ChemCraft basics

            ChemCraft comprises a set of graphical tools for facilitating working with quantum-chemical calculations. It provides convenient utilities, which help to prepare new jobs for calculation and analyze computed results. Among the main functions of the program is visualization of output files produced by quantum-chemical packages. For this time, the main supported packages are GAMESS (US version) and Gaussian94-03.

1. Interface of ChemCraft.

ChemCraft for Gamess users

ChemCraft provides very detailed visualization of Gamess-US output files. The following data from the files can be presented graphically:

-         Atomic coordinates (corresponding to either all or symmetry unique atoms, if corresponding tables are presented in the file);

-         If bond order analysis is presented in the file, bonds from the file are shown on the image (otherwise, bonds are calculated by distance algorithm);

-         Energy gradient can be shown in the form of pointers (fig. 2);

-         Different atomic properties can be shown as labels on atoms: mulliken populations and charges, spin densities, valences;

-         Bond orders (as labels on bonds);

-         Molecular orbitals are visualized as isosurfaces or colored planes;

-         Vibrational modes can be animated or shown in the form of pointers (displacement vectors);

-         Dipole moment can be visualized as pointer.

The program provides structured presentation of output files. The file being read is divided into separate elements, such as individual geometries or vibrational modes. For each element all available data is extracted from the file: atomic coordinates, energy gradient, etc. All elements are presented in hierarchical list (see fig. 1). Clicking on the elements of the list automatically displays individual geometries or modes on the image and allows to visualize different properties. This interface provides reliable visualization of computational data, including non-standard types of calculation, incomplete calculations, etc. It also allows to visualize complicated files with multiple calculation jobs. For IRC-calculations, all geometries are divided into groups by IRC-steps. Besides graphical presentation of data, ChemCraft outlines most essential parts of output file and shows a brief “abstract” for each element of the file.  

2. Example of energy gradient visualization.

ChemCraft extracts molecular orbital coefficients together with basis set information from Gamess output files and renders molecular orbitals in the form of isodensity surfaces or  surfaces (planes, spheres) colored by density value (see fig. 3). ChemCraft provides some possibilities to perform operations with orbitals (e.g. to multiply one orbital by another). The formulas for building the orbitals (creation) are taken from the source code of program PLTORB. The calculation of density values is well-optimized. Note that if there are several tables of molecular orbital coefficients in the file, ChemCraft extracts each of them and allows them to be rendered (for instance, in MCSCF calculations either canonical or natural orbitals can be shown). Besides visualization of orbitals, ChemCraft provides a simple utility for automatic determination of atomic orbitals forming each molecular orbitals, which can be useful for analysis of the orbitals.

3. Examples of molecular orbitals visualization.

ChemCraft supports an interface to quickly create sections of Gamess input files with non-standard basis sets (fig. 4). The basis sets are extracted from their description, which can be obtained at PNNL's webpage (http://www.emsl.pnl.gov/forms/basisform.html). They can be also supplemented with additional gaussians specified by the user.

4. Basis set creation form.

ChemCraft for Gaussian users

We recommend to type #P GFINPUT POP(FULL, NBO) in Gaussian input files for visualization of Gaussian output files via ChemCraft. #P option enables extended printout; GFINPUT option enables printout of basis set information (description of primitives in basis set), while POP(FULL) enables printout of all molecular orbitals coefficients (POP(REGULAR) can be also used). The last two keywords allow ChemCraft to visualize molecular orbitals. POP(NBO) enables printout of Natural Bond Orbitals analysis, in which the bonds in molecule are computed. All these keywords are advisable but not necessary. As for Gamess files, different data from the file can be visualized: forces on nucleus (energy gradient), atomic charges, spin densities and other atomic properties, NBO bond properties (occupations, energies), normal modes, molecular orbitals (either Cartesian (6d, etc) or internal (5d) functions can be visualized). Coordinates in either standard or input/Z-matrix orientation can be read from the file and shown on the image (it is necessary for correct visualization of forces on nucleus, because they are usually printed in different orientation than other properties). For energy surface scan and IRC jobs, all geometries are grouped by scan steps. For each individual geometry or vibrational mode, most essential data is outlined and shown as an “abstract” (SCF energy, convergence criteria, etc). ChemCraft reads multi-step jobs and presents then as the list of several expanding nodes, each node representing individual job in the file.

In addition to Gaussian output files, ChemCraft can read Formatted Checkpoint files (.fch), extracting molecular structure and orbitals from the file. For visualization of molecular orbitals and other properties, Gaussian Cube files can be also read.

ChemCraft reads isotropic shielding values from Gaussian log files with NMR calculations (GIAO, CSGT). A simple utility for recounting them into chemical shifts and averaging within specified groups of atoms is provided.  

Working with other formats

Besides Gamess and Gaussian files, ChemCraft can read HyperChem files, files of MSI or PDB formats (these formats are not comprehensively supported), MolDraw and Priroda programs format, ADF ASCII TAPE41 files, and simple text files with Cartesian coordinates of atoms. ChemCraft provides an interface to import/export coordinates of atoms in text format through clipboard, which helps to use data from any types of calculations. Export of atomic coordinates into clipboard can be also useful for creating input files.  

ChemCraft comprises an utility for conversion of fractional coordinates, used in crystallographic measurements, into Cartesian, and conversely, using unit cell parameters (a,b, etc).

Constructing molecules

            ChemCraft supports a set of tools for constructing molecular structures, which can be used for preparing an initial guess for calculations and other purposes:

-         Constructing molecule from standard molecular fragments (radicals, etc). The possibility to supplement the set of fragments with custom ones and to copy/paste individual fragments via clipboard is provided;

-         Modifying any geometrical parameter in the molecule (distance, angle, dihedral). The modification can be accompanied with displacement of one atom, two atoms or selected group of atoms;

-         The possibility to “drag” an atom or a fragment on the molecule’s image or rotate a fragment using the mouse (fig. 5);

-         Iterative algorithm for applying an arbitrary set of geometrical parameters (fig. 6);  

-    An easy to use utility for applying a point group to the molecule.

5. Examples of “dragging” an atom or rotating a fragment along a bond.

When “dragging” an atom or performing other structural modifications, any geometrical parameter can be controlled on the image (see fig. 5). ChemCraft’s interface allows to easily alter the type of any atom or insert/remove a bond.

ChemCraft provides an utility for quick obtaining z-matrix. The z-matrix is build by clicking on atoms in molecule and specifying some additional information (fig. 7). Before using this utility one should first obtain the structure of molecule in Cartesian coordinates. All above-mentioned tools for constructing molecules can be used for this purpose.

6. Applying a specified set of geometrical parameters.

7. Visual construction of Z-matrix.

Molecule rendering possibilities

                 ChemCraft produces high-quality 32-bit pictures of molecules. It is designed as a program for creating publication-ready images, which does not require any additional modification. The pictures can be easily supplemented with captions on atoms/bonds and additional objects, such as labels and lines. ChemCraft comprises a collection of standard graphical schemes. Each scheme represents a set of parameters defining the appearance of the molecule: lighting parameters, colors and sizes of individual atoms and bonds, etc. Fig. 8 illustrates four schemes of the collection. ChemCraft allows the user to change the parameters of individual schemes or add his own schemes to the collection.

The graphical engine of ChemCraft does not require any graphical acceleration either as additional graphical libraries. It is well-optimized and provide high rendering speed even on outdated computers.  

8. Examples of rendering a molecule in different graphical

schemes and with different labels style.