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build codecov DOI Maven Central

nanojava

Java library for descriptor calculation for (nano)materials.

The library can be used either as a JAR file or through Docker. It can also either print the calculated descriptors to the terminal or write them to a file using TSV format (tab-separated file).

It is also available on DockerHub (https://hub.docker.com/r/aammar/nano-java) for direct usage without compilation or Docker build!!

Build with Docker

  1. Make sure that Docker is installed and ready to go (https://docs.docker.com/)

  2. Clone the current repository

  3. Enter the repository with "cd" command

    cd nanojava

  4. Run the following command:

    docker build -t nanojava .

  5. Now, you can use the library through Docker as in the Usage section (use "docker run nanojava" instead of "docker run aammar/nano-java" in this case).

Build with maven

If you do not have Docker or if it is an overhead for your use case, you can bundle nanojava library as a standalone jar file.

  1. Make sure that JDK 8 and Maven 3.x are installed and ready to go

  2. Clone the current repository

  3. Enter the repository with "cd" command

    cd nanojava

  4. Run the following command:

    mvn package

  5. Now, you will have the standalone jar file in the "target" folder named:

    nanojava-1.2.0-SNAPSHOT-jar-with-dependencies.jar

  6. The JAR file is used in the same way as the Docker image in the "Usage" section with replacing:

    "docker run" with "java -jar nanojava-1.2.0-SNAPSHOT-jar-with-dependencies.jar"

    and make sure you provide the absolute paths for your files in this case.

Usage

NOTE: descriptor names are the class names of the descriptors available under the package io.github.egonw.nanojava.descriptor:

  • ParticleSizeDescriptor
  • MetalElementMassDescriptor
  • ZetaPotentialDescriptor
  • MetalAtomCountDescriptor
  • MetalGroupDescriptor
  • EnergyBandDescriptor
  • HeatOfFormationMopac2012Descriptor
  • MolecularWeightDescriptor
  • MetalPeriodDescriptor
  • HeatOfFormationDescriptor
  • OxygenAtomCountDescriptor

Example 1: Calculate a single descriptor for a nano material formula provided through command line, and output the results to the terminal.

docker run aammar/nano-java -d OxygenAtomCountDescriptor -m Al2O3

Output:

Nano Material OxygenAtomCountDescriptor
Al2O3 3

Example 2: Calculate all available descriptors in nanojava library for a nano material formula provided through command line, and output the results to the terminal.

docker run aammar/nano-java -d all -m Al2O3

Example 3: Calculate a single descriptor for all nano materials provided as an XML file (you can find an example of that in this repository "materials.xml") , and output the results to the terminal. Pay attention to the volume mapping between the folder on your PC where the XML file resides and the a path of your choice inside the Docker container!!

docker run -v XML_PATH_ON_YOUR_PC:/data aammar/nano-java -d OxygenAtomCountDescriptor -f /data/materials.xml

Output:

Nano Material OxygenAtomCountDescriptor
Al2O3 3
CeO2 2
CoO 1
Co3O4 4
Cr2O3 3
CuO 1
Fe2O3 3
Fe3O4 4
Gd2O3 3
HfO2 2
In2O3 3

Example 4: Calculate all available descriptors in nanojava library for all nano materials provided as an XML file (you can find an example of that in this repository "materials.xml") , and output the results to the terminal. Pay attention to the volume mapping between the folder on your PC where the XML file resides and the a path of your choice inside the Docker container!!

docker run -v XML_PATH_ON_YOUR_PC:/data aammar/nano-java -d all -f /data/materials.xml

Example 5: If you want to write the descriptors calculation results as a TSV file, add the argument "-o OUTPUT_FILE_ABSOLUTE_PATH". For the following examples, the output file path will be used "/data/descriptors.tsv"

That results the following commands for the previous examples:

docker run aammar/nano-java -d OxygenAtomCountDescriptor -m Al2O3 -o /data/descriptors.tsv

docker run aammar/nano-java -d all -m Al2O3 -o /data/descriptors.tsv

docker run -v XML_PATH_ON_YOUR_PC:/data aammar/nano-java -d OxygenAtomCountDescriptor -f /data/materials.xml -o /data/descriptors.tsv

docker run -v XML_PATH_ON_YOUR_PC:/data aammar/nano-java -d all -f /data/materials.xml -o /data/descriptors.tsv