XMD is a program for performing molecular dynamic simulations on metals and some ceramics materials at the atomic scale. It models atomic energies and dynamics using user defined pair potentialsl, EAM potentials and some hard coded potentials.
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# 2007-07-31 8:25 am Finish calc_strain() # 2007-08-04 11:09 am (x) Code matrix.eigen subroutine. # (x) Use SingularMarix exception in matrix3.py. # (x) Convert R to axis,angle # (x) Calculate overall fit. # 2007-08-05 (x) Write command line interface. # (x) Convert R to axis polar angles. # (x) Make no header option (-h) # (x) Make efficient neighbor function. # (x) Apply boundary conditions # (x) Use boundary conditions in nlist. # (x) Adjusted jcell calculation. # (x) Adjust rsq calculation. # (x) Read 'box x x x' from file # (x) Apply box to calc_strain() # 2007-08-12 # (x) Read cor files. # (_) Read rcv files. # (_) Test large lattice (1000+) with shift # boundary. # 2007-09-01 Added option to apply_boundary() called origin, # which translates input particles so that # coordinates of origin become 0,0,0. # # Using this option causes the calculated # displacement to not include the bulk motion # of the atoms. Currently, we do not use it. # 2009-04-14 - When taking sqrt() of evalues, set negative # arguments to 0, because typically these # negative values are due to roundoff-error, this # prevents taking the sqrt() of negative values. # - The read_any_file() returned a tuple of coordx3 # tuples, changed it to a tuple of coordx3 lists so that # their values change change when they are wrapped for # repeating boundary conditions. # - Updated test output file strain.out.orig to account # for sign changes (-0.0 went to 0.0) due to sqrt() # change above.
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