A utility tool is provided to analyze the difference between
two geometrical coordinates in two xyz files which store
Cartesian coordinates. The following three analyses are supported:
a root mean square of deviation (RMSD) between two Cartesian
coordinates defined by
% gcc diff_geo.c -lm -o diff_geoWhen the compile is completed normally, then you can find an executable file 'diff_geo' in the directory 'source'. Please copy the executable file to the directory 'work'.
usage: ./diff_geo file1.xyz file2.xyz -d rmsd option -d rmsd a root mean square of deviation -d md a mean deviation -d mdbl 2.2 a mean deviation between bond lengths, 2.2 (Ang) means a cutoff bond length which can be taken into account in the calculationIf you want to know RMSD between two Cartesian coordinates, run as follows:
% ./diff_geo file1.xyz file2.xyz -d rmsdThe calculated result appears in the standard output (your display). Also, a xsf file 'dgeo_vec.xsf' is generated in the XCrySDen format, which stores the difference between Cartesian coordinates of each atom in a vector form. This file can be visualized using 'DisplayForces' in XCrySDen. When MDBL is calculated, please give a cutoff bond length (Å). Bond lengths below the cutoff bond length are taken into account for the RMSD calculation. Figure 44 shows vectors corresponding to the deviation of atomic coordinates in optimized structures and the difference of total charge density between a neutral and one electron doped glycine molecule. We see that the large structural change seems to take place together with the large charge deviation. This example illustrates that the tool would be useful when we want to know how the structure is changed by the charge doping and the electric field.