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Add instructions for installing the squadgen conda package #8

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b12fec9
Remove png.h include and libpng dependency
xylar May 14, 2024
77a17c9
Clean up Markdown in README.md
xylar May 14, 2024
51e9ec4
Add conda instructions
xylar May 14, 2024
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271 changes: 172 additions & 99 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
\file README.md
```
\file README.md
\author Paul Ullrich
\version May 8, 2024
```

Copyright 2024 Paul Ullrich

Expand All @@ -10,149 +12,220 @@ source code and its documentation under the terms of the GNU General
Public License. This software is provided "as is" without express
or implied warranty.

Spherical Quadrilateral Mesh Generator (SQuadGen)
=================================================
# Spherical Quadrilateral Mesh Generator (SQuadGen)

REQUIRED EXTERNAL LIBRARIES
libpng
libnetcdf
## REQUIRED EXTERNAL LIBRARIES

BUILDING
Modify src/Makefile to specify NetCDF paths
make all
libnetcdf

SYNOPSIS
## BUILDING

Modify `src/Makefile` to specify NetCDF paths

```sh
make all
```

## INSTALLING FROM CONDA PACKAGE

An alternative to building SQuadGen from source is to install a pre-built Linux
verison from a conda package.

If you don't already have a conda base environment set up, you can install
[miniforge3](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge3).

To add SQuadGen to an existing conda environment, activate the environment and
run:
```sh
conda install squadgen
```

To create a new conda environment with SQuadGen in it (and any other packages
you like, run:
```sh
conda create -n <env_name> squadgen <package> <package>
```
Then, activate the environment with:
```sh
conda activate <env_name>
```
The `SQuadGen` executable will be in your path.

## SYNOPSIS
```sh
./SQuadGen <Parameter List>
```

## PARAMETERS

PARAMETERS
```
--grid_type <string> ["CS"] (Options: CS | ICO | OCT1 | OCT2)
--refine_type <string> ["LOWCONN"] (Options: LOWCONN | CUBIT | LOWCONNOLD)
--refine_level <integer> [2]
--resolution <integer> [10]
--refine_file <string> [""]
--refine_rect <string> [""]
--output <string> [""]
--loadcsrefinementmap <bool> [false]
--refine_level <integer> [2]
--resolution <integer> [10]
--refine_file <string> [""]
--refine_rect <string> [""]
--output <string> [""]
--loadcsrefinementmap <bool> [false]
--smooth_type <string> ["NONE"] (Options: NONE | SPRING | PRESSURE)
--smooth_dist <integer> [1] (Smooth distance, -1 = smooth entire mesh)
--smooth_iter <integer> [10]
--lon_base <double> [-180.000000]
--lat_base <double> [0.000000]
--x_rotate <double> [0.000000]
--y_rotate <double> [0.000000]
--lon_ref <double> [0.000000]
--lat_ref <double> [0.000000]
--orient_ref <double> [0.000000]
--tessellate <integer> [0]
--subcellres <integer> [0]
--invert <bool> [false]
--block_refine <bool> [false]


DESCRIPTION
SQuadGen is a mesh generation utility that uses a cubed-sphere base mesh to
--smooth_iter <integer> [10]
--lon_base <double> [-180.000000]
--lat_base <double> [0.000000]
--x_rotate <double> [0.000000]
--y_rotate <double> [0.000000]
--lon_ref <double> [0.000000]
--lat_ref <double> [0.000000]
--orient_ref <double> [0.000000]
--tessellate <integer> [0]
--subcellres <integer> [0]
--invert <bool> [false]
--block_refine <bool> [false]
```

## DESCRIPTION

`SQuadGen` is a mesh generation utility that uses a cubed-sphere base mesh to
generate quadrilateral meshes with user-specified enhancements. In order to
determine where enhancement is desired, the user provides a PNG file which
corresponds to a latitude-longitude grid. Raster values with higher brightness
(whiter values) are tagged for refinement. The algorithm uses a basic paving
technique and supports two paving stencil types: Low-connectivity (LOWCONN)
and CUBIT-type transition regions.
technique and supports two paving stencil types: Low-connectivity (`LOWCONN`)
and `CUBIT`-type transition regions.

## OPTIONS

`--grid_type (CS) | ICO`
<dd>

Type of base mesh to use for refinement: cubed-sphere (`CS`) or icosahedral
(`ICO`). If `ICO` is specified, generate a basic icosahedral flag mesh. All
refinement criteria will be ignored in this case.
</dd>

`--refine_type (LOWCONN) | CUBIT | LOWCONNOLD`
<dd>

OPTIONS
--grid_type (CS) | ICO
Type of paving stencil to use `LOWCONN`, `CUBIT` or `LOWCONNOLD`. `LOWCONN` provides
a few enhancements over the previous `LOWCONN` old template by removing
spurious elements with high aspect ratios (typically near interior corners).
</dd>

Type of base mesh to use for refinement: cubed-sphere (CS) or icosahedral
(ICO). If ICO is specified, generate a basic icosahedral flag mesh. All
refinement criteria will be ignored in this case.
`--refine_level <integer>`
<dd>

--refine_type (LOWCONN) | CUBIT | LOWCONNOLD
Number of levels of refinement to use in grid generation. Each refinement
level corresponds to a 2x refinement of the mesh.
</dd>

Type of paving stencil to use LOWCONN, CUBIT or LOWCONNOLD. LOWCONN provides
a few enhancements over the previous LOWCONN old template by removing
spurious elements with high aspect ratios (typically near interior corners).
`--resolution <integer>`
<dd>

--refine_level <integer>
Base resolution of the mesh. For cubed-sphere meshes this corresponds to the
number of faces along each edge of the cubed-sphere.
</dd>

Number of levels of refinement to use in grid generation. Each refinement
level corresponds to a 2x refinement of the mesh.
`--refine_file <filename>`
<dd>

--resolution <integer>
Filename of the PNG file to use for specifying refinement regions.
</dd>

Base resolution of the mesh. For cubed-sphere meshes this corresponds to the
number of faces along each edge of the cubed-sphere.

--refine_file <filename>
`--refine_rect <string>`
<dd>

Filename of the PNG file to use for specifying refinement regions.
An argument specifying rectangular regions on the cubed-sphere where
refinement should be applied. Each refine_rect should be separated by a
semi-colon and consists of five arguments:

--refine_rect <string>
```
<lon1>,<lat1>,<lon2>,<lat2>,<level>
```

An argument specifying rectangular regions on the cubed-sphere where
refinement should be applied. Each refine_rect should be separated by a
semi-colon and consists of five arguments:
<lon1>,<lat1>,<lon2>,<lat2>,<level>
where `<lon1>,<lat1>` are the longitude-latitude coordinates of the lower-right
corner of the refinement region, `<lon2>,<lat2>` are the longitude-latitude
coordinates of the upper-right corner of the refinement region, and `<level>`
is the number of levels of refinement.
</dd>

where <lon1>,<lat1> are the longitude-latitude coordinates of the lower-right
corner of the refinement region, <lon2>,<lat2> are the longitude-latitude
coordinates of the upper-right corner of the refinement region, and <level>
is the number of levels of refinement.
`--output <filename>`
<dd>

--output <filename>
Filename for the output EXODUS-format grid file.
</dd>

Filename for the output EXODUS-format grid file.
`--loadcsrefinementmap`
<dd>

--loadcsrefinementmap
(ADVANCED) If specified, the refinement map will be reloaded from the
previously generated refine_map.dat file. This option allows for manual
editing of the cubed-sphere refine map.
</dd>

(ADVANCED) If specified, the refinement map will be reloaded from the
previously generated refine_map.dat file. This option allows for manual
editing of the cubed-sphere refine map.
`--smooth_type (NONE) | SPRING`
<dd>

--smooth_type (NONE) | SPRING
If `SPRING` is specified, use spring-dynamics type mesh smoothing once the
refined mesh has been generated.
</dd>

If SPRING is specified, use spring-dynamics type mesh smoothing once the
refined mesh has been generated.
`--smooth_dist <integer>`
<dd>

--smooth_dist <integer>
By default (smooth dist 1) only nodes which are part of the transition region
will be smoothed. Larger values of smooth_dist includes nodes of distance
smooth_dist away from the transition region (by edge connectivity). If
smooth_dist is set to -1 then the entire mesh will be subjected to smoothing.
</dd>

By default (smooth dist 1) only nodes which are part of the transition region
will be smoothed. Larger values of smooth_dist includes nodes of distance
smooth_dist away from the transition region (by edge connectivity). If
smooth_dist is set to -1 then the entire mesh will be subjected to smoothing.
`--smooth_iter <integer>`
<dd>

--smooth_iter <integer>
Number of smoothing iterations to perform. A larger value will typically
result in a smoother mesh.
</dd>

Number of smoothing iterations to perform. A larger value will typically
result in a smoother mesh.
`--lon_base <double>`
<dd>

--lon_base <double>
Longitude coordinate (in degrees) of the left-most edge of the PNG image.
</dd>

Longitude coordinate (in degrees) of the left-most edge of the PNG image.
`--lon_shift <double>`
<dd>

--lon_shift <double>
Amount of rotation (in degrees) to apply to the base mesh.
</dd>

Amount of rotation (in degrees) to apply to the base mesh.
`--lon_ref <double>`
<dd>

--lon_ref <double>
The central longitude of the first panel of the cubed-sphere (in degrees).
</dd>

The central longitude of the first panel of the cubed-sphere (in degrees).

--lat_ref <double>
`--lat_ref <double>`
<dd>

The central latitude of the first panel of the cubed-sphere (in degrees).
The central latitude of the first panel of the cubed-sphere (in degrees).
</dd>

--orient_ref <double>
`--orient_ref <double>`
<dd>

The orientation of the cubed sphere at <lon_ref>,<lat_ref> in degrees.
A value of 0 means the cubed-sphere is aligned perfectly zonal at the\
reference point. A value of 45 means the cubed-sphere is inclined by 45
degrees at this point.

--invert
The orientation of the cubed sphere at `<lon_ref>,<lat_ref>` in degrees.
A value of 0 means the cubed-sphere is aligned perfectly zonal at the
reference point. A value of 45 means the cubed-sphere is inclined by 45
degrees at this point.
</dd>

Invert the base image (so black identifies regions of refinement).
`--invert`
<dd>

--block_refine
Invert the base image (so black identifies regions of refinement).
</dd>

Turn on block-wise tagging of elements for refinement.
`--block_refine`
<dd>

Turn on block-wise tagging of elements for refinement.
</dd>
1 change: 0 additions & 1 deletion src/SQuadGen.cpp
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Expand Up @@ -14,7 +14,6 @@
/// or implied warranty.
/// </remarks>

#include <png.h>
#include "netcdfcpp.h"

#include <string>
Expand Down