README.md

Morphokinetics

This is Morphokinetics software developed at the Donostia International Physics Center. Morphokinetics is a software to simulate kinetics Monte Carlo (KMC) processes. It can simulate etching, CVD growing and catalysis processes. To specify simulation mode "parameters" file must be present in the current working directory (more details in {@link Parser}).

You can either compile the code automatically using ant or manually invoking javac.

Papers using Morphokinetics

• Multiscale Analysis of Phase Transformations in Self-Assembled Layers of 4,4′-Biphenyl Dicarboxylic Acid on the Ag(001) Surface, ACS Nano, 2020. https://doi.org/10.1021/acsnano.0c02491
• Dominant contributions to the apparent activation energy in two-dimensional submonolayer growth: Comparison between Cu/Ni(111) and Ni/Cu(111), Journal of Physics: Condensed Matter, 2020. https://doi.org/10.1088/1361-648X/ab9b50
• Microscopic Origin of the Apparent Activation Energy in Diffusion-Mediated Monolayer Growth of Two-Dimensional Materials, The Journal of Physical Chemistry C, 2017. https://doi.org/10.1021/acs.jpcc.7b05794
• A microscopic perspective on heterogeneous catalysis, arVix, 2018. https://arxiv.org/abs/1812.11398

ANT (simpler and faster)

Next two steps should be enough to run Morphokinetics:

ant jar 
java -jar dist/morphokinetics.jar

MANUAL COMPILATION

Alternatively, you can use javac commands to compile the code. Instructions to compile the code manually:

cd src/
javac -source 8 -target 8 -encoding "UTF-8" -cp .:../lib/json-20141113.jar:../lib/j3dcore.jar:../lib/j3dutils.jar:../lib/jtransforms-2.4.jar:../lib/vecmath.jar:../lib/colt.jar graphicInterfaces/growth/GrowthKmcFrame.java main/PcConfigurator.java main/Morphokinetics.java
mkdir ../perimeterData
cp ../scripts/perimeterStatistics/*txt ../perimeterData/

Run

Run the code: In order to be able do a simulation with Morphokinetics, a file called "parameter" have to exits in the current directory. If there is not any file, default simulation is carried out.

java -Xss100M -cp  .:../lib/json-20141113.jar:../lib/j3dcore.jar:../lib/j3dutils.jar:../lib/jtransforms-2.4.jar:../lib/vecmath.jar:../lib/colt.jar main.Morphokinetics

Jar

Beforehand creating a jar file, java code must be compiled (with the above instruction). To manually create a portable JAR file, follow this instructions:

cd src
jar cfm morphokinetics.jar manifest.txt . ../lib/jtransforms-2.4.jar ../lib/j3dcore.jar  ../lib/j3dutils.jar ../lib/vecmath.jar ../lib/colt.jar  ../lib/json-20141113.jar

If you want to move the JAR file to another folder, you have to also move the lib, perimeterData and resources/png/ folders.

TESTING

ant test

or

cd test/
javac -encoding "UTF-8" -cp .:../lib/colt.jar:../lib/json-20141113.jar:../lib/j3dcore.jar:../lib/j3dutils.jar:../lib/jtransforms-2.4.jar:../lib/vecmath.jar:../lib/junit-4.13.jar:../src TestRunner.java

java -cp .:../lib/json-20141113.jar:../lib/j3dcore.jar:../lib/j3dutils.jar:../lib/jtransforms-2.4.jar:../lib/vecmath.jar:../lib/junit-4.13.jar:../lib/hamcrest-core-1.3.jar:../src TestRunner

PROFILING

To profile this code within NetBeans 8.1 next line has to be added:

-XX:+UseLinuxPosixThreadCPUClocks -agentpath:$NETBEANS_DIR/profiler/lib/deployed/jdk16/linux-amd64/libprofilerinterface.so=$NETBEANS_DIR/profiler/lib,5140

TUTORIAL

A tutorial is provided in the following link: https://github.com/dipc-cc/Morphokinetics/wiki/User-guide#5-examples-parameters-files