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gsjaardema committed Apr 6, 2019
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70 changes: 35 additions & 35 deletions NetCDF-Mapping.md
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Expand Up @@ -4,64 +4,64 @@

The distributed version of netcdf sets the following limits
on dimensions and variables:
* `#define NC_MAX_DIMS 1024`
* `#define NC_MAX_VARS 8192`
* `#define NC_MAX_DIMS 1024`
* `#define NC_MAX_VARS 8192`

For use with Exodus, it is recommended that these be increased to:
* `#define NC_MAX_DIMS 65536`
* `#define NC_MAX_VARS 524288`
* `#define NC_MAX_DIMS 65536`
* `#define NC_MAX_VARS 524288`

The reason for these increases is due to the mapping of Exodus onto
NetCDF. The sections below show the number of Dimensions (controlled
by NC_MAX_DIMS) and Variables (controlled by NC_MAX_VARS) that are
used in an Exodus file.

## Entities
* A mesh-entity is an individual node, edge, face, or element.
* An entity is a set or block consisting of a single mesh-entity type.
* Each entity can have variables, maps, and attributes which contain an entry per mesh-entity.
* Each entity has an optional name and a required id (32-bit or 64-bit )which is non-negative.
* A mesh-entity can be in one and only one entity block,
* A mesh-entity can be in zero or more entity sets.
* Currently there is only a single implicit node block containing all nodes in the model.
* A mesh-entity is an individual node, edge, face, or element.
* An entity is a set or block consisting of a single mesh-entity type.
* Each entity can have variables, maps, and attributes which contain an entry per mesh-entity.
* Each entity has an optional name and a required id (32-bit or 64-bit )which is non-negative.
* A mesh-entity can be in one and only one entity block,
* A mesh-entity can be in zero or more entity sets.
* Currently there is only a single implicit node block containing all nodes in the model.

## Dimensions: (NC_MAX_DIMS)
* There are about 10 standard dimensions in every file.
* plus one for each set plus one if any attributes
* plus two for each block plus one if any attributes
* plus one for each transient variable on an entity (node, node set, element block, element set, ...)
* There are about 10 standard dimensions in every file.
* plus one for each set plus one if any attributes
* plus two for each block plus one if any attributes
* plus one for each transient variable on an entity (node, node set, element block, element set, ...)

## Variables: (NC_MAX_VARS)
* There are a few standard dimensions
* times
* names of each entity type (block set)
* ids of each entity type (block set)
* status of each entity type (block set)
* #ndim coordinates (1,2,3)
* There are a few standard dimensions
* times
* names of each entity type (block set)
* ids of each entity type (block set)
* status of each entity type (block set)
* #ndim coordinates (1,2,3)

* Each block adds 1 + 2*#attr_on_block + #var_on_block
* Each block adds 1 + 2*#attr_on_block + #var_on_block

* Each set adds 2 + 2*#attr_on_set + #var_on_set
* Each set adds 2 + 2*#attr_on_set + #var_on_set

* Each sideset add 3 + 2*#attr_on_sset + #var_on_sset
* Each sideset add 3 + 2*#attr_on_sset + #var_on_sset

* Each map adds 1
* Each map adds 1

## Example
If we have an exodus file with:
* Nodes
* Nodes

* 5 Element blocks
* 4 transient variables per element block
* 2 attributes per element block
* 5 Element blocks
* 4 transient variables per element block
* 2 attributes per element block

* 4 Node Sets
* Distribution Factors defined on each set
* 3 transient variables
* 4 Node Sets
* Distribution Factors defined on each set
* 3 transient variables

* 3 Side Sets
* Distribution Factors defined on each set
* 2 transient variables
* 3 Side Sets
* Distribution Factors defined on each set
* 2 transient variables

Then there would be about:
`10 + 5*(2+1) + 4*(2) + 3*(2) + 1 + 1 + 1 = 42` Dimensions
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16 changes: 8 additions & 8 deletions README-PARALLEL.md
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Expand Up @@ -31,7 +31,7 @@ For all of the libraries, there should exist a
* cd to the parmetis directory and enter the command:
```bash
MPI=ON sh ../runconfigure.sh
make && make install
make && make install
```

### Parallel-NetCDF
Expand All @@ -51,16 +51,16 @@ For all of the libraries, there should exist a

* `cd` to the parallel-netcdf source directory and enter the command:
```bash
sh ../runconfigure.sh
make && make install
sh ../runconfigure.sh
make && make install
```

### HDF5
* `cd` to the hdf5 source directory and enter the command:

```bash
MPI=ON sh ../runconfigure.sh
make && make install
make && make install
```

### NetCDF
Expand All @@ -69,10 +69,10 @@ For all of the libraries, there should exist a
* `cd netcdf-4.6.1` and enter the command:

```bash
mkdir build
cd build
MPI=ON sh ../../runcmake.sh
make && make install
mkdir build
cd build
MPI=ON sh ../../runcmake.sh
make && make install
```

## Configure, Build, and Install SEACAS
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4 changes: 2 additions & 2 deletions packages/seacas/NetCDF-Mapping.md
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Expand Up @@ -4,8 +4,8 @@ If you are using NetCDF-4.5.1 or later, then you can ignore the information in t

The distributed version of netcdf sets the following limits
on dimensions and variables:
* `#define NC_MAX_DIMS 1024`
* `#define NC_MAX_VARS 8192`
* `#define NC_MAX_DIMS 1024`
* `#define NC_MAX_VARS 8192`

For use with Exodus, it is recommended that these be increased to:
* `#define NC_MAX_DIMS 65536`
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12 changes: 6 additions & 6 deletions packages/seacas/README.md
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Expand Up @@ -110,12 +110,12 @@ The most recent released version is recommended. For use with Exodus, some local
```bash
# Features
--------
NetCDF-2 API: no
NetCDF-4 API: yes
CDF-5 Support: yes
HDF5 Support: yes
PNetCDF Support: yes
NC-4 Parallel Support: yes
NetCDF-2 API: no
NetCDF-4 API: yes
CDF-5 Support: yes
HDF5 Support: yes
PNetCDF Support: yes
NC-4 Parallel Support: yes
```
There will be other features, but their settings are not important
for seacas. For a serial build, `PNetCDF` and `NC-4 Parallel Support`
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50 changes: 25 additions & 25 deletions packages/seacas/libraries/exodus/include/polyhedra.md
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Expand Up @@ -19,27 +19,27 @@ consisting of 3 elements is shown below.
The three elements have the following geometry:

* Element 1: 5 faces.
* Face 1: triangle with nodes 5, 6, 8
* Face 2: triangle with nodes 2, 1, 4
* Face 3: quadrilateral with nodes 6, 2, 4, 8
* Face 4: quadrilateral with nodes 8, 4, 1, 5
* Face 5: quadrilateral with nodes 1, 2, 6, 5
* Face 1: triangle with nodes 5, 6, 8
* Face 2: triangle with nodes 2, 1, 4
* Face 3: quadrilateral with nodes 6, 2, 4, 8
* Face 4: quadrilateral with nodes 8, 4, 1, 5
* Face 5: quadrilateral with nodes 1, 2, 6, 5

* Element 2: 5 faces.
* Face 6: triangle with nodes 5, 8, 7
* Face 7: triangle with nodes 1, 3, 4
* Face 8: quadrilateral with nodes 7, 8, 4, 3
* Face 9: quadrilateral with nodes 7, 3, 1, 5
* Face 4: quadrilateral with nodes 8, 4, 1, 5 (shared with element 1)
* Face 6: triangle with nodes 5, 8, 7
* Face 7: triangle with nodes 1, 3, 4
* Face 8: quadrilateral with nodes 7, 8, 4, 3
* Face 9: quadrilateral with nodes 7, 3, 1, 5
* Face 4: quadrilateral with nodes 8, 4, 1, 5 (shared with element 1)

* Element 3: 7 faces.
* Face 8: quadrilateral with nodes 7, 8, 4, 3 (shared with element 2)
* Face 10: pentagonal with nodes 8, 4, 14, 10, 12
* Face 11: pentagonal with nodes 7, 11, 9, 13, 3
* Face 12: quadrilateral with nodes 7, 8, 12, 11
* Face 13: quadrilateral with nodes 11, 12, 10, 9
* Face 14: quadrilateral with nodes 9, 10, 14, 13
* Face 15: quadrilateral with nodes 12, 14, 4, 3
* Face 8: quadrilateral with nodes 7, 8, 4, 3 (shared with element 2)
* Face 10: pentagonal with nodes 8, 4, 14, 10, 12
* Face 11: pentagonal with nodes 7, 11, 9, 13, 3
* Face 12: quadrilateral with nodes 7, 8, 12, 11
* Face 13: quadrilateral with nodes 11, 12, 10, 9
* Face 14: quadrilateral with nodes 9, 10, 14, 13
* Face 15: quadrilateral with nodes 12, 14, 4, 3

The Exodus model is created via the following calls:

Expand Down Expand Up @@ -79,9 +79,9 @@ The Exodus model is created via the following calls:
block_id = 10;
ex_put_block (exoid, EX_FACE_BLOCK, block_id, "nsided",
num_face_in_block[0],
num_total_nodes_per_blk[0],
0, 0, 0);
num_face_in_block[0],
num_total_nodes_per_blk[0],
0, 0, 0);
ex_put_name(exoid, EX_FACE_BLOCK, block_id, block_name);
~~~~

Expand Down Expand Up @@ -155,11 +155,11 @@ The Exodus model is created via the following calls:
block_id = 10;

ex_put_block (exoid, EX_ELEM_BLOCK, block_id, "nfaced",
num_elem_in_block,
0, /* nodes */
0, /* edges */
num_total_faces_per_blk,
0); /* attribute count */
num_elem_in_block,
0, /* nodes */
0, /* edges */
num_total_faces_per_blk,
0); /* attribute count */
ex_put_name(exoid, EX_ELEM_BLOCK, block_id, block_name);
~~~~
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