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

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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

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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

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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

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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