COMPUTATIONAL CHEMISTRY COLUMN 766

CHIMIA 2000,54, No.12

Computational Chemistry Column Column Editors: Prof. Dr. H. Huber, University of Basel Prof. Dr. K. MOiler, F. Hoffmann-La Roche AG, Basel Prof. Dr. H.P. LUthi, Univ. of Geneva, ETH-ZOrich

Chimia 54 (2000) 766-769 © Neue Schweizerische Chemische Gesellschaft ISSN 0009-4293

MOLEKEL: An Interactive Tool

Stefan Portmann*a,b and Hans Peter LUthia

Abstract: MOLEKEL is an interactive ('postprocessing') program for molecular and electronic structure data, generating high-quality graphics for use in research and education. MOLEKEL has been ported to OpenGL and is now available on a number of platforms, including PC (http://www.cscs.ch/molekelf). We describe details of its implementation, capabilities and the new added features. Keywords: Computational chemistry' Molecular graphics' OpenGL . ' Visualization

Visualization Tools capabilities. Among those are very com- in Computational Chemistry plex applications, such as Cerius2, Unichem, Titan, Spartan [1-3J, that lead The chemical building set and a pencil the user through the complete process of with a piece of paper have always been a chemical computation (Fig. 1). Some of popular tools in the chemistry laboratory, these, however, only support one specific set up and submit a computation but the this set has recently been extend- application or are able to communicate ed by the very powerful visualization with one particular server type only. If programs on computers. These programs you work in a heterogeneous environ- are not only able to fully replace the tra- ment with different kinds of compute ditional tools, but they also offer many servers and applications available, these additional features. highly integrated may be lack- These visualization programs allow ing flexibility when it comes to distribut- MOLEKEL us to interactively modify the view of a ing calculations over more than one serv- model, to overlay molecular and elec- er, or when the exchange of data with tronic structure information, to dynami- other becomes an issue. In that Fig. 1. A typical work flow of a chemical com- cally display molecular vibration and to case, simple connectivity between the putation and MOLEKEL's position in the proc- prepare illustrations for presentations and visualization tool and the hardware and ess. publications. Today, one has the choice software resources present in the network between many visualization programs will be a definite advantage. Its easy inte- properties for research and education. It vastly differing in price, performance and gration in a distributed environment was is mainly designed for generating a de- one of the main reasons why we decided tailed, easily interpretable and esthetical- ·Coffespondence:S.Portmann to further develop our visualization soft- ly appealing graphical output based on "ETH-Zurich ware MOLEKEL. structural data and the results of calcula- Laboratory of Physical Chemistry Universitiitsstr. 16 MOLEKEL was originally developed tions. To allow us high flexibility in a CH-8092 Zurich by Peter F. Fltikiger at the University of heterogeneous compute environment, the Tel.: +41 1 6325782 Fax; +4116321615 Geneva in the context of a Ph.D. thesis connection to the data is made via easily E-Mail: [email protected] [4] under the direction of Prof. J. Weber. transferable text logfiles. MOLEKEL bAffiliate with the Centro Svizzero di Calcolo The purpose of the molecular graphics was developed further by Fltikiger and Scientifico (CSCS) Galleria 2. Via Canton ale package is the interactive visual repre- Portmann at CSCS (Centro Svizzero di CH-6928 Manno sentation of molecular structures and Calcolo Scientifico, Manno), where the COMPUTATIONAL CHEMISTRY COLUMN 767

CHIMIA 2000. 54. No. 12

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Fig. 2. Screenshot of MOLEKEL: The main graphics window containing the , the main interface window on the right side, the popup menu containing submenus within the main graphics window and two of the popup windows giving control over the surfaces and the representation of the vibrational normal modes. The graphics window is resizable. The main interface window contains a scrollable info text area (log info). program was made available to the public. independent graphics library and there- available, it can easily be replaced by the In the present article we describe fore does not contain the equivalents to freely available Mesa 3D Graphics li- some of the most recent developments, the event handling and window manage- brary [12] (no change in the source code including the port of the software from ment functions of IRIS GL. This func- needed). The new MOLEKEL version high performance graphics stations to tionality needs to be covered by other li- consists of two main windows, the graph- generally available platforms. braries, such as the OpenGL Utility ical window and a main interface win- Toolkit GLUT [8] for event handling and dow, plus a popup menu and several pop- window management. up windows (Fig. 2). MOLEKEL GLUT is available for X-Windows This choice of the libraries made the systems [9] (all UNIX) and for WIN- new version of MOLEKEL basically Implementation and System DOWS PCs [10]. The library gives easy platform independent. The new version Requirements access to an OpenGL rendering context, 4.0 has been successfully ported to IRIX The original version of MOLEKEL handles mouse and keyboard events and SGI [5], SUN [13], [14] and was written in C and was based on the offers easy implementation of a popup WINDOWS PCs [10] using the systems IRIS GL graphics library of Silicon menu. To make common graphical user standard C++ or the GNU gcc compilers Graphics, Inc. (SGI) [5]. As a conse- interface (GUI) building blocks such as [15]. It should also run without major dif- quence, the program was able to run on buttons and checkboxes available, the ficulties on other UNIX systems. The use SGI platforms only. The IRIS GL graph- GLUT-based C++ user interface library of a gcc compiler together with a mini- ics library found its successor in the GLUI [II] was used in addition. As a malist GNU for Windows (MinGW) set- OpenGL graphics system [5-7], whose consequence, MOLEKEL became a C++ up [16] on the WINDOWS PC platform availability is no longer limited to SGI code, even though major parts are still in made the port to that platform a rather systems. OpenGL is designed as a system plain C. On systems where no OpenGL is straightforward task. COMPUTATIONAL CHEMISTRY COLUMN 768

CHIMIA 2000, 54, No.12

Table. Supported file formats. Capabilities and Features In the current version, MOLEKEL is quantum chemistry code comment a pure interactive postprocessing tool (Fig. 1), designed to visualize the output [17] logfile of a number of electronic structure pro- GAMESS (US) [18] loglile grams (Table). The focus is on the analy- sis of computational data and on the prep- ADF [19) only coordinates read from logfile. aration of photorealistic graphics for ADF utilities used to generate grid data presentations and publications. It has no capabilities to build molecules from ZINDO [20] logfile scratch or to generate input for external MOS [21] logfile electronic structure programs. Only the text output of the electronic structure cal- HONDO [22] log and punch file culation program is required to visualize PRDDO[23] loglile properties (exception ADF [19]). This makes MOLEKEL very flexible, espe- MKL MOLEKEL's own format cially in a environment of heterogeneous hardware and software resources. coordinate file format In terms of features, MOLEKEL of- PDB. also multiple protein data base file fers the common wire, stick, -and- stick and spacefill (CPK) representation structure [24) format of the atomic structure of molecules (Fig. 3). Several molecules can be loaded XYZ. also multiple as in XMol of MSC simultaneously and can be rotated and structure [25] translated interactively and independent- Iy. In the new version it is now possible to grid file format reference the to take action on with the click of the mouse, instead of GAUSSIAN CUBE [17] grid file format of Gaussian stepping through the complete reference- ADF TAPE41 [19] text dump of TAPE41 list of molecules. Geometrical parame- ters like bond lengths, angles and torsion- MACU MOLEKEL's own format al angles can be measured interactively and are displayed directly on the model. Two molecules can be superimposed by defining the matching atoms explicitly. Based on the information parsed from an electronic structure calculation output, the application text logfile, isosurfaces of the electron density, spin density and mo- lecular orbitals can be generated. The fact that these computations are started as in- dependent processes allows us to run them in the background, a feature very useful when working with very large sys- tems (no independent process is started on WINDOWS PCs). Connolly surfaces are also available [27][28]. The external original FORTRAN program of Connol- ly is used for this purpose. Any surface can be activated and manipulated by the click of the mouse. The active surface can be deleted independent of its position in the list of surfaces. Previously only the last surface generated could be deleted. Properties like the molecular electrostatic potential can be mapped on any isosur- face using texture mapping [7][29][30]. The minimal and maximal value of the range over which the color spectrum or the texture is mapped can be set manual- Fig. 3. An output generated by MOLEKEL illustrating its capabilities. The molecular structure is represented as a ball and stick model, the orbitals are rendered transparent using alpha blending. ly. In the old version the minimal and Non standard colors and materials are assigned to the background and the different objects. The maximal value of the current data was displayed example structure, an anti-(P)-hydrogen peroxide R-2-methyl oxirane complex, is taken, without having the possibility to taken from a work published elsewhere [26]. intervene. This new feature is particular- COMPUTATIONAL CHEMISTRY COLUMN 769 CHIMIA 2000,54, No. 12

downloads of the old version. Its wealth of features and high-quality graphics, its platform independence and easy integra- tion into almost any compute infrastruc- ture make the new version of MOLEKEL an attractive tool for researchers and edu- cators performing or teaching chemical computation. The new, self-explanatory GUI along with manuals available in pdf, postscript or html format, MOLEKEL is even more simple to use. It is based on a up-to-date software technology, which makes the code also an interesting start- ing point for further development. Among the options considered are the extension of supported file formats, the addition of a molecular builder, and the upgrade of MOLEKEL to a collaborative engineering tool [33]. MOLEKEL can be downloaded from http://www.cscs.ch/molekel/ free of charge (precompiled executables). The copyright for the software is owned by CSCS. It is possible to obtain the source code in the framework of a collaborative agreement with CSCS (please contact Dr. D. Maric; E-Mail: [email protected])

Acknowledgment We would like to thank CSCS for their sup- port and the opportunity to work on the MOLE- KEL project. Fig. 4. The same example as for Fig. 3 is taken to illustrate the possibilities of displaying grid data. Received: November 7,2000 The molecular electrostatic potential is mapped on the clipplane cut isosurface of the electron density, projected along an axis and cut with a plane. The potential is color coded using a predefined contour texture. [1] http://www.msi.com/life/product~/cerius2/ [2] http://www.oxmol.comls(!ftware/unicheln/ [3] http://www.wavefun.com/S(!ftwllre/ software.html ly useful when comparing a series of Vibrational normal modes can be [4] Peter F. Fli.ikiger, 'Development of the molecules. To view areas behind mole- viewed statically using arrows indicating molecular graphics package MOLEKEL cule covering surfaces, surfaces can be the direction of the motion of a mode or and its application to selected problems in opened using movable and rotatable clip- dynamically through animation. The ar- organic and organometallic chemistry', planes (one clipplane per surface; only rows can now also be rendered as solid These No 2561, Departement de chimie one clipplane per molecule in the old ver- objects not just as lines (Fig. 2). Sequenc- physique, Universite de Geneve, Gencve, sion) and also be rendered transparent, es of coordinates, e.g. from a geometry 1992. [5] http://www.sgi.com either using polygon stippling or alpha optimization, can also be animated. Co- [6] http://www.opengl.org blending [7]. The computed three-dimen- ordinates are exportable in the original [7] OpenGL Programming Guide, 'The Offi- sional grid data used for the isosurface orientation or the current orientation in cial Guide to Learning OpenGL', M. generation is saved in a external file in PDB and new also in XYZ format Woo, l. Neider, T. Davis, D. Shreiner MOLEKEL's own 'macu' format for lat- [24][25]. The colors and materials of the (OpenGL Architecture Review Board), er use. As a new feature, grid data of objects are flexible (Fig. 3), textures us- Addison-Wesley, 1999. Gaussian (cube files) [17] and ADF ing any picture, available in SGl's RGB [8] http://reality.sgi. eOIll/mjk/g/ut3/g lut3.hunl [9] http://www.x.org (TAPE41 files) [19] can also be read into file format [31], can be assigned to vari- [10] http://www.microsoft.eol11/windows/ MOLEKEL. Besides rendering isosur- ous objects. As a new feature, four, in- [II] http://www.cs.une.edu/-rademach/glui/ faces from grid data, the data can also ei- stead of only one, predefined contour tex- [] 2] http://www.mesa3d.org ther be projected on a normal plane along tures are already compiled into the exe- [13] http://www.sun.com anyone of the principal axes or on a mov- cutable. It is possible to save the content [14] hllp://www./illux.org able plane along a principal axes cutting of the graphics window in SGI's RGB [15] http://www.gnu.org/software/gcc/gce.htm/ through the object. Using texture map- [31] or in TIFF format [32]. [16] http://www.mingw.org/; the mingw32 dis- ping, the plains are color coded according tribution available from ftp://ftp.xraylith. wise. edu/pllb/khan/g 1l11- w in3 2/lIlingw3 2/ to the projected values of the grid points Conclusion, Program Availability gce-2.95.2/was used. or according to the values of the grid at MOLEKEL is already an established [17] Gaussi.m 98, M.J. Frisch, G.W. Trucks, the planes actual position, respectively interactive molecular graphics program, H.B. Schlegel, G.E. Scuseria, M.A. Robb, (Fig. 4). a fact illustrated by the large number of J.R. Cheeseman, V.G. Zakrzewski, l.A. COMPUTATIONAL CHEMISTRY COLUMN 770

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Montgomery, Jr., R.E. Stratmann, J.e. Nguyen, S.J. Su, T.L. Windus, together [25] Xmol of Minnesota Supercomputer Cent- Burant, S. Dapprich, J. M. Millam, A.D. with M. DupuiS: J.A. Montgomery, J. er, Inc., http://www.msc.edulmscldocs/ Daniels, K.N. Kudin, M.C. Strain, O. Far- Comput. Chem. 1993,14, 1347. xmol/ XMol.html kas, J. Tomasi, V. Barone, M. Cossi, R. http://www. ms g. ames lab. gov/G AM ESS/ [26] S. Portmann, A. Inauen, H.P. Luthi, S. Cammi, B. Mennucci, C. Pomelli, C. Ada- GAMESS.html Leutwyler, J. Chem. Phys. 2000,21. mo, S. Clifford, J. Ochterski, G.A. Peters- [19] E.J. Baerends, D.E. Ellis, P. Ros, Chem. [27] M.L. Connolly, J. Appl. Cryst. 1983, 16, son, P.Y. Ayala, Q. Cui, K. Morokuma, Phys. 1973,2,41; L. Versluis, T. Ziegler, 548. D.K. Malick, A.D. Rabuck, K. Raghava- J. Chem. Phys. 1988,322,88; G. te Velde, [28] M.L. Connolly, Quantum Chemistry Pro- chari, J.B. Foresman, J. Cioslowski, J.V. E.J. Baerends, J. Comput. Phys. 1992, gram Exchange Bull. 1981,1,74. Ortiz, B.B. Stefanov, G. Liu, A. Liash- 99(1), 84; e. Fonseca Guerra, J.G. Snij- [29] P.S. Heckbert, IEEE Computer Graphics enko, P. Piskorz, 1. Komaromi, R. Gom- ders, G. te Velde, E.J. Baerends, Theor. and Applications 1986, 56. perts, R.L. Martin, DJ. Fox, T. Keith, Chem. Ace. 1998, 99, 391, http://www. [30] P.S. Heckbert, 'Fundamentals of Texture M.A. AI-Laham, C.Y. Peng, A. Nanay- scm. com! Mapping and Image Warping', M.Sc. akkara, C. Gonzalez, M. Challacombe, [20] J. Ridley, M.e. Zemer, Theoret. Chim. Thesis, Department of Electrical Engi- P.M.W. Gill, B. Johnson, W. Chen, M.W. Acta 1976,42,223. neering and Computer Science, Universi- Wong, J.L. Andres, e. Gonzalez, M. [21] by H. Baumann ETHZ. ty of California, Berkeley, 1989. Head-Gordon, E.S. Replogle, and J.A. [22] M. Dupuis, J.D. Watts, H.O. Villar, G.J.B [31] http://reality.sgi.com!graficalsgiimage. Pople, Gaussian, Inc., Pittsburgh PA, Hurst, Comput. Phys. Comm., 1989, 52, html 1998. http://www.gaussian.com 415. [32] http://www.libtiff.org [18] M.W. Schmidt, K.K. Baldridge, J.A. [23] A. Derecskei-Kovacs, D. S. Marynick, In- [33] P.P. Flilkiger, S. Portmann, H.P. Uithi, Boatz, S.T. Elbert, M.S. Gordon, J.H. ternat. J. Quantum Chem., 1996,58, 193. 1999 Proceedings, Lecture Notes in Com- Jensen, S. Koseki, N. Matsunaga, K.A. [24] http://www.pdb.org puter Science 1615, Springer, 11.

Chimia 54 (2000) 770 © Neue Schweizerische Chemische Gesellschaft ISSN 0009-4293

Verleihung des Hellmann-Preises fur Theoretische Chemie

schlossen, jahrlich einen Hellmann-Preis sich Andreas Gorling von Prof. Levy in fi.ir hervorragende Leistungen in diesem die theoretische Analyse der Grundlagen Gebiet an Nachwuchswissenschafter und der Dichtefunktionale einfi.ihren.Andreas -wissenschafterinnen zu vergeben. Nach Gorling hat dann sowohl den grundlegen- der ersten Verleihung an Wim Klopper den Formalismus wie die anwendungs- 1999 wurde der Preis dieses Jahr an And- technischen Rechenverfahren weiterent- reas Gorling vergeben. Wir publizieren wickelt und wurde mit diesen Ergebnis- nachstehend die Laudation verbunden sen, zuruck in Mi.inchen, im Jahre 1995 mit unserer Gratulation an den Preistra- habilitiert. Seither hat er weitere Beitrage geL zur verbesserten dichtefunktionaltheore- Andreas Gorling, Jahrgang 1960, tischen Behandlung von Grund- und ins- studierte Chemie an der Technischen besondere von angeregten Zustanden in Universitat Mi.inchen.Ende der 80er Jahre kleineren Moleki.ilen wie in ausgedehn- rankten sich seine Dissertationsarbeiten ten Festkorpern, mittels selbstwechsel- bei Prof. Rosch urn verschiedene anwen- wirkungsfreier Austauschpotentiale und dungsorientierte Themenstellungen der unter Losung des Symmetriedilemmas, Theoretischen Chemie. Dabei machte er neuerdings auch zur Untersuchung nicht- erste Bekanntschaft mit der damals auch linearer optischer Phanomene, erarbeitet. Aus Anlass des 95. Geburtstages und des bei Chemikern in Mode gekommenen Die vornehmlich in Physical Review er- 60. Todestages des Quantenchemie-Pio- Dichtefunktionalmethode (deren Forde- schienenen Arbeiten wurden am 11. Sep- niers Hans G.A. Hellmann hatten 1998 rung durch Kohn und Pople 1998 mit tember 2000 auf dem 36. Symposium fi.ir die deutsche, osterreichische und schwei- dem Nobelpreis fUr Chemie ausgezeich- Theoretische Chemie in Litschau, Nie- zerische Tragerorganisation des 'Sympo- net wurde). Wahrend eines Hingeren derosterreich, mit dem 'Hans G.A. Hell- siums fi.ir Theoretische Chemie' be- Gastaufenthaltes in New Orleans liess mann-Preis 2000' ausgezeichnet.