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YAeHMOP - Yale Department of Chemistry

1. 17 If a molecular calculation is being done the data necessary to construct an FMO interaction diagram will be written to a separate output file 3 22 FCO optional Perform Fragment Crystal Orbital analysis The lines following this keyword are identical to those for the FMO keyword 3 23 Average Properties optional Do an average properties calculation for the system This consists of e Generating a total DOS curve e Finding Ey the Fermi energy e Determining the average overlap population and reduced over lap population matrices within the unit cell if the printing option for these is set e Finding average orbital occupations and net charges e Reporting the average values of any COOPSs specified see key word COOP e Show average occupations of Fragment MO s if FMO analysis is being done NOTE if you are doing an average properties calculation on an extended system you must provide a set of K points see keyword K Points Specifying an average properties calculation for a molecular prob lem will allow the generation of MOOP Molecular Orbital Overlap Population diagrams and the RCM Reduced Charge Matrix as for extended syatems 18 3 24 No Total DOS optional Turns off printing of the total DOS into the output file This option can be used to conserve disk space when the total DOS isn t going to be looked at Note If this keyword is specified neither total DOS nor pro jected DOS calc
2. definitions of the COOPS type which contribi contrib2 abc Atom 1 1 2 000 Atom 1 2 1 010 20 Note If you are doing a COOP calculation on a high symmetry system where you are using K points within the irreducible wedge of the first Brillouin zone it is very important that you average all symmetry equivalent bonds 11 If you do not do so your results may be inaccurate 3 30 Printing optional This keyword controls what information is printed into the output file In most cases this also controls what things the program ac tually calculates For example if the user doesn t request that the reduced overlap population matrix be printed then there s no rea son to calculate it We have tried to make the program smart about what it calculates but there may be problems here Please let us know if you see strange behavior This keyword is different from all the others in that the program expects it to be followed by another list of keywords In fact any keyword following Printing is assumed to be controlling what gets printed The way to tell bind that you are done giving it printing options is to either let it hit the end of the file i e to have Print ing as the last keyword in your input file or to put the keyword End_Print at the end of the printing options Each of the printing keywords is described below e Distance Print the distance matrix e Overlap Population Print the Mulliken overlap population ma t
3. 15 Crystal Spec say Dee 1 1 1000 alpha beta gamma 90 90 90 3 4 Electrons potentially required The line following this keyword should have the number of valence electrons in the molecule or unit cell for an extended system 3 5 Charge potentially required The line following this keyword should have the charge on the molecule or unit cell for an extended system Either the Charge or Electrons keywords must appear in the input file 3 6 Alternate Occups This keyword is for looking at the effects of changing the number of electrons in the unit cell upon the position of the Fermi level the average energy and orbital occupations This is a far more efficient way of probing these changes than rerunning the calculation with alternate electron numbers 11 On the line following the keyword the number of alternate occu pations num_occups should be given The next line contains the step that is to be taken between occupations For example the following input fragment would result in the program doing a calculation with 5 electrons then printing out the Fermi level average energy net charges and orbital occupations for 4 8 4 6 4 4 4 2 and 4 0 electrons per unit cell Electrons 5 Alternate Occup num_occups the step 3 7 Parameters optional NOTE If this keyword appears in the file it must follow the Geom etry keyword in the input file There should be a line following this keyword for each ty
4. For example the following section would print out the entire overlap population matrix and all the net charges at every step into the main output file and then print the overlap population between orbitals 13 and 23 into the Walsh output file start dealing with printing options Print Overlap Population Net charges this is a Walsh printing value Overlap Population Walsh Orbital 13 23 End_Print 3 31 MO Print optional This keyword controls creation of a MO file This can be read in by viewkel to produce iso surface plots of molecular and crystal orbitals The first line following the keyword contains the number of MO s to be printed num_MOs The next num_MOs lines contain the numbers of the individual MO s that should be printed If you are doing an extended calculation the MO s will be printed at each k point If you are doing a Walsh diagram the MO s will be printed at each step along the reaction coordinate 23 3 32 Orbital Occupations optional This section is used to change the occupations of molecular orbitals This is primarily useful for trying to model open shell systems or molecules in excited states The first line following the keyword should contain the number of orbital occupations to change num_occups The next num_occups lines consist of an integer specifying the orbital whose occupation should be changed and a real number specifying what the new oc cupation should be For example
5. overlap chem cornell edu 8080 Citing YAeHMOP If you publish calculations and or figures that you produce using either bind or viewkel we d appreciate it if you d cite the program in your references section At this point there are no print publi cations describing YAeHMOP so there s no obvious citation to give Please use the following citation for bind G A Landrum and W V Glassey bind ver 3 0 bind is distributed as part of the YAeHMOP extended Hiickel molecular orbital package and is freely available on the WWW at http sourceforge net projects yaehmop and the following citation for viewkel G A Landrum viewkel ver 3 0 viewkel is distributed as part of the YAeHMOP extended Hiickel molecular orbital package and is freely available on the WWW at http sourceforge net projects yaehmop 54 Specifying your geometry with a Z Matrix A Z Matrix is a convenient way to specify the geometry of a molecule or crystal in terms of bond lengths bond angles and di hedral angles There are several styles of Z matrix used in various programs bind uses a format similar to that used in Gaussian This is intended to be a brief introduction to how a Z matrix works If you already know how to use a Z matrix here s all you need to know about the implementation in bind e The first atom is put at the origin e The second atom is put along the Z axis e The third atom is in the XZ plane e Dihedrals are evalua
6. Determine the center of mass and principle axes of the molecule and transform the atoms into the principle axis frame This can allow the program to find more symmetry elements Note Principle axes are only found if the meschach library was linked with bind If you do not have meschach then the program will just translate the molecule into the center of mass frame before finding symmetry elements 3 14 Zeta optional Toggles self consistent variation of radial exponents This is under development and if you don t know what it means you probably shouldn t be using it 3 15 Nonweighted optional Use the non weighted H form 6 By default the weighted H form is used in order to reduce problems arising from counter intuitive orbital mixing gasp 7 8 3 16 The Constant optional Allows replacement of the value K used in evaluating the H el ements The next line should contain the new value for K By default K 1 75 3 17 Zero Overlap optional Set some elements of the overlap matrix to zero The next line should contain the number of different types of overlap being set to zero num_to_zero The next num_to_zero lines should consist of type contribl contrib2 which type should be either Atom or Orbital to indicate which type of overlap is being zeroed If which is set to Intercell then overlaps between contribl and contrib2 between cells will be zeroed If 15 which is set to Intracell then the overlap
7. e example status status information about the job e example out the main output file Contains energies occu pations average properties etc e example walsh the values of variables which were printed out along each step of a reaction coordinate e example band the information needed by viewkel for con structing a band diagram e example DOS generated by fit_dos the information needed by viewkel to generate DOS curves e example COOP generated by fit_coop the information needed by viewkel to generate COOP curves e example WALSH generated by fit_walsh the information needed by viewkel to generate Walsh diagrams e example FMO contains the information needed by viewkel to generate FMO diagrams e example MO contains the information needed by viewkel to generate MO pictures e example DMAT generated when the dump distance matrix key word is used contains the information needed by cooperate to automatically generate COOP specifications for crystals Those Damn Bugs One thing to be aware of is that YAeHMOP is under develop ment so there are some features built into it which may or may not be permanent We ve tried to indicate wherever possible when things are not finished or are in the testing stages 32 10 What is a bug There are two possible reasons for a calculation to screw up a bug in the program or a user error Please make sure that your input file is correct before you send in a bug
8. 16 8 Walsh button window a aoa a a a 48 16 9 Band button window ooo a aa 49 16 10Properties button window 49 16 11Graph button window oaoa aa sa eke ad 50 17 Using viewkel from a Tek terminal 50 What is YAeHMOP and why should I use it YAeHMOP isa group of programs for performing extended Hiickel calculations 1 2 and analyzing and visualizing the results The programs bind and viewkel form the core of the package 1 bind bind is the program which performs the actual extended Hiickel calculations It can be used to perform calculations on both isolated molecules and extended systems of 1 2 or 3 dimensions bind is an almost complete rewrite of the program new3 and is written almost entirely in C the routines for evaluating overlap ma trix elements and diagonalizing the Hamiltonian matrix from new3 remain Because of the fact that all memory used in the program is allocated dynamically there are no restrictions on the number of atoms K points or orbitals which can be used this isn t totally true there is a limit of 20 user defined atom types The only lim itation is the amount of memory that your computer has and the length of time which you are willing to wait for the run to finish Because of the fact that bind is written to be easy to maintain and understand we have not spent a lot of time trying to make it fast This isn t to say that it s slow but it certainly could be faster The input f
9. Grigoriy Vajenine who pointed out that I 51 should be evaluating the radial parts of wavefunctions in atomic units and Kazunari Yoshizawa In addition the students and au ditors of Chemistry 798 in the fall of 1994 and the spring of 1995 acted as unwitting beta testers and uncovered a few problems I never would have found Roald Hoffmann my advisor was very support ive of my efforts and never chastised me for how much time I was devoting to this project Of course he did accuse the program of being vaporware but this should nip that criticism in the bud Thanks Roald Edgar M ller has provided a number of helpful suggestions as well as some Fortran code which served as the template for the code to deal with crystallographic coordinates Edgar also came up with a consistent parameter set for the entire periodic table This parameter set is distributed with this release of the program as muller_parms dat Paul Kogerler has also provided suggestions for features which are now integrated and has even agreed to add some features himself Expect to see these in a future release The function used to diagonalize the inertia tensor as part of the symmetry analysis is taken from the meschach library This is a freely available package of functions written in C for working with matrices meschach was written by David Stewart and Zbigniew Leyk at the Australian National University If you want to use this function in your own code please obt
10. actual character of the wavefunction with respect to the symmetry operation not just a symmetric anti symmetric label It is important to realize that the results of this method of displaying the results of symmetry analysis can give results which are at first confusing for degenerate orbitals If you are looking at the charac ters of a set of degerate orbitals and trying to compare them to the characters given in a character table it is very important that you sum the characters of each of the members of the degenerate set When a reaction coordinate is being followed bind first gener ates all the geometries along the coordinate and determines the sym metry elements which they possess The only symmetry elements 26 reported are those which are conserved along the entire distortion This means that you don t have to worry about moving from high to low symmetry geometries or vice versa Note It is possible that loss of symmetry elements will lead to problems in constructing a Walsh diagram In these cases fit_walsh will warn you If the dia gram as constructed is incorrect you can either change your reaction coordinate to not include geometries with problematic degeneracies or edit the WALSH file by hand to fix it This is explained in more detail below in the section on fitting programs YAeHMOP on the Macintosh As of version 1 2 of YAeHMOP there is a Macintosh port of everything At the moment the Mac version only runs on Powe
11. average contributions make the sum of the individual contributions add up to 1 0 To add contributions make each of the contributions 1 0 In general it is a good idea to add projected DOS curves rather than average them 3 29 COOP optional Do a Crystal Orbital Overlap or Hamilton Population analysis 2 5 9 10 Note the COOP option results in a Molecular Or bital Overlap or Hamilton Population analysis when the molecular keyword is specified The line following the keyword has the total number of COOPs specified not just the number of different types tot_num_COOPs The next tot_num_COOPs lines should contain the definitions of the COOPs themselves in the form type which contribl contrib2 a b c type should be either Atom Orbital or FMO to indicate whether the COOP between atoms orbitals or fragment MO s is being projected Setting type to H Atom H Orbital or H FMO will generate the corre sponding Hamilton population between atoms orbitals or fragment MO s respectively which is the number of the COOP Multiple COOPs with the same value of which will be averaged The COOP reported is between contribl in the unit cell and contrib2 in a cell defined by the vector a b c For example the following sample section will average the COOP between atoms 1 and 2 in the unit cell with that between atom 2 in the unit cell and atom 1 in the adjacent cell in the b direction COOP the total number of lines here 2
12. data to label the X axis This is particularly useful for integrated DOS data There are problems with using this option for COOP and COD data These will be fixed in the next version of the program e Fermi E allows you to change the value of the Fermi energy For DOS and COOP data the value of the Fermi energy is stored in the output file so viewkel will know the proper value 16 11 Graph button window This controls displays of graph data There are no new buttons for control of graph data 17 Using viewkel from a Tek terminal When you are sitting at a Tek terminal Tek 4014 compatible viewkel will use a command line driven interface and will use the graphics capabilities of the terminal to display graphs You can get help in the Tek version of the program by typing help or at the prompt This will list all the commands along with a brief description Since this is available I will not describe all the features here Though it can be convenient the Tek interface does have some limitations e You can not look at either molecules or MO s e Not all features of each type of graph are modifiable e Once a new graph has been opened previously opened and displayed graphs cannot be modified e Due to limitations of the technology the graph you see onscreen is not nearly as similar to what comes out of the printer as in the X windows version of viewkel Note It has been a long time since I have worked on th
13. number of electrons in the system any special information needed the ranges of Walsh variables any special pa rameters you may want to use etc and any printing options that you want to set Here s a minimal input file example called foo bind the name of the job A silly example a square of H atoms specification that this is a molecular problem Molecular the geometry geometry 4 1 H 0 0 0 0 0 0 2 H 1 0 0 0 0 0 3 H 1 0 1 0 0 0 4 H 0 0 1 0 0 0 The number of electrons Electrons 4 printing options PRINT Overlap Population Reduced overlap population charge matrix wavefunction end_print The contents of this file will be explained later To run the file execute the following command bind foo bind This will create two output files foo bind status has some status information foo bind out has all the results in it That s it If you had done a Walsh diagram or an average properties cal culation then there are some utility programs that need to be run to get the data in shape to be displayed These will be discussed a later The data and results are now ready to be displayed using viewkel or your favorite plotting program The input file Like many other programs the input file for bind is based on keywords This allows the file to be broken into logical blocks and makes the format for constructing the file a little less rigid Each keyword is described below Note that the input routine
14. the left side e Right Fragment Controls which fragment is displayed on the right side of the interaction diagram Set this to zero or 1 to not show a fragment on the right side e Y min This is the minimum energy displayed e Y max This is the maximum energy displayed e Level Width The width horizontal length of the levels drawn e Thickness The thickness of the lines used to draw the levels e Electron len The length of the lines used to represent elec trons e Y tics Toggles the display of tic marks on the y axis e Frame Toggles the display of a frame around the interaction diagram e Show Title Toggles display of the title of the graph if one has been entered e Title Allows you to enter a new title to be displayed across the top of the graph e Main Label Allows you to enter a new label for the central set of levels those of the full molecule e Frag n Label There will be one of these buttons for each fragment used in the calculation These are used to enter labels to be displayed under each fragment displayed 16 8 Walsh button window This window is used to control the display of Walsh diagrams The coordinate used to label the x axis is specified when fit_walsh is run e MO s Toggles display of the MO levels e Total E Toggles display of the total energy 48 e X tics Toggles display of X tics e MO tics Toggles display of Y axis tic marks for the energies of the MO s display
15. values of the second variable are specified explicitly Walsh the number of variables and number of steps 25 use Auto Walsh for the first variable 1 0 2 0 100 0 100 1 100 2 100 3 100 4 Please note that while there are two Walsh variables they are varied simultaneously There is not at this point a capability to vary the Walsh variables independently in order to automatically generate a multi dimensional potential energy surface 3 11 Symmetry optional Find and report all the symmetry elements possessed by the molecule The characters of all wave functions with respect to these operations will also be reported Note As is explained in the section of this manual on symmetry elements bind does not actually find all symmetry elements It only finds those which are aligned with the Cartesian axes You can increase the number of symmetry elements which the program finds by making sure that it align with the axes in a reasonable manner 3 12 Symm Tol optional Allows the user to adjust the value of the tolerance used for de termining whether or not symmetry elements are present in the molecule The next line should contain the new value of symm_tol If the position of an atom after a symmetry operation differs from that of an atom before the symmetry operation is applied by 14 less than symm_tol A then the two atoms are considered to be equivalent under the symmetry operation 3 13 Principle Axes optional
16. 12 1 3112 7 2 90 0 4112 7 2 90 0 3 90 0 5112 7 2 90 0 3 180 0 6112 7 2 90 0 3 270 0 7H21 1 1109 5 3 0 0 8 H 2 1 1 1 109 5 3 120 0 9H21 1 1 109 5 3 240 0 Let s look at the first few entries in more detail 1 The first atom is a Bi and it s placed at the origin Cartesian 0 0 0 2 Atom two is a C It s placed on the Z axis 2 1 A away from atom 1 Cartesian 0 0 2 1 56 3 Atom three is an I It s placed 2 7 A away from atom 1 and the angle between atoms 3 1 2 in the XZ plane is 90 0 degrees Cartesian 2 7 0 0 Atom four is an I It s placed 2 7 A away from atom 1 the angle 4 1 2 is 90 degrees This angle puts us in the XY plane At this point we know that atom 4 lies on a circle in the XY plane with radius 2 7 A The dihedral 4 1 2 3 90 degrees tells us where on the circle we are This dihedral is particularly easy to see if we look down the bond 2 1 which is looking down the Z axis the angle between the bond 3 1 and the bond 4 1 is 90 degrees So atom 4 lies on the Y axis Taking the right handedness of dihedrals into account we know that atom 4 lies on the negative Y axis Cartesian 0 2 7 0 Atom five is an I It s 2 7 A away from atom 1 making an angle of 90 degrees with 2 and a dihedral of 180 with 3 This puts us on the negative X axis Cartesian 2 7 0 0 If you find the handedness of dihedrals confusing just play around with a couple of molecules defined using Z matrices y
17. Numerous bug fixes e Much improved MO plotting Including Jorgenson and Salem or CACAO style plots that can be rotated in real time to find the optimal viewing angle Also included are contour plots of MOs e Fragment Crystal Orbital analysis a new interpretive tool for crystalline systems e A new keyword allowing diagonalization of the hamiltonian without including the overlap matrix e viewkel now provides distances angles and dihedral angles between selected atoms in molecules e There are several new options for display of molecules in viewkel Including tube bonds and pseudo 3D crosses What s new in version 1 2 Support for using LAPACK routines to diagonalize the matri ces e A version for Power Macs I have more faith in the MO drawings now The normalization constants were right and now that I evaluate them in atomic units the pictures look right too Thanks Grisha e More juicy raisins in every bite e Other things that escape me at the moment Overview of how a calculation is done So you ve come up with a cool problem or it was assigned in class and you want to do an extended Hiickel calculation using YAeHMOP The goal of this section is to get you familiar with the basic process for moving from initial idea to final graphs and pictures The first step is to set up your input file Basically the input file contains a specification of the geometry of your molecule or ex tended system the
18. Turning on all the printing options can lead to a huge output file if you have a lot of K points or steps in a Walsh diagram Placing the keyword Transpose after a printing option for a matrix will result in the transpose of the matrix being printed This feature has been introduced to appease those who think that the default way of printing is stupid To facilitate the construction of graphs of various quantities over lap populations net charges etc along a reaction coordinate there is a second option that can be used with printing options If you place the keyword Walsh on the same line as a printing option then you can select a particular quantity to monitor along the Walsh di agram These values are put into a separate file If you are using an 22 input file named foo bind then the values of these quantities would be put into foo bind walsh To use this feature place Walsh after your printing keyword then on the next line put the following three pieces of information type contribl contrib2 Once again type is one of Atom Orbital or FMO and contribl and contrib2 refer to particular atoms orbitals or fragment MO s NOTE there are certain combinations of these Walsh printing options which do not make sense For example specifying that you want to monitor the reduced overlap population between 2 orbitals is nonsensical The program will notice this and complain so just think a bit before you start printing everything out
19. Yet Another Extended Htickel Molecular Orbital Package YAeHMOP Version 3 0 User Manual Greg Landrum and Wingfield Glassey July 27 2006 Contents 1 bind 2 viewkel 3 Keywords 3 1 3 2 3 3 3 4 3 9 3 6 3 7 3 8 3 9 3 10 3 11 3 12 3 13 3 14 3 15 3 16 Geometry required o Lattice mandatory for extended systems Crystal Spec required for use of crystallographic co dinat s of A Eats anges a GIB A ene ia le A ald Electrons potentially required Charge potentially required Alternate ccups 22 02 aaa ek hoe es Parameters optional oo 44 4 844 wwe Molecular mandatory for molecular calculations Just Geom optional f46e 44 4 wae ode PR Walsh optional So o od sete sia ah esas onl ad aha alae a Symmetry optional 2 2 crate 2d woe 2 ee Symm Tol optional soo et ee A ee Principle Axes optional 2 2 n p aai Saws amp ee Zeta optional e a Videcace git ga Os 8d eat A BRO 8 Nonweighted optional The Constant optional 25 425 2 2s 3 17 Zero Overlap optional 3 4 2 56 2 4 2 44 eee a 15 3 18 Nearest Neighbor Contact optional 16 3 19 K Points mandatory for Average Properties calcula tions on extended systems 0 0 16 3 20 Band optional uc 2 Sova a de ee eS 16 3 21 FMO optional i bo ah aa i a oe ae PR 17 3 22 RCO optional ero a os Soa lt in ie od ves weld as ala
20. age Numerous options for displaying molecules and MO surfaces Automatic generation of input files for rayshade a freeware raytracing program This can be used to get extra gratuitous color 3D plots The official Roald Hoffmann seal of approval on the way the output looks NOTE this feature is still under development Both bind and viewkel were written to be as easy to port to other flavors of UNIX as possible This is one of the reasons why viewkel doesn t use any of the snazzy user interface libraries which are available What s new in version 3 0 Quite a few new features have been added to YAeHMOP and one or two problems have gone away The YAeHMOP development team has also increased in size as of this release so please use the version 3 0 citations when publish ing results generated with YAeHMOP Thanks Additions to bind include e f orbitals at last e COOP s in a fragment molecular orbital FMO basis e Hamilton population analysis a tool for total energy partition ing built on the orbital atom and fmo COOP options offered in YAeHMOP 3 4 5 also the known bugs section of the those damn bugs chapter of the version 2 0 manual has vanished so there are absolutely NO bugs left in YAeHMOP What s new in version 2 0 A bunch of stuff has been added to this version This is almost certainly the last non bug fix release of the programs until I gradu ate e
21. ailable on your machine because of the demands of the average properties cal culation the band structure calculation will take much much longer than it has too You are better off if you do the two runs sepa rately It s also a good idea to do the band structure once then comment out the band part of the input file That way if you add projected DOS s or COOPs later you won t accidentally redo the band structure which won t have changed Using viewkel viewkel is written to display results on either X Windows dis plays or Tektronix terminals The program will automatically de tect whether or not X Windows are available and will use them if they are Printing is handled by generating Postscript files which can then be directly printed or included in documents The actual graphics calls used to draw the data are all included in a separate file so it should be reasonably easy to port the program to other graphics systems 35 Since the use of the X and Tek versions of viewkel is different they will be dealt with separately Note I haven t put much work into the command line Tek tronix version of viewkel recently so it doesn t have a lot of the features mentioned below and some of the features it purportedly does have may not work 16 Using viewkel in X When you start viewkel under X it will open 2 windows The first and larger window the graphics window is used to display output The second window the main butt
22. ain a copy of the entire library I want to go ahead and take the chance to thank David Stewart for making this library freely available At this point I can t help but interject a piece of propaganda free software is top quality stuff find out about it and use it The basis of the code to calculate solid isosurfaces was taken from the article An Implicit Surface Polygonalizer by Jules Bloo menthal in Graphics Gems IV Academic Press 1994 If you do graphics taking a look at these books is a really good idea The algorithm used to do hidden line removal in the Jorgenson and Salem style MO plots is a slight modification of that used in Jorgenson s PSI88 program Because PSI88 is written in Fortran none of the code from the program was used I just used PSI88 to figure out the algorithm The enhanced postscript code is adapted from the file enhpost trm for gnuplot version 3 5 The original code was written by David Den 52 holm and Matt Heffron both of whom have given me permission to distribute this adaptation The code used to contour data both for FCO and MO plots is adapted from that used in gnuplot version 3 5 I love borrowing code from gnuplot The original code was written by Gershom Elber and this modification is distributed with his permission Using the LAPACK diagonalizer bind can now use a function from the LAPACK library zhegv to diagonalize the hamiltonian This diagonalizer is significantly faster than t
23. automatically along each of these symmetry lines The program will produce an additional output file containing 16 the information needed by viewkel to plot the band structure If your input file is called foo bind then the band file will be called foo bind band For example the following segment will generate a band diagram with symmetry lines containing 40 K points running from I to X to M and then back to IP Band the number of points along each line 40 the number of special points 4 Gamma 0 0 0 0 0 0 X 0 5 0 0 0 0 M 0 5 0 5 0 0 Gamma 0 0 0 0 0 0 3 21 FMO optional Perform Fragment Molecular Orbital analysis The next line should contain the number of fragments num_FMO_frags Note that num_FMO_frags should be gt 1 There is no upper limit on the number of fragments The next line consists of a comma delimited list of the number of electrons in each fragment The following num_FMO_frags lines consist of comma delimited lists of the numbers of the atoms in each fragment In the specification of atoms for each fragment you can use a hyphen dash to indicate groups of sequentially numbered atoms For example the following segment will generate 2 fragments the first fragment containing atoms 1 2 3 4 5 and 8 and the second fragment containing atoms 6 and 7 FMO the number of fragments 2 the number of electrons in each fragment 12 2 the lists of atoms contained in each fragment 1 5 8 6 7
24. c needs to be developed to warn the user when lobes of the MO might have been missed I have some ideas here but I m still working on them When the surface is first read in the user is prompted for values used in constructing the radial lookup table This is a table of values for the radial part of the wavefunctions Use of this lookup table results in a tremendous gain in speed The default values should be fine for almost any calculations One important note about both solid and contour isosurfaces viewkel does not deal with the imaginary part of wavefunctions yet I will put this in later until then limit yourself to pure real wave functions You ll always be okay with molecular wavefunctions but general k points for extended systems will be problematic Well with my salvo of disclaimers fired here are the explanations of the buttons in the MO options window e Surface Toggles display of the solid isosurface once it has been calculated e Molecule Toggles display of the molecule e Isosurface This is the isosurface value that is displayed on screen This is applies to both solid and contour isosurfaces e Voxel Size The spacing of the grid used to calculate the solid surface e Search Rad The size of the cube around each atom used to provide starting points for the solid surface search e Slop Used to determine how far past the end of the molecule s bounding box the solid isosurface grid extends 44 e E
25. cribed above is switched on MO contour plots are real three dimensional objects just like the molecule they are associated with and will rotate translate and scale in three dimensions along with the molecule This feature seems gratuitous but it s kind of fun to play with and it was a lot easier to implement than having the contour be a fixed 2D object It can even be useful if you rotate the molecule so that you are looking at the edge of the contour plot you can see exactly where it cuts through your molecule e Contour Surf Evaluates an MO contour plot e Invert Phase This toggle allows you to invert the phase of the MO displayed on screen This can be helpful when you want to visually compare two similar MO s that have opposite phases just invert the phase of one of them e Hidden Toggles the use of the hidden line removal algorithm for contour plots and MO surfaces When Hidden is on you 46 should no longer be able to see through the MO isosurface However this can make it take a lot longer to draw plots so you may want to have Hidden turned off when you are rotating your molecule The hidden line removal does not work particu larly well for normal contour plots but viewkel will still allow you to use it if you wish Note there are still some boundary conditions that get screwed up sometimes in the hidden line re moval If a plot looks bad rotate the molecule a small amount that should clear things up Ver
26. d in an Ap pendix Font Size Allows specification of the standard text font size in points The default is 12 Scale Allows scaling of the whole output This does not affect the size of the text font to change that use the Font Size button Note None of the changes made in this window will be visible on screen 16 5 The molecule button window This is the window which is popped up when a molecule is opened It is used to control the viewing options for the molecule being displayed Hydrogens Toggles drawing of hydrogens Dummies Toggles drawing of dummy atoms Center When this is pressed the molecule is moved so that it is centered at the center of mass Note since viewkel doesn t actually know what the masses of your atoms are the center of mass is actually calculated assuming all the atoms have the same mass The resulting positioning is usually still right Hide Atoms Allows you to make it so that some atoms in the molecule aren t displayed You will be prompted for a list of atoms to hide Enter a comma delimited list You can use the dash hyphen just as it was used in the FMO specification For example the following list will hide atoms 1 23 and 99 1 23 99 Show Atoms Allows you to unhide atoms you may have hidden before Axes Toggles display of a set of axes on screen Al Outlines Toggles the drawing of dark circles around the atoms being displayed Shading Toggles shading of t
27. down shift while hitting any of these keys results in a larger rotation step In versions of viewkel greater than or equal to 2 0 you can also rotate molecules in rotate mode by left clicking and dragging in the graphics window This is easier to do than it is to explain so try it out Note Rotations only apply to displayed molecules and MO s not to graphs because that would be silly Translate the control keys translate the active object i and k move along the y axis j and 1 move along x and p and move along z Holding down shift while hitting any of these keys results in a larger step Center the control keys translate the center of the active object i and k move along the y axis j and move along x and p and move along z Holding down shift while hitting any of these keys results in a larger step This is different from the Translate mode for molecules and MO surfaces in that the molecule and the point that the camera used to construct the perspective view looks at are move simulta neously This allows the molecule to be moved about the screen without the view changing In versions of viewkel greater than or equal to 2 0 you can also change the center of your molecule by left clicking in the graphics window When you do this the center of the molecule will be moved to where you clicked If you then drag the molecule will move Note For anything other than molecules and MO surfaces Translate and Center are equiva
28. e E 18 3 23 Average Properties optional 18 3 24 No Total DOS optional 02 19 3 25 Dump Overlap optional 2 2 e2i 423 8 ees 19 3 26 Dump Hamil optional ge ety SS eg 19 3 27 Dump Dist optional 3 1 4 5 2522 4 alate 19 3 28 Projected DOS optional ooa aaa 19 3 29 COOP optional at ace wtp a 20 3 30 Printing optional a a 21 3 31 MO Print optional o a aa 23 3 32 Orbital Occupations optional 24 3 33 Charge Iteration optional 24 3 34 Sparsify optional sao kate Barats e246 eo eats 25 3 35 Just Average E optional o o aaa 25 3 36 Just Matrices optional o oa a aaa 25 3 37 Diagwo optional ooa a 25 4 A couple of disclaimers 27 5 Using bind on a Macintosh 28 6 The fitting programs 28 7 General Mac hints 28 8 sub_dos and add_dos 31 9 cooperate 31 10 What is a bug 33 11 What to do if you find a bug 33 12 Choosing how many overlaps to use 34 13 Choosing the number of k points to use 34 14 Choosing the number of points in band structures 35 15 Calculations on big systems 35 16 Using viewkel in X 36 16 1 Special keys in viewkel 36 16 2 General use of buttons 37 16 3 The main button window 37 16 4 The PS options button window AO 16 5 The molecule button window 41 16 6 The MO button window 43 16 7 FMO button window ooo a aa 47
29. e Tek tronix version of viewkel so it s not guaranteed to work at all 50 Using the enhanced Postscript features in viewkel It is now possible to include superscripts subscripts different fonts and all kinds of other wacky stuff in output from viewkel This is accomplished using an adaptation of the enhpost terminal type from gnuplot If you are familiar with this then you don t have to read this section everything is exactly the same here except that you can t do rotated text To get a superscript use the symbol only holds for one char acter unless a group of characters is enclosed in squiggly brackets and so the line X710 comes out looking like X10 while the line X 10 gives XM To get a subscript use the symbol _ behaves in the same manner as To change font put a backslashed version of the name of the font inside squiggly brackets with the text to be changed For example look at Symbol G now gives look at I now There are some other features of the enhpost drivers but these are the most important A word or two from Greg some acknowledgements The members of the Hoffmann group were invaluable in the devel opment and testing of these programs They provided moral sup port bug reports featur suggestions and esthetic criticisms that were invaluable The group members most involved were Hugh Genin Norman Goldberg Kimberly Lawler Qiang Liu Erika Mer schrod Udo Radius
30. ed on the left side of the diagram e Tot E tics Toggles display of Y axis tic marks for the total energy curve on the right side of the diagram e X Legend Allows you to enter a legend to be displayed under the X axis e Y Legend Allows you to enter a legend to be displayed beside the Y axis 16 9 Band button window Controls the display of band structure data on screen e Bands toggles display of the bands e Show Fermi toggles display of the Fermi energy on the band graph e Fermi E allows you to enter a value for the Fermi energy The location of the Fermi energy is not stored in the band file so you must enter this yourself to get an accurate value 16 10 Properties button window This is used to control display of average properties data DOS COOP or COD data e Curve n where n is an integer This is a toggle to control display of each curve in the file The numbering of the curves varies from type to type DOS data Curve 1 is the total DOS Projections are la beled starting from Curve 2 The projections are in the order in which they were specified in the input file COOP data The curves are numbered in the same way as the COOPs were numbered in the input file COD data There is only one curve per COD file this is curve 1 49 e Integration n where n is an integer These toggle display of the integration of the corresponding curve e Integ Scale toggles use of the integration
31. er the name of the file in the window from which you started up viewkel The program will read in the geometry of the molecule itself from the out file and the MO specification from the MO file You will be prompted for which MO you which to use if there are multiple MO s in the MO file Note To use this option you must have specified MO printing when bind was run e Read Contours Reads in a contour plot You will be prompted for the name of the file containing the contour data This op tion is primarily intended for dealing with FCO plots e Read FMO Reads in FMO data and constructs an interaction diagram You will be prompted for the name of a FMO file viewkel will read in the FMO data construct an interaction diagram and open an FMO options window e Read Props Reads in average properties DOS COOP or COD data and displays it You will be prompted for the name 39 of a data file either DOS COOP or SUB The program will read in the data and open a property options window e Read Walsh Reads in data for a Walsh diagram You will be prompted for the name of a WALSH file viewkel will read in the data and open a walsh option window e Read Bands Reads in the data to display a band structure You will be prompted for the name of a bands file viewkel will display and band structure and open a bands option window e Read Graph Reads in raw data for a graph You will be prompted for the name of the file contai
32. he atoms being displayed Crosses Toggles display of pseudo 3D crosses on the atoms If this is turned on and shading is turned off the interiors of the atoms are drawn as solid white with the cross superimposed Connectors Toggles drawing of lines connecting atoms which are a distance within bond_tol see below of the sum of their covalent radii apart Fancy Lines When this is on lines between atoms are drawn as if they are intersecting the sphere of the atoms When off the lines are drawn all the way to the center of the atoms Turning Fancy Lines off is useful when drawing a structure without the atoms being displayed Breaking Lines When this is turned on lines cut those behind them that they intersect Tube Lines Toggles display of bonds as tubes instead of lines Tubes are drawn as a white center with a black edges and cut lines behind them just like breaking lines Note if both Tube Bonds and Breaking Lines are turned on only the Breaking Lines will be drawn Numbers Toggles display of the numbers of atoms Symbols Toggles display of atomic symbols Line Width Used to control the thickness of the lines drawn between atoms Bond Tol Used to enter a new value of bond_tol When this is changed the lines between atoms are recalculated Rad Scale Used to control the scaling of the circles drawn for atoms Grow Xtal This button only appears for molecules that have lattice parame
33. he default routine cboris In addition zhegv can be used to generate just the eigenvalues of a matrix This speeds up band structure calculations and properties calculations with the Just Average E keyword enormously If you have a binary distribution of the program it will use zhegv to diagonalize this is unfortunately not true of the Mac version of the program which still uses cboris If you have a source distribution you can turn on the LAPACK diagonalizer by including DUSE_LAPACK in the CFLAGS line of the makefile Most of the functions necessary to use LAPACK with YAeHMOP are distributed in the file zhegv f This is the good news The bad news is that zhegv f will not work unless you have an implemen tation of the Basic Linear Algebra Subroutines BLAS library in stalled on your machine this is why the Mac version doesn t cur rently support LAPACK Most modern distributions of UNIX in clude a specially tuned version of the BLAS library it s usually usr 1ib libblas a so you should be able to use LAPACK In addition many UNIX implementations will include as an optional product a tuned version of LAPACK The name of this library is very system dependant so you ll have to determine if it exists if you have an SGI it s usr lib libcomplib sgimath so If you do have a vendor supplied version of LAPACK it s advisable to use it instead of the zhegv f distributed with YAeHMOP the vendor product tends to be faster If
34. iles to bind are keyword based so with a few excep tions it doesn t really matter what order things are in In addition white space spaces tabs etc in the input are ignored Here are just a few reasons to use bind e Built in parameters for most elements e Gaussian style Z matrix standard Cartesian or crystallographic coordinate input e Automatic generation of points along a reaction coordinate for Walsh diagrams e Particular pieces of information can be monitored at each step along a reaction coordinate e g the reduced overlap popula tion between two atoms can be printed at each step along a Walsh diagram e Automagic generation of K points along symmetry lines for band structures 2 Orientation independent determination of symmetry elements More symmetry elements are found up through Ss DOS and COOP data are in ASCII format so you can plot the data with any plotting program though you will want to use viewkel viewkel viewkel is an X Windows based interactive program for displaying and printing the results obtained using bind though there s no reason that it can t be made to display data from other programs Some of viewkel s features are Interactive 3 D manipulation of molecular structures Support for extended systems grow crystals of any size Postscript output It doesn t use Motif Ability to place as many structures and graphs as desired on the same p
35. in the form atoml atom2 where atom is the beginning of the vector it is inside the unit cell and atom2 is the end of the vector it is outside the unit cell NOTE The ends of the lattice vectors must be the highest num bered atoms in the geometry specification For example if there are are 6 atoms defined for a 3 dimensional unit cell then the ends of the three lattice vectors must be numbers 4 5 and 6 Only a number of lattice vectors equal to the dimensionality of the crystal need to be provided If you feel like putting in zeroes for the other lattice vectors go ahead we can t stop you 3 3 Crystal Spec required for use of crystallographic coor dinates This section has the stuff needed to define the crystal lattice so that crystallographic coordinates can be used The first line following the Crystal Spec keyword should contain the lengths of each of the lattice vectors The next line should contain the crystallographic angles a 8 and 9 Variables in the Crystal Spec section can be used as variables in Walsh diagrams in exactly the same way as variables in the Geometry section i e by using integer multiples of 1000 as values For example the following Geometry Lattice and Crystal Spec sections define a body centered lattice of H atoms where the length of the c lattice vector is the first Walsh Variable 10 Geometry Crystallographic 1HOOO 2H 0 5 0 5 0 5 3H100 4HO10 5HOO1 Lattice 3 555 13 14
36. is 25 The symmetry analysis performed by bind is relatively extensive and flexible While the program doesn t find all of the symmetry elements possessed by molecules it does get a lot of them In order to make the symmetry analysis as flexible as possible the molecule can first be moved to the center of mass frame of reference The moments of inertia are then found and the whole molecule is rotated into the principle axis frame This allows molecules which are not located exactly at the origin or aligned perfectly with the Cartesian axes to be analyzed The transformation to the principle axis frame is controlled by the keyword Principle Axes If this keyword is not specified the symmetry analysis will be done in the orientation specified in the Geometry section The program searches for the following symmetry elements e an inversion center e rotation axes from C through Cg about the three Cartesian axes e improper rotation axes from 3 through Ss about the three Cartesian axes e mirror planes perpendicular to the Cartesian axes The elements found their axes and atoms which are equivalent under each operation are printed to the output file The characters of the wavefunctions with respect to each opera tion are determined by constructing the appropriate transformation matrix for each operation and transforming the vector of atomic or bital coefficients for each molecular orbital The result of this pro cess is the
37. le which was given to bind as an argument Here is a sample session bind H_mesh bind fit_dos H_mesh bind Enter E min 30 0 Enter E max 30 0 Enter broadening 10 0 Enter Energy Step 0 5 The broadening parameter given to the fitting programs is the exponent of the normalized Gaussian smoothing function A larger broadening parameter gives rise to sharper lines in the DOS COOP curves After this smoothing process which produces either a DOS or COOP file the data is ready for viewing with viewkel In order to view a Walsh diagram the program fit_walsh must be run fit_walsh is run the same way as fit_dos or fit_coop 30 you give it the name of the input file which was given to bind If you lose symmetry elements along the distortion coordinate and de generacies are broken it is possible that fit_walsh will get confused and generate a silly looking Walsh diagram fit walsh will warn you if this happens If the output looks wrong in viewkel you can ei ther manually edit the WALSH file created by fit_walsh or rerun the calculation with more points along the distortion and use the pro gram dumb_walsh which ignores symmetry operations If you take the dumb_walsh route we recommend you use at least 30 40 points along the distortion Hopefully a future version of the program will have a smarter version of fit_walsh so that these contortions are no longer necessary Other Utility Programs There are a number of other uti
38. lent Scale the control keys change the size of the active object j shrinks along x grows along x k shrinks along y i grows along y shrinks along z and p grows along z Once again holding down shift while hitting a key increases the size of the step 38 Choose Left clicking on atoms selects them Right clicking then either displays the distance between those atoms two selected the angle between them three selected or the relevant dihedral angle four selected A label is placed at the location of the right click and lines are drawn to the controlling atoms If you right click with just a single atom selected the coordinates and identity of that atom will be printed in the window from which you ran viewkel This is a convenient way to find the coordinates of a particular atom if you forget or if you have centered the molecule using the center button in the molecule option window The labels displayed in Choose mode remain on screen until the Clear Labels button is hit e Read Molecule Reads in the atomic positions of a molecule You will be prompted for the name of the output file contain ing the geometry Enter the name of the file in the window from which you started up viewkel The molecule will be read in and displayed and a molecule button window will be opened e Read MO Reads in the specification of an MO You will be prompted for the name of the input file used to perform the calculation Ent
39. lities distributed with YAeHMOP These are described below 8 sub _ dos and add _dos These are used to manipulate DOS files sub_dos is used to subtract two DOS curves from each other This is the basic operation needed for the Crystal Orbital Displacement COD analysis developed by Eliseo Ruiz and Santiago Alvarez 12 COD is a very sensitive tool for tracking complicated interactions in the solid state Running sub_dos without any arguments will give you the correct ordering of arguments add_dos is like sub_dos except that it adds two DOS curves to gether Note It is very important that the DOS curves used for sub_dos are fit using fit_dos within the same energy window and with the same broadening and energy step The programs will warn you about this 9 cooperate cooperate reads in the DMAT file generated when bind is given the keyword Dump Distance Matrix and generates a COOP specification that can be pasted into an input file for bind The output from cooperate needs very little modification before incorporation into 31 an input file The necessary modifications are fairly obvious Once again running the program without any arguments will give you a complete list of possible arguments Contents of Files The various programs in YAeHMOP produce different output files the names of the files may be confusing For a run on a file named example here are the names of the files produced and the contents of those files
40. means that the buttons aren t necessarily the most beautiful things you ve ever seen and sometimes they behave in ways which are just plain wrong for example text can overflow out of the button The most important thing from my perspective is that these buttons do work and the code to deal with them is simple and small To activate a button left click on it If it is a toggle button then the toggle will be changed If the button is for changing the value of some variable you will be prompted to enter a new value for that variable no I didn t write dialog box code Buttons which are for toggling the display of lines will show a sample of the line style to the right of the button You can change this line style by right clicking in the toggle button 16 3 The main button window The buttons in the main button window are described below e the Mode button This is the top button in the window It displays what mode the program is using to manipulate the graphics displayed in the graphics window Left clicking in this window changes the active mode This mode determines what action the control keys have The control keys are i j k l p and 37 The first four of these form an inverted arrow on a standard keyboard The possible modes are None the control keys do nothing Rotate the control keys rotate the active object i and k rotate about the y axis j and rotate about x and p and rotate about z Holding
41. n t have enough overlaps the diagonalization procedure will fail This will be reported in the status file after the program finishes running 13 Choosing the number of k points to use This is a tricky question The right answer is that you should always do a k point convergence test for every calculation i e you should try using a variety of different sampling densities and stop when you get convergence However this isn t always practical or possible The general guideline we use is that the number of crystal orbitals 34 number of orbitals in the unit cell times the number of k points should be equal to 1000 This criterion is highly questionable when doing slab models of interfaces or surfaces so be careful with these systems 14 Choosing the number of points in band struc tures Generally using 40 k points per symmetry line works fine If your bands are flat you can use less than this If you are really worried about seeing weakly avoided crossings and you can t tell if you are seeing one use more points 15 Calculations on big systems When doing calculations on large systems where the meaning of large depends on how much memory your computer has it s very good idea to do the average properties and band structure calcula tions separately This is because average properties calculations use a lot more memory and band structure calculations use a lot more k points If you are nearing the limit of the memory av
42. n do 11 What to do if you find a bug In order for us to be able to fix bugs we have to be able to reproduce the circumstances that gave rise to them In order to do this we 33 need a copy of the input file that caused the problem Please include the following in any bug report that you send 1 A description of what went wrong or why you think the an swers you got are wrong 2 Copies of the input file essential and the status and output files optional but extremely useful 3 Information about what kind of computer you are using ma chine type and operating system version if possible 4 Some way to get in touch with you Please send bug reports to the following email address yaehmopOxtended chem cornell edu Some hopefully helpful hints 12 Choosing how many overlaps to use The overlaps specified determine how many unit cells the program uses when building the overlap matrix in K space The important thing when answering this question is to remember that the goal is to include all unit cells surrounding the home cell that have a non zero contribution to the overlap matrix The general criterion here is that you should go out far enough that the length of the lattice vector times the number of overlaps is between 10 and 20 A Some systems don t require this many overlaps and some require more It s safe to go with too many overlaps though this causes bind to use more memory and go slower If you do
43. ning the graph data This allows construction of very primitive graphs This option just exists because it was easy to do viewkel is not intended to be a general purpose graphing program Fill Proj s Toggles filling of projected DOS curves On screen these will be shown shaded in the printed output they will be lined Note in the Macintosh version of viewkel this keyword has no effect on the way things are displayed on screen it does still affect the Postscript output Purge Deletes all currently displayed objects and closes all of their button windows Printing Options Opens a window which allows you to change some of the default behavior for the Postscript printing e Print Prompts for the name of a file then redraws the screen writing its contents to the file as Postscript This file can then be printed however you normally print ps files e Clear Labels Removes labels from the display They will not be refreshed so once you clear them they are gone 16 4 The PS options button window This window allows you to control some of the default behavior of the Postscript printing from viewkel e Location This button controls where the graph is located on the output page There are three possible values Top Middle and Bottom The default is Bottom 40 Font Allows specification of the standard text font The de fault is Times Roman Note This option can be overridden using the enhanced Postscript commands describe
44. ollowed by a single line specifying the tolerance used to terminate the iteration lambda followed by a single line specifying the step size for the iteration process max iter followed by a single line specifying the maximum number of iterations 3 34 Sparsify optional This is used to set small elements of the hamiltonian and overlap matrices to zero The next line should contain the value which is considered to be zero NOTE This is primarily here for development purposes and we d encourage you not to use this 3 35 Just Average E optional Tells bind to only generate the average energy total DOS and Fermi level of the system This causes the program to require considerably less memory when run on systems with a lot of orbitals If you are using a version of bind that uses the LAPACK libraries to diagonalize the matrices then only eigenvalues will be generated This can result in a significant speed increase A factor of 10 de crease in execution time for sufficiently large systems is possible 3 36 Just Matrices optional Generate just the overlap and hamiltonian matrices then exit This is basically useless unless it is used in conjunction with either the Dump Overlap or Dump Hamil keywords or the Hamiltonian or Over lap printing options 3 37 Diagwo optional Performs the matrix diagonalization without using the overlap ma trix so that a calculation is similar to a simple Huckel calculation Symmetry analys
45. oms 2 4 6 7 and 8 will use the same parameters as atom 1 Clarification The parameters specified here for O are the default parameters 3 8 Molecular mandatory for molecular calculations Indicates that a molecular calculation not an extended one is being performed Otherwise it is assumed that the calculation is on an extended system 3 9 Just Geom optional Do not actually do a calculation just generate the molecular ge ometry This is useful to check whether or not an input file is okay before running a calculation It will also print the estimated memory requirements of bind for this run into the status file 3 10 Walsh optional Do a series of calculations along a reaction coordinate The next line should contain the number of variables reaction coordinates num_Walsh_var and the number of steps to be taken along each coordinate num_steps There should then be num_Walsh_var lines consisting of a list of comma separated num_steps values 13 To generate the values of a variable automagically place an ex clamation point at the beginning of the line for that variable followed by the starting and ending values of the variable separated by a comma The program will generate num_steps values between those values For example the following sample section will generate a reaction with coordinate with 5 steps and 2 variables The values of the first variable will be automatically generated between 1 0 and 2 0 the
46. on window has buttons which are used to control the program The individual button windows and the functions of the buttons found therein are described below Each button is only described once so though many different windows have a X Legend button it is only described once You can cause the program to redraw at any time except when an isosurface is being evaluated by middle clicking in any of the windows 16 1 Special keys in viewkel There are a number of keys that can be used in viewkel some of these duplicate features found in button windows some are unique e q will cause viewkel to quit e r switches into rotate mode e t switches into translate mode e c switches into center mode e s switches into scale mode e the spacebar switches into choose mode e h in choose mode hides the selected atoms e in choose mode shows previously hidden atoms 36 z rotates the selected molecule so that you are looking along the Z axis y rotates the selected molecule so that you are looking along the Y axis x rotates the selected molecule so that you are looking along the X axis e 1 viewkel will prompt you for a file name to use then write an input file for rayshade e d writes the cartesian coordinates of the molecule to standard output 16 2 General use of buttons In order to avoid having to use a user interface library that may not exist on some machines I wrote all the button code myself This
47. ontour plot is evaluated Discrete you will be prompted to enter the num_contours contour values when you evaluate the contour plot e Contour it Evaluates a contour plot You will be prompted for the orientation of the plane used to evaluate the contours i e perpendicular to X Y or Z the height and width of the plane in which the MO will be evaluated 45 the number of steps to take along each side of the evalua tion plane the number of contours you want to use an offset this shifts the evaluation plane off the origin useful if you want to contour an MO where most of the density isn t at X Y or Z 0 Whether or not you want to do a stack of contour plots If you say yes here you will be prompted for the number of planes you want in the stack the location of the start of the stack and the distance between planes in the stack What this does is generate a series of plots which are parallel to each other and located at different heights This is a quick and dirty way to get a feeling for the shape of an MO Note if the contour mode is Auto viewkel will generate the contour levels automatically in the first plane of the stack but then will use those contour values in all other planes viewkel will then go off and evaluate the values of the MO in the plane contour that data show you the values of the contours it found and finally display those contours if the Contours toggle des
48. osurface is taken from a section by Jules Bloomenthal at Xerox PARC in the book Graphics Gems IV The algorithm as published is suitable for polygonaliza tion of continuous surfaces Unfortunately isosurfaces of molecular and crystal orbitals are rarely continuous They are instead made up of a number of discrete parts usually lobes centered on partic ular atoms In order to work around this problem Bloomethal s algorithm has been modified to look for individual pieces of the sur face around each atom in the molecule The algorithm starts at the corners of a cube of side length search_radius centered on each atom The default value of search_radius seems to work most of the time if you see that lobes are obviously missing try changing the value of search_radius The algorithm evaluates the MO values on a grid of spacing voxel_size Increasing voxel_size results in quicker evaluation and drawing of the surface less triangles are found so the surface can be drawn more rapidly but the resolution suffers Decreasing voxel size gives a smoother surface but it takes much 43 longer to calculate and to draw My best advice here is to start with the default value 0 2A and then play around with it to see what size suits your purpose Some Cautions about solid isosurfaces e I haven t had a chance to do shading simulated lights of the isosurfaces I think that this will improve the appearance of the final images e A heuristi
49. ou ll get the hang of it fairly quickly References 1 A w a R Hoffmann W N Lipscomb J Chem Phys 36 2179 1962 ibid 36 3489 1962 b R Hoffmann W N Lipscomb J Chem Phys 37 2872 R Hoffmann J Chem Phys 39 1397 1963 d R Hoffmann J Chem Phys 40 2474 1964 ibid 40 2745 1964 T A Albright J K Burdett and M H Whangbo Orbital Interactions in Chemistry Wiley Interscience 1985 R Dronskowski J Am Chem Soc 114 7230 1992 R Dronskowski and P E Blochl J Phys Chem 97 8617 1993 W V Glassey G A Papoian and R Hoffmann accepted for publication in J Chem Phys 57 D M Wolfsberg and L Helmholtz J Chem Phys 20 837 1952 M H Whangbo and R Hoffmann J Chem Phys 68 5498 1978 8 J H Ammeter H B Burgi J C Thibeault and R Hoffmann J Am Chem Soc 100 3686 1978 9 R S Mulliken J Chem Phys 23 1841 1955 10 T Hughbanks and R Hoffmann J Am Chem Soc 105 3528 1983 11 G A Landrum Ph D dissertation Cornell University 1997 Greg s thesis is also available on the WWW via a link from the YAeHMOP home page http www overlap chem cornell edu 8080 yaehmop html 12 E Ruiz S Alvarez R Hoffmann and J Bernstein J Am Chem Soc 116 8207 1994 N 58
50. parameter file usually called eht_parms dat it ll pop up another dialog box You should use that dialog box to find and select the parameter file You can avoid this by having a copy of the parameter file in the same folder as the input file To work around this make an alias for eht_parms dat copy it to the input folder and then rename it eht_parms dat 6 The fitting programs The fitting programs will open a file choice dialog on start up You should pick the input file used to run the calculation 7 General Mac hints If you get errors about the programs not having enough memory or not being able to allocate matrices increase the size of the memory allocation for the troublesome program If you don t know how to do this select the application you want to change select Get Info from the File menu or hit CMD I then increase the Preferred Size entry Sample Extended System Input File This is an input file for doing a band structure and average prop erties calculation on a square 2 dimensional mesh of hydrogen atoms the title 2 D mesh of hydrogen the geometry Geometry number of atoms Wee WNrR S Seewta h osi n oroo ooow eoon ooogt oOoo0oo0oo ooon 28 lattice parameters Lattice dimension of lattice 2 number of overlaps along each lattice vector 44 the lattice vectors begin atom gt end atom 1 2 1 3 number of electrons per unit cell Electrons 1 band st
51. pe of custom atom which is being defined Recall that a custom atom is defined by replacing the first occurance of that atom s label in the Geometry specification with an asterix If there are multiple custom atom types then define them in this section in the order in which they occurred in the Geometry section The format of a parameter specification is Symbol Atomic _Number Num_Valence_Electrons ns Cs IPs np Gp IPp na Cla IPa cl 62a c2 and if you re dealing with f elements which like d orbitals are de scribed by a double zeta expansion add ny ly IPs cl 27 c2 to the end of the parameter specification In this specification the values are the radial exponents of the Slater type orbitals and the H values are the valence state ioniza tion potentials diagonal elements of the hamiltonian for each AO Here s an example of a section of input file where 3 different custom atoms are defined 12 Geometr y 8 1 x 000000000 000000000 000000000 20 1 952000000 1 952000000 000000000 3 1 952000000 000000000 23 40 1 952000000 000000000 1 4862 5 0 000000000 1 952000022 1 9422 6 0 3 904000044 000000000 000000000 7 0 000000000 3 904000044 000000000 8 0 000000000 0 0 4 152 Parameters 0 8 6 2 2 275 32 3 2 2 275 14 8 Ti 22 4 4 1 075 8 970 4 1 075 5 400 3 4 55 10 81 4206 1 400 7839 Pb 82 4 6 2 50 16 70 6 2 06 8 000 In this example atom 1 is an O atom 3 is a Ti and atom 5 is a Pb At
52. r Macs A port to the 68K based Macs is not suported The Mac port was done using the CodeWarrior compiler from Metrowerks Source code and project files for the Metrowerks IDE are available upon request Codewarrior is fantastic Metroworks prices it reasonably includes a ton of useful examples and libraries and has an excellent upgrade policy In addition the MW technical support is excellent The Fortran bits of the program were converted using f2c on our workstations and then compiled on the Mac using a port of the f2c libraries All input and output that would normally go to the console on a workstation is handled by the SIOUX library included with CodeWarrior The basic structure of the graphics stuff used in viewkel was done using the EasyApp application shell distributed with CW 4 lt A couple of disclaimers The Mac version of YAeHMOP is not the most beautiful thing that the world has ever seen Some of the operations are handled in an ugly non Mac way This is a direct consequence of the program s Unix heritage Hopefully in some future version these difficulties will be eliminated The Mac version of the programs are not nearly as stable as the UNIX version principally because the MacOS isn t a protected mode operating system 27 5 Using bind on a Macintosh When bind starts up it will open a standard file choice dialog you should choose the input file in that dialog box If the program has problems opening the
53. report Any of the following things could indicate a bug 1 bind gives you answers that don t make any sense at all 2 bind does something funny like not printing out something you told it to print out 3 bind wanders off into space and never comes back i e it runs forever 4 bind crashes without giving you some idea of what happened 5 bind seg faults and dies You see the message Segmentation Fault core dumped We have yet to see bind do anything like 3 above If you do think that the run is taking too long check the status file and make sure that it is still doing something bind should never do either 4 or 5 above If either of these happen you have definitely found a bug Please report it The major cause of segmentation faults seems to be problems in the input files given to bind Error checking routines are in place to catch many of these problems but we probably missed a few So please let us know if you find input file formats that give rise to segmentation faults without generating a warning viewkel is a slightly different story The code for viewkel isn t nearly as clean or carefully written as that in bind The result is that viewkel occasionally will dump core and or die unexpectedly We re aware of some of these problems and are working on them If you can make viewkel dump core reproducibly please let us know Similarly if the output from viewkel just looks wrong tell us and we ll see what we ca
54. rix e Reduced Overlap Population Print the Mulliken reduced overlap population matrix e Charge Matrix Print the charge matrix e Wave Functions Print the wavefunctions for the molecule e Net Charges Print the net charges on the atoms as determined using Mulliken population analysis e Overlap Print the overlap matrix 21 e Hamil Print the hamiltonian matrix e Electrostatic Print the electrostatic contribution to the total energy NOTE this is under development and is not to be considered reliable e Levels Toggles the printing of energy levels at each k point in an extended calculation e Fermi Print the Fermi energy this is primarily useful in com bination with the Walsh option described below e Orbital Energy Allows the energy of a particular orbital to be printed this is primarily useful in combination with the Walsh option described below e Orbital Coeff Allows the coefficient of a particular atomic or bital in a given molecular orbital to be printed this is pri marily useful in combination with the Walsh option described below e Orbital Mapping Generates the scheme used to number the individual atomic orbitals in a calculation especially useful when working out the contributions for COOP s e Levels Print out the calculated energy levels at each k point in an extended calculation Each of these options control printing at every K point and or step along a reaction coordinate
55. ructure details Band K points per symmetry line 40 number of special points 4 special points Gamma 0 0 0 0 0 0 X 0 5 0 0 0 0 M 0 5 0 5 0 0 Gamma 0 0 0 0 0 0 do average properties calculation Average Properties do a COOP COOP number of COOP s 2 COOP specifications type which contribi contrib2 cell orbital 1 1 1 100 orbital 1 1 1 010 this averages H H COOP s between cells 0 0 0 gt 1 0 0 and 0 0 0 gt 0 1 the K points K points number of K points 10 the K points and respective weights 29 0 0625 0 0625 0 0000 1 0 1875 0 0625 0 0000 2 0 1875 0 1875 0 0000 1 0 3125 0 0625 0 0000 2 0 3125 0 1875 0 0000 2 0 3125 0 3125 0 0000 1 0 4375 0 0625 0 0000 2 0 4375 0 1875 0 0000 2 0 4375 0 3125 0 0000 2 0 4375 0 4375 0 0000 1 end of file The Fitting Programs In order to generate nice looking DOS and COOP curves it is necessary to either use hundreds of k points in the calculation or to smooth the data which is generated by bind For obvious reasons it is far more common to adopt the latter approach Smoothing of DOS and COOP curves is done by putting a gaus sian on each data point then summing up the contributions from each of the gaussians between the data points This process gives rise to the type of curves we are used to seeing The parts of YAeHMOP which perform this smoothing operation are called fit_dos and fit_coop These both take the name of the input fi
56. s inside the cell will be zeroed NOTE This option should be used with caution as it can result in a non positive definite overlap matrix and non physical results 3 18 Nearest Neighbor Contact optional Determines the longest contact between atoms in nearest neighbor cells that will be reported in the output file The next line should contain the new value The default is 2 5 A NOTE This keyword only makes sense for extended systems 3 19 K Points mandatory for Average Properties calcula tions on extended systems A K point set for an average properties calculation If you want to do a band structure we recommend that you use the Band keyword The keyword is followed by a line containing the number of K points num_KPOINTS The next num KPOINTS lines should contain the coordinates and weights of the K points themselves in the following form a b c weight Each K point should go on its own line 3 20 Band optional Generate a band structure The line following the keyword should contain the number of K points to use along each symmetry line points_per_line The next line should have the number of special points to be used num_special_points The following num_special_points lines should have the names and locations of the special points in the form label x y z The program will generate symmetry lines connecting the special points in the order in which they are defined points_per_line K points will be generated
57. tain the atomic coor dinates and types in the following fashion e Z matrix Input number atom_label refl r ref2 alpha ref3 beta e Cartesian Input number atom_label X Y Z e Crystallographic Input number atom_label X Y Z number is the number of the atom There is no reason why the atoms in the list have to be in increasing numeric order atom_label is the label for the atom it should be one or two characters long If the atom label is a single asterix then the atom is taken to be a custom type and a symbol and parameters should be provided for it in the Parameters section If the atom label is an ampersand amp then the atom is taken to be a dummy atom The other variables are the coordinates for the atom in whatever system is being used If a reaction coordinate is being traced out see keyword Walsh below any coordinate which is an integer multiple of 1000 is assumed to be variable For example placing 2000 as the X coordinate of some atom would cause that coordinate to take on the values of the second Walsh variable 3 2 Lattice mandatory for extended systems NOTE If this keyword appears in the file it must follow the Geom etry keyword in the input file These are the lattice parameters The keyword should be followed by a line containing the dimensionality of the crystal The next line contains the number of overlaps considered along each lattice direction The following lines should contain the lattice vectors
58. ted using the right hand rule The easiest way to explain a Z matrix is to show one and then explain it so that s what we ll do Before we start however we need to briefly define a dihedral angle A dihedral is specified by 4 atoms we ll call them A B C and D The dihedral A B C D is the angle between the plane defined by A B C and the plane defined by B C D Here s an alternative explanation the dihedral A B C D is the angle between the lines C D and B A if you are looking down the line C B There s one more piece of information we need to fully understand the dihedral there is a handedness associate with them If you think about it looking down the line C B there are two different angles between lines C D and B A 6 and 360 0 The dihedrals in bind are defined using the right hand rule Take your right hand and point the thumb down the line C B now align your fingers with the line C D curling your fingers shows the direction in which the dihedral angle is measured This is all about a million times easier to understand using a picture here s a picture demonstrating both views of dihedrals and their handedness 55 7 Z lL x A x n C D D The Molecule The dihedral A B C D With that definition under our belt here s the Geometry speci fication for a square pyramidal CH3 Bil fragment where the CH3 group is along the Z axis and the Bi and four I s lie in the XY plane Geometry Z Matrix 9 1 Bi 2C
59. ters in the output file i e extended systems Clicking this allows you to show more than one unit cell 42 16 6 The MO button window Note This section is substantially changed since viewkel version 1 2 When an MO isosurface is opened two button windows are opened One of these windows is a Molecule window as described above The other window is used to control the drawing of MO isosurfaces on screen These options are described below There are two ways to draw isosurfaces in viewkel version 2 The first method draws the isosurface just as it was done in version 1 2 a solid isosurface made up of filled triangles is drawn These iso surfaces do not look particularly good when drawn in viewkel but generate very nice illustrations when rayshade is used to raytrace the object The second method draws Jorgenson and Salem style con tour plots of the surface with hidden line removal These plots are similar to those generated by CACAO and PSI88 I will refer to these as solid surfaces and contour surfaces respectively Finally this button window is also used to generate a two dimensional contour plot of an MO Pll refer to these as contour plots While some buttons apply to both types of figures the majority control only solid or contour surfaces To explain what the solid surface buttons do it is necessary to understand how the calculation of solid isosurfaces is done The algorithm used to generate the polygonal is
60. the following piece of an input file would place 1 electron in both orbitals 49 and 50 Orbital Occupations the number of occupations to change 2 the orbitals and new occupations 49 1 0 50 1 0 3 33 Charge Iteration optional bind has the capability to perform charge iteration a self consistent adjustment of the H s in order to lessen the amount of charge flow The charge iteration algorithm in bind is somewhat experimental so beware and is discussed in the file charge ps For those of you who know no fear here s a summary of the CI keywords The keywords controlling the CI process are sandwiched between the charge iteration and end charge keywords The keywords within the CI block are Param followed by a line giving the number of different atoms that parameters will be specified for num_CI_parms each of the next num_ClI_parms lines should contain the charge iteration parameters in the form Atomic_symbol s4spscpapsppcdadgdc i e the A B and C parameters for each of the orbitals These are the same parameters used in the old programs for single configu ration CI and are NOT distributed with YAeHMOP Note charge iteration for f orbitals is not supported Vary follows Param followed by a single line containing the num bers of the atoms whose parameters are to be varied This is a 24 comma delimited list you can use to abbreviate series of atoms i e 1 4 and 1 2 3 4 are equivalent Tolerance f
61. the parser is not case sensitive when dealing with keywords i e Electrons electrons and ELECTRONS will all work Any line in the input file which begins with a semicolon is ig nored This allows comments to be put into the input file It also makes it easy to temporarily change the contents of a file just put a semicolon in front of anything you don t want the program to read Blank lines and spaces in the input are also ignored The first non empty line should contain the title of the job 3 Keywords The remainder of the file contains the keywords which control the job These keywords are all described below The notation used is as follows e Words in sans serif style such as foo are keywords e Words in slanted type such as bar are variable names used within the program They are used for convenience 3 1 Geometry required The line following this keyword should have the number of atoms num_atoms If the line containing the keyword Geometry also contains the string Z Matrix then the input is take to be in Gaussian style Z ma trix format If the line containing Geometry also contains the string Crystallographic then the input is taken to be in fractional coordi nates and the Crystal Spec keyword must be specified Otherwise the input is assumed to be in Cartesian coordinates If you are un familiar with Z matrix input it is described in a later chapter of this document The following num_atoms lines should con
62. ulations will be done 3 25 Dump Overlap optional Toggles creation of a binary file containing the overlap matrix at each K point This file can be used with the matrix_view utility to generate pictures of overlap matrices 3 26 Dump Hamil optional Toggles creation of a binary file containing the hamiltonian matrix at each K point This file can be used with the matrix_view utility to generate pictures of hamiltonian matrices 3 27 Dump Dist optional Toggles creation of a binary file containing the distance matrix for the system This DMAT file can be used by the utiltity cooperate to generate specifications for COOPs automatically 3 28 Projected DOS optional This section contains the list of densities of states DOS s that will be projected Each DOS can have multiple contributions which will be added up The keyword is followed by a line containing the number of dif ferent projections num_proj DOS The next num_proj DOS lines should consist of type contribl weight1 contrib2 weight2 type should be either Atom Orbital or FMO to indicate whether the contribution from an entire atom a single orbital or a fragment MO is being projected out There can be as many contributions to each projection as you like just put it all on one line and separate the contrib weight pairs by commas Entries for a single projection can be spread over 19 multiple lines by placing a at the end of each line To
63. xclude Atoms Used to remove atoms from the calculation of the isosurface For example if you are doing a 7 layer metal slab and are only interested in the surface states a topic near and dear to my heart you can exclude the atoms which are in the middle of the slab This will result in a cleaner looking more quickly evaluated isosurface You will be prompted to enter a list of atoms the syntax here is the same as for the Hide Atoms button described in the Molecule options section e Include Atoms This is used if you make a mistake when you exclude atoms It turns the atoms you switched off back on e Surf Evolve Starts the calculation of a solid isosurface e Change MO Allows you to change which MO you are looking at without having to reload the whole molecule e Tri Shading Toggles filling of the triangles which make up the displayed solid isosurface e Tri_Outlines Toggles the drawing of outlines around the triangles which make up the solid isosurface e Contours Toggles display of the calculated contours that make up either a contour plot of an MO or a contour isosurface e Contour Mode This mode button determines the method which is used to generate contour levels in contour plots There are three possibilities Auto num_contours contour levels are automatically selected between the maximum and minimum values in the data set Incremental you will be prompted for a starting value and a step between contours when the c
64. y Very Important Note The hidden line removal algorithm is not guaranteed to work at all if you have some contours displayed which are not closed this can arise if the plane in which you evaluated the MO was too small Sometimes it works sometimes it does stuff that is very very wrong Grow Xtal This grows the crystal and propagates the MO coefficients with the correct phase factors for the given k point If you want to display the MO of an extended system in more than one unit cell you must use this button to grow the crystal Using the Grow Xtal button in the Molecule button window will not correctly propagate the MO coefficients Note If are looking at an extended system and you want to see the crystal orbital in more than the home unit cell you must evaluate the isosurface after growing the crystal 16 7 FMO button window This window contains buttons for controlling the display of an FMO interaction diagram e Electrons Controls the drawing mode for the electrons in the interaction diagram Each mode is described below None Do not draw electrons HOMO Draw electrons only in the highest occupied level of each fragment and the molecule All Draw electrons in all occupied levels on screen e Levels Toggles display of the levels in the FMO diagram AT e Left Fragment Controls which fragment is displayed on the left side of the interaction diagram Set this to zero or 1 to not show a fragment on
65. you are willing to compile BLAS for your system or if you want the full LAPACK distribution you can get them from the netlib server http netlib att com Netlib is a great source for numerical routines Distributing and Modifying YAeHMOP You can distribute YAeHMOP to anybody you like It s intended 53 to be given away However you cannot charge others for the dis tribution We are firm believers in free software and would like YAeHMOP to remain freeware The programs which make up YAeHMOP are available in source form If there is a feature lacking which you feel really should be there feel free to add it If you think that others might like to use this feature let us know and we ll see about integrating it into the main distribution This is much easier if you clearly indicate in the source code where you have made changes and if possible send a context sensitive diff of the modified source files If you find and fix bugs please do the same thing Updates YAeHMOP is still under development The next version will con tain bug fixes and other great stuff If you send us email yaehmop xtended chem cornell ed and let us know that you have the program we can send you mail and let you know when the next version is done If you don t let us know that you have the program you ll just have to keep checking our anonymous ftp site ftp overlap chem cornell edu dist yaehmop or the YAeHMOP home page on the World Wide Web http

YAeHMOP - Yale Department of Chemistry

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