README

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+Nstrophy is a tool to solve the two-dimensional Navier-Stokes equation as well
+as Gallavotti's reversible Navier-Stokes equation and compare them.
+
+**Nstrophy is under active development**
+
+# Building
+
+Compile Nstrophy with
+```bash
+make
+```
+which will place a binary at `build/nstrophy`.
+
+The syntax for the execution of Nstrophy is
+```bash
+./build/nstrophy [-p parameters] [-s savefile] <command>
+```
+
+Nstrophy is written in C. The Makefile uses the GNU C Compiler.
+
+Nstrophy depends on `fftw`: [https://fftw.org]
+
+
+# Commands
+
+The available commands are
+
+* `enstrophy`: to compute the enstrophy, the parameter alpha and
+  alpha times the enstrophy. This command prints
+  `step_index time average_alpha average_enstrophy average_alphaxenstrophy alpha enstrophy alphaxenstrophy`
+  where the averages are running averages over `print_freq` steps.
+
+* `uk`: to compute the Fourier transform of the solution.
+
+* `quiet`: does not print anything, useful for debugging.
+
+
+# Parameters
+
+The parameters can be specified using the `-p` flag. The parameter string
+should be a `;` sperated list of `key=value` pairs. The possible keys are
+
+* `equation`: either `irreverisible` (default) or `reversible`.
+
+* `K` (int, default 16): cutoff in momentum space: -K<=k_i<=K
+
+* `K1` (int, default `K`): cutoff in momentum space for the x component:
+  -K<=k_x<=K
+
+* `K2` (int, default `K`): cutoff in momentum space for the y component:
+  -K<=k_y<=K
+
+* `N` (int, default smallest power of 2 that is larger than 3`K`): size of fft
+  vectors: must be at least 3 times `K` to avoid aliasing.
+
+* `N1` (int, default `N`): same as `N` but only for x component.
+
+* `N2` (int, default `N`): same as `N` but only for y component.
+
+* `nsteps` (long int, default 10000000): number of steps in the computation.
+  Set to 0 to keep on going forever.
+
+* `nu` (double, default 0.00048828125): viscosity.
+
+* `delta` (double, default 0.0001220703125): step size.
+
+* `L` (double, default 2pi): size of box.
+
+* `print_freq` (long int, default 1000): only print every `print_freq` steps.
+
+* `starting_time` (long int, default 0): start the computation at this step.
+
+* `driving`: either `zero` for no driving, `test` (default) for a testing
+  driving force or `file:<filename>` or `file_txt:<filename>` to read the
+  driving force from a file. When using `file:<filename>` the file should be
+  binary, whereas with `file_txt:<filename>` it should be plaintext. The binary
+  file format is `(double)(double)` for each entry of the driving force,
+  excluding kx<0 and kx=0&&ky<=0. The plaintext file format is
+  `kx ky real_part imag_part`.
+
+* `init`: either `random` for a random initialization, `gaussian` (default) for
+  a Gaussian initial condition or `file:<filename>` or `file_txt:<filename>` to
+  read the driving force from a file. When using `file:<filename>` the file
+  should be binary, whereas with `file_txt:<filename>` it should be plaintext.
+  The binary file format is `(double)(double)` for each entry of the driving
+  force, excluding kx<0 and kx=0&&ky<=0. The plaintext file format is
+  `kx ky real_part imag_part`.
+
+* `init_en` (double, default 1.54511597324389e+02): initial value of the energy if
+  `equation=irreversible` or of the enstrophy if `equation=reversible`.
+
+* `random_seed` (int, default ): seed for random initialization.
+
+* `algorithm`: either `RK4` for Runge-Kutta 4, or `RK2` for Runge-Kutta 2.
+
+
+# Interrupting/resuming the computation
+
+The computation can be interrupted by sending Nstrophy the `SIGINT` signal
+(e.g. by pressing `Ctrl-C`.) When Nstrophy receives the `SIGINT` signal, it
+finishes its current step and writes the value of uk, either to `savefile` if
+such a file was specified on the command line (using the `-s` flag), or to
+`stderr`. In addition, when a `savefile` is specified it writes the command
+that needs to be used to resume the computation (which essentially just sets
+the appropriate `starting_time` and `init:file:<savefile>` parameters. The data
+written to the `savefile` is binary.