Hi, > See the attached POSCAR and POTCAR. When opened in Avogadro, the cell > is displayed as shown in the screenshot. The atoms are given in > fractional coordinates -- there should not be any outside the cell! At > a glance, it seems Avogadro is calling GetCellVectors, which > constructs the vectors from GetOrthoMatrix, which ignores the "real" > vectors, instead rebuilding them from a,b,c, etc.
Why is it that the lattice parameters are not equivalent to the orthonormalization matrix in the first place ?? Does that mean that the matrix is not a true orthonormalization matrix (B, with a standard convention of a parellel to Ox, b in the OxOy plane and c deduced to make a direct reference frame), but rather a UB matrix, where U is an orientation matrix ? Removing the a,b,c in favor of a matrix seems somewhat strange to me - in crystallography the reference values always are the lattice parameters - the rest should be derived. If the atoms are rotated, there should be an orientation matrix, so that the orthonormal coordinates are given by: (xyz)_ortho = U B (xyz)_frac -- Vincent Favre-Nicolin CEA / INAC http://inac.cea.fr Université Joseph Fourier http://www.ujf-grenoble.fr http://vincefn.net ObjCryst & Fox : http://objcryst.sourceforge.net ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
