Offers molecular dynamics solutions, including core computations, visualization, and experimental integrations with third-party tools. Facilitates environment manipulation and visualization using Kool engine.
various solutions for molecular dynamics and related fields using Kotlin Multiplatform
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.
To use this library in your Maven project, add the following to your pom.xml file:
Replace VERSION with the latest version of the library.
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
| 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 | |
<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>
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