The best way to proceed is to set the boundary conditions using Physical 
Entities in GMSH.
An example is always better. For example, the following GMSH code :

 lc = 2.0e-1;
 lf = 2.0e-1;
 RO=1;
 RI=0.25;
 
 Point(0) = {0, 0, 0, lc};
 Point(1) = {RO, 0, 0, lc};
 Point(2) = {0, -RO , 0, lc};
 Point(3) = {-RO, 0, 0, lc};
 Point(4) = {0, RO, 0, lc};
 
 Point(5) = {RI, 0, 0, lf};
 Point(6) = {0, -RI , 0, lf};
 Point(7) = {-RI, 0, 0, lf};
 Point(8) = {0, RI, 0, lf};
 
 Circle(1)={1,0,2};
 Circle(2)={2,0,3};
 Circle(3)={3,0,4};
 Circle(4)={4,0,1};
 
 Circle(5)={5,0,6};
 Circle(6)={6,0,7};
 Circle(7)={7,0,8};
 Circle(8)={8,0,5};
 
 Line Loop(1) = {1,2,3,4};
 Line Loop(2) = {5,6,7,8};
 
 Plane Surface(1) = {1,2} ;
 //Transfinite Surface{1}={1,2,3,4};
 Recombine Surface{1,2};
 
 // Creates a physical entity 1 (i.e. for a BC)
 //Physical Point(1) = {1,2} ;
 Physical Line(0)={1,2,3,4};
 Physical Line(1)={5,6,7,8};
 
 Physical Surface(0) = {1};


Produces a 2D mesh of a single surface with id 0. It has two boundary 
conditions (0) and (1). One on the outer circle and the other on the inner 
circle. We use it to simulate a Taylor-Couette flow.
If you wanted to use a 3D mesh, then you would make a Physical Volume(0) 
and you would use the Physical Surface for the boundary conditions

Best
Bruno



On Wednesday, 5 August 2020 20:36:09 UTC-4, yuesu jin wrote:
>
> Dear all,
>   I want to set up one Dirchlet boundary condition and one Neumann 
> boundary condition on a 2d  mesh, which is generated by gmsh. How can I set 
> up the mesh file in order to tell dealii with the boundary id when I input 
> the .msh file into dealii? Thanks!
> Best regards,
> -- 
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008 
> 346-404-2062
>
>

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