moleKool

various solutions for molecular dynamics and related fields using Kotlin Multiplatform

sample code for above screenshop

fun main() {

    // your world
    val env = Environment()

    // read monkey stl
    val data = STL(STL::class.java.classLoader.getResource("monkey.stl")!!.readBytes())
    val monkeyFace = TriangleMeshClosedSurface(data.triangles)

    // sample inside monkey
    Grid3D(20, 20, 20)
        .points.spanInAllDirections()
        .filter { it isInside monkeyFace }
        .map { it.rotateX(90.toRad()) }
        .map { it.copy(z = -it.z) }
        .map { atomOf(AtomicMass.Fe, it) }
        .forEach { env.add(it) }

    // update box based on monkey face
    env.boundingBox = with(env.enclosingBox) {
        val edgeLen = listOf(xBoundary.length, yBoundary.length, zBoundary.length).max() * 1.5
        Box(-edgeLen to edgeLen, -edgeLen to edgeLen, -edgeLen to edgeLen)
    }

    // sphere to cut out from
    val sphere = Sphere(Point(0, 0, 0), 0.2 * env.enclosingBox.xBoundary.length)

    // a famous grid
    Grid2D(50, 50)
        .points
        .spanInAllDirections()
        .usingCrystal(Crystal.graphene.armchair(1.0))
        .flatMap { listOf(it, it.rotateZ(5.6.toRad())) }
        .filter { it isInside env.boundingBox!! }
        .filter { it isOutside sphere }
        .map { atomOf(AtomicMass.H, it) }
        .forEach { env.add(it) }

    // visualize
    KoolVisualizer()
        .withDefaultConfig()
        .addPlugin(BoxViewerPlugin(env.enclosingBox))
        .init()
        .addEnvironment(env)
        .runAndWaitUntilExit()

}

run this for yourself from

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Modules

Name	Description	Platforms
molekool-core	base computation for manipulation
molekool-visual	minimal embedded visualization tool based on kool-engine
molekool-bind	basic integrations with third party tools experimental

Install

Gradle

To use this library in your Gradle project, add the following to your build.gradle(.kts) file:

dependencies {
    // Various generators
    implementation("io.github.nort3x:molekool-core:$molekoolVersion")
    // Using Kool engine to visualize environments
    implementation("io.github.nort3x:molekool-visual:$molekoolVersion")
    // Basic bindings to various MD third-party tools (experimental)
    implementation("io.github.nort3x:molekool-bind:$molekoolVersion")
}

Replace $molekoolVersion with the latest version of the library.

Maven

To use this library in your Maven project, add the following to your pom.xml file:

<dependencies>
    <!-- Various generators -->
    <dependency>
        <groupId>io.github.nort3x</groupId>
        <artifactId>molekool-core</artifactId>
        <version>VERSION</version>
    </dependency>
    <!-- Using Kool engine to visualize environments -->
    <dependency>
        <groupId>io.github.nort3x</groupId>
        <artifactId>molekool-visual</artifactId>
        <version>VERSION</version>
    </dependency>
    <!-- Basic bindings to various MD third-party tools (experimental) -->
    <dependency>
        <groupId>io.github.nort3x</groupId>
        <artifactId>molekool-bind</artifactId>
        <version>VERSION</version>
    </dependency>
</dependencies>

Replace VERSION with the latest version of the library.