### Configuring Output Times with New Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/changes.rst.txt

This example demonstrates how to configure output intervals using the updated parameter system. It sets the starting redshift, a list of target redshifts, and specifies one step for each interval.

```python
dRedFrom = 49               # Start at z=49
dRedTo = [10,2,1,0.5,0]     # Step to z=10, 2, 1, 0.5 and 0
nSteps = [1] * len(dRedTo)  # Taking one step for each interval
iOutInterval = 1            # Output every interval
```

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

### Specifying Steps for Redshift Intervals

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/changes.rst.txt

This example shows the new method for specifying simulation steps across different redshift intervals. It defines the starting redshift and a list of target redshifts, with corresponding steps for each interval.

```python
dRedFrom = 40
dRedTo = [10,0]
nSteps = [60,100]
```

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

### Configure Output Times using Redshift in pkdgrav3

Source: https://pkdgrav3.readthedocs.io/en/latest/changes.html

Set output times based on redshift. This example demonstrates specifying a start redshift, a list of target redshifts, and the number of steps for each interval.

```python
dRedFrom = 49               # Start at z=49
dRedTo = [10,2,1,0.5,0]     # Step to z=10, 2, 1, 0.5 and 0
nSteps = [1] * len(dRedTo)  # Taking one step for each interval
iOutInterval = 1            # Output every interval

```

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

### Build and Install pkdgrav3 Manually

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Commands to set up a virtual environment, build the project using CMake, and install the executable.

```bash
cd $HOME/project/project1

python -m venv .venv
source .venv/bin/activate
python -m pip install -r $HOME/sources/pkdgrav3/requirements.txt

cmake -S $HOME/sources/pkdgrav3 -B build
cmake --build build
cmake --install build --prefix $HOME/project/project1
```

```bash
$HOME/project/project1/bin/pkdgrav3
```

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

### Install dependencies on Ubuntu

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Install necessary build tools and libraries for PKDGRAV3 on Ubuntu 20.04 and 22.04.

```bash
sudo apt update
sudo apt install -y autoconf automake pkg-config cmake gcc g++ make gfortran git
sudo apt install -y libfftw3-dev libfftw3-mpi-dev libgsl0-dev libboost-all-dev libhdf5-dev libmemkind-dev libhwloc-dev
sudo apt install -y python3-dev cython3 python3-pip python3-numpy python3-ddt python3-nose python3-tomli
```

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

### Verify Homebrew Package Installation

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Checks the installation path and version of Python, FFTW, and Boost installed via Homebrew.

```bash
brew --prefix python@3.12 fftw boost

```

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

### Install Python Dependencies

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Install all necessary Python packages for compiling, running, and testing pkdgrav3 using pip and the provided requirements.txt file.

```bash
python -m pip install -r requirements.txt
```

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

### Locate Installed Executable

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Path to the pkdgrav3 binary after installation.

```bash
$HOME/project/project1/bin/pkdgrav3
```

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

### Project-Specific Build Workflow

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

A complete sequence for setting up a project-specific environment, building, and installing the pkdgrav3 executable.

```bash
cd $HOME/project/project1

python -m venv .venv
source .venv/bin/activate
python -m pip install -r $HOME/sources/pkdgrav3/requirements.txt

cmake -S $HOME/sources/pkdgrav3 -B build
cmake --build build
cmake --install build --prefix $HOME/project/project1
```

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

### Install xmlrunner on Ubuntu

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Install the xmlrunner package required for running the test suite.

```bash
sudo apt install -y python3-xmlrunner
```

```bash
pip3 install xmlrunner
```

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

### Configure Parallel Tipsy Output Path

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Example format string for achIoPath to enable parallel writing to separate files.

```text
{name}.{step:05d}{type}.{i}
```

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

### Ubuntu Dependency Installation

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Commands to install required system packages and test suite dependencies on Ubuntu.

```bash
sudo apt update
sudo apt install -y autoconf automake pkg-config cmake gcc g++ make gfortran git
sudo apt install -y libfftw3-dev libfftw3-mpi-dev libgsl0-dev libboost-all-dev libhdf5-dev libmemkind-dev libhwloc-dev
sudo apt install -y python3-dev cython3 python3-pip python3-numpy python3-ddt python3-nose python3-tomli
```

```bash
sudo apt install -y python3-xmlrunner
```

```bash
pip3 install xmlrunner
```

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

### Install Homebrew Packages for pkdgrav3

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Installs essential development packages using Homebrew on MacOS. Ensure Xcode is installed and launched at least once.

```bash
brew install cmake boost fftw git gsl open-mpi hdf5-mpi python pyenv pyenv-virtualenv

```

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

### Verify Homebrew package paths

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Check the installation prefix for specific Homebrew packages.

```bash
brew --prefix python@3.12 fftw boost
```

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

### Execute pkdgrav3 via uenv

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Commands to start the pkdgrav3 view or configure Slurm for batch execution.

```bash
uenv start --view=pkdgrav3 pkdgrav3
pkdgrav3 cosmology.par
```

```bash
#SBATCH --uenv=pkdgrav3 --view=pkdgrav3
```

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

### Manage Python Virtual Environment

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Commands to create, activate, and install required Python dependencies for the project.

```bash
python -m venv /path/to/pkdgrav3/.venv
```

```bash
source /path/to/pkdgrav3/.venv/bin/activate
```

```bash
python -m pip install -r requirements.txt
```

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

### Install dependencies on MacOS via Homebrew

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Install required packages for PKDGRAV3 on MacOS using Homebrew.

```bash
brew install cmake boost fftw git gsl open-mpi hdf5-mpi python pyenv pyenv-virtualenv
```

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

### Sample Unit Conversions for Planetary Simulations

Source: https://pkdgrav3.readthedocs.io/en/latest/units.html

Example output sets for dKpcUnit and dMsolUnit based on specific length, velocity, or mass unit inputs.

```text
Length unit: 1 Earth radius, Velocity unit: 1 km/s
dKpcUnit = 2.064688206889847e-13
dMsolUnit = 4.8006351375833994e-08

Length unit: 1 Astronomical unit, Velocity unit: 1 km/s
dKpcUnit = 4.848101587970315e-09
dMsolUnit = 0.0011272388129170855

Length unit: 1 Astronomical unit, Mass unit: 1 Jupiter mass
dKpcUnit = 4.848101587970315e-09
dMsolUnit = 0.0009548380607523638
```

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

### Verify uenv2 on Piz Daint

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Check the installed version of uenv on the Daint system.

```bash
[daint]$ uenv --version
8.1.0
```

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

### Measure Power Spectrum

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Example workflow for loading a simulation file, decomposing the domain, building the tree, and measuring the power spectrum.

```python
time = msr.load(name,nGridPk=nGridPk)
msr.domain_decompose()
msr.build_tree()
(K,PK,N,*rest) = msr.measure_pk(nGridPk,L=L)

with open(f'{name}.pk','w') as f:
  for k,pk,n in zip(K,PK,N):
    if n>0: f.write(f'{k} {pk} {n}\n')
```

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

### PKDGrav3 Cosmology Parameter File Configuration

Source: https://pkdgrav3.readthedocs.io/en/latest/quickstart.html

This is an example of the cosmology.par file used to configure PKDGrav3 simulations. It sets initial conditions, cosmological parameters, simulation behavior, and accuracy settings.

```python
from accuracy import classic_theta_switch,classic_replicas_switch

achOutName      = "example"

# Initial Condition
dBoxSize        = 2000          # Mpc/h
nGrid           = 128           # Simulation has nGrid^3 particles
iLPT            = 2             # LPT order for IC
iSeed           = 314159265     # Random seed
dRedFrom        = 49            # Starting redshift

# Cosmology
achTfFile       = "euclid_z0_transfer_combined.dat"
h               = 0.67
dOmega0         = 0.32
dLambda         = 0.68
dSigma8         = 0.83
dSpectral       = 0.96

iStartStep      = 0
nSteps          = 100
dRedTo          = 0.0

# Cosmological Simulation
bComove         = True          # Use comoving coordinates
bPeriodic       = True          # with a periodic box
bEwald          = True          # enable Ewald periodic boundaries

# Logging/Output
iOutInterval    = 10
#iCheckInterval = 10
bDoDensity      = False
bVDetails       = True

bOverwrite      = True
bParaRead       = True          # Read in parallel
bParaWrite      = False         # Write in parallel (does not work on all file systems)
#nParaRead      = 8             # Limit number of simultaneous readers to this
#nParaWrite     = 8             # Limit number of simultaneous writers to this

# Accuracy Parameters
bEpsAccStep     = True          # Choose eps/a timestep criteria
dTheta          = classic_theta_switch()        # 0.40, 0.55, 0.70 switch
nReplicas       = classic_replicas_switch()     # 1 if theta > 0.52 otherwise 2

# Memory and performance
bMemUnordered   = True          # iOrder replaced by potential and group id
bNewKDK         = True          # No accelerations in the particle, dual tree possible

```

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

### Configure SLURM for pkdgrav3

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/quickstart.rst.txt

Example SLURM scripts for running pkdgrav3 on different node architectures. Ensure the MPI and thread counts match the hardware configuration.

```bash
#!/bin/bash -l
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=1 --cpus-per-task=16 --ntasks-per-core=1
srun pkdgrav3 cosmology.par
```

```bash
#!/bin/bash -l
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=8 --cpus-per-task=16 --ntasks-per-core=1
srun pkdgrav3 cosmology.par
```

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

### Configure CMake for Dependencies

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Specify installation paths for optional libraries like FFTW and GSL when CMake fails to detect them automatically.

```bash
cmake -DFFTW_ROOT=/path/to/fftw
```

```bash
cmake -DGSL_ROOT_DIR=/opt/gsl/2.5
```

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

### uenv2 Version Verification

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Check the installed version of uenv on Eiger and Piz Daint systems.

```bash
[eiger]$ uenv --version
8.1.0
```

```bash
[daint]$ uenv --version
8.1.0
```

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

### Check CMake Version

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Verify that CMake version 3.24 or newer is installed. This is a prerequisite for building pkdgrav3.

```bash
pkdgrav3:~> cmake --version
cmake version 3.26.0
```

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

### Specify Redshift Intervals and Steps in pkdgrav3

Source: https://pkdgrav3.readthedocs.io/en/latest/changes.html

Define simulation steps and redshift intervals. This example shows the new method for specifying synchronized steps and redshifts, replacing older parameters.

```python
dRedFrom = 49
dRedTo = 0
nSteps = 160
nStepsSync = 60
dRedSync = 10

```

```python
dRedFrom = 40
dRedTo = [10,0]
nSteps = [60,100]

```

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

### Configure Spack for Homebrew packages

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Instruct Spack to use existing Homebrew installations for dependencies.

```bash
spack external find --not-buildable cmake git gmake gsl hdf5 openmpi apple-clang gcc
```

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

### Units Calculator Sample Set 2

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/units.rst.txt

Example configuration for the units calculator tool, setting length unit to 1 Astronomical unit and velocity unit to 1 km/s. Provides the resulting dKpcUnit and dMsolUnit values.

```text
Length unit: 1 Astronomical unit, Velocity unit: 1 km/s
dKpcUnit = 4.848101587970315e-09
dMsolUnit = 0.0011272388129170855
```

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

### Units Calculator Sample Set 3

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/units.rst.txt

Example configuration for the units calculator tool, setting length unit to 1 Astronomical unit and mass unit to 1 Jupiter mass. Provides the resulting dKpcUnit and dMsolUnit values.

```text
Length unit: 1 Astronomical unit, Mass unit: 1 Jupiter mass
dKpcUnit = 4.848101587970315e-09
dMsolUnit = 0.0009548380607523638
```

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

### Units Calculator Sample Set 1

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/units.rst.txt

Example configuration for the units calculator tool, setting length unit to 1 Earth radius and velocity unit to 1 km/s. Provides the resulting dKpcUnit and dMsolUnit values.

```text
Length unit: 1 Earth radius, Velocity unit: 1 km/s
dKpcUnit = 2.064688206889847e-13
dMsolUnit = 4.8006351375833994e-08
```

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

### I/O Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Configuration options for handling input and output files in PKDGrav3.

```APIDOC
## I/O Parameters

### Description
Configuration options for handling input and output files in PKDGrav3.

### Parameters

#### Input Parameters
- **achInFile** (string) - Optional - Input file name. Defaults to 'none'.
- **bInFileLC** (boolean) - Optional - Enable input light cone data. Defaults to False.

#### Output Parameters
- **achOutName** (string) - Optional - Base name for output files. Defaults to 'pkdgrav3'.
- **achOutPath** (string) - Optional - Full path and name for output files, must include `{name}`, `{step}`, and `{type}`. Defaults to '{name}.{step:05d}{type}'.
- **achIoPath** (string) - Optional - Overrides path for Tipsy outputs. Behaves like `achOutPath` but can include `{i}` for parallel writing. Defaults to `achOutPath`.
- **achCheckpointPath** (string) - Optional - Overrides path for checkpoint outputs. Behaves like `achOutPath`. Defaults to `achOutPath`.
- **achDataSubPath** (string) - Optional - Sub-path for data. Defaults to 'none'.
- **bHDF5** (boolean) - Optional - Output in HDF5 format. Defaults to False.
- **bDoublePos** (boolean) - Optional - Input/output double precision positions (standard format only). Defaults to False.
- **bDoubleVel** (boolean) - Optional - Input/output double precision velocities (standard format only). Defaults to False.
- **bDoSoftOutput** (boolean) - Optional - Enable soft outputs. Defaults to False.
- **bDoDensity** (boolean) - Optional - Enable density outputs. Defaults to False.
- **bDoAccOutput** (boolean) - Optional - Enable acceleration outputs. Defaults to False.
- **bDoPotOutput** (boolean) - Optional - Enable potential outputs. Defaults to False.
- **bDoRungOutput** (boolean) - Optional - Enable rung outputs. Defaults to False.
- **bDoRungDestOutput** (boolean) - Optional - Enable rung destination outputs. Defaults to False.
- **bStandard** (boolean) - Optional - Output in standard TIPSY binary format. Defaults to True.
- **iCompress** (integer) - Optional - Compression format: 0=none, 1=gzip, 2=bzip2. Defaults to 0.

#### Parallel Processing Parameters
- **bParaRead** (boolean) - Optional - Enable parallel reading of files. Defaults to True.
- **bParaWrite** (boolean) - Optional - Disable parallel writing of files. Defaults to False.
- **nParaRead** (integer) - Optional - Number of threads for parallel read (0=unlimited). Defaults to 0.
- **nParaWrite** (integer) - Optional - Number of threads for parallel write (0=unlimited). Defaults to 0.

#### Interval Parameters
- **iOutInterval** (integer) - Optional - Number of timesteps between snapshots. Defaults to 0.
- **iCheckInterval** (integer) - Optional - Number of timesteps between checkpoints. Defaults to 0.
- **iLogInterval** (integer) - Optional - Number of timesteps between logfile outputs. Defaults to 1.
- **iPkInterval** (integer) - Optional - Number of timesteps between pk outputs. Defaults to 1.
- **iDeltakInterval** (integer) - Optional - Number of timesteps between DeltaK outputs. Defaults to 0.

#### Runtime Parameters
- **iWallRunTime** (integer) - Optional - Maximum Wallclock time in minutes to run. Defaults to 0.
- **iSignalSeconds** (integer) - Optional - Time in seconds before USR1 signal is sent for termination. Defaults to 0.

#### Other Parameters
- **lstOrbits** (list) - Optional - List of particle IDs to write to orbit file. Defaults to 'none'.
```

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

### Manage pkdgrav3 with Spack

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Commands for cloning Spack, adding the repository, and building within a local environment.

```bash
git clone -c feature.manyFiles=true --depth=2 https://github.com/spack/spack.git
source spack/share/spack/setup-env.sh
```

```bash
spack repo add spack_repo
==> Added repo with namespace 'pkdgrav3'.
```

```bash
spack spec pkdgrav3
```

```bash
cd /path/to/pkdgrav3
spack env activate  .
spack install pkdgrav3
```

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

### Running and Developing with uenv

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Commands to execute pkdgrav3 via uenv or load development modules.

```bash
uenv start --view=pkdgrav3 pkdgrav3
pkdgrav3 cosmology.par
```

```bash
#SBATCH --uenv=pkdgrav3 --view=pkdgrav3
```

```bash
[daint]$ uenv start --view=modules pkdgrav3
[daint]$ module load boost cmake cray-mpich fftw gcc gsl hdf5 pkdgrav3-python
```

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

### Specify GSL Installation Path

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

If CMake cannot find GSL, provide the installation directory using the GSL_ROOT_DIR variable. Ensure gsl-config is in your PATH.

```bash
cmake -DGSL_ROOT_DIR=/opt/gsl/2.5
```

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

### Specify FFTW Installation Path

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

If CMake does not automatically detect FFTW, specify its root directory using the FFTW_ROOT variable.

```bash
cmake -DFFTW_ROOT=/path/to/fftw
```

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

### Create Python Virtual Environment

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Create a dedicated Python virtual environment for pkdgrav3 to manage dependencies.

```bash
python -m venv /path/to/pkdgrav3/.venv
```

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

### Configure and Build pkdgrav3 with CMake

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Use CMake to configure the build environment and then build the pkdgrav3 code. This process detects dependencies and compiles the project.

```bash
cd /path/to/pkdgrav3
cmake -S . -B build
cmake --build build
```

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

### Develop pkdgrav3 with uenv

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Use the modules view to access development tools within a user environment.

```bash
[daint]$ uenv start --view=modules pkdgrav3
```

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

### Add Custom Analysis Hook

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/analysis.rst.txt

Example of adding a custom analysis hook using PKDGRAV.add_analysis. This class outputs a density grid at each simulation step.

```python
from PKDGRAV import add_analysis, ASSIGNMENT_ORDER

class MassGrid:
    grid = 0
    order = ASSIGNMENT_ORDER.PCS
    def __init__(self,grid,order=ASSIGNMENT_ORDER.PCS):
        self.grid = grid
        self.order = order
    def __call__(self,msr,step,time,**kwargs):
        print('calculating density grid')
        msr.grid_create(self.grid)
        msr.assign_mass(order=self.order)
        msr.grid_write('output.{:05d}'.format(step))
        msr.grid_delete()
    def ephemeral(self,msr,**kwargs):
        return msr.grid_ephemeral(self.grid)


# To enable it, use:
# add_analysis(MassGrid(nGrid))

```

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

### Load PKDGRAV3 modules on Daint

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Load the required environment modules for compiling and running PKDGRAV3 on the Daint system.

```bash
[daint]$ module load boost cmake cray-mpich fftw gcc gsl hdf5 pkdgrav3-python
```

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

### Override Restore Parameters in pkdgrav3

Source: https://pkdgrav3.readthedocs.io/en/latest/changes.html

Modify the `msr.restore` call to override parameters. This example shows how to enable parallel reading and set the number of readers.

```python
msr.restore(__file__)

```

```python
msr.restore(__file__,bParaRead=True,nParaRead=100)

```

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

### Derive Mass Unit (kpc & km/s)

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/units.rst.txt

Calculates the mass unit when length is in kpc and velocity is in km/s, with G=1. This is a common setup for cosmological simulations.

```math
G = 4.30091727063\times 10^{-9}~	ext{Mpc}~M_⊙^{-1}(\text{km}/\text{s})^2
      = 4.30091727063\times 10^{-6}~	ext{kpc}~M_⊙^{-1}(\text{km}/\text{s})^2
```

```math
M_{unit} = \frac{1}{4.30091727063\times 10^{-6}} = 2.32508541103\times 10^5~M_⊙
```

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

### Initial Conditions Generation

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Configure the Initial Condition (IC) generator, supporting various perturbation theory orders and gas properties.

```APIDOC
## Initial Conditions Generation

### Description
Configure the Initial Condition (IC) generator, which supports first order (Zeldovich), second order, and third order Lagrangian perturbation theory. Ensure cosmological parameters are properly set.

### Parameters
#### Path Parameters
- **dRedFrom** (float) - Optional - Specifies initial redshift for the simulation.
- **nGrid** (integer) - Optional - Sets the grid size and hence the number of particles in the IC. For a grid size of N there will be N^3 particles.
- **iSeed** (integer) - Optional - Random seed for IC generation. Default is 0.
- **iLPT** (integer) - Optional - LPT order for IC generation. Default is 2.
- **dInitialT** (float) - Optional - Initial temperature of the gas for generated ICs. Default is 100.0.

#### Query Parameters
- **bWriteIC** (Boolean) - Optional - Write IC after generating. Default is False.
- **bFixedAmpIC** (Boolean) - Optional - Use fixed amplitude of 1 for ICs. Default is False.
- **dFixedAmpPhasePI** (float) - Optional - Phase shift for fixed amplitude in units of PI. Default is 0.0.
- **bICgas** (Boolean) - Optional - Enable/disable gas in the ICs. Default is False.
```

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

### Overriding Parameters During Restore

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/changes.rst.txt

To override parameters during a restore call, add them as arguments. This example shows how to enable parallel reading and set the number of readers to 100.

```python
msr.restore(__file__,bParaRead=True,nParaRead=100)
```

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

### Run pkdgrav3 with Checkpoint File

Source: https://pkdgrav3.readthedocs.io/en/latest/changes.html

Use this command to restart a simulation using a checkpoint file. The '.chk' file is the primary input.

```bash
srun pkdgrav3 checkpoint.00010.chk

```

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

### SimpleCosmology Class Initialization

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Initializes the SimpleCosmology object with various density parameters and cosmological constants.

```APIDOC
## POST /cosmology/SimpleCosmology

### Description
Initializes a new instance of the SimpleCosmology class with specified density parameters and physical constants.

### Method
POST

### Parameters
#### Request Body
- **omega_matter** (number) - Required - Matter density Ωm
- **omega_lambda** (number) - Optional - Dark energy density ΩΛ
- **omega_baryon** (number) - Optional - Baryon density Ωb
- **omega_radiation** (number) - Optional - Radiation density Ωγ
- **omega_dark_energy** (number) - Optional - Dark energy density ΩDE
- **w0** (number) - Optional - Dark energy equation of state parameter w0
- **wa** (number) - Optional - Dark energy equation of state parameter wa
- **running** (number) - Optional - Running of the spectral index dns/dln k
- **pivot** (number) - Optional - Pivot scale for the power spectrum kp
- **comoving** (bool) - Optional - Whether to use comoving or physical units
- **sigma8** (number) - Optional - Sigma8 σ8
- **As** (number) - Optional - Amplitude of the power spectrum As
- **ns** (number) - Optional - Spectral index ns
- **h** (number) - Optional - Hubble parameter h
- **k** (number) - Optional - Array of wavenumbers k
- **Tk** (number) - Optional - Array of transfer functions T(k)
- **transfer_file** (str) - Optional - File name of the transfer function
- **usecols** (tuple) - Optional - Columns to use in the transfer function file
```

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

### PKDGRAV.grid_create

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Creates a grid structure for mass assignment.

```APIDOC
## PKDGRAV.grid_create

### Description
Create a grid for the mass assignment.

### Method
PKDGRAV.grid_create

### Parameters
#### Path Parameters
- **grid** (integer) - The grid configuration or size.

### Request Example
```python
PKDGRAV.grid_create(grid=128)
```

### Response
This method does not return a value.
```

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

### Spack Package Manager Commands

Source: https://pkdgrav3.readthedocs.io/en/latest/install.html

Commands for cloning Spack, adding the pkdgrav3 repository, and managing local development environments.

```bash
git clone -c feature.manyFiles=true –depth=2 https://github.com/spack/spack.git source spack/share/spack/setup-env.sh
```

```bash
spack repo add spack_repo
```

```bash
spack spec pkdgrav3
```

```bash
cd /path/to/pkdgrav3 spack env activate . spack install pkdgrav3
```

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

### Configure dynamic accuracy parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/extensions.rst.txt

Use these functions to set dTheta and nReplicas for cosmological simulations.

```python
from accuracy import classic_theta_switch,classic_replicas_switch

dTheta          = classic_theta_switch()
nReplicas       = classic_replicas_switch()
```

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

### Stellar Initial-Mass Function (IMF) Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Configure the stellar initial-mass function, including type and mass limits.

```APIDOC
## Stellar Initial-Mass Function (IMF)

### Parameters

- **achIMFType** (string) - Optional - Type of IMF. Default: "chabrier"
- **dIMFMinMass** (float) - Optional - Lower-mass limit of the IMF in Msol. Default: 0.1
- **dIMFMaxMass** (float) - Optional - Upper-mass limit of the IMF in Msol. Default: 100.0
- **dCCSNMinMass** (float) - Optional - Minimum mass for a star to end its life as a Core Collapse Supernova in Msol. Default: 6.0
- **dCCSNMaxMass** (float) - Optional - Maximum mass for a star to end its life as a Core Collapse Supernova in Msol. Default: 100.0
```

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

### Periodic Boundary Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Settings for enabling and configuring periodic boundary conditions.

```APIDOC
## Periodic Boundaries

### bPeriodic
- **Default**: False (Boolean)
- **Description**: Enables periodic boundary conditions. If gravity is enabled, Ewald correction should also be enabled.

### dPeriod
- **Default**: [1.0, 1.0, 1.0]
- **Description**: The length of the periodic box in code units. Can be a single float for uniform dimensions or a list of three floats for x, y, and z dimensions.
```

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

### Import PKDGRAV for Analysis Mode

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Import the PKDGRAV module to enter analysis mode instead of simulation mode. This script is used to measure the power spectrum of a periodic simulation output.

```python
# simulation mode is skipped when PKDGRAV imported
import PKDGRAV as msr
from sys import argv,exit

# Name and grid size are required; box size is optional
if len(argv)<=2:
    print(f"Usage: {argv[0]} <filename> <grid> [box-length]")
    exit(1)
name=argv[1]
nGridPk = int(argv[2])
L = 1 if len(argv)<4 else int(argv[3])

```

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

### PKDGRAV.simulate

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Enters simulation mode directly. This is typically disabled when PKDGRAV is imported.

```APIDOC
## PKDGRAV.simulate

### Description
Directly enter simulation mode. Normally simulation mode is disabled if PKDGRAV has been imported. Calling this function proceeds normally.

### Method
APIDOC

### Endpoint
PKDGRAV.simulate(**kwargs)

### Parameters
#### Query Parameters
- **kwargs** - Additional parameters to set for the simulation.
```

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

### Output and Logging Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/quickstart.rst.txt

Parameters governing simulation output frequency, checkpointing, and logging behavior.

```APIDOC
## Output and Logging Parameters

### Parameters
- **iOutInterval** (int) - Frequency of output writes in steps.
- **iCheckInterval** (int) - Frequency of checkpoint writes in steps.
- **bDoDensity** (bool) - Calculate and output SPH densities. Default: False.
- **bVDetails** (bool) - Enable additional progress information. Default: True.
- **bOverwrite** (bool) - Disable abnormal exit check.
- **bParaRead** (bool) - Enable parallel file reading. Default: True.
- **bParaWrite** (bool) - Enable parallel file writing. Default: False.
- **nParaRead** (int) - Limit number of simultaneous readers.
- **nParaWrite** (int) - Limit number of simultaneous writers.
```

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

### Gravity, Domains, Trees Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Parameters controlling gravitational softening, domain decomposition, and tree memory layout.

```APIDOC
## Gravity, Domains, Trees Parameters

### Description
Parameters in this section are used to override the gravitational softening 𝜖, control the tree memory layout, as well as to control how often domain decomposition and tree building occur.

### Parameters

- **dSoft** (float) - Default: 0.0 - Sets the gravitational softening length globally for all particles.
- **dSoftMax** (float) - Default: 0.0 - Maximum comoving gravitational softening length (absolute or multiplier).
- **bPhysicalSoft** (Boolean) - Default: False - Physical gravitational softening length.
- **bSoftMaxMul** (Boolean) - Default: True - Use maximum comoving gravitational softening length as a multiplier.
- **bDoGravity** (Boolean) - Default: True - If false, accelerations due to gravitational forces are not applied.
- **nGridLin** (integer) - Default: 0 - Grid size for linear species (0=disabled).
- **bDoLinPkOutput** (Boolean) - Default: False - Enable power spectrum output for linear species.
- **dFracNoDomainDecomp** (float) - Default: 0.1 - Fraction of Active Particles for no domain decomposition.
- **dFracNoDomainRootFind** (float) - Default: 0.1 - Fraction of Active Particles for no domain decomposition root finding.
- **dFracNoDomainDimChoice** (float) - Default: 0.1 - Fraction of Active Particles for no domain decomposition dimension choice.
- **iMaxRungDomainDecomp** (integer) - Default: 2147483648 - Rung above which no domain decomposition is performed.
```

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

### PKDGRAV.generate_ic

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Generates initial conditions for a cosmological simulation.

```APIDOC
## PKDGRAV.generate_ic

### Description
Generate initial conditions for a cosmological simulation.

### Method
PKDGRAV.generate_ic

### Parameters
#### Path Parameters
- **cosmology** (Cosmology) - The cosmology object.
- **grid** (integer) - Grid size of the initial conditions.
- **seed** (integer) - Random seed.
- **z** (number) - Starting redshift.
- **L** (number) - Length unit of the box.
- **order** (integer) - Optional. IC order (1=Zeldovich, 2=2LPT, 3=3LPT). Defaults to None.
- **fixed_amplitude** (Boolean) - Optional. Use fixed amplitude for the power spectrum. Defaults to False.
- **phase_pi** (number) - Optional. Phase of the initial conditions in units of pi radians (normally 0 or 1). Defaults to 0.0.

### Request Example
```python
from pkdgrav import Cosmology
cosmo = Cosmology(Omega_m=0.3, Omega_L=0.7, H0=70)
PKDGRAV.generate_ic(cosmology=cosmo, grid=512, seed=42, z=50.0, L=100.0, order=2)
```

### Returns
- **time** (number) - The simulation time.
```

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

### Restarting Simulation with Checkpoint File

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/changes.rst.txt

Use the .chk file as input to restart a simulation. This command assumes the checkpoint file is named 'checkpoint.00010.chk'.

```bash
srun pkdgrav3 checkpoint.00010.chk
```

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

### Configure uenv2 on Eiger

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Verification and shell configuration for uenv2 on the Eiger system.

```bash
[eiger]$ uenv --version
8.1.0
```

```bash
export PATH=$HOME/.local/$(uname -m)/bin:$PATH
if test ${HOST##eiger} != $HOST ; then
    unset -f uenv
fi
```

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

### Import HYDRO_MODEL

Source: https://pkdgrav3.readthedocs.io/en/latest/parameters.html

Import the HYDRO_MODEL enum to specify the hydrodynamics model. This is required before setting the hydro_model parameter.

```python
from PKDGRAV import HYDRO_MODEL
```

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

### PKDGRAV.build_tree

Source: https://pkdgrav3.readthedocs.io/en/latest/extensions.html

Builds a tree structure within each domain of the simulation, potentially for Ewald summation.

```APIDOC
## PKDGRAV.build_tree

### Description
Builds a tree in each domain.

### Method
PKDGRAV.build_tree

### Parameters
#### Path Parameters
- **ewald** (Boolean) - Optional. Construct a moment for Ewald if true.

### Request Example
```python
PKDGRAV.build_tree(ewald=True)
```

### Response
This method does not return a value.
```

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

### Manage pkdgrav3 Images with uenv

Source: https://pkdgrav3.readthedocs.io/en/latest/_sources/install.rst.txt

Commands to find and pull specific pkdgrav3 images on Daint and Eiger systems.

```bash
[daint][dpotter@daint-ln003 ~]$ uenv image find service::pkdgrav3
uenv                     arch   system  id                size(MB)  date
pkdgrav3/3.4:1824353160  gh200  daint   ee775978c79587fb   4,044    2025-05-19
pkdgrav3/3.4:1825038404  gh200  daint   5e0b0ac41d73e4e5   3,866    2025-05-19
```

```bash
[daint]$ uenv image pull service::pkdgrav3/3.4:1825038404
pulling 5e0b0ac41d73e4e5 100.00% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3867/3867 (0.00 MB/s)
updating pkdgrav3/3.4:1825038404@daint%gh200
```

```bash
[eiger]$ uenv image find service::pkdgrav3
uenv                     arch  system  id                size(MB)  date
pkdgrav3/3.4:1825268321  zen2  eiger   09cbc44a4026a1f6     643    2025-05-19
pkdgrav3/3.4:1826427762  zen2  eiger   c3268965cf74074c     643    2025-05-20
[eiger]$ uenv image pull service::pkdgrav3/3.4:1826427762
pulling c3268965cf74074c 100.00% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 644/644 (0.00 MB/s)
updating pkdgrav3/3.4:1826427762@eiger%zen2
```

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

### PKDGRAV3 Parameters

Source: https://pkdgrav3.readthedocs.io/en/latest/genindex.html

A list of parameters used in the PKDGRAV3 simulation code.

```APIDOC
## Parameters

### General Parameters
- **dSNIaExpScale** (float) - Description not available
- **dSNIaFBDelay** (float) - Description not available
- **dSNIaMaxMass** (float) - Description not available
- **dSNIaNumPerMass** (float) - Description not available
- **dSNIaPLFinalTime** (float) - Description not available
- **dSNIaPLInitTime** (float) - Description not available
- **dSNIaPLScale** (float) - Description not available
- **dSoft** (float) - Description not available
- **dSoftMax** (float) - Description not available
- **dSpectral** (float) - Description not available
- **dStellarWindSpeed** (float) - Description not available
- **dTau** (float) - Description not available
- **dTheta** (float) - Description not available
- **dTheta2** (float) - Description not available
- **dTheta20** (float) - Description not available
- **dTimeStepSmin** (float) - Description not available
- **dVelocityDamper** (float) - Description not available
- **dVelocityDamperEnd** (float) - Description not available
- **dVelocityDamperEndTime** (float) - Description not available
- **dxPeriod** (float) - Description not available
- **dyPeriod** (float) - Description not available
- **dzPeriod** (float) - Description not available
- **fH_reion_eV_p_H** (float) - Description not available
- **fH_reion_z** (float) - Description not available
- **fHe_reion_eV_p_H** (float) - Description not available
- **fHe_reion_z_centre** (float) - Description not available
- **fHe_reion_z_sigma** (float) - Description not available
- **fT_CMB_0** (float) - Description not available
- **h** (float) - Description not available
- **hLCP** (float) - Description not available
- **hxLCP** (float) - Description not available
- **hydro_model** (string) - Description not available
- **hyLCP** (float) - Description not available
- **hzLCP** (float) - Description not available
- **iCacheMaxInflight** (integer) - Description not available
- **iCacheSize** (integer) - Description not available
- **iCheckInterval** (integer) - Description not available
- **iCompress** (integer) - Description not available
- **iDeltakInterval** (integer) - Description not available
- **iKernelType** (integer) - Description not available
- **iLogInterval** (integer) - Description not available
- **iLowerGroupSizeThreshold** (integer) - Description not available
- **iLPT** (integer) - Description not available
- **iMaxRung** (integer) - Description not available
- **iMaxRungDomainDecomp** (integer) - Description not available
- **iOutInterval** (integer) - Description not available
- **iPkInterval** (integer) - Description not available
- **iPkOrder** (integer) - Description not available
- **iSeed** (integer) - Description not available
- **iSignalSeconds** (integer) - Description not available
- **iStartStep** (integer) - Description not available
- **iTimeStepCrit** (integer) - Description not available
- **iUpperGroupSizeThreshold** (integer) - Description not available
- **iWallRunTime** (integer) - Description not available
- **iWorkQueueSize** (integer) - Description not available
- **lstLightConeOctants** (list) - Description not available
- **lstOrbits** (list) - Description not available
- **nBinsPk** (integer) - Description not available
- **nBucket** (integer) - Description not available
- **nFoldPk** (integer) - Description not available
- **nGrid** (integer) - Description not available
- **nGridLin** (integer) - Description not available
- **nGridPk** (integer) - Description not available
- **nGroup** (integer) - Description not available
- **nMemEphemeral** (integer) - Description not available
- **nMinMembers** (integer) - Description not available
- **nParaRead** (integer) - Description not available
- **nParaWrite** (integer) - Description not available
- **nPartColl** (integer) - Description not available
- **nPartRhoLoc** (integer) - Description not available
- **nReplicas** (integer) - Description not available
- **nSideHealpix** (integer) - Description not available
- **nSmooth** (integer) - Description not available
- **nSteps** (integer) - Description not available
- **nTreeBitsHi** (integer) - Description not available
- **nTreeBitsLo** (integer) - Description not available
- **nTruncateRung** (integer) - Description not available
- **sqdegLCP** (float) - Description not available
- **time_step** (float) - Description not available
- **w0** (float) - Description not available
- **wa** (float) - Description not available
```