My PhD take home qualifying exam. 2 Computational projects.
========= Basin Hopping:
Main is in basinhop.cpp, as is the Monte Carlo step. The total energy calculation and minimization methods (A&B) are in the localMin.cpp file. The structure 'state' stores all relevant information for a cluster including: -Atomic Coordinates -Center of mass -Energy -Storage space for calcuations
Powell's method was taken from Numerical Recipes this includes the files: f1dim.c linmin.c nr.h nrutil.c nrutil.h powell.c mnbrak.c
Several python scripts were written for visualization the results and making graphs to answer posted questions. The script viz.py takes as its only arguement the location of a log file, e.g.:
./viz.py ../basinhopping_data/finalstate_N104_A_0.dat.
Which prints total energy and plots the lowest energy atomic structure with bonded neighbors highlighted by a line. The others can be run as follows
./viz12.py [#atoms] //prints energies and rmsd(i)
./viz3.py [#atoms] //plots phase space
./viz4.py [#atoms] //plots density of states
./viz5.py -no args- //plots min-rmsd(i) vs average rmsd-neighbor