### Compile pkdgrav3 with Specific GCC and FFTW

Source: https://github.com/dpotter/pkdgrav3/blob/master/README.md

A detailed example of compiling pkdgrav3 with a specific GCC version (5.3) and FFTW3 installation path. This is useful for ensuring compatibility and reproducibility.

```bash
mkdir build
cd build
CC=/scratch/isaacaa/opt/gcc53/bin/gcc CXX=/scratch/isaacaa/opt/gcc53/bin/g++ cmake -DFFTW_ROOT=/scratch/isaacaa/opt/fftw3  ..
make
```

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

### Configure and install project files

Source: https://github.com/dpotter/pkdgrav3/blob/master/mdl2/CMakeLists.txt

Configures a header file (mdl_config.h) from a template and installs the main project target and header files. This includes the main executable/library, configuration headers, and MPI-related stub headers.

```cmake
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/mdl_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/mdl_config.h)
install(TARGETS ${PROJECT_NAME} DESTINATION "lib")
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/mdl_config.h mpi/mdl.h mpi/mdlstubs.h mdlbase.h DESTINATION "include")
```

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

### Set Target Include Directories and Installation

Source: https://github.com/dpotter/pkdgrav3/blob/master/CMakeLists.txt

Configures include paths for the 'tostd' target and defines installation rules for the project binaries.

```cmake
target_include_directories(tostd PUBLIC ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
install(TARGETS ${PROJECT_NAME} ${PROJECT_NAME} DESTINATION "bin")
install(TARGETS ${PROJECT_NAME} tostd DESTINATION "bin")
```

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

### Install {fmt} via Conda

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Command to install the {fmt} library using the conda-forge channel. This is the recommended method for Linux, macOS, and Windows environments.

```bash
conda install -c conda-forge fmt
```

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

### CMake: Configure Installation Targets

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/CMakeLists.txt

Configures installation targets for the fmt library and its headers. It sets up installation directories for libraries, headers, and CMake configuration files, and generates necessary package configuration files.

```cmake
if (FMT_INSTALL)
  include(GNUInstallDirs)
  include(CMakePackageConfigHelpers)
  set_verbose(FMT_CMAKE_DIR ${CMAKE_INSTALL_LIBDIR}/cmake/fmt CACHE STRING
              "Installation directory for cmake files, a relative path "
              "that will be joined to ${CMAKE_INSTALL_PREFIX}, or an arbitrary absolute path.")
  set(version_config ${PROJECT_BINARY_DIR}/fmt-config-version.cmake)
  set(project_config ${PROJECT_BINARY_DIR}/fmt-config.cmake)
  set(pkgconfig ${PROJECT_BINARY_DIR}/fmt.pc)
  set(targets_export_name fmt-targets)

  set (INSTALL_TARGETS fmt)
  if (TARGET fmt-header-only)
    set(INSTALL_TARGETS ${INSTALL_TARGETS} fmt-header-only)
  endif ()

  set_verbose(FMT_LIB_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
              "Installation directory for libraries, a relative path "
              "that will be joined to ${CMAKE_INSTALL_PREFIX}, or an arbitrary absolute path.")

  set_verbose(FMT_INC_DIR ${CMAKE_INSTALL_INCLUDEDIR}/fmt CACHE STRING
              "Installation directory for include files, a relative path "
              "that will be joined to ${CMAKE_INSTALL_PREFIX}, or an arbitrary absolute path.")

  set_verbose(FMT_PKGCONFIG_DIR ${CMAKE_INSTALL_LIBDIR}/pkgconfig CACHE PATH
              "Installation directory for pkgconfig (.pc) files, a relative path "
              "that will be joined to ${CMAKE_INSTALL_PREFIX}, or an arbitrary absolute path.")

  # Generate the version, config and target files into the build directory.
  write_basic_package_version_file(
    ${version_config}
    VERSION ${FMT_VERSION}
    COMPATIBILITY AnyNewerVersion)

  join_paths(libdir_for_pc_file "\${exec_prefix}" "${CMAKE_INSTALL_LIBDIR}")
  join_paths(includedir_for_pc_file "\${prefix}" "${CMAKE_INSTALL_INCLUDEDIR}")

  configure_file(
    "${PROJECT_SOURCE_DIR}/support/cmake/fmt.pc.in"
    "${pkgconfig}"
    @ONLY)
  configure_package_config_file(
    ${PROJECT_SOURCE_DIR}/support/cmake/fmt-config.cmake.in
    ${project_config}
    INSTALL_DESTINATION ${FMT_CMAKE_DIR})
  # Use a namespace because CMake provides better diagnostics for namespaced
  # imported targets.
  export(TARGETS ${INSTALL_TARGETS} NAMESPACE fmt::
         FILE ${PROJECT_BINARY_DIR}/${targets_export_name}.cmake)

  # Install version, config and target files.
  install(
    FILES ${project_config} ${version_config}
    DESTINATION ${FMT_CMAKE_DIR})
  install(EXPORT ${targets_export_name} DESTINATION ${FMT_CMAKE_DIR}
          NAMESPACE fmt::)

  # Install the library and headers.
  install(TARGETS ${INSTALL_TARGETS} EXPORT ${targets_export_name}
          LIBRARY DESTINATION ${FMT_LIB_DIR}
          ARCHIVE DESTINATION ${FMT_LIB_DIR}
          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})

  install(FILES $<TARGET_PDB_FILE:${INSTALL_TARGETS}> 
          DESTINATION ${FMT_LIB_DIR} OPTIONAL)
  install(FILES ${FMT_HEADERS} DESTINATION ${FMT_INC_DIR})
  install(FILES "${pkgconfig}" DESTINATION "${FMT_PKGCONFIG_DIR}")
endif ()
```

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

### PKDGRAV3 Parameter Configuration

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/quickstart.md

An example parameter file (cosmology.par) defining initial conditions, cosmological constants, simulation accuracy settings, and I/O preferences for a PKDGRAV3 run.

```default
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
```

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

### Restarting Pkdgrav3 Simulation

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/changes.md

Demonstrates how to restart a Pkdgrav3 simulation using the updated checkpoint file format. The example shows the command-line usage for specifying the checkpoint file and how to override restart parameters.

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

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

### Run pkdgrav3 Simulation

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Commands to start the pkdgrav3 simulation using the provided environment view. Includes instructions for interactive use and SLURM queue submission.

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

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

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

### Install C++ Format via APT

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Installs the C++ Format library on Debian-based systems using the apt-get package manager. This command is useful for developers who need the library for system-wide use.

```bash
$ sudo apt-get install libcppformat1-dev
```

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

### Configure GSL Path with CMake

Source: https://github.com/dpotter/pkdgrav3/blob/master/README.md

Example of how to specify the GSL installation directory to CMake if it's not found automatically. This is crucial for linking against the GNU Scientific Library.

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

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

### Spack External Package Configuration for macOS

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Example configuration for Spack's packages.yaml file to specify external installations of Python, FFTW, and Boost on macOS, disabling Spack's build process for these packages.

```yaml
python:
  externals:
  - spec: python@3.12
    prefix: /opt/homebrew/opt/python@3.12
  buildable: false
fftw:
  externals:
  - spec: fftw@3.3.10
    prefix: /opt/homebrew/Cellar/fftw/3.3.10_2
  buildable: false
boost:
  externals:
  - spec: boost@1.88.0
    prefix: /opt/homebrew/Cellar/boost/1.88.0
  buildable: false
```

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

### Run pkdgrav3 Simulation

Source: https://github.com/dpotter/pkdgrav3/blob/master/README.md

Example of how to execute the pkdgrav3 simulation using MPI. The 'mpiexec' command is used to launch the executable with a simulation parameter file.

```bash
mpiexec pkdgrav3 simfile.par
```

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

### Install macOS Dependencies with Homebrew

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Commands to install necessary development tools and libraries for pkdgrav3 on macOS using Homebrew, including cmake, boost, fftw, and python.

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

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

### Verify macOS Homebrew Package Locations

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Command to verify the installation path and version of Python, FFTW, and Boost installed via Homebrew on macOS.

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

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

### Joining Container Elements with fmt::join (C++)

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Illustrates the use of fmt::join to format elements of a range, separated by a specified string. This example uses fmt/format.h and demonstrates formatting a vector of doubles.

```c++
#include "fmt/format.h"

std::vector<double> v = {1.2, 3.4, 5.6};
// Prints "(+01.20, +03.40, +05.60)".
fmt::print("({:+06.2f})", fmt::join(v.begin(), v.end(), ", "));
```

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

### SLURM Execution Scripts for PKDGRAV3

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/quickstart.md

Example bash scripts for submitting PKDGRAV3 jobs to a SLURM scheduler, demonstrating configurations for standard nodes and NUMA-aware node architectures.

```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
```

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

### Install C++ Format via Homebrew

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Installs the C++ Format library on OS X using the Homebrew package manager. This command is convenient for developers working on macOS.

```bash
$ brew install cppformat
```

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

### Configure Blitz Library Build with CMake

Source: https://github.com/dpotter/pkdgrav3/blob/master/blitz/CMakeLists.txt

This CMake configuration initializes the project, defines the static library target, sets up include directories for both build and public interfaces, and handles header file installation.

```cmake
cmake_minimum_required(VERSION 3.12)
cmake_policy(VERSION 3.12...3.27)
project(blitz)

set(BLITZ_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
set(BLITZ_HEADERS
    ${BLITZ_INCLUDE_DIR}/blitz/array.h
)

add_library(blitz STATIC globals.cpp)
target_include_directories(blitz INTERFACE ${BLITZ_INCLUDE_DIR})
target_include_directories(blitz PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/bzconfig.h.in ${CMAKE_CURRENT_BINARY_DIR}/bzconfig.h)
install(FILES ${BLITZ_HEADERS} DESTINATION "include/blitz")
```

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

### Configure Boost Path with CMake

Source: https://github.com/dpotter/pkdgrav3/blob/master/README.md

Demonstrates how to set the BOOST_ROOT environment variable for CMake to locate the Boost C++ libraries. This is often necessary for custom installations.

```bash
cmake -DBOOST_ROOT=/path/to/boost ...
```

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

### C++ fmt::print with Core API

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Example of using the lightweight fmt::print function from the core API for simple console output. This API is designed to improve compile times and reduce code bloat by minimizing dependencies on standard headers.

```c++
#include <fmt/core.h>

fmt::print("The answer is {}.
", 42);
```

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

### Basic Printing with {fmt}

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/README.rst

Demonstrates basic printing to stdout using {fmt}'s print and printf functions. It supports Python-like format string syntax and traditional printf syntax.

```c++
fmt::print("Hello, {}!", "world");  // Python-like format string syntax
fmt::printf("Hello, %s!", "world"); // printf format string syntax
```

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

### Basic String Formatting

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates how to format a string using fmt::format with a std::string_view.

```c++
auto message = fmt::format(std::string_view("The answer is {}."), 42);
```

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

### Install Ubuntu Test Suite Dependency

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Commands to install the python3-xmlrunner package for running the pkdgrav3 test suite on Ubuntu 22.04. For older versions, a pip installation within a virtual environment is suggested.

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

```bash
pip3 install xmlrunner
```

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

### Initialize static strings with fmt

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates the use of fmt::format for global or static string initialization on compilers supporting constexpr.

```c++
// This works on compilers with constexpr support.
static const std::string answer = fmt::format("{}", 42);
```

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

### Use experimental string_view with fmt

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates how to print an experimental string_view using the fmt library.

```c++
#include <fmt/core.h>
#include <experimental/string_view>

fmt::print("{}", std::experimental::string_view("foo"));
```

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

### Develop pkdgrav3 with User Environment

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Instructions for compiling a custom version of pkdgrav3 using a user environment and loading necessary modules like boost, cmake, and fftw.

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

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

### Execute PKDGRAV3 via Command Line

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

Demonstrates the command-line interface for executing the PKDGRAV3 binary with a specific FOF configuration. The command takes the filename, linking length, and minimum member count as arguments.

```bash
./build/pkdgrav3 fof.py example.00100 0.0015625 10
```

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

### Install Ubuntu Dependencies for pkdgrav3

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/install.md

Commands to update package lists and install essential development packages for pkdgrav3 on Ubuntu 20.04 and 22.04. Includes packages for compilation, MPI, and Python.

```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
```

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

### Select and Analyze Particles

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

Demonstrates loading a simulation snapshot and preparing the environment for particle selection and property retrieval.

```python
import PKDGRAV as msr
import numpy as np

time = msr.load("example.00100")
msr.domain_decompose()
msr.build_tree()
```

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

### Run fmt Library Benchmarks

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/README.rst

Commands to clone the benchmark repository, generate build files with CMake, and execute speed or bloat tests.

```bash
git clone --recursive https://github.com/fmtlib/format-benchmark.git
cd format-benchmark
cmake .
make speed-test
make bloat-test
```

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

### C++ printf Enum Formatting Example

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates the corrected formatting of enums with numeric format specifiers in fmt::(s)printf. This example highlights a fix for a breaking change related to enum formatting.

```c++
enum {
    ANSWER = 42
};
fmt::printf("%d", ANSWER);
```

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

### Format Pointers with fmt

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Illustrates how to format C strings as pointers using the p specifier.

```c++
fmt::print("{:p}", "test"); // prints pointer value
```

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

### GET /config/blackholes

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/parameters.md

Configures black hole physics, including accretion, mergers, and AGN feedback mechanisms.

```APIDOC
## GET /config/blackholes

### Description
Configures the behavior of black hole particles within the simulation environment.

### Method
GET

### Endpoint
/config/blackholes

### Parameters
#### Query Parameters
- **bBlackholes** (boolean) - Optional - Enable black hole particles
- **dBHAccretionAlpha** (float) - Optional - Accretion boost parameter
- **dBHRadiativeEff** (float) - Optional - AGN radiative efficiency

### Response
#### Success Response (200)
- **config** (object) - Black hole physics parameters
```

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

### Check CMake Version

Source: https://github.com/dpotter/pkdgrav3/blob/master/README.md

Command to verify the installed version of CMake. pkdgrav3 requires version 3.14 or newer.

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

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

### Project Initialization

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/CMakeLists.txt

Initializes the project with the name 'FMT' and specifies CXX as the primary language. This command must appear after all CMake version and policy settings.

```cmake
project(FMT CXX)
```

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

### GET /config/star-formation

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/parameters.md

Manages parameters related to star formation, including density thresholds and Kennicutt-Schmidt law settings.

```APIDOC
## GET /config/star-formation

### Description
Defines the conditions under which gas particles are converted into stellar particles.

### Method
GET

### Endpoint
/config/star-formation

### Parameters
#### Query Parameters
- **bStars** (boolean) - Optional - Enable stellar particles
- **dSFThresholdDen** (float) - Optional - Minimum density for star formation
- **dSFindexKS** (float) - Optional - Index of the Kennicutt-Schmidt law

### Response
#### Success Response (200)
- **settings** (object) - Star formation configuration
```

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

### GET /config/eos

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/parameters.md

Retrieves or defines the effective equation of state (EOS) parameters for gas pressurization at high densities.

```APIDOC
## GET /config/eos

### Description
Configures the polytropic effective EOS to handle gas pressure at high densities.

### Method
GET

### Endpoint
/config/eos

### Parameters
#### Query Parameters
- **bDoEOS** (boolean) - Optional - Enable polytropic effective EOS
- **dEOSFloornH** (float) - Optional - Minimum density for energy floor (nH cm-3)
- **dEOSPolyFloorIndex** (float) - Optional - Index of the polytropic effective EOS

### Response
#### Success Response (200)
- **status** (string) - Configuration status
- **params** (object) - Current EOS settings
```

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

### Apply Runtime Width Specification

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Illustrates how to dynamically specify the width of a formatted output at runtime using the fmt library's formatting syntax.

```cpp
fmt::format("{0:{1}}", 42, 5); // gives "   42"
```

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

### Configure PKDGRAV3 Simulation Parameters

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

Sets up fundamental parameters for PKDGRAV3 simulations, including unit systems for mass and length, gas physics properties like initial temperature, star formation criteria, supernova feedback parameters, and memory allocation flags for hydrodynamics. These parameters control the simulation's physical behavior and computational resource usage.

```python
# Unit system for galaxy simulations
dMsolUnit = 1.0e10      # Mass unit: 10^10 solar masses
dKpcUnit = 1.0          # Length unit: 1 kpc

# Gas physics
bDoGravity = True
dInitialT = 10000.0     # Initial gas temperature (K)

# Cooling (requires GRACKLE compilation flag)
# bGrackle = True
# achGrackleDataFile = "CloudyData_UVB=HM2012.h5"

# Star formation parameters
bStarForm = True
dTempMax = 30000.0      # Temperature threshold for SF
dOverDensity = 100.0    # Overdensity threshold
dSFEfficiency = 0.01    # Star formation efficiency

# Supernova feedback
bFeedback = True
dESN = 1.0e51           # Supernova energy (erg)
dDeltaStarForm = 1.0e6  # Minimum time between SF events (years)

# Memory flags for hydrodynamics
bMemVelocity = True
bMemAcceleration = True
bMemMass = True
bMemSoft = True
```

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

### Argument ID Validation

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Example of an invalid format string that triggers an error due to repeated leading zeros in an argument ID.

```c++
fmt::print("{000}", 42); // error
```

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

### Enable and Use RGB Color Output in fmt

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates how to enable experimental RGB color support using the FMT_EXTENDED_COLORS macro and print colored text to the console.

```c++
#define FMT_EXTENDED_COLORS
#define FMT_HEADER_ONLY
#include <fmt/format.h>

fmt::print(fmt::color::steel_blue, "Some beautiful text");
```

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

### Setup Rockstar Symbolic Links

Source: https://github.com/dpotter/pkdgrav3/blob/master/CMakeLists.txt

Creates symbolic links for Rockstar header files to resolve naming conflicts and includes them in the project build process.

```cmake
if(ROCKSTAR_PATH)
    set(HAVE_ROCKSTAR TRUE)
    file(REAL_PATH ${ROCKSTAR_PATH} rdir EXPAND_TILDE)
    foreach(file particle.h halo.h io/io_internal.h)
        add_custom_command(
            OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/rockstar/${file}
            COMMAND ${CMAKE_COMMAND} -E create_symlink ${rdir}/${file} ${CMAKE_CURRENT_BINARY_DIR}/rockstar/${file}
        )
        target_sources(${PROJECT_NAME} PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/rockstar/${file})
    endforeach()
endif()
```

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

### Chrono Duration Formatting

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Examples of formatting chrono durations, including precision control and extracting specific units or values using %Q and %q specifiers.

```c++
auto s = fmt::format("{:.1}", std::chrono::duration<double>(1.234));
auto value = fmt::format("{:%Q}", 42s);
auto unit  = fmt::format("{:%q}", 42s);
auto s2 = fmt::format("{0:{1}%H:%M:%S}", std::chrono::seconds(12345), 12);
```

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

### String Formatting with Positional Arguments in {fmt}

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/README.rst

Shows how to format strings and utilize positional arguments for localization or reordering. This allows for flexible string construction.

```c++
std::string s = fmt::format("I'd rather be {1} than {0}.", "right", "happy");
// s == "I'd rather be happy than right."
```

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

### Configure GoogleTest and Test Executables with CMake

Source: https://github.com/dpotter/pkdgrav3/blob/master/tests/CMakeLists.txt

This script sets up the GoogleTest framework using FetchContent and defines several test executables. It configures C++17 standards, links necessary libraries like mdl2, blitz, and fmt, and registers tests with the CTest framework.

```cmake
cmake_minimum_required(VERSION 3.14)
set(USE_GTEST "no" CACHE STRING "Should we provide the tests using gtest framework")
if(USE_GTEST)
  FetchContent_MakeAvailable(googletest)
  enable_testing()
  add_executable(cache cache.cxx)
  set_target_properties(cache PROPERTIES CXX_STANDARD 17 CXX_STANDARD_REQUIRED YES CXX_EXTENSIONS NO)
  target_link_libraries(cache mdl2 gtest_main)
  add_test(NAME cache COMMAND $<TARGET_FILE:cache> WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
endif()
```

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

### Configure FFTW3 Path with CMake

Source: https://github.com/dpotter/pkdgrav3/blob/master/README.md

Shows how to inform CMake about the location of the FFTW3 library installation using the FFTW_ROOT variable. This is required if FFTW3 is not found in standard system paths.

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

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

### Format date and time

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Shows how to use the fmt/time.h header to format current system time using strftime-like specifiers.

```c++
#include "fmt/time.h"

std::time_t t = std::time(nullptr);
fmt::print("The date is {:%Y-%m-%d}.", *std::localtime(&t));
```

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

### Gravity, Domains, and Trees Parameters

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/parameters.md

Configuration options for gravitational softening, domain decomposition, and tree building in PKDGRAV3.

```APIDOC
## Gravity, Domains, Trees

### Description
Parameters in this section control gravitational softening, tree memory layout, and the frequency of domain decomposition and tree building.

### Parameters

- **dSoft** (float) - Default: 0.0 - Sets the global gravitational softening length in code units.
- **dSoftMax** (float) - Default: 0.0 - Maximum comoving gravitational softening length (absolute value or multiplier).
- **bPhysicalSoft** (boolean) - Default: False - Specifies if the gravitational softening length is physical.
- **bSoftMaxMul** (boolean) - Default: True - Indicates if the maximum comoving gravitational softening length is used as a multiplier.
- **bDoGravity** (boolean) - Default: True - If false, gravitational accelerations are not applied, useful for hydrodynamical simulations.
- **nGridLin** (integer) - Default: 0 - Grid size for linear species; 0 disables this feature.
- **bDoLinPkOutput** (boolean) - Default: False - Enables power spectrum output for linear species.
- **dFracNoDomainDecomp** (float) - Default: 0.1 - Fraction of active particles below which domain decomposition is not performed.
- **dFracNoDomainRootFind** (float) - Default: 0.1 - Fraction of active particles below which domain root finding is not performed.
- **dFracNoDomainDimChoice** (float) - Default: 0.1 - Fraction of active particles below which domain dimension choice is not performed.
- **iMaxRungDomainDecomp** (integer) - Default: 2147483648 - The maximum rung level above which domain decomposition is not performed.
```

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

### Enabling Grisu Floating-Point Formatting

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Shows how to enable the experimental Grisu algorithm for faster floating-point formatting by defining the FMT_USE_GRISU macro.

```c++
#define FMT_USE_GRISU 1
#include <fmt/format.h>

auto s = fmt::format("{}", 4.2);
```

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

### Run FOF Group Finder in Python

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

This script demonstrates how to load a simulation snapshot, configure the FOF algorithm with a specific linking length, and export group statistics. It requires the PKDGRAV Python module and assumes standard simulation data inputs.

```python
import PKDGRAV as msr
from PKDGRAV import OUT_TYPE

# Load with group finding enabled
time = msr.load("example.00100", bFindGroups=True, bMemGlobalGid=True, nMemEphemeral=8)
msr.domain_decompose()
msr.build_tree()

# Run FOF algorithm
msr.fof(0.0015625, 10)
msr.reorder()

# Write group statistics
msr.write_group_stats("example.00100.fofstats")
```

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

### Overriding Restart Parameters in Pkdgrav3

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/changes.md

Illustrates how to override specific parameters during a Pkdgrav3 simulation restart. This example shows how to enable parallel reading and set the number of parallel readers by modifying the `restore` call.

```python
msr.restore(__file__)
# Changed to:
msr.restore(__file__,bParaRead=True,nParaRead=100)
```

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

### Project Options Definition

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/CMakeLists.txt

Defines various boolean options for the project, such as enabling pedantic warnings, halting on warnings, generating documentation, installation targets, testing, fuzzing, CUDA testing, and OS-specific core features.

```cmake
option(FMT_PEDANTIC "Enable extra warnings and expensive tests." OFF)
option(FMT_WERROR "Halt the compilation with an error on compiler warnings."
       OFF)

# Options that control generation of various targets.
option(FMT_DOC "Generate the doc target." ${MASTER_PROJECT})
option(FMT_INSTALL "Generate the install target." ${MASTER_PROJECT})
option(FMT_TEST "Generate the test target." ${MASTER_PROJECT})
option(FMT_FUZZ "Generate the fuzz target." OFF)
option(FMT_CUDA_TEST "Generate the cuda-test target." OFF)
option(FMT_OS "Include core requiring OS (Windows/Posix) " ON)
```

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

### Include fmt library headers

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates the updated include path for the fmt library following its rename from cppformat.

```c++
#include "fmt/format.h"
```

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

### Safe Printf Implementation with Positional Arguments in C++

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Provides an example of using fmt::printf, a safe implementation of printf that supports positional arguments. This allows for more flexible and robust string formatting, especially in internationalized applications.

```c++
fmt::printf("Elapsed time: %.2f seconds", 1.23);
fmt::printf("%1$s, %3$d %2$s", weekday, month, day);
```

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

### Format Wide String with Date in C++

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Example of formatting a wide string literal with a Date object using fmt::format. This showcases the library's ability to handle wide characters and custom types for output.

```c++
fmt::format(L"The date is {0}", Date(2012, 12, 9));
```

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

### Apply Terminal Colors and Emphasis

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Shows how to use fmt/color.h to apply foreground colors, background colors, and text emphasis like bold or italic to console output.

```c++
#include <fmt/color.h>

int main() {
  print(fg(fmt::color::crimson) | fmt::emphasis::bold,
        "Hello, {}!\n", "world");
  print(fg(fmt::color::floral_white) | bg(fmt::color::slate_gray) |
        fmt::emphasis::underline, "Hello, {}!\n", "мир");
  print(fg(fmt::color::steel_blue) | fmt::emphasis::italic,
        "Hello, {}!\n", "世界");
}
```

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

### Configure Custom Unit Systems for Simulations

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

Defines custom unit systems for non-cosmological simulations, such as planetary dynamics, by setting length and mass units. Provides examples for AU-based, Earth-radius-based, and Galactic-scale units, emphasizing the G=1 convention.

```Python
# units_custom.par - Custom unit system for planetary simulations
# Use dKpcUnit and dMsolUnit to define G=1 unit system

# Astronomical Unit scale (AU, km/s, ~Jupiter masses)
dKpcUnit = 4.848101587970315e-09    # Length unit in kpc (= 1 AU)
dMsolUnit = 0.0011272388129170855   # Mass unit in solar masses

# This gives:
# Length: 1 AU
# Velocity: 1 km/s
# Mass: ~1130 Earth masses
# Time: ~0.978 years (derived from G=1)

# Earth radius scale (for collision simulations)
# dKpcUnit = 2.064688206889847e-13   # 1 Earth radius
# dMsolUnit = 4.8006351375833994e-08 # ~48 micro solar masses

# Galactic scale (kpc, km/s)
# dKpcUnit = 1.0                     # 1 kpc
# dMsolUnit = 232508.541103         # ~2.3e5 solar masses
# Time unit: ~0.978 Gyr

# Unit conversion formulas (with G=1):
# Velocity^2 = G * Mass / Length
# Time = Length / Velocity
# Density = Mass / Length^3

# Use tools/calculate_units.py to compute dKpcUnit and dMsolUnit
# from your desired length/mass/velocity/time combinations
```

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

### Implementing Variadic Formatting Functions in C++

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates how to implement variadic formatting functions using C++11 variadic templates or lightweight wrapper functions with the FMT_VARIADIC macro. This approach improves performance by avoiding temporary formatter objects and argument lifetime management.

```c++
void report_error(const char *format, const fmt::ArgList &args) {
  fmt::print("Error: {}");
  fmt::print(format, args);
}
FMT_VARIADIC(void, report_error, const char *)

report_error("file not found: {}", path);
```

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

### Configure Dynamic Accuracy Parameters

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/extensions.md

Demonstrates how to initialize dynamic accuracy switches for cosmological simulations. These switches automatically adjust theta and replica parameters based on simulation state.

```python
from accuracy import classic_theta_switch,classic_replicas_switch

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

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

### Pkdgrav3 Synchronized Redshift Steps

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/changes.md

Demonstrates the new method for specifying synchronized steps to reach specific redshifts in Pkdgrav3, replacing `nStepsSync` and `dRedSync`. This example shows how to define multiple redshift targets and the number of steps for each interval.

```python
# Old way:
dRedFrom = 49
dRedTo = 0
nSteps = 160
nStepsSync = 60
dRedSync = 10
# This would take 60 steps to redshift 10, then 100 steps to redshift 0.

# New way:
dRedFrom = 40
dRedTo = [10,0]
nSteps = [60,100]
```

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

### Convert Integer to String using fmt::to_string (C++)

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Demonstrates how to convert an integer to a string using the fmt::to_string function from the fmt/string.h header. This provides an alternative to std::to_string.

```c++
#include "fmt/string.h"

std::string answer = fmt::to_string(42);
```

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

### CMake Visual Studio MSBuild Setup Script

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/CMakeLists.txt

Generates a `run-msbuild.bat` script for Visual Studio builds when using the MS SDK. It includes logic to set up the build environment using `SetEnv.cmd` and calls `msbuild`, overriding the .NET Framework path to avoid specific warnings.

```cmake
if (MASTER_PROJECT AND CMAKE_GENERATOR MATCHES "Visual Studio")
  # If Microsoft SDK is installed create script run-msbuild.bat that
  # calls SetEnv.cmd to set up build environment and runs msbuild.
  # It is useful when building Visual Studio projects with the SDK
  # toolchain rather than Visual Studio.
  include(FindSetEnv)
  if (WINSDK_SETENV)
    set(MSBUILD_SETUP "call \"${WINSDK_SETENV}\"")
  endif ()
  # Set FrameworkPathOverride to get rid of MSB3644 warnings.
  join(netfxpath
       "C:\\Program Files\\Reference Assemblies\\Microsoft\\Framework\\
       ".NETFramework\\v4.0")
  file(WRITE run-msbuild.bat "
    ${MSBUILD_SETUP}
    ${CMAKE_MAKE_PROGRAM} -p:FrameworkPathOverride=\"${netfxpath}\" %*")
endif ()
```

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

### PKDGRAV Initial Condition Generation

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

Programmatically generates initial conditions for cosmological simulations using the PKDGRAV interface. Allows customization of cosmology, grid size, redshift, box size, and perturbation order (e.g., 2LPT). Includes options for saving to Tipsy format.

```python
# generate_ic.py - Generate initial conditions
import PKDGRAV as msr
from cosmology import SimpleCosmology

# Define cosmology
cosmology = SimpleCosmology(
    omega_matter=0.32,
    omega_lambda=0.68,
    omega_baryon=0.05,
    sigma8=0.83,
    ns=0.96,
    h=0.67,
    transfer_file="euclid_z0_transfer_combined.dat"
)

# Generate initial conditions
time = msr.generate_ic(
    cosmology=cosmology,
    grid=256,              # 256^3 particles
    seed=42,               # Random seed
    z=49,                  # Starting redshift
    L=1000,                # Box size in Mpc/h
    order=2,               # 2LPT (1=Zeldovich, 2=2LPT, 3=3LPT)
    fixed_amplitude=False, # Use random amplitudes
    phase_pi=0             # Phase offset (0 or 1)
)

print(f"Generated ICs at time={time}")

# Save to file
msr.save("ic_z49.tipsy", time=time)

# Can also generate with gas particles
# In parameter file: bICgas = True, dInitialT = 100.0
```

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

### Capturing Formatting Arguments with `make_format_args`

Source: https://github.com/dpotter/pkdgrav3/blob/master/fmt/ChangeLog.rst

Explains how to use `fmt::make_format_args` to capture formatting arguments, often used in variadic functions.

```APIDOC
## Capturing Formatting Arguments with `make_format_args`

### Description
The `make_format_args` function is used to create a `format_args` object from a variable number of arguments. This is particularly useful when implementing functions that accept arbitrary formatting arguments, such as logging or reporting functions.

### Method
N/A (Library function usage)

### Endpoint
N/A

### Parameters
N/A

### Request Example
```cpp
// Prints formatted error message.
void vreport_error(const char *format, fmt::format_args args) {
  fmt::print("Error: ");
  fmt::vprint(format, args);
}

template <typename... Args>
void report_error(const char *format, const Args & ... args) {
  vreport_error(format, fmt::make_format_args(args...));
}
```

### Response
N/A (Internal function usage)

### Response Example
N/A
```

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

### Configure Light Cone Output

Source: https://github.com/dpotter/pkdgrav3/blob/master/docs/parameters.md

These parameters control the generation and format of light cone outputs. They allow enabling/disabling the feature, setting the starting redshift, configuring HEALPix map output, controlling particle output, specifying octants to include, defining the sky coverage in square degrees, and setting the light cone direction vector.

```default
bLightCone = False
dRedshiftLCP = 0.0
nSideHealpix = 0
bLightConeParticles = False
bBowtie = False
lstLightConeOctants = all
sqdegLCP = 50.0
hLCP = [0.749, 0.454, 1.0]
```

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

### Build and Execute Simulation on HPC

Source: https://context7.com/dpotter/pkdgrav3/llms.txt

Commands to compile the PKDGRAV3 source code using CMake and execute the simulation using SLURM job scheduling on a high-performance computing cluster.

```bash
cd /path/to/pkdgrav3
cmake -S . -B build
cmake --build build -j 16
#!/bin/bash -l
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=1 --cpus-per-task=16 --ntasks-per-core=1
srun ./build/pkdgrav3 cosmology.par
```