### Run Meissner example with noisy d-wave start guess

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Demonstrates using command-line arguments to remove the s-wave component and add a noisy dxy-wave component to an existing configuration.

```bash
python superconga.py simulate -C examples/swave_disc_meissner/ --no-s-wave --dxy-wave 1.0 0.0 2.0
```

--------------------------------

### Simulating and plotting a solenoid setup

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Commands to simulate a d+is superconductor with a solenoid gauge and plot the resulting simulation data. Note that this setup may require higher numerical discretization for convergence.

```bash
python superconga.py simulate -C examples/dwave_plus_swave -S data/dwave_plus_swave_modified -g solenoid --remove-regular-polygon 0 0 8 0.333 5 -B 3.7 -N 10 -p 64 -c 2.5e-5

python superconga.py plot-simulation -L data/dwave_plus_swave_modified --view {D,J}
```

--------------------------------

### Change Meissner-state example via command-line arguments

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example of overriding configuration settings using command-line flags to set flux, temperature, penetration depth, output folder, and order-parameter symmetry.

```bash
python superconga.py simulate -C examples/swave_disc_meissner -S data/dwave_disc_meissner -B 1 -T 0.05 -k 4 --dx2-y2-wave 1 0 0 --no-s-wave -N 10 -p 64
```

--------------------------------

### Postprocessing configuration file

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example of a postprocess_config.json file defining spectroscopy, numerical, and miscellaneous settings.

```json
 {
     "spectroscopy": {
         "energy_max": 0.5,
         "energy_min": 0.0,
         "energy_broadening": 0.008,
         "num_energies": 128
     },
     "numerics": {
         "convergence_criterion": 1e-4,
         "norm": "l2",
         "num_energies_per_block": 32,
         "num_fermi_momenta": 720,
         "num_iterations_burnin": -1,
         "num_iterations_max": 1000,
         "num_iterations_min": 0
     },
     "misc": {
         "data_format": "h5",
         "load_path": "data/examples/swave_disc_vortex",
         "save_path": "",
         "verbose": true
     }
 }
```

--------------------------------

### Plot the custom d-wave Meissner example

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Command to visualize simulation results saved in a specific data directory.

```bash
python superconga.py plot-simulation -L data/dwave_hexagon_meissner
```

--------------------------------

### Geometry section of the config file

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example of the geometry list structure in a JSON configuration file.

```json
"geometry": [
     {
         "regular_polygon": {
             "add": true,
             ...
         }
     }
 ],

```

--------------------------------

### Compile SuperConga with tests

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Run this command after the setup process to compile the project and automatically execute unit tests.

```bash
python superconga.py compile --type Release --test
```

--------------------------------

### Simulate and plot modified chiral d-wave example

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Run a simulation with opposite chirality by modifying the phase shift and plot the results using the chiral transformation.

```bash
python superconga.py simulate -C examples/dwave_chiral/ --dxy-wave 1 -0.25 0 -S data/examples/dwave_chiral_opposite/
python superconga.py plot-simulation --chiral-transform -L data/examples/dwave_chiral_opposite/ --view {D,J}
```

--------------------------------

### Run Abrikosov-vortex simulation with superconga.py simulate

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Runs the Abrikosov-vortex example from the repository root. The -C flag specifies the config file path, and -T overrides the temperature to 0.5Tc. Command-line arguments take priority over config-file values.

```bash
python superconga.py simulate -C examples/swave_disc_vortex/simulation_config.json -T 0.5

```

--------------------------------

### Run Abrikosov-vortex lattice simulation

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Runs the SuperConga simulation for the Abrikosov-vortex lattice example, saving data to data/vortex_lattice/. Required before plotting with plot-simulation or plot-convergence.

```bash
python superconga.py simulate -C examples/swave_abrikosov_lattice/ -S data/vortex_lattice/
```

--------------------------------

### Add multiple vortices via config file

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Demonstrates adding four singly-quantized vortices to the simulation start guess by extending the vortices list in the JSON configuration.

```json
 "vortices": [
     {
         "center_x": 5.0,
         "center_y": 5.0,
         "winding_number": -1.0
     },
     {
         "center_x": 5.0,
         "center_y": -5.0,
         "winding_number": -1.0
     },
     {
         "center_x": -5.0,
         "center_y": -5.0,
         "winding_number": -1.0
     },
     {
         "center_x": -5.0,
         "center_y": 5.0,
         "winding_number": -1.0
     }
 ]
```

--------------------------------

### Disc geometry configuration

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example of defining a disc geometry in a JSON configuration file using radius and center coordinates.

```json
 "geometry": [
     {
         "disc": {
             "add": true,
             "center_x": 0.0,
             "center_y": 0.0,
             "radius": 15.0
         }
     }
 ],

```

--------------------------------

### Plot d+is vortex simulation results

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Plots the converged simulation results for the d+is vortex example.

```bash
python superconga.py plot-simulation -L data/dwave_plus_swave_vortices
```

--------------------------------

### Simulate d+ig superconductor with spontaneous symmetry breaking

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Modifies the dwave_plus_swave example to study a d+ig superconductor by replacing the s-wave component with a g-wave and applying a phase shift.

```bash
python superconga.py simulate -C examples/dwave_plus_swave/simulation_config.json --no-s-wave --g-wave 0.5 0.01 0 -T 0.1 -k 80 -S data/dwave_plus_gwave
```

--------------------------------

### Example postprocess_config.json for swave_disc_vortex

Source: https://superconga.gitlab.io/superconga-doc/technical_reference.html

JSON configuration file for running postprocessing with SuperConga. Contains spectroscopy, numerics, and misc parameter groups. The spectroscopy group defines the energy range and broadening; numerics controls convergence and memory usage; misc specifies data format and paths. Note that energy_min is often set to 0.0 because negative energies can be obtained by symmetry.

```json
{
    "spectroscopy": {
        "energy_max": 0.5,
        "energy_min": 0.0,
        "energy_broadening": 0.008,
        "num_energies": 128
    },
    "numerics": {
        "convergence_criterion": 1e-4,
        "norm": "l2",
        "num_energies_per_block": 32,
        "num_fermi_momenta": 720,
        "num_iterations_burnin": -1,
        "num_iterations_max": 1000,
        "num_iterations_min": 0
    },
    "misc": {
        "data_format": "h5",
        "load_path": "data/examples/dwave_chiral",
        "save_path": "",
        "verbose": true
    }
}
```

--------------------------------

### Run chiral d-wave simulation

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Execute the simulation using the configuration file located in the examples/dwave_chiral/ directory.

```bash
python superconga.py simulate -C examples/dwave_chiral/
```

--------------------------------

### Arbitrary polygon geometry: d-wave phase crystal example

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example geometry section from examples/dwave_phase_crystal/simulation_config.json defining an irregular polygon.

```json
 "geometry": [
     {
         "polygon": {
             "add": true,
             "vertices_x": [
                 25.0,
                 0.0,
                 0.0,
                 5.0,
                 25.0
             ],
             "vertices_y": [
                 25.0,
                 25.0,
                 0.0,
                 0.0,
                 20.0
             ]
         }
     }
 ],

```

--------------------------------

### Regular polygon geometry: an octagon

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example geometry section from examples/dwave_octagon/simulation_config.json defining an octagon.

```json
 "geometry": [
     {
         "regular_polygon": {
             "add": true,
             "center_x": 0.0,
             "center_y": 0.0,
             "num_edges": 8,
             "rotation": 0.0,
             "side_length": 10.0
         }
     }
 ],

```

--------------------------------

### Simulate a chiral d-wave in a slab geometry via CLI

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Runs a simulation with noise to seed domain walls, setting the temperature to 0.1Tc and constructing a slab geometry from five squares.

```bash
python superconga.py simulate -C examples/dwave_chiral/ --dxy-wave 1 0.25 20 --dxy-wave 1 0.25 20 -T 0.1 -S data/dwave_chiral_slab/ --clear-geometry --add-regular-polygon 0 0 4 0 10 --add-regular-polygon 10 0 4 0 10 --add-regular-polygon 20 0 4 0 10 --add-regular-polygon 30 0 4 0 10 --add-regular-polygon 40 0 4 0 10
```

--------------------------------

### Geometry with a circular hole

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Example configuration showing how to add a square and remove a circular disc to create a hole.

```json
     "geometry": [
             {
                     "regular_polygon": {
                             "add": true,
                             "center_x": 0.0,
                             "center_y": 0.0,
                             "num_edges": 4,
                             "rotation": 0.0,
                             "side_length": 20.0
                     }
                     "disc": {
                             "add": false,
                             "center_x": 0.0,
                             "center_y": 0.0,
                             "radius": 5.0
                     }
             }
     ],

```

--------------------------------

### Run vortex-core spectroscopy simulation

Source: https://superconga.gitlab.io/superconga-doc/guides/vortex-core-spectroscopy.html

Execute the shell script from the project root directory to calculate the spectra of vortex cores.

```bash
./examples/guides/vortex_core_spectroscopy/vortex_core_spectroscopy.sh
```

--------------------------------

### Run Abrikosov-vortex core simulation script

Source: https://superconga.gitlab.io/superconga-doc/guides/abrikosov-vortex-core.html

Execute the shell script from the project root to perform a parameter sweep for the penetration depth.

```bash
./examples/parameter_sweeps/swave_disc_vortex_kappa_sweep.sh
```

--------------------------------

### Change Meissner-state example to a hexagon geometry

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

JSON configuration snippet to modify the geometry entry to a hexagon with side-length 10ξ0.

```json
     "geometry": [
         {
             "regular_polygon": {
                 "add": true,
                 "center_x": 0.0,
                 "center_y": 0.0,
                 "num_edges": 6,
                 "rotation": 0.0,
                 "side_length": 10.0
             }
         }
     ],
```

--------------------------------

### Plot chiral d-wave simulation results

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Visualize the simulation data stored in the data/examples/dwave_chiral/ directory.

```bash
python superconga.py plot-simulation -L data/examples/dwave_chiral/ --view {D,J}
```

--------------------------------

### Run the thermodynamics simulation

Source: https://superconga.gitlab.io/superconga-doc/guides/basic-thermodynamics.html

Command to execute the parameter sweep script from the project root directory. Launches multiple simulations with varying penetration depth.

```bash
./examples/parameter_sweeps/swave_and_dwave_temperature_sweep.sh

```

--------------------------------

### View SuperConga noise tool help

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Run the noise tool from the SuperConga root directory to display its help message. The tool is located at tools/noise.py.

```bash
python tools/noise.py --help

```

--------------------------------

### Simulate d-wave superconductor with subdominant s-wave

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Shows how to define multiple order parameters by adding both a dxy-wave and a subdominant s-wave component with a lower critical temperature.

```bash
python superconga.py simulate -C examples/swave_disc_meissner/ --dxy-wave 1 0 0 --s-wave 0.1 0 0 -S data/dwave_plus_swave_meissner
```

--------------------------------

### Bash script for penetration depth sweep

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

This script executes a series of SuperConga simulations with varying penetration depth values, using the output of the previous simulation as the starting point for the next.

```bash
 #!/bin/bash

 # Note, this script is meant to be executed from the root folder of the project.
 # ./examples/parameter_sweeps/swave_disc_vortex_kappa_sweep.sh

 # The configuration file to use.
 CONFIG="examples/parameter_sweeps/kappa_sweep_config.json"

 # Base path to save the data to.
 DATA_PATH="data/examples/swave_disc_vortex_kappa_sweep"

 # The number of burn-in iterations.
 BURNIN=-1

 python superconga.py simulate -C $CONFIG -S $DATA_PATH/kInf --no-visualize -k -1 --vortex 0 0 -1
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k64 -L $DATA_PATH/kInf -b $BURNIN --no-visualize -k 64
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k32 -L $DATA_PATH/k64 -b $BURNIN --no-visualize -k 32
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k16 -L $DATA_PATH/k32 -b $BURNIN --no-visualize -k 16
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k8 -L $DATA_PATH/k16 -b $BURNIN --no-visualize -k 8
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k4 -L $DATA_PATH/k8 -b $BURNIN --no-visualize -k 4
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k2 -L $DATA_PATH/k4 -b $BURNIN --no-visualize -k 2
 python superconga.py simulate -C $CONFIG -S $DATA_PATH/k1 -L $DATA_PATH/k2 -b $BURNIN --no-visualize -k 1
```

--------------------------------

### git remote: adding upstream parent

Source: https://superconga.gitlab.io/superconga-doc/contribute.html

Adds the parent SuperConga repository as a remote named 'upstream'. Run this in the directory created by git clone. Multiple remotes can be added, for example to other forks.

```bash
git remote add upstream https://gitlab.com/superconga/superconga

```

--------------------------------

### Interactive spectroscopy of vortex cores

Source: https://superconga.gitlab.io/superconga-doc/guides/vortex-core-spectroscopy.html

Run the interactive plotter for s-wave and d-wave vortex cores.

```bash
python3 ldos_plotter.py --file examples/guides/vortex_core_spectroscopy/swave_vortex.json
python3 ldos_plotter.py --file examples/guides/vortex_core_spectroscopy/dwave_vortex.json
```

--------------------------------

### Resume Abrikosov-vortex simulation with same parameters

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Resumes a simulation using the exact same configuration and data path as the original run.

```bash
python superconga.py simulate -L data/examples/swave_disc_vortex/ -C data/examples/swave_disc_vortex/
```

--------------------------------

### Parameter sweep shell script for s-wave and d-wave simulations

Source: https://superconga.gitlab.io/superconga-doc/guides/basic-thermodynamics.html

Bash script that loops over temperatures, runs s-wave and d-wave simulations using superconga.py, and uses previous data as start guess with burn-in. Requires execution from project root.

```bash
#!/bin/bash

# Note, this script is meant to be executed from the root folder of the project.
# ./examples/parameter_sweeps/swave_and_dwave_temperature_sweep.sh

# Force decimal separator to be point (instead of e.g. comma).
export LC_NUMERIC="en_US.UTF-8"

# Note, this script is meant to be executed from the root folder of the project.

# The configuration file to use.
CONFIG="examples/parameter_sweeps/temperature_sweep_config.json"

# Base path to save the data to.
DATA_BASE_PATH="data/examples/temperature_sweep"

# The number of burn-in iterations. Negative: run until boundary is converged.
BURNIN=-1

# String containing load path (including flag). Empty for first run.
LOAD_STRING_SWAVE=""
LOAD_STRING_DWAVE=""

# Loop over temperatures. Manually add T=0.999 at end.
T_MIN=0.01
T_MAX=0.99
T_STEP=0.02
T_IDX=0
for T in $(seq $T_MIN $T_STEP $T_MAX; seq 0.999 $T_STEP 0.999); do
    DATA_PATH_SWAVE=`printf "$DATA_BASE_PATH/swave/T%2.3f/" $T`
    DATA_PATH_DWAVE=`printf "$DATA_BASE_PATH/dwave/T%2.3f/" $T`

    # Run simulation: s-wave.
    python superconga.py simulate -C $CONFIG -S $DATA_PATH_SWAVE --no-visualize -T $T $LOAD_STRING_SWAVE
    # Run simulation: d-wave.
    python superconga.py simulate -C $CONFIG -S $DATA_PATH_DWAVE --no-visualize -T $T $LOAD_STRING_DWAVE --no-s-wave --dx2-y2-wave 1 0 0

    # Use data as start-point for next simulation, with burnin.
    LOAD_STRING_SWAVE="-L $DATA_PATH_SWAVE -b $BURNIN"
    LOAD_STRING_DWAVE="-L $DATA_PATH_DWAVE -b $BURNIN"
done

```

--------------------------------

### Run simulation with save frequency -F 50

Source: https://superconga.gitlab.io/superconga-doc/tutorials.html

Saves data every 50th iteration during the vortex example. Use from the root directory. Positive integer frequency saves during simulation and at the end; negative saves only at the end; zero disables saving.

```bash
python superconga.py simulate -C examples/swave_disc_vortex/ -F 50

```