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1. SCFTYP RHF RUNTYP ENERGY EXETYP RUN MPLEVL 0 CITYP NONE CCTYP NONE MULT 1 ICHARG 0 NZVAR 0 COORD ZMT ECP NONE RE LWFN NONE LOCAL NONE NUMGRD F ISPHER 1 NOSYM 0 MAXIT 30 UNITS ANGS PLTORB E MOLPLT E AIMPAC E FRIEND NPRINT 7 IREST 0 GEOM INPUT NORMF 0 NORMP 0 BT OTs 20 ICUT 9 INTTYP POPLE QMTTOL 1 0E 06 SSYSTEM OPTIONS REPLICATED MEMORY 100000 WORDS ON EVERY NODE DISTRIBUTED MEMDDI 0 MILLION WORDS IN AGGREGATE MEMDDI DISTRIBUTED OVER 2 PROCESSORS IS 0 WORDS PROCESSOR TOTAL MEMORY REQUESTED ON EACH PROCESSOR 100000 WORDS TIMLIM 2 00 MINUTES OR 0 00 DAYS PARALL T BALTYP NXTVAL KDIAG 0 COREFL F PROPERTIES INPUT MOMENTS FIELD POTENTIAL DENSITY IEMOM 1 IEFLD 0 IEPOT 0 IEDEN 0 WHERE COMASS WHERE NUCLEI WHERE NUCLEI WHERE NUCLEI OUTPUT BOTH OUTPUT BOTH OUTPUT BOTH OUTPUT BOTH IEMINT 0 IEF INT 0 IEDINT 0 MORB 0 DONE SETTING UP THE RUN Each ab initio calculation starts from guessed orbitals In GAMESS the default starting point is to use Extended Huckel orbitals KKKKKKKKKKKKKKKKKKKK 1 ELECTRON INTEGRALS KKKKKKKKKKKKKKKKKKKK Sera ee END OF ONE ELECTRON INTEGRALS
2. 85 Post Processing Visualization The isotope of each atom for the analysis is listed in the following way NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION ATOMIC WEIGHTS AMU 1 O 15 99491 2 H 1 00782 3 H 1 00782 Since water molecule has three n 3 atoms there are 3n 6 3 vibrations GAMESS calculates all 3n modes includ ing the For good optimization these 6 three translations and three rotations should be close to zero Otherwise the optimization was poor And better optimized structure for frequency analysis is needed All 3n 9 modes are listed with frequency reduced mass and IR intensity MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS FREQUENCIES IN CM 1 IR INTENSITIES IN DEBYE 2 AMU ANGSTROM 2 REDUCED MASSES IN AMU 1 2 3 4 5 FREQUENCY 193 0 28 0 00 0 00 4 75 REDUCED MASS 1 12589 5 24028 6 00352 6 00356 1 07762 IR INTENSITY 4 03724 0 00545 0 00000 0 00000 1 54682 1 O x 0 00000000 0 23214557 0 00000000 0 00000000 0 06573974 Y 0 08364703 0 00000000 0 00000341 0 23563332 0 00000000 Z 0 00000000 0 00000000 0 23563315 0 00000341 0 00000000 2 H x 0 00000000 0 25960863 0 00000004 0 00000000 0 39690549 Y 0 66377371 0 00000000 0 00000341 0 23563178 0 00000000 Z 0 00000000 0 03274502 0
3. ON NODE 0 STEP CPU TIME 0 01 TOTAL CPU TIME 0 0 0 0 MIN TOTAL WALL CLOCK TIME 0 0 SECONDS CPU UTILIZATION IS 100 00 GUESS OPTIONS GUESS HUCKEL NORB 0 NORDER 0 MIX E PRTMO E PUNMO E TOLZ 1 0E 08 TOLE 1 0E 05 SYMDEN E PURIFY F INITIAL GUESS ORBITALS GENERATED BY HUCKE ROUTINE HUCKEL GUESS REQUIRES 2569 WORDS SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW BOTH SET S 5 ORBITALS ARE OCCUPIED 1 CORE ORBITALS 80 Post Processing Visualization 2 Al 3 B1 4 Al 5 B2 6 B1 7 Al END OF INITIAL ORBITAL SELECTION The following section shows the progress of the iterative SCF process RHF SCF CALCULATION NUCLEAR ENERGY 8 3134263274 MAXIT 30 NPUNCH 2 EXTRAP T DAMP F SHIFT F RSTRCT F DIIS F DEM F SOSCF F DENSITY MATRIX CONV 1 00E 05 MEMORY REQUIRED FOR RHF STEP 30441 WORDS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR To 0 74 781696591 74 781696591 0 565508269 0 000000000 2 1 0 74 941109404 0 159412813 0 171859293 0 000000000 3 2 0 74 954504200 0013394796 0 053897963 0 000000000 4 3 0 74 955895555 0 001391355 0 018056178 0 000000000 5 0 0 74 956098156 0 000202601 0 011639084 0 000000000 6 1 0 74 956144781 0 000046625 0 000894164 0 000000000 7 2 0 74 956145797 0 000001016 0 000338739 0 000000000 8 3 0 74 956145930 0
4. Once the job has completed it is possible to look at the output file To view the data available graphically click on the MONITOR JOB OUTPUT button in the GridChem Manage Jobs window The job that is highlighted in the left hand side of the window will be the job whose output is being fetched and displayed Prepare for NWChem Input File 48 Pre processor Molecule Builder In progress 49 Chapter 8 Job Management Managing GridChem Jobs For GridChem jobs there are two types of management capabilities inquiry and actions Job inquiries tell the user information about the job Is the job running now On what HPC cluster for how long etc Job management ac tions DO something to the job Actions on jobs include creating submitting and killing them It is assumed from this point forward that a job has been successfuly submitted The Job Management Window The GridChem user can access all job managemnet capabilities iquiries and actions from the Job Management Window shown below In turn this window is displayed by clicking on the button labelled Manage Jobs in the GridChem startup window a k a the Main Control Panel Figure 8 1 GridChem Job Manager Grd GhemManaee dos Ge pro deiat test COQHOGILE ag pos Sandeep p defaut test isdxukyedu gauss Sandeep p defaut test cunesauiu debuy Sandeep p detaut test cuncsa uiu debug Shashank Alanine test sdxuky edu gauss 09 21 2005 11 49 Sh
5. 0 0 0 0 MIN CPU UTILIZATION IS 100 00 30 5032997846 6 9853469741 E 00 0 00000E 00 Mulliken population analysis shows the charge distribution in molecular orbitals The Lowdin population analysis calculates the charge distribution in a way that more reflects the difference in electronegativity of the atoms MULLIK EN AND LOWDIN POPULATION ANALYSES MULLIK EN ATOMIC POPULATION IN EACH MOL ECULAR ORBITAL 82 Post Processing Visualization 1 2 3 4 3 2 000000 2 000000 2 000000 2 000000 2 000000 1 2 000921 1 673462 1 054744 1 545576 2 000000 2 0 000461 0 163269 0 472628 0 227212 0 000000 3 0 000461 0 163269 0 472628 0 227212 0 000000 Sncas POPULATIONS IN EACH AO MULLIKEN LOWDIN T cO de YS 1 99816 1 99662 2 O 1 3S 1 86833 1 75974 3 0 le 1 05474 1 07681 47 0r EL Y 2 00000 2 00000 JI O A A 1 35347 1 36404 6 H 2 S 0 86265 0 90139 To lt 3 8 0 86265 0 90139 SSeS MULLIKEN ATOMIC OVERLAP POPULATIONS OFF DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2 1 2 3 iL 7 7970869 2 0 2388082 0 6581371 3 0 2388082 0 0342969 0 6581371 TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS ATOM MULL POP CHARGE LOW POP CHARGE ne 8 274703 0 274703 8 197214 0 197214 2 H 0 862648 0 137352 0 901393 0 098607 3 H 0 862648 0 137352 0 901393 0 098607 At the end of the output file the bond analysis and dipole moment are listed in
6. gt home gt consulting gt administration gt preferences gt search gt about gt add user gt browse users gt modify user gt delete user gt install new module gt view modules gt module instances gt backup site These options allow the administrator to 1 add user 2 list or browse users 3 modify user information 4 delete user 5 create new module plugins not discussed here The following window shows the fields for add user Individual fields of an existing user can be modified through the modify user link 105 Technical Support Figure 10 11 Graphic11 add user indicates a required field usermame email address Password verify password group Select Group w first name last name location current date time in GMT UTC Frei 04 Feb 2005 23 19 00 GMT user s GMT UTC offset 0 hours wt hide status hide profile notify via email on change remember login website clear form create user 106 Technical Support lt site gt consult _MailAutoSig Figure 11 Add user view form for updating user database entries The required information for adding a user is indicated by stars both white and yellow fields accept text see Figure 11 The administrator is responsible for providing a new user with a username and password The user has the op tion to c
7. Delete Selected Job ptao_proj butaneopt Gaussian cu ncsa uiuc edu Submit Selected Jobs to Queue Submit All Jobs to Queue Close Click the job in the job list if it is not highlighted Then click the SUBMIT SELECTED JOBS TO QUEUE button to submit this job After a small pop up window Figure 7 22 indicating that your job is being submitted disappears you will see your job in the queuing window Figure 7 23 Figure 7 22 GridChem Job Submission Progress CI x butanegAMESSOpt monitor Job submission progress Making connection Figure 7 23 GridChem Submit Jobs Window 47 Pre processor Molecule Builder 2101 Edit a job a create New too New Job Delete Selected Job Selected Job AMESSOpt GAMESS longhorn tacc ut Submit Selected Jobs to Queue test_proj butane Click on the CLOSE button in the Submit Jobs window The only GridChem window that should be up is the main GridChem window Click on the MANAGE JOBS button in the main GridChem window A window will appear that contains a list of all of the jobs that you have submitted The most recent job submission should be at the top of the list Figure 7 24 Figure 7 24 GridChem Manage Jobs Window ix jobName _Machine jowo Get Job Status 1005 2005 01 39 test_proj butaneGAMESSOpt longhorn tac normal longhorn 16 Monitor Job Output Kil Selected Job Retrieve Job Output Delete Job from List Close
8. 99 99 2 9 110 2 Bf Sd 626 t gt 654 3021 14245 1723 4 5 5 16 3 1 5 5 2 38 5 2 TIA 4 2437 268 1 14 1 18 20 3 5 2 9 110 2 6 7 2 8 2 9 2 10 2 19 2 28 1 1 99 9 1 99 Symbolic Z matrix Charge 0 Multiplicity 1 F Os 0 0 F 1 5 0 0 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad After the initialization of the program running Gaussian is ready to start the real calculation In this case the struc ture of fluorine molecule F2 will be optimized The following section gives the initial setup of Berny optimization Berny optimization Initialization pass Initial Parameters Angstroms and Degrees Name Definition Value Derivative Info R1 R 1 2 L5 estimate D2E DX2 Trust Radius 3 00D 01 FncErr 1 00D 07 GrdErr 1 00D 06 Number of steps in this run 20 maximum allowed number of steps 100 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Input orientation Center Atomic Atomic Coordinates Angstroms Number Number Type X Y Z 1 9 0 0 000000 0 000000 0 000000 2 9 0 1 500000 0 000000 0 000000 Stoichiometry F2 Framework group D H C F F Deg of freedom 1 Full point group D H NOp 8 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 54 Post Processing Visualization The standard orientation is the coordinate system chosen by
9. I noticed that I cannot respond to a ticket once the consultant has responded to me What is wrong Thanks John kent Response Date Fri 04 Feb 2005 10 22 40 Responder Ken Milfeld Response Cc d N A Hi John I will take care of this I found another problem with single quotes rrrr Kent Response Date Fri 04 Feb 2005 16 45 32 Responder John Doe2 Response Cc d N A Thanks for the help Just one more thing When will GridMech be available Add Response The table presents all the relevant information about the ticket category creation date status etc Note the ticket owner is the consultant that is responsible for resolving your problem After the table the original problem report is displayed followed by the consultant s response Below the correspondence is an Add Response link for updating the ticket requesting additional information or clarification If you have a different problem please submit a differ 99 Technical Support ent ticket do not use the ticket as a general form to directly connect a consultant for all your needs Creating a Ticket After you login click on consulting in the Main Menu and then select create ticket in the Consulting menu The follow form appears in the Display panel Figure 10 6 Create Ticket view User Ticket form Create New Ticket Your First Name Your Last Name Doer2 Your Phone Number 859 257 1111 Your E mail Address milfeld
10. email firstname lasmame logic between fields browse users The search results are posted in a new panel as shown in figure 14 Figure 10 14 Search results from Modify user view 1 total results 10 results per page lt lofi gt milfeld Ken Milfeld milfeld tacc utexas edu Mon 31 Jan 2005 08 42 08 NM 1 total results 10 results per page lt lofi gt Selection of an ID in the search results panel will create a panel similar to the add user panel for the selected user The administrator can then change any of the user s entries in the database 109 Technical Support Summary The Portable Consulting System PCS is written in PHP and includes wrapper calls for MySQL and MSSQL Hence the system can be installed on any Windows or Unix platform that supports PHP and either database service A configuration HTML paged is also included with the distribution PCS was developed by Patrick Hurley at the Texas Advanced Computing Center phurley tacc utexas edu mailto phurley tacc utexas edu The system will become publicly available in the near future Thanks to Patrick for creating a generic version for the NSF GridChem project References This work integration of PCS into the Computation Chemistry Grid has been sponsored by the NSF project Col laborative Research NMI Deployment CHE GridChem Cyberinfrastructure for Computation Chemistry award number SCI 0438312
11. 0 01 TOTAL CPU TIME 0 1 0 0 MIN TOTAL WALL CLOCK TIME 1 3 SECONDS CPU UTILIZATION IS 7 03 ENERGY GRADIENT ATOM E X EY E Z 10 0 000000000 0 000000000 0 000001002 2 H 0 000001762 0 000000000 0 000000501 3 H 0 000001762 0 000000000 0 000000501 CARTESIAN FORCE CONSTANT MATRIX f 2 O H X Y Z X Y Z 1 O X 0 803951 0 000000 0 000000 0 401975 0 000000 0 337134 Y 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 Z 0 000000 0 000000 0 634895 0 216310 0 000000 0 317447 2 H X 0 401975 0 000000 0 216310 0 438910 0 000000 0 276722 Y 0 000000 0 000000 0 000000 0 000000 0 000001 0 000000 Z 0 337134 0 000000 0 317447 0 276722 0 000000 0 300101 3 H X 0 401975 0 000000 0 216310 0 036935 0 000000 0 060412 Y 0 000000 0 000000 0 000000 0 000000 0 000001 0 000000 Z 0 337134 0 000000 0 317447 0 060412 0 000000 0 017347 3 H X Y Z 3 H X 0 438910 0 000000 0 276722 Y 0 000000 0 000001 0 000000 Z 0 276722 0 000000 0 300101 DIPOLE DERIVATIVE TENSOR DEBYE ANGSTROM ATOM MU X MU Y MU Z O D DX 0 149608308 0 000000000 0 000000000 D DY 0 000000000 2 688297407 0 000000000 D DZ 0 000000000 0 000000000 0 401211797 H D DX 0 074818152 0 000000000 0 754405971 D DY 0 000000000 1 344148703 0 000000000 D DZ 1 064569806 0 000000000 0 200609876 H D DX 0 074818152 0 000000000 0 754405971 D DY 0 000000000 1 344148703 0 000000000 D DZ 1 064569806 0 000000000 0 200609876
12. For more information please visit https www gridchem org Manage Jobs Save Data View License Exit ETH Authentication The first action you will want to take is to authenticate yourself with the GridChem middleware server To do this click on the AUTHENTICATE button You will be prompted for your username and password These are the GridChem username and passwords that you were either e mailed or given by a principal investigator Figure 3 8 GridChem Login 21 Software Installation Configuration ix GridChem Welcome to GridChem Portal to the Computational Chemistry Grid Authenticate Developed by GridChem Get Access to GridChem Read Announcements ccs University of CCT Louisiana Sta agin to GridChem with your username and password CS4 University o OSC Ohio Supercom TACC University o Username img For more informati Password rrna Juthentication req Check Preferences Submit Jobs Manage Jobs Save Data Login Cancel View License Exit UE If authentication is unsucessful you will be given an appropriate error message Once authentication is successful a corresponding message will be displayed in the main window and it will indicate for how long your certificate is valid Figure 3 9 GridChem Successful Authentication o GridChem mj x Welcome to GridChem Portal to the Computational Chemistry Gri
13. Vili Chapter 1 GridChem Overview Introduction What is the Computational Chemistry Grid e A virtual organization that will provide access to distributed high performance computing resources for the com putational chemistry community with distributed support and services intuitive interfaces and a measurable quality of service What is GridChem e GridChem is an open source Java based desktop client that allows the researcher to submit jobs to high perform ance compute resources without learning the intricacies of the different operating systems environments or re sources e GridChem will present what is available on the chosen system to you It interfaces with the Grid Middleware Server GMS for authentication allocations and resources e GridChem will act as your client for a community allocation or allow you sacrificing some of the job manage ment capabilities will allow you to login as an external user An external user is a scientist with allocations on CCG resources to be used You can use our client with your current certificates to authenticate to your current accounts Scope of the Computational Chemistry Grid e Computational chemistry research community users invoke the execution of modules withing large packages through inputs that specify the chemistry and the physical model to determine structure dynamics and proper ties e There is very little need to login to these systems for the bat
14. Add Hydrogen 36 Pre processor Molecule Builder g amp Nanocad F Group I T Forces _Help structure clear undo Ald Frrinze Fore Fe eeotwen zl The last step for building butane is minimizing the current structure Click the MINIMIZE pull down menu at the bottom of the Nanocad window and choose either the CONJ GRAD Conjugate Gradients method or the STP DESC Steepest descent method to minimize the current molecule If the first time minimization doesn t give a satisfied structure the minimization can be repeated multiple times until a reasonable structure obtained Figure 7 10 Figure 7 10 Molecule Minimization 37 Pre processor Molecule Builder Nanocad loj x Summary of Nanocad Commands About Rotate drag gray space Translate Shift drag gray space Zoom Ctrl drag empty space Move Atom drag atom Add Atom Shift click gray space Delete Atom Sluft click atom Add Bond Shift dragatomtoatom Delete Bond Ctrl drag atom to atom Select Atom Alt click atom Add double bond Sluft drag between bonded atoms Select Group Ctrl Alt click atom I Group Geometry Forces Help Structure Clear Undo Add H Get Potential J Minimize x Force Field 7 Export Menu x SD done Max force 1 04442 Potential 1 6925 Hint Nanocad has lots of template molecules to choose from In the Import Structure window click on ION FUNCTION GROUP or MOLECULE to c
15. Alpha occ eigenvalues 0 51301 0 51301 0 41241 0 41241 Alpha virt eigenvalues 0 19705 1 04774 1 04774 ELIS 1 22730 Alpha virt eigenvalues t425294 1 25294 1 37450 1 86482 Condensed to atoms all electrons 1 2 1 F 8 924099 0 075901 2 oF 0 075901 8 924099 Mulliken atomic charges 1 1 F 0 000000 2 F 0 000000 Sum of Mulliken charges 0 00000 Atomic charges with hydrogens summed into heavy atoms 1 1 E 0 000000 55 Post Processing Visualization 2 E 0 000000 Sum of Mulliken charges 0 00000 Electronic spatial extent au R 2 56 4125 Charge 0 0000 electrons Dipole moment field independent basis Debye X 0 0000 Y 0 0000 Z 0 0000 Tot 0 0000 Quadrupole moment field independent basis Debye Ang XX 9 3410 YY 9 3410 ZZ 8 5623 XY 0 0000 XZ 0 0000 YZ 0 0000 Traceless Quadrupole moment field independent basis Debye Ang XX 0 2596 YY 0 2596 ZZ 0 5191 XY 0 0000 XZ 0 0000 YZ 0 0000 Octapole moment field independent basis Debye Ang 2 XXX 0 0000 YYY 0 0000 ZZZ 0 0000 XYY 0 0000 XXY 0 0000 XXZ 0 0000 XZZ 0 0000 YZZ 0 0000 YYZ 0 0000 XYZ 0 0000 Hexadecapole moment field independent basis Debye Ang 3 XXXX 4 8704 YYYY 4 8704 ZZZZ 31 1436 XXXY 0 0000 XXXZ 0 0000 YYYX 0 0000 YYYZ 0 0000 ZZZX 0 0000 ZZZY 0 0000 XXYY 1 6235 XXZZ 6 7859 YYZZ 6 7859 XXYZ 0 0000 YYXZ 0 0000 ZZXY 0 0000 After each optimization step the summary of calculation
16. END v gt Cancel Modify the GAMESS input file according to the Gamess manual http www msg ameslab gov GAMESS doc menu htmlto set up your GAMESS job Modify the default GAMESS input file as CONTRL SCFTYP RHF RUNTYP OPTIMIZE NZVAR 0 END SYSTEM TIMLIM 60 MEMORY 500000 END DFT DFTTYP B3LYP END BASIS GBASIS N31 NGAUSS 6 NDFUNC 1 END GUESS GUESS HUCKEL END STATPT OPTTOL 0 00001 END 45 Pre processor Molecule Builder In DATA section only change the line which defines the molecular symmetry Dnh 4 C11 Since Cartesian coordinates are used in this case section ZMAT or LIBE is not needed in input file Please dis card these two sections if they can be found in input file Change other settings in this window if necessary For example a Change job name from default_test to butaneGAMESS Opt b Choose GAMESS as Application c Choose batch as queue choice d Change number of processors from default value 4 to 1 Now you are ready to submit your GAMESS job for running Click OK button at the bottom right of GridChem Job Editor window Then this window will disappear In the GridChem Submit Jobs window you will see your job User_proj butaneGAMESSOpt GAMESS in the job list Figure 7 21 Figure 7 21 GridChem Submit Jobs Window 46 Pre processor Molecule Builder io x Edit a job Create New Job ptao_proj butaneGAMESSOpt GAMESS cu ncsa uiuc edu
17. Semi Empirical Computational Method The main aim of the semi empirical methods is to replace the computationally expensive Hartree Fock integrals with parameters chosen to fit experimental data This is why the term semi empirical has been used The most common semi empirical methods are based on the neglect of diatomic differential overlap NDDO form alism which uses parameters to replace the one center two electron and two center two electron integrals One of the NDDO based methods uses a modified neglect of differential overlap MNDO algorithm To improve the poor predictions of hydrogen bonding which is the major drawback of the MNDO method the Aus tin Model 1 AM1 was developed this model modifies the nuclear repulsion terms in the NDDO model to attempt to improve the bond length prediction Parameterized Model 3 PM3 uses the same NDDO functional form with that of AM1 The PM3 method aims to simultaneously optimize the overlap integral parameters for more atoms based on larger data set than AM1 uses The main improvement of PM3 is that the optimization algorithms applied in this method permitted an efficient search of parameter space which brings the possibility that the PM3 parameter set may actually be the global min imum in the parameter space Basis Set The basis set is the set of mathematical functions from which the wave function is constructed N w Peah j The use of Gaussian type orbital GTO is very common
18. i g ppt is g 2 Pry A mtd gta _ fin eh a giy i 2 jw 2 Fhe 4 Beary By solving the equation for each order of lambda the correction of energy and wave function at corresponding order can be obtained Actually the Hartree Fock energy is the energy correct through first order in M ller Plesset perturbation theory With the second order correct it is called MP2 level of theory Similarly MP3 level of theory includes the correc tion through the third order and so on All orders of MPn theory are size consistent but not variational Coupled cluster CC Theory The central tenet of coupled cluster CC theory is that the full CI wave function can be described as es Poe Fe The cluster operator T is defined as Eq 6 14 ToT bos Where n the total number of electrons and the various Ti operators generate all possible determinants having I excit ations from the reference If we make the approximation that T T 2 Taylor expansion of the exponential function in the full CI wave function 13 Introduction to Computational Chemistry gives ATT oft al Where CCD implies coupled cluster with only the double excitation operator Similarly CC SD method use the approximation that T T 1 T 2 which adds more accuracy than CCD However CCSDT is very computationally costly for most system but very molecules The most robust and thus most commonly used is CCSD T method which includes a singles triples coupling term
19. menu was added to the Main Menu not show above This menu is a gateway for users with PI status status derived from the CCG database to add users to their project or request a community project or external project if they have one type of project but not the other Since the panels are self explanatory and are not concerned with consulting their content is not discussed here PCS is used as the gateway because it is a con venient and secure interface that is familiar with the CCG users How the Ticketing System Works After a user enters a ticket a notification is sent to an administrator s email as a backup and a mechanism to ascer tain that PCS is operating accepting tickets Consultants login to PCS in the same manner as do users but the con sultants have a special status and have additional menus and capabilities that users don t have When a consultant logs in he sees three listings one is for all recent tickets whether they be new assigned or closed another shows all the open tickets that he owns the third panel shows tickets that he created New tickets are perused by the con sulting staff usually a consultant of the day The consultant either takes ownership or assigns a ticket to a site manger for further handling The manager is notified of the assignment by automatic email When the consultant re sponds to a user problem the user is immediately notified the email contains a copy of the consultant s response W
20. new Consulting panel appears identical to a normal user s menu The consultant s display of the tickets ticket ta ble however has three panels one with the new tickets another showing tickets owned by the consultant and an other showing tickets created by the consultant often empty The last display entries are created when a consultant fields a problem from a phone call and must respond at a later time after further analysis The panels are shown below Figure 10 7 Consulting view the Ticket Table 102 Technical Support New Tickets 1 out of 1 2 Mon 31 Jan 2005 12 46 20 GridChem Operation New John Doe2 Open Tickets You Own or Have Responded To 4 out of 4 Fri 04 Feb 2005 GridcChem 10 09 22 Operation wed 02 Feb 2005 GridChem Pending User Sadhakar Ken 16 47 46 Operation Response Pamidighantam Milfeld Mon 31 Jan 2005 GridChem Job Pending User John Doe2 Ken 13 10 36 Submission Response Milfeld Mon 31 Jan 2005 GridcChem Pending User John Doe2 Ken 12 07 35 Operation Response Milfeld Ken In Progress John Doe2 Milfeld Open Tickets You Have Submitted 0 out of 0 No open tickets Clicking on a Ticket number Ticket will open a new window with a display of the ticket problem text and re sponse s New tickets only have the problem text The consultant s window has an Update Ticket panel at the bot tom which allows the consultant to take owners
21. 0000 XZZ 0 0000 YZZ 0 0000 YYZ 0 0000 XYZ 0 0000 Hexadecapole moment field independent basis Debye Ang 3 XXXX 4 8704 YYYY 4 8704 ZZZZ 31 1436 XXXY 0 0000 XXXZ 0 0000 YYYX 0 0000 YYYZ 0 0000 ZZZX 0 0000 ZZZY 0 0000 XXYY 1 6235 XXZZ 6 7859 YYZZ 6 7859 XXYZ 0 0000 YYXZ 0 0000 ZZXY 0 0000 N N 2 857556924820D 01 E N 5 336431655183D 02 KE 1 984792247777D 02 Symmetry AG KE 8 818960539513D 01 Symmetry B1G KE 0 000000000000D 00 Symmetry B2G KE 7 325365943605D 00 Symmetry B3G KE 7 325365943605D 00 Symmetry AU KE 0 000000000000D 00 Symmetry B1U KE 8 320825368179D 01 Symmetry B2U KE 6 215316906775D 00 Symmetry B3U KE 6 215316906775D 00 xx x x x Axes restored to original set 61 Post Processing Visualization Center Atomic Forces Hartrees Bohr Number Number X Y Z t 9 0 020072532 0 000000000 0 000000000 2 9 0 020072532 0 000000000 0 000000000 Cartesian Forces Max 0 020072532 RMS 0 011588882 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization Internal Forces Max 0 020072532 RMS 0 02006D 7F There are 5 symmetry adapted basis functions of AG symmetry There are 0 symmetry adapted basis functions of B1G symmetry There are 2 symmetry adapted basis functions of B2G symmetry There are 2 symmetry adapted basis functions of B3G symmetry There are 0 symmetry adapted basis functions of AU symmetry
22. 110
23. 142 675995 171 735001 155 876007 205 045001 410 15 7 013 430 65 990 461105935 402 100006 Scale Factor 0 100000 Visualization of Gaussian03 Output File by Gauss View 1 2 5 d 5 B T a J Mm e C se DCDC Des Hl GaussView is a graphical interface designed to help users prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces GaussView is not integrated with the computational module of Gaus sian and needs to be purchased separately GaussView has three main applications for Gaussian users First GaussView allows users to build their own molecules then rotate translate and zoom in on these molecules Secondly Gauss View can be used to set up many types of Gaussian calculations Finally GaussView can examine the results of Gaussian calculations using a variety of graphical techniques Gaus sian results that can be viewed graphically include the following 1 Optimized molecular structures 2 Molecular orbitals 3 Electron density surfaces from any computed density 4 Electrostatic potential surfaces 73 Post Processing Visualization 5 Surfaces for magnetic properties 6 Atomic charges 7 Animation of the normal modes corresponding to vibrational frequencies 8 IR Raman NMR VCD and other spectra 9 Animation of geometry optimizations IRC reaction path following potential energy surface scans and ADMP and BOMD traje
24. 23563320 0 00000341 0 55162447 3 H x 0 00000000 0 25960863 0 00000004 0 00000000 0 39690549 Y 0 66377371 0 00000000 0 00000341 0 23563178 0 00000000 Z 0 00000000 0 03274502 0 23563319 0 00000341 0 55162447 TRANS SAYVETZ X 0 00000000 4 23642756 0 00000003 0 00000001 0 25147870 Y 0 00000877 0 00000001 0 00006141 4 24388501 0 00000000 Z 0 00000000 0 00000003 4 24388501 0 00006141 0 00000000 TOTAL 0 00000877 4 23642756 4 24388501 4 24388501 0 25147870 ROT SAYVETZ X 1 60751331 0 00000000 0 00000000 0 00000332 0 00000000 Y 0 00000000 0 15361933 0 00000000 0 00000000 2 58788182 Z 0 00000000 0 00000000 0 00000000 0 00000000 0 00000000 TOTAL 1 60751331 0 15361933 0 00000000 0 00000332 2 58788182 6 7 8 9 FREQUENCY 6 33 2170 04 4139 99 4391 06 REDUCED MASS 1 00782 1 07849 1 04909 1 07736 IR INTENSITY 0 00000 0 17128 1 04807 0 70926 1 O X 0 00000000 0 00000000 0 00000000 0 06562478 Y 0 00000000 0 00000000 0 00000000 0 00000000 Z 0 00000000 0 06612201 0 05123270 0 00000000 2 H X 0 00000000 0 43140643 0 55678216 0 52075644 Y 0 70435636 0 00000000 0 00000000 0 00000000 Z 0 00000000 0 52470184 0 40654994 0 43675633 3 H X 0 00000000 0 43140643 0 55678216 0 52075644 Y 0 70435636 0 00000000 0 00000000 0 00000000 Z 0 00000000 0 52470184 0 40654994 0 43675633 TRANS SAYVETZ X 0 00000000 0 00000000 0 00000000 0 00000023 Y 0 00000000 0 00000000 0 00000000 0 00000000 oo eN Post Processing Visualization 00000 0 00000037 00
25. 6 31 G d OPT Butane optimization O 1 Change other settings in this window if necessary For example a Change job name from default_test to butaneopt b Choose batch model for queue c Change number of processors from the default value of 4 to 1 Now you are ready to submit your Gaussian job for running Click OK button at the bottom right of GridChem Job Editor window Then this window will disappear And you will see your new job is in the GridChem Submit Jobs window and ready for submit Figure 7 14 41 Pre processor Molecule Builder Figure 7 14 GridChem Submit Jobs Window io x ptao_proj butaneopt Gaussian cu ncsa uiuc edu Edit a job _ Create New Job Delete Selected too Selected Job Submit Selected Jobs to Queue Submit AlJobs to Queue All Jobs to Queue cose Click the job in the job list if it is not highlighted Then click the SUBMIT SELECTED JOBS TO QUEUE button to submit this job After a small pop up window indicating that your job is being submitted disappears Figure 7 15 you will see your job in the queuing window Figure 7 16 Figure 7 15 GridChem Submitting Jobs Progress Window CT x butaneopt monitor Job submission progress Making Connection Figure 7 16 GridChem Submit Jobs Window 42 Pre processor Molecule Builder io x Edit a job __createnew ob New Job Dete Selected Jon Selected Job Submit Selected Jobs to Queue Sub
26. Hratchian J B Cross M K V G R H k C Adamo J Jaramillo R Gomperts R E Stratmann O Yazyev A J Austin R Cammi C Pomelli J W Ochterski P Y Ayala K Morokuma G A Voth P Salvador J J Dannenberg V O J J I B G G Zakrzewski S Dapprich A D Daniels M C Strain Farkas D K Malick A D Rabuck K Raghavachari B Foresman J V Ortiz Q Cui A G Baboul S Clifford Cioslowski B B Stefanov G Liu A Liashenko P Piskorz Komaromi R L Martin D J Fox T Keith M A Al Laham Y Peng A Nanayakkara M Challacombe P M W Gill Johnson W Chen M W Wong C Gonzalez and J A Pople aussian Inc Wallingford CT 2004 The following section gives the version of Gaussian 03 that is running For example this version is Revision C 02 of Gaussian 03 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Gaussian 03 IA32L GO3RevC 02 12 Jun 2004 27 Sep 2005 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK The following section displayed the input information for this job such as route section IOp setup title section and molecule specification B3LYP 6 31G Opt 1 14 1 18 20 26 3 38 1 1 3 2 9 110 17 6 18 5 40 1 2 3 5 1 6 6 11 2 16 1 25 1 30 1 74 5 1 2 3 4 1 53 Post Processing Visualization 5 5 2 38 5 2 6 1 2 8 2 9 2 1042 2841 13 Td Lp 2p oy Or 1 14 1 18 20 3 1
27. The general functional form of a normalized GTO in atom centered Cartesian coordinates is given A i itk KA go Bra 4 Bex i il jl scl oa ok x2 2 nF Z t fn Ee ee Sear eee tal ale P Ux Y 2 i 1 CACA E ae Where alpha is an exponent controlling the width of the GTO and i j and k are non negative integers that dictate the nature of the orbital When all of i j and k are zero the GTO has spherical symmetry and is called an s type GTO When only one of these three indices is one it is called p type GTO And there are three possible choices for which index is one corresponding to the p x p y and p z orbitals 14 Introduction to Computational Chemistry If one basis function primitive or contracted in a given basis set is selected for every atomic orbital that is required to describe the free atom the basis is called the minimal basis set The minimal basis set is always inefficient to describe the interaction between atoms more importantly the chemic al bonds If the basis set formed by doubling all functions of in a minimal basis set it is usually termed double zeta basis set In most cases doubling the basis functions of inner shell electrons doesn t gain much accuracy Therefore it is more efficient that only double the number of basis functions for the valence shell electrons This basis set is also called split valence basis set The most common use split valence basis sets include 3 2
28. There are 5 symmetry adapted basis functions of B1U symmetry There are 2 symmetry adapted basis functions of B2U symmetry There are 2 symmetry adapted basis functions of B3U symmetry Integral buffers will be 262144 words long Raffenetti 2 integral format Two electron integral symmetry is turned on 18 basis functions 44 primitive gaussians 18 cartesian basis functions 9 alpha electrons 9 beta electrons nuclear repulsion energy 29 2017096340 Hartrees NAtoms 2 NActive 2 NUniq 1 SFac 5 66D 00 NAtFMM 60 Big F One electron integrals computed using PRISM NBasis 18 RedAO T NBF 5 0 2 2 0 5 2 2 NBsUse 18 1 00D 06 NBFU 5 0 2 2 0 5 2 2 Initial guess read from the read write fil Initial guess orbital symmetries Occupied SGU SGG SGG SGU SGG PIU PIU PIG PIG Virtual SGU PIU PIU SGU SGG PIG PIG SGG SGU Requested convergence on RMS density matrix 1 00D 08 within 128 cycles Requested convergence on MAX density matrix 1 00D 06 Requested convergence on nergy 1 00D 06 No special actions if energy rises Keep R1 integrals in memory in canonical form NReq 452820 SCF Done E RB HF LYP 199 477833730 A U after 5 cycles Convg 0 1833D 08 V T 2 0047 S 2 0 0000 xx x x Axes restored to original set Center Atomic Forces Hartrees Bohr Number Number X Y Z I 9 0 000000136 0 000000000 0 000000000 2 9 0 000000136 0 000000000 0 000000000 Cartesian Forces M
29. as HF 7 Please notice that this energy is the total electronic energy of the final geometry based on the give theory level and basis set This number does not involve and thermodynamics property of the system To obtain more thermodynamics properties please read the following section about calculation of thermodynamics properties from Gaussian output At the end of each successful Gaussian job output file a random quotation is chosen from the internal collection The CPU time and other resource usage information is also listed at the end of the output file The last line is always starts with Normal termination of Gaussian for a successful Gaussian job Otherwise the calculation is not termin ated normally The output shouldn t be considered as meaning results And further investigation is needed until Gaussian job ends normally 57 Post Processing Visualization IF MATHEMATICALLY YOU END UP WITH THE INCORRECT ANSWER TRY MULTIPLYING BY THE PAGE NUMBER Job cpu time 0 days 0 hours 0 minutes 11 0 seconds File lengths MBytes RWF 11 Int 0 D2E 0 Chk 4 Scr 1 Normal termination of Gaussian 03 at Tue Sep 27 15 34 37 2005 Appendix The complete Gaussian 03 output file used in this section piv180 Tue Sep 27 15 34 24 EDT 2005 Entering Gaussian System Link 0 usr local g03c02 g03 g03 Initial command usr local g03c02 g03 11 exe tmp pbstmp 356045 Gau 13469 inp scrdir tmp pbstm
30. controls how and when their job waits e H gt Job is being Held by the batch system software not the user If the job is finished the status windows states that in a simple text line If the user wishes to see if their job is working correctly before it is finished the Monitor Job Output button can be used It brings up a graphics window that say shows the conformation of a molecule at this particular point in the calculation or a 2 D graph of iteration residual and number at this particular point in the minimization Action Buttons It has been said that after submission there is precious little one can do to a batch job One can either kill it or let it finish If the user realizes that a mistake has been made in their job they can terminate it before it is finished with the Kill Selected Job button The user will be prompted to make sure they want to kill the job If the user instead chooses to let the job finish they will naturally be curious about the output By clicking on the Retrieve Job Output button a browser box will appear allowing the user to download the output file to the desired location on their home machine The actual batch job GridChem ran can also be viewed and saved The action button yet to be discussed does not perform a task on the user s batch job but rather of the list of batch jobs shown in the text window GridChem will leave finished jobs in this list as a log for the user In fact this job log is mainta
31. is listed in the following way The information of optimiz ation includes the step number second derivative matrix corresponding to the force and converging situation Please notice that at the first step none of four criteria for optimization is met GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization Internal Forces Max 0 020072532 RMS 0 020072532 Search for a local minimum Step number 1 out of a maximum of 20 All quantities printed in internal units Hartrees Bohrs Radians Second derivative matrix not updated first step The second derivative matrix R1 R1 032377 Eigenvalues 0 32377 RFO step Lambda 1 23966358D 03 Linear search not attempted first point Iteration 1 RMS Cart 0 04367035 RMS Int 0 00000000 Iteration 2 RMS Cart 0 00000000 RMS Int 0 00000000 Variable Old X DE DX Delta X Delta X Delta X New X Linear Quad Total R1 2 83459 0 02007 0 00000 0 06176 0 06176 2 77283 Item Value Threshold Converged Maximum Force 0 020073 0 000450 NO RMS Force 0 020073 0 000300 NO Maximum Displacement 0 030880 0 001800 NO RMS Displacement 0 043670 0 001200 NO Predicted change in Energy 6 221960D 04 And we can see that at the last step of optimization all of the converging criteria were met And the optimization 56 Post Processing Visualization process ended accordingly GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGra
32. motion is so much slower than electron motion that they can be considered to be fixed After applying the Born Oppenheimer approximation the time independent Schrodinger equation can be reduced Introduction to Computational Chemistry for electrons in the field of fixed nuclei H electrons Tomoi r R mE E affective CRS nee rR Eq 6 3 Here is the effective electronic energy which depends on the nuclear coordinates The major E effective efforts in quantum chemistry have been applied to solve the reduced time independent Schrodinger equation Hartree Fock HF Method The Hartree Fock calculation scheme is self consistent iterative procedure to calculate the single determinant solu tion to the time independent Schrodinger equation of a many electron system in a Coulombic potential of fixed nuc lei According to the variational theorem for a time independent Hamiltonian operator any trial wavefunction will have an energy expectation value that is greater than or equal to the true ground state wavefunction corresponding to the given Hamiltonian Therefore the Hartree Fock energy is an upper bound to the true ground state energy of a given system The limit of the Hartree Fock energy as the basis set becomes infinite is called the Hartree Fock limit It is also said that the Hartree Fock method is variational At the beginning of Hartree Fock calculation a set of approximate orbitals needs to be created as the star
33. of GAMESS Output File 20 0 0 eee cence ee cenece een eeneeeeeeeeeeeeeeeeeeaees 78 Calculate Thermodynamics Properties from Gaussian Output 2 0 0 0 cece eee eee ee ence eeeeeeeeeeee ees 84 Visualization of GAMESS Output File by Molden 00 oe eee ec eee eee eeeeeeeeeeeeeeeeeaees 88 10 Technical Support stesse onean seas cesag eas e tastes sherk ssa aicag E A E E EE EER 95 PES User Gude p a rE E R E NEE A E AN E bees E AE E E pa ENRE 95 User Interface deoi eeo ai E E E EE A EEE E shes EE E TE AE essen 95 OVERVIEW eee e a a N E E a eE a EEEa 95 LO BUM E a E E E etek GOT T 95 The Cons lting Menu Mtemi ysiyernsesp ens es e eea EE EAE E Or EN EE EEOSE 97 Creating a Tieke terere ea vie sch EE E EEE N EN E EOE EEEE AEAT 100 Management sss onae bas E E E E E E aa R ETES 101 Consultant Interface sec e ern deine EEE EEE ee deine EEE EEEE ERE EEKE ET EEEE EEEE 101 Manager and Administrator Interface 2 0 0 0 cece sereisepsst tiritas Sieis s s usud kera ros ips EPT r tasses 103 SUMIMALY esera E E E E E ten ces EE E EEEN O EESE EEE EEEE E N ai 110 References 355 03 scsa ss enii aa e E E E E desu baa oes EE TRE a E E 110 List of Figures 1 1 Current CCG Three Tiered Architecture 0 0 0 0 ccc cccccccccececcccee cece eeceeeeeesceeeeueeeeeesseeeeneeaeeeeseeeaenes 2 1 2 CCG Second Generation Architecture srir nnn e EE E E E ER EE iei 4 2 1 Hartree Fock Calculation Procedure c cece cceccccccecececeeecceesueeeeeesceeeeeeeaeee
34. or site managers are sent email when a ticket is created but in general the consultant of the day monitors the new ticket panel in the consultant view and quickly responds to problems The consultant s response is emailed to the user If the user needs to correspond further up date the information or close the ticket they MUST login to PCS and make an entry into the ticket They CANNOT simply respond to the email Using email as a protocol for monitoring and communicating information is prone to many uncertainties created by filters email forwarding accidental deletion or neglect PCS will notify the user of correspondence by sending the consultant s response but PCS expects the user to connect directly to PCS to re spond Problem reporting systems such as Intel s Premier Support use the same mechanisms Login Users interact with the consulting system through the web at the URL _ lt site gt consult http www gridchem org consult A username and password are required to enter the site The mechanism and policy for assigning and distributing the pair are left up to the site management If you have a username and pass word type them in the Login window and click Login button Figure 10 1 Login 95 Technical Support username Loo password If the username is unknown or the incorrect password has been entered you are given the opportunity to re enter a different value or click the forgot password lin
35. tacc utexas edu Cc Category Select Category Priority Select Priority Y Subject Description 100 Technical Support Your contact information name phone number and email is retrieved from the database and inserted into the yel low fields If it is incorrect please correct the information in the supplied fields CCG users cannot change the email address If you want to send a copy of the ticket to a colleague include their email address in the Cc field Next select an appropriate category and priority for your problem Supply a short concise description of the problem in the Subject field In the Description text area describe your problem Include the following information if applic able 1 Time the problem occurred 2 Command and Input script jobscript 3 Version of software application used 4 Machine of execution Finally click the submit command to enter your information into the ticket system You will be notified when a con sultant responds the response will be included in the notification Please return to the PCS and add a response to the ticket consulting Ticket add response Indicate whether the problem has been solved so that the consultant can close the ticket or include further correspondence in the ticket for the consultant The consultant is immediately notified of the new correspondence Management Recently a Management
36. text SP RHF STO 3G punch archive trakio scf conventional Gaussian Test Job 00 ater with archiving ol C 3 603043530424603 2 1119859522730913 2 982856162973117 C 2 250886549930942 2 77074271450858 2 73562699055859 C 1 3408591984268021 1 8907277573753343 1 6763236019299638 C 0 016248117297188683 2 528605433888812 1 6081181022104691 4 242656983446934 2 780451133229639 3 60807460408959 zi A 1920nNAICOCcICEcENnA 1 NVABVECONVINAANDD 2 N1IP91TLANeSNeINAVE lolx wee Load Data File Save Data to File Create Default Job OK Cancel Figure 7 13 IMPORTANT Add Blank Line Be sure to add an ADDITIONAL blank line at the end of the input file press enter at the file end Figure 7 13 40 Pre processor Molecule Builder 1 1736774634016185 0 9110448060870714 2 3889294199533504 1 8362865110213342 1 6909096262764574 0 8936701331395179 0 5559937742414238 2 7166833383907045 2 567694694269497 0 10624235242450163 3 495743151132968 1 062774653091984 0 633360626248914 1 8407971838263295 0 9810897059697277 OK Additional blank line at the end of gaussian input file Modify the gaussian input file according to the gaussian manual http www gaussian com g_ur g03mantop htm to set up your gaussian job Here change the default file head from SP RHF STO 3G punch archive trakio scf conventional Gaussian Test Job 00 Water with archiving O 1 to B3LYP
37. the export passphrase for your PKCS 12 converted certific ate Please choose a passphrase that you can remember you will need to use it in the future Then you will be asked to enter a pass phrase 1 Your pass phrase is like a traditional password You must choose a pass phrase that is very secure and that can be easily remembered 2 Your pass phrase must be at least 8 characters long should contain at least one numeric digit 0 9 and at least one non alphanumerica character 3 If you forget your pass phrase you will have to revoke your certificate and request a new one 4 This will look something like this Next you will be prompted to enter a passphrase which will serve as both the encryption key for your certificate s private key and as the export passphrase for your PKCS 12 converted certificate Please choose a passphrase that you can remember you will need to use it in the future Please enter your private key encryption passphrase Verifying private key passphrase please reenter passphrase After typing in your passphrase the second time you will see You now have a u ac userid globus directory containing the following files usercert pl2 Your digital certificate and private key in a PKCS 12 format certificate usercert pem Your digital certificate signed by the CA daemon userkey pem Your encrypted private key matching the public key contained in your usercert pem KKKKKKKKKKKKKKKKKK
38. 0 51875 0 40890 0 40890 Alpha virt eigenvalues 0 18115 1 05032 1 05032 L107 9 1 22651 Alpha virt eigenvalues 1 25330 1 25330 1 39874 1 86170 Condensed to atoms all electrons 1 2 TB 8 935365 0 064635 Ze 0 064635 8 935365 Mulliken atomic charges 1 Ly E 0 000000 2 FEF 0 000000 Sum of Mulliken charges 0 00000 Atomic charges with hydrogens summed into heavy atoms 1 EF 0 000000 2 F 0 000000 Sum of Mulliken charges 0 00000 Electronic spatial extent au R 2 54 9247 Charge 0 0000 electrons Dipole moment field independent basis Debye X 0 0000 Y 0 0000 Z 0 0000 Tot 0 0000 Quadrupole moment field independent basis Debye Ang XX 9 3286 YY 9 3286 ZZ 8 6491 XY 0 0000 XZ 0 0000 YZ 0 0000 Traceless Quadrupole moment field independent basis Debye Ang XX 0 2265 YY 0 2265 ZZ 0 4530 XY 0 0000 XZ 0 0000 YZ 0 0000 Octapole moment field independent basis Debye Ang 2 XXX 0 0000 YYY 0 0000 ZZZ 0 0000 XYY 0 0000 XXY 0 0000 XXZ 0 0000 XZZ 0 0000 YZZ 0 0000 YYZ 0 0000 XYZ 0 0000 Hexadecapole moment field independent basis Debye Ang 3 XXXX 4 8606 YYYY 4 8606 ZZZZ 30 1196 XXXY 0 0000 63 Post Processing Visualization XXXZ 0 0000 YYYX 0 0000 YYYZ 0 0000 ZZZX 0 0000 ZZ2ZY 0 0000 XXYY 1 6202 XXZZ 6 5726 YYZZ 6 5726 XXYZ 0 0000 YYXZ 0 0000 ZZXY 0 0000 N N 2 920170963405D 01 E N 5 349230662400D 02
39. 000 0 00000037 00000 0 00000000 00000 0 00000000 87122 0 00000000 87122 0 00000000 O1O SAYVETZ CONDITIONS A SAYVETZ 0 000 TOTAL 0 000 ROT SAYVETZ xX 0 000 Y 0 000 Zi 2033 TOTAL 2 033 REFERENCE ON NOTE THE MODES J K ARE ORTHONORMALIZI SUM ON I M I X I Jd The thermodynamics properties calculated by GAMESS are under 298 15K and 1 01325 x 10 5 Pascal X I K THERMOCHEMISTRY AT T 298 15 K USING IDEAL GAS RIGID ROTOR HARMONIC NORMAL MOD 1 01325E 05 PASCAL ALL FREQUENCIES ARE SCALED BY 1 00000 THE MOMENTS OF INERTIA ARE 2 58410 4 13663 6 72073 THE ROTATIONAL SYMMETRY NUMBER IS 2 0 THE ROTATIONAL CONSTANTS ARE IN GHZ 697 76283 435 88315 268 28751 THE HARMONIC ZERO POINT EN 379 HARTREE MOL ELEC ROT VIB TOT ELEC ROT VIB TOTAL ELEC ROT VIB TOTAL TRANS TRANS TRANS IN AMU BOHR 2 ERGY IS SCALED BY 00000002 00000002 00000000 00000000 00000000 00000000 J CHEM PHYS ED ACCORDING TO Y I J Y I K 1 000 OOOO O O 00000000 00000023 00000000 00000213 00000000 00000213 7 383 389 1939 Z I J Z I K E APPROXIMATIONS 0 024 ECULE 5350 543918 CM 1 MOLECULE 15 297988 KCAL MOL 64 006782 KJ MOL
40. 000000133 0 000154849 0 000000000 9 4 0 74 956145954 0 000000024 0 000074540 0 000000000 FO 5 20 74 956145959 0 000000005 0 000035092 0 000000000 11 6 0 74 956145960 0 000000001 0 000016519 0 000000000 12 7 0 74 956145960 0 000000000 0 000007747 0 000000000 132 Bs tO 74 956145960 0 000000000 0 000003631 0 000000000 After the SCF iterative results the orbital energies and the coefficients of the basis functions for each molecular or bital are listed in the following way DENSITY CONVERGED TIME TO FORM FOCK OPERATORS 0 0 SECONDS 0 0 SEC ITER TIME TO SOLVE SCF EQUATIONS 0 0 SECONDS 0 0 SEC ITER FINAL RHF ENERGY IS 74 9561459604 AFTER 13 ITERATIONS EIGENVECTORS 1 2 3 4 5 20 2616 1 2273 0 5602 0 4508 0 3905 Al Al Bl Al B2 If Os ch cS 0 994367 0 237063 0 000000 0 098812 0 000000 Ze 1 ty S 0 024632 0 870930 0 000000 0 507158 0 000000 3 Or SM XK 0 000000 0 000000 0 613299 0 000000 0 000000 4 O 1 Y 0 000000 0 000000 0 000000 0 000000 1 000000 5 1 2 0 003543 0 099900 0 000000 0 742445 0 000000 6 He 425 4S 0 004904 0 148411 0 452257 0 320128 0 000000 Ty Bod S 0 004904 0 148411 0 452257 0 320128 0 000000 6 7 81 Post Processing Visualization YOUR WNHE TTETOOO0OO0OO WNHRRRERE The energy related terms are summarized in the following section 0 5181 Al L15775 0 714725 0 000000 000000 0 758415 72603
41. 1G 6 31G Since minimal basis set or split valence basis set couldn t represent the polarizability of the atom the polarization functions need to be added to represent the atom more properly The addition of polarization functions is usualy denoted by an asterisk indicating that polarization functions is added for heavy atoms not hydrogen or helium Two asterisks indicate that polarization functions are also ad ded to light atoms hydrogen and helium The common used basis sets with polarization functions includes 3 21G 6 31G 6 31G etc Another common addition to basis sets is the addition of diffuse functions denoted by a plus sign Two plus signs indicate that diffuse functions are also added to light atoms hydrogen and helium These are very shallow Gaussian basis functions which more accurately represent the tail portion of the atomic orbitals which are distant from the atomic nuclei These additional basis functions can be important when considering anions and other large soft molecular systems Some commonly used basis sets with diffuse functions 3 21 G 6 31 G 6 31 G The polarization functions and diffuse functions can be combined together to achieve better performance For ex apmle user can use 6 31 G 6 31 G 6 31 G as basis set for their calculations etc 15 Chapter 3 Software Installation Configuration Introduction GridChem is a Java application that can be used to laun
42. 2 726032 NONKKnNN je 0 0 0 0 0 Pigi sah DO CTCGOLQTGTGO ON NODE 0 STEP CPU TIME 0 02 TOTAL CPU TIME TOTAL WALL CLOCK TIME 0 0 SECONDS ENERGY COMPONENTS WAVEFUNCTION NORMALIZATION 0000000000 ONE ELECTRON ENERGY 1207582136523 TWO ELECTRON ENERGY 37 4886463645 NUCLEAR REPULSION ENERGY 13134263274 TOTAL ENERGY 74 9561459604 ELECTRON ELECTRON POTENTIAL ENERGY 37 4886463645 NUCLEUS ELECTRON POTENTIAL ENERGY 195 1479483346 NUCLEUS NUCLEUS POTENTIAL ENERGY 3134263274 TOTAL POTENTIAL ENERGY 149 3458756427 TOTAL KINETIC ENERGY 74 3897296823 VIRIAL RATIO V T 0076141731 eS Oats PI ENERGY ANALYSIS ENERGY ANALYSIS FOCK ENERGY 45 7809251349 BARE H ENERGY 120 7582186523 ELECTRONIC ENERGY 83 2695718936 KINETIC ENERGY 74 3897296823 N N REPULSION 8 3134263274 TOTAL ENERGY 74 9561455662 SIGMA PART 1 2 75 5031666243 K V1 2 69 3322672303 175 3387336392 PI PART 1 2 7 7664052693 K V1 2 5 0574624520 19 8092146954 SIGMA SKELETON ERROR 67 1897402969 0 0000000000 MIXED PART 0 00000E 00 0 00000E 00 0 00000 6173 Bl 00000 00000 925864 00000 00000 61831 61831
43. 616 47 4 4058 3761 5 8 8115 TD Show Dipole Wenvatve Unit Vector hs fi eit Le E By choose Show Displacement Vectors option in Display Vibrations window displacement vector associated with the vibrational motion can be displayed in the view window Figure 9 9 Figure 9 9 Displacement Vectors 76 Post Processing Visualization fy GS M1 1 rese loj x Read Only Read Only 2 The Spectrum button in Display Vibrations window presents Gaussian s estimate of the spectrum in line format Figure 9 10 According to Gaussian online document the intensity values are relative to the highest value in the present set and bear no precise relationship to experimental band intensities Figure 9 10 Vibrational Frequency Spectrum 77 Post Processing Visualization Infrared Spectrum 1500 2000 2500 S000 3500 4000 Frequency Please refer to GaussView online user help for more information Post Processing of GAMESS File General Introduction of GAMESS Output File In this section we will have an overlook of a general GAMESS output file to give reader a basic understanding of the structure of GAMESS output file Please notice that only part of typical GAMESS output file has been listed for annotation At the very beginning of GAMESS output file the basic system information of the running job is listed piv116 Tue Oct 4 16 09 27 EDT 2005 eee GAMESS execution script This job is ru
44. 69 Post Processing Visualization If the calculation in the selected output file is optimization of the structure Molden can show the details of optimiza tion process by clicking button Geom conv Figure 9 4 shows the optimization of energy and force for cysteine Figure 9 4 Molden Optimization Results 70 Post Processing Visualization 2101 x E n e r 9 y Aver Force If the calculation includes vibration frequencies Molden is also able to visualize each vibratoinal mode Click Norm Mode check box the IR spectrum based on the calculated vibrational frequencies will be shown first Figure 9 5 Figure 9 5 Molden Vibrational Results 71 Post Processing Visualization Spectrum Taxi Spectrum InfraRed Half Width Eo hin Freq esse a aa ee Scale Fac Max Freq mo nnn Max Ints In the second window Molden Frequency Select Figure 9 6 each vibrational normal mode can be selected And the cartoon of corresponding vibrational normal mode will be shown in the main Molden window Molden can also measure any atom distance bond angle and dihedral angle upon the corresponding selection To learn more about the Molden s ability to visualize the molecule please refer to the Molden user manual Figure 9 6 Molden Frequency Select 72 Post Processing Visualization Molden Frequency Select a oj x 11 151000 42 505001 E0 619999 r5 292999 101 100998
45. 9 4155 990234 1 2 5 d 5 B Fi a to Scale Factor 7 0 100000 Figure 9 17 Vibrational Normal Modes 94 Chapter 10 Technical Support PCS User Guide The Portable Consulting Service PCS was designed with the HPC system users in mind It is used to submit and track problem reports found in the GridChem client at the resource sites and within the CCG infrastructure The PCS User Guide has three sections the User Interface the Consultant Interface and the Manager and Administrator Interface The User Interface describes the login mechanism ticket problem report creation and updates and viewing con sultant responses The Consulting Interface and Manager and Administrator Interface are for the consultants and site administrator and GridChem users need not concern themselves with these section but a quick read will give in sights on how tickets are handled User Interface Overview A user with a problem enters the PCS ticketing system clicks the create ticket button and then fills in the form with information about a problem Specific radio buttons and pull down menus allow the user to easily categorize the problem for the consultant A text area is used to insert the details the user should include Personal information email username etc is automatically included in the ticket This information is acquired from the database at PCS login from the user s preferences and login data Consultants and
46. Cal Mol Kelvin Total 24933 5 346 48 522 Electronic 0 000 0 000 0 000 Translational 0 889 2 981 36 834 Rotational 0 592 1 987 P5595 Vibrational 1 452 0 378 0 094 Q Log10 Q Ln Q Total Bot 0 104734D 09 8 020088 18 466936 Total V 0 0 116746D 10 9 067243 20 878099 Vib Bot 0 904387D 01 1 043646 2 403083 Vib V 0 0 100811D 01 0 003509 0 008081 Electronic 0 100000D 01 0 000000 0 000000 Translational 0 920610D 07 6 964076 16 035377 Rotational 0 125794D 03 2 099658 4 834642 From the beginning we can see that all the thermodynamics properties in this output section are at 298 150K and 1 00000 Atm After list of atomic number and mass of each atom in the system some characteristics of the system based on the moments of inertia including rotational temperature and constants zero point vibrational energy and vibrational temperature are listed as well Zero point correction is the zero point energy in the unit Hartree Particle In this case zpe is 0 002277 Hartree Particle Zero point correction 0 002277 Hartree Particle Thermal correction to energy is the correction to the internal thermal energy The correction is sum of the correction of internal thermal energy from molecular translational rotational and vibrational motion This correction includes the zero point correction Thermal correction to Energy 0 004674 Thermal correction to enthalpy is sum of thermal correction to energy and k B T where k B is Boltzmann con
47. E EES EE ESEE E Os ie 24 NCSA Certificate RegUest eresia a eane a E e a R a E E oa 24 Creating a Passphrase cosseccstey i een sa a E aa a E Ea EE E TE SE S 25 Grid ProXy sss tacte sot aie e a E E a e e T aa E e a E AEE 26 5 Interface Fundamentals sossen en aneren ties iee eeo EEEE EE EE EES it ence E E EE I rE EE Soe 27 The Fundamentals of Using the GridChem Portal ss sseessesesssesessrerrrrrsrrererrsrrerreresrrresrreersse 27 Overview of a GridChem Session c ccc ceeece cece ence ence eeceeecaeeca seca eeaeceae eeu eeneeeeeceeeeeeeeeeeeaees 27 Getting Started GridChem Main Control Panel 00 ce cece neces ee ence een eeeeeeeeeeeeeeeeeaees 27 Getting Started Control Buttons 2 0 0 0 eee cence nec eee ceeeca seca esau eeaa eens ecu eeneeeeeeeeeeeeeeeeeeaees 27 Text Area Running Lor ee r E E ben cdita baste ite T E EE acddtab E T ENE cers 28 6 Chimistry Applications yesin r E e a E a E aa e E A E doen aeae 29 7 Pre processor Molecule Boulder ec e2 csc ti ds sed othe weg ocd are e E eb wd ET E SS A 30 Prepare for a Case Computational Chemistry Study 0 0 ceee cece sce eceneeeeeeeeeeeeeeeeeaeeeaes 30 Prepare Structure For Your System 2 2 0 0 cece cece cee onein iee aa T EEEE e TEESE ESERE E Ta 30 Prepar for Gaussian Input File reedene hat oa aae a E E a EA EES ASS 38 Prepare for GAMESS Input File ites 0 0 oe ee eee eeeccescneecnecen seen ereeecneeece scan scan sce consesssenseensesnees 44 Prepare for N
48. Gaussian internally The absolute coordinate might be different from the input orientation but the real geometry remains the same Gaussian chooses the different orienta tion to optimize performance Standard orientation Center Atomic Atomic Coordinates Angstroms Number Number Type X Y Z 1 9 0 0 000000 0 000000 0 750000 2 9 0 0 000000 0 000000 0 750000 The following section indicates the predicted energy computed by Gaussian The convergence criteria in SCF com putation is also listed SCF Done E RB HF LYP 199 477206381 A U after 8 cycles Convg 0 1473D 08 V T 2 0050 S Z 0 0000 Population analysis section gives Mulliken population analysis results This analysis partitions the charge of mo lecule to each atom i e the partial charge of each atom is computed based on the SCF calculation In addition the dipole moment and multipole moment including quadrupole moment octapole moment and hexadecapole moment are also listed in the standard orientation KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Population analysis using the SCF density KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Orbital symmetries Occupied SGU SGG SGG SGU SGG PIU PIU PIG PIG Virtual SGU PIU PIU SGU SGG PIG PIG SGG SGU The electronic state is 1 SGG Alpha occ eigenvalues 24 80230 24 80230 1 30712 1 11790 0 57244
49. GridChem User s Manual GridChem User s Manual Published November 18 2005 DRAFT Table of Contents I GidChem Overview oc 25s53 siete ieoor a nen Oeren E EEIE EE TE E E SEEE EE EET EKE 1 INtHOMUCTION ORAS SE E EE EEEE T voietds sea neeuesvlotessseetenaged sone 1 Scope of the Computational Chemistry Grid essseseeeessesesesrestrstreerresrrerreerrreteerresrresererere 1 D sisn of CCG ia iis css Se een a ee AS sae ead se EE eee ee 2 Future Changes tothe Architecture syss enren e re e o EEE eseaueshe Sed shed vem esenyetagbey 4 2 Introduction to Computational Chemistry seeessseesseesereresrerrerrerrerrerrsresrrresrreersrrerrsresereeerrrerereet 6 Q nt m Chemisty Iae iet E E a a R R E EEE E R 6 Foundations of Quantum Chemistry esesseseiesesrsrsereessrrrrsrrerrsresereresrerresreresrrerrrresrreresrerert 6 Hartree Fock HE Methodi ici iis5ci ci estes nin dase ena oan adenine aacteevonede N EEEE seaade vis caades OEE EEEREN 7 Density Functional Theory DFT 00 0 0 cece cece cc ee ce en E E EESE eeu e o 8 Electron Correlation Methods tssirini arisen osie betta ss euanea se paiva sds TEP ETE S 11 Configuration Interaction CI ieis nacenan see eE EE EEE SRE EEEE EEEa 12 M ller Plesset Perturbation Theory oein mai aoe n a RE SE ASe UPE UER SENISES 12 Coupled cluster CC Theory 2 0 0 0 cece cece anssen E EEE S EEEE S EO EEEE 13 Semi Empirical Computational Method seesesseessseessseresrrerrsre
50. GridChem without having to go back to the web site The current GridChem client uses Java Web Start 1 2 Configuring GridChem for the First Time Once you launch the GridChem web start client it will check to see if the application jar files have been downloaded to your computer previously Jar files that have not been previously downloaded or newer jar files exist on the Grid Chem server will be downloaded to your computer The download progress window looks like Figure 3 3 Download it Java Web Start K GridChem Portal to the CCG Computational Chemistry Grid Validating Stream Adaptor jar From load gridchem org Scanning entries 100 done 18 Software Installation Configuration Once the software has been downloaded the GridChem client will start automatically Before it can start there are three certificats that you will be prompted to accept It is important that you accept all three The three are the CCG middleware server certificate a security certificate from the Legion of the Bouncy Castle and the third is another certificate from the Computational Chemistry Grid The three screen windows you should see are given below Figure 3 4 GridChem Middleware Server Certificate Warning Security Ga xj ccg mw 1 ncsa uiuc edu For the purpose of exchanging encrypted T Do you want to accept the certificate From web site information Publisher authenticity can not be verified A The secu
51. KE 1 985435752769D 02 Symmetry AG KE 8 820800488532D 01 Symmetry B1G E 0 000000000000D 00 Symmetry B2G KE 7 359570501461D 00 Symmetry B3G KE 7 359570501461D 00 Symmetry AU KE 0 000000000000D 00 Symmetry B1U KE 8 323455722276D 01 Symmetry B2U KE 6 190936082959D 00 Symmetry B3U KE 6 190936082959D 00 1 1 GINC PIV180 FOpt RB3LYP 6 31G F2 0SU3112 27 Sep 2005 0 B3LYP 6 31G OPT test F2 0 1 F 0 7339185686 0 0 F 0 7339185686 0 0 Vers ion IA32L G03RevC 02 State 1 SGG HF 199 4778337 RMSD 1 833e 09 RMSF 7 871e 08 Dipole 0 0 0 PG D H C F1 F1 IF MATHEMATICALLY YOU END UP WITH THE INCORRECT ANSWER TRY MULTIPLYING BY THE PAGE NUMBER Job cpu time 0 days 0 hours 0 minutes 11 0 seconds File lengths MBytes RWF 11 Int 0 D2E 0 Chk 4 Scr Normal termination of Gaussian 03 at Tue Sep 27 15 34 37 2005 Calculate Thermodynamics Properties from Gaussi an Output If thermodynamic properties such as enthalpy and free energies need to be calculated based on Gaussian output it is very important to make sure that the structure has been completely optimized to a minimum or transition states One simple way to confirm this is that four convergence criteria are all met at the end of the optimization process i e you get four YES at the last step of optimization To calculate the meaningful thermodynamics properties you also need to compute the frequencies of all the vibrational modes of y
52. KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK YOUR CERTIFICATE IS VALID FOR TWO YEARS DO NOT FORGET T 25 Authentication Authorization and Allocations t YOUR PRIVATE KEY ENCRYPTION PASSWORD AND DO NOT DELETE YOUR u ac userid globus DIRECTORY KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK The next step on the NCSA machine is to get a grid proxy To do this you will Testing your certificate by typing 1 grid cert info subject you will see C US O National Center for Supercomputing Applications CN John Doe 2 grid cert info enddate you will see Jun 5 17 22 19 2005 GMT 3 The above tests prove your certificate is working properly Grid Proxy You will request a grid proxy by entering 1 grid proxy init at the command prompt 2 You will respond to the request for the grid pass phrase to create this pass phrase you use the same rules as for the certificate pass phrase Your identity C US O National Center for Supercomputing Applications CN John Doe Enter GRID pass phrase for this identity Creating PLORKY 6 ee beeceveee o ete ise ele Wel we Se Babe byes lee e elaine yee Done Your proxy is valid until Thu Jun To see your proxy information type the following at the command prompt grid proxy info all You will see subject C US O National Center for Supercomputing Applications CN John Doe CN proxy issuer C US O Nat
53. Main Control panel allows the user to control all aspects of using GridChem from logging in to creating and submitting jobs for computational Chemistry software packages to accessing viewing saving the results These stages and others are activated by the buttons shown When one of these buttons are clicked a new window appears related to that particular task Getting Started Control Buttons Below is a list of the Main Control panel buttons and a brief description of what each one does In other sections of this Help Documenation there is a full detailed description of how to perform the tasks each button is labelled with e Authenticate Allows the user to logon to the GridChem portal At the same time a check is performed on the user s account to see if it has valid certification That is does the user have permission to use the GridChem portal and the software and hardware it leads too 27 Text Interface Fundamentals NOTE This must be the first procedure the user goes through Without authentication the other Main Panel but tons won t even work except Exit e Read Announcements Directs the user to the Announcements section of the GridChem home page The Grid Chem announcemnts can cover a variety of topics upgrades problems with the present GridChem version post ings of GridChem events such as conferences and presentations details of upcoming improvements to Grid Chem etc e Check Preferences Allows the us
54. Molden Display Molecule 90 Post Processing Visualization MOLDEN If the calculation in the selected output file is optimization of the structure Molden can show the details of optimiza tion process by clicking button Geom conv Figure 9 14 shows an example of optimization of energy and force from GAMESS optimization Figure 9 14 Energy and Force Optimization 91 Post Processing Visualization IAE 92 Post Processing Visualization If the calculation includes vibration frequencies Molden is also able to visualize each vibratoinal mode Click Norm Mode check box the IR spectrum based on the calculated vibrational frequencies will be shown first Figure 9 15 Figure 9 15 Vibrational Frequencies Spectrum Ma x Spectrum InfraRed Half Width Feo din Freq bo Max Ints In the second window Molden Frequency Select Figure 9 16 each vibrational normal mode can be selected And the cartoon of corresponding vibrational normal mode will be shown in the main Molden window Figure 9 17 Molden can also measure any atom distance bond angle and dihedral angle upon the corresponding selection To learn more about the Molden s ability to visualize the molecule please refer to the Molden user manual Figure 9 16 Molden Frequency Select 93 Post Processing Visualization Molden Frequency Select EE x 1 930000 0 200000 0 OOOO 0 OOOO 4 foQ000 E 35000 2170 04003
55. One of the quantum mechanics postulates states that all the basic properties including energy of a stationary state of a molecule can be obtained by solving the time independent Schrodinger equation Here is the time independent Hamiltonian a differential operator representing the total energy E is the eigen Al value of the state which is also the energy of the state Y is the wavefunction It is the function of the Cartesian Eq 6 1 coordinates of all particles nuclei and electrons in the molecule and also the spin coordinates of these particles Unfortunately except very small systems such as helium atom or hydrogen atom the time independent Schrodinger equations cannot be solved analytically for neither any other atom nor any molecule To tackle this difficulty one important approximation which is called Born Oppenheimer approximation has been made to simplify the Schrodinger equation The Born Oppenheimer approximation is the assumption that the elec tronic motion and the nuclear motion in molecules can be separated It leads to a molecular wave function in terms of electron positions a and nuclear positions a gt n Eq 6 2 Prorun s t F 7A PR CaA There is following assumption involved in this approximation That is the electronic wavefunction depends upon the nuclear positions but not upon their velocities One common explanation of this assumption is that the nuc laefrans lear
56. Q LN Q 1 00000E 00 0 000000 3 00431E 06 14 915558 4 79731E 01 3 870640 1 00003E 00 0 000028 1 44130E 08 18 786227 E H G CV CP S KJ MOL KJ MOL KJ MOL J MOL K J MOL K J MOL K 0 000 0 000 0 000 0 000 0 000 0 000 Bi TL8 6 197 2396975 124472 20 786 144 800 3 718 3 718 9 595 12 472 12 472 44 654 64 008 64 008 64 007 0 026 0 026 0 003 71 444 73 923 17 437 24 969 33 283 189 456 E H G CV CP S KCAL MOL KCAL MOL KCAL MOL CAL MOL K CAL MOL K CAL MOL K 0 000 0 000 0 000 0 000 0 000 0 000 0 889 1 481 8 837 2 981 4 968 34 608 0 889 0 889 2 293 2 981 2 981 10 672 15 298 15 298 15 298 0 006 0 006 0 001 17 076 17 668 4 168 5 968 7 955 45 281 D ELTA J K The zero point energy calculated by GAMESS is 0 024379 Hartree Particle GAMESS also calculated the correction for internal energy enthalpy Gibbs free energy and entropy Combined with the total energy listed in the first half of output file user will be able to calculate the thermodynamics properties for the whole molecule For more details about the thermodynamics properties calculation please refer to the section Calculate Thermodynamics Properties from Gaussian Output 87 Post Processing Visualization The scaling factor used by GAMESS for frequency analysis is 1 000 But due to the systematic error of some elec tronic structure theory it is very common to scale the ab initio calculation of vibrational frequencies to obtain better results with respect to the experiments The
57. S CPU UTILIZATION IS 4 69 TWO ELECTRON INTEGRAL DERIVATIVE CONTRIBUTIONS 7909 WORDS REQUIRED 100000 WORDS AVAILABLE THE COARSE FINE SCHWARZ SCREENINGS SKIPPED 0 0 BLOCKS THE NUMBER OF DERIVATIVE INTEGRAL BLOCKS COMPUTED WAS 27 ON NODE 0 STEP CPU TIME 0 02 TOTAL CPU TIME O 1 0 0 MIN TOTAL WALL CLOCK TIME 1 3 SECONDS CPU UTILIZATION IS 6 25 mode se tigen el END OF 2 ELECTRON GRAD HESS FOCKDER ON NODE 0 STEP CPU TIME 0 00 TOTAL CPU TIME Q s le of 0 0 MIN TOTAL WALL CLOCK TIME 1 3 SECONDS CPU UTILIZATION IS 6 25 COUPLED PERTURBED CLOSED SHELL HARTREE FOCK THE CPHF HAS 10 INDEPENDENT ORBITAL ROTATIONS SOLVING FOR 6 NUCLEAR RESPONSES AND 0 ELECTRIC FIELD RESPONSES 84 Post Processing Visualization FA WILL USE 553 WORDS TA WILL USE 1097 WORDS FCK WILL USE 31139 WORDS WXY AND YA WILL USE 30987 WORDS THERE ARE 100000 WORDS AVAILABLE TIME FOR FA 0 000 TIME FOR TA 0 000 TIME FOR FCK 0 000 PRECONDITIONED CONJUGATE GRADIENT SOLVER CONV TOLERANCE 5 00E 05 ITER RESPONSE ERROR IMPROVED I 4 97703E 01 6 2 6 92844E 02 3 1 01932E 02 5 4 1 22498E 03 4 9 2 65793E 04 4 6 3 58112E 05 2 THE CPHF HAS CONVERGED AFTER 6 ITERATIONS IT REQUIRED 27 FOCK LIKE BUILDS TO FIND THE 6 SYMMETRY UNIQUE RESPONSES TIME FOR YA 0 000 wile Bei DONE WITH CPHF CONTRIBUTIONS ON NODE 0 STEP CPU TIME
58. S HUCKEL SEND CARD gt SDATA CARD gt Water RHF STO 3G CARD gt Cnv 2 CARD gt CARD gt O CARD gt H 1 roH CARD gt H 1 rOH 2 aHOH CARD gt CARD gt rOH 1 06 CARD gt aHOH 100 0 CARD gt SEND T E HHHH HHHHAHHHHHHHHZ ZAZA AZAZAZAA A An U o g T a g a g a g tg g te AAA al Sar dar Uar Sa S Ba Bar E ar Sa V NNNUNN N The following section shows the formation of the STO 3G basis set from the 3 primitive Gaussians in each case The L symbol means both S and P The same exponents of the Gaussians are used but with difference coefficients S coefficients are listed first then P ATOMIC BASIS SET THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENTS O 1 S 1 130 7093214 0 154328967295 1 S 2 23 8088661 0 535328142282 1 S 3 6 4436083 0 444634542185 2 L 4 5 0331513 0 099967229187 0155916274999 2 L 5 1 1695961 0 399512826089 0 607683718598 2 L 6 0 3803890 0 700115468880 0 391957393099 H 4 S 7 3 4252509 0 154328967295 4 S 8 0 6239137 0 535328142282 79 Post Processing Visualization 4 S 9 0 1688554 0 444634542185 There are many more options are set to default values by GAMESS SCONTRL OPTIONS
59. W Chem Input File ccs ccscsoess ec eessaesdsoiaa de snd snasashotsaapsatvneasberieagssnaseusesboteagesedebageas 48 8 Job Management isoine iorno erae ccnsebonsacsenin Gets gubeness aes E S E EEES EGEE EEE EEG 50 Managing GridChem Jobs 3s c0 c025 ai i e a ea p EEG AEE e E TGE ESS 50 The Job Management Window ssseesssesrseresrrresrrrresrrerrsrrerrrresrrrerrerrsrrerrsrrerreeesreresrreeest 50 Inquity Buttons ss csc sccen ss Scbasag oad teadk sebap tg saci aban ss sete agess sene da shoms OSATEN E EPIR geen ieau de sebaadeveaaber gate 51 ACHON BULONS eee AEE NEEE E E TAE SE AE E EEEE E E TOET 51 9 Post Processing V ISNA Za O a a a A Mawel e a A ee Ae eee 52 General Introduction e presea EE OE E E E AENT SREE OE EE E EPEE E TVE AN E Ei 52 GridChem User s Manual Post Processing of Gaussian03 Output File 2 0 0 0 cece eee cece cece cena een eeneeeeeeeeeeeeeeeeeeaeeeaes 52 General Introduction of Gaussian03 Output File ccc eeeeeeeeceeeceeeeeceeeeeeeeececueeeeneeeeeeeeeuneeeees 52 Calculate Thermodynamics Properties from Gaussian Output 0 cece eee cece eeceeeceeeeeeeeeeeeaees 64 Visualization of Gaussian03 Output File by Molden 0 0 0 cece cence eee eceeeeeeeeeeeeeeeeeeeenees 67 Visualization of Gaussian03 Output File by GaussView 2 0 0 0 ccc cece ce cece ce ence ence eeeeeeceeeeeeeeeeeaees 73 Post Processing of GAMESS File teses prinssiin r erene GEEET E ve EEE e TE E PEGEDE 78 General Introduction
60. X G 3204 180012 Oct 4 16 09 tmp pbstmp 362347 exam09H20 F08 rw r r 1 xxxx G 3204 180012 Oct 4 16 09 tmp pbstmp 362347 exam09H20 F08 rw r r 1 XXXX G 3204 1571328 Oct 4 16 09 tmp pbstmp 362347 exam09H20 F10 0 176u 0 261s 0 04 99 8 6 0 0k 0 0io Opf 0w Calculate Thermodynamics Properties from Gaussi an Output Similar to Gaussian 03 calculation to calculate thermodynamic properties such as enthalpy and free energies based on GAMESS output it is very important to make sure that the structure has been completely optimized to a minim um or transition states To calculate the meaningful thermodynamics properties you also need to compute the fre quencies of all the vibrational modes of your molecule The keyword in GAMESS for vibration calculation is RUNTYP HESSIAN in CONTRL section Except the output of the energy and properties calculation at the input geometry Hessian is also calculated for fre quency analysis ON NODE 0 STEP CPU TIME 0 00 TOTAL CPU TIME 0 1 0 0 MIN TOTAL WALL CLOCK TIME 1 3 SECONDS CPU UTILIZATION IS 4 69 1ST AND 2ND INTEGRAL DERIVATIVE CONTRIBUTIONS TEET END OF 1 ELECTRON GRAD HESS FOCKDER ON NODE 0 STEP CPU TIME 0 00 TOTAL CPU TIME OxI 0 0 MIN TOTAL WALL CLOCK TIME 1 3 SECOND
61. als with certificates for the machines you are working on The GridChem Client is designed to al low the user to concentrate on his or her science and not worry about computers schedulers etc External User If you have an account on one of the accepted machines of the involved schools you can use the GridChem client with your account This will allow you to use the GridChem client with your existing account You will not have to request a community allocation Digital Certificate To obtain a digital certificate you must be an authorized user on one of the machines in question for a list of ma chines see follow the link on the left menu titled CCG Resources NCSA Certificate Request To receive a certificate on NCSA s copper cu ncsa uiuc edu Log into the machine from which you will be requesting your NCSA certificate At the command line type ncsa cert request If you get output like 24 Authentication Authorization and Allocations ncsa cert request Command not found Then your environment needs to be configured properly If the certificate request works you will be asked to enter your NCSA Kerberos password The text will look something like this To continue pleas nter your NCSA Kerberos password Creating a Passphrase After entering your Kerberos password you will be prompted to enter a passphrase which will serve as both the en cryption key for your certificate s private key and as
62. applying of scaling factor is fairly easy What needs to be done is just multiply the zero point energy from GAMESS output file by the scaling fact For the different theory level and basis set the different scaling factors need to be used Here are some common used scaling facts Table 9 2 GAMESS Vibrational Frequency Scaling Factors Level Basis Scale HF 6 31G d 0 9135 HF 6 31 G d 0 9163 HF 6 31G d p 0 9181 HF 6 311G d p 0 9248 HF 6 311G df p 0 9247 HF 6 31 G d p 0 9173 B3LYP 6 31G d 0 9806 B3LYP 6 31 2df 2p 0 983 Data taken from http comp chem umn edu database freq_scale htmAn Extended list can also be found here Visualization of GAMESS Output File by Molden Molden is a package for displaying Molecular Density from the Ab Initio packages Gaussian GAMESS UK and GAMESS US and the Semi Empirical packages Mopac Ampac Molden reads all the required information from the GAMESS GAUSSIAN output file And Molden is capable of displaying Molecular Orbitals and the electron dens ity Molden supports contour plots 3 d grid plots with hidden lines and a combination of both It also can animate reaction paths and molecular vibrations Derived Electrostatic Potential and atomic charges can be fitted to the Elec trostatic Potential calculated on a Connolly surface Molden has a Z matrix editor which gives full control over the geometry and allows you to build molecules from scratch including polypep
63. artree Fock and DFT calculation In this section several multiple determinant methods are introduced briefly Configuration Interaction Cl Configuration Interaction CI methods proceed by constructing more than one determinants by replacing one or more occupied orbitals in Hartree Fock determinant with a virtual orbital The wave function of the system is repres ented as the linear combination of these multiple determinants In a single substitution a virtual orbital replaces an occupied orbital within the Hartree Fock determinant This de terminant corresponds to the excitation state with one electron to a higher energy orbital In a double substitution two occupied orbitals are replaced by virtual orbitals The determinant corresponds to the excitation state with two electrons to higher energy orbitals Similarly triple substitutions would exchange three or bitals and so on The full CI method constructs wave functions by the linear combination of the Hartree Fock determinant and all possible substituted determinants W 0 he ay Where the first term in right hand side is the Hartree Fock determinant and s runs over all possible substitutions Full CI is size consistent and variational But it is too expensive to be practical for most systems Therefore limited Configuration Interaction methods which are more practical use the linear combination of Hartree Fock determin ant and a limited set of substitutions as
64. ashank default test cuncsauu debug 0932005 05 02 ptaomk ptao metha cunesa ui debug 02Sa 0438 ropoj defaut fest cuncsauu debug 0872472005 0327 kyriacou proj default test cuncsa uiu debug The columns in the text window provide job inquiry information In order from left to right the column headings and explanationsa are e Date Date job was sumitted e Time How long the job has been running e ResProj The research project the job is a part of e jobName Name user chose for the job 50 Job Management e Machine The IP address of the HPC cluster the job used e Queue The batch processing queue the job is in e jobID The internal job ID number used by the batch processing system Just by glancing at the columns the user can quickly confirm or not that the job specifications they entered were indeed used Inquiry Buttons On the left hand side of the Job Management window are buttons some which are inquiry in nature and others of which are action oriented Clicking on the Get Job Status button will do just that show the status of the job in a pop up window The status of a batch job is typically an upper case letter For example if an R is shown in the status window it means the users job is Running Other possible states include Q W and H e Q gt Job is Queued and will be run in turn e W gt Job is Waiting for an event e g a certain time of day to occur before it is run The user
65. ax 0 000000136 RMS 0 000000079 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization Internal Forces Max 0 000000136 RM 0 000000136 Search for a local minimum Step number 3 out of a maximum of 2 R1 RAL 2 1 4678 DE DX 0 0 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Input orientation Center Atomic Atomic Coordinates Angstroms Number Number Type X Y Z 62 Post Processing Visualization 1 9 0 0 016081 0 000000 0 000000 2 9 0 1 483919 0 000000 0 000000 Stoichiometry F2 Framework group D H C F F Deg of freedom 1 Full point group D H NOp 8 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 Standard orientation Center Atomic Atomic Coordinates Angstroms Number Number Type X y Z a 9 0 0 000000 0 000000 0 733919 2 9 0 0 000000 0 000000 0 733919 Rotational constants GHZ 0 0000000 24 6930279 24 6930279 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK KKK KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Population analysis using the SCF density KKEKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Orbital symmetries Occupied SGU SGG SGG SGU SGG PIU PIU PIG PIG Virtual SGU PIU PIU SGU SGG PIG PIG SGG SGU The electronic state is 1 SGG Alpha occ eigenvalues 24 80102 24 80102 1 32083 1 11174 0 57847 Alpha occ eigenvalues 0 51875
66. be used in any manner that competes with the business of Gaussian Inc or will provide assistance to any competitor of Gaussian Inc The licensee of this program is prohibited from giving any competitor of Gaussian Inc access to this program By using this program the user acknowledges that Gaussian Inc is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the 58 Post Processing Visualization licensee that it is not a competitor of Gaussian Inc and that it will not use this program in any manner prohibited above Cite this work as Gaussian 03 Revision C 02 M J Frisch G W Trucks H B Schlegel G E Scuseria M A Robb J R Cheeseman J A Montgomery Jr T Vreven K N Kudin J C Burant J M Millam S S Iyengar J Tomasi V Barone B Mennucci M Cossi G Scalmani N Rega G A Petersson H Nakatsuji M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai M Klene X Li J E Knox H P Hratchian J B Cross C Adamo J Jaramillo R Gomperts R E Stratmann O Yazyev A J Austin R Cammi C Pomelli J W Ochterski P Y Ayala K Morokuma G A Voth P Salvador J J Dannenberg V O J J I Cc B G G Zakrzewski S Dapprich A D Daniels M C Strain Farkas D K Malick A D Rabuck K Raghavacha
67. bout Note that this is a live test environment You may occassionally see strange text or broken features for a short period of time The CCG Portable Consulting System is in testing mode Last update 11 3 2004 Thank you for your patience Support Kent Milfeld milfeld tacc utexas edu to report any issues you encounter Developer Patrick Hurley phurley tacc utexas edu The Consulting Menu Item When consulting is selected from the main menu a ticket table is displayed in the Display panel and a new Consult ing menu appears left The links in the new menu allow you to create a ticket go home or browse tickets An ex ample snapshot of the new window is shown below The ticket table has six headers Ticket Date Created Category Status Requestor and Owner The Owner is the name of the consultant who has responded and is responsible for the ticket The Status is New when the ticket is still awaiting a consultant to take ownership of respond to the ticket In Progress means that the user has respon ded to the ticket and PCS is waiting for the consultant to act on the new information Pending User Response means that the consultant has responded to the ticket and is waiting for the user to respond or close the ticket Once a user is satisfied with the resolution of the problem he should respond with an acknowledgement so that the con sultant can immediately close the ticket Figure 10 4 Consulting
68. ch and monitor computational chemistry calculations on high performance supercomputers from a user s personal machine The GridChem interface allows users to submit and monitor quantum chemistry jobs run on any computer on which they have an allocation without having to log in or to remember the unique features of each system In future releases when the Computational Chemistry Grid has taken full form we envision making this process even more transparent to the user but for now we depend on the users to know which machines they are able to access GridChem can submit input text files to Gaussian 03 GAMESS and NWChem applications currently We intend to implement several other quantum chemistry applications such as Molpro Qchem Aces etc in this interface in the future Please use the online user survey http www gridchem org project GridChem_survey htm form to provide feed back on which chemistry applications you would like to see supported through GridChem A molecular editor is integrated into GridChem and can be used to generate input files In addition output files can be obtained from the remote hosts and parsed to create graphs and geometries extracted and viewed as molecular models GridChem relies upon Grid and Java security technologies to ensure security System Requirements Java GridChem requires Java If you do not have Java on your machine or the version of Java on your machine is old download and install Java fr
69. ch executions that usually happen If you have a desktop client that submits these batch requests remotely the user can submit their work remotely without having to spend time learning different types of operating systems local environments and batch environment specific ations of various HPC systems e GridChem s desktop client provides a single GUI interface for researchers to authenticate to a machine or even tually grid of machines and submit jobs Each machine in the grid stores its information in a middleware server so that the client can provide the user with all necessary system information e Currently a user generally logs into a command line interpreter and writes scripts for the machine logged into e There is none of the ease of use of a desktop machine and the scientist must learn the system details of the ma chine e queues e number of nodes and processors e how to set a time limit GridChem Overview e amount of memory storage etc e CCG and the GridChem client allows the user to do chemistry research without having to learn system details about one or more machines Design of CCG The CCG is designed as a 3 tier architecture consisting of a client side GUI application a middleware service and a resource layer The client GridChem is a Java application that remotely launches and monitors computational chemistry applications on CCG supercomputers at remote sites GridChem is a lightweight application dist
70. community users external users basic settings for each ap plication on each machine etc is stored The GMS interacts with the grid utilities to pass information from the client to the machines at each site Currently we are changing the architecture at this level and the resources level We will be relying more on grid technologies and less on the CGI scripts The grid technologies are easier to add to and scale much more reliably than CGI scripts therefore as the second year of the project progresses each CGI script will be replaced with a grid technology The third level of the architecture is the resource layer This layer is made up of the necessary scripts applications and the actual machine resources that a community user may draw upon Therefore using the client allows you to work on any of the machines in the grid regardless of whether or not you have an account on that specific machine or any knowledge of what type hardware operating system or scheduler the system has Future Changes to the Architecture In the future there will be many changes to the GMS and Resource layer of the CCG architecture While we may continue to add functionality to the GridChem client it is not the focus of the remainder of this project The re mainder of this project is focused on developing the existing resources into a fully functional grid application that will allow any community user complete access to all of the CCG resources The anticipated future a
71. ctories 10 Plots of the total energy and other data from the same jobs types as in the previous item A detailed GaussView user help documentary can be found on Gaussian official website ht tp www gaussian com g_gv gvtop htm Here we just briefly show how GaussView can display Gaussian calculation results GaussView can read in both of Gaussian log file and checkpoint file and display calculations results The Results gt Summary menu item displays summary data about the results of the Gaussian calculation available when a Gaussian log file or checkpoint file is opened Figure 9 7 shows the summary of optimization of water mo lecule Figure 9 7 Optimization Summary 74 Post Processing Visualization fa G2 M1 1 Calculation Summary q x Water Opt File Type log Calculation Type FREQ Calculation Method FABSLY P Basis Set 6 316 E RB HF LYP 76 38611663 a u AHS Gradient Norm 0 00000988 a u Imaginary Freq 0 Dipole Moment 2 3988 Debye Point Group Cay Job cpu time O days hours O minutes 13 1 seconds The Results gt Vibrations menu item is used to vibration frequency calculation resutls It allows calculated vibration al data to be displayed as dynamic screen motions based on information from a frequency calculation Figure 9 8 shows the Display Vibrations window which contains the H 2 O molecule vibration data Figure 9 8 Vibration Frequency Results 75 Post Processing Visualization 3
72. d Authenticate Developed hy Read Announcements University of Kentucky Louisiana State University University of Illinois at Urbana Champaign Ohio Supercomputer Center University of Texas at Austin Check Preferences Submit Jobs For more information please visit https www gridchem org Manage Jobs Authentication requested Save Data GridChem Authentication Valid for 2 hours starting from Mon Nov 14 13 46 33 ES Error saving credentials to local machine 0 View License HERI Exit It will also display an allocations summary window This window will display all of the allocations which this ac count is listed under and what their current balances are Figure 3 10 Allocation Summary 22 Software Installation Configuration GridChem Allocation Information 23 Chapter 4 Authentication Authorization and Allocations Authentication 1 Before you start 2 Community User 3 External User 4 Digital Certificate 5 NCSA Certificate Request 6 Creating a Passphrase 7 Grid Proxy Before You Start Make sure you follow all the steps in the GridChem Manual http www gridchem org GCmanual You especially need to make sure that you carefully follow each step in the System Requirements and Installation sections Community User With the new client if you are a Community User you do not need any external authentication actions You install the client and it de
73. dGrad Berny optimization Internal Forces Max 0 000000136 RMS 0 000000136 Search for a local minimum Step number 3 out of a maximum of 20 All quantities printed in internal units Hartrees Bohrs Radians Update second derivatives using D2CorX and points 3 Trust test 9 26D 01 RLast 9 80D 04 DXMaxT set to 3 00D 01 The second derivative matrix R1 R1 0 33072 Eigenvalues 0 33072 RFO step Lambda 0 00000000D 00 Quartic linear search produced a step of 0 00039 Iteration 1 RMS Cart 0 00000027 RMS Int 0 00000000 Variable Old X DE DX Delta X Delta X Delta X New X Linear Quad Total R1 2 17381 0 00000 0 00000 0 00000 0 00000 2 77381 Item Value Threshold Converged Maximum Force 0 000000 0 000450 YES RMS Force 0 000000 0 000300 YES Maximum Displacement 0 000000 0 001800 YES RMS Displacement 0 000000 0 001200 YES Predicted change in Energy 2 792449D 14 Optimization completed Stationary point found The following section is the archive entry corresponding to this job All the calculation results are summarized in a compact format style 1 1 GINC PIV180 FOpt RB3LYP 6 31G F2 0SU3112 27 Sep 2005 0 B3LYP 6 31G OPT test F2 0 1 F 0 7339185686 0 0 F 0 7339185686 0 0 Vers ion IA32L G03RevC 02 State 1 SGG HF 199 4778337 RMSD 1 833e 09 RMSF 7 871e 08 Dipole 0 0 0 PG D H C F1 F1 For each Gaussian output file archive section the total electronic energy is always listed
74. e Bi Eloy fei Vie ai lan i 2 i k h nl F 2 a Tee dro taleg nor Here N is the number of electrons The ground state energy can be found by varying ro so as to minimize the functional A 2 r Equivalently instead of varying ro we can vary the Kohn Sham orbitals to minimize the functional The first term on the right hand side of the DFT energy equation is the kinetic energy of the non interacting elec trons which is in equation 6 4 The second term is the nuclei electron attraction which is aLe pr Le 5 in equation 6 4 This term is as same as nuclear electron interaction in the real system The third term is the classical electron electron repulsion which is Le 5 in equation 6 6 The fourth term Introduction to Computational Chemistry i ferred h h lati which i d E Lew is referred to as the exchange correlation energy which contains ATT ocr an AF in equation 6 4 Since the first term is close to the kinetic energy of the real system and the third ee LOlr term is close to the electron electron interaction of the real system the correction of the kinetic energy ATT i and non classical corrections to the electron electron repulsion energy are not Or AM LO main contributions to the functional ET fa cr Unfortunately the exchange correlation energy cannot be calcu lated exactly and approximations need to be applied for its calculation The most popular method to calculat
75. e a ee eee ieee 74 9 8 Vibration Frequency Results cc s sseics saostesssavescadaieacvassesoctapsensesa EE TE E a Ea S 75 9 9 Displacement Vectors secto lesrr ericson ret eerk o na ESEE EEE I TEENE EES IA EE ERES EEEE EEEIEE RETTES 76 9 10 Vibrational Frequency Spectrum o is is ionisere si s iroi rosessi RSS snI EEEE ties dsensssesesevtesseeadebeadebs 77 OV Te Molden Interface vs 225 odvs gos an a Steves Gio huie ge ees cena Ross Woe bs ae eeu dele bulge where a a bowen e need 88 912 Mold n File Select rim enes a n e a a e e a sae sn deeasieaessie udaveusdersdeseenedGssiuneceatee 89 9 13 Molden Display Molecule 2 0 0 0 r a eea E a E EER ee i ose 90 9 14 Energy and Force Optimization ese isee ireann eiee NEEE S EA E ESES KERE S EE R RSSA Ei 91 vi GridChem User s Manual 9 15 Vibrational Frequentie S 2 sect sts oee sid e baitie gs save mh andedesMvard ha Seu UG ee mate edad eed sige oie ees 93 9 16 Molden Frequency Select 152 4 0 ssaccee Pag e a beatae teat gad aes less sheet haa dh euaa tee aetaseh laceeterans 93 9 17 Vibrational Normal Modes 23 3 sf 8incote dss use na buck Bel aa cetacean ss ae eG OS A 94 LODE Logi nn Seer acon ss waked e Ge tea gees tugs ss gant eats oh A Sea tesh Wore sedbeds aed semaeetyven tees E NEEE 95 10 2 F iled logi Panel sisser foe bores bebe cesdete gonegecees on E S EREE sous Meas E ESEA E SEE OSS 96 10 3 PCS Panels home VEM e sided seg e A Ea tote E E E a a EEEa 97 10 4 Cons
76. e ex change correlation energy is called the hybrid method in which the HF exchange energy is introduced into DFT the ory to calculate the exchange correlation energy B3LYP is one of the most popular hybrid methods In B3LYP method there are three parameters have been used to give satisfied theoretical results compared to the experimental results in many cases A generalized procedure of DFT calculation is illustrated below Figure 2 2 Generalized DFT Proceedure 10 Introduction to Computational Chemistry Input data atom coordinates and the number of electrons Theory level specified Figure 6 2 The Procedure of Density Functional Theory Calculation Electron Correlation Methods Introduction to Computational Chemistry In Hartree Fock calculation scheme the wavefunction of each electron is optimized under the mean potential aver aged over all the other electrons in the system as well as the electrostatic potential generated by the fixed nuclei In another words during the Hartree Fock calculation the electron cannot see other electrons in stead of averaged electron gas The primary deficiency of Hartree Fock method is that the correlation of electron motion cannot be accounted adequately To take such correlation in account so called multiple determinants method should be applied The name multiple determinants reflects the fact that a single Slater determinant wave function is formed in H
77. e of analysis to be performed The general purpose text based job creation tool is the Job Editor naturally With the Job Editor the user will spe cify the information GridChem needs to run the job For example the user will choose the Computational Chemistry package they want to use and what HPC machine they want to run it on The user must also specify information GridChem needs to set up your job Required informaton includes the estimated run time which job queue to use and if parallel processing the number of processors needed Every Computational Chemistry package requires an input file that details the acutal chemistry to be done The Job Editor allows the user to type in or load the text comprising this input file The user is now ready to submit the job into GridChem and have GridChem run it Like a proud parent or con cerned programmer the user can check up on their job The user can verify submission and execution check the job status stop the job before it is finished if desired and even monitor the job s output while it is still running When finished GridChem provides the job s complete output in a downloadable file If curious the user can also view the job file created The above is a description of an entire GridChem session for logging on in the beginning to checking the results at the end What follows next is some information to get the user going Getting Started GridChem Main Control Panel The
78. eeeeeeeeeceesceeeeueeeeeeesceeaeueeaeneeseeeaenes 42 7 17 GridChem Manage Jobs Window 0 ccc ceeceeeceeeceeeceeeceeeceeeea seca ceca eeaeeeae een ceneceeeeeeeeeeeeeeeeaees 43 TAB JOD S tats 4 fice dee ered hows eg eedeivn ededty eh Seta teh dice Shoes a ge Sunes Ne A edase atone het devunpes hee dets gee Maw ateenne 44 7 19 Nanocad Export Molecule 2 321032 a Gua nuh aie sete Re a eee 44 7 20 GridChem Job Editor Window serere aen ae a e e a E a e a e e Aa 44 7 21 GridChem Submit Jobs Window menossa a E E E TE I E AEE 46 7 22 GridChem Job Submission Progress ccecceeceeeceeeceeece a ceca sean E TTE E GEE Ss 47 7 23 GridChem Submit Jobs Window cccccce cece ec cceseeceeeeeeseeceseeeeeceescseeeeeeeeeeesceeeeueeueneeseneneees 47 7 24 GridChem Manage Jobs Window isc os ssscscsssccsdsa sist stoed rers spesa neos osina ERES thea gees serosa TEPO ESTORNES SES 48 8 1 GndChem Job Manager essiri ro ie eE E REES ETE EEES SI EESE EEE EEE 50 91 Molden Interlace hts aaa a a a a e a aa e a aa SG hoe E 67 92 Molden File SelesEnrssrn ennn a e AE E e a a e AE a NE n tone se eed 68 9 3 Molden Display Molecule scs ee i E TE E KEE a EE TE seca eee oe 69 9 4 Molden Optimization Results sgrnan o dae Eaa EE aene 70 9 5 Molden Vibrational Results eeren rse en n ai eE E E E E E a 71 9 6 Mo lden Frequency Select isyeri rn e E EEE TEREE NE E EE TE EEI EER ES nE 72 9 7 Optimization Summary aisee rE E E EN ey EEEE sec ae en be
79. er to view and change the manner in which they have customized GridChem User preferences include how the available GridChem machines are displayed which Mass Storage System to use and the default directory user output should go to e Submit Jobs Where a user can create a new job and or edit an existing job file Either can then be submitted to the batch processing system of one of GridChem machines e Manage Jobs After job submission this button lets the user check the status of a job kill or remove the job and monitor then retrieve the output from the job e Save Data In this task the user can choose to save log files of the GridChem session They can also specify the where these history files are stored e View License If it is desired the user can read the license agreement for the GridChem software by clicking this button e Exit Close the GridChem package User will be prompted to insure they really do want to exit Area Running Log When the Main Control panel first appears the text box contains a greeting from the institutions that created Grid Chem As the user clicks on the various control buttons described above the text box keeps a running history of what happens during the user s session with GridChem This log can be read in real time by the user to remind them what tasks they have accomplished and what tasks still need to be performed 28 Chapter 6 Chimistry Applications On hold at the present t
80. esseeeeeeaeeseseeeneaeaeess 7 2 2 Generalized DET Proceed re trni eene een aE vad duvets E E EEEE ESE EE EEES EEEE nS 10 3 1 GridChem Website Certificate se e O cand N EA E N AA E 17 3 2 Downloading Web Start Bile ccc c 3ss6 hake deus taeousodtdcocesuanct aged aa fauegaws SaueeaascewegaeSs suena dae Maetgoe ess 17 3332 Download RETE E ost oe A E E ee pecel eects ood Gob aaa tab eanebus buco aoanes Uasaeet ub eaten 18 3 4 GridChem Middleware Server Certificate ccccccccccececeeeceeececeeueeeeeesceeeeueeeeeeeseseeeeeeueaeesenees 19 3 5 Security Certificaten enen a sete es seed ch E EE E sede e A eer oad E ae dttatberamuyets 19 3 6 GridChem Website Certificate irren drene eaen a a E E A Sa 20 3 7 G dChbem Main Sereen eies kenn oe Ee EEEE E E E E EESE 21 3 8 GnidChem Logi sses eines he tieondass ges vote Sees OET EAE donates EREE I EEEE EEE SES ES RORE o Rae e 21 3 9 GridChem Successful Authentication ccc cece cece cc ceseceeeeecsceceeueeeeeeseseeegeeeeeeseseeeneeueeesenees 22 3 10 Allocation Summary sosise eeren e dea es dashes pas setae EEE oye sw ds sees ab ae Ded E E EEE E EEEE 22 7 1 Nanocad Molecule Builder Main Interface cece cece cc cccececeeeceeeceeeeeeeaeeesceeesueeueueeseeenenees 30 7 2 Nanocad Import Structure irens sas sedans sass rai rers EEE OESTRA E SPISAR seaedesebaeageeessbes sabe 31 7 34 Nanocad IMmport StrUCture a kava Ueaaen ste iaos daved see EE A E NEE 32 TAs Carbon Ato
81. etter results with respect to the experiments The applying of scaling factor is fairly easy What needs to be done is just multiply the zero point energy from Gaussian output file by the scaling 66 Post Processing Visualization fact For the different theory level and basis set the different scaling factors need to be used Here are some common used scaling facts Table 9 1 Gaussian Vibrational Frequency Scaling Factors Level Basis Scale Factor HF 6 31G d 0 9135 HF 6 31 G d 0 9163 HF 6 31G d p 0 9181 HF 6 311G d p 0 9248 HF 6 311G df p 0 9247 HF 6 31 G d p 0 9173 B3LYP 6 31G d 0 9806 B3LYP 6 31 2df 2p 0 983 Data taken from http comp chem umn edu database freq_scale htmAn Extended list can also be found here Visualization of Gaussian03 Output File by Molden Molden is a package for displaying Molecular Density from the Ab Initio packages Gaussian GAMESS UK and GAMESS US and the Semi Empirical packages Mopac Ampac Molden reads all the required information from the GAMESS GAUSSIAN output file And Molden is capable of displaying Molecular Orbitals and the electron dens ity Molden supports contour plots 3 d grid plots with hidden lines and a combination of both It also can animate reaction paths and molecular vibrations Derived Electrostatic Potential and atomic charges can be fitted to the Elec trostatic Potential calculated on a Connolly surface Molden has a Z matrix editor
82. exe PID 13470 Copyright c 1988 1990 1992 1993 1995 1998 2003 2004 Gaussian Inc All Rights Reserved This is the Gaussian R 03 program It is based on the the Gaussian R 98 system copyright 1998 Gaussian Inc the Gaussian R 94 system copyright 1995 Gaussian Inc the Gaussian 92 TM system copyright 1992 Gaussian Inc the Gaussian 90 TM system copyright 1990 Gaussian Inc the Gaussian 88 TM system copyright 1988 Gaussian Inc usr local g03c02 g03 1l exe tmp pbstmp 356045 Gau 13469 inp scrdir tmp pbstmp 356045 52 Post Processing Visualization the Gaussian 86 TM system copyright 1986 Carnegie Mellon University and the Gaussian 82 TM system copyright 1983 Carnegie Mellon University Gaussian is a federally registered trademark of Gaussian Inc The citation section gives the official citation for the Gaussian 03 program This citation should be included in the scientific articles presenting calculation results by running Gaussian 03 Cite this work as Gaussian 03 Revision C 02 M J Frisch G W Trucks H B Schlegel G E Scuseria A Robb J R Cheeseman J A Montgomery Jr T Vreven N Kudin J C Burant J M Millam S S Iyengar J Tomasi Barone B Mennucci M Cossi G Scalmani N Rega A Petersson H Nakatsuji M Hada M Ehara K Toyota Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao Nakai M Klene X Li J E Knox H P
83. hange his profile every time he submits a ticket The features next to the NO YES boxes will be discussed later when they are implemented For CCG PCS user accounts are created automatically when a PI requests a project PIs add users to the project and PCS when they use the add user link in their Management menu For a complete listing of the users click on the browse users link Usernames biographical names and emails are listed as shown below Figure 10 12 Browse users view List of users and important information 107 Technical Support browse users 16 total results 10 results per page lt Lotz gt af sere stat Kaacoul _kyiacoudossedu ope 503 af user sohn Deez mifelezetaccutenas edu aot 53 153153 CE ee 07 4200 O2 milfeld Ken ilfeld mifleld tacc utexas edu PE ape a a l E mi Mon 31 Jan chona Chona Guiang chona tacc utexas edu 2005 10 44 26 i Mon 31 Jan kyriacou Stelios Kyriacau kyriacoumlosaedu 2005 10 44 26 Mon 31 Jan gazula Vikrum Gazula gazulam ccs UKY EDU 2005 10 41 26 16 total results 10 results per page lt Lof2 gt Other important characteristics of a user s profile will be considered for the next revision The modify module first brings up a search engine for finding users Figure 10 13 Modify users view List of users and important information 108 Technical Support modify user search At least one field is required username
84. he SCF density KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK KKK KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Orbital symmetries Occupied SG PI Virtual SG U G SGG SGG U PIU PIU SGU SGG PIU PIU PIG SGU SGG PIG PIG SGG 0 57244 1 22730 SGU The electronic state is 1 SGG Alpha occ eigenvalues 24 80230 24 80230 1 30712 1 11790 Alpha occ eigenvalues 0 51301 0 51301 0 41241 0 41241 Alpha virt igenvalues 0 19705 1 04774 1 04774 1 11574 Alpha virt eigenvalues 1 25294 1 25294 1 37450 1 86482 Condensed to atoms all electrons 1 2 1 F 8 924099 0 075901 2 F 0 075901 8 924099 Mulliken atomic charges 1 LE 0 000000 2 E 0 000000 Sum of Mulliken charges 0 00000 Atomic charges with hydrogens summed into heavy atoms 1 T Et 0 000000 Zo ak 0 000000 Sum of Mulliken charges 0 00000 Electronic spatial extent au R 2 56 4125 Charge 0 0000 electrons Dipole moment field independent basis Debye X 0 0000 Y 0 0000 Z 0 0000 Tot 0 0000 Quadrupole moment field independent basis Debye Ang XX 9 3410 YY 9 3410 ZZ 8 5623 XY 0 0000 XZ 0 0000 YZ 0 0000 Traceless Quadrupole moment field independent basis Debye Ang XX 0 2596 YY 0 2596 ZZ 0 5191 XY 0 0000 XZ 0 0000 YZ 0 0000 Octapole moment field independent basis Debye Ang 2 XXX 0 0000 YYY 0 0000 ZZZ 0 0000 XYY 0 0000 XXY 0 0000 XXZ 0
85. heck them out Now the building of the butane molecule is finished You are ready to get an input file for this molecule Prepare for Gaussian Input File After you finish the minimization of the new structure in NanoCad click the EXPORT MENU button and choose GAUSSIAN INPUT for a Gaussian input file After you do this the Nanocad window will disappear and there will be a small window pop up to warn you that the molecule information is correct but you need to edit the other parts of your job file to make sure the calculation is under the way you want Gaussian to do Figure 7 11 Click OK to close this warning window Figure 7 11 Exporting the Molecule 38 Pre processor Molecule Builder GridChem Job Editor xj WARNING The input appearing here is taken From a template The molecule information is correct but make sure to edit the other parts of the text You will see your GridChem Job Editor window has a Gaussian input file for butane in the editing area below In put text Figure 7 12 Figure 7 12 GridChem Job Editor 39 Pre processor Molecule Builder gt Project Job name Research project name ftac _ proj Job name defaut test Application Gaussian v cu nesa uiuc edu un nesa uiuc edu X ita zi Requirements Choose a project mjk Estimated time for job hh mm ss 0 4 30 0 Choose a queue fiebug Number of processors 4 Input
86. hen the user is satisfied with the response he should login and update the ticket to let the consultant know or up date the ticket to request additional information A consultant is notified of the update If the user doesn t respond within a few days his state of satisfaction will be inquired through email Consultant Interface 101 Technical Support The consultant login panel is identical to the user login Every username has a group level category associated with their ID There are 4 categories of logins Table 10 1 Consult System Categories of Users Login Category Purpose User Users can submit tickets and respond to the replies only through http www gridchem org consult NOTE Users must login to PCS to SUBMIT and RESPOND to tickets but they are sent via e mail any response that a con sultant makes to the ticket Staff Consultant Staff can take ownership of tickets and respond to them Manager Managers have staff privileges and can reassign owner ship and create users If you have a staff consultant lo gin you cannot reassign a ticket after you take ownerh sip but you have one chance to assign a new ticket to anybody Administrator Administrators have manager privileges and can delete tickets Table 1 Categories of users The Consulting Menu Item When a consultant selects consulting from the main menu the consulting system is displayed In the menu area a
87. hip and add a response In addition the consultant can view all of the requestor s tickets Ticket dependencies will be included in the documentation later after the implementation is completed very soon Also the Category Priority and Status can be changed The update panel is shown below Figure 10 8 Consulting view Update Ticket command panel below the Ticket Table Update Ticket Category GridChem Operation v Status In Progress Priority High Date Due day mon yr update Edit Dependencies Requestor s Tickets Take Ownership Add Response Manager and Administrator Interface Usernames with Manager or Administrator status have extract privileges At login their Main Menu has an adminis tration link different from the normal User administration link as shown below 103 Technical Support Figure 10 9 Admin s Main Menu Administration view for administrators managers lagged in as pcsadmin logout gt home gt consulting gt administration gt preferences gt search gt about When the administration link is clicked a new menu panel is displayed with management and administration op tions as shown below Figure 10 10 adminSpace menu Created by clicking the administration view of the Main menu 104 Technical Support adminSpace logged in as some kind of admin stats pcsadmin logout
88. ime Chapter 7 Pre processor Molecule Builder Prepare for a Case Computational Chemistry Study When applying Computational Chemistry method in research the very basic information needed include the struc ture of the molecular system the geometry of the system for input which state the system is for example the ground state or the first excited state and multiplicity When the user has a molecular structure in mind he needs a file which is called structure file to describe the mo lecule There are many formats of molecular structure files One of the most popular formats is PDB file Originally PDB file is used by Protein Data Base to describe the pro tein structure Now the PDB file format can be used for any molecular system The other one is XYZ file This format is very simple Each line contains the element symbol and Cartesian coordinates for each atom in the system The XYZ file doesn t contain any information about the connection between atoms The one Gaussian 03 favors is Z Matrix file This format doesn t contain the absolute coordinates of each atom but the relative position of each atom according to other atoms Either XYZ or Z Matrix file can be used as Gaussian in put There are many other file formats such as mol mol2 which are also commonly used to molecular structures The input geometry for quantum chemistry calculation is recommended but not required to be a local minimum structure The initial str
89. ined between GridChem sessions If the user wants to clean up the list the can deleted selected jobs with the Delete Job from List button Unlike job termination no confirmation window appears 51 Chapter 9 Post Processing Visualization General Introduction After the computation is completed we need to extract information we need from the output files Usually the out put information are determined by software applied type of calculation and theory level etc According to the computation task the general calculation results include e Single point energy and properties e Optimized geometry e Frequencies of each vibration mode and intensities e Reaction path following searching e Calculated spectra such as IR UV Vis e Molecualr orbitals e Charge distribution e Spin Density distribution We will briefly introduce some very general methods to process and or visualize output files Post Processing of Gaussian03 Output File General Introduction of Gaussian03 Output File In this section we will have an overlook of a general Gaussian03 output file to give reader a basic understanding of the basic structure of Gausian03 output file At the beginning of Gaussian output file there is the copyright notice for Gaussian03 ntering Gaussian System Link 0 usr local g03c02 g03 g03 ntering Gaussian System Link 0 usr local g03c02 g03 g03 Initial command i Fi Entering Link 1 usr local g03c02 g03 1l
90. ional Center for Supercomputing Applications CN John Doe type full strength 512 bits path tmp x509up_u27031 timeleft 11 59 32 After finishing all steps on the NCSA machine you will update your work machine where you will be running the GridChem client Using scp copy your globus directory from the NCSA machine into the machine and account you willbe using Gridchem in The directory will be globus just like on the NCSA machine 26 Chapter 5 Interface Fundamentals The Fundamentals of Using the GridChem Portal The GridChem Portal is a Java based interface that allows the user to run a job that uses a Computational Chemistry software package The job is executed on a HPC cluster computer provided by one the sponsoring institutions Overview of a GridChem Session Before even starting GridChem the user needs to get an authenticated login ID and password The authentication procedure is described elsewhere in this help document It is also explained at the GridChem home page http www gridchem org Once armed with an identity the user s first task is to create the job they want executed There are three methods for job creation text based graphics base and use of a custom interface A custom interface is designed for one specif ic Computational Chemistry package such as Gaussian A user can use a graphics package such as Nanocad to visually design the molecule to be analyzed and at the same time specify the typ
91. k You will be prompted for a correct email or user name and if correctly identified as a valid entry in the database email instructions for updating and validation are sent to the user The failed login panel is show below Figure 10 2 Failed login Panel sername password Login forgot password login failed Once you have been authorized four different panels in the consulting window appear a Header Login Menu and a Display area Their functions are 1 Header Shows the site logo 2 Login This panel shows your login username and a logout button 3 Main Menu The menu allows you to go home the present window with announcements in the display area to invoke the consulting to change your preferences font size and time zone more later to search implemented yet and to view information about the installed PCS version 4 Display The area lower right is where information is displayed and forms are presented for interacting with the tickets The Main and PCS Support News announcements are shown below for the home view of the display 96 Technical Support Figure 10 3 PCS Panels home view 6 1 do Oo Ticket g E 1 d Computational System Chemistry Grid cheme e oO Welcome to PCS Portable Consulting System PCS Support News Fri 04 Feb 2005 17 20 55 logged in as user2 logout gt home gt consulting gt preferences gt search gt a
92. ll temporarily change their color to the back ground color indicating that you are doing an active operation When you move your cursor over the other carbon release in this order 1 your mouse 2 the shift key The bond will exist between two carbons And the atom color will change back to deep gray Figure 6 6 33 Pre processor Molecule Builder Figure 7 6 Create Carbon Atom Bond 22 Nanocad Tora o Hap sructro cer uno asst winimize Force Fieid x Export Menu To build butane we need two more carbon atoms Please Shift Click the appropriate space to add two more carbon atoms Figure 7 7 Figure 7 7 Create Two Addtional Carbon Atoms 34 Pre processor Molecule Builder f 2 Nanocad Group I T Forces Heip structure clear undo aaan Get Potential mrimize Force Fie z Export menu z Then use Shift drag to add missing C C bond Figure 7 8 Figure 7 8 Create Additional Bonds 35 Pre processor Molecule Builder gt Nanocad F Group T T Forces Helo structure clear undo aaan Fiz Force Fen z emotes Now we have all the heavy atoms in butane The only missing atoms are hydrogen Adding hydrogen is relatively easy click ADD H button at the bottom of the Nanocad window You will see that NanoCad adds the missing hy drogen to your unfinished butane molecule Figure 7 9 Figure 7 9
93. mic 35s se E E E EE au veto yobs Seek Solem ae ae wands R Sadeuder sues ke bogies 32 Jo SeCond Carbon Atom 5025 eds ese on a a toons cuawes du e tettecse E neuen sd ones onda oe tebtee e towels Geetens 33 71 6 Create Carbon A tom Bond 55 suseteg tee ccc rir ces tben o pSu de bebe vee e E EE a ea pees dose i or ita 34 7 7 Create Two Addtional Carbon Atoms ccccccceccccececececceeecceseeeeeceesceeneueeeeeeesceeaeeeeueneeseeeaenees 34 7 8 Create Additional Bonds i 033 ses osecor tose te bel Sasa cet veetacek oa Bacon vow aae ce las csh A oe eae od AE E EE ERSS 35 TY Add Hydrogen ss arae nenies ro ngs es ib nseseoca sessed sone ss esta nda se sees Teves ba presse ERETI PIESE ISERE PO NESNESE EEES 36 ATO Molecule MinimiZation 22 soos eccsceseees ase ea besos banka calvduies deaescubedslots nugese sien E EA RES 37 TII Exporting the Molecule s cccscts shock ss acsdaas ss ee e a a a e A siaandag sss oste des 38 7 12 Grid hem Job Editor insat reee od dees wate cbse E eee Sued EE E ued debe pVewebow se eedew dea weeds 39 7 13 IMPORTANT Add Blank Line 2 0 0 ccc ccccc eee ceecee cece nR NaS EEEE PIRIS PENRE ERS 40 7 14 GridChem Submit Jobs Window cccccceecccec cc ceeeceeeeeesceceeeeeeeceesceeneueeueneesceeeegeeueueeseeeaenees 42 7 15 GridChem Submitting Jobs Progress Window 0 0 0 0 cece cece cece eee c tec e cece cena cena eeneeeaeeeeeeeeeeaeeeaees 42 7 16 GridChem Submit Jobs Window ccccc cece ec ecccceseceeeeeeec
94. mit All Jobs to Queue ptao_proj bute ssian cu nesa uiuc edu Click on the CLOSE button in the Submit Jobs window The only GridChem window that should be up is the main GridChem window Click on the MANAGE JOBS button in the main GridChem window A window will appear that contains a list of all of the jobs that you have submitted The most recent job submission should be at the top of the list Figure 7 17 Figure 7 17 GridChem Manage Jobs Window GridChem Manage Jobs loj x Time ResProj joName Machine ETARE Get Job Status 0944 2005 eae ptao_proj butaneopt cu ncsa uiu batch cu12 35758 Monitor Job Output Kill Selected Job Retrieve Job Output Delete Job from List Close If Get Job Status button is clicked the system will return the current status of the submitted job In Figure 7 18 it is shown that the job has been completed in 5 seconds 43 Pre processor Molecule Builder Figure 7 18 Job Status x fs i JOB Id cu12 357585 0 Status Completed CPU_time 00 00 05 Peak Memory 68 72 Total Sus 0 00 Once the job has completed it is possible to look at the output file To view the data available graphically click on the MONITOR JOB OUTPUT button in the GridChem Manage Jobs window The job that is highlighted in the left hand side of the window will be the job whose output is being fetched and displayed Prepare for GAMESS Input File After you finish the minimization of
95. nning on host pivll6 under operating system Linux at Tue Oct 4 16 09 28 EDT 2005 Available scratch disk space Kbyte units at beginning of the job is Filesystem 1K blocks Used Available Use Mounted on dev hda3 64530948 223692 64307256 tmp Distributed Data Interface kickoff program Initiating 2 compute processes on 1 nodes to run the following command usr local gamess current gamess 01 x exam09H20 78 Post Processing Visualization After the job running information there is a brief introduction of GAMESS KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKAKKKKKKKKKK GAMESS VERSION 19 MAY 2004 R4 FROM IOWA STATE UNIVERSITY M W SCHMIDT K K BALDRIDGE J A BOATZ S T ELBERT M S GORDON J H JENSEN S KOSEKI N MATSUNAGA K A NGUYEN S J SU T L WINDUS TOGETHER WITH M DUPUIS J A MONTGOMERY J COMPUT CHEM 14 1347 1363 1993 KEKE KKK KKKKKKKKKKKE PC UNIX VERSION KEKE KK KKK KKKKKKKKHK SINCE 1993 STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT Ea HF a The whole input file will be listed completely for user s reference UT CARD gt H2O energy CARD gt SCONTRL SCFTYP RHF RUNTYP ENERGY COORD ZMT SEND CARD gt SSYSTEM TIMLIM 2 MEMORY 100000 SEND CARD gt BASIS GBASIS STO NGAUSS 3 SEND CARD gt GUESS GUES
96. om http java sun com j2se Select the appropriate JRE download for your platform For a Mac version of Java see http www apple com java The version of Java used to develop this software is JDK 1 4 1 Installing Java Run the Java installation for your platform If you are on a workstation or shared machine root access may be re quired For details on how to install Java and how to set the environment variables properly please see the Java web pages Java 1 4 1 is required as well as Java Web Start 1 2 Installing GridChem GridChem is launched using the Java Web Start technology Click here http download gridchem org webstart gridchem jnlp to load the latest version of the GridChem client You can either launch it directly from the web browser or save the Java Web Start file to your desktop and launch the applic ation from there The first time you visit the http www gridchem org web site you will be prompted to trust the GridChem certi 16 Software Installation Configuration ficate Please click ALWAYS so that the browser will remember to trust the http www gridchem org web site on future visits An example of the screen you will see is given below Figure 3 1 GridChem Website Certificate Website Certified by an Unknown Authority Unable to verify the identity of www gridchem org as a trusted site Possible reasons For this error Your browser does not recognize the Certificate Authority tha
97. omputational Chemistry molecular and condensed matter systems It has been proved that for molecules the ground state molecular energy is uniquely determined by the ground state electron probability density Therefore all the ground state molecular properties can be calculated from the electron density without having to find the molecular wave function In addition according to the Hohenberg Kohn vari ational theorem the true ground state electron density minimizes the energy functional The DFT method is vari ational The Kohn Sham method provides a practical way to conduct DFT calculations Hypothetically a fictitious reference system with the same number of electrons and the same electron density as the real molecule system but no electron electron interactions are considered to aid the DFT calculation The energy calculated by DFT can be written as ELEGI fale H LO Kl eG 477 er HA Ler Here the term is the kinetic energy of the non interacting electrons is the nuclear Talari Piel OV electron interaction is the classical electron electron repulsion energy A is the cor Leir fe rection to the kinetic energy deriving from the interaction nature of the electrons and AF e 5 is all non classical corrections to the electron electron repulsion energy The electron density a can be expressed by Kohn Sham orbitals Therefore a by ae Slee i l the energy calculated by DFT can be rewritten as iy 1 N mach
98. our molecule To do so you need to put keyword Freq in your Gaussian 03 input file After successful optimization and vibrational frequency calculation you will find the following part of your Gaussi an 03 output file Example comes from F 2 molecule calculation Thermochemistry Temperature 298 150 Kelvin Pressure 1 00000 Atm Atom 1 has atomic number 9 and mass 18 99840 Atom 2 has atomic number 9 and mass 18 99840 Molecular mass 37 99681 amu Principal axes and moments of inertia in atomic units 1 2 3 EIGENVALUES 0 00000 73 08708 73 08708 X 0 00000 0 90398 0 42757 Y 0 00000 0 42757 0 90398 Z 1 00000 0 00000 0 00000 This molecule is a prolate symmetric top Rotational symmetry number 2 Rotational temperature Kelvin 1 18508 Rotational constant GHZ 24 693028 64 Post Processing Visualization Zero point vibrational energy 5977 2 Joules Mol 1 42858 Kcal Mol Vibrational temperatures 1437 78 Kelvin Zero point correction 0 002277 Hartree Particle Thermal correction to Energy 0 004674 Thermal correction to Enthalpy 0 005618 Thermal correction to Gibbs Free Energy 0 017436 Sum of electronic and zero point Energies 199 475557 Sum of electronic and thermal Energies 199 473160 Sum of electronic and thermal Enthalpies 199 472216 Sum of electronic and thermal Free Energies 199 495270 E Thermal CV S KCal Mol Cal Mol Kelvin
99. p 356045 Entering Link 1 usr local g03c02 g03 11 exe PID 13470 Copyright c 1988 1990 1992 1993 1995 1998 2003 2004 Gaussian Inc All Rights Reserved niversity the Gaussian 82 TM system copyright 1983 arnegie Mellon University Gaussian is a federally registered rademark of Gaussian Inc This is the Gaussian R 03 program It is based on the the Gaussian R 98 system copyright 1998 Gaussian Inc the Selena ee 94 system copyright 1995 Gaussian Inc the Gaussian 92 TM system copyright 1992 Gaussian Inc the Gaussian 90 TM system copyright 1990 Gaussian Inc the Gaussian 88 TM system copyright 1988 Gaussian Inc the Gaussian 86 TM system copyright 1986 Carnegie Mellon U nd C H his software contains proprietary and confidential information including trade secrets belonging to Gaussian Inc This software is provided under written license and may be used copied transmitted or stored only in accord with that written license The following legend is applicable only to US Government contracts under FAR RESTRICTED RIGHTS LEGEND Use reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraphs a and c of the Commercial Computer Software Restricted Rights clause in FAR 52 227 19 Gaussian Inc 340 Quinnipiac St Bldg 40 Wallingford CT 06492 Warning This program may not
100. rchitecture can be seen below Figure 1 2 CCG Second Generation Architecture GridChem Overview Credential Management Hardware Resource Descriptions Software Resource Descriptions Job Descriptions Accounting Information Monitoring Data Machine Load Accounting Job Logging Historical Job Information Aggregated Resource Usage Resources Grid Middleware osc Ncsa Uky In the uppermost layer the GridChem client there are no changes from the previous architecture However in the GMS and Resource layers you will find grid technologies replacing the CGI scripts This makes for a more efficient maintainable scalable resource Chapter 2 Introduction to Computational Chemistry Quantum Chemistry According to w ikipedia the free encyclopedia online computational chemistry is the branch of theoretical chemistry whose major goals are to create efficient computer programs that calculate the properties of molecules such as total energy dipole moment vibrational frequencies reactivity and other diverse spectroscopic quantities and to apply these programs to concrete chemical objects The basic theory underlines this field is called quantum mechanics In this section a very brief introduction is trying to be made up to give GridChem users basic idea about this field Fur ther reading to obtain better understanding about the quantum chemistry is highly recommended Foundations of Quantum Chemistry
101. ri B Foresman J V Ortiz Q Cui A G Baboul S Clifford Cioslowski B B Stefanov G Liu A Liashenko P Piskorz Komaromi R L Martin D J Fox T Keith M A Al Laham Y Peng A Nanayakkara M Challacombe P M W Gill Johnson W Chen M W Wong C Gonzalez and J A Pople aussian Inc Wallingford CT 2004 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKAKKKKKKKKKK Gaussian 03 IA32L GO3RevC 02 12 Jun 2004 27 Sep 2005 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK B3LYP 6 31G Opt 1 14 1 18 20 26 3 38 1 1 3 2 9 110 17 6 18 5 40 1 2 3 5 1 6 6 11 2 16 1 25 1 30 1 74 5 1 2 3 4 1 5 5 2 38 5 2 6 7 2 8 2 9 2 10 2 28 1 1 TIAL 237 168 1 14 1 18 20 3 1 99 99 2 9 110 2 3 5 1 6 6 11 2 16 1 25 1 30 1 74 5 1 2 3 4 5 5 16 3 1 5 5 2 38 5 2 TAA ZT SALG 1 14 1 18 20 3 5 2 9 110 2 6 7 2 8 2 9 2 10 2 19 2 28 1 1 99 9 1 99 test F2 Symbolic Z matrix Charge 0 Multiplicity 1 F 0 0 0 F 15 0 0 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization Initialization pass Initial Parameters Angstroms and Degrees 59 Post Processing Visualization Name Definition Value Derivative Info R1 R 1 2 175 estimate D2E DX2 Trust Radius 3 00D 01 FncErr 1 00D 07 GrdErr 1 00D 06 Number of steps in this r
102. ributed as a Java web start executable jar file Currently once the client is downloaded it takes care of all security for a com munity user The current incarnation of the client allows users to easily submit monitor and manage their jobs using a a restricted set of computational chemistry applications on a diverse set of resources Figure 1 1 Current CCG Three Tiered Architecture GridChem Overview CCG Architecture NANNAN TI Project sh Shay N RA GLOBUS j N RNN NANAON ee OOO Sems i e s o As you can see in the top level we have the GridChem client The client gives you access to all the resources with a minimal store of knowledge about a particular machine It still helps to have an HPC background on some machine so you know what the difference between a node and a processor is how to estimate needed memory and actual pro cessing time but it is not absolutely necessary The GridChem architects have created basic requests that you can use 3 GridChem Overview if you don t have that background The client allows you to authenticate create submit and manage jobs and to ex plore your data with visualizations The second level of the architecture is the Grid Middleware Server GMS The GMS is the underlying grid utilities the actual database with user and machine information and the CGI scripts needed to provide the functionality for the GridChem client This is where all information on
103. rity certificate was issued by a company that is not trusted Lod a i 1 The security certificate has not expired and is still valid Figure 3 5 Security Certificate 19 Software Installation Configuration Warning Security x Do you want to trust the signed extension distributed by The Legion of the Bouncy Castle Publisher authenticity can not be verified A The security certificate was issued by a company that is not trusted E n L The security certificate has not expired and is still valid Figure 3 6 GridChem Website Certificate Warning Security xX Do you want to trust the signed application distributed by Computational Chemistry Grid Publisher authenticity can not be verified a The security certificate was issued by a company that is not trusted The security certificate has not expired and is still valid Select ALWAYS for all three 20 Software Installation Configuration Once all of the certificates are trusted The application should start and leave you at the main screen Figure 3 7 GridChem Main Screen GridChem DEAR Welcome to GridChem Portal to the Computational Chemistry Grid Authenticate Developed by Read Announcements ccs University of Kentucky ICCT Louisiana State University NCSA University of Illinois at Urbana Champaign OSC Ohio Supercomputer Center TACC University of Texas at Austin Submit Jobs Check Preferences
104. sis functions 9 alpha electrons 9 beta electrons nuclear repulsion energy 28 5755692482 Hartrees NAtoms 2 NActive 2 NUniq 1 SFac 5 66D 00 NAtFMM 60 Big F One electron integrals computed using PRISM NBasis 18 RedAO T NBF 5 0 2 2 0 5 2 2 NBsUse 18 1 00D 06 NBFU 5 0 2 2 0 5 2 2 Harris functional with IExCor 402 diagonalized for initial guess ExpMin 3 58D 01 ExpMax 7 00D 03 ExpMxC 1 05D 03 IAcc 1 IRadAn 1 AccDes 1 00D HarFok IExCor 402 AccDes 1 00D 06 IRadAn 1 IDoV 1 ScaDFX 1 000000 1 000000 1 000000 1 000000 Initial guess orbital symmetries Occupied SGU SGG SGG SGU SGG PIU PIU PIG PIG Virtual SGU PIU PIU SGU SGG PIG PIG SGG SGU The electronic state of the initial guess is 1 SGG Requested convergence on RMS density matrix 1 00D 08 within 128 cycles Requested convergence on MAX density matrix 1 00D 06 Requested convergence on nergy 1 00D 06 No special actions if energy rises 60 Post Processing Visualization Keep R1 integrals in memory in canonical form Integral accuracy reduced to 1 0D 05 until Initial convergence to 1 0D 05 achieved E RB HF LYP SCF Done Convg SAEZ 0 0000 199 477206381 0 1473D 08 final NRe q 452820 iterations A U V T 2 0050 Increase integral accuracy after 8 cycles KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Population analysis using t
105. srrresrrrrrsrrerrsrrerrseesrereesrreesreet 14 BaS18 Sets e ne feat veden terns dub Ssanse py Sune os E E sh subaesnevae tes E ss dawe eaves eetues A teh ARS EROTS 14 3 Software Installation Configuration ccc ceeeceee cece ence ce ec ce eeae cen eeneeeeneeeeeeeseeseeeeeaeeea esau sean eeaes 16 Introduction uc 325 5 85 dates soe ot e e ac eee aaa dau ebdas ga yed se dee same ried aes ase Sawa rent ae ean SE 16 System Requirements Ar in rae Le Rae eee ee ak en ee eek as at a ea EAN AE IEN 16 VaV aiscasSeu ston vanes ey nga atopy suanesng ed E A EEE ssugeeshuSel obs huvenepe nveee ties eamesboted sbopseumeeosentete 16 Installing Java 2205 ics icoss codes tacecs heels lavas EEIE bia gecs EEEE dessa OE EEEE devas oncsteebouy debvagecedeseneede 16 Installing GridC hem sorcen er ses ospau bes aE E s a E a ANE E 16 Configuring GridChem for the First Time ees sseesseersrrerrsrsrrrrsrrrersrerrsrrerrsrreereresrereerreresrt 18 AUPHENU CANON ais esecceg deters Teese psiles Pte seeds are st REE sad EEEE PR a eE REEE EEES Sa E PENE SER nS ENE 21 4 Authentication Authorization and Allocations ssse sseeseseresseresrrerrsrrsrrrresrerrsrreersrrerrererrreeereeees 24 A thentication serene e eaea e a a e e E a E R E E e OE ES 24 Before You Starte rner yen Er E nes dda OREERT nEs 24 Community US Pes aen E E E N E E E E E E A E ES 24 External SGP sic sich r E R E a E E E A E A sucess aa gt 24 Dipital OSA UED a CO Ire ea a EEE EE E
106. stant 65 Post Processing Visualization and T is the temperature Thermal correction to Enthalpy 0 005618 Thermal correction to Gibbs free energy is the thermal correction to enthalpy subtract TS tot where T is the temper ature and S fot is total entropy of the system Thermal correction to Gibbs Free Energy 0 017436 Sum of electronic and zero point energies are the sum of the total electronic energy and the zero point correction Please refer the previous section about the total electronic energy Sum of electronic and zero point Energies 199 475557 Sum of electronic and thermal energies are the sum of the total electronic energy and the thermal correction to en ergy Sum of electronic and thermal Energies 199 473160 Sum of electronic and thermal enthalpies are the sum of the total electronic energy and the thermal correction to en thalpy Sum of electronic and thermal Enthalpies 199 472216 Sum of electronic and thermal free energies are the sum of the total electronic energy and the thermal correction to Gibbs free energy Sum of electronic and thermal Free Energies 199 495270 Please notice that the unit of energy is Hartree Particle if not explicitly indicated The conversion factor is 1 Hartree Particle 627 5095 kcal mol Due to the systematic error of some electronic structure theory it is very common to scale the Gaussian calculation of vibrational frequencies to obtain b
107. t default element is H is the atom you will be able to put into the Nanocad window To change the current element you can type the element name after Change current element to and click SELECT to the current element In this case type C and click SELECT button to change the current element to carbon Figure 7 3 31 Pre processor Molecule Builder Figure 7 3 Nanocad Import Structure 3 Import Structure Shift click in the gray area of Nanocad window a gray carbon atom will appear after your click Figure 7 4 Figure 7 4 Carbon Atom B Nanocad Group I Forces Helo structure clear unao agan Minimize Force Fiel Export meru Z 32 Pre processor Molecule Builder Then Shift click the area close to your previous carbon atom you will get your second carbon atom close to your first one Figure 7 5 Figure 7 5 Second Carbon Atom ER a 2 Nanocad l F Group I T Forces Help Structure clear Undo Agan wininize Force Fieid Export menu You may notice that there is no bond between two carbons To build bond between your two carbons you need Shift drag from one carbon to the other carbon Detailed operation press shift key and do not release it then drag one atom to the other You will see there is a line with one end attached to the starting carbon the other end you move with your cursor While you move your cursor the two atoms wi
108. t issued the site s certificate The site s certificate is incomplete due to a server misconfiguration You are connected to a site pretending to be www gridchem org possibly to obtain your confidential information Please notify the site s webmaster about this problem Before accepting this certificate you should examine this site s certificate carefully Are you willing to to accept this certificate for the purpose of identifying the Web site www gridchem org Examine Certificate Accept this certificate temporarily for this session Do not accept this certificate and do not connect to this Web site Cancel Help You can also get to the download page by going to the main GridChem web site http www gridchem org and then click on SOFTWARE and the DOWNLOAD link Once you click on the client link you will see a download box similar to the following Figure 3 2 Downloading Web Start File 17 Software Installation Configuration Opening gridchem jnip _ x The file gridchem jnlp is of type application x java jnlp file JNLP Filei and a Mozilla does not know how to handle this File type This File is located at https haw gridchem org What should Mozilla do with this File i Open it with Choose f Save it to disk Always perform this action when handling files of this type cma If the option to save to a file is chosen then running the JNLP web start file will launch
109. the following way BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD 0 050 BOND BOND BOND ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER 1 2 1 060 0 974 ae 3 1 060 0 974 TOTAL BONDED FREE ATOM VALENCE VALENCE VALENCE 10 1 949 1 949 0 000 2 H 0 981 0 981 0 000 3 H 0 981 0 981 0 000 ELECTROSTATIC MOMENTS POINT ab X Y Z BOHR CHARGE 0 000000 0 000000 0 000000 0 00 A U DX DY DZ D DEBYE 0 000000 0 000000 1 608889 1 608889 In each GAMESS output file some accounting information is normally appended at the very end ON NODE 0 STEP CPU TIME 0 01 TOTAL CPU TIME Oni 0 0 MIN TOTAL WALL CLOCK TIME 0 0 SECONDS CPU UTILIZATION IS 100 00 100000 WORDS OF DYNAMIC MEMORY USED EXECUTION OF GAMESS TERMINATED NORMALLY Tue Oct 4 16 09 29 2005 DDI 920 bytes 0 0 MB 0 MWords used by master data server 83 Post Processing Visualization CPU timing information for all processes 0 0 022996 0 050992 0 073988 1 0 019996 0 025996 0 045992 ddikick x exited gracefully a alee accounting info Tue Oct 4 16 09 32 EDT 2005 Files used on the master node pivll6 were rw r r 1 xxxx G 3204 1716 Oct 4 16 09 tmp pbstmp 362347 exam09H20 dat rw r r 1 XXXX G 3204 1213 Oct 4 16 09 tmp pbstmp 362347 exam09H20 F05 rw r r 1 XXX
110. the new structure in NanoCad click the EXPORT MENU button and choose GAMESS INPUT for a GAMESS input file After you do this the Nanocad window will disappear and there will be a small window pop up to warn you that the molecule information is correct but you need to edit the other parts of your job file to make sure the calculation is under the way you want GAMESS to do Click OK to close this warning window Figure 7 19 Figure 7 19 Nanocad Export Molecule GridChem Job Editor xj WARNING The input appearing here is taken From a template The molecule information is correct but make sure to edit the other parts of the text You will see your GridChem Job Editor window has a GAMESS input file for acetaldehyde in the editing area be low Input text Figure 7 20 Figure 7 20 GridChem Job Editor Window 44 Pre processor Molecule Builder ioi xi ProjectJob name Research project name etac proj i Job name defaut test Load Data File Application Save Data to File Gaussian v Create Default Job cu nesa uiuc edu un nesa uiuc edu M 3 Requirements Choose a project mik Choose a queue hiebug Estimated time for job hh mm ss oJ 3044 4 Number of processors 4 Input text SCONTRL SCFTYP RHF RUNTYP OPTIMNIZE NZVAaR 5 SEND SSYSTEM TIMLIM 20 MEMORY 500000 SEND DFT DFTTYP SVUN END BASIS GBASIS N31 NGAUSS 6 NDFUNC 1 END OK GUESS GUESS HUCKEL
111. the wave function When only single excitations are considered it is called CI singles CIS method In CID method only double excit ations are accounted CISD adds both of single and doubles excitations CISDT adds singles double and triples Unfortunately these limited CI methods are not size consistent The Quadratic Configuration Interaction QCD method was developed using the quadratic expansion coefficients for higher excitation terms This method forces the size consistency For example QCISD method adds terms to CISD to restore size consistency Moller Plesset Perturbation Theory The perturbation theory of M ller and Plessetis is also an electron correlation method Closely related to many body 12 Introduction to Computational Chemistry perturbation theory this method introduces correction of Hamiltonian corresponding to the perturbation of the sys tem 4 f a The exact ground state wave function and energy psi lambda and E lambda of a system described by the full Hamiltonian H lambda can be expanded in power of lambda Eq 6 10 P 4 AP Pe E H ak PRP Plug the exact wave function and energy into Schrodinger equation we have A sarto s ape Je a0 agmg Yoo ayy After expanding the products we can equate the coefficients on each side of the equation for each power of lambda leading to a series of relations representing successively higher orders of perturbation Ai Bt Ju 9
112. tial Guess Molecular Orbitals Fock Matrix 1 electron vectors Formation Fock Matrix Diagonalization Calculate Properties End In a closed shell system each spatial orbital contains two electrons one is alpha and one is beta The spin restricted closed shell Hartree Fock RHF can be applied on such a system In this case two electrons in same spatial orbital share the same wavefunction and the same eigenvalues In an open shell system there is at least one unpaired electron There are two ways to treat open shell system One is called spin restricted open shell Hartree Fock ROHF theory In this approach a single set of molecular or bitals is used some being doubly occupied and some being singly occupied Therefore two electrons in the same spatial orbital still share the same wavefunction and the same eigenvalues The other one is spin unrestricted open shell Hartree Fock UHF In this approach different spatial orbitals are as signed to alpha and beta electrons Thus there are two distinct sets of molecular orbitals for alpha and beta respect ively Please note that in this approach two electrons in the same spatial orbital no longer share the same wavefunc tion And they may have different eigenvalues even though they are in the same spatial orbital Density Functional Theory DFT DFT is one of the most popular approaches to quantum mechanical many body electronic structure calculations of Introduction to C
113. tides Molden is free of charge and can be obtained at the website http www cmbi ru nl molden molden html Molden is available on most UNIX systems Linux Mac OS and Windows systems User can download the binary executable package uncompress if necessary and directly run the molden program More details about installation and using of Molden can be obtained from Molden website Figure 9 11 shows the user interface of Molden running on Windows Figure 9 11 Molden Interface 88 Post Processing Visualization Molden Control ioj xi E a a a g ea g a H a aum Y Hi Teea H Ii El elol al Status line First point Click Button Read a browse window will pop out to select the GAMESS output file Figure 9 12 Figure 9 12 Molden File Select 89 Post Processing Visualization Molden File Select Oo x examQL inp examQ1 log examQLfreg inp examQLfreg log examQLfrequroang log exam inp exami log exam inp exam log examQ3He0 inp Bx an i SH 0 F l m g After click the correct GAMESS output file for water calculation Molden will try to read in the file and visualize the structure Please notice that any time a file is clicked in Molden file browser Molden will try to read into that file And it will take a while for Molden to do so Therefore please be careful to choose the file which needs to be read in Figure 9 13 shows the structure of water Figure 9 13
114. ting point If the system has only one atom these are typically the orbitals for a hydrogenic atom which is an atom with only one electron but the appropriate nuclear charge For a molecular or crystalline calculation the initial guess is typic ally a linear combination of atomic orbitals Once an initial wavefunction is constructed an arbitrary electron is selected The effect of all the other electrons on the selected electron can be summed up based on the initial guess of wavefunctions This calculation leads to an av eraged potential for the selected electron This gives selected single electron a defined potential for which the single electron Schr dinger equation can be solved And the solution is alwasy a slightly different wavefunction from the initial guess The same process is then repeated for each of the other electrons which completes one step of the iter ative procedure In each iterative procedure the wavefunction of each electron is updated based on the updated wavefunctions of other electrons This is why the Hartree Fock calculation is also called self consistent field SCF calculation The whole procedure is then repeated until the change from one step to the next is sufficiently small i e the calculation is converged The procedure of Hartree Fock calculation is illustrated below Figure 2 1 Hartree Fock Calculation Procedure Introduction to Computational Chemistry Input 3D Coordinates of atomic nuclei Ini
115. uctures are usually prepared manually And user usually has more than one option to build structures Some programs are distributed under fee based license such as GaussView Chem3D Some are free under certain license NanoCad which comes with GridChem is one of free molecule builders After having a structure file of the interested system user always need a set up file to tell the computational program the requirements of the job Generally these requirements include but not limited to charge and multiplicity of the molecule theory level basis set and job type such as single point calculation optimization transition state search etc To run a computational job on a given operation system a job control file is needed sometimes The job control file can set up number of CPU estimated running time and size of memory allocated for job running This file highly depends on the type of operation system to execute the computational job In GridChem structure file and set up file are combined together as one file No job control file is needed in Grid Chem since the system will generate such a file for selected system automatically Prepare Structure For Your System User may have his her own favorite molecular structure editing software Here we will choose NanoCad which is integrated into GridChem as example for structure editing Here we choose b utane CH 3 CH 2 CH 2 CH 3 as example to show how to use NanoCad to build a new molec
116. ule Here we assume that you already have an active account of GridChem and knew how to start GridChem and Nano Cad After launch the NanoCad in GridChem you will see the main interface of this molecule builder as in figure 7 1 As it can be seen the main interface the basic manipulation commands have been listed in Summary of Nanocad Com mands section which is located in the upper part of the Nanocad window Figure 7 1 Nanocad Molecule Builder Main Interface 30 Pre processor Molecule Builder oxi Summary of Nanocad Commands About Rotate drag gray space Translate Shift drag gray space Zoom Ctrl drag empty space Move Atom drag atom Add Atom Shift click gray space Delete Atom Shift click atom Add Bond Shift drag ator to atom Delete Bond Ctrl drag atom to atom Select Atom Alt click atom Add double bond Shift drag between bonded atoms Select Group Ctrl Alt click atom J Group J Geometry J Forces Help Structure Clear Undo Add H Get Potential Minimize z Force Field x Export Menu 7 To build a new structure you need to click the STRUCTURE button at the bottom of the Nanocad window A new small window with the title Import Structure will pop up Figure 7 2 Figure 7 2 Nanocad Import Structure SIRI Atom Database hy Files Function Group lon Molecule Change current element to H l i Current Element H In the Import Structure window the current elemen
117. ulting view new Consulting Table and new Ticket Table osneensseessseeerrsessrerrsrrerrerrerrsees 97 10 5 Ticket Ticket information and correspondence cece cece seen eee ee cece ne eeneeeneeeeeeeeeeeeeeeeeaees 98 10 6 Create Ticket view User Ticket form 0 ceec cee cceeceeeceeecaeeea seca eeaa sean eeu eeaeeeneeeneees 100 10 7 Consulting view the Ticket Tables ss c0 s202 fc icssdesscbevsessseteaa ses yest ds csentapeesesvastemeoag A Ee eha 102 10 8 Consulting view Update Ticket command panel below the Ticket Table eee 103 10 9 Admin s Main Menu Administration view for administrators managers seeeeeeeee eee ee eee 104 10 10 adminSpace menu Created by clicking the administration view of the Main menu 104 LOA sGraphied 1 x tsb si ay a et oh ech hapa E baa ee Piece deh Uae be Mu A te eat eee Ae Peete 106 10 12 Browse users view List of users and important information cseeeeeeeceeeeeeeeeeeeeeeeeaneeeens 107 10 13 Modify users view List of users and important information cece ects cc eeceeeceeee nena es 108 10 14 Search results from Modify user View 20 0 0 cece cece c cee ce ence ence eeceeecaeeea seen eeea scan eeaeceueeeneeeenees 109 Vil List of Tables 9 1 Gaussian Vibrational Frequency Scaling Factors 9 2 GAMESS Vibrational Frequency Scaling Factors 10 1 Consult System Categories of Users
118. un 20 maximum allowed number of steps 100 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Input orientation Center Atomic Atomic Coordinates Angstroms Number Number Type X Y Z 1 9 0 0 000000 0 000000 0 000000 2 9 0 1 500000 0 000000 0 000000 Stoichiometry F2 Framework group D H C F F Deg of freedom 1 Full point group D H NOp 8 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 Standard orientation Center Atomic Atomic Coordinates Angstroms Number Number Type X Y Z 1 9 0 0 000000 0 000000 0 750000 2 9 0 0 000000 0 000000 0 750000 Rotational constants GHZ 0 0000000 23 6454494 23 6454494 Standard basis 6 31G 6D 7F There are 5 symmetry adapted basis functions of AG symmetry There are 0 symmetry adapted basis functions of B1G symmetry There are 2 symmetry adapted basis functions of B2G symmetry There are 2 symmetry adapted basis functions of B3G symmetry There are 0 symmetry adapted basis functions of AU symmetry There are 5 symmetry adapted basis functions of B1U symmetry There are 2 symmetry adapted basis functions of B2U symmetry There are 2 symmetry adapted basis functions of B3U symmetry Integral buffers will be 262144 words long Raffenetti 2 integral format Two electron integral symmetry is turned on 18 basis functions 44 primitive gaussians 18 cartesian ba
119. view new Consulting Table and new Ticket Table 97 Technical Support logged in as user2 logout gt home gt consulting gt preferences gt search gt about gt home gt create ticket gt browse tickets A listing of your tickets is presented with relevant information in the display area Click on a Ticket number under the Ticket header to display the correspondence submitted ticket problem and consultant response and other Fri O4 6 Feb 2005 10 09 22 GridChem Operation In Progress John Doe2 Open Tickets You Have Submitted 4 out of 4 Ken Milfeld Mon 31 Jan 2005 13 10 36 GridChem Job Submission Pending User Response John Doe2 Milfeld Ken Mon 31 2 Jan 2005 12 46 20 Gridchem Operation New John Doe2 None Mon 31 ijJan 2005 12 07 35 GridChem Operation Pending User Response John Doe2 Ken Milfeld details The figure below shows the interaction between the user and consultant after selecting ticket number 6 Figure 10 5 Ticket Ticket information and correspondence 98 Technical Support Ticket 6 Fri 04 Feb John Doe2 Date Created 2005 10 09 22 Requestor s Email Requestor s Phone 859 257 8748 milfeld2 tacc utexas edu GridChem Operation In Progress N A High Ticket Owner Ken Milfeld Mi Subject Fest
120. which gives full control over the geometry and allows you to build molecules from scratch including polypeptides Molden is free of charge and can be obtained at the website http www cmbi ru nl molden molden html Molden is available on most UNIX systems Linux Mac OS and Windows systems User can download the binary executable package uncompress if necessary and directly run the molden program More details about installation and using of Molden can be obtained from Molden website Figure 9 1 shows the user interface of Molden running on Windows Figure 9 1 Molden Interface 67 Post Processing Visualization Molden Control ioj xi E a a a g ea g a H a aum Y Hi Teea H Ii El elol al Status line First point Click Button Read a browse window will pop out to select the Gaussian output file Figure 9 2 Figure 9 2 Molden File Select 68 Post Processing Visualization Molden File Select Cysteine log cus eclipse After click the correct Gaussian 03 output file Molden will try to read in the file and visualize the structure Please notice that any time a file is clicked in Molden file browser Molden will try to read into that file And it will take a while for Molden to do so Therefore please be careful to choose the file which needs to be read in Figure 9 3 shows the optimized structure of cysteine Figure 9 3 Molden Display Molecule

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