Toolkit-Help Files

Help for Toth's Materials Toolkit version 2.0

Goals:

The main goal of the Toolkit is to lower the learning barrier for the application of quantum methods to materials or chemistry problems. This is achieved through simple-to-use dialogs that control fully general and powerful tools performing modular tasks whose objective can be understood by any user. From users' feedback, we gather that this goal has been mostly achieved, with novices performing after a couple hours operations and manipulations that are conceptually simple to grasp but whose application to a given problem might challenge even experienced modelers.

Organization:

The Toolkit is a flexible, integrated, graphic, interactive and seamless environment of modular data-manipulation tools oriented towards materials characterization and modeling, with a strong emphasis on ab initio modeling. It does not attempt to duplicate widespread tools that are available elsewhere, like X-ray single-crystal or powder data reduction and refinement. It rather tries to complement them by putting at the users' fingertips powerful software automating often neglected areas of model creation, manipulation and use, such as twinning, clusters, surfaces, epitaxy and catalysis, including periodicity and symmetry manipulation in view of quantum modeling for physical or chemical properties.

In order to achieve the complementary goals of simplicity and completeness, the tools are laid out on two screens. The main screen, which groups the tools that are frequently used by the modeler, clearly separates in two frames the tools that operate on triperiodic objects from those that operate on finite objects. In-between the two frames are three directional tools that can be used to create a finite object from a triperiodic one or vice-versa.

A second screen, accessible through the "More tools" tool at the bottom of the main screen, offers a variety of tools, all extremely useful to the materials scientist, but not needed as frequently. The button "Back to modeling" brings back the main screen.

Input
The input to the Toolkit initially comes from its integrated CRYSTMET database environment currently containing ~93000 entries corresponding to an up-to-date compilation of crystal structure data for intermetallic compounds since 1915 augmented by the inorganic structures reported since 2000. After a Search, an entry is selected with Results. Clicking on the "Toolkit" tab, which is the rightmost tab in the same menu, transfers the selected entry data to the Toolkit and pops up a menu of available tools. Each tool operates on the selected entry as modified by the tools run previously. The current description can be viewed in text form by selecting "Edit entry" or in graphic form by selecting "PLOT", and running the tool. If wanted, the modifications can change all aspects of the selected entry, replacing for example a quartz structure entry by structure data for NaCl, typed in a few free-format keystrokes. Users can also enter their own structure data into the Toolkit as explained under the "ASCII structure editors" heading below. Data from ICSD, CSD etc.. database entries can easily be imported into the Edit screens of the Toolkit through cut-and-paste from corresponding database screens, or through importing the CIF output files those databases produce from any entry.

Hardware requirements
The implementation has been tested with Windows XP, NT and 2000 only, but it should also run with Windows 95 and 98. We do not know the minimum requirements, but the Toolkit runs nicely on a 128MB, 1.4GHz Pentium 4 with a Windows 2000 system, and even faster on a more recent Athlon with Windows XP.

Number crunching
The Toolkit prepares data files for quantum jobs. Those quantum jobs can be run and interpreted on the Windows modeling machine, but that would offer limited number-crunching power. It is more efficient to have one modeling machine that could be a PC laptop with a ~20GB hard drive, a CD-ROM drive, a USB port and Microsoft Office on one hand, and any number of number-crunching Windows or Linux serial or parallel machines with a 20GB hard drive, a USB port and corresponding ab initio executables. The ab initio executables are NOT distributed with the Toolkit. The user must get those executables from the ab initio package developers at their terms and conditions.

It is then most convenient to create a directory with the problem, including the command files to run it with the operating system of the target machine, and then move it to the number-crunching machine with a USB flash drive (or ftp). Execution is started by executing the RunJob.bat command file. After execution, the directory with the files created by the quantum software gets moved back to the modeling machine. Irrespective of whether execution was performed under Windows or Linux, results get analyzed by executing a Windows command file called PostProc.bat. This operation transfers the important results of the run to a plain-English JOBreport file that then serves as a condensed Toolkit archive for the run and as a record for writing papers.

Software requirements for plots__[CosmoPlayer tutorial]
Contrary to the database part, where plots are performed with GL, the Toolkit part plots with VRML2.1, allowing full-screen plots as an option, as well as the capture of the 3D plot scripts, e.g. for manual editing or later reference. The Toolkit expects to find the Internet Explorer executable stored as file \Program Files\Internet Explorer\IEXPLORE.exe. If it does not find it there, it will ask for its full path upon the first execution, and then remember it. As a viewer, we suggest Cosmo(TM) Player, a widespread VRML viewer that can be downloaded for no charge from URL http://cic.nist.gov/vrml/cosmoplayer.html or other sites. At CosmoPlayer installation time, the puzzling question about "unsupported software" should be answered YES, and "Internet Explorer" should be clicked on the next window. Besides that item, the installation of Cosmoplayer is usually straightforward.

Security settings for plots
The default settings of the current Internet Explorer allows users to view VRML plots on their own computer only after clicking on a dialog, which can become frustrating in the long run. To turn off this feature, click on "Tools", "Internet options", "Advanced", and tick the check box for the line "Allow active content to run in files on My Computer", as shown below. To implement the change, click on button "Apply", and then on "OK'.

Tools
Although the tools are grouped more-or-less logically under headings like "Crystallographic", "Materials", "Model Building" and "Ab-Initio" for clarity, they can be selected in pretty much any order dictated by the problem. Some tools like "Quantum Edit" include some data verification and should preferably, but not necessarily, be run before "ABINIT" for example.

The tools in the "Ab-initio" section are labeled with the names of well-known ab-initio packages. Those packages can be obtained from their respective developers at their own terms and conditions. The present Toolkit tools only prepare input files and command files for basic running of those packages, freeing the Toolkit user from all the tedium. This freedom allows the user to focus instead on the selection of options and flags that will efficiently produce accurate results for the problem at hand.

ASCII structure editors
The tools comprise three specialized ASCII editors and three specialized structure viewers, each with a different function. The crystallographic editor, which may have to handle disordered atoms and partial occupancy necessarily differs from the quantum editor which flags such features as inadequacies in the model. They both differ from the cluster editor which deals with finite, and therefore non-periodic objects in Cartesian axes.

Those editors use the left-justified mnemonics "SPGNAM=", "CELEDG=", "CELANG=" and "ATOM=" to indicate the information content of the line. Besides the mnemonic, those lines can be edited in free-format, with for example reordering of atoms through cut-and-paste, new atoms typed in, atoms deleted etc... The complete structure data in the edit dialog can be cut and pasted to a Notepad file for example and vice-versa, allowing in this way the easy transfer of numerical structure data to and from other data manipulation systems, with presumably limited editing each way. /p>

Only the "ATOM=" lines need explanations. The numbering scheme, the site multiplicity, the Wyckoff letter and the site symmetry are output values, derived on the fly. Upon reading, only the element, the atom coordinates [and optionally the occupancy in the crystallographic editor] are read in at Update time. The other fields can be omitted from the input or entered wrong with no harm. They will be output correctly upon the next cycle.

Quantum modeling tools

Open JOBreport__Tutorial

When the Toolkit submits a quantum job, it creates a job directory. In addition to data files and command files, that directory contains a JOBreport file. This file includes a paragraph with the specifics of the job submission parameters for later reference or publication. It also echoes the starting model in a format that is clear to the reader and suited for publication with minimal editing. That model can also be cut-and-pasted directly into a Toolkit Edit dialog.

After job execution, the PostProc.bat command file analyses the ab initio output files and extracts the total energy and the stress state of the material. It also extracts the crystallographic description for the optimized model. In case of an elastic job, the elastic tensor is extracted and printed together with its derived quantities. The JOBreport file is therefore the pivot archive for the job, especially when writing papers.

This tool can do four things:

Quantum Edit__Tutorial
For quantum calculations, atom disorder is not allowed and occupancies must be full. This editor checks that this is the case and flags corresponding problems or fixes them in the background, facilitating the task to edit out such imperfections.

Ball Plot__Tutorial__[CosmoPlayer tutorial]
This simple but powerful plot option is meant to be used in conjunction with the quantum edit tool. Clicking on an atom with the "Seek" Cosmoplayer option that looks like a crosshair on the left of the dashboard both magnifies the plot and places its center of rotation at the center of that atom, making it easy to read its label. The number part of the atom label corresponds to the sequence number at the beginning of the "ATOM=" printed record of the editor. Typing e.g. "Cl" instead of "Ni" in this record and depressing the UPDATE button changes the nature of that atom on the edit list, and later in the plot as well, including the ball color. For very crowded plots, the ball diameter can be made smaller. As labels scale with the ball diameter, they then require a larger magnification with the "Seek" option, but cause reduced interference with other atom labels. To identify graphically several atoms, the initial orientation and magnification can be recreated as many times as desired by clicking on "Viewpoint" at the complete left of the CosmoPlayer dashboard.

Supercells__Tutorial
This option provides two routes, a simple one where the supercell edges are integer multiples of conventional cell edges, and a general one where supercell edges are translations of the primitive lattice expressed in terms of the conventional cell. Both produce a P1 description of the atomic contents of the selected supercell. The result of a request for a 1x1x1 superstructure is then a transformation to P1 of the content of the conventional cell. The general supercell route checks both that the requested edges are indeed primitive lattice translations and that the requested transformation is right-handed. This option will refuse to implement left-handed transformations. There is more than one way to create the enantiomorph of a structure, but you can for example transform it to P1 with the "Supercells" tool, change the sign of all coordinates for all atoms with the "Edit" tool and then run the "Symmetry" tool.

Users should be careful with this option because implementing a 4x4x4 supercell (or 2 times a succession of 2x2x2 supercells) creates a P1 model with 64 times the number of atoms in the conventional cell. Options which involve calculation of distances in the background (crystallographic plot and quantum edit) can become slow. The Toolkit is geared towards quantum simulations that become extremely slow beyond 50 to 70 atoms per primitive cell. Models with no more than 200 or 250 atoms are manipulated in an eyeblink by the Toolkit tools, which fulfils this goal. The user is advised that, although Toolkit functions would work for much larger numbers of atoms, this may slow down the computing to impractical speeds or may exceed the capabilities of interactive edit screens provided by the operating system.

Surfaces__Tutorial
This tool is oriented towards quantum modeling of surfaces. A slice of the requested orientation and thickness (often slightly thicker) is prepared and described crystallographically in a reference system where a and b are the two shortest repeats in the crystallographic plane. The third repeat, perpendicular to the slab, is selected with a length equal to the sum of the actual slab thickness and the requested vacuum gap, measured from atom centre to atom centre. If the material is centrosymmetrical, the slice will also be created centrosymmetrical. The user is then expected to transform graphically this surface built using geometrical criteria into the actual desired surface of the solid. For this, the user alternatively identifies atoms with the ball plot tool and deletes them with the quantum edit tool until the desired surface is obtained. The nature of some atoms can then be changed and extra atoms or molecules can be added. See the Tutorial example for the preparation of a Pt/Ru surface.

Symmetry__Tutorial
This powerful tool establishes the conventional description of a structure model, including its shortest translations and its space group, within a distance tolerance in Angstroms. That distance tolerance applies to periodicities as well as atom positions. It keeps track of such things as axial transformations and change of origin. If applied to a P1 description in a supercell, it will find the cell and space group of the substructure. If applied to an alternate setting of a structure, it will reset it using the conventional cell and space group symbol.

Epitaxy__Tutorial
Epitaxy is about pairs of surfaces with approximately equal meshes or supermeshes with low multiplicity, which, when superposed with an adequate origin, establish bonds across the interface, leading to their adhesion. This utility allows to model just that in two steps.

In a first step an atom from the epitaxial surface is placed over one, two or three atoms of the substrate surface much in the same way as in step 1 of Adsorption. After that, the two surfaces can rotate about the common axis parallel to Z that this operation defines for the two surfaces.

In a second step, the "lattice match" is defined interactively in terms of the two meshes of the surface, not of the materials they are made of, that are to be brought into coincidence, possibly with application of a small strain. The a, b, gamma parameters of the two supermeshes are output to decide whether the lattice match is convincing or not.

Models built in this way can be processed ab-initio to study for example the adhesion of coatings. After an appropriate epitaxial model has been built, it can be input as the substrate model and a new epitaxial layer placed on top of it, leading to models for multilayer systems. Twinning by 180 deg rotation about the perpendicular to a lattice plane that is also the composition plane, can be viewed as a case of epitaxy of the substrate material on the substrate material and be easily modeled with this utility. A twin where the twin operation is a mirror plane can be processed as the epitaxy of a (-h-k-l) slab over an (hkl) slab. Together, those cases constitute the majority of known twins.

Eventually, a third modeling step can be used to create 3-periodical systems from multilayer models by specifying the bonding distances of an atom from the bottom of the substrate slab to atoms on the top of the multilayer model. This defines a third repeat for a crystalline multilayer system.

Prepare ab initio jobs

Each quantum package has its own spectrum of functionalities, many of which are not harnessed by the Toolkit. The Toolkit only uses the very basic functionalities that are common to all modern quantum packages: total energy calculation for a given model, minimization of total energy through optimization of just atom coordinates, and minimization of total energy through optimization of both cell parameters and atom coordinates. Combined, those functionalities are sufficient to process many problems ranging from structure optimization to catalysis through calculation of elastic data. Users wishing to use additional functionalities of a given package can easily do so by editing with Notepad the ASCII input files prepared by the Toolkit before submitting the job.

Single point__Tutorial
Single point is modeling jargon for the total energy calculation of a model with fixed cell data and fixed atom coordinates. This simple function can decide quickly about e.g. site preference by a given atom.

Atom coordinates__Tutorial
This is the key function for the extraction of the elastic tensor. This optimization often involves symmetry constraints on specific atom coordinates. Those constraints, which are applied to fractional atom coordinates referred to the selected primitive reference system, are worked out in the background by the Toolkit, thus relieving the user of a significant hurdle.

In the case of Catalysis problems, constrainment is used to compute the energy of stepped atom configurations where some atoms are allowed to relax while others are not. Within the Toolkit, this is implemented through the Catalysis dialog below.

Cell and coordinates__Tutorial
This is the key function for crystallographic modeling of materials. Failure to reproduce the experimental cell data within about 2% raises a very serious question mark about the validity of the structure model.

Elasticity__Tutorial
For full details about this easy-to-use but internally complex tool, see Phys. Rev. B63, 174103 (2001) and Phys. Rev. B65, 104104 (2002). This tool prepares the distorted models that are required for extraction of the independent elastic coefficients for the material. Those coefficients, and therefore the distortions to be quantum-optimized, depend on the point-group symmetry of the material. The tool prepares the input files and the command files that will execute the quantum optimizations. Those command files also activate the extraction of the strain and its resulting stress for each simulation. After execution of the last simulation, the independent stiffness-tensor coefficients are extracted by least-squares analysis of the accumulated stress/strain pairs. The complete least-squares analysis is available in a file called slasco.out.

The essential results are reimported to JOBreport.out, with display of the symbolic and numerical values of the constrained stiffness tensor. The Voigt, Reuss, and Hill values for equivalent isotropic bulk, shear and Young's moduli are extracted from them and printed. From those and the density, the speed of sound for the longitudinally and transversely polarized vibrations. Finally, the Debye temperature is extracted from the "average" speed of sound and printed.

Catalysis__Tutorial
Catalysis studies are performed by computing energy curves and energy barriers for non-equilibrium conformations of molecules adsorbed on the surface of catalysts, e.g. while the distance between the two atoms constituting an oxygen molecule is increased until their distance becomes such that no O=O bond still exists. Such studies are performed through the constrained optimization of the system. The dialog proposes to move up to two atoms in a concerted way while constraining the optimization of up to four atoms. For efficient constraining, a different selection of axes for the cell (performable with the "Supercells" tool) may be needed.

Ccp solid solutions__Tutorial
Many binary alloy systems are known to be cubic close-packed solid solutions. Some such solutions obey Vegard's law while others do not. The competing requirements of exploring the compositions with a sufficiently fine step within affordable computing time are best accommodated by retaining cubic symmetry for all compositions. Le Page, Bock and Rodgers (2006) show that only three schemes are feasible: a 4x4x4 supercell allows stepping compositions in 64ths in Fm-3m except 5, 11, 17, 23, 29, 35, 41, 47, 53 and 59/64th; a 3x3x3 supercell with space group Pm-3m allows stepping of compositions in 108ths except 2, 5, 103 and 106/108ths; a 4x4x4 supercell with Im-3m symmetry allows stepping compositions in 128ths except 2 and 126/128ths. The next solution involves 216ths and will remain computationally inaccessible for a while. The ccp solid-solution tool implements this strategy with both VASP and ABINIT. Its use is computation-intensive in 2005, but Moore's law should bring those computations within easy reach of state-of-the-art PCs by 2010.

Interfaced ab initio packages

Those tools create commented ab initio input files corresponding to the data being manipulated, i.e. as printed by the structure editors and as viewed with the viewers. These files also reflect the relatively simple interactive user directives on the submission form. Relieved in this way from most of the tedium of data file preparation, users can then focus on the best selection of pseudopotentials, flags and possibly stepping that will result in the most accurate answers to the problem. If the corresponding flexibility or sophistication is not proposed on the submission dialog, it can be entered either in the interactive window before file writing to disk, or later, with e.g. Notepad before batch-file job submission.

ABINIT
This tool is called ABISUB and creates commented input files for ABINIT versions 4.1.5, 4.2.4 or 4.3.3. The ABINIT program itself is open-source GNU software that can be downloaded from URL http://www.abinit.org/ABINIT/ in either source form or compiled form under the terms and conditions stated there. The same pages contain information about importing available pseupotentials or creating your own.

The ABISUB interface assumes the following directory structure:

The execution is then as follows:

The ".files" file generated by ABISUB points to existing pseudopotentials that are referenced on the ABINIT Web page and can be imported from Internet, for example from http://www.abinit.org/ABINIT/Psps/LDA_TM/lda.html. It is easy to edit the reference to the pseudopotential file of an element with e.g. Notepad, but it is crucial to retain the order of the reference to such files in the ".files" file because the ".in" file refers to pseudopotentials by their sequence number in ".files", with no safeguards.

VASP
This tool is called VASPSUB and produces input files for VASP versions 4.5 or 4.6. VASP is licensed software that can be bought under the terms and conditions detailed at http://cms.mpi.univie.ac.at/vasp/vasp/node14.html. It can be compiled with e.g. Portland's PGI workstation compiler for a variety of Intel and AMD-based platforms running Linux or Microsoft Windows. PGI Windows setups include a UNIX-like BASH shell in which users can generate Windows executables under UNIX makefile control.

Similar to ABINIT, a directory tree is created by the Toolkit for VASP. Pseudopotentials should be stored in subdirectories Ac, Ag, .. Zr of directory ~\VASP\pot. Each subdirectory contains up to 3 potentials for the element, each called POTCAR with a trailer (not an extension) that can be any of: &ltnone>, sv, pv, s, p, d, h, 2 or 3. Potentials named in this systematic way are presented for user selection at job creation time. It is important to adhere to this naming convention because the resulting POTCAR file in the job directory is an ordered concatenation of individual potentials for the elements. If the user wants to create this POTCAR file by hand, the order of the elements in the INCAR file created by VASPSUB is ALWAYS the order of decreasing Z values. Jobs are numbered automatically and appear in subdirectories ~\VASP\jobs. Provided that the directory structure is preserved, that the VASP directory contains a VASP executable and that potentials for all elements in the material were available, jobs can be started by double-clicking on the batch file.

Windows execution
The execution system, either Windows or Linux, is selectable from a button on the quantum engine submission form. Creation of a directory with the problem is dependent on the availability of appropriate potential files at the appropriate location at job creation time. Execution is dependent on the availability of an executable for the execution system, at the location where the full path in the RunJob.bat command file points. As explained above, this executable is obtainable from the ab initio package developers either as an executable or as sources with ready-to-be-adapted compilation makefiles.

Execution on the modeling machine__Tutorial
Provided that the above requirements are satisfied, starting the execution of the quantum program becomes just a matter of double-clicking the RunJob.bat command file in the job directory that was indicated on the form at job creation time. A DOS window appears, showing the single-line command in RunJob.bat. The DOS window disappears when the execution is finished or terminated, either by a crash or actively using the Task manager. The execution time is extremely dependent on the problem and the selected k-mesh. While a cell optimization for diamond requires a few seconds on a laptop, a single catalytic step on a Pt63Ag surface may require two weeks on an AMD Athlon64.

When the execution is finished (or even terminated), results are imported from complete or partial results files and deposited in the JobReport.OUT file by double-clicking on the PostProc.bat command file. Not only the data in JobReport then constitutes an archive that is often sufficient for publications, but it is also sufficient to restart from where it ended a job that would have either crashed or not fully converged.

Execution on a Windows machine other than the modeling machine __Tutorial
Only two things are required: an ab initio Windows executable in the location that is pointed at by the RunJob.bat batch file. Usually, that is:
C:\Program files\Toth\Materials Toolkit\VASP\vasp.exe for VASP or
C:\Program files\Toth\Materials Toolkit\ABINIT\abinis.exe for ABINIT.
Just create such a directory prior to the first execution, and deposit the executable in it together with any Fortran DLL is required for its execution. To find out which DLLs are required, double click on the executable. If any is required, a dialog will appear. You should import that file from the Windows machine you used for compilation. If it is impossible to use the path in RunJob.bat, you will have to edit each RunJob.bat file for the full or relative DOS path to the ab initio executable on the execution machine. The directory with the problem is most conveniently moved to the execution machine with a USB flash drive. Starting the execution of the quantum program is just a matter of double-clicking the RunJob.bat command file in the job directory that has been moved. A DOS window appears, showing the single-line command in RunJob.bat. The DOS window disappears when the execution is finished or terminated.

Linux execution__Tutorial
The item is conceptually similar to execution on a Windows machine that is not the modeling machine. At job creation time, a dialog requests the full path to the ab initio Linux executable. Usually, it will be something like:
$HOME/VASP/vasp for VASP and
$HOME/ABINIT/abinis for serial ABINIT.
The job directory is moved to the target machine with either a flash drive or ftp. The RunJob.bat is made executable through:
chmod 555 RunJob.bat . After that, the job is launched with the command:
./RunJob.bat
When the execution is complete, the whole directory is moved back to the modeling machine. Results are then interpreted by double-clicking on the batch file PostProc.bat. Users should not perform format changes when moving ASCII files between Windows and Linux. They should be moved as if they were binary files. The Toolkit and Internet Explorer are comfortable with both formats, but Windows or Linux may not be.

Cross checks

Distances & Angles__Tutorial
In addition to the fact that it operates on users' data, this tool incorporates more flexibility than the corresponding tool included with the "Browse" menu of CRYSTMET. For example, the Cartesian coordinates of the neighbours are optionally listed in the output, providing data for e.g. separate studies of anisotropic effects.

Crystal-chemical plot__Tutorial__[CosmoPlayer tutorial]
This tool is similar to the View tool in Browse, but it differs on the following points:

Requested plotting options like new colors for atoms remain requested as long as a different request is not formulated for the same atom. Options are remembered even if the coordinates are edited. However, changing the chemical nature of an atom, or reading in another entry, causes the plotting defaults to be entirely refreshed.

Powder Diffraction__Tutorial
Without incorporating all possible sophistications like anisotropic thermal motion for individual atoms or an extinction parameter, this Tool computes Debye-Scherrer powder patterns for a range of anticathodes, beam divergence and overall thermal motion. The available anticathode elements are: V, Cr, Mn, Fe, Co, Ni, Cu, Zn and Mo. The radiations available are: KA, KA1 and KA2 for each of the above elements. A radiation wavelength in Å can also be input in the radiation window for e.g. synchrotron work. The pattern is calculated in the range 5-165 degrees 2-theta and plotted for any 2-theta range comprised within the above 2-theta limits.

In combination with "Supercells", "Ball plot" and "Edit entry", this robust utility is extremely useful for modeling e.g. low-intensity reflections due to ordering or atom displacement. Possible superstructure models can be created at a high rate and the resulting effect on the powder pattern viewed interactively.

View property__Tutorial
Physical properties of crystals are numerically expressed by tensor coefficients, but they can be baffling. For example, it is easy to grasp that sound in isotropic matter can have either of two speeds, one for longitudinal waves and one for transverse waves. It is not so easy to grasp that sound in even cubic crystals can have either of three speeds, one for longitudinal waves and two for transverse waves except along three-fold, fourfold and sixfold symmetry axes where the two transverse speeds must coalesce.

Upon entry in the Toolkit, one of a half-dozen stored sets of elastic coefficients and density for reference materials gets picked at random and stored in the editable window. The user can then view radial plots for any of the three speeds of sound, or for the longitudinal modulus or the two principal shear moduli. Through editing, the user can enter tensor coefficients and density for any desired material and visualize the anisotropy of its elasticity or speed of sound. If wanted, the user interface also allows numerical output of values along specific Cartesian or crystallographic directions rather than radial plots.

Elasticity is a rank-4 physical property. It is our intention to program similar radial plots for visualizing rank-3 properties like piezoelectricity, rank-2 properties like thermal conductivity and rank-1 properties like pyroelectricity.

Cluster preparation__Tutorial
This tool aids in the preparation of raw clusters, i.e. of lumps made of those atoms whose centers are inside a limiting surface. The limiting surface can currently be a sphere, a cylinder or a cell-like box. Depending on the parameters in the request, the cylinder option can produce rods or slabs at will. Although powerful, this limited selection of options can of course only rarely produce in one shot the exact cluster the user has in mind, but it can produce one that contains it plus a few additional atoms. The user is then expected to identify and delete interactively those extra atoms, and/or coat the surface with adatoms, molecules etc..

The raw cluster is then crudely displayed as an assemblage of spheres with default color and uniform adjustable diameter. Upon return, the user is indicated the cluster formula and proposed the option to keep or not the cluster just viewed in a new directory. If the option is turned down, that directory is not created, allowing the interactive trial-and-error generation of many tentative models without cluttering the disk. If the option is accepted, a directory is created with a single file, called clus.dat written to it.

Editing of the cluster in view of e.g. its deposition on a surface can then be performed with the "Molecules" Tool.

Edit molecule__Tutorial
This tool allows either the assembling of simple molecules in view of their adsorption on a surface or simply the import of the Cartesian model of a molecule throug cut-and-paste followed by minor editing.

Creation of molecules starts with a methane molecule in memory. One can:

This list may sound limited, but it allows creation in a few keystrokes of the molecules most likely to be of interest for adsorption and catalysis like alkanes (branched or not, staggered or not), alcohols, CFCs, silicones etc.. For the time being, for compounds containing one cycle or polycycle, it is best to start from a Cartesian model of the cycle or polycycle pasted in the editable window, and use the utility to attach ligands to it.

Nanotubes__Tutorial
This tool prepares nanotubes based on their length, diameter and pitch. Nanotubes with even pitch must have a circumference close to a multiple of 3 times the C-C distance, while tubes with an odd pitch have a circumference that is close to an odd multiple of 3/2 C-C. Accordingly, the tool produces the tube with the requested pitch and the next possible diameter that is larger than the requested diameter.

After they have been created and viewed within the tool, the nanotubes can be edited for e.g. dangling C-C bonds at the tube edge, and then treated like molecules for adsorption on surfaces.

C₆₀__Tutorial
This tool prepares ideal C₆₀ molecules where all bonds have same length. Later, we intend to offer the option to differentiate between bonds involved in a pentagon and bonds not involved in a pentagon.

After they have been created and viewed within the tool, the C₆₀ molecules can be quantum-optimized, and then treated like any other molecule for adsorption on surfaces.

Cluster Diffraction__Tutorial
This tool operates on the ASCII clus.dat file, which is just made of the symbol of the element and Cartesian coordinates for each atom in the cluster, one atom per line. The cluster does not have to be a nanocrystal with internal repeats or have any symmetry. It can be glassy. One can liberally delete or add atoms, or even replace the clus.dat file prepared with the Toolkit by another file prepared externally, but it has to be called clus.dat.

The scattering pattern is computed through the exact Debye formula [P. Debye, Ann. Phys. (Leipzig) 46, 809-823 (1915)] and not as the convolution of discrete Bragg peaks with a Debye-Scherrer broadening function. The quantity in wrapup.xls is the "powder pattern" in electron**2 vs the reciprocal length R in Å**-1. This means that the result of this calculation for a scattering object made of a single free electron at a fixed point would be 1 across the whole range of the reciprocal length R. Through use of a spreadsheet, it is then easy to apply a global temperature factor and transform this result into a calculated pattern for a given radiation and a given instrument through transformation of reciprocal lengths into Bragg angles followed by application of the appropriate Lorentz-polarization factor for the instrument/detector combination.

Incorporate finite object

Periodic model from finite object__Tutorial
This tool produces a periodic model by placing a finite Cartesian object in an oversize cell of any shape. Such a periodic model will be accepted for optimization by the quantum software. Due to the large vacuum gap between the finite objects, they do not interact much. This means that quantum software designed for optimization of periodic objects can be persuaded in this way to optimize finite objects.

Adsorption__Tutorial
Quantum modeling of adsorption on a surface involves the combination of a surface and a finite object, both prepared or fetched before, and currently in memory. The molecule is then deposited on the surface in three steps through use of interactive graphics.

First, an atom of the molecule is positioned on top of the surface by specifying one, two or three distances to the same number of surface atoms. If only one distance is specified, the molecule atom is placed in apical position over that surface atom. If two distances are specified, the atom is placed in the "bridging plane", ie the plane parallel to the Z axis containing the two surface atoms. The solution outside the slab is of course selected. The coordinates of this molecule atom, which we designate the "peg atom" below, remain fixed in following steps.

In a second step, the vector from the "peg atom" to a second atom from the molecule (or cluster) gets aimed at a point in space defined in the same way as the first atom was defined. It does not matter whether this aim point is closer or farther than the atom. In the last step, the vector from the "peg atom" to the second atom becomes a pivot around which the molecule can rotate.

In a third and last step, the distance from a third atom in the molecule to an atom on the surface is specified. This problem can have two solutions, both outside the slab. Normally, the algorithm converges on the solution closest to the starting point. A button on the form allows to converge on the other solution.

This simple but amazingly powerful procedure allows to position molecules in relevant orientations on surfaces in three simple steps, each of which can be repeated as many times as wanted provided any following step is also repeated. Viewing the combined model puts it in memory, allowing one to temporarily exit the utility, run distances and angles, produce a crystal-chemical plot, save the model, twitch the molecule etc.. before returning to the adsorption utility with no loss of prior information. The solution of relatively easy problems like placing an atom or diatomic molecules at known bonding distances in ccp or hcp position over alloy surfaces becomes trivial, while the solution for a more complex problem of positioning eg methanol on a Pt-Ru surface or octane on clay in chemically sensible orientations takes a couple minutes, mostly spent gazing at atom numbers on 3-D plots. The preparation of a methanol molecule or an octane molecule takes about the same time.

Crystallographic tools

Structure editor__Tutorial__[Quantum Edit Tutorial]
This editor allows ASCII modification of any aspect of the structure description, space group, cell data, atom positions and chemical nature, as well as atom ordering. Cut-and-paste is enabled, allowing transfer of data to and from e.g. Notepad.

In addition to the "SPGNAM=", "CELEDG=", "CELANG=" and "ATOM=" mnemonics, there is an additional command allowing the selection of the origin at the point whose coordinates are specified. Typing a line with the left-justified content:
ORIGAT= 1/3 2/3 0.772
and depressing the "UPDATE" button performs the change. This command, which can be used freely in space group P1 where any point can be selected to be the origin, should be used with caution for all other space groups, precisely because that origin cannot be selected anywhere. If the space group is not P1, it is wise to save first the structure data as detailed under "Save/Fetch".

Atom coordinates are printed as decimal values, irrespective of whether they are constrained or not. Similarly, they can be input as decimal values or fractions, irrespective of whether they are constrained or not. Fraction numerators or denominators do not have to be integers. Engineering notation, e.g. 12.34E3 (or 43.21D-3) are understood. All digits typed are interpreted up to 64-bit accuracy.

Morphology__Tutorial
The first attempt at crystal morphology came from Ha&uumly (1784). In modern language, crystal faces were due to steps of different integer height, width or depth in the parallel stacking of tiny identical parallelepipedic blocks. This early pre-atomistic concept thus contained the seed for the cell and for Miller indices. In 1848, Bravais extended this concept by postulating that the crystal faces with large development corresponded to lattice planes containing a high density of nodes of a Bravais lattice. It is equivalent to state that they are the planes with largest d-spacings, again of the Bravais lattice. In spite of a few glaring exceptions, this law of observation was extremely successful, allowing for example the distinction at a glance of rhombohedral crystals from hexagonal ones and the description of minerals based on a Bravais lattice with axial ratios from goniometric measurements which rivaled in accuracy modern diffractometer measurements. Combined with crystal point-group symmetry, this law allowed a scientific and nearly modern development of mineralogy in the second half of the XIXth century, i.e. long before X-ray diffraction. In 1937, Donnay and Harker clarified Bravais' concept of the large d-spacings. By postulating that those d-spacings could not be those of glide-element extinctions in the space group, they reconciled a large proportion of the exceptions to Bravais' law with actual morphological observations on minerals.

MISSYM__Tutorial
It is the same tool as in Browse, operating on user structure data if desired.

Space Groups__Tutorial
This tool displays the general and special positions, including Wyckoff positions and site symmetry for all space group symbols in Chapter 4 of International Tables for Crystallography Vol. A (1983). This tool lists the equivalents in the same order as ITVA prints them. It also develops many symbols that are listed but not developed in ITVA.

Materials tools

Twin laws__Tutorial
This tool lists all lattice row/lattice plane pairs satisfying Mallard's law for binary twins within maximum obliquity and maximum twin index. The list includes all such possible twin laws by merohedry, reticular merohedry, pseudo merohedry and reticular pseudomerohedry.

Those Mallard conditions are necessary but not sufficient for the existence of a binary or ternary twin. Possible twins by 60 deg or 90 deg rotation are in the list of binary twins. The unusual twins by 120 deg rotation are listed among the binary twins with an index that is a multiple of 3. The converse is rarely true: few binary twins with an index that is a multiple of 3 are also possible twins by 120 degs rotation. The usually short list printed by this tool is then a big help for the interpretation of existing twins in terms of Mallard's law. For details, see: Journal of Applied Crystallography 35, 175-181 (2002) and also Chapter 3.3 in Volume D of International Tables for Crystallography (2003).

Voronoi polyhedra__Tutorial
Given a set of points, each with known (x_i,y_i) pairs of coordinates in 2 dimensions, Voronoi polygons are the locus of points closer to a given point from that set than to any other point from the same set. This powerful concept allows for example an analysis of simple cases of the traveling salesman problem. In a 3-D crystal, Voronoi polyhedra are the locus of points closer to a given atom than to any other atom. Their faces help define an objective list of neighbours of a given atom, or an objective integration volume for the extraction of an atomic property. They also provide an elegant and relatively straightforward non trial-and-error solution to the problem of finding the centres of the largest voids and the axes of the largest channels in a given crystal structure.

CBED index
This tool helps microscopists put a handle on the problem of identifying the crystalline material that produced a given convergent-beam electron diffraction (CBED) pattern. Usually, the microscopist has partial knowledge of elements that are actually present in stoichiometric amounts, absent elements and possibly present elements. A database search then discloses the known materials satisfying those chemical criteria. The lengths and the angle between two reciprocal vectors in the zero-order Laue zone (ZOLZ) are then measured, with estimation of their maximum error. Running the tool using those lengths, angle and tolerances criteria on materials in the selected entries produces an output.

Most of the times, that output indicates that no solution is possible because, unless maximum errors are unusually large, that combination of chemical and geometric criteria is amazingly stringent. When solutions exist, all the symmetry-independent ones are printed, and only those. They list the Miller indices for the two reflections, their calculated d-spacings (or reciprocal lengths as requested) and inter-vector angle. The short ZOLZ translations are printed with their lengths and inter-vector angles, as well as the indices and d-spacing of the shortest repeat ending in the first order Laue zone (FOLZ). This wealth of often difficult-to-guess information constitutes both the starting point of a careful diffraction and chemistry comparison of the sample with the entry, and a handle on the literature of the material.

Voids__Tutorial
Voids are all solutions to the problem of a sphere with a minimum diameter passing through at least 4 non-coplanar atom centres and containing no atom centre in its interior. They are plotted in 3-D over a range that is not necessarily identical to that of the crystal structure. Voids are the key to the stable positions of carbon in carbides or lithium in intercalated materials etc..

Channels__Tutorial
Channels in a crystal structure are the locus of points that are at a distance greater than a threshold from all atoms. Channels have to do with the path that small atoms like hydrogen or lithium can take in order to diffuse within a given material, and especially with the bottlenecks in that path. They are accordingly the key to phenomena like intercalation, hydrogen storage, diffusion etc..

Import/Export

Save/Fetch__Tutorial
Quantum modeling produces numerous intermediate or alternate models that the user may wish to keep. This tool allows to save up to 10 such models in memory or to write those models to a single disk file that can be recovered later, allowing a quick restart for a given problem. This feature can be a safety net against a disastrous request.

As it is easy to overwrite such a restart file, which is written to the "Storage" directory, the Toolkit creates a copy of the file under a unique name in the "avatars" subdirectory, where it cannot be accidentally overwritten. Those avatars are named in chronological order and never deleted automatically. It is sensible practice though to clean up the avatars directory once in a while, after making sure that all saved files are OK.

Read/Write CIF__Tutorial
Public-domain structure data can be imported from Internet, e.g. from Crystallography Open Database. Such CIF files can be imported directly into the Toolkit by cutting them from the browser window and pasting them into the edit window of this utility. After clicking "UPDATE", they can be viewed, manipulated and stored like any entry from CRYSTMET. Conversely, a "Write CIF" utility is supplied for users who need one.

Handy tools__Tutorial
This dialog groups in Swiss Army knife fashion a collection of handy little tools performing simple chores like selecting representatives with coordinates that obey the parametrization for the first position in the Wyckoff site. For example, Wyckoff position 4a in SG P2₁3 is parametrized x,x,x. Atom coordinates 0.6,0.9,0.1 belong to the 4a site but correspond to the third equivalent position -x,x+1/2,-x+1/2. This tool accordingly produces the more convincing coordinates 0.4,0.4,0.4 from the coordinates 0.6,0.9,0.1. Another tools brackets coordinates between a chosen minimum and that minimum + 1. Another tool orders atoms first on the criterion of decreasing atomic numbers, and then on increasing z coordinates. This tool is most useful for editing the atomic content of slabs created by the Surfaces tool. Another tool lets the user select the nicest-looking equivalent for each atom etc.

Internal Toolkit tools

Administration__Tutorial
Upon installation, the first Toolkit run will let the first user in with Administrator privileges, allowing that user to configure the Toolkit and play with it. If the installation is standard, i.e. with Toolkit software in directory "\Program Files\Toth\Materials Toolkit" of any hard disk attached to the computer, and the Internet Explorer executable as "\Program Files\Internet Explorer\IEXPLORE.exe", the Toolkit will not ask any questions and produces transparently configuration and restart files. If the installation is not standard, those questions are asked the first time only, with the Toolkit leaving its location in a bootstrap file in the Windows directory on the system disk.

Another file with users, called "config.tkt" is also created in Materials Toolkit. Upon the first execution, a super-user called "Administrator", password "Administrator", is transparently created. Upon subsequent executions, the user is then faced with a "Username/Password" dialog, which at first, can only be answered "Administrator".

Additional users with individual passwords can be created by the Administrator in existing directories of any disk unit attached to the computer. Only the top directory has to exist. Provided it has sufficient privilege, the Toolkit then creates a tree of subdirectories of that directory to store user data only. Only one copy of the software exists, and it is in the Materials Toolkit directory, but there is no limit to the number of users. This user scheme is meant as a way to compartment data into data areas and not as a safe way to protect data from fraudulent activities. In fact, this "user" concept can be a convenient way to compartment various projects of a single person and store them separately rather than require systematic bookkeeping.

User login/off__Tutorial
Answering the "Username/password" dialog with any valid user's login information ascribes a distinct data area to the user, always the same area that was ascribed by the Administrator at user creation time. All data created during the run will be deposited in the corresponding data tree.

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