Nmag

Nmag cheat sheet¶

Mesh generation¶

Create mesh with Netgen from command line (Geometry specification to Neutral Mesh)

netgen -geofile=in.geo -moderate -meshfiletype="Neutral Format" \
       -meshfile=out.neu -batchmode

Convert from one mesh format to the other¶

Neutral format (Netgen) to Nmag format:

nmeshimport --netgen in.neu out.nmesh.h5
nmeshimport --netgen in.neu out.nmesh

Binary Nmag format to ASCII Nmag format and viceversa:

nmeshpp -c in.nmesh.h5 out.nmesh
nmeshpp -c in.nmesh out.nmesh.h5

Binary Nmag format to AVS format (Magpar):
```
nmeshpp -m in.nmesh.h5 out.inp
```

Inspect and visualise mesh¶

Getting generic info on the mesh

nmeshpp in.nmesh.h5 -i   # show general information, num points, num simplices, etc
nmeshpp in.nmesh.h5 -a   # show a distribution of lengths of the edges of the simplices
nmeshpp in.nmesh.h5 -q   # show a distribution of simplex quality

Transforming the mesh to a VTK file for visualisation (with Mayavi2 or Paraview):
```
nmeshpp --vtk in.nmesh.h5 out.vtk
```

Visualising the mesh from the VTK file obtained from command above (using Mayavi2 or Paraview)

mayavi2 -d out.vtk -m Surface
paraview --data=out.vtk # click on apply when Paraview windows is shown

Running simulations¶

Run simulation file ``mysim.py``
```
nsim mysim.py
```

Run simulation and confirm that existing data files should be overridden
```
nsim mysim.py --clean
```

Continue simulation from stage where it was interrupted before (only for hysteresis command)
```
nsim mysim.py --restart
```

Running MPI simulations¶

Start a parallel run (on 2 machines):
```
mpirun -np 2 nsim mysim.py
```

For MPICH2 you need to launch the daemon first (not required for Nmag VM as it is using OpenMPI):
```
cd nmag-0.1 # here we assume you installed from source
~/lib/mpich2/bin/mpd &
```
If you launch mpd for the first time take a look at the instructions in the manual

Visualise mesh partitioning¶

When you run the simulation in parallel you get:

...
nfem.ocaml:2010-07-26 15:54:50,578    INFO Processor 0: 1065 nodes
nfem.ocaml:2010-07-26 15:54:50,578    INFO Processor 1: 1052 nodes
...

These numbers are recorded in the log file (example simulation_log.log).
We here assume that your fields are saved in the file simulation_dat.h5.
You can produce a VTK file with the partitioning (and visualise it) using:

nmeshpp simulation_dat.h5 --partitioning=[1065,1052] partitioning.vtk
mayavi2 -d partitioning.vtk -m Surface

Postprocessing data¶

Inspect field data file simulation_dat.h5:

nmagpp simulation --fieldlist # get the list of field stored inside the file
nmagpp simulation --idlist    # get the list of the IDs for the stored fields

Convert data from mysim_dat.h5 file to vtk-files with name myvtk-000000.vtk, myvtk-000001.vtk, etc.
```
nmagpp --vtk myvtk.vtk mysim
```

Write VTK files containing only the specified fields (faster than command above):
```
nmagpp --vtk myvtk.vtk --fields=m,H_demag mysim
```

Visualising data from the VTK obtained above
```
mayavi2 -d myvtk-000000.vtk -m Vectors
```

Get a list of fields stored in NDT file mysim.ndt
```
ncol mysim
```

Get a list of the fields whose name starts with H or H_e
```
ncol mysim H
ncol mysim H_e
```

Extract external field (spatial average against time) from ``mysim.ndt`` file
```
ncol mysim time H_ext_0 H_ext_1 H_ext_2
```

Extract magnetisation against time (with ncol) and plot it with Gnuplot:

ncol mysim time m_Py_0 m_Py_1 m_Py_2 > outfile.dat
gnuplot
plot "./outfile.dat" u 1:2 t "m_x" w l, "" u 1:3 t "m_y" w l, "" u 1:4 t "m_z" w l

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