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# Simulation of nanoparticles formation
# written by Eunseok Lee
# v1: Sep 01, 2017
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The program simulates the formation of silver nanoparticles. The number of nanoparticles is counted by classifying the structure of nanoparticles into single-crystal and icosahedral structures. For further information, refer to The Journal of Physical Chemistry C 122, 1333-1344 (2018).

To compile the code, move to 'src' directory and type 'make' at the prompt as follows.

>> make

The program was written in C and in parallel version using MPI. Hence, an MPI C-compiler should be pre-installed for compilation. The provided Makefile uses mpicc.

The compilation will build an executable, kmc_ccp_mpi. You can copy this executable to other location but two supplemental files (param.dat and ef_atoms) must be provided in the same directories the executable.

To run the executable, the following parameters must be provided.

1) Nparticles: the number of particles at initial step
2) Natoms_per_particle_ini: the number of atoms per particle at initial step
3) Natoms_instant_trans: the critical number of atoms for instantaneous coalescence
4) maxKMCstep: the maximum number of KMC steps
5) T: simulation temperature, corresponding to the synthesis temperature of nanoparticles
6) eb0: the activation energy barrier for atom's hopping on surface
7) dispfreq: the frequency of displaying and storing the results
8) store_range_to_finalstep: the results will be stored at every KMC step after KMC step of this parameter.

These parameters should be provided in param.dat and param.dat must be placed in the same directory as the executable.

In addition to the parameters in param.dat, the enthalpy of formation (Ef) of nanoparticles as a function of the number of atoms and the structure of particles must be provided. The included ef_atoms.dat is the parametrized Ef for the silver nanoparticles based on first-principles calculations - column 1 and 2 are for single crystal and icosahedral structure of silver nanoparticles. This ef_atoms.dat also need to be placed in the same directory as the executable.

The results from running the program will be stored in the directory, dir_result, (it will be created if not existing). The following list shows the results to be stored.

1) event_time.dat: the log of event and time at each KMC step
2) final_result.dat: row 1 - the last KMC step and the simulation time, row 2-end - the number of atoms (column 1) and structure type (column 2) of each particle
3) on_the_fly_data****.dat: row 1 - the current KMC step and the simulation time, row 2-end - the number of atoms (column 1) and structure type (column 2) of each particle
4) almost_final_data****.dat: row 1 - the current KMC step and the simulation time, row 2-end - the number of atoms (column 1) and structure type (column 2) of each particle

The file 1) contains the information as follows.
Col1&2,  the number of atoms and structure type of particle from which atoms transfer
Col3&4,  the number of atoms and structure type of particle to which atoms transfer
Col5&6,  the number of atoms and structure type of resultant particle
Col7,    the simulation time
Col8,    random number that was used for event selection
Col9&10, the ids of two coalescent particles

The files 2)-4) have the same format but store the information at different KMC steps.

The included example inputs, outputs, and .dat files are for silver nanoparticles in two structures (single-crystal vs. icosahedral) up to 12,000 atoms. However, thee program can be applied for other nanoparticle systems with bigger size and more kinds of structures if ef_atoms.dat is provided correctly.

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The current version doesn't account for the facet dependence of atom's hopping on particle surface. It will be implemented into the next version.