### Execute RASPA3 Simulation Example

Source: https://github.com/iraspa/raspa3/blob/main/README.md

This snippet demonstrates how to run a basic RASPA3 simulation for methane in a box. It involves navigating to the example directory and executing the run script. Ensure you have RASPA3 installed and configured.

```bash
cd examples/basic/1_mc_methane_in_box
./run
```

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

### Install RASPA3 on OpenSUSE 15.5 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.5 with AVX512 support using `zypper`. This command installs the RPM package from a specified URL and then runs the unit tests for `raspakit`. Ensure all listed dependencies are met before installation.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.5.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA 3 on Debian/Ubuntu

Source: https://github.com/iraspa/raspa3/blob/main/INSTALLATION.md

Installs a pre-built RASPA 3 package on Debian-based systems like Ubuntu using the apt package manager. Requires a .deb file.

```bash
apt install ./raspa3-<VERSION>-<OS>-<ARCH>-<AVX>.deb
```

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

### Install RASPA3 on OpenSUSE 15.2 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.2 with AVX2 support using `zypper`. This command installs the RPM package from a specified URL and then runs the unit tests for `raspakit`. Verify that all listed dependencies are met before proceeding with the installation.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.2.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA 3 using Conda

Source: https://github.com/iraspa/raspa3/blob/main/INSTALLATION.md

Installs RASPA 3 and its library using the Conda package manager. This is a cross-platform method suitable for most users.

```bash
conda install -c conda-forge raspa3 raspalib
```

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

### Install RASPA3 on OpenSUSE 15.3 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.3 with AVX2 support using `zypper`. This command installs the RPM package from a specified URL and then runs the unit tests for `raspakit`. Ensure all specified dependencies are installed before running this command.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.3.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on OpenSUSE 15.3 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.3 with AVX512 support using `zypper`. This command installs the RPM package from a specified URL and then executes the `raspakit` unit tests. It is advisable to check for and install all listed dependencies beforehand.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.3.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA 3 on RPM-based Linux

Source: https://github.com/iraspa/raspa3/blob/main/INSTALLATION.md

Installs a pre-built RASPA 3 package on RPM-based Linux distributions using the rpm command. Requires an .rpm file.

```bash
rpm -i raspa3-<VERSION>-<OS>-<ARCH>-<AVX>.rpm
```

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

### Install RASPA3 on OpenSUSE 15.2 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.2 with AVX512 support using `zypper`. This command installs the RPM package from a specified URL and then executes the `raspakit` unit tests. Ensure all specified dependencies are installed before running this command.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.2.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Build RASPA with Conda (Recommended)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_from_source.md

This snippet demonstrates the recommended method for building RASPA using Conda. It involves cloning the repository, creating a Conda environment from `env.yml`, activating the environment, configuring the build with CMake presets, and finally building with Ninja. It also includes notes on environment variable setup for dynamic libraries.

```bash
git clone https://github.com/raspa3/raspa3.git
cd raspa3
conda env create -f env.yml
conda activate raspa
cmake --preset=linux_conda  # or mac_conda / windows_conda_raspa3
ninja -C build
ninja -C build install      # optional
```

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

### JSON Configuration for RASPA Simulation

Source: https://context7.com/iraspa/raspa3/llms.txt

Example of a JSON file used to configure a RASPA simulation. It specifies simulation type, cycles, systems, and components. This file allows for reproducible and scriptable simulation setups.

```json
{
  "SimulationType": "MonteCarlo",
  "NumberOfCycles": 10000,
  "NumberOfInitializationCycles": 1000,
  "PrintEvery": 1000,
  "Systems": [
    {
      "Type": "Box",
      "BoxLengths": [30.0, 30.0, 30.0],
      "ExternalTemperature": 300.0,
      "ChargeMethod": "None",
      "OutputPDBMovie": true,
      "SampleMovieEvery": 10
    }
  ],
  "Components": [
    {
      "Name": "methane",
      "MoleculeDefinition": "ExampleDefinitions",
      "TranslationProbability": 1.0,
      "CreateNumberOfMolecules": 100
    }
  ]
}
```

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

### Doxygen Comment Example for Function

Source: https://github.com/iraspa/raspa3/blob/main/STYLE_GUIDE.md

This snippet demonstrates the use of Doxygen-style comments to document a function. It includes a brief description, notes on side effects, parameter descriptions, and return value information. This enhances code readability and facilitates automatic documentation generation.

```cpp
/// Inserts a molecule into the vector of atoms.
///
/// Note: updates the numberOfMoleculesPerComponent, numberOfIntegerMoleculesPerComponent,
///       numberOfPseudoAtoms, totalNumberOfPseudoAtoms.
/// - Parameters:
///   - selectedComponent: the index of the component
///   - atoms: vector of atoms to be inserted
/// - returns:
```

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

### Install RASPA3 on Fedora-39 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX2 support on Fedora 39. The command uses DNF to install the RPM from the provided URL and then executes unit tests. Root privileges are needed for this installation.

```shell
dnf install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.fc39.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Fedora-39 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX512 support on Fedora 39. This command utilizes DNF to install the RPM from the specified URL and then runs unit tests to verify the installation. Root privileges are required.

```shell
dnf install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.fc39.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Fedora-40 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX2 support on Fedora 40. This command uses DNF to install the relevant RPM package from the given URL and then executes unit tests. Root privileges are necessary for this installation.

```shell
dnf install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.fc40.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Allman Style Brace Formatting Example

Source: https://github.com/iraspa/raspa3/blob/main/STYLE_GUIDE.md

Illustrates the Allman style of brace formatting, where opening braces are placed on a new line, aligned with the control statement. This style is recommended for its readability and consistency.

```cpp
while (x == y)
{
  foo();
  bar();
}
```

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

### Install Unit Tests Executable - CMake

Source: https://github.com/iraspa/raspa3/blob/main/tests/foundationkit-tests/CMakeLists.txt

Installs the 'unit_tests_foundationkit' executable to the 'share/raspa3/tests' directory as part of the 'unit_tests' component. This makes the tests available after installation.

```cmake
install(TARGETS unit_tests_foundationkit DESTINATION share/raspa3/tests COMPONENT unit_tests)
```

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

### CFCMC Binary Mixture Adsorption Example

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/examples_advanced.md

An example configuration for CFCMC binary mixture adsorption of CO2 and N2 in DMOF.

```APIDOC
## CFCMC Binary Mixture Adsorption Example

### Description
Configuration example for simulating binary mixture adsorption using the CFCMC method.

### Method
Monte Carlo (CFCMC)

### Endpoint
N/A (Configuration Example)

### Parameters
N/A

### Request Example
```json
{
  "SimulationType": "MonteCarlo",
  "NumberOfCycles": 10000,
  "NumberOfInitializationCycles": 5000,
  "NumberOfEquilibrationCycles": 5000,
  "PrintEvery": 1000,
  "Systems": [
    {
      "Type": "Framework",
      "Name": "MFI_SI",
      "NumberOfUnitCells": [
        2,
        2,
        2
      ],
      "ExternalTemperature": 353.0,
      "ExternalPressure": 1.0e5,
      "ChargeMethod": "Ewald",
      "HybridMCProbability": 0.01,
      "HybridMCMoveNumberOfSteps": 100,
      "TimeStep": 0.005,
      "Ensemble": "NVE"
    }
  ],
  "Components": [
    {
      "Name": "CO2",
      "MoleculeDefinition": "ExampleDefinitions",
      "FugacityCoefficient": 1.0,
      "ThermodynamicIntegration": true,
      "TranslationProbability": 0.5,
      "RotationProbability": 0.5,
      "CFCMC_CBMC_SwapProbability": 1.0,
      "CreateNumberOfMolecules": 0
    }
  ]
}
```

### Response
#### Success Response (200)
N/A (Configuration Example)

#### Response Example
N/A
```

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

### Install and Sign Executable (CMake)

Source: https://github.com/iraspa/raspa3/blob/main/cli/CMakeLists.txt

This snippet defines installation rules for the raspa3-cli executable and conditionally performs code signing on macOS builds. The executable is installed to the 'bin' directory.

```cmake
if(BUILD_MAC_PACKAGE)
install(CODE "execute_process(COMMAND
    codesign --force --options runtime --timestamp --sign \"Developer ID Application: David Dubbeldam (24U2ZRZ6SC)\"  
    \"cli/${PROJECT_NAME}\")" COMPONENT cli)
endif()
install(TARGETS ${PROJECT_NAME} DESTINATION bin COMPONENT cli)
```

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

### Install RASPA3 on Debian 12 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Debian 12 with AVX512 support. This process includes updating apt, downloading the specific .deb file, installing it, and running unit tests.

```bash
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_amd64_debian-12_skylake-avx512.deb
apt-get install ./raspa_3.0.16_amd64_debian-12_skylake-avx512.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Debian 13 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Debian 13 with AVX512 support. This procedure requires updating apt, downloading the specified .deb file, installing it, and running unit tests.

```bash
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_amd64_debian-13_skylake-avx512.deb
apt-get install ./raspa_3.0.16_amd64_debian-13_skylake-avx512.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Debian 11 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Debian 11 with AVX512 support. The steps are to update apt, download the correct .deb file, install it, and run unit tests.

```bash
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_amd64_debian-11_skylake-avx512.deb
apt-get install ./raspa_3.0.16_amd64_debian-11_skylake-avx512.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Fedora-41 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX2 support on Fedora 41. This command directly installs the RPM package from the specified URL using DNF and then executes the unit tests. This operation requires root privileges.

```shell
dnf install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.fc41.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Fedora-38 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX2 support on Fedora 38. The process involves using DNF to install the RPM from the given URL, followed by running unit tests. Root privileges are necessary for this operation.

```shell
dnf install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.fc38.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Debian 10 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Debian 10 with AVX2 support. This process requires adding a specific repository, updating package lists, downloading the .deb package, installing it, and running unit tests.

```bash
echo "deb http://archive.debian.org/debian stretch main contrib non-free" > /etc/apt/sources.list
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_amd64_debian-10_core-avx2.deb
apt-get install ./raspa_3.0.16_amd64_debian-10_core-avx2.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Unpack RPM file without installation

Source: https://github.com/iraspa/raspa3/blob/main/INSTALLATION.md

Extracts the contents of an RPM package without performing a system-wide installation. Useful for inspecting package contents.

```bash
rpm2cpio raspa3-*.rpm | cpio -idmv
```

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

### Install RASPA3 on OpenSUSE 15.4 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.4 with AVX2 support using `zypper`. This command installs the RPM package from a specified URL and then executes the `raspakit` unit tests. Verify that all listed dependencies are satisfied prior to execution.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.4.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Build RASPA on Fedora 40

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_from_source.md

This snippet outlines the steps to build RASPA on Fedora 40. It begins by installing necessary development packages with `dnf`. Subsequently, it clones the RASPA repository, configures the build with a Fedora 40-specific CMake preset, and compiles the project using Ninja.

```bash
sudo dnf install -y git llvm lld cmake clang clang-tools-extra ninja-build \
  libomp-devel libcxx libcxx-devel libcxxabi libcxxabi-devel \
  lapack64 blas64 python3 python3-devel pybind11-devel

git clone https://github.com/raspa3/raspa3.git
cd raspa3
cmake -B build --preset=linux-x86_64-core-avx2-fedora-40
ninja -C build
ninja -C build install
```

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

### Execute RASPA3 Simulations via Command Line (Bash)

Source: https://context7.com/iraspa/raspa3/llms.txt

This bash script demonstrates how to execute RASPA3 simulations from the command line. It includes navigating to an example directory, running a local simulation script, and directly executing the `raspa3` executable with a JSON configuration file.

```bash
# Navigate to example directory
cd examples/basic/1_mc_methane_in_box

# Run simulation using local run script
./run

# Or run directly with raspa3 executable
raspa3 simulation.json
```

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

### Fetch and Configure Googletest for CMake

Source: https://github.com/iraspa/raspa3/blob/main/tests/CMakeLists.txt

This snippet demonstrates how to use CMake's FetchContent module to download and integrate the Googletest framework. It specifies the Git repository and tag for Googletest and includes a setting to force shared CRT on Windows to prevent build conflicts. Finally, it makes Googletest available for use in the build.

```cmake
include(FetchContent)
FetchContent_Declare(googletest
      GIT_REPOSITORY https://github.com/google/googletest.git
      GIT_TAG v1.16.0
      EXCLUDE_FROM_ALL)
# For Windows: Prevent overriding the parent project's compiler/linker settings
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
FetchContent_MakeAvailable(googletest)
```

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

### Install RASPA3 on Debian 12 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Debian 12 with AVX2 support. The installation involves updating package lists, downloading the correct .deb package, installing it using apt-get, and running the unit tests.

```bash
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_amd64_debian-12_core-avx2.deb
apt-get install ./raspa_3.0.16_amd64_debian-12_core-avx2.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Build RASPA on Ubuntu 24.04

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_from_source.md

This section provides commands to build RASPA on Ubuntu 24.04. It first installs the required system packages using `apt`, then clones the RASPA repository, configures the build using a specific CMake preset for Ubuntu 24.04 with AVX2 support, and finally builds the project using Ninja.

```bash
sudo apt install -y git ca-certificates cmake ninja-build \
  llvm lld clang clang-tidy libc++-dev libc++abi-dev \
  libomp-dev libclang-rt-dev python3 python3-dev pybind11-dev \
  liblapack64-dev libblas64-dev

git clone https://github.com/raspa3/raspa3.git
cd raspa3
cmake -B build --preset=linux-x86_64-core-avx2-ubuntu-24
ninja -C build
ninja -C build install
```

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

### Install RASPA3 on OpenSUSE 15.4 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs the RASPA3 package for OpenSUSE 15.4 with AVX512 support using `zypper`. This command installs the RPM package from a specified URL and subsequently runs the unit tests for `raspakit`. It is recommended to confirm all listed dependencies are present before proceeding.

```shell
zypper install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.opensuse-leap-15.4.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Code Signing and Installation - CMake

Source: https://github.com/iraspa/raspa3/blob/main/app/CMakeLists.txt

This CMake snippet handles the installation of the Raspa3 executable and conditionally performs code signing for macOS application bundles. The `install(TARGETS)` command places the executable in the 'bin' directory, while the `install(CODE)` block executes a shell command for code signing if the `BUILD_MAC_PACKAGE` flag is set. This ensures the application is properly signed for distribution on macOS.

```cmake
if(BUILD_MAC_PACKAGE)
install(CODE "execute_process(COMMAND
    codesign --force --options runtime --timestamp --sign \"Developer ID Application: David Dubbeldam (24U2ZRZ6SC)\"  
    \"app/${PROJECT_NAME}\")" COMPONENT app)
endif()
install(TARGETS ${PROJECT_NAME} DESTINATION bin COMPONENT app)
```

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

### Install RASPA3 on Ubuntu 20.04 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Ubuntu 20.04 with AVX512 support. This process involves updating package lists, downloading the specific .deb package, and then installing it. It also includes a command to run unit tests.

```bash
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_amd64_ubuntu-20_skylake-avx512.deb
apt-get install ./raspa_3.0.16_amd64_ubuntu-20_skylake-avx512.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 Unit Tests Executable

Source: https://github.com/iraspa/raspa3/blob/main/tests/raspa3-tests/CMakeLists.txt

Installs the `unit_tests_raspa3` executable to the `share/raspa3/tests` directory as part of the `unit_tests` component.

```cmake
install(TARGETS unit_tests_raspa3 DESTINATION share/raspa3/tests COMPONENT unit_tests)

```

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

### Simulate Multi-Component Adsorption with Charges using Python API

Source: https://context7.com/iraspa/raspa3/llms.txt

Shows how to simulate multi-component adsorption of charged molecules in frameworks using the raspalib Python API. This example enables electrostatic interactions (Ewald summation) and defines charged components. Requires 'force_field.json', 'CO2.json', and a CIF file (e.g., 'Cu-BTC.cif').

```python
import raspalib

# Load force field with charges enabled
ff = raspalib.ForceField("force_field.json")

# Define MC moves for molecular adsorbate
mcmoves = raspalib.MCMoveProbabilities(
    translationProbability=0.5,
    rotationProbability=0.5,
    reinsertionCBMCProbability=0.5,
    swapProbability=1.0,
    widomProbability=1.0,
)

# Define CO2 component (with charges)
co2 = raspalib.Component(
    componentId=0,
    forceField=ff,
    componentName="CO2",
    fileName="CO2.json",
    particleProbabilities=mcmoves,
)

# Load Cu-BTC framework
cubtc = raspalib.Framework(
    frameworkId=0,
    forceField=ff,
    componentName="Cu-BTC",
    fileName="Cu-BTC.cif",
    numberOfUnitCells=raspalib.int3(1, 1, 1),
)

# Create system with Ewald summation for charges
system = raspalib.System(
    systemId=0,
    externalTemperature=300.0,
    externalPressure=1e4,
    forceField=ff,
    components=[co2],
    initialNumberOfMolecules=[0],
    frameworkComponents=[cubtc],
)

# Run simulation
mc = raspalib.MonteCarlo(
    numberOfCycles=10000,
    numberOfInitializationCycles=2000,
    systems=[system],
    outputToFiles=True
)
mc.run()
```

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

### Gibbs Ensemble Monte Carlo Simulation Setup with Python API

Source: https://context7.com/iraspa/raspa3/llms.txt

Provides the initial setup for simulating phase equilibria using Gibbs Ensemble Monte Carlo with the raspalib Python API. This ensemble involves two simulation boxes that exchange particles and volume. Requires a 'force_field.json' file.

```python
import raspalib

# Load force field
ff = raspalib.ForceField("force_field.json")

```

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

### Install RASPA3 on Redhat-6 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX512 support on Red Hat 6 systems. The process includes setting up EOL repositories, updating the system, and installing the specific AVX512 RPM. Unit tests are executed to validate the installation. Root privileges are necessary for this operation.

```shell
curl https://www.getpagespeed.com/files/centos6-eol.repo --output /etc/yum.repos.d/CentOS-Base.repo 
curl https://www.getpagespeed.com/files/centos6-epel-eol.repo --output /etc/yum.repos.d/epel.repo
yum -y install centos-release-scl
curl https://www.getpagespeed.com/files/centos6-scl-eol.repo --output /etc/yum.repos.d/CentOS-SCLo-scl.repo
curl https://www.getpagespeed.com/files/centos6-scl-rh-eol.repo --output /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo
yum update -y && \
yum install --nogpgcheck https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.el6.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Redhat-6 (AVX2)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX2 support on Red Hat 6 systems. This involves configuring EOL repositories for CentOS 6, updating the system, and then installing the specified RPM package. Unit tests are run to confirm the installation. This procedure requires root privileges.

```shell
curl https://www.getpagespeed.com/files/centos6-eol.repo --output /etc/yum.repos.d/CentOS-Base.repo 
curl https://www.getpagespeed.com/files/centos6-epel-eol.repo --output /etc/yum.repos.d/epel.repo
yum -y install centos-release-scl
curl https://www.getpagespeed.com/files/centos6-scl-eol.repo --output /etc/yum.repos.d/CentOS-SCLo-scl.repo
curl https://www.getpagespeed.com/files/centos6-scl-rh-eol.repo --output /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo
yum update -y && \
yum install --nogpgcheck  https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.el6.x86_64.core-avx2.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Install RASPA3 on Redhat-7 (AVX512)

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 with AVX512 support on Red Hat 7 systems. It first updates the system's package repositories by modifying yum configurations and then installs the necessary RPM package. Finally, it runs unit tests to verify the installation. This process requires root privileges.

```shell
sed -i -e "s|mirrorlist=|#mirrorlist=|g" /etc/yum.repos.d/*
sed -i -e "s|#baseurl=|baseurl=|g" /etc/yum.repos.d/*
sed -i -e "s|http://mirror.centos.org|https://vault.centos.org|g" /etc/yum.repos.d/*
yum update -y
yum install epel-release
yum install blas
yum install https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa-3.0.16-1.el7.x86_64.skylake-avx512.rpm
/usr/share/raspa3/tests/unit_tests_raspakit
```

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

### Run Monte Carlo Simulation with Python API

Source: https://context7.com/iraspa/raspa3/llms.txt

Demonstrates how to perform standard Monte Carlo simulations using the raspalib Python API. It covers loading force fields, defining molecule components, setting up the simulation box and system, and initiating the simulation. Requires a 'force_field.json' and 'methane.json' file.

```python
import raspalib

# Load force field parameters
ff = raspalib.ForceField("force_field.json")
ff.useCharge = False

# Define Monte Carlo move probabilities
mcmoves = raspalib.MCMoveProbabilities(translationProbability=1.0)

# Define molecule component
methane = raspalib.Component(
    componentId=0,
    forceField=ff,
    componentName="methane",
    fileName="methane.json",
    particleProbabilities=mcmoves,
)

# Create simulation box
box = raspalib.SimulationBox(30.0, 30.0, 30.0)

# Set up system
system = raspalib.System(
    systemId=0,
    externalTemperature=300.0,
    forceField=ff,
    components=[methane],
    initialNumberOfMolecules=[100],
    simulationBox=box,
    sampleMoviesEvery=10,
)

# Run Monte Carlo simulation
mc = raspalib.MonteCarlo(
    numberOfCycles=10000,
    numberOfInitializationCycles=1000,
    systems=[system],
    outputToFiles=True,
)
mc.run()
```

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

### Install RASPA3 on Debian 13 ARM64

Source: https://github.com/iraspa/raspa3/blob/main/docs/manual/installing_binary_packages.md

Installs RASPA3 on Debian 13 ARM64 by updating package lists, downloading the .deb package, and installing it. This method is specific to the arm64v8/debian:13 environment and requires wget.

```bash
apt update
apt install wget 
wget https://github.com/iRASPA/RASPA3/releases/download/v3.0.16/raspa_3.0.16_arm64_debian-13.deb
apt-get install ./raspa_3.0.16_arm64_debian-13.deb
/usr/share/raspa3/tests/unit_tests_raspakit
```