![]() We would expect that conventions prefixed with "ISO" would be useful, Use of convention will normally require non-STMML semantics, and should be used withĬaution. It may be useful to create conventions with namespaces (e.g. So that a convention for molecule would by default extend to its bond and atom children. The convention is inherited by all the subelements, ![]() There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. Example - these are exactly equivalent representations It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_ The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info. The _atomIDArray_ attribute is mandatory. It also cannot be checked as easily by schema- and schematron validation. This is NOT suitable for complexType atom children such as _atomParity_. This requires all arrays to be of identical lengths with explicit values for all atoms in every array. of _elementTypeArrayType_ under _atomArray_. This gives the greatest flexibility but is the most verbose. There are two strategies: Create individual _atom_ elements under _atomArray_ (in any order). A child of _molecule_ and contains _atom_ information. Mikolaj, that is a complex question that you should pursue with a vigorous lit search.A container for a list of atoms. Do you think, that crystallography structure is good (experimental) reference point for comparing with computed results? My software (Gaussian) does geom optimization in gas phase, crystallography geometry is in solid state, i’m confused if it is good idea to compare those 2 results. I am also doing some studies on comparing geometries obtained using different basis set. Always nice to have corroboration!Īnyway, it’s a really nice program and maybe you should ask for it from him if you need a raw comparison of two geometries. This is a much more elegant and simple program than mine, but doesn’t allow you to see which parts in the geometry are actually wrong (or ignore unimportant errors), which I need to be able to do.Īnyway, his and my program made the same (qualitative) results about which level of theory and basis set I should be using for my calculations. Julius Su, in the Goddard lab at Caltech, emailed me a copy of his C++ program that first rotates two molecules (rigidly), then calculates the root-mean-squared distances between all the atoms. %Now copy the three columns of absolute differences and paste into %This separates the three types of values by when in the column theyĭiff_bondlengths=ĭiff_angles= %Need the transform of the result of the above loop: %This loop corrects for angles larger than 180: These read in the variables at the end of theĭifference_uncorr=abs(reference-calculation) Use the z-matrix that Molden outputs (e.g. %correct these far negative angles to their corresponding positive angles %Molden defines a dihedral of -190 as +170. %original crystal structure z-matrix to the calculation. %dihedrals are defined the same (I was having trouble comparing the %compare the starting structure to the optimized structure (before and %Because I used the crystal structure as the starting z-matrix, I can %Z-matrix Editor in Molden, click “US” and “Gaussian,” then save the %at a file this prevents Molden from rewriting the z-matrix. Be sure to use “molden -A ‘structure'” when looking ![]() %differences in the bond lengths, angles, and dihedrals directly from a %different levels of theory or different basis sets. %This program compares the z-matrices for multiple QC calculations using Let me know if you find errors or if you find ways to make it better. If you want to check it out or try it, I’ll post it below. For instance, I remove the dihedrals that don’t really matter (some light atoms and some artificially inflated dihedral errors) and just look at the mean and standard deviation for different method/basis set combinations. Then I just throw those outputs into SigmaPlot or Excel ( ew!) or whatever and do the error analysis I want. It just imports the variables from a Molden z-matrix and takes the absolute difference in them, sorting my type. It’s not perfect, I’m pretty happy with it. It took me a while to get what I wanted out of Molden and make MatLab spit out the right set of numbers, but I finally got it to do what I wanted (I think). So I wrote a MatLab M-file that outputs the absolute differences in the bond lengths, angles, and dihedrals between two structures. But I couldn’t find one, and I wanted control over how to compare the structures (for instance, I wanted to be able to ignore the errors in the dihedrals for light atoms). Now, there’s probably already a program out there that will compare the optimized structures of quantum-chemistry calculations (e.g. Comparing gaussian structures at 12:53 am | sam | everyday science, software ![]()
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