GAMESS-UK USER'S GUIDE and REFERENCE MANUAL Version
Contents
1. n successive F fields The omission of the integer n before a letter code implies that n 1 More complicated descriptors are used for example iA jl kF describes a line consisting of i A fields followed by j l fields followed by k F fields Consider the following line ATOM 10 1 0 12 HCH read to the variables TEXT X J BTEXT in format A I F I A TEXT will be set to the character string ATOM will be set to the decimal integer 10 X will be set to the floating point value 1 0 J will be set to the decimal integer 12 BTEXT will be set to the character string HCH The same line could be read to variables TEXT X Y ATEXT BTEXT in format A 2F 2A so that TEXT will be set to the character string ATOM X will be set to the floating point value 10 0 Y will be set to the floating point value 1 0 ATEXT will be set to the character string 12 BTEXT will be set to the character string HCH 6 RESTRICTIONS 11 Consider reading the following line GENERALISED ATOMIC AND MOLECULAR ELECTRONIC STRUCTURE SYSTEM to A I 1 7 in format 7A e A 1 will be set to the string GENERALI Note the truncation e A 2 will be set to the string ATOMIC e A 3 will be set to the string AND e A 5 will be set to the string ELECTRON Note the truncation 1 2 3 e A 4 will be set to the string MOLECULA Note the truncation 5 e A 6 will be set to the string STRUCTUR Note the truncation 7 e A2. 2 Changes introduced in GAMESS UK Version 6 3 15 7 3 Changes introduced in GAMESS UK Version 6 2 17 8 Enquiries 17 9 Acknowledgement 18 1 About This Manual This manual is divided into sixteen parts or chapters which may be broadly classified as follows 1 ABOUT THIS MANUAL 2 e Part 1 this part describes the general features of the program detailing the file system employed and the directive structure associated with the free format data input e Part 2 presents a series of example data files designed to provide a broad outline of the various capabilities of the program Subsequent chapters provide a more detailed description of the data input formats e Parts 3 and 4 describe the directives required in performing SCF Mgller Plesset CASSCF MCSCF DFT and associated gradient calculations e Part 5 deals with integral transformation and Direct Cl calculations e Part 6 covers conventional and semi direct Table Cl calculations e Part 7 describes the data required in performing RPA and MCLR calculations e Part 8 describes the various analysis capabilities of the code plus the directives and scope of the DRF solvation module e Part 9 presents a brief summary of possible problem areas in running the code e Part 10 provides a brief summary of the utility functions associated with GAMESS UK e Part 11 describes the way formatted output may be obtained from GAMESS UK for use by other pro
3. 7 will be set to the string SYSTEM 5 3 GAMESS UK Directives Data input is largely structured as a sequence of directives Directives sometimes extend over many lines sometimes they comprise a single line and usually contain some reasonably self contained data built up out of A l and or F fields The first field of a directive is invariably an A field carrying the name of the directive Note that only the first four characters of such an identifier are in practice required The directives group into two classes with Class 1 directives see Part 3 specified before Class 2 directives see Part 4 note that the order within each class may be important and the user is recommended to follow the order outlined in the relevant sections of the manuals or example inputs where available 5 3 1 INCLUDE Including external files in an input file As of version 7 0 it is possible to include external text files into a GAMESS UK input file through the use of the include directive Thus the line include home wab inputs geometry txt placed in a GAMESS UK input file would cause the geometry txt file to be inserted at that point in the input file 6 Restrictions The restrictions which the present program place on the user are as follows e Gaussian functions of s p d f and g may be used 7 RELEASE NOTES FOR GAMESS UK 12 The maximum number of contracted orbitals depends in general on the functionality re quested Con
4. Rys Polynomial or Rotation techniques 2 to evaluate repulsion inte grals over s p d f and g type Cartesian Gaussian orbitals Open and closed shell SCF treatments are available within both the RHF and UHF framework with convergence controls provided through a hybrid scheme of level shifters and the DIIS method 3 In addition generalised valence bond 4 complete active space SCF 5 and more general MCSCF 6 MASSCF 8 and M ller Plesset MP2 and MP3 7 calculations may be performed The original limitation to cartesian basis sets is lifted through the provision of spherical harmonic basis sets for all options within the programme The most recent additions to the code available from Version 6 0 onwards include a full featured Density Functional Theory DFT module with access to a wide variety of functionals S VWN B LYP B P86 B3 LYP HCTH B97 B97 1 B97 2 FT97 etc This module is subject to on going developments under the auspices of CCP1 The analytic energy gradient is available for each class of wavefunction above Gradients for s and p Gaussians are evaluated using the algorithm due to Schlegel 9 while gradients involving d f and g Gaussians utilise the Rys Polynomial Method 2 GENERAL FEATURES 4 Geometry optimisation may be carried out using the DL FIND module that is included into GAMESS UK see Part 4 for information about DL FIND Alternatively GAMESS UK has it s own optimisation capabilities using a quasi New
5. file creation file manipulation etc The program also includes version 7 0 of the MOPAC 38 semi empirical code enabling the calculations with the semi empirical Hamiltonians MNDO MINDO 3 AM1 PM3 PM5 and MNDO d The interface between GAMESS UK and MOPAC allows coordinates calculated with MOPAC to be imported into GAMESS UK for a subsequent ab initio calculation A free Graphical User Interface the CCP1GUI has also been developed to simplify the use of the code and to graphically display the results of calculations Further information on the CCP1GUI as well as downloadable packages for a number of different operating systems can be found on the web at http www cse scitech ac uk ccg software ccplgui Areas of application for GAMESS UK include e Theoretical studies of reaction surfaces SCF and MCSCF calculations of equilibrium and transition state geometries and the evaluation of force constants and vibrational frequencies at these stationary points e Energy assignments in the entire field of electronic spectroscopy Calculation of spectro scopic properties of highly excited molecular and ionic states Evaluation of transition moments e Graphical and numerical analysis of Hartree Fock and post Hartree Fock wavefunctions e Generation of zero order wavefunctions required in the more extensive treatments of dy namical correlation energy Applicability to general systems with many electrons in this treatment of dynamical c
6. file delimited by the keywords newscf and end following the specification of the runtype This functionality is available in serial and within the parallel MPI ScaLAPACK driver Changes to the DFT Module e New DFT Functionals Several new functionals have been added PBE exchange correlation functional HCTH120 HCTH147 HCTH407 KT1 and KT2 functionals PW92 local correlation functional RELEASE NOTES FOR GAMESS UK 13 PW91 exchange correlation and exchange correlation functionals B95 meta GGA correlation functional BB95 B1B95 and BB1K meta GGA functionals NB for the meta GGA func tionals only the energies and gradients can be calculated the second derivatives of the energy are not available e More flexible DFT grid specifications The atom size is used in a number of tests within in the DFT code Previously the same size was used for all tests however it is now possible to specify the atomic size for each test separately as shown in the examples below a The atomic radii for the angular grid pruning schemes pradii 3 0 b The atomic size adjustment radii for the weighting scheme wradii 3 0 c The screening radius sradii 3 0 d The radial grid scale factor radii 3 0 It is also now possible to specify the grid size for a row of the periodic table previously this had to be done on a per element basis For example to specify the grid size for the Lebedev Laikov angular grid
7. for logging and querying bugs with the code has also been added The new URL for the main GAMESS UK website is http www cfs dl ac uk CCP1GUI The CCP1GUI is a free extensible Graphical User Interface to various computational chemistry codes Although it has interfaces to other codes such as Dalton and Mopac the CCP1GUI has been developed around GAMESS UK and provides a powerful tool for setting up and viewing the results of calculations with GAMESS UK The CCP1GUI website can be found at http www cse scitech ac uk ccg software ccp1lgui Changes introduced in GAMESS UK Version 6 3 Section numbers for vectors enter can now be omitted DMA analysis now uses Slater radii table 7 RELEASE NOTES FOR GAMESS UK 16 3 10 11 12 13 The old option of performing a DFT energy calculation on a HF density a posteriori is no longer in the default build This can still be accessed using the old dft keyword in the configure response at build time Changes to the DFT module e More flexible grid input e Additional DFT functionals FT97 HCTH B97 B97 1 and B97 2 etc e Optimisations to coulomb fit DFT code e Built in DFT Orbital sets DZVP DZVP2 and TZVP and Auxiliary Coulomb Fitting Basis sets DGauss Al and A2 DeMon and those due to Ahlrichs e Gradient term from derivative of quadrature weights included Reduced functionality build options SCF DFT and MP2 for use on parallel machines with limi
8. 003 doi 10 1063 1 1615954 9 H B Schlegel J Chem Phys 77 1982 3676 doi 10 1063 1 444270 10 S Bell and J S Crighton J Chem Phys 80 1984 2464 doi 10 1063 1 446996 11 C J Cerjan and W H Miller J Chem Phys 75 1981 2800 doi 10 1063 1 442352 12 J Simons P Jorgensen H Taylor and J Ozment J Phys Chem 87 1983 2745 doi 10 1021 j100238a013 A Banerjee N Adams J Simons and R Shepard J Phys Chem 89 1985 52 doi 10 1021 j100247a015 13 J Baker J Comp Chem 7 1986 385 doi 10 1002 jcc 540070402 14 J A Pople R Krishnan H B Schlegel and J S Binkley Int J Quant Chem 14 1978 545 doi 10 1002 qua 560140503 Y Osamura Y Yamaguchi P Saxe M A Vincent J F Gaw and H F Schaefer Chem Phys 72 1982 131 doi 10 1016 0301 0104 82 87073 0 15 R M Stevens R M Pitzer and W N Lipscomb J Chem Phys 38 1963 550 doi 10 1063 1 1733693 16 R D Amos Adv Chem Phys 67 1987 99 17 P J Hay and W R Wadt J Chem Phys 82 1985 270 doi 10 1063 1 448799 284 doi 10 1063 1 448800 299 doi 10 1063 1 448975 18 Ph Durand and J C Berthelat Theoret Chim Acta 38 1975 283 doi 10 1007 BF00963468 19 R J Buenker in Proc of the Workshop on Quantum Chemistry and Molecular Physics Wollongong Australia 1980 R J Buenker in Studies in Physical and Theoretical Chem istry 21 1982 17 20 P E M Siegbahn J Chem Phys 72 1980 164
9. 7 doi 10 1063 1 439365 V R Saunders and J H van Lenthe Mol Phys 48 1983 923 doi 10 1080 00268978300100661 21 S Zarrabian and R J Harrison Chem Phys Lett 81 1989 393 398 doi 10 1016 0009 2614 89 87358 0 22 T J Lee and J E Rice Chem Phys Lett 150 1988 406 415 doi 10 1016 0009 2614 88 80427 5 23 G E Scuseria A C Scheiner T J Lee J E Rice and H F Schaefer J Chem Phys 86 1987 2881 doi 10 1063 1 452039 24 T J Lee A P Rendell and P R Taylor J Phys Chem 94 1990 5463 doi 10 1021 j100377a008 25 A P Rendell T J Lee and A Komornicki Chem Phys Lett 178 1991 462 470 doi 10 1016 0009 2614 91 87003 T REFERENCES 20 26 T J Lee J E Rice and A P Rendell The TITAN Set of Electronic Structure Programs 1991 27 L S Cederbaum and W Domcke Adv Chem Phys 36 1977 205 28 J Schirmer and L S Cederbaum J Phys B11 1978 1889 doi 10 1088 0022 3700 11 11 006 29 C Fuchs V Bonati Koutecky and J Kouteck J Chem Phys 98 1993 3121 doi 10 1063 1 464086 30 Based upon Version 3 0 of the NBO program from the Quantum Chemistry Program Exchange No 408 1980 A E Reed L A Curtiss and F Weinhold Chem Rev 88 1988 899 926 doi 10 1021 cr00088a005 F Weinhold and J E Carpenter in R Naaman and Z Vager eds The Structure of Small Molecules and lons Plenum New York 1988 pp 227 236 31 Interface to Version 94 Rev
10. Computing for Science CFS Ltd CCLRC Daresbury Laboratory Generalised Atomic and Molecular Electronic Structure System SSS Se GAMESS UK USER S GUIDE and REFERENCE MANUAL Version 8 0 June 2008 PART 1 INTRODUCTION and GENERAL FEATURES M F Guest J Kendrick J H van Lenthe P Sherwood and J M H Thomas Copyright c 1993 2008 Computing for Science Ltd This document may be freely reproduced provided that it is reproduced unaltered and in its entirety Introduction to GAMESS UK GAMESS UK is a general purpose ab initio molecular electronic structure program for perform ing SCF DFT and MCSCF gradient calculations together with a variety of techniques for post Hartree Fock calculations The program is derived from the original GAMESS code obtained from Michel Dupuis in 1981 then at the National Resource for Computational Chemistry NRCC and has been extensively modified and enhanced over the past decade This work has included contributions from nu merous authors see below and has been conducted largely at the former EPSRC Engineering and Physical Sciences Research Council and now CCLRC Daresbury Laboratory under the auspices of Collaborative Computational Project No 1 CCP1 Other major sources that have assisted in the on going development and support of the program include various academic funding agencies in the Netherlands and ICI plc All publications resulting from use of this program must include
11. IS DMA A J Stone Chem Phys Letters 83 1981 233 doi 10 1016 0009 2614 81 85452 8 e OUTER VALENCE GREENS FUNCTION OVGF L S Cederbaum and W Domcke Adv Chem Phys 36 1977 205 e TAMM DANCOFF METHOD TDA J Schirmer and L S Cederbaum J Phys B11 1978 1889 L H Hillier K Rigby M Vincent M F Guest and W von Niessen Chem Phys Lett 134 1987 403 doi 10 1016 0009 2614 87 87162 2 e EFFECTIVE CORE POTENTIALS LOCAL ECPs P J Hay and W R Wadt J Chem Phys 82 1985 270 284 299 doi 10 1063 1 448800 iii e EFFECTIVE CORE POTENTIALS NON LOCAL ECPs Ph Durand and J C Berthelat Theoret Chim Acta 38 1975 283 doi 10 1007 BF00963468 N A Burton I H Hillier M F Guest and J Kendrick Chem Phys Lett 155 1989 195 doi 10 1016 0009 2614 89 85348 5 e INFRA RED AND RAMAN INTENSITIES R D Amos Adv Chem Phys 67 1987 99 doi 10 1002 9780470142936 ch2 e MULTI CONFIGURATION LINEAR RESPONSE MCLR C Fuchs V Bonati Koutecky and J Kouteck J Chem Phys 98 1993 3121 doi 10 1063 1 464086 e COUPLED CLUSTER CCSD anD CCSD T T J Lee J E Rice and A P Rendell The TITAN Set of Electronic Structure Programs 1991 DENSITY FUNCTIONAL THEORY DFT The initial DFT module within GAMESS UK was developed by Dr P Young under the auspices of EPSRC s Collaborative Computational Project No 1 CCP1 1995 1997 Subsequent developments have been undertaken by staff at the D
12. _id 14 e The gamess uk users email list is the place to raise any queries about the code or to ask for advice on using the code The homepage for the list can be found at http ccpforge cse rl ac uk mailman listinfo gamess uk users 9 ACKNOWLEDGEMENT 18 Note that an electronic copy of this manual is available under the CFS web pages http www cfs ac uk docs index shtml 9 Acknowledgement This program resulted from the efforts of many researchers we gratefully acknowledge the on going collaborative efforts of those colleagues detailed in the preface to this manual References 1 M F Guest I J Bush H J J van Dam P Sherwood J M H Thomas J H van Lenthe R W A Havenith J Kendrick The GAMESS UK electronic structure pack age algorithms developments and applications Molecular Physics 103 2005 719 747 doi 10 1080 00268970512331340592 M F Guest J Kendrick GAMESS Users Manual SERC Daresbury Laboratory CCP1 86 1 1986 M Dupuis D Spangler and J Wen doloski NRCC Software Catalog Vol 1 Program No QG01 GAMESS 1980 M F Guest R J Harrison J H van Lenthe and L C H van Corler Theor Chim Acta 71 1987 117 doi 10 1007 BF00526413 Note The CDC version of the GAMESS code was obtained from M Dupuis in June 1981 Serious development work on the program com menced in January 1982 after conversion to VAX and IBM systems All sections of the original code have either been extensively modified or re
13. ances however it may be necessary to keep the files in question between jobs This activity should be controlled through the appropriate FILE pre directives see Part 3 of this manual 5 Data Input The Directive Structure Data input for GAMESS UK consists of a sequence of data lines where a GAMESS UK data line consists of a number of data fields the fields being separated by at least one space character The separating spaces are not considered part of the data field 5 1 Data Lines Data lines normally end at column 72 assuming a carriage return is used as the line terminator although this can be altered by means of the pre directive WIDTH see Part 3 of this manual In fact there are several valid terminators recognised for a data line These include 5 DATA INPUT THE DIRECTIVE STRUCTURE Table 1 Direct Access Files and Default LFNs used by GAMESS UK File Contents Default LFN Mainfile Two electron integrals ED2 Dumpfile Eigenvectors restart information ED3 Hessians Cl coefficients etc Scratchfile Temporary file for program ED7 housekeeping Libraryfile Pseudopotential Library File EDO Symmetry Adapted Two electron integrals in a symmetry ED1 Mainfile adapted basis Secondary Mainfile Partially transformed two electron ED4 integrals Direct CI file Direct Cl file for restarts ED5 and symbolic hamiltonian etc Transformed Integral Transformed two electron integrals ED6 File Overflow file Direct C
14. aresbury Laboratory e DIRECT REACTION FIELD DRF A H de Vries P Th van Duijnen A H Juffer J A C Rullmann J P Dijkman H Merenga and B T Thole J Comp Chem 16 1995 37 55 doi 10 1002 jcc 540160105 erratum 1445 1446 doi 10 1002 jcc 540161113 P Th van Duijnen and A H de Vries Int J Quant Chem 60 1996 1111 doi 10 1002 SIC1 1097 461X 1996 60 6 1111 AID QUA2 3 0 CO 2 2 Additional key references and background material on each of the modules are provided at appropriate points throughout this manual CONTENTS 1 Contents 1 About This Manual 1 2 General Features 3 3 Units used in the manual 6 ay WORD e oe em ER eed bo ees a be es ee PRN ns Set oe es Bot Se ee ss ts See een es oe 6 4 The File System 4 1 Direct Access Data Sets 2 aa a a a a a a a a a 4 2 FORTRAN Data Sets o ca 044680 d i aaea 48 eE 45 2 8e 5 T 5 Data Input The Directive Structure 7 51 Data LNE 23 a4 ook eao AEM Se eS he a eh ws i f 52 Data Feds 2 ced ganein a aoe we ae we a ee e a E d 9 5 3 GAMESS UK Directives 2 oscsaac eceran ee 11 5 3 1 INCLUDE Including external files in an input file 11 6 Restrictions 11 7 Release Notes for GAMESS UK 12 7 1 Changes introduced in GAMESS UK Version 7 0 12 7 1 1 Changes to GAMESS UK functionality 12 7 1 2 Changes to the structure of the code 0 14 7 3 Peripheral Changes o co ece cia sea ow Gea we eta ee Ee 15 7
15. ated to the program using logical file names LFNs in the range EDO ED1 ED19 and MTO MT1 MT19 In Table 1 we list those files used by the program and define the default LFN associated with each file A full description of data set management will not be given here for the present it suffices to note the following 1 The Dumpfile which in default is routed to ED3 is crucial to the program and controls all restart activities This file is organised into variable length sections with the user nom inating various sections for data storage e g eigenvectors The sections are characterised by integers in the range 1 350 which are specified by the user through data input 2 The Scratchfile which is routed to ED7 is used in all runs of the program as a file for house keeping activities While this data set need never be maintained across separate runs of the program the user should be aware of the role of ED7 and avoid any attempts to use the data set in for example the re routing of integral output 5 DATA INPUT THE DIRECTIVE STRUCTURE 7 3 Each data file is block addressable 1 block 512 words In default output of each file commences at block 1 of the associated data set and continues in uninterrupted fashion until output is complete With certain exceptions the user may control file usage in several ways e redefine the LFN to be associated with a given data file e redefine the starting block for the file all
16. ded to the MRDCI module The use of the HARMONIC directive has been extended to the Valence Bond code allowing spherical harmonic basis sets to be used for d f and g functions A simple solvation model has been implemented in the Valence Bond code Arbitrary not spinadapted wavefunctions are now possible in the Valence Bond code The Valence Bond module can be compiled with 8 byte integers The RESTORE option has been added to the ZORA module to allow zora relativis tic atomic corrections to be stored and restored on the current and foreign dumpfile This permits easy restart calculations when the ZORA corrections do not need to be recalculated New distributed data MPI HF DFT driver A distributed data HF and DFT module has been developed using MPl based tools such as ScaLAPACK All data structures except those required for the Fock build are fully distributed The functionality of this code is currently limited to closed shell and unrestricted open shell To build this code BLACS and ScaLAPACK available from http www netlib org must be installed on the target machine and the mpi build option selected when configuring the code Taskfarming Harness A taskfarming harness has been developed This is an MPI program designed to be run on a large number of processors on a parallel machine and batch processes numerous small GAMESS UK jobs The taskfarming harness is currently only available as a
17. electric to model bulk response both static and electronic of the surroundings and iv by an enveloping ionic solution characterized by its Debye screening length The treatment of relativistic effects is provided within the ZORA scheme Zeroth Order Regular Approximation 36 a two component alternative to the full 4 component Dirac equation 2 GENERAL FEATURES 5 While much cheaper than the latter ZORA recovers a large part of the relativistic effects The scalar 1 component form is now available with the full 2 component implementation including spin orbit coupling in progress The current implementation will allow all usual Ab Initio and DFT methods to be performed incorporating the major relativistic effects The restriction of a maximum of 255 basis functions when performing conventional processing of two electron integrals has been removed in nearly all modules in Version 7 0 of the code The program structure is open ended in both direct SCF DFT and direct MP2 mode so that direct SCF calculations up to 22 000 basis functions have been performed Version 7 0 also features a significant extension to the parallel capabilities of GAMESS UK In addition to the functionality outlined above the program provides for i Hybrid QM MM calculations through an interface to the CHARMM QM MM code developed in collaboration with B Brooks and E Billings of the NIH and ii a Utilities module concerned with house keeping library
18. field consists of a succession of non space characters on a single line Three types of field are in use e A fields are used for the introduction of textual material in the form of character strings The maximum length of an A field is 8 characters A fields of less than 8 characters are padded to the right with spaces while if more than 8 characters are found the field is truncated from the right so that only the leftmost 8 characters are significant e fields are used for the introduction of numeric data in the form of integers and consist of a succession of decimal digits possibly preceded by a or sign The sign character may be omitted when the integer is assumed to be positive The following are examples of valid I fields 762 4033 6149 5 DATA INPUT THE DIRECTIVE STRUCTURE 10 F fields are used for the input of floating point numbers They are as I fields except that a decimal point character may appear to the right of the sign character To introduce a decimal exponent a concatenation of a F field followed by the character E or D followed by an I field without intervening blanks is allowed The following are equivalent F fields o 0 0 0 0 0 0 as are 0 0003 3E 4 3D 4 0 3E 3 30E 5 and 500 0 500 5E2 5E 2 5D 2 Format descriptors are used to describe a data line The simplest of these takes the form nA or nl or nF where n is a decimal integer Thus the format nF describes a line consisting of
19. for the first row of the periodic table lebedev row 1 194 6 Changes to the Post HF Modules e The 255 basis function limit in the MRDCI code has been removed so that the code is effecively open ended in the number of basis functions permitted e Configuration Interaction Transformation between AO and MO basis has been ex tended to g functions e A facility to allow the punching of both transformed integrals and Cl coefficients from the full Cl code has been introduced This uses i the cards directive and ii an extension of the current print facility within the Full Cl module Thus the data file core 10000000 title h2co 3 21g basis valence full ci super off nosym cards trans fullci zmatrix angstrom c o 1 1 203 h 1 1 099 2 121 8 h 1 1 099 2 121 8 3 180 0 end active 5 to 22 end core 1 to 4 end runtype ci fullci 18 4 4 punch 1 8 enter Would result in a complete list of transformed le and 2e integrals to the file moints ascii and all ci coefficients greater than 1 10 8 to the file civecs ascii 7 RELEASE NOTES FOR GAMESS UK 14 10 11 12 13 e The filenames for the files use in Cl calculations can now be set through file directives in the input file as well as environment variables e MR ACPF Multireference Averaged Coupled Pair Functional MR AQCC Multi Reference Average Quadratic Coupled Cluster and the CEPAO coupled electron pair approximation methods have been ad
20. grams e Part 12 presents a sequence of worked examples on a UNIX machine using the specially provided script rungamess e Part 13 provides a series of worked examples invoking the GAMESS UK binary directory from a UNIX shell C shell e Part 14 describes the capabilities and running of the parallel version of GAMESS UK on both MPP and SMP hardware e Turtle describes how to run the GAMESS UK Valence Bond module e Mopac describes the GAMESS UK MOPAC interface The user who wishes to acquire rapid familiarity and a sufficient subset of knowledge to use the program albeit perhaps in a somewhat restricted fashion should concentrate initially on Parts 1 and 2 together with any appropriate examples from Parts 12 14 The example input files described in Part 2 are supplied with GAMESS UK and can can be found in the scripts labelled c2001_a c2035 in the directory GAMESS UK examples chap2 NB this documentation describes features available in the current release of the code Version 8 0 some of the features described herein may not function as described in earlier releases of the program 2 GENERAL FEATURES 3 2 General Features GAMESS UK 1 is a general purpose ab initio molecular electronic structure program for performing SCF DFT and MCSCF gradient calculations together with a variety of techniques for post Hartree Fock calculations On going development of the code is co ordinated from Daresbury with the program curren
21. ision B of AIMPAC F W Biegler Konig R F W Bader and T H Tang J Comp Chem 3 1982 317 328 doi 10 1002 jcc 540030306 32 A J Stone Chem Phys Lett 83 1983 233 239 doi 10 1016 0009 2614 81 85452 8 33 A H de Vries P Th van Duijnen A H Juffer J A C Rullmann J P Dijkman H Merenga and B T Thole J Comp Chem 16 1995 37 55 doi 10 1002 jcc 540160105 erratum 1445 1446 doi 10 1002 jcc 540161113 34 P Th van Duijnen and A H de Vries Int J Quant Chem 60 1996 1111 doi 10 1002 SICI 1097 461X 1996 60 6j1111 AID QUA2 3 0 CO 2 2 35 H J J van Dam J H van Lenthe and P Pulay Mol Phys 93 1998 431 doi 10 1080 002689798169122 36 S Faas J G Snijders J H van Lenthe E van Lenthe E J Baerends Chem Phys Lett 246 1995 632 640 doi 10 1016 0009 2614 95 01156 0 37 D Moncrieff and V R Saunders ATMOL Introduction Notes UMRCC May 1986 Cyber 205 Note Number 32 UMRCC September 1985 V R Saunders and M F Guest ATMOL3 Part 9 RL 76 106 1976 M F Guest and V R Saunders Mol Phys 28 1974 819 doi 10 1080 00268977400102171 38 MOPAC 1993 Version 7 00 J J P Stewart Fujitsu Limited Tokyo Japan
22. l file for ED8 symbolic hamiltonian Loop Formulae Tape Symbolic formulae used in CASSCF ED9 Reordered Formulae Reordered symbolic formulae ED10 Tape Density Matrix File Two particle density matrix ED11 used in CASSCF geometry optimisation Hamiltonian File Derivative Fock Operators ED12 Reordered Integral Reordered two electron integrals ED13 File used in MCSCF Scratchfiles Temporary files used in ED16 ED19 derivative integral calculations Sortfile Temporary file for sorting SORT integrals P Sortfile Temporary file for sorting molecular PSORT integrals Tablefile Table CI file for storing data base TABLE of pattern matrix elements 5 DATA INPUT THE DIRECTIVE STRUCTURE 9 e the conventional carriage return CR e the back slash character e the colon character Thus the following sequence of data lines TITLE H2CO 3 21G DEFAULT BASIS CLOSED SHELL SCF ZMATRIX ANGSTROM N 0 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END ENTER could be presented as TITLE H2C0 3 21G DEFAULT BASIS CLOSED SHELL SCF ZMATRIX ANGSTROM C O 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END ENTER Note also that a data line with one of the characters gt or lt in the first column will be treated by the program as comment lines being merely echoed to the output file It goes without saying that the character should be avoided in any TITLE data 5 2 Data Fields A data
23. lence ionization energies may be performed though Green s function techniques using either the outer valence Green s function OVGF 27 or the two particle hole Tamm Dancoff method 2ph TDA 28 Calculations of electronic transition energies and corresponding oscillator strengths may also be performed using either the Random Phase Approximation RPA method or the Multiconfigura tional Linear Response MCLR procedure 29 The RPA calculations may be performed either within the conventional approach where the two electron integrals are transformed or with a direct implementation A variety of wavefunction analysis methods are provided including population analysis Natural Bond Orbital NBO 30 and distributed multipole analysis 32 localised orbitals graphical analysis and calculation of 1 electron properties An interface to the AIMPAC code of Bader is provided 31 for SCF DFT MCSCF MP2 MP3 MRDCI and Direct Cl calculations The treatment of solvation effects is now based on the DRF Direct Reaction Field model 33 34 an embedding technique enabling the computation of the interaction between a quantum mechanically described molecule and its classically described surroundings The clas sical surroundings may be modelled in a number of ways i by point charges to model the electrostatic field due to the surroundings ii by polarizabilities to model the electronic re sponse of the surroundings iii by an enveloping di
24. ncluded in Release 6 3 1 Work on CHARMM interface code Changes introduced in GAMESS UK Version 6 2 New functionality available includes e Alpha release of Direct Reaction Field module e Gaussian functions of s p d f and g may now be used e Alpha release of ZORA Relativistic treatment e Production release of Density Functional Theory DFT module e Alpha release of semi direct Table Cl module Change to the default behaviour of the DFT module Users of alpha releases of the DFT module should note that now e the default functional is now B LYP e the default grids are now constructed from the logarithmic grid of Knowles and Mura previously the SG1 grid was selected by default Point charge calculations using BQ centres the nuclear energy now excludes the term arising from BQ BQ interactions This should simplify the construction of QM MM models by allowing the classical electrostatic energy to be computed entirely within the MM code The original behaviour may be restored with the BQBQ directive 8 Enquiries All enquiries regarding the availability of the program documented herein should be directed in the first instance to the following E Mail address at Daresbury gamess_uk_contact dl ac uk For any problems arising from use of the program there are two sources of help e There is a bug tracker that lists known problems with the code which can be found at http ccpforge cse rl ac uk tracker group
25. orrelation energy Benchmark treatments of correlation energy using Full Cl calculations e Theoretical mechanistic studies of chemisorption in heterogeneous catalysis e Treatment of bio organic and related molecules through Direct SCF calculations and electrostatic potential analysis 3 UNITS USED IN THE MANUAL 6 3 Units used in the manual Throughout the manual use is made of the units of words and blocks to describe the sizes of files and or memory These are defined as follows 3 1 WORD A word is defined as a FORTRAN DOUBLE PRECISION or INTEGER 8 datatype and is 8 bytes 64 bits long 3 2 BLOCK The definition of BLOCK is derived from the ATMOL 37 file system where a BLOCK is 512 words 4096 bytes long 4 The File System In this section we provide a brief overview of the file system used by GAMESS UK Note at this stage that both direct access and FORTRAN sequential data sets may be used by the program the exact usage being a function of the particular activity in hand Manipulation of these files e g keeping deleting etc is described in the pre directives section of Part 3 of this manual and also under the rungamess script in Part 13 4 1 Direct Access Data Sets Extensive use is made of the system of disk and tape handling originally developed within the ATMOL 37 program system with the various files of integral data output to one or more direct access data sets Such data sets are alloc
26. owing several files of data to be stored on the same data set e partition output of a given file over several data sets specifying the associated LFNs and the starting and terminal blocks of each LFN This feature is particularly useful in controlling the output of two electron integrals It is not possible however to fragment the Dumpfile Scratchfile or Direct Cl file e while mainly of historical interest we note that direct access files needed on an IBM Mainframe running the MVS or VM CMS operating system to be preallocated This process assumed the user had some idea of the overall space requirements since any attempt to route file output beyond the terminal block of a preallocated file was viewed as an unrecoverable error condition Preallocation was not required when using the more restrictive sequential data sets which may be accessed though the LFNs MTO MT19 Note that these considerations refer only to GAMESS UK usage on an IBM mainframe On other machines no formal distinction is made between direct EDO ED19 and sequential MTO MT19 files 4 2 FORTRAN Data Sets In addition to the direct access data sets described above GAMESS UK will in certain phases of computation e g Table Cl make use of the more conventional FORTRAN unformatted sequential data sets In the majority of cases this usage is restricted to scratch activities and the user need not be concerned with for example FORTRAN unit specification In some inst
27. placed in the present GAMESS UK code 2 M Dupuis J Rys and H F King J Chem Phys 65 1976 111 doi 10 1063 1 432807 J A Pople and W J Hehre J Comp Phys 27 1978 161 doi 10 1016 0021 9991 78 90001 3 3 P Pulay Chem Phys Lett 73 1980 393 doi 10 1016 0009 2614 80 80396 4 P Pulay J Comp Chem 3 1982 556 doi 10 1002 jcc 540030413 4 F W Bobrowicz and W A Goddard in Modern Theoretical Chemistry Vol 3 ed H F Schaefer Plenum New York 1977 79 5 B Jonsson B O Roos P R Taylor and P E M Siegbahn J Chem Phys 74 1981 4566 doi 10 1063 1 441645 B O Roos P Linse P E M Siegbahn and M R A Blomberg Chem Phys 66 1982 197 doi 10 1016 0301 0104 82 88019 1 P J Knowles G J Sexton and N C Handy Chem Phys 72 1982 337 doi 10 1016 0301 0104 82 85131 8 The original CASSCF module as developed by Dr P J Knowles was incorporated into GAMESS in April 1983 6 P J Knowles and H J Werner Chem Phys Lett 115 1985 259 doi 10 1016 0009 2614 85 80025 7 7 N C Handy and H F Schaefer J Chem Phys 81 1984 5031 doi 10 1063 1 447489 J E Rice R D Amos N C Handy T J Lee and H F Schaefer J Chem Phys 85 1986 963 doi 10 1063 1 451253 REFERENCES 19 8 Direct configuration interaction and multiconfigurational self consistent field method for multiple active spaces with variable occupations Method J Ivanic J Chem Phys 119 9364 9376 2
28. separate binary of the mpi build of the code and is selected by choosing the taskfarm keyword when configuring the mpi code 7 1 2 Changes to the structure of the code 1 New Ports The code has been ported to several new platforms e Macintosh OSX G3 G4 and G5 processors e Windows XP e AMD Opteron and Athlon processors running Linux e Intel Xeon EM64T and Itanium processors running Linux e HP UX running on Itanium processors 7 RELEASE NOTES FOR GAMESS UK 15 e Sunfire v880 server e SGI Altix e Cray XD1 Global Arrays The version of the Global Arrays supplied with GAMESS UK has been updated from 3 3 to GA 3 4b MOPAC The MOPAC code within GAMESS UK has been updated to version 7 0 Configuring GAMESS UK A new configure process has been developed to ease porting the code to new platforms and making it easier for users to configure the build on their own machine All platform specific variables for the make process are stored in a file with an mk suffix in the GAMESS UK config directory and the configuration process is run by the configure script in the main GAMESS UK directory There are further notes in the file GAMESS UK INSTALL 7 1 3 Peripheral Changes 1 7 2 Demo Binaries Free Windows Macintosh and Linux demo versions are available for users who wish to try out the code Changes to the website The website has been updated and moved to a new url and a Bugzilla facility
29. ted node memory and for benchmark porting exercises Major changes to all ECP related code with re writes of the integrals and derivatives code This has sped the energy integrals by between 2 3 and the gradients by a factor of at least 5 Addition of 4 sets of ECPs to internal libraries e LANL2 including all inner valence TM ECPs etc to library the original HW ECP s are now code named lanl e CRENBS and CRENBL Christiansen et al Small and Large core ECPs e STRLC and STRSC Stuttgart RLC and RSC sets all ECPs associated basis sets added for all elements New Ports e Linux PowerPC e Windows95 e Parallel version for Alpha Linux clusters e 64 bit build supported on a range of platforms Origin Alpha Linux AIX Solaris Global Array and Peigs source for parallel builds has been updated supporting a wider range of platforms Ability to read in hessian information under runtype optx Ability to use include directive in input files Extensions enhancements to ZORA Alpha release of Multi Reference Moller Plesset module NBO analysis extended to UHF wavefunctions Interface provided to Bader s AIMPAC code 8 ENQUIRIES 17 14 15 16 17 7 3 Alpha release of newscf module allowing more flexible treatment of cases showing poor SCF convergence Reduction in memory usage for systems with many nuclear centres e g for QM MM studies Developments to support VB code under development not i
30. the following acknowledgement GAMESS UK is a package of ab initio programs See http www cfs dl ac uk gamess uk index shtm M F Guest I J Bush H J J van Dam P Sherwood J M H Thomas J H van Lenthe R W A Havenith J Kendrick The GAMESS UK electronic structure package algorithms develop ments and applications Molecular Physics Vol 103 No 6 8 20 March 20 April 2005 719 747 doi 10 1080 00268970512331340592 Depending on which modules are used the following references should be cited e MCSCF CASSCF P J Knowles G J Sexton and N C Handy Chem Phys 72 1982 337 doi 10 1016 0301 0104 82 85131 8 P J Knowles and H J Werner Chem Phys Lett 115 1985 259 doi 10 1016 0009 2614 85 80025 7 e M LLER PLESSET PERTURBATION THEORY MP2 MP3 J E Rice R D Amos N C Handy T J Lee and H F Schaefer J Chem Phys 85 1986 963 doi 10 1063 1 451253 J D Watts and M Dupuis J Comput Chem 9 1988 158 doi 10 1002 jcc 540090208 e FULL CI FCI S Zarrabian and R J Harrison Chem Phys Letts 81 1989 doi 10 1016 0009 2614 89 87358 0 e DIRECT CI DCI V R Saunders and J H van Lenthe Mol Phys 48 1983 923 doi 10 1080 00268978300100661 e CONVENTIONAL CI MRDCI R J Buenker in Studies in Physical and Theoretical Chemistry 21 1982 17 e MULTIPLE ACTIVE SPACE SCF MASSCF J lvanic J Chem Phys 119 9364 9376 2003 doi 10 1063 1 1615954 e DISTRIBUTED MULTIPOLE ANALYS
31. tly available on a wide range of machines including e a wide variety of UNIX workstations including those from SGI R4000 R4400 R8k and R10k Indigo R5k R10k and R12k O2 Challenge and Power Challenge Origin200 Origin2000 Origin300 and Origin3800 Hewlett Packard Model 9000 7xx PA8000 PA8200 PA8500 PA8600 and PA8700 IBM RS 6000s PowerPC Powerl Power2 P2SC Power3 Power4 and Power5 Compaq Digital EV5 EV6 EV67 and EV68 AXP under Tru64 OSF 1 OpenVMS and Linux and SUN Super Hyper and Ultra SPARC e a number of IA 32 IA 64 and AMD PCs e g Pentium Pentiumll Pentium III Pentium 4 Xeon EM64T Itanium1 and Itanium2 Athlon and Opteron under Linux FreeBSD and Windows NT 2000 and XP e Mac OSX running on Power 3 4 and 5 processors e Parallel versions of the code are available on both MPP and SMP platforms MPP versions include those for the IBM p series TN2 P2SC WH2 and Regatta nodes and a variety of 1A32 IA64 EM64T AMD64 and Alpha based Beowulf Systems SMP versions are available for the SGI Origin and Altix Compaq AlphaServer SC and Cray XD1 Ports to the Fujitsu VPP300 and NEC SX 5 are also available e Versions for other machines of mainly historical interest include the Intel iPSC 860 Am dahl VP IBM 3090 VF Convex C2 and C3 series and Kendall Square KSR 2 Cray Y MP C90 and J90 T3D and T3E Cray T3E 900 and Cray T3E 1200 VAX VMS and Hitachi SR2201 The program utilises the
32. ton rank 2 update method while transition state location is available through either a synchronous transit 10 trust region 11 or hill walking 12 13 method Force constants may be evaluated ana lytically 14 and by numerical differentiation coupled Hartree Fock CHF calculations provide for a range of molecular properties including polarisabilities and molecular hyperpolarisabilities 15 and through the calculation of dipole moment and polarisability derivatives the computa tion of infra red and Raman intensities 16 Ab initio core potentials are provided in both semi local 17 and non local 18 formalism for valence only molecular orbital treatments Conventional Cl treatments using the table driven selection algorithms within the framework of MR DCI calculations 19 have been extended to include an implementation of the semi direct table driven MRDCI module This provides more extensive capabilities in the treatment of electronic spectra and related phenomena The variety of correlation treatments available include Direct Cl 20 Full Cl 21 and both CCSD 22 23 and CCSD T 24 25 coupled cluster calculations the latter being limited to closed shell systems 26 A size consistent variant of Multi Reference MP2 theory popularized in its CASPT2 form by Roos et al is also available 35 With no restriction to CAS wavefunctions the module also provides MR MP3 capabilities The direct calculation of molecular va
33. ventional SCF and DFT energy and gradient calculations are now effectively open ended the default being 1024 functions Note that lifting this restriction to an arbitrary number is trivially performed by changing the build size when configuring the code The maximum number of primitive functions within a contraction is 25 The maximum number of centres is 1000 allowing for the use of extensive point charge arrays 7 Release Notes for GAMESS UK 7 1 Changes introduced in GAMESS UK Version 7 0 7 1 1 Changes to GAMESS UK functionality 1 Fermi dirac smearing implemented Normally orbitals are filled according to a step function but this can cause convergence problems if it is uncertain which state to converge on Fermi smearing allows orbitals to be partially filled which can improve convergence in some problematic cases Atomic Guess extended It is now possible to specify the per atom electron configuration or charge for the atomic guess It is also possible to specify alpha and beta populations for atoms in UHF calcu lations Update of the Graphics Module The graphics modules have been revised to enable both density and potential codes to drive through full s p d f g basis sets User defined convergence schemes It is now possible for a user to specify a particular convergence scheme rather than the default one within GAMESS UK This is activated by placing the convergence criteria within a block in the input
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