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Manual NWCHEMRATE – version 2007

1. The IVTST M algorithm is used for this sample run with the fu31 input file that is generated in the ch5tr3 test run The information used for interpolations is read from fu31 input file by specifying the keyword POTENTIAL UNIT31 in ENERGETICS section The rj reaction path is calculated at the s range of 2 00 to 2 00 angstrom by using the interpolation of information provided in fu31 file There is no electronic structure calculation by nwchem in this test run NWCHEMRATE I O files NWCHEMRATE file names ch5tr4 dat poly fu5 Input data for POLYRATE ch5tr4 61 esp fu l POLYRATE output file containing information about the stationary points ch5tr4 fu6 poly fu6 Long output file ch5tr4 ful5 poly ful5 Summary output file ch5tr3 fu31 poly fu31 Input data for IVTST M algorithm December 26 2007 NWCHEMRATE version 2007 5 8 2 9 Test Run ch4ohtr1 Tunneling none Number of levels single level M05 2X 3 21G Hindered rotation none IVTST M off This is the first of a series of tests that try to show how NWCHEMRATE would usually be used We study the CH4 OH CH H50 reaction The sequence actually has five stages The first four stages may be thought of a complete single level calculation or as runs 1 4 of a five run dual level calculation The first step we will take is the calculation of the first reactant CH4 In the fu5 input file we only include the REACTI sect
2. Example RSTTOL 0 00000001 December 26 2007 NWCHEMRATE version 2007 33 7 4 2 The NWRCOMMON Section The NWRCOMMON section reads the information common to all the NWCHEM calculations for the stationary points and points along the reaction path excepting the NWCHEM geometry optimizations which are totally controlled by the u71 through u78 input file The options selected in this section will be applied to all the NWCHEM calculations unless a different keyword is specified in the section corresponding to a specific point This section needs to precede the specific sections NWRREACTI NWRREACT2 NWRPRODI NWRPROD2 NWRSTART NWRWELLR NWRWELLP and NWRPATH The following keywords are allowed in the NWRCOMMON section NWRMETHOD This keyword determines which type of electronic structure calculation is to be performed by NWCHEM This should be the option used in the NWCHEM task statement NWCHEMRATE was primarily written to handle DFT calculations by HF SCF and post HF methods are also possible In the case of DFT the value of NWRMETHOD should be simply DFT rather than a specific exchange correlation functional which should be defined in the NWRMETHOP section below At this point most of the electronic structure methods available in NWCHEM are available for use in NWCHEMRATE Nonetheless certain methods are not available because they require specialized options These include TDDFT MCSCF and PSPW These methods ma
3. u70 input file is divided into sections which like the u5 sections are denoted by a header preceded by an asterisk There are ten sections each starting with NWR in order to avoid confusion with similar sections in the u5 input file These sections are NWRGENERAL NWRCOMMON NWRREACTI NWRREACT2 NWRPRODI NWRPROD2 NWRWELLR NWRWELLP NWRSTART and NWRPATH In these sections the appropriate keywords need to be specified Section name Description NWRGENERAL General options NWRCOMMON NWCHEM options common to all the stationary points NWRREACTI NWCHEM options specific to the first reactant NWRREACT2 NWCHEM options specific to the second reactant if any NWRPRODI NWCHEM options specific to the first product NWRPROD2 NWCHEM options specific to the second product if any NWRWELLR NWCHEM options specific to the reactant well if any NWRWELLP NWCHEM options specific to the product well if any NWRSTART NWCHEM options specific to the starting or saddle point NWRPATH NWCHEM options common to all the nonstationary points along the reaction path NWRNWREND signals last line of the esp fu70 file mandatory There are three types of keywords switch which does not have any argument variable which requires one argument following the keyword and list which requires a list of options with an NWREND line See the POLYRATE manual for a more thorough discussion of the three types of keywords Note that a list termina
4. will need to calculate numerical Hessians GEOM The ordering of the atoms in the GEOM keyword in sections REACTI REACT2 PRODI PROD2 and START must be consistent with the ordering in units u71 fu72 fu73 fu74 and u75 when they are used and also the ordering in u75 also must be consistent with the one in ATOMS in the GENERAL section December 26 2007 NWCHEMRATE version 2007 27 CONSTANT If the user selects NWCHEM for optimizing the geometries this is accomplishing with the OHOOK option for the OPTMIN and OPTTS keywords in the OPTIMIZATION section of the POLYRATE fu5 input the CONSTANT keyword in the REACT1 REACT2 PRODI PROD2 WELLR WELLP and START sections of the fu5 input file is meaningless The frozen parameters must be indicated in units fu71 fu78 according to the instructions explained in the NWCHEM manual If a user selects POLYRATE 9 7 for optimizing the geometries this keyword has the same function as in any other POLYRATE calculation fixing the value of the selected coordinates and avoiding their optimization as explained in Section 11 A 6 of the POLYRATE 9 7 manual INITGEO and STATUS There are two options for reading the initial geometries of reactants products wells and saddle point The first is by means of units fu71 through fu78 if a NWCHEM optimization is desired OHOOK option for the OPTMIN and OPTTS keywords in the OPTIMIZATION section In this case the INITGEO keyword sh
5. SCT Hindered rotation none IVTST M on The IVTST M algorithm is used for this sample run with hooks The step size of s is set to 0 01 angstrom and s range is set to 0 20 to 0 20 angstrom The keywords EXFIRST and EXSECOND are used for IVTST M algorithm The reaction coordinate s is extended to 2 0 42 0 angstrom with a 0 01 angstrom step size The keyword FIXMUEF is used to apply a global interpolation to estimate the effective reduced mass of the SCT algorithm at the saddle point The geometries for the reactants products and saddle point are given in the u5 input file 1 NI TG EO is set to GI EOM and STATUS set to 2 in the RI REACT2 PROD1 PROD2 and START sections of the fu5 input file Fu31 file is EACTI written by using keyword writefu31 in the fu5 input file which will be used for the next test run NWCHEMRATE I O files ch5tr3 dat ch5tr3 e61 ch5tr3 fu6 ch5tr3 ful15 ch5tr3 fu31 50 NWCHEMRATE file names poly fu5 Input data for POLYRATE esp fu61l POLYRATE output file containing information about the stationary points poly fu6 Long output file poly ful5 Summary output file poly fu31 Input data for IVTST M algorithm NWCHEMRATE version 2007 December 26 2007 8 2 8 Test Run ch5tr4 Tunneling SCT Number of levels single level M05 6 31G Hindered rotation none IVTST M on with fu31
6. u78 must be consistent with the index specifications in the GEOM keyword in the REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections of the u5 input file For the sake of consistency the method chosen for the electronic structure calculations for a given reaction must be the same in all the esp f u71 through esp fu78 files representing the species for that reaction Only if one of the species is the hydrogen atom and electronic correlation is included can the quantum methods be different since no correlation energy can be calculated for the hydrogen atom The electronic structure method must also be consistent with the options related to energy and first and second derivatives chosen in the u70 input file When studying a reaction with no saddle point the user must insure that the optimization procedures chosen for the starting point will not lead the system to reactants or products This can be accomplished by freezing the appropriate geometrical parameters If no geometrical parameter is kept fixed the optimization will lead to a point where the gradients are zero and the procedure for following the reaction path will not work successfully December 26 2007 NWCHEMRATE version 2007 31 7 4 DESCRIPTION OF Esp FU70 INPUT FILE Along with the input u5 file which controls the POLYRATE options the u70 input file will control all of the NVCHEMRATE options and some of the NWCHEM input options The
7. 7 Note that running two NWCHEMRATE calculations or a NWCHEM and a NWCHEMRATE calculation in the same directory can cause problems due to overwriting of some of the temporary files NWCHEMRATE makes use of system calls in order to have NWCHEM perform the needed energy gradient and or Hessian calculations The capability to make system call is available in most FORTRAN compilers Any user of NWCHEMRATE should make sure that this utility subroutine is available with their compiler and if necessary install any missing libraries 8 NWCHEMRATE version 2007 December 26 2007 4 DISTRIBUTION NWCHEMRATE is a Set of subroutines for interfacing POLYRATE and NWCHEM The user needs to obtain four items of code POLYRATE The POLYRATE code is a licensed code available from the University of Minnesota Currently the license fee is waived for all users For further information see http comp chem umn edu polyrate NWCHEM NWCHEM is a licensed code available from Pacific Northwest National Laboratories For further information see http www emsl pnl gov docs nwchem nwchem main html NWCHEMRATE The NWCHEMRATE code is a licensed code available from the University of Minnesota Currently the license fee is waived for all users For further information see http comp chem umn edu nwchemrate system This utility code is also required It is available in most FORTRAN libraries Prospective users of NWCHE
8. IVTST M calculations is in conjunction with the hooks this requires some additional keywords namely EXFIRST and EXSECOND A calculation with the hooks involves two stages At the end of the first stage one has stored s Vuep s and the gradients on the fine grid and s VMEp s oX5 Bmpr s and I s are stored on the save grid The grids are defined in Sect 7 A of the POLYRATE manual Both grids extend from s SLM on the reactant side to s SLP on the product side and there are G 1 points including the saddle point but excluding reactants and products on the fine grid and H 1 points including the saddle point but excluding reactants and products on the save grid Then mapped interpolation is carried out to add EXNSTEP EXSTEP points on each side of the grids Furthermore SLM is replaced by SLM EXNSTEP EXSTEP and SLP is replaced by SLP EXNSTEP EXSTEP December 26 2007 NWCHEMRATE version 2007 41 8 TESTING NWCHEMRATE 8 1 TESTS PERFORMED We tested version 2007 of NWCHEMRATE using version 9 7 of POLYRATE and the indicated versions of NWCHEM on the following machines the operating system is indicated in parentheses IBM Regatta with Power4 processors AIX 5 3 NWCHEM version 5 0 2 SGI Altix with Itanium 2 processors Linux NWCHEM version 5 0 4 IBM BladeCenter with AMD Opteron processor SuSE Linux NWCHEM version 5 0 The code is expected to work with all NWCHEM versions that
9. be set to BFGS NR and or EF and INITGEO has to be set to GEOM and STATUS set to 0 in the corresponding REACTI REACT2 PRODI PROD2 WELLR WELLP and or START sections of the fu5 input file The initial geometries are given in the appropriate sections of the fu5 input file If the geometry of one of the stationary points is already optimized the only parameter that has to be changed is the value of the STATUS keyword in the corresponding section of the u5 input file A value greater than 0 for the STATUS keyword in any of the REACTI REACT2 PRODI PROD2 and or START sections results in no optimization of the input geometry in the u5 file If a value greater than 2 is selected no Hessian calculation is performed If STATUS is set to 4 in the START section of the u5 input file the Hessian matrix as it appears in a NWCHEM formatted checkpoint file can be input according to the instructions in the POLYRATE manual ANHARMONICITY Although anharmonic calculations can be carried out the user must keep in mind the extremely high cost of numerical third or fourth derivatives of the energy when using ab initio or DFT methods With the anharmonicity options available in POLYRATE 9 7 this extra cost is not usually warranted We therefore recommend not using anharmonic options in the REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections when they require derivatives of order higher than two at least until some later version of POLYRATE
10. information is stored in this same file If one of these conditions is not fulfilled an NWCHEM calculation is run to obtain the desired information If both conditions are fulfilled then the information is read from esp u83 and no NWCHEM job is spawned The geometry check is performed by comparing each of the Cartesian coordinates of the desired geometry with the Cartesian coordinates in esp fu83 If the values differ by more than a criterion given by RSTTOL the geometries are considered to be different It is important to have an appropriate value for 18 NWCHEMRATE version 2007 December 26 2007 RSTTOL if the criterion is too tight the check might fail due to the numerical round off and the fact that the precision of the written information is limited and redundant calculations could be carried out unnecessarily increasing the CPU time of the calculation However if this criterion is too loose the check could be passed for two geometries that are only slightly different thereby resulting in erroneous results from NWCHEMRATE The latter case can be especially true when performing reaction path calculations with very small step sizes numerical differentiations or accurate geometry optimizations Therefore the user must be very careful about changing this parameter The default value is 1 D 8 which is very conservative but safe For very expensive calculations one might want to use a higher value but too high a value can give unphysi
11. is thus not recommended e So far NWCHEMRATE has only been tested using DFT and MP2 e In NWCHEM a number of methods do not have analytical second derivatives Hessians inter alia open shell DFT and meta GGA functionals Likewise the TCE engine used for correlated post Hartree Fock methods does not have analytical gradients We generally recommend that NWCHEMRATE only be run with methods that have analytical gradients but this is a recommendation not a requirement 20 NWCHEMRATE version 2007 December 26 2007 7 DESCRIPTION OF INPUT FILES We will assume that the user knows how to use POLYRATE 9 7 and NWCHEM and is familiar with their keywords Therefore when talking about the common input files we will only discuss the differences between running POLYRATE 9 7 and running NWCHEMRATE 2007 December 26 2007 NWCHEMRATE version 2007 21 7 1 FILE USAGE In addition to the POLYRATE 9 7 and NWCHEM input files NWCHEMRATE uses several files of its own for input data for storing restart information and for output All these files have the name esp fu where denotes an integer esp esp esp esp esp esp esp esp esp 22 fu70 sf u72 u73 fu74 fu75 fu76 fu77 fu78 General NWCHEMRATE input data NWCHEM input file for geometry optimization of reactant 1 if such optimization is going to be carried out NWCHEM input file for geometry optim
12. modified for running this program Likewise separate licenses for these codes need to be obtained before using NWCHEMRATE This NWCHEMRATE manual covers only material that is not covered in the POLYRATE and NWCHEM manuals The user of NWCHEMRATE should first be familiar with these programs The interface between POLYRATE and NWCHEM is made by a series of FORTRAN subroutines included in the files hooks nwr f and hooks mdepnw f which are specialized versions of the routines in the hooks f file in POLYRATE 9 7 and by a C shell script for running NWCHEM This C shell script named taxi equivalent to shuttle in GAUSSRATE the name was changed to avoid confusion between the two codes is called from inside NWCHEMRATE and it has to be able to start running NVCHEM using an input file named as the first argument given to taxi It produces an output file named as the second argument given to taxi The third argument passed to taxi is the number of processors on which NWCHEM will be run For the user s convenience a well documented script is provided and in most cases the user will only need to change one line set the nwpath variable to the appropriate path where NWCHEM is located In the provided script the variable scratchdir which indicates the directory where the temporary and scratch NWCHEM files are going to be located is set to the working directory if desired the user can also change this December 26 2007 NWCHEMRATE version 2007
13. not exist and the program will calculate the frequencies for all the stationary points and the optimum geometry for the saddle point instead of reading them from the restart file It should be noted that the u75 file is required and it is used by NWCHEMRATE although not by NWCHEM At the end of the calculation a new restart file including the information calculated for the first time in the present run will take the name of oh3t r2 rst while the old restart file will be renamed as oh3tr2 rst old and this will be unchanged from what was in file oh3tr1 rst at the start of the present run NWCHEMRATE I O files NWCHEMRATE file names oh3tr2 70 esp fu70 Input data for NWCHEMRATE oh3tr2 75 esp fu75 Input data for the saddle point oh3tr2 dat poly fu5 Input data for POLYRATE oh3tr2 61 esp fu l POLYRATE output file containing information about the stationary points oh3tr2 fu6 poly fu6 Long output file oh3tr2 ful5 poly ful5 Summary output file oh3tr2 rst old esp fu83 Restart file read by NWCHEMRATE oh3tr2 rst esp fu84 Restart file written by NWCHEMRATE December 26 2007 NWCHEMRATE version 2007 45 8 2 3 Test Run oh3txr3 Tunneling none Number of levels single level MPW1K 3 21G Hindered rotation none IVTST M off This test run uses the oh3tr2 rst file written by the oh3tr2 test run copying it as oh3tr3 rst and it performs the same calculation as the oh3tr1 test Since more informa
14. or site will redistribute the source code or executable code to a third party in original or modified form without written permission of the principal investigator Donald G Truhlar A license does not entitle the licensee to relicense the code or distribute it in original or modified form to parties not covered by the license The licensee has no ownership rights in the NWCHEMRATE software or in any copyrights for the NWCHEMRATE software or documentation through this license A user license covers the work of a single research group and the code may be shared and disseminated within a group without requiring permission Site licenses are also available Publications resulting from using this package or the POLYRATE or NWCHEM subsystems used by this package will cite the corresponding program The required references are given in the documentation see Section 2 for the required references for NWCHEMRATE No guarantee is made that this program is bug free or suitable for specific applications and no liability is accepted for any limitations in the mathematical methods and algorithms used within the program No consulting or maintenance services are guaranteed or implied The POLYRATE and NWCHEM codes required to use NWCHEMRATE are covered by separate licenses December 26 2007 NWCHEMRATE version 2007 5 2 REQUIRED REFERENCES Publications based on results obtained with this computer code should include the following
15. paths would be different There is only one parameter related to the path that should not be changed between an original calculation and a restart calculation namely the value of SCALEMASS Changing this parameter will cause a miscalculation of the frequencies It is important to note that its default value is 1 0 amu and this is the value assumed if no reaction path calculation is desired Therefore if a restart calculation including the reaction path is based on a restart file written by a TST only calculation SCALEMASS must be set to 1 amu in order to obtain the correct frequencies In general we recommend always using a value of 1 0 amu for SCALEMASS in NWCHEMRATE A NWCHEMRATE restart run requires that all the information about all the stationary points be present in file esp u83 and this data cannot be updated in this kind of restart run However the use of the STATUS keyword in the REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections of the POLYRATE fu5 input file can alleviate this inconvenience Thus the user can calculate reactants and products separately and include the information obtained in the u5 input file See the ch4oh test runs in the Section 8 2 and Sections 7 C and 11 A of the POLYRATE manual The restart option works in the following way when POLYRATE needs an energy gradient and or Hessian for a given geometry it first checks if the geometry is stored in esp fu83 and then checks if the required
16. references Additional references for specific methods used are given in the documentation for POLYRATE and NWCHEM J Zheng M A Iron B A Ellingson J C Corchado Y Y Chuang E L Coitifio and D G Truhlar NWCHEMRATE version 2007 University of Minnesota Minneapolis MN 2007 J C Corchado Y Y Chuang P L Fast W P Hu Y P Liu G C Lynch K A Nguyen C F Jackels A Fernandez Ramos B A Ellingson B J Lynch J Zheng V S Melissas J Villa I Rossi E L Coitifio J Pu T V Albu R Steckler B C Garrett A D Isaacson and D G Truhlar POLYRATE version 9 7 University of Minnesota Minneapolis MN 2007 and either 3A or 3B or both 3A E J Bylaska W A de Jong K Kowalski T P Straatsma M Valiev D Wang E 3B Apr T L Windus S Hirata M T Hackler Y Zhao P D Fan R J Harrison M Dupuis D M A Smith J Nieplocha V Tipparaju M Krishnan A A Auer M Nooijen E Brown G Cisneros G I Fann H Fr chtl J Garza K Hirao R Kendall J A Nichols K Tsemekhman K Wolinski J Anchell D Bernholdt P Borowski T Clark D Clerc H Dachsel M Deegan K Dyall D Elwood E Glendening M Gutowski A Hess J Jaffe B Johnson J Ju R Kobayashi R Kutteh Z Lin R Littlefield X Long B Meng T Nakajima S Niu L Pollack M Rosing G Sandrone M Stave H Taylor G Thomas J van Lenthe A Wong and Z Zhang NWChem A Computati
17. use input and output files with the same structure as the above mentioned versions 42 NWCHEMRATE version 2007 December 26 2007 8 2 TEST SUITE The purpose of the test suite is to provide some examples of the way NWCHEMRATE works and to check the most important NWCHEM and POLYRATE 9 7 options for direct dynamics Therefore the number of tests included is only fifteen and the tests illustrate only the most basic features of NWCHEMRATE The level of calculation size of the systems and computational requirements of the test runs have been chosen in such a way that running the whole suite does not consume an inordinate amount of computing time All the test runs were run after compiling NWCHEMRATE using the param4 inc file The test suite is located in the test run directory which contains four subdirectories Each subdirectory contains one or more tests based on the same reaction The summary output files for these test runs that are distributed in the current version of the program are located in the testo directory The output files were obtained from runs on an IBM Power4 Regatta computer The Korn shell script checknw in the testrun directory allows for an easy comparison between the poly fu15 output files obtained after running all the test runs using NWCHEM and the equivalent poly fu15 files in the testo directory Each directory in testrun includes one or more tests based on one of the following re
18. with better anharmonicity options becomes available The only anharmonicity options that do not require derivatives higher than second are Morse I and hindered rotator December 26 2007 NWCHEMRATE version 2007 29 SCALEMASS SCALEMASS is the reduced mass to which all isoinertial coordinates are scaled If restart calculations are desired the value of the SCALEMASS variable keyword must be the same for the whole series of calculations See also the discussion of SCALEMASS in Section 6 2 30 NWCHEMRATE version 2007 December 26 2007 7 3 DESCRIPTION OF EsP FU71 THROUGH EeP FU78 INPUT FILES The data files esp fu71 through esp fu78 are NWCHEM type data files They are used only as input files for NWCHEM optimization on reactants 1 and 2 esp fu71 and esp fu72 respectively products 1 and 2 esp u73 and esp fu74 of the wells on the reactant esp u77 and product esp u78 sides and of the saddle point or other starting geometry esp fu75 If no optimization using NWCHEM is desired these files are not needed For constructing these files the user should consult the NWCHEM manual The user can also use examples of these files in the NWCHEMRATE test suite As mentioned above when creating these files the order of the atoms in unit u75 must be consistent with the order of the atoms input in the ATOMS keyword in the GENERAL section of the POLYRATE fu5 input file and the order of the atoms in units u71
19. 823 3 Test run oh3tr3 0 0 0 0 Test run oh3tr4 995 4 523 4 Test run ch4ohtr1 287 8 167 6 Test run ch4ohtr2 413 8 241 4 Test run ch4ohtr3 2080 3 1433 4 Test run ch4ohtr4 9997 0 5750 0 Test run ch4ohtr5 10174 8 6804 0 Test run ch4ohtr6 11640 5 7100 3 Test run nh3ohtr1 3251 3 1795 4 60 NWCHEMRATE version 2007 December 26 2007 8 4 COMPARISON BETWEEN NWCHEMRATE AND GAUSSRATE We performed the same calculations using NWCHEMRATE and GAUSSRATE The results of forward rate constants are shown in the following table The reaction is CH H5 5 CH4 H The forward rate constants were calculated at the PBE0 6 31G level PBEO are chosen because PBEO also called PBEIPBE or PBEh in some places in the literatures is a popular functional defined uniformly in most electronic structure packages Here we used 0 01 A for step size of s and s range from 0 30 0 30 A These values should be enough for purpose of testing program Summary of forward rate constants cm3 molecule s T K TST CVT CVT ZCT CVT SCT GUASSRATE 298 0 4 90E 17 4 79E 17 4 82E 15 5 90E 14 400 0 7 46E 16 7 33E 16 1 01E 14 5 86E 14 667 0 1 88E 14 1 86E 14 4 83E 14 1 03E 13 1000 0 1 15E 13 1 15E 13 1 76E 13 2 50E 13 1550 0 5 98E 13 5 95E 13 7 11E 13 8 25E 13 NWCHEMRATE 298 0 4 88E 17 4 78E 17 4 81E 15 5 87E 14 400 0 743E 16 7 31E 16 1 01E 14 5 84E 14 667 0 1 87E 14 1 85E 14 4 83E 14 1 03E 13 1000 0 1 15
20. E 13 1 14E 13 1 75E 13 2 49E 13 1550 0 5 97E 13 5 93E 13 7 09E 13 8 23E 13 The numbers in the tables show that two programs give the identical results using the same electronic structure method and basis set December 26 2007 NWCHEMRATE version 2007 61 9 COMPUTERS OPERATING SYSTEMS AND NWCHEM VERSIONS ON WHICH THE CODE HAS BEEN DEVELOPED AND TESTED In each case we give the NWCHEMRATE version number then the computers and operating system on which NWCHEMRATE was tested For each computer and operating system we also specify the NWCHEM version that was used for testing NWCHEMRATE VERSION 2007 P9 7 NW5 0 Machine OS Compilers NWCHEM Version IBM Regatta Power4 procs XLF v10 1 5 0 AIX 5 3 IBM BladeCenter g77 from gcc v3 3 3 5 0 AMD Opteron procs SuSE Linux SGI Altix Itanium 2 procs g77 from gcc v3 3 3 5 0 SuSE Linux 62 NWCHEMRATE version 2007 December 26 2007 10 VERSION INFORMATION 11 1 NWCHEMRATE VERSION NUMBERS NWCHEMRATE version numbers have the general form 200x Px y Z NWx y where 200x is the NWCHEMRATE version number x y Z is version of POLYRATE to which it is linked and x y is the number of the version of NWCHEM being used In general the lowest level revisions y or z are bug fixes while the higher level revisions x x or y are significant feature enhancements The part of the version number before the solidus is unique that is it changes if the version of POLYRATE c
21. E restart option is off Usually the user would calculate the stationary points one by one instead of calculating three in a row Thus if some problem is encountered in any stationary point calculation the user can check the error in that particular point instead of repeating several optimizations The fu61 input file will contain all the information about the reactants and products needed for the next run This includes both the information calculated in test run ch4ohtr1 and the information calculated in the present test run NWCHEMRATE I O files NWCHEMRATE file names ch4ohtr2 70 esp fu70 Input data for NVCHEMRATE ch4ohtr2 72 esp fu72 Input data for reactant 2 optimization ch4ohtr2 73 esp fu73 Input data for product 1 optimization ch4ohtr2 74 esp fu74 Input data for product 2 optimization ch4ohtr2 dat poly fu5 Input data for POLYRATE ch4ohtr2 61 esp fu l POLYRATE output file containing information about the stationary points ch4ohtr2 fu6 poly fu6 Long output file December 26 2007 NWCHEMRATE version 2007 53 8 2 11 Test Run ch4ohtr3 Tunneling none Number of levels Hindered rotation none IVTST M off single level M05 2X 3 21G This is the third step in the four stage single level calculation for the CH4 OH CH3 H50 reaction In this test run we calculate the saddle point properties and evaluate the conventional TST rate constant including all the information on reactants and pr
22. HEMRATE I O files oh3tr1 70 oh3tr1 75 oh3trl dat oh3tr1 601 oh3trl fu6 oh3trl fu15 nstri rst 44 NWCHEMRATE file names esp fu70 Input data for NWCHEMRATE esp fu75 Input data for the saddle point optimization poly fu5 Input data for POLYRATE esp fu61 POLYRATE output file containing information about the stationary points poly fu6 Long output file poly fu15 Summary output file esp fu84 Restart file written by NWCHEMRATE NWCHEMRATE version 2007 December 26 2007 8 22 Test Run oh3tr2 Tunneling none Number of levels single level MPWIK 3 21G Hindered rotation none IVTST M off This is a test run that by making use of the on3tr1 rst file previously written by the oh3tr1 test run restarts the calculation performed by the previous test run and makes a canonical variational theory CVT calculation without tunneling by following the reaction path using the variational reaction path algorithm based on the Euler method VRPE option of RPM keyword with a step size of 0 012 Angstrom The reaction path is calculated between 0 15 Angstrom and 0 15 Angstrom Nonredundant internal coordinates are used for describing the vibrations The user must run the oh3t r1 test run before running oh3t r2 since the restart file to be read oh3tr2 rst will be a copy of the oh3trl rst file generated by the previous run and located in the same directory Otherwise the on3tr2 rst file will
23. MRATE must first obtain and install POLYRATE and NWCHEM before proceeding with NWCHEMRATE The NWCHEMRATE program is distributed as a compressed tar file named either nwrate2007 tar Z or nwrate2007 tar gz The distributed file either one of the above files should be uncompressed and untarred in the polyrate9 7 directory To uncompress type uncompress nwrate2007 tar Z or gunzip nwrate2007 tar gz December 26 2007 NWCHEMRATE version 2007 9 The uncompressed file will be named nwrate2007 tar After extracting the files from the tar file which can be done with the command tar xvf nwrate2007 tar a new directory nwrate is created This directory contains all the files included in the distribution package If these instructions are followed correctly the directory structure should be the following tree structure polyrate9 7 doc exe nwrate obj poten script src testo testrun util doc script source testo testrun ch4oh ch5 oh3 nh3oh The files will be distributed among the directories as follows nwrate the C shell script taxi and five subdirectories doc NWCHEMRATE manual nwchemrate pdf script 1 file nwrcompile source 4 files comprising the source code for NWCHEMRATE nwrate inc head nwr f hooks nwr f and hooks nwr wks f testo This directory contains selected output files of the test runs 15 files ch4ohtrl fu6 ch4ohtr2 fu6 ch4ohtr3 fu15 ch4ohtr4 fu
24. Manual NWCHEMRATE version 2007 Jingjing Zheng Mark A Iron Benjamin A Ellingson Jos C Corchado Yao Yuan Chuang and Donald G Truhlar Department of Chemistry and Supercomputing Institute University of Minnesota Minneapolis Minnesota 55455 Program version 2007 P9 7 NWS 0 Program version date December 26 2007 Manual version date December 26 2007 Copyright 2007 Abstract NWCHEMRATE is a set of FORTRAN subroutines and Unix scripts for interfacing the POLYRATE and NWCHEM computer programs for the purpose of carrying out direct dynamics calculations of gas phase chemical reaction rates of polyatomic species and also atoms and diatoms as special cases using the electronic structure methods available in NWCHEM to calculate the potential energy surface and POLYRATE for the dynamics The interface is based on the POLYRATE hooks protocol The dynamical methods used are variational or conventional transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection Rate constants may be calculated by any of the methods available in POLYRATE for canonical or microcanonical ensembles or for specific vibrational states of selected modes with translational rotational and other vibrational modes treated thermally Bimolecular and unimolecular reactions are included Both single level and dual level calculations may be carried out In single level mode optimized geometries potential energie
25. TST M Usage 40 8 Testing NWGCHEMBA TE 0o oed beetutr en ite esed e A tabac duet atas du ee ra Cab es 42 Sd Tests Performed arrena tese dea omn EP om amis 42 December 26 2007 NWCHEMRATE version 2007 3 8 2 Test SUlte xit ted ae 8 2 1 Test Run oh31 8 2 2 Test Run oh31 8 2 3 Test Run oh31 8 2 5 Test Run ch5 8 2 6 Test Run ch5 8 2 7 Test Run ch5 8 2 8 Test Run ch5 8 2 9 Test Run ch4oht r1 esee 8 2 10 Test Run ch4oht r2 eian 8 2 11 Test Run ch4oht r3 eeeee 82 12 Test Run chA6htr4 vist daisies 8 2 13 Test Run ch4oht r Dae a aai 8 2 14 Test Run ch4ONTY Oristano ra naa 8 2 15 Test Run nhiSohit rl ec eed 8 3 Test Run Timings sud tereti eere te 8 4 Comparison between NWCHEMRATE and GAUSSRATE 3 3 3 8 2 4 Test Run oh3t r4 essesssssesssssssessserersssseserereessssss 5 5 5 5 9 Computers Operating Systems and nwchem Versions on which the Code has been Developed and Lested uan reete des 10 Version Informoatiofi a cutie io rra bed eria vise hx 11 1 NWCHEMRATE Version Numbers sss 10 2 NWCHEMRATE Revision History ssss 11 Acknowledgments cono ora Ier redit on ts 4 NWCHEMRATE version 2007 December 26 2007 1 USER AGREEMENT NWCHEMRATE is a licensed program and the use of this program implies acceptance of the terms of the license which are repeated here for convenience A No user
26. actions Reaction Directory Test Names OH H gt H2O H oh3 oh3trl oh3tr2 oh3tr3 oh3tr4 CH H5 gt CH4 H ch5 ch5trl ch5tr2 ch5tr3 ch5tr4 CH OH gt CH4 H50 ch4oh ch4ohtr1 ch4ohtr2 ch4ohtr3 ch4ohtr4 ch4ohtr5 ch4ohtr6 NH OH gt NH H2O0 nh3oh nh3ohtr1 The test runs are run in a subdirectory created for each run In this way problems that could be caused when running other NWCHEM or NWCHEMRATE calculations in the same directory that NWCHEMRATE is using are avoided After the test run is completed the directory is removed and the temporary files created are moved to the NWRTEMPFILES directory December 26 2007 NWCHEMRATE version 2007 43 8 2 1 Test Run oh3tr1 Tunneling none Number of levels single level MPWIK 3 21G Hindered rotation none IVTST M off This is a test run for a conventional TST calculation for the reaction OH H5 gt H50 H The geometries for the reactants and products are given it is assumed that they already are fully optimized in the u5 input file INITGEO is set to geom and STATUS set to 2 in the REACTI REACT2 PRODI and PROD2 sections of the u5 input file while the saddle point optimization is carried out using NWCHEM requiring therefore the esp fu75 input file and STATUS set to 0 and the option hooks for the INITGEO keyword in the START section of the input file u5 The NWCHEMRATE restart file esp fu84 is written NWC
27. ae 25 R OAR S ecu E E T oe 25 ATOMS 5 dessen M e e ei M UE 23 NOSUPERMUQL quec icen ete tci oec eel Radiant having 25 219 PLUR ENS 26 POTENTIS acie ne a bete R Mc EL 26 OPTTS ait OP TM IN out tte e n e dei 26 SECOND ERES 27 GEOM T i E 27 CONSTAN Pateat iaee De N N a eed o D End 28 INITGEO and STATUS s occ R a rae a a E E 28 ANHARMONIC r ec ie en o ED E EE AER ad 29 SCALEMA SS i usevteabssi eaa etian AE a bu AAEE ONAE AAE ESARET NSG 30 7 3 Description of esp fu71 Through esp fu78 Input Files 31 7 4 Description of esp fu70 Input File onc ep de t re aepo tele ce 32 T4 T The NWGENERAL SEC Ofte secs tsvisetevpied a bibe p IN D editae 33 NWRRESTART NONWRRESTART csccssecssecssecssecssucessecsteestecesecesecesecesseeesecs 33 INW PROC 41 i eaten tuens isa corel dem ee lad eas rea a aaa 33 RSTTOL x sic n po e ueste E Obr UM Med 33 7 4 2 The NWRCOMMON SOCIO cesta rre eterne peter deine er EREE ere eie als 34 NWRMETHOD m 34 NWRTOP aorar Gutes rec te RN UU HERE Penis pa i een e ada Eus 34 DISMISS e EL LE EE 35 NWRMETHOP srecne det etai E E e ARRETE 35 NWRSCBOP aaen n a aN EE E ETER e EREE 36 NWROPTOP rn a a a a a 36 7 4 3 The NWRREACTI NWRREACT2 NWRPROD1 NWRPROD2 NWRWELLR NWRWELLP NWRSTART and NWRPATH Sections 38 CHARGE MULTIPLICITY and SCFTYPE ccssscssssrcesseeceseseesseneees 38 7 5 Description of Interpolated VTST by Mapping IV
28. arting geometry and if they are specified in the NWRPATH section they will also be ignored 38 NWCHEMRATE version 2007 December 26 2007 These are variable keywords that must be followed by an integer which is the value of the charge and multiplicity of the system The default values are 0 and 1 respectively which correspond to a neutrally charged singlet Multiplicities of 2 and 3 correspond to doublets and triplets Example CHARGE a MULTIPLICITY 2 SCFTYPE UHF December 26 2007 NWCHEMRATE version 2007 39 7 5 DESCRIPTION OF INTERPOLATED VTST BY MAPPING IVTST M USAGE IVTST M is a method for obtaining the information required for a VTST calculation all along the reaction path from the information available at an arbitrary but small number of points The only limitations on using the IVTST M algorithm are that a saddle point exists and reaction path information is available at least one nonstationary point on each side of the saddle point In addition as in all IVTST methods information is required for 3 5 stationary points reactants saddle point products and optionally one or two wells The level of IVTST M is denoted by two numbers H and G indicating respectively the number of nonstationary points at which Hessians are available and the number of nonstationary points at which gradients are available Thus IVTST M 6 54 indicates that the interpolation is based in 6 nonstationary Hessian points at
29. cal results If the user increases this parameter he or she has to be very aware of the risk it posses in the calculation and all the results must be carefully checked Therefore only experienced users are advised to change this parameter One should not confuse the restart options of NWCHEMRATE with those of NWCHEM NWCHEM also has the ability to restart jobs that were stopped in the middle for various reasons In principle one could include NWCHEM s restart options in a NWCHEMRATE job but this has not been tested Therefore this practice is not recommended December 26 2007 NWCHEMRATE version 2007 19 6 3 LIMITATIONS OF NWCHEMRATE There are a number of limitations in the initial release of NWCHEMRATE some of which associated with this program while others are associated with NWCHEM We hope that most of these limitations will eventually be eliminated The limitations of NWCHEM are listed here are for version 5 0 for full details see the NWCHEM User s Manual Earlier versions of NWCHEM may have additional limitations e Due to potentially complicated input required to be passed between NWCHEMRATE and NWCHEM certain model chemistries in NWCHEM are not compatible with NWCHEMRATE and any attempt to use them will result in an error message from NWCHEMRATE These currently include MCSCF TDDFT and PSPW e The use of dummy atoms Bq or X in the input specification may confuse NWCHEMRATE when it tries to read the output and
30. ction path if it exists in NWRWELLP the options for a well on the product side if it exists section NWRSTART will indicate the options for the saddle point or starting geometry and NWRPATH will indicate the options for NVCHEM calculations on the non stationary points along the reaction path If no changes from the options selected in the NWRCOMMON section are wanted these sections can be skipped Currently only three keywords are allowed in these sections CHARGE MULTIPLICITY and SCFTYPE CHARGE MULTIPLICITY and SCFTYPE If NWCHEM optimization is required NWCHEMRATE will read the charge the multiplicity of each species and the type of SCF if HF or post HF method is used from the NWCHEM optimization output Nevertheless if no optimization is selected or if POLYRATE 9 7 is selected for carrying out the optimizations NWCHEMRATE will need to know the charge and multiplicity of the system and type of SCF before making any NWCHEM calculation The way to input these characteristics is by means of the CHARGE MULTIPLICITY and SCFTYPE keywords These keywords are not allowed in the NWRCOMMON section since they are dependent on the species and are only required for the systems that will not be optimized using NWCHEM being ignored if they are specified for a species that is going to be optimized using NWCHEM For the points along the reaction path the charge and multiplicity are assumed to be the same as the values for the saddle point or st
31. e previous run was calculated using the SCT approach The frequencies are calculated using Cartesian coordinates instead of the set of redundant curvilinear coordinates from the ch4oht r4 run Since the different choice of coordinates does not affect the reaction path calculation the restart option does not prevent us from changing the coordinate system from one run to another The hindered rotor approximation is used for computing the partition function of the lowest vibrational mode The lowest four frequencies are interpolated directly by the IVTST O interpolation algorithm The restart file to be read is copied from the ch4ohtr4 rst file generated by the previous run ch4ohtr4 The user should therefore run the previous run ch4oht r4 in this set of tests before running this one A new restart file which includes all the previous information plus the additional calculations needed for estimating the LCT tunneling is generated by this test run NWCHEMRATE I O files NWCHEMRATE file names ch4ohtr5 70 esp fu70 Input data for NVCHEMRATE ch4ohtr4 rst esp fu83 Restart file read by NVCHEMRATE ch4ohtr5 dat poly fu5 Input data for POLYRATE ch4ohtr5 50 poly fu50 Additional input data for the POLYRATE VTST IC calculation ch4ohtr5 61 esp fu l POLYRATE output file containing information about the stationary points 56 NWCHEMRATE version 2007 December 26 2007 ch4ohtr5 fu6 ch4ohtr5 ful5 ch4ohtr5 r
32. ems due to the reorientation of the system A restart file is created NWRRESTART keyword and all the input of the geometries is done by means of files u71 through fu74 in order to allow NWCHEM to optimize the stationary points ohook option in OPTTS and optmin in the OPTIMIZATION section of the u5 input file and INITGEO set to hooks in the REACTI REACT2 PRODI and PROD2 in the input file u5 INITGEO is set to GEOM and STATUS is set to 2 in START sections in the input file fu5 NWCHEMRATE I O files NWCHEMRATE file names oh5trl 70 esp fu70 Input data for NVCHEMRATE ah5trl 71 esp fu71 Input data for reactant 1 optimization ch5trl 72 esp fu72 Input data for reactant 2 optimization ech5trl 73 esp fu73 Input data for product 1 optimization ch5tr1 74 esp fu74 Input data for product 2 optimization ch5tril dat poly fu5 Input data for POLYRATE ch5tr1 61 esp fu61 POLYRATE output file containing information about the stationary points ch5tr1 fu6 poly fu6 Long output file ch5trl ful5 poly ful5 Summary output file eh5trl rst esp fu84 Restart file written by NVCHEMRATE 48 NWCHEMRATE version 2007 December 26 2007 8 2 6 Test Run ch5tr2 Tunneling Number of levels Hindered rotation IVTST M SCT dual level none off This test run uses the restart file created by the previous run and performs a calculation using the ISPE technique by using eight MP2 6 31G energies input i
33. en the SCF options should be given in the NWRMETHOP section and not here Example NWRSCFOP SCF Maxiter 200 END NWREND NWROPTOP This section lists any options needed for using NWCHEM to optimize geometries The first one should be the selection of either the DRIVER or STEPPER NWCHEM module In the current version NWCHEMRATE does not generate NWCHEM optimization files but rather requires them to be already generated by the user prior to starting NWCHEMRATE This feature will be implemented in the next version of NWCHEMRATE 36 NWCHEMRATE version 2007 December 26 2007 Example NWROP TOP DRIVER MAXITER 100 XYZ INHESS 2 END NWREND December 26 2007 NWCHEMRATE version 2007 37 7 4 3 The NWRREACTI NWRREACT2 NWRPROD1 NWRPROD2 NWRWELLR NWRWELLP NWRSTART and NWRPATH Sections Since in some cases the options selected in the NWRCOMMON section might not be the most useful for all the points to be calculated these eight sections allow us to select different keywords for the energy gradients and Hessian calculations by means of the NWRENER NWRFIRST and NWRSEC list keywords The options for the first reactant should be specified in the NWRREACTI section in the NWRREACT2 the options for the second reactant if it exists in NWRPRODI and NWRPROD2 the options for the first product and if it exists the second one in NWRWELLR the options for a well on the reactant side of the rea
34. for future calculations in the u84 file It should be noted that since no NWCHEM calculations are carried out for the saddle point in this particular run the charge and multiplicity for the nonstationary points along the reaction path must be provided in the START section of the u70 file since the program assumes that these nonstationary points have the same charge and multiplicity as the saddle point NWCHEMRATE I O files NWCHEMRATE file names ch4ohtr4 70 esp fu70 Input data for NVCHEMRATE ch4ohtr4 dat poly fu5 Input data for POLYRATE ch4ohtr4 61 esp fu l POLYRATE output file containing information about the stationary points ch4ohtr4 fu6 poly fu6 Long output file ch4ohtr4 ful5 poly ful5 Summary output file ch4ohtr4 rst esp fu84 Restart file written by NVCHEMRATE December 26 2007 NWCHEMRATE version 2007 55 8 2 13 Test Run ch4ohtr5 Tunneling LCT Number of levels dual level Hindered rotation mode 14 IVTST M off This test run completes a IOC dual level calculation of the CH4 OH CH3 H 0 reaction The lower level information is read from the restart file from the previous run The higher level data is included by means of the u50 file Tunneling is calculated by the microcanonical optimized multidimensional tunneling method muOMT requiring therefore some calculation in the reaction swath region that are not present in the restart file since the tunneling for th
35. hanges or the version of NWCHEM changes or the interface changes Thus the part after the solidus is redundant and may be omitted for brevity Note We sometimes update one or more of the manuals without updating the version number The manual version is determined by the date of its most recent change and is given on its first page Any changes other than the manual s always involve a change in version number of the code December 26 2007 NWCHEMRATE version 2007 63 10 2 NWCHEMRATE REVISION HISTORY This section contains the revision history as of version 2007 December 2007 the first version of the code Version 2007 1 This is the initial release version of NVCHEMRATE 64 NWCHEMRATE version 2007 December 26 2007 11 ACKNOWLEDGMENTS The development of NWCHEMRATE has been supported in part by grants from the U S Department of Energy Office of Basic Energy Sciences which supports research on VTST MT and the Office of Naval Research which supports the development of integrated software tools December 26 2007 NWCHEMRATE version 2007 65
36. he A Wong and Z Zhang NWChem A Computational Chemistry Package for Parallel Computers Version 5 0 2006 Pacific Northwest National Laboratory Richland Washington 99352 0999 USA High Performance Computational Chemistry An Overview of NWChem A Distributed Parallel Application Kendall R A Apra E Bernholdt D E Bylaska E J Dupuis M Fann G I Harrison R J Ju J Nichols J A Nieplocha J Straatsma T P Windus T L Wong A T Computer Phys Comm 2000 128 260 283 2 NWCHEMRATE version 2007 December 26 2007 Table of Contents t Ust Agreement sises T ot alg eee ws sae DT I ND 5 2 Requited Referentes nsns tete erec a divae biduo dhus iip e aides 6 Sx IGECOLUCHOBL ois eb testi teles tuae eas ud p a ce ale ihe RUE 7 d JDuisbribUtotic Cus tetro Coa o pendet inen ees EA he ewes 9 2o MAAS PAULO So eode onore o m is On avere ta etse tuos rompre itr 12 Gz Program DESC TOM oi es ikea ane p bd eee renes es aa tot ere inl ed a asta e lada eaii 13 6 1 Description of NVCHEMRATE Subprograms sseesseeeeenenes 14 6 2 Restarting a Calculations o rotis dede node d rtg on nti made o eO naa 17 6 37 Limitations of NWOHEMRBATE 5 ensscieecru denda mceleudenia i cedi en a Miel iba estie 20 7 Description of Input BESS o e Aonconse sedebat utu tette Mss esc eee E DEM 21 Tl Pale ISAC osea iecit edebat E tests eee utex nt a Dad tego ee 22 Tubs Description of urbe Utilis a eoe qe n to i i dde onda E a oye
37. ion and only the additional input files u70 and fu71 are required The NWCHEMRATE restart option is off since the restart is only available when all the information about the stationary points is read from the restart file or written in it The output file esp u61 will contain the information calculated for this reactant and this information will be included in the u5 input file for the following runs NWCHEMRATE I O files NWCHEMRATE file names ch4ohtr1 70 esp fu70 Input data for NVCHEMRATE ch4ohtrl 7 esp fu71 Input data for reactant 1 optimization ch4ohtrl dat poly fu5 Input data for POLYRATE ch4ohtrl 6 esp fu l POLYRATE output file containing information about reactant 1 ch4ohtrl fu6 poly fu6 Long output file 52 NWCHEMRATE version 2007 December 26 2007 8 2 10 Test Run ch4ohtr2 Tunneling none Number of levels single level M05 2X 3 21G Hindered rotation none IVTST M off This is the second step in the four stage single level calculation for the CH4 OH gt CH H50 reaction The information included in the u61 output file from the previous run is cut and pasted to the u5 input file for the present run The properties of the other reactant OH and the products CH4 and H5O are calculated here Therefore the u5 input file will not contain the START section and the input files u70 u72 u73 and fu74 are required Once again the NWCHEMRAT
38. ions are required the POLYRATE restart is recommended since it is faster than the NWCHEMRATE restart See Section 6 2 of this manual for further information ATOMS The ordering in the ATOMS keyword list of the GENERAL section of the input file for unit fu5 must be consistent with the ordering in unit u75 if this unit is used in the calculation NOSUPERMOL Because of the way the interface is constructed the NOSUPERMOL keyword is required note that SUPERMOL is the default option in POLYRATE Therefore only size consistent methods should be used in NWCHEMRATE Both DFT and MP2 are size consistent December 26 2007 NWCHEMRATE version 2007 25 EZERO Because of the way the interface is constructed the user must use the calculate option for the EZERO keyword of the ENERGETICS section note that calculate is the default option POTENTIAL The hooks option is required if the program will perform any NWCHEM calculations The option can also be unit29 unit30 unit31 or unit40 but the geometries of reactants products and saddle point should be given in fu5 file and keywords INITGEO GEOM and STATUS 2 must be used in order to avoid any NWCHEM calculations OPTTS and OPTMIN In NWCHEMRATE there are two ways to optimize the geometries by means of NWCHEM routines or by means of POLYRATE 9 7 routines The choice between the two methods is made in the OPTIMIZATION section of the fu5 input file Choosing the option BFGs NR
39. ization of reactant 2 if the reaction studied is bimolecular and if such optimization is going to be carried out by means of the NWCHEM program NWCHEM input file for geometry optimization of product 1 if such optimization is going to be carried out NWCHEM input file for geometry optimization of product 2 if the reaction studied has two products and if such optimization is going to be carried out by means of the NWCHEM program NWCHEM input file for geometry optimization of the saddle point or constrained optimization of a reaction path starting geometry if such optimization is desired reserved NWCHEM input file for geometry optimization of a well on the reactant side of the reaction path if it exists and its optimization is going to be carried out by means of the methods in NWCHEM NWCHEM input file for geometry optimization of a well on the product side of the reaction path if it exists and its optimization is going to be carried out by means of the methods in NWCHEM NWCHEMRATE version 2007 December 26 2007 esp esp esp f esp f esp esp esp fu81 u82 u83 fu85 fu86 fu87 NWCHEM temporary input file generated by NWCHEMRATE NWCHEM temporary output file generated by NWCHEM If the NWCHEM calculation fails it can be examined in order to find out why the failure occurred Restart file to be read during a restart calculation see Section 6 1 Restart file to be w
40. l geometries given in the fu71 through fu75 input files and setting INITGEO equal to HOOKS A further explanation of these keywords will be provided below SECOND The calculation of the Hessian matrices can be done by numerical differentiation of the gradients either using the POLYRATE 9 7 methods or the NWCHEM modules The latter option is strongly recommended The choice is made by means of the GHOOK or HHOOK options in the HESSCAL keyword in the SECOND section of the fu5 input file If HHOOK is selected the remaining keywords of the SECOND section are ignored and the Hessian calculations will be controlled by the options selected in the u70 input file If GHOOK is selected the Hessian calculation will be carried out following the options indicated in the SECOND section ignoring the options for the Hessian calculation selected in the u70 input file Although NWCHEM can calculate a Hessian for any of the electronic structure methods available in NWCHEM the option of performing the Hessian calculation using POLYRATE methods is implemented for completeness However the user is advised for efficiency reasons using NWCHEM for the Hessian calculations because frequent system calls can lower the program efficiency when using POLYRATE for the numerical Hessian calculations The user should be aware that analytical Hessian is available in NWCHEM only for certain methods for more details see Section 6 3 For other method NWCHEM
41. l5 ch4ohtr5 ful5 ch4ohtr6 fuld5 chStr1 ful5 ch5tr2 ful5 ch5tr3 ful5 10 NWCHEMRATE version 2007 December 26 2007 ch5tr4 ful5 oh3trl ful5 oh3tr2 ful5 oh3tr3 ful5 oh3tr4 ful5 nh3ohtrl ful5 testrun 2 files checknwr and run all jc and 4 subdirectories ch4oh ch5 oh3 and nh3oh with the input files for the test calculations December 26 2007 NWCHEMRATE version 2007 11 5 INSTALLATION The user should first obtain and install licensed copies of the POLYRATE and NWCHEM packages Next the user should obtain a licensed copy of the NWCHEMRATE package After downloading uncompressing and untarring the file as described in Section 4 the NWCHEMRATE package should appear as a subdirectory of polyrate9 7 There are a few parameters such as NATOMS maximum number of atoms NSDM maximum number of saved points along the minimum energy path and so forth that have to be set large enough to accommodate the system or systems to be studied These variables are set in the include file param inc in the POLYRATE side of the interface The user should consult the POLYRATE manual for additional details The installation of the NWCHEMRATE program is carried out by running a C shell script configure The script will copy the file hooks_nwr wks f to the hooks_mdepnw f file the nw was appended to the file name to avoid potential conflicts with GAUSSRATE will compile the POLYRATE 9 7 files substituting
42. lectronic structure calculations employing density functional theory DFT or Moller Plesset second order perturbation theory MP2 The NWCHEMRATE program follows the POLYRATE hooks protocol which is explained in the POLYRATE manual The hooks protocol means that if an energy a gradient and or a Hessian calculation is required by POLYRATE the program calls the appropriate hooks subroutine which will return the requested information The user may read more about hooks in the POLYRATE manual December 26 2007 NWCHEMRATE version 2007 13 6 1 DESCRIPTION OF NWCHEMRATE SUBPROGRAMS This is a brief description of the NWCHEMRATE subroutines In most of the cases a more detailed description is given in the comment cards at the beginning of the FORTRAN code for each subprogram ehook enatin escener escfirst eSCSEC geoin ghook nwinpfl rdnwout grest headr hhook 14 Equivalent to the ehook subroutine in the POLYRATE hooks For a given set of coordinates it calculates the energy using NWCHEM Calculates the energy for atomic systems Carries out NWCHEM energy calculations using NWCHEM Carries out energy and first derivative calculations using NWCHEM Carries out Hessian calculations using NWCHEM Carries out geometry optimizations using NWCHEM Equivalent to the ghook subroutine in the POLYRATE hooks For a given geometry calculates the energy and first derivatives Creates the NWCHEM i
43. n the esp fu51 input file Of these eight energies two are for products and the saddle point and six are for nonstationary points Since the ISPE technique does not modify the reaction path the calculation can be restarted successfully The user must run the ch5tr1 test run before running ch5t r2 in order to create the restart file to be read ch5t r2 rst which will be a copy of the ch5tri rst file generated by the previous run and located in the same directory NWCHEMRATE I O files ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 ch5tr2 December 26 2007 51 70 72 33 74 dat 61 rst rst fue ful5 old NWCHEMRATE file names poly fub5l esp esp f esp esp esp poly esp poly poly ful5 esp esp fu70 u71 fu72 fu73 fu74 fu5 fuel fu6 fu83 fu84 Input data for ISPE information Input data for NVCHEMRATE Input data for reactant 1 optimization Input data for reactant 2 optimization Input data for product 1 optimization Input data for product 2 optimization Input data for POLYRATE POLYRATE output file containing information about the stationary points Long output file Summary output file Restart file read by NVCHEMRATE Restart file written by NVCHEMRATE NWCHEMRATE version 2007 49 8 2 7 Test Run ch5tr3 Number of levels single level M05 6 31G Tunneling
44. n up any work directories The use of such a file although not necessary is highly recommended A general example is provided in December 26 2007 NWCHEMRATE version 2007 23 the exe directory and each test job see Section 8 also has a jc file that can be used as a template 24 NWCHEMRATE version 2007 December 26 2007 7 2 DESCRIPTION OF Fu5 UNIT A NWCHEMRATE calculation requires some input from input units for POLYRATE At the very least an fu5 input file is required for indicating several options such as electronic degeneracies temperatures for the rate constant calculations etc Therefore an fu5 file must be written just as 1f we were using an analytical potential energy surface If the calculation requires some additional input files the user must provide them following the instructions in the POLYRATE 9 7 manual Here we clarify some points about preparing the input file for unit u5 RESTART If a POLYRATE 9 7 restart run is selected option readful or readful 2 for the RESTART keyword in the GENERAL section the program will not modify any characteristic of the calculated reaction path We therefore advise the user to use only the restart option in NWCHEMRATE controled by the NWRRESTART keyword in NWRGENERAL section of the esp u70 input file until the reaction path calculation is completely converged and all the desired tunneling options are calculated When no more electronic structure calculat
45. nput file for all calculations Reads the output file generated by NWCHEM and extracts the geometry energy and first and second derivatives of the energy with respect to atomic coordinates Reads and writes the information in the restart files of a NWCHEMRATE restart calculation Prints out the program header Equivalent to the hhook subroutine in the POLYRATE hooks For a given geometry calculates the Hessian matrix using either NWCHEM or POLYRATE methods NWCHEMRATE version 2007 December 26 2007 ohook prep prepj rchmul rcodnw redinf rinpnw rlingr rstatnw rdnwtop rdnwmid rdnwmethop rdnwoptop Equivalent to the ohook subroutine in the POLYRATE hooks Optimizes a given initial geometry using either POLYRATE or NWCHEM methods Prepares the calculation and depending on the selected options carries out certain geometry optimizations and Hessian calculations Initialize variables dependent on each stationary point Reads the charge and multiplicity of a system from the NWCHEM output file Reads the input option for the NWCHEM runs from file esp u70 Reads the information about reactants products and saddle point calculated in the prep subroutine Reads the esp u70 NWCHEMRATE input file Utility program for reading in a line of the esp fu70 input file and parsing off comments and extra spaces Reads the input options given in the esp fu70 input file for the stationar
46. ntional TST rate constant without tunneling is calculated NWCHEMRATE I O files NWCHEMRATE file names nh3ohtr1 70 esp fu70 Input data for NWCHEMRATE nh3ohtr1 71 esp fu71 Input data for reactant 1 optimization nh3ohtr1 72 esp fu72 Input data for reactant 2 optimization nh3ohtr1 73 esp fu73 Input data for product 1 optimization nh3ohtr1 74 esp fu74 Input data for product 2 optimization nh3ohtr1 75 esp fu75 Input data for the saddle point optimization nh3ohtr1 77 esp fu77 Input data for the reactant well optimization nh3ohtr1 78 esp fu78 Input data for the product well optimization nh3ohtr1 dat poly fu5 Input data for POLYRATE nh3ohtr1 61 esp fu61 POLYRATE output file containing information about the stationary points nh3ohtr1 fu6 poly fu6 Long output file nh3ohtrl ful5 poly ful5 Summary output file December 26 2007 NWCHEMRATE version 2007 59 8 3 TEST RUN TIMINGS Here are the timings for the test runs in CPU seconds These timings are sum of user and system time on a single processor The following timings apply to version 2007 P9 7 with NWCHEM version 5 0 These calculations are all run on a single processor IBM Regatta Computer IBM BladeCenter With Power4 Processors with AMD Opteron Processors Test run chStr1 13036 5 6985 9 Test run ch5tr2 3 4 1 3 Test run ch5tr3 3143 6 1758 1 Test run ch5tr4 0 1 0 0 Test run oh3tr1 548 3 253 4 Test run oh3tr2 1875 8
47. oducts in the u5 input file as they appeared in the NWCHEMRATE I O files ch4ohtr3 70 ch4ohtr3 dat ch4ohtr3 61 ch4ohtr3 fu6 54 Fu61 output file from the previous run NWCHEMRATE file names esp fu70 esp fu75 poly fub5b esp fu6l poly fu6 NWCHEMRATE version 2007 Input data for NVCHEMRATE Input data for the saddle point optimization Input data for POLYRATE POLYRATE output file containing information about the stationary points Long output file December 26 2007 8 2 12 Test Run ch4ohtr4 Tunneling SCT Number of levels single level M05 2X 3 21G Hindered rotation mode 14 IVTST M off This is the fourth and final step in the four stage calculation for the CH4 OH CH H5O reaction Actually this fourth stage may be considered either as stage 4 of a complete four stage single level calculation or as the fourth stage in five stage dual level calculation In this test run we use the information about the stationary points appearing in the u61 output file from the ch4oht x3 test run and evaluate the reaction path CVT CVT ZCT and CVT SCT rate constants using Euler method We assumed the hindered rotor approximation for treating the lower vibrational mode along the reaction path and we calculated the vibrational frequencies by using redundant internal coordinates The NWCHEMRATE restart option was selected in the fu70 input file writing the information
48. onal Chemistry Package for Parallel Computers Version 5 0 2006 Pacific Northwest National Laboratory Richland Washington 99352 0999 USA High Performance Computational Chemistry an Overview of NWChem a Distributed Parallel Application Kendall R A Apr E Bernholdt D E Bylaska E J Dupuis M Fann G L Harrison R J Ju J Nichols J A Nieplocha J Straatsma T P Windus T L Wong A T Computer Phys Comm 2000 128 260 283 NWCHEMRATE version 2007 December 26 2007 3 INTRODUCTION NWCHEMRATE is a program for the analysis of reactants products and transition states of chemical reactions and for direct dynamics calculations of variational transition state theory VTST rate constants and multi dimensional semiclassical tunneling probabilities using the electronic structure methods in the NWCHEM package to represent the potential energy of interaction and its first and second derivatives whenever they are needed This version 2007 P9 7 NWS5 0 interfaces POLYRATE version 9 7 which is a program for dynamical rate calculations with the electronic structure program NWCHEM any version although version 5 0 or later is recommended Using NWCHEMRATE presupposes that the user has both POLYRATE 9 7 and NWCHEM version 5 0 preferred but any version should suffice on the same computer working properly before attempting to run NWCHEMRATE No part of POLYRATE 9 7 or NWCHEM is contained in NWCHEMRATE or needs to be
49. or EF for the OPTMIN or OPTTS keywords in the OPTIMIZATION section will cause NWCHEMRATE to use the methods native to POLYRATE 9 7 using as starting geometries those in the fu5 input file and controlling the optimization procedure by means of the keywords selected in the OPTIMIZATION section of the u5 input file In these cases the input files u71 through fu75 will not be required The INITGEO keyword needs to take the option GEOM in the REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections of the u5 input file If the option OHOOK is chosen for both the OPTTS and OPTMIN keywords in the OPTIMIZATION section of the fu5 input file NWCHEMRATE will optimize the geometries of the stationary points using NWCHEM according to the options selected in the u70 input file and the u71 u78 input files The initial geometries for the optimization will be those indicated in the u71 fu78 input files and the options selected in the OPTIMIZATION section in the u5 input file will be ignored INITGEO should take the value HOOKS in the REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections of the u5 input file 26 NWCHEMRATE version 2007 December 26 2007 If the user wishes to optimize the stationary points we recommend the use of NWCHEM methods in particular this is accomplished by using the OHOOK option for both the OPTMIN and the OPTTS keyword in the OPTIMIZATION section of the u5 input file using initia
50. or example a task dft energy statement followed by the larger basis set definition Example NWRMID basis library aug cc pVTZ end NWREND NWRMETHOP This list type keyword contains all the options required in the NWCHEM method section This may include special convergence options or method specification options For December 26 2007 NWCHEMRATE version 2007 35 instance when using DFT one would define here the specific exchange correlation method desired One normally would also specify here the multiplicity of the system in those cases where the system is not a singlet but when using NWCHEMRATE this option must not be set Rather the multiplicity statements are inserted automatically by NWCHEMRATE and unpredictable results may be obtained if the user were to also specify the multiplicity in the NWRMETHOP section Also note that when using post HF methods this section refers to the post HF method options and any options required for the SCF calculation should be specified in the NWRSCFOP section Note that only the options should be provided and not the method as this is set with NWRMETHOD keyword Example NWRME THOP XC M05 ITERATIONS 200 NWREND NWRSCFOP NWRSCFOP is a list keyword for specifying any options related to the SCF part of a post HF calculation In all other circumstances this section should be absent If one were only doing an HF SCF calculation instead of post HF calculation th
51. ould be set to HOOKS and the files fu71 fu78 should be the appropriate input files for a NWCHEM optimization The second is by means of the GEOM keyword if a POLYRATE 9 7 optimization BFGS NR or EF options in the OPTMIN or OPTTS keyword in the OPTIMIZATION section or no optimization is going to be carried out In this case the INITGEO keyword needs to be set to GEOM The combination of the keywords INITGEO STATUS and OPTTS and OPTMIN therefore will indicate the procedure of the initial and or optimized geometries for the stationary points The combinations are For optimizing the geometries using the methods in NWCHEM OPTTS and OPTMIN in the OPIMIZATION section have to be set to OHOOKS INITGEO has to be set to HOOKS and STATUS set to 0 in the corresponding REACTI REACT2 PRODI PROD2 WELLR WELLP and or START sections The initial geometries should be provided in the files u71 through fu78 If the geometry optimization of one of the stationary points is not desired the INITGEO keyword should be set to GEOM and the STATUS keyword should be set to 28 NWCHEMRATE version 2007 December 26 2007 the appropriate values in the corresponding REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections of the u5 input file The optimized geometry will be read from the u5 input file For optimizing the geometries using the methods in POLYRATE not recommended OPTTS and OPTMIN in the OPTIMIZATION section should
52. ritten during a restart calculation see Section 6 1 NWCHEMRATE uses the NWCHEM database file to extract the final data after an NWCHEM run This file esp db is however machine readable only Therefore a subsequent NWCHEM job esp fu87 is run in order to convert this file to a human readable format the result of this file is esp fu85 NWCHEM Hessian output file generated by NWCHEM An NWCHEM input file with only two NWCHEM statements restart and task rtdbprint This file must be present in the work directory prior to starting the NWCHEMRATE job although the supplied version of taxi will generate this file if it is missing Note that this file usage is consistent with Section 17 of the POLYRATE manual Note also that esp stands for electronic structure package and fu stands for FORTRAN unit Finally note that esp u76 is reserved for future use In addition there are two additional files to be discussed The first discussed in Section 3 is taxi This shell script is used by NWCHEMRATE to call NWCHEM The second is the job control script the jobname jc file This file prepares an NWCHEMRATE job for execution by making a working directory with a unique name copying all files to the appropriate names and making sure all necessary files are present and all environmental variables are defined It also after the NWCHEMRATE run copies all the relevant output files back to their final destination and clea
53. s gradients and Hessians can be calculated by any of the density functionals in the NWCHEM package or with the MP2 ab initio method In dual level mode the lower level data is calculated by NWCHEM and the higher level data is read in from an external file December 26 2007 NWCHEMRATE version 2007 1 NWCHEMRATE version 2007 provides an interface between two programs POLYRATE version 9 7 by J C Corchado Y Y Chuang P L Fast W P Hu Y P Liu G C Lynch K A Nguyen C F Jackels A Fernandez Ramos B A Ellingson B J Lynch J Zheng V S Melissas J Vill I Rossi E L Coitifio J Pu T V Albu R Steckler B C Garrett A D Isaacson and D G Truhlar University of Minnesota Minneapolis MN 2007 and E J Bylaska W A de Jong K Kowalski T P Straatsma M Valiev D Wang E Apr T L Windus S Hirata M T Hackler Y Zhao P D Fan R J Harrison M Dupuis D M A Smith J Nieplocha V Tipparaju M Krishnan A A Auer M Nooijen E Brown G Cisneros G I Fann H Fr chtl J Garza K Hirao R Kendall J A Nichols K Tsemekhman K Wolinski J Anchell D Bernholdt P Borowski T Clark D Clerc H Dachsel M Deegan K Dyall D Elwood E Glendening M Gutowski A Hess J Jaffe B Johnson J Ju R Kobayashi R Kutteh Z Lin R Littlefield X Long B Meng T Nakajima S Niu L Pollack M Rosing G Sandrone M Stave H Taylor G Thomas J van Lent
54. scribe some effect for example tunneling one can extend the calculated reaction path without having to repeat the calculation of the points included in the previous NWCHEMRATE run One should rename the esp fu84 file provided by the first run as esp fu83 and then run again with the NWRRESTART option on In a similar way if one finds problems in the SCF convergence at some points along the reaction path one can repeat the calculation including some of the options for improving SCF convergence available in NWCHEM without recalculating the well converged points Another possibility is computing one side of the reaction path with one computer or one processor of a December 26 2007 NWCHEMRATE version 2007 17 multiprocessor computer and the other side with a different computer or different processor a new restart file combining the information from both calculations can be constructed by just appending one restart file to the end of the other restart file allowing a calculation using the whole reaction path with no duplication of effort at least in principle in practice due to the different precision of two different machines and round off errors some recalculation might be needed One should be aware though that if a calculation is made using a step size that is too large giving a non converged reaction path a restart calculation using a different step size would probably be unsuccessful since the points along the two reaction
55. st December 26 2007 poly fu6 Long output file poly ful5 Summary output file esp fu84 Restart file written by NVCHEMRATE NWCHEMRATE version 2007 57 8 2 14 Test Run ch4ohtr6 Tunneling LCT Number of levels dual level Hindered rotation mode 14 IVTST M off This test run completes an IOC dual level calculation of the CH4 OH CH H 0 reaction The lower level information is read from the restart file from the ch4ohtr4 run The higher level data is included by means of the u50 file Tunneling is calculated by the microcanonical optimized multidimensional tunneling method muOMT with LCT method being calculated using the LCG4 approach The frequencies are calculated using Cartesian coordinates instead of the set of redundant curvilinear coordinates from the ch4oht r4 run Since the different choice of coordinates does not affect the reaction path calculation the restart option does not prevent us from changing the coordinate system from one run to another The hindered rotor approximation is used for computing the partition function of the lowest vibrational mode The lowest four frequencies are interpolated directly by the IVTST 0 interpolation algorithm The restart file to be read is copied from the ch4ohtr4 rst file generated by the previous run ch4oht r4 The user should therefore run the previous run ch4oht r4 in this set of tests before running this one A new restart file which incl
56. tes with an NWREND line rather than an END line to avoid confusion with NWCHEM blocks that also end with an END statement 32 NWCHEMRATE version 2007 December 26 2007 7 4 1 The NWGENERAL Section The NWRGENERAL section controls NWCHEMRATE s own options There are only four keywords allowed in this section NWRRESTART and NONWRRESTART with NWRRESTART being the default NWPROC and RSTTOL NWRRESTART NONWRRESTART This is a switch keyword that tells the program to check the restart file esp fu83 and search for information about the point to be calculated If it finds the required information about that point the program writes it in the esp fu84 file and uses the stored information instead of calculating it If the information needed is not present in the u83 file NWCHEMRATE runs NWCHEM and writes the NWCHEM output information to unit u84 If NONWRRESTART is selected neither reading file u83 nor writing file u84 will be performed NWPROC NWPROC is the number of processors on which to run NWCHEM Example NWPROC 16 RSTTOL RSTTOL is a variable keyword that must be followed by a real number which is the value of the tolerance in the comparison of geometries between the geometry currently used by NWCHEMRATE and the geometry found in a restart file esp fu83 The meaning of this keyword is explained in detail in Section 6 2 The inexperienced user is advise not to change this value from its default value 1 E 8
57. the NWRRESTART keyword in the NWRGENERAL section of the unit esp fu70 input file The NWCHEMRATE restart option is designed to take advantage of any previous calculations that may have been made on the same system so that the number of NWCHEM calls is minimized As long as the information on the stationary points from previous calculations is still applicable a restart calculation can be made if there is a change in any stationary point input or option the program will not read this information as the results of trying to restart such calculation are unpredictable This restart option allows the user to change any parameter related to the reaction path calculations using as much information as possible from previous calculations Two restart files are used in this kind of restart calculation esp u83 which stores the information to be read as originated in a previous NWCHEMRATE calculation and esp fu84 where the useful information read from esp fu83 is stored along with the information calculated for the first time in the present NWCHEMRATE run esp fu84 is the file to be used for future restart runs The esp fu84 file has to be created by NWCHEMRATE so if the program finds that this file exists it will stop to prevent overwriting a restart file One important practical point related to this restart option is that if one finds that the range of the reaction path calculated in a NWCHEMRATE run is not large enough to de
58. the hooks f file of standard POLYRATE by hooks_nwr f and hooks_mdepnw f and will create the executable file nwrate exe in the exe subdirectory of the polyrate9 7 directory The executable nwrate exe will then be accessible for all the NWCHEMRATE calculations In Section 9 the computers and operating systems are listed on which the code has been tested The installation of NWCHEMRATE on other platforms should be straightforward requiring only changes in the compiler and loader options in any one of the compilation scripts Before running NWCHEMRATE one line of the C shell script taxi should be changed as described in Section 1 The user needs to set the nwpath variable to the appropriate path where NWCHEM is located Likewise one can also change the scratchdir from the working directory to one s own scratch space 12 NWCHEMRATE version 2007 December 26 2007 6 PROGRAM DESCRIPTION NWCHEMRATE program performs direct dynamics calculations by variational transition state theory with multidimensional tunneling contributions VTST MT Full details of VTST MT are given in the POLYRATE manual and in Variational Transition State Theory with Multidimensional Tunneling A Fernandez Ramos B A Ellingson B C Garrett and D G Truhlar in Reviews in Computational Chemistry Vol 23 edited by K B Lipkowitz and T R Cundari Wiley VCH Hoboken NJ 2007 pp 125 232 The potential energy surface is obtained directly by e
59. tion can be carried out using reactants and or products If the well is ignored then since for bimolecular reactions or bimolecular sides of the reaction path the interpolation is based on an Eckart potential no point on the reactant side of the reaction path can be used that has an energy lower than the reactants energy and no point on the product side can be used that is more stable than the products 40 NWCHEMRATE version 2007 December 26 2007 The IVTST M algorithm has been implemented to be used with the hooks and the electronic structure input files unit fu30 fu31 and fu40 The method is fully operational when using the hooks and the unit fu31 input file When using units fu30 and fu40 only the IVTST M default options are available To use the IVTST M algorithm with unit fu30 LOPT 2 must be set equal to 1 and with fu40 MAXLPTS must be set equal to 1 Therefore we recommend users to use an fu31 input file instead of fu30 and fu40 files The first way to perform IVTST M calculations in NWCHEMRATE is to use electronic structure input file fu30 fu40 or fu31 fu31 is recommended This method is described fully in the POLYRATE manual The input file fu31 can be generated by a preliminary run with the keyword writefu31 in the General section In this preliminary run one only needs to use a very small range of s to get some points along the reaction path that will be used for interpolations in IVTST M The second way to perform
60. tion is stored in the oh3tr2 rst file than is required for the calculation the restart file created by this test run oh3tr3 rst will be smaller than the file oh3tr2 rst This is the reason why it is convenient to keep the file from which a restart calculation reads the information in the executable scripts of these test runs such files are renamed with the extension old No NWCHEM calculations are needed for this test run so it is the fastest test run of the suite NWCHEMRATE I O files NWCHEMRATE file names oh3tr3 70 esp fu70 Input data for NVCHEMRATE GB3EES 75 esp fu75 Input data for the saddle point oh3tr3 dat poly fu5 Input data for POLYRATE oh3tr3 61 esp fu l POLYRATE output file containing information about the stationary points oh3tr3 fu6 poly fu6 Long output file oh3tr3 fu15 poly ful5 Summary output file oh3tr3 rst old esp fu83 Restart file read by NVCHEMRATE Gh8tr3 rst esp fu84 Restart file written by NVCHEMRATE 46 NWCHEMRATE version 2007 December 26 2007 8 2 4 Test Run oh3tr4 Tunneling Number of levels Hindered rotation IVTST M SCT single level MP2 6 31G none off This is a test run that uses the MP2 method for direct dynamics with NWCHEMRATE The reaction path is calculated between 0 60 Angstrom and 0 60 Angstrom Nonredundant internal coordinates are used for describing the vibrations The geometries of stationary points are provided in the fu5 inp
61. udes all the previous information plus the additional calculations needed for estimating the LCT tunneling is generated by this test run NWCHEMRATE I O files NWCHEMRATE file names ch4ohtr6 70 esp fu70 Input data for NVCHEMRATE ch4ohtr4 rst esp fu83 Restart file read by NVCHEMRATE ch4ohtr6 dat poly fu5 Input data for POLYRATE ch4ohtr6 50 poly fu50 Additional input data for the POLYRATE VTST IC calculation ch4ohtr6 61 esp fu l POLYRATE output file containing information about the stationary points ch4ohtr6 fu6 poly fu6 Long output file ch4ohtr6 ful5 poly fulb Summary output file ch4ohtr6 rst esp fu84 Restart file written by NVCHEMRATE 58 NWCHEMRATE version 2007 December 26 2007 8 2 15 Test Run nh3ohtr1 Tunneling none Number of levels single level B3LYP 3 21G Hindered rotation none IVTST M off This is a test run for the NH3 OH NH H50 reaction including wells on the reactant and product sides The geometries are optimized by NWCHEM Therefore the initial geometries and keywords for the optimization are given in the input files esp fu71 75 esp u77 and esp fu78 and INITGEO is set to hooks and STATUS to 0 in the REACTI REACT2 PRODI PROD2 WELLR WELLP and START sections of the u5 input file The Hessian matrices are also calculated as recommended using NWCHEM With the information for the stationary points obtained in this way a conve
62. ut file Because the current version of NWCHEM cannot perform a calculation for the one electron hydrogen atom when specifying any post HF method in the NWCHEM input file the PROD 1 hydrogen atom is calculated at the HF level although MP2 method is specified in 70 file NWCHEMRATE I O files O y W O y W tr4 tr4 1 70 l dat 61 fu6 ful5 L rst December 26 2007 esp fu70 poly fu5 esp fu61 po po ly fu6 ly ful5 esp fu84 NWCHEMRATE file names Input data for NVCHEMRATE Input data for POLYRATE POLYRATE output file containing information about the stationary points Long output file Summary output file Restart file written by NVCHEMRATE NWCHEMRATE version 2007 47 8 2 5 Test Run ch5tr1 Tunneling SCT Number of levels single level M05 6 31G Hindered rotation none IVTST M off This sample run for the reaction CH3 H5 CH4 H is based on the test run ch5fu30tr5 included in the POLYRATE 9 7 test suite It performs calculations of the TST CVT and ICVT rate constants and it is based on following the reaction path using the Euler steepest descents method also called Euler single step method For all of the stationary points symmetry is employed in all the NWCHEM calculations which is the default for NWCHEM calculations nevertheless this option is turned off when calculating points along the reaction coordinate in order to avoid possible probl
63. which geometries energies gradients and Hessians are available and 48 points which is 54 minus 6 for which only geometries energies and gradients are available The method employs different approaches for the interpolation of Vygp s depending on the number of reactants and products in the reaction If the reaction is unimolecular in either the forward or reverse direction a cubic polynomial for estimating 10 energies between the reactant or product and the first or last point on the reaction path or between the reactant and the first point and between the product and the last point is calculated before carrying out the spline under tension fit The user can choose not to calculate the 10 extra energies however the default is to calculate them If the forward reaction is bimolecular the interpolation on the reactant side of the saddle point is based on the energies from the input plus 10 additional energies estimated from an Eckart polynomial with a range parameter which is a function of s Similar considerations apply on the product side if there are two products If there are wells on the reactant and or product side the interpolation can be done using the information on these stationary points with the unimolecular procedures which at least in principle can make the interpolation more accurate especially when the well is deep and or close to the saddle point But if a well is present it can also be ignored and the interpola
64. y be implemented in future versions Example NWRMETHOD DFT NWRTOP This is a list type keyword and therefore it must include an NWREND line to indicate the end of the list see the POLYRATE manual for a description of list keywords NWRTOP includes many of the keywords that NWCHEM will use for carrying out an energy calculation Everything here will be written before NWCHEMRATE writes the geometry and method sections 34 NWCHEMRATE version 2007 December 26 2007 Example NWRTOP memory 24 mw echo basis library 6 311 g3df_3pd usr local nwchem nwchem 5 0 data libraries end NWREND Note that in NWCHEM the backslash V at the end of a line concatenates the current line with the next This can be very useful as the maximum line length in NWCHEMRATE is 80 characters NWRMID This optional list type keyword contains any part of the NWCHEM input file that may come between the geometry and methods sections which are automatically generated by NWCHEMRATE and the final NWCHEM task statement The use of the NWRMID keyword is probably rare but occasionally necessary For instance one may want to do a single point energy calculation in a smaller basis set before any calculation in a larger basis set This is often required for example in order to improve SCF convergence when using large basis sets In such a situation the smaller basis set would go in the NWRTOP section while the NWRMID section would include f
65. y points Reads the NWCHEM input file section that precedes the geometry Reads the NWCHEM input file section that after the geometry but before the NWCHEM task statement s Reads the NWCHEM options for the method dft scf ccsd etc section of the NWCHEM input file Reads the NWCHEM options for the geometry optimization section of the NWCHEM input file December 26 2007 NWCHEMRATE version 2007 15 rdnwscfop rgennw secin setup store Reads the NWCHEM options for the scf section of the NWCHEM input file for post Hartree Fock methods Reads the general NVCHEMRATE options Carries out NWCHEM Hessian calculations for stationary points Initializes some variables and calls the subroutines for reading in the esp fu70 input file Stores some information that could be useful in future calculations in order to avoid duplicate NWCHEM calls Note that NWCHEMRATE does not use any of the utility routines routines starting with y of the generic hooks package of POLYRATE 16 NWCHEMRATE version 2007 December 26 2007 6 2 RESTARTING A CALCULATION The NWCHEMRATE restart option should not be confused with the POLYRATE restart options see Section 7 C of the POLYRATE manual The POLYRATE restart options can be used with NWCHEMRATE but NWCHEMRATE also has its own unique restart capability The rest of this section concerns this NWCHEMRATE restart capability The NWCHEMRATE restart option is controlled by

Manual NWCHEMRATE – version 2007

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Manual NWCHEMRATE &ndash; version 2007

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Manual NWCHEMRATE – version 2007