edges. I also wanted to be able to convert
between them. Thus it made sense to leave the cell
and vertex numbers invariant under this change. I still think
this
is
the best pragmatic alternative.
2 What does coneOrientations contain? For two counterclockwise
oriented triangles sharing an edge e={v0,v1}, I understand that
{v0,v1} is the right oriented edge for the second triangle (and
e
for the first one) but what is the meaning of value -2? I read
that
it is -(o+1) with o=1 but why does o equal 1 in this case?
Right now, orientation o = signstart means:
sign: + means traverse in cone order
- means traverse in the reverse of cone order
start: cone point to start iteration on
if sign is -, then start on point -(start+1)
Thus -2 means start on point 1 and go in reverse order, so
for an edge that would be {1, 0} which is what you want.
What we should really have is start identify a group element
from
the symmetry
group of the point, and sign indicate inversion. However, that
will
be a big rewrite
and needs to be motivated by applications.
Matt
Thank you very much for your help!
Best regards,
Cédric Doucet
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to
which
their experiments lead.
-- Norbert Wiener
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments
Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Fri, Jan 31, 2014 at 5:55 AM, Cedric Doucet cedric.dou...@inria.frwrote:
Hello,
DMPlexInterpolate is very interesting!
Is it slow?
It is as fast as I know how to make it. It uses hashing to find the matches.
If I want to call DMplexInterpolate, just after DMPlexCreateFromDAG call,
for the example of two triangles sharing an edge, I only have to specify
cells and vertices like this in DMPlexCreateFromDAG:
PetscIntnumPoints[3] = {4, 0, 2};
PetscIntconeSize[11] = {3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5,
0.5};
and let cones and coneOrientations be empty?
cones[] would be the vertices in each cell, and coneOrientations would be
all zeros.
Matt
Cédric
--
*De: *Matthew Knepley knep...@gmail.com
*À: *Cedric Doucet cedric.dou...@inria.fr
*Cc: *petsc-users@mcs.anl.gov
*Envoyé: *Vendredi 31 Janvier 2014 12:21:40
*Objet: *Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Fri, Jan 31, 2014 at 3:23 AM, Cedric Doucet cedric.dou...@inria.frwrote:
Thank you for your answer.
I understand well the reason why coneSize begins with faces of cells and
vertices first.
However, I am not sure to understand how cone points are numbered in the
definition of start.
For example, in CreateSimplex2D in ex5.c (two triangles sharing an edge),
we have:
PetscIntnumPoints[3] = {4, 5, 2};
PetscIntconeSize[11] = {3, 3, 0, 0, 0, 0, 2, 2, 2, 2, 2};
PetscIntcones[16] = {6, 7, 8, 9, 7, 10, 2, 3, 3,
4, 4, 2, 5, 4, 3, 5};
PetscIntconeOrientations[16] = {0, 0, 0, 0, -2, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5,
0.5};
The fact that coneOrientations[4] equals -2 means that edge cones[4]=7
must be oriented in reverse order starting at vertex 1.
However, edge 7 is defined by vertices (3,4). Does it mean that a local
numbering is used here: (3,4)~(v0,v1)?
Yes, exactly the numbering from cones[8-9].
In algebraic topology, a convenient way to orient simplices is to number
their vertices in ascendant order.
For example, an edge (i,j) is oriented so that ij, a face (i,j,k) is
oriented so that ijk, etc.
Can we adopt the same convention here and does it simplify something?
No, because we do not have exclusively simplices.
You can simplify by only specifying cells and vertices, which need no
orientations, and then calling DMPlexInterpolate().
Matt
Best regards,
Cédric Doucet
--
*De: *Matthew Knepley knep...@gmail.com
*À: *Cedric Doucet cedric.dou...@inria.fr
*Cc: *petsc-users@mcs.anl.gov
*Envoyé: *Jeudi 30 Janvier 2014 19:26:36
*Objet: *Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Thu, Jan 30, 2014 at 12:19 PM, Cedric Doucet
cedric.dou...@inria.frwrote:
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM structure
from a hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not understand.
1. Why does coneSize lists faces of cells first, then faces of vertices
and finally faces of edges (in 2D)? Listing faces of vertices, then faces
of edges and finally faces of cells is not simpler?
This is really about what order you number points. I wanted to support
meshes with just cells and vertices, as well as
those with face and edges. I also wanted to be able to convert between
them. Thus it made sense to leave the cell
and vertex numbers invariant under this change. I still think this is the
best pragmatic alternative.
2 What does coneOrientations contain? For two counterclockwise oriented
triangles sharing an edge e={v0,v1}, I understand that {v0,v1} is the right
oriented edge for the second triangle (and e for the first one) but
what is the meaning of value -2? I read that it is -(o+1) with o=1 but why
does o equal 1 in this case?
Right now, orientation o = signstart means:
sign: + means traverse in cone order
- means traverse in the reverse of cone order
start: cone point to start iteration on
if sign is -, then start on point -(start+1)
Thus -2 means start on point 1 and go in reverse order, so
for an edge that would be {1, 0} which is what you want.
What we should really have is start identify a group element from the
symmetry
group of the point, and sign indicate inversion. However, that will be
a big rewrite
and needs to be motivated by applications.
Matt
Thank you very much for your help!
Best regards,
Cédric Doucet
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
--
What most experimenters take for granted before they begin their
experiments
Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
Thank you very much for your help!
I will test this solution.
Best regards,
Cédric
- Mail original -
De: Matthew Knepley knep...@gmail.com
À: Cedric Doucet cedric.dou...@inria.fr
Cc: petsc-users@mcs.anl.gov
Envoyé: Vendredi 31 Janvier 2014 13:11:14
Objet: Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Fri, Jan 31, 2014 at 5:55 AM, Cedric Doucet
cedric.dou...@inria.fr wrote:
Hello,
DMPlexInterpolate is very interesting!
Is it slow?
It is as fast as I know how to make it. It uses hashing to find the
matches.
If I want to call DMplexInterpolate, just after DMPlexCreateFromDAG
call, for the example of two triangles sharing an edge, I only have
to specify cells and vertices like this in DMPlexCreateFromDAG:
PetscInt numPoints[3] = {4, 0, 2};
PetscInt coneSize[11] = {3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5,
0.5};
and let cones and coneOrientations be empty?
cones[] would be the vertices in each cell, and coneOrientations
would be all zeros.
Matt
Cédric
De: Matthew Knepley knep...@gmail.com
À: Cedric Doucet cedric.dou...@inria.fr
Cc: petsc-users@mcs.anl.gov
Envoyé: Vendredi 31 Janvier 2014 12:21:40
Objet: Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Fri, Jan 31, 2014 at 3:23 AM, Cedric Doucet
cedric.dou...@inria.fr wrote:
Thank you for your answer.
I understand well the reason why coneSize begins with faces of
cells
and vertices first.
However, I am not sure to understand how cone points are
numbered
in
the definition of start.
For example, in CreateSimplex2D in ex5.c (two triangles sharing
an
edge), we have:
PetscInt numPoints[3] = {4, 5, 2};
PetscInt coneSize[11] = {3, 3, 0, 0, 0, 0, 2, 2, 2, 2, 2};
PetscInt cones[16] = {6, 7, 8, 9, 7, 10, 2, 3, 3, 4, 4, 2, 5,
4,
3,
5};
PetscInt coneOrientations[16] = {0, 0, 0, 0, -2, 0, 0, 0, 0, 0,
0,
0,
0, 0, 0, 0};
PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0,
0.5,
0.5};
The fact that coneOrientations[4] equals -2 means that edge
cones[4]=7 must be oriented in reverse order starting at vertex
1.
However, edge 7 is defined by vertices (3,4). Does it mean that
a
local numbering is used here: (3,4)~(v0,v1)?
Yes, exactly the numbering from cones[8-9].
In algebraic topology, a convenient way to orient simplices is
to
number their vertices in ascendant order.
For example, an edge (i,j) is oriented so that ij, a face
(i,j,k)
is
oriented so that ijk, etc.
Can we adopt the same convention here and does it simplify
something?
No, because we do not have exclusively simplices.
You can simplify by only specifying cells and vertices, which
need
no
orientations, and then calling DMPlexInterpolate().
Matt
Best regards,
Cédric Doucet
De: Matthew Knepley knep...@gmail.com
À: Cedric Doucet cedric.dou...@inria.fr
Cc: petsc-users@mcs.anl.gov
Envoyé: Jeudi 30 Janvier 2014 19:26:36
Objet: Re: [petsc-users] Input arguments of
DMPlexCreateFromDAG
On Thu, Jan 30, 2014 at 12:19 PM, Cedric Doucet
cedric.dou...@inria.fr wrote:
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM
structure
from a hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not
understand.
1. Why does coneSize lists faces of cells first, then faces
of
vertices and finally faces of edges (in 2D)? Listing faces
of
vertices, then faces of edges and finally faces of cells is
not
simpler?
This is really about what order you number points. I wanted
to
support meshes with just cells and vertices, as well as
those with face and edges. I also wanted to be able to
convert
between them. Thus it made sense to leave the cell
and vertex numbers invariant under this change. I still think
this
is
the best pragmatic alternative.
2 What does coneOrientations contain? For two
counterclockwise
oriented triangles sharing an edge e={v0,v1}, I understand
that
{v0,v1} is the right oriented edge for the second triangle
(and
e
for the first one) but what is the meaning of value -2? I
read
that
it is -(o+1) with o=1 but why does
[petsc-users] Input arguments of DMPlexCreateFromDAG
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM structure from a
hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not understand.
1. Why does coneSize lists faces of cells first, then faces of vertices and
finally faces of edges (in 2D)? Listing faces of vertices, then faces of edges
and finally faces of cells is not simpler?
2 What does coneOrientations contain? For two counterclockwise oriented
triangles sharing an edge e={v0,v1}, I understand that {v0,v1} is the right
oriented edge for the second triangle (and e for the first one) but what is the
meaning of value -2? I read that it is -(o+1) with o=1 but why does o equal 1
in this case?
Thank you very much for your help!
Best regards,
Cédric Doucet
Re: [petsc-users] Input arguments of DMPlexCreateFromDAG
On Thu, Jan 30, 2014 at 12:19 PM, Cedric Doucet cedric.dou...@inria.frwrote:
Hello,
I tried to use DMPlexCreateFromDAG function to create a DM structure from
a hybrid mesh.
To understand how it works, I look at ex5.c file.
Unfortunately, there are some things that I do not understand.
1. Why does coneSize lists faces of cells first, then faces of vertices
and finally faces of edges (in 2D)? Listing faces of vertices, then faces
of edges and finally faces of cells is not simpler?
This is really about what order you number points. I wanted to support
meshes with just cells and vertices, as well as
those with face and edges. I also wanted to be able to convert between
them. Thus it made sense to leave the cell
and vertex numbers invariant under this change. I still think this is the
best pragmatic alternative.
2 What does coneOrientations contain? For two counterclockwise oriented
triangles sharing an edge e={v0,v1}, I understand that {v0,v1} is the right
oriented edge for the second triangle (and e for the first one) but what
is the meaning of value -2? I read that it is -(o+1) with o=1 but why does
o equal 1 in this case?
Right now, orientation o = signstart means:
sign: + means traverse in cone order
- means traverse in the reverse of cone order
start: cone point to start iteration on
if sign is -, then start on point -(start+1)
Thus -2 means start on point 1 and go in reverse order, so
for an edge that would be {1, 0} which is what you want.
What we should really have is start identify a group element from the
symmetry
group of the point, and sign indicate inversion. However, that will be a
big rewrite
and needs to be motivated by applications.
Matt
Thank you very much for your help!
Best regards,
Cédric Doucet
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
