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TmoleX—A Graphical User Interface for TURBOMOLE CLAUDIA STEFFEN,1 KLAUS THOMAS,1 UWE HUNIAR,1 ARNIM HELLWEG,1 OLIVER RUBNER,2 ALEXANDER SCHROER3 1
COSMOlogic GmbH & Co. KG, Burscheider Strasse 515, D-51381 Leverkusen, Germany 2 Institut für Physikalische Chemie, Universität Münster, D-48149 Münster, Germany 3 Physikalisches Institut, Universität Bonn, D-53115 Bonn, Germany Received 19 February 2010; Accepted 11 April 2010 DOI 10.1002/jcc.21576 Published online 31 May 2010 in Wiley Online Library (wileyonlinelibrary.com).
Abstract: We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.
J Comput Chem 31: 2967–2970, 2010
Key words: tmoleX; TURBOMOLE; quantum chemistry; GUI; DFT; MP2; PES; java
Introduction Quantum chemical programs are widely used in nearly all fields of chemistry, and there is also growing application in cognate disciplines, such as physics, biology, material science, or medicine. No longer the domain of just theoretical chemists scientists of all disciplines are now using quantum chemistry tools to aid their research. Hence, it is an important challenge for all program developers to consider the requirements of real-life applications in their work. In the late 1970’s, quantum chemical methods could be applied to only small, mainly organic molecules. In those days, the methods used were mostly Hartree–Fock (HF) or semiempirical, but in the following decade, it became possible to incorporate electron correlation effects at MP2 level for small systems. Because of the important advances in the methodology and algorithms in the 1990’s, density functional theory (DFT) became the workhorse of first principle studies throughout the whole periodic table. See refs. 1, 2 for some more historical information. With the recent advances in modern computer hardware, highly accurate methods like coupled cluster theory are becoming practical for medium sized molecules.3 TURBOMOLE4 is a quantum chemical program package covering single reference methods. It has pioneered significant reduction in CPU timings, disk space, and memory demands by various methods. The two most important methods are the two electron integral screening5 and the resolution of the identity (RI) approximation,6 which are now used in almost every quantum chemistry program. These and other efficient and robust approximations can turn a normal desktop or notebook to a powerful virtual laboratory or spectrometer.
To use TURBOMOLE, it is necessary to become acquainted with the collection of programs and scripts and to have some basic UNIX skills to handle this collection. TmoleX, as a Java-based graphical front–end has been developed to facilitate the usage of TURBOMOLE in both research and education.
Features and Philosophy TURBOMOLE development has always been focused on solving real life chemistry problems. The key points that result from this focus are: • • • • •
implementation of generally applicable methods, robust and efficient implementations, rigorous bounds and stable approximations, optimised compilation for all kinds of hardware, transparent modular program structure to enable customization for specific user needs.
The requirement for efficiency and robustness narrows the choice to specific methods. The keynote of the TmoleX program design was to retain this philosophy and present it graphically. The define Paradigm
The core functionality of TmoleX has to map the capabilities of the TURBOMOLE program define, which interactively creates
Correspondence to: A. Hellweg; e-mail:
[email protected]
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the required input files. Figure 1 displays a flowchart of how this is handled in TmoleX. The operations are Java swing panels. In each panel, settings can be adjusted or specific actions can be invoked. In Table 1 an overview of the panels and the actions is given. The usage of TURBOMOLE differs from many other quantum chemistry codes because of its input and output paradigm. Other programs often use one input and one output file. Requisite steps, such as the generation of initial molecular orbitals (MOs) or loading basis sets from a database, are processed during job execution. Job types (e.g., single point calculations or geometry optimization) are integrated in the programs. TURBOMOLE uses one input/output file called control which collects all information in a markup language style. Initial MOs and basis sets are loaded before the actual calculation is started using the user interactive define program. Job types or workflows are driven by scripts. This modus operandi
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Table 1. The Main Panels.
Panels
Possible actions
Geometry
Atomic attributes
Molecular attributes
Method
Load and manipulate structure; detect or change the molecular symmetry group; create internal coordinates; fix coordinates. Assign one electron basis sets for all atoms, per element, or for individual atoms; choose between all basis sets of the TURBOMOLE basis set library. Set molecular charge and optionally the multiplicity; create start MOs; by default the multiplicity is automatically determined by the energy of the start orbitals; the occupation can be changed or Fermi pseudo smearing can be used to lift multiplicity constraints and optimize to the lowest spin state; visualize the orbital energies; set the frozen core for correlated methods. Choose level of theory (HF, DFT, DFT-D, MP2, CC2, SCS-MP2, CCSD, CCSD(T)); select auxiliary basis sets for the RI-approximation; switch the continuum solvation model COSMO on or off; expert settings for SCF convergence and solvation.
has a lot of benefits for experts, but often is cumbersome for nonexpert users. With TmoleX, the complexities are considerably reduced, making it much easier for nonexperts. General Workflow
The define paradigm is flanked on one side (before define) by a 3D molecule builder and preoptimization tools, and on the other side (after define) by interfaces for job submission and job administration and tools to visualize the results. In Figure 2, an overall flowchart of TmoleX is sketched. 3D Molecular Builder
The 3D builder offers the possibility to create a molecule atom by atom or by adding and merging fragments from a customizable library. The 3D representations of the molecules as well the orbitals and densities (see below) are being generated using the OpenGL (Open Graphics Library) programming interface. This standard ensures platform independence, supports 3D hardware acceleration if present, and, because Java Bindings for OpenGL (JOGL) has been introduced, a suitable interface to Java programs is available. Preoptimization
Figure 1. Flowchart of the define paradigm.
In many cases, a fast preoptimization step can save a lot of time for the following DFT or ab initio calculation. For this purpose, the semi empirical molecular orbital package MOPAC77 is integrated in the 3D builder. With MOPAC7, geometry optimizations and transition state searches can be performed on various levels. Semiempirical approaches are a mixed blessing. They are fast, but only perform well for systems similar to the ones for which they are parametrized. Sometimes, they simply fail. Thus, the results should be scrutinized closely.
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Figure 2. Flowchart of TmoleX.
Figure 3. Flowchart of the job submission.
Job Submission
Potential Energy Surfaces
Once a production run is prepared, a TURBOMOLE calculation can be started. This is a straightforward task if the job is started on the same computer that is running TmoleX. However, for many applications, it is preferable to run TURBOMOLE on a remote computer or even parallel on remote compute clusters because the computational costs can be too demanding for desktop computers. The flowchart of job submission is sketched in Fig. 3. The scp and ssh implementations of PuTTY8 are being used. An advantage of this particular implementation is that passwords can be transferred to the remote computer as a command line flag. Thereby, the user needs to type the login data only once per session. It should be pointed out that passwords are not stored anywhere in TmoleX. They are kept in the memory only during a session and are deleted afterward.
The calculation of potential energy surfaces (PES) is a very important task in computational chemistry. For example, a PES can be used to calculate spectroscopic parameters, identify stationary points, or to understand dissociation channels. Automated scans of a PES are
Visualization of Results
The visualization of computational results can be very helpful for analysis and interpretation. In TmoleX, results from geometry optimizations and vibrational frequency calculations can be animated as movies. In addition, IR, Raman, UV/Vis, and CD spectra can be plotted as line spectra or with superimposed Gaussian functions. If data, such as MOs, densities, or electrostatic potentials, has been calculated on grids, this can be visualized with the 3D OpenGL viewer. An example of visualized MOs is given in Fig. 4. Journal of Computational Chemistry
Figure 4. The HOMO of thiophene.
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usually done by varying one or more internal coordinates systematically while performing either single point calculations (unrelaxed PES scans, sometimes also called rigid PES scan) or constrained geometry optimizations (relaxed PES scan) for each point. TmoleX lets the user to select the desired internal coordinates, to set start and end values, and the stepsize. Then, the scan is performed automatically. If only one coordinate is scanned then the energy curve is plotted for convenience. Templates
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functional version for the remote operation mode, called “client version,” is freely available for download.9 The future development of TmoleX has three directions. First, more TURBOMOLE functionality will be accomodated. Second, the scripting capability of Java will be exploited to create more sophisticated workfows for application such as reaction path modelling, QM/MM calculations, or molecular dynamic simulations. Third, the postprocessing tools will also be extended.
Acknowledgments
Often computations have to be performed for different systems at the same level of theory and using the same job types (mainly geometry optimizations). For such tasks, TmoleX offers a set of predefined templates. If a template is selected for a given molecule, the calculation can be started directly, without having to execute the steps in between. This allows for a fast setup of calculations. In many cases, users have their own preferred setting for performing quantum chemical calculations. Hence, user defined templates can also be created for TmoleX.
The authors thank David A. Gallagher, CAChe Research LLC, and Hirotaka Ikeda, Ryoka Systems Inc., and all colleagues at COSMOlogic GmbH & Co. KG for valuable discussions.
References 1. 2. 3. 4.
Summary and Outlook We have developed a Java application that facilitates the setup and execution of TURBOMOLE calculations. Additionally, an integrated 3D molecule builder and tools for the visualization of results have been designed. TmoleX enables nonexpert users to perform state-of-the-art quantum chemical calculations, and it allows experienced users the flexibility to handle nonstandard tasks. A fully
5. 6. 7. 8. 9.
Pople, J. A. Angew Chem Int Ed 1999, 38, 1894. Friesner, R. A. Proc Natl Acad Sci USA 2005, 102, 6648. Bartlett, R. J.; Musial, M. Rev Mod Phys 2007, 79, 291. TURBOMOLE, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com. Häser, M.; Ahlrichs, R. J Comput Chem 1989, 10, 104. Vahtras, O.; Almlöf, J. E.; Feyereisen, M. W. Chem Phys Lett 1993, 213, 514. Stewart, J. J. P. J Comput Aided Mol Des 1990, 4, 1. PuTTY, available from http://www.chiark.greenend.org.uk/∼sgtatham/ putty. TmoleX Client, available from http://www.cosmologic.de/tmolexclient.
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