Revision History - Climate & Space Research
Contents
1. The only drawback to using very large numbers of array elements is that the execution time increases as more energy grains have to be visited via collisions in the lower half of the double array Note that Egrain1 Imax1 and Isize must still be identical for all of the wells and transition states in a given model just as in previous versions of MultiWell 4 MultiWell enhancement The multiwell out and multiwell sum output formats have been changed slightly The fractional abundance of each well is now reported with 4 significant digits instead of 3 while the statistical errors are now reported with 2 significant digits instead of 3 5 MultiWell enhancement lower case time and coll keywords are now accepted 6 DenSum enhancement this version now lists in densum out the lowest values of Imax1 index number of the highest element in the lower portion of double arrays and corresponding energy where the maximum relative fluctuations in state density are always below 1 2 3 4 and 5 If the fluctuations are not small the extrapolation and interpolation routines are not accurate Relative 15 MultiWell Program Suite Revision History fluctuations are defined by the following where pi and pi 1 are adjacent elements in the array of densities of states Ap i Pi Pil P P b This version automatically gives a non fatal warning on the terminal screen and in the title line of the species dens output fil2. have resulted in errors in the sums of states of as much as 5 10 at energies near and above the dissociation limit These bugs have been fixed DenSum new feature a new type of degree of freedom kro has been defined in order to calculate sums and densities of states when the K rotor is included as an active quantized degree of freedom According to this feature the K quantum number is restricted to the 2J 1 values in the range from J to J for a specified value of J Normally we recommend the pragmatic approximation that the K rotor be treated as an ordinary quantized or classical 1 D rotor with quantum number K that is restricted only by conservation of energy dens output file which is used as input by MultiWell has been modified to include a succinct summary of the input data and the DenSum version number This helps users keep a better record of the vibrational assignments used to generate sums and densities of states This new version of the MultiWell master equation module is compatible with both the old format and this new one DenSum new feature It is now possible to run DenSum in a batch mode in which calculations can be carried out all at one time for multiple species with a minimum amount of effort This feature is useful when changing the energy grain or array boundaries for a complicated chemical system See the MultiWell User Manual for details 14 MultiWell Program Suite Revision History NEW IN VER
3. the new format is not compatible with previous data files Enhancement Thermo now reports A H 298 15 K and A G 298 15 K for each chemical species It also reports AGreaction at every temperature Enhancement Thermo now reports the electronic partition function Qel as a function of temperature The non integer Qel can be used for input in MultiWell instead of the integer electronic degeneracy previously required Other Changes 12 MultiWell Program Suite Revision History 1 The default compiler has been changed from g77 to gfortran GNU The g77 compiler is now considered obsolete and gfortran is currently supported by the GNU software project Of course other fortran compilers may be used instead 2 User Manual updated to include a more complete discussion of simulating the competition between unimolecular and bimolecular reactions NEW IN VERSION 2008 3 May 2008 1 MultiWell Revision the maximum array size Imax and lsize was reduced from 20000 to 14000 array elements to allow for storage limitations on some computer platforms 2 MultiWell Revision the code was revised so that it reports the same kinf k high pressure rate constant whether or not centrifugal corrections are selected Note that kinf is formally identical to the canonical transition state theory rate constant NEW IN VERSION 2008 2 March 2008 1 A minor bug resulted in incorrect calculated A factor and activation energy for kinf al
4. and densities of states that were only 58 of the correct values This error has been now been fixed DenSum revision Previously classical rotations and translations were treated using a semi classical approximation where the sum of states at E 0 was set to unity This has been changed so that they are treated as purely classical the sum of states is zero at E 0 This revision will have negligible effects for most 17 MultiWell Program Suite Revision History users MultiWell revision subroutines Colnorm and Colstep were revised to improve accuracy of collisional energy transfer at low energies The revised subroutines are less unstable and produce thermal energy distributions that are more accurate than previous versions This revision is expected to affect unimolecular decay constants and fractional yields by up to 10 20 depending on the system MultiWell revision when tunneling or slow IVR are not invoked the k E array at energies below the critical energy and the IVR coefficient array are empty set equal to zero The empty portions of these arrays are no longer included in the output files since they were just a waste of space Gauss2Multi Bug Fix the code has been revised so that it now works properly for atoms and linear molecules as well as for non linear polyatomics NEW IN VERSION 2 03 August 2006 1 MultiWell Bug Fix in ratearray f The barrier to reaction in the reverse direction was improperly
5. anharmonic non separable vibrations Three practical algorithms programs for calculating densities of states for fully coupled non separable vibrations have been added to the MultiWell Program Suite This new capability is an important advance beyond separable models which up until now were the standard for RRKM and master equation calculations The three algorithms are compared with each other and with accurate benchmarks in a new manuscript which has been submitted for publication available by request Program doloops exact counts of states for small molecules 3 4 atoms Program adensum an automated version of the Wang Landau and Basire et al random walk algorithm for computing approximate sums and densities of states Appropriate for most molecules 24 atoms Program ansum uses an efficient Monte Carlo algorithm for computing approximate sums and densities of states Appropriate for small molecules 3 6 atoms New code Program lamm computes the effective mass or reduced moment of inertia for large amplitude motions as a function of the internal coordinate e g dihedral angle This implementation of lamm is for non rigid hindered internal rotation The results are used with the flexible hindered internal rotor option type hrd which is already available in DenSum and Thermo for computing sums and densities of states DenSum and thermodynamic functions Thermo from the energy eigenvalues which are obtained by diagonal
6. calculated in the last version This only affected simulations that calculated tunneling corrections to k E MultiWell revision in ratearray f The calculation of k E was modified when the density of states of the reactant is less than a fixed constant DScrit 0 000001 Egrain1 Thus in the sparse density of states regime if an energy grain does not contain a reactant state k E is set to zero This change applies for k E calculated using both the tunneling and the non tunneling subroutines It protects against numerical overflow and unrealistic values for k E in reactions that have low energy barriers and very sparse densities of states MultiWell maintenance in ratearray f The calculation of the reverse reaction rate constant was changed when tunneling is used so that the tunneling modified sum of states of the transition state calculated for the forward direction is stored in an array and not re calculated when computing the reverse reaction rate This reduces execution times MultiWell maintenance in multiwell f A fatal error is now returned when the CENT and TUN keywords are used simultaneously This is because the tunneling subroutine is implemented only for reactions without centrifugal corrections This change will have little practical effect in simulations since tunneling is important only for tight transition states where centrifugal corrections are not important and centrifugal corrections are important only for loos
7. effect when tunneling was not chosen 2 MultiWell Bug Fix corrected error in calculated reverse reaction threshold energy in subroutine ratearray f This error affected the magnitude of the tunneling transmission coefficients calculated in eckart f The magnitude of the difference in the transmission coefficient between the new version and the earlier version depends on the enthalpy of the reaction and the reaction threshold energy This bug had no effect when tunneling was not chosen 3 Gauss2Multi Bug Fix minor bug fix to account properly for the Gaussian key word RESTART VERSION 2 01 April 2006 1 MultiWell Bug Fix corrected error in calculated strong collider low pressure rate constant 2 MultiWell maintenance modified subroutines colnorm f and colstep f to improve their accuracy when exceptionally large energy transfer step sizes are specified These changes will result in small changes in the calculated pressure dependence for all step sizes VERSION 2 0 March 2006 40 MultiWell Program Suite Revision History 3 MultiWell Program Suite User Manual New the README files for the four components of the MultiWell program Suite and the Frequently Asked Questions FAQ have been consolidated in a User Manual distributed as a pdf file 4 New gauss2multi New this new code contributed by Andrea Maranzana reads GAUSSIAN output files and automatically stes up data files for Momlinert DenSum Thermo and
8. includes the ratio of the moments of inertia of the transition state and reactant when using the Inverse Laplace Transform ILT method for calculating k E s It is assumed that the ratio of moments of inertia has been included in the A factor which is required input for the ILT method Revision execution is now stopped and fatal errors are reported when incompatible combinations of key words and input data are entered These include the following incompatible combinations ILT and CENT ILT and TUN RKE and TUN CENT and TUN CENT and TSmom 0 0 moment of inertia of transition state Bug Fix fixed a small bug in the part of Estart f that selects initial active energies Occasionally initial energies were chosen in low energy grains that 11 MultiWell Program Suite Revision History did not contain any states This bug had very little effect since a test is applied and corrections are made for energies in empty grains each time a collision step size is selected in subroutine colstep Changes to DenSum 1 Enhancement now uses exact within 1 cm energy eigenvalues for one dimensional hindered rotors Can treat both symmetrical and unsymmetrical rotors For symmetrical rotors this change results in only small changes in the sums and densities of states the previous approximate method was quite accurate for symmetrical rotors Enhancement information on molecular free rotations internal and external can now be
9. input in any of four equivalent forms moment of inertia in units of amu A or g cm rotational constants in units of cm or MHz All of the rotational information except for hindered internal rotors in a Densum data file must use the same form of input Changes to Thermo 1 Enhancement now uses exact within 1 cm energy eigenvalues for one dimensional hindered rotors when computing the partition function Can treat both symmetrical and unsymmetrical rotors For symmetrical rotors this change results in only small changes in the sums and densities of states the previous approximate method was quite accurate for symmetrical rotors Enhancement information on molecular rotations internal and external can now be input in any of four equivalent forms moment of inertia in units of amu or g cm rotational constants in units of cm or MHz All of the rotational information except for hindered internal rotors for a single chemical species must use the same form of input Different species in the same Thermo data file may use different forms of input Enhancement instead of the molecular weight it is now required that the empirical formula be input This enables Thermo to calculate the molecular weight and to report the AfH 298 15 K and A G 298 15 K for each species Common isotopes of major elements can be entered individually See the User Manual for details This change has resulted in a change in the data file format
10. set equal to A inf 4 MINOR FORMAT CHANGES MultiWell the moment of inertia for the 2 dimensional adiabatic external rotation has been re labeled in the output files in order to avoid confusion with the rotational quantum number 5 MORE EXAMPLES more examples have been included Test data sets for DenSum taken from the literature have been added to the examples directory NEW IN VERSION 1 2 3 SEP 2002 1 BUG FIX in MultiWell fixed bug in bookkeeping subroutine that gave anomalous reaction at very short times when the collision frequency was much smaller than all of the k E s This bug may have had a small effect on low pressure fall off calculations 2 BUG FIX in Densum fixed bug that prevented calculation using Whitten Rabinovitch approximation This bug was probably introduced in version 1 1 2 It had no effect on the exact count option 3 BUG FIX in MultiWell fixed bugs related to reading a file containing Pstart the initial cumulative energy distribution function NEW IN VERSION 1 2 2 MAY 2002 1 BUG FIX Revised averaging of kuni so that only one sample per time bin per 23 MultiWell Program Suite Revision History trial is included in the average The previous algorithm resulted in over weighting faster k E s and gave erroneously high average kuni values reported in multiwell out NEW IN VERSION 1 2 1 MARCH 2002 1 BUG FIX in Thermo vibrational state degeneracies were not handled correctly when n
11. transition frequencies This feature is useful when using observed fundamental frequencies and estimated anharmonicities NOTE THIS NEW OPTION AFFECTS ONE LINE OF THE DATA FILE 6 BUG FIX MultiWell the centrifugal corrections to k E and k inf were revised They now correspond to Equations 4 31 and 4 30 respectively in P J Robinson amp K A Holbrook Unimolecular Reactions Wiley London 1972 The threshold energy including the centrifugal correction for each reaction is listed in file multiwell array above the column of k E values for each reaction Eo Rot A future version will incorporate a more accurate representation of centrifugal effects 7 BUG FIX DenSum and Thermo bugs were fixed in the sums and densities of rotational and hindered rotor states and the corresponding partition functions NEW IN VERSION 1 1 1 JULY 2001 Note that all revised codes are compatible with the previous data file formats BUG FIXES 1 Collision frequency error of 0 6 in MultiWell f 2 Chemical activation option in MultiWell f ENHANCEMENTS MultiWell 25 MultiWell Program Suite Revision History 1 Numerous minor output format revisions were made to improve clarity and convenience 2 The vibrational population distribution that is output in file MultiWell DIST was revised to give instantaneous snapshots of the population distribution Previously the distribution was obtained by averaging over the entire
12. we needed to use more grid points in order to achieve the desired accuracy at very high eigenvalue energies As a result we increased the number of grid points from 201 to 501 This slows down execution times but achieves better accuracy at high energies The eigenvalues at lower energies were already quite accurate and thus this change had very little effect on practical calculations Thanks go to the MESMER Team for participating in this master equation inter comparison MEIC activity For more information about the MEIC activities contact jroarker umich edu Only the above programs were modified for this particular release NEW IN VERSION 2014 January 2014 1 MULTIWELL Bug Fix when densities of states are sparse e g for small molecules at low energies tunneling from one Well to another was allowed to take place even when tunneling into an energy grain that did not contain a state an empty grain In this event the stochastic trial did not terminate correctly This problem has now been addressed by forbidding tunneling into an empty grain and issuing a warning in the rate constant tables in the output files However note that this pragmatic fix 1 MultiWell Program Suite Revision History does not address the more fundamental problem that wells connected by tunneling should possess states in matching energy grains Fortunately the effects of this problem are small except at very low energies in very small mol
13. MUST BE ADDED TO LINE 15 FOR EACH FORWARD REACTION NEW IN VERSION 1 1 3 NOVEMBER 2001 1 BUG FIX minor bugs in the hindered rotor subroutines were fixed in Thermo and in DenSum The bugs prevented execution on some platforms MultiWell itself was not affected NEW IN VERSION 1 1 2 SEPTEMBER 2001 24 MultiWell Program Suite Revision History 1 For convenience input and output file names were changed to all lower case 2 NEW OPTION MultiWell and Thermo energies can be read in units of cm 1 kJ mole or kcal mole Previous versions were only capable of reading the latter two units 3 NEW OPTION MultiWell the maximum time simulated can be specified directly or it can be specified as a maximum number of collisions key word TIME or COLL This feature is particularly useful for efficient calculation of fall off curve and other pressure dependent quantities NOTE THIS NEW OPTION AFFECTS THE LAST LINE OF THE DATA FILE 4 NEW FEATURE MultiWell output file multiwell is generated that gives all of the header material in the full output file but instead of the time dependent results gives only the final results of each simulation in the form of a summary table This feature is particularly convenient for calculating fall off curves and other pressure dependent quantities 5 NEW OPTION DenSum and Thermo by specifying a key word HAR or OBS vibrational frequencies can be input as harmonic or as observed 0 1
14. MultiWell See the MultiWell Program Suite User Manual for details 5 MultiWell New quantum mechanical tunneling transmission coefficients for the Eckart unsymmetrical barrier can now be included in k E The data file multiwell dat format has been revised and a KEYWORD is used for this purpose 6 MultiWell New The enthalpy of final products is now entered in the data file This feature is used with the new tunneling feature 7 MultiWell New The effects of slow intramolecular vibrational energy redistribution IVR on k E can now be included 8 MultiWell New Two new collision models have been added see MultiWell Program Suite User Manual for info a Exponential Model with Alpha E linear exponential b Exponential Model with alpha E switching function 9 MultiWell Maintenance Revision Subroutine gkinf f was revised to improve its accuracy in calculating k infinity 10 MultiWell Maintenance Revisions subroutines Estart Pdown Colnorm and Colstep were revised to improve accuracy of the initial distribution and of energy transfer at low energies The revisions also ensure that the selected energies are aligned with energy grains at energies below Emax1 11 MultiWell Maintenance Revisions subroutine qudint f converted to linear instead of quadratic interpolation in order to improve stability in Colnorm f and Colstep f numerical integrations 12 MultiWell Bug Fix the conversion factor for converting k
15. MultiWell Program Suite Revision History If you notice surprising behavior it may indicate a bug Please let us know right away We try very hard to fix bugs as soon as we know about them and then post the latest MultiWell release on the website THANK YOU FOR REPORTING BUGS NEW IN VERSION 2014 1 June 2014 1 MultiWell new feature by optionally adding a single keyword energy transfer is treated in the traditional manner instead of the default which is to attenuate the inelastic collision frequency and hence the rate of energy transfer at low energies where the densities of states are very sparse see J R Barker Int J Chem Kinetics 41 748 2009 The traditional method was based on the convenient assumption that the inelastic collision frequency is independent of internal energy This feature facilitates inter comparisons between multiwell and other master equation codes DENSUM new feature an additional output file is now generated by the code densum lev This file summarizes all of the energy levels utilized in computing the sums and densities of states for each built in quantized degree of freedom vibration particle in a box free rotation and hindered rotation LAMM Improvement the output was revised in order to write out more significant digits Hindered Rotor Treatment Improvement From a comparison between the hindered rotor treatments in MultiWell and MESMER it was apparent that
16. SION 2 08 February 2007 a Gauss2Multi Bug Fix when compiled with older versions of the GNU GCC compiler this module sometimes did not execute correctly This bug has been corrected b MultiWell Bug Fix Previously the tunneling correction was not correct when the energy grain size was not an integer multiple of 1 0 e g 1 0 3 0 10 0 etc This error only affected k E significantly in the lower portion of the double array when Egrain1 was not an integer e g if Egrain1 2 45 then the value was truncated to 2 0 before calculating the tunneling correction This bug has been fixed 2 MultiWell Bug Fix Previously in simulations at zero pressure zero collision frequency an error could occur if the energy in a well was below all of the reaction thresholds for that well zero rates of reaction For this condition the sum of the rates of all processes is equal to zero but MultiWell would erroneously report reaction via the channel with the lowest index number This error probably affected very few users This bug has been fixed 3 MultiWell enhancement This version of the MultiWell Suite should give the same results as v 2 07 but it is now much simpler to change Isize the dimension of the double arrays in MultiWell since it is no longer necessary to recompile the code in order to do so Now Isize can be set at any value up to 20000 array elements This makes it possible to use a very small grain size up to high energies
17. cal mole to kJ mole was corrected from 4 1855 international calorie to 4 184 thermochemical calorie This correction also affected conversion from kcal mole to cm units 13 MultiWell Deleted option to use the Whitten Rabinovitch method for calculating sums and densities of states within MultiWell It is still possible to use DenSum to calculate sums and densities of states via the W R approximation if desired In short parameters related to the Whitten Rabinovitch method for calculating densities of states are no longer input 20 MultiWell Program Suite Revision History 14 MultiWell Deleted the un tested feature that was intended to enable one to include elastic collisions has been removed because it did not work correctly 15 DenSum New added the capability to calculate sum and density of translational states new type of degree of freedom trn This enables one to use Densum to calculate microcanonical k E s for bimolecular reactions which can in turn generate microcanonical pseudo first order reactions for use in MultiWell See the MultiWell Program Suite User Manual for details 16 DenSum Maintenance Revision Densities of states are now calculated using double sided numerical finite differences instead of the single sided differences used earlier originally described by Stein and Rabinovitch This change does not affect the sums of states but may affect calculated densities of states by 1 2 17 Ther
18. ces initial population in energy grains where k E 0 NOTE no other changes were made in this release Thus DenSum Mominert Thermo and Gauss2Multi are still version 2 06 NEW IN VERSION 2 06 January 2007 1 MultiWell Bug Fix An indexing error in multiwell 2 05 resulted in erroneous identification of the reaction channel in some multi channel simulations This bug was not present in previous versions and had no effect on single channel reactions but it could have affected some multi channel simulations 16 MultiWell Program Suite Revision History NEW IN VERSION 2 05 December 2006 2 MultiWell Bug Fix A subtle error became apparent when using chemact at very low pressures in MultiWell The error was due to an array element index error that in effect shifted the initial energy distribution to lower energy by an amount equal to Egrain1 In tests using models of the Cl NO2 and CIO CIO recombination reactions at 300 K this resulted in about 0 01 of the initial energies being selected erroneously below the dissociation energy of the reaction forming the chemically activated intermediate The error first became noticeable at k k lt 10 and resulted in k k approaching a constant value at very low pressures It is possible that this bug has lurked in the bowels of MultiWell since its early days It has now been fixed In addition the rate constants at energies in the lower half of the double array are now treate
19. d as constant within each energy grain Egrain1 instead of using linear interpolation within the grain Linear Interpolation is still used at energies in the upper half of the double array For k k gt 10 this bug fix is expected to affect results by no more than 10 25 in most models the relative effects are larger at k k lt 10 3 MultiWell Revision because densities of states are not calculated at reactant active energies greater than Emax2 and densities at higher energies are obtained by extrapolation the k E values at the higher energies are not accurate Previously the higher energy k E values were printed in the output file To eliminate the chance that the inaccurate k E values at high energy might be taken seriously the output has been revised so that k E is not calculated at energies higher than is the reactant state density but is instead set equal to 1 e 20 This revision will have no effect on any aspect of the calculations other than the listing of k E in the multiwell array output file NEW IN VERSION 2 04 December 2006 1 DenSum Bug Fix Previously the qro quantum rotations option worked properly for 2 D rotors but not for other dimensions Essentially instead of the correct symmetry number sig was replaced by sig d 2 where d rotor dimension The effect of this error depends on the symmetry number and on the dimensionality of the rotor For a 3 fold 1 D internal rotation it gave sums
20. data filename was broken in a previous revision although the default filename multiwell dat still worked correctly This bug has been fixed 5 MULTIWELL enhancement The centrifugal corrections were extended to include up to three adiabatic rotors as in spherical tops like methane by using Keyword CENT3 When CENTS is invoked none of the external rotors is active and none should be included with the vibrations when computing the sum and density of states 6 MULTIWELL enhancement The numerical integration subroutines used to compute the informational k and kose high and low pressure limiting rate constants were improved significantly Depending on the temperature and the energy grain in the upper part of the double arrays k inf and kosc printed in the table describing the transition states were in error by amounts varying from 1 up to nearly a factor of x2 The largest errors occurred when the maximum energy in the lower part of the double array Emax1 was less than kT and at the same time the energy grain in the upper part of the double array Egrain2 was a substantial fraction of kT The code has been revised in order to greatly reduce the dependence on user choices for energy For best accuracy Egrain1 should be smaller than 10 of kT 5 to 10 cm is usually a good choice and the double arrays should be constructed so that Egrain2 is less than kT 2 7 SCTST bug fix A minor bug resulted in a very small error in the c
21. e the 11 MultiWell Program Suite Revision History are still named multiwell xxx where xxx out etc just as in previous versions See Section 2 5 of the latest MultiWell User Manual for details MultiWell Bug Fix the lower energy limits of the numerical integrations for kinf and kO high and low pressure limiting rate constants were Egrain1 in energy below the correct values This caused very small errors typically lt 0 5 in the calculated values for the limiting rate constants Thermo new feature introduction of new types of degrees of freedom gor and fit enables Thermo to find the hindered Gorin model that fits a user supplied recombination rate constant Three new examples illustrating the use of this feature were added to directory examples thermo examples See the User Manual for details DenSum Bug Fix when quantized rotation qro was selected DenSum incorrectly neglected all rotor levels except the zero point level in the lowest energy bin densities of states in all other energy bins were correct This error has been fixed DenSum Bug Fix for Morse oscillators the quantum number for the highest bound state was erroneously calculated to be about one state higher than it should have been This bug had only a small effect at high energies and probably was negligible in most applications In addition there was a bug in the way anharmonicity was included For strongly anharmonic molecules this bug may
22. e transition states where tunneling is not important In a multichannel model it is still possible to designate centrifugal corrections keyword CENT for some reactions e g barrier less reactions while designating no centrifugal corrections keyword NOCENT for others 18 MultiWell Program Suite Revision History NEW IN VERSION 2 0 March 2006 2 03 August 2006 This is a major upgrade We recommend that all users stop using older versions and use the latest version even though it may require revising some input data files The items marked with an asterisk have necessitated changes in the input data files See the MultiWell Program Suite User Manual for details Please use the following citations to acknowledge results obtained using this version of the MultiWell Program Suite a MultiWell 2 03 Software 2006 designed and maintained by John R Barker with contributions from Nicholas F Ortiz Jack M Preses Lawrence L Lohr Andrea Maranzana and Philip J Stimac University of Michigan Ann Arbor MI http aoss engin umich edu multiwell b John R Barker Int J Chem Kinetics 33 232 45 2001 VERSION 2 02 July 2006 1 MultiWell Bug Fix modified subroutine eckart f so that tunneling corrections to k E terminate properly for both endothermic and exothermic reactions and for reactions with very low barriers This error significantly affected the k E calculated for low barrier reactions This bug had no
23. e default names defaults densum out and mominert out 6 ADENSUM Bug Fix ADENSUM can be used with THERMO to compute thermodynamic data and canonical TST rate constants for fully vibrationally coupled anharmonic molecules and transition states It does this by passing a data file with the qvib suffix which contains partition functions zero point energy etc When separable degrees of freedom e g hindered rotors are included in the ADENSUM calculation their zero point energies should have been added to the anharmonic zero point energy but were not This omission has now been fixed 7 gauss2multi revision When using gauss2multi to create data files for the MultiWell codes Users must specify pressure units which are used only for creating multiwell dat The thermo dat data file requires specifying the standard state but TOR pressure units are not an allowed standard state and previous versions would give error messages when creating thermo dat The gauss2multi code has been revised so that thermo dat is created with BAR as default when TOR units are specified by Users thus avoiding unnecessary error messages Other data files created by gauss2multi are not affected in particular multiwell dat can still be created with TOR pressure units when they are specified MultiWell Program Suite Revision History 8 In the User Manual and in the output files from the various codes the hindered rotor degree of freedom that was p
24. e if you choose a value for Imax1 where the density of states fluctuations are greater than 5 the species dens output file can still be used as input for MultiWell whether or not a warning is issued This feature gives helpful guidance regarding the choice of Imax1 when changing energy grain sizes since the choice of Imax1 depends on the grain size and when setting up a model for the first time All input and output files are completely compatible with previous versions all sums and densities of states are the same as in v 2 07 7 NOTE no other changes were made in this release Thus Mominert and Thermo are still version 2 06 NEW IN VERSION 2 07 February 2007 ile MultiWell Bug Fix In versions 2 05 and 2 06 an error occurred when the reaction critical energy Eo was lower than Emax1 when CHEMACT was selected Essentially when k E O in some energy grains part of the initial population distribution was erroneously placed in those energy grains This could lead to calculating yields of stabilized product that are too high The magnitude of this error depends on temperature and on the size of the excited reactant molecule For CIOOCI and CIONO at 250 K the erroneous excess yield was of the order of 1 e 03 This bug has been fixed The revised version gives results for the cases when Eo gt Emax1 that are almost indistinguishable from those obtained using version 2 06 When Eo lt Emax1 the revised version no longer pla
25. ecules it does not occur at all in models that do not contain empty grains Probably very few users have been affected If more information is needed contact jroarker umich edu 2 MULTIWELL Improvement the format of output file multiwell dist was revised to make it more convenient for users although the file is now larger than before 3 MULTIWELL Improvement For convenience the temperature dependence of the collisional energy transfer parameter ALPHA has been revised to the following form Alpha C 1 E C 2 E E C 3 T 300 C 8 Previously the constant term C 1 was not multiplied by the temperature dependent factor Furthermore the temperature dependent factor was changed by replacing T with the ratio T 300 All of the temperature dependent factors have been changed analogously The revised form is expected to be more convenient for users 4 DENSUM Bug fix A minor bug prevented calculation of sums and densities of states using the KRO degree of freedom This bug has been fixed Since this degree of freedom is not employed routinely this bug probably did not affect any users 5 THERMO MOMINERT improvement in both of these codes it is now an option to use user defined filenames with extension dat for the data file e g C2H5 dat in place of the default names defaults densum dat and mominert dat The output files take the user defined file name with extension out e g C2H5 out in place of th
26. eginning of this program This problem has been fixed Probably very few users were affected by this problem 12 User Manual update The User manual has been updated In addition a new How to section has been added and will be further extended in future releases NEW IN VERSION 2011 1 March 2011 1 MULTIWELL error found and corrected It was discovered that we did not implement the centrifugal corrections correctly Although we used the approximate centrifugal correction described by Marcus 1966 the approximate k E was not properly averaged over the thermal rotational distribution As a result the following factor was omitted C I l exp 1 I l where I and are the moments of inertia of the adiabatic rotors in the transition state and in the reactant molecule respectively For tight transition states I 1 C is nearly equal to unity but it can be much smaller than unity for loose transition states Thus k E was larger than it should have been which made collisions less competitive when all other factors were held constant This had several effects a larger values of the energy transfer parameter alpha average energy transferred in deactivating collisions were required in order to fit experimental data b at low pressures collisions were less efficient than they should have been affecting the rate constant at low pressures c the relative rates in competitive multi channel reactions may have been affected to
27. er 10 More such descriptions will be added in future releases 2 MULTIWELL bug fix The option to include the effects of slow intramolecular vibrational energy redistribution slow IVR was not working correctly possibly due to an earlier maintenance revision of the code The option has been fixed 3 MULTIWELL revision The code now issues a warning when centrifugal corrections cause the critical energy Eor to be less than zero for RRKM input with key word SUM The warning is issued because in most cases Eor lt 0 0 is non physical 4 MULTIWELL extension A new key word has been implemented CRP for Cumulative Reaction Probability designates a new category of input created using Semi Classical Transition State Theory SCTST This new key word is analogous to SUM except that no warnings are issued when centrifugal corrections cause the critical energy Eor to be less than zero this condition is usually not non physical when using SCTST to generate the CRP The input file is designated using suffix crp instead of dens and has the same format as files with suffix dens 5 THERMO bug fix The option to include symmetric top rotations with the proper constraint on the K quantum number for specified total angular momentum J was not working correctly The option has been fixed 6 GAUSS2MULTI bug fix Occasionally the name and energy fields in some data lines would run together causing errors This problem has been fi
28. g fix when rotational information moments of inertia or rotational constants were entered the proper unit conversions were not carried out but all entries were treated as if they were expressed in units of amu A This bug has been fixed Enhancement rotational constants in units of GHz are now accepted in addition to MHz or cm and moments of inertia in units of amu A and g cm Enhancement the potential function that is needed for the unsymmetrical hindered rotor input type hrd is no longer required to have its zero of energy at the minimum of the potential this former requirement had not been stated previously in the manual Because it could lead to problems we eliminated this limitation Changes to MultiWell 1 Enhancement for convenience rotational information can now be entered as rotational constants in units of GHz MHz or cm and moments of inertia in units of amu A and g cm This change requires that a third KEYWORD be added to Line 3 of the input file in additon to keywords for pressure units and energy units It is important that the three keywords be given in this exact order Changes to Thermo 1 Enhancement the potential function that is needed for the unsymmetrical hindered rotor input type hrd is no longer required to have its zero of energy at the minimum of the potential this former requirement had not been stated previously in the manual Because it could lead to problems we el
29. iles generated by program adensum full vibrational anharmonicity can be incorporated in computed thermodynamic functions e g entropy and heat capacity By employing files generated by program sctst Thermo can compute thermal rate constants using SCTST formulated by W H Miller and coworkers When files from both program MultiWell Program Suite Revision History adensum and program sctst are utilized rate constants are produced using the fully coupled anharmonic version of the semi classical transition state theory 6 thermo New Feature Quantum mechanical tunneling through an unsymmetrical Eckart potential energy barrier can now be included when using program Thermo to calculate rate constants using Canonical Transition State Theory CTST The imaginary frequency and the barrier heights for forward and reverse directions must also be specified As a result the thermo input data file format for CTST calculations has been modified slightly but the other types of Thermo calculations are not affected 7 Rotational Parameters densum thermo adensum and sctst Parameters for free rotations and hindered internal rotations most of the optional formats can now be entered in these programs in any of the following user selected units Rotational constants GHz MHz and cm Moments of inertia amu A and g cm 8 mominert New Feature any specified atom now can be assigned an arbitrary mass allowing calculations for arbitrary isot
30. ill soon be updated to reflect these changes NEW IN VERSION 2011 January 2011 New Capabilities 3 New computer code sctst This code implements the semi classical transition state theory SCTST formulated by W H Miller and coworkers With this new program the SCTST can be applied to polyatomic systems containing up to dozens of atoms It includes full non separable coupling among all vibrations including the reaction coordinate and treats rotations as separable degrees of freedom The SCTST automatically includes multidimensional quantum mechanical tunneling along the curved reaction path The new code generates a standard output file a file intended as input for MultiWell for master equation calculations and a file intended for input for Thermo for computing thermal rate constants 4 adensum New Feature Because computation of fully coupled vibrational states may be time consuming the new version of adensum now allows the user to re start the density of states calculation from a checkpoint file which is generated automatically at the end of the coupled states calculation but before the convolution with separable degrees of freedom This feature speeds up the computation if the user wishes to change the number of separable degrees of freedom e g the number of external rotational degrees of freedom in subsequent calculations The code now outputs a file intended for input for Thermo 5 thermo New Feature By employing f
31. iminated this limitation 10 MultiWell Program Suite Revision History NEW IN VERSION 2009 1 April 2009 Changes to Mominert 1 Bug fix for some molecular geometries Momlnert failed to compute the reduced moment of inertia for internal rotation i e it produced NAN in the output although it still computed the principal moments of inertia correctly This bug has been fixed NEW IN VERSION 2009 0 February 2009 Changes to MultiWell 2 Revision converted to new collision ansatz where collision frequency depends on active energy A paper on this subject has been submitted contact jroarker umich edu for a copy At energies above the lowest reaction threshold the effects of this revision are small At very low energies however the collision frequency can be significantly lower than calculated by previous versions leading to different energy transfer rates incubation times etc See the user manual for details Revision in light of the preceding revision we revised the energy transfer parameters in the MultiWell examples to give results roughly similar to previous versions Revision instead of integer electronic degeneracies for wells and transition states now the non integer electronic partition functions can be entered instead The electronic partition functions are now reported as a function of temperature by Thermo Revision the code was revised so that kinf k high pressure rate constant never
32. izing the quantum Hamiltonian In future we plan to extend program lamm and the eigenvalue solutions to inversion modes and ring puckering New script gauss2lamm sh this script reads Gaussian output files and automates in part creation of the data file for lamm Starting with this version the MultiWell User Manual the Examples and the compressed package of computer codes are down loaded separately This is to reduce the size of the individual compressed files Changes to Mominert 1 Bug fix due to a bug in a Fortran write statement the rotational constants i e Ba Bb and Bc for the external rotations were too large by a factor of 10 while the moments of inertia i e la Ib and Ic were correct This bug has been fixed NEW IN VERSION 2009 3 May 2009 MultiWell Program Suite Revision History Changes to Densum and Thermo 1 Bug fix the symmetry of the unsymmetrical hindered rotor was incorrectly set equal to the symmetry of the potential energy function This bug has been fixed by adding an explicit input of the rotor symmetry number which depends on both the potential energy symmetry and the mass distribution symmetry Changes to the User Manual 1 Sections 7 4 and 7 5 have been revised in order to amplify the discussion of the treatment of external rotations internal rotations optical isomerization and the connections between them NEW IN VERSION 2009 2 May 2009 Changes to DenSum 1 Bu
33. mo New a new chemical species type ctst designating canonical transition state enables direct calculation of Canonical Transition State Theory rate constants See the MultiWell Program Suite User Manual for details 18 Thermo New electronic states and degeneracies are now listed explicitly This change improves accuracy for species with low energy excited electronic states Note that there is no provision for changes in vibrational frequencies and moments of inertia for the excited electronic states 19 Thermo New added provision for reading a comment line up to 50 characters for each chemical species 20 Thermo Improvement parameters for van t Hoff expression of equilibrium constants Kequi T A exp B T and rate constant Arrhenius parameters ktst T A exp B T are now obtained using an improved numerical derivative 21 Thermo Bug Fix the conversion factor for converting kcal mole to kJ mole was corrected from 4 1855 international calorie to 4 184 thermochemical calorie This correction also affected conversion from kcal mole to cm units 22 Thermo Bug Fix for anharmonic oscillators the vibrational partition function entropy heat capacity and enthalpy functions were not being calculated correctly This error was greatest at high temperature for low frequency highly anharmonic vibrations 23 MomlInert New from a single input file the code now will calculate reduced moments of inertia for multi
34. opologues Many isotopes are already included in the atomic mass data base and are recognized by programs Mominert and Thermo 9 multiwell New Feature A new collision model has been added Type 14 this collision model is motivated by the recent detailed trajectory analysis of 2 D i e E J energy transfer involving argon collisions with pyrazine and ethane J R Barker and R E Weston Jr J Phys Chem A 114 10619 2010 This new 1 D energy transfer model is expected to behave much like the conventional exponential model except the temperature dependence may be somewhat different Calculations are underway to investigate its behavior 10 densum bug fix the option intended for unsymmetrical hindered rotors type hrd did not work properly for symmetrical rotors although it worked correctly for unsymmetrical rotors The symmetry parameter NG was ignored i e assumed to equal unity The code has been fixed so that the hrd type no longer ignores NG and now generates the correct results for symmetrical hindered rotors as well as for unsymmetrical This bug did not affect program adensum NEW IN VERSION 2010 1 February 2010 Changes to adensum 1 Bug fix a minor bug in rare cases for some molecules was found to interfere with the initialization This bug has been fixed MultiWell Program Suite Revision History NEW IN VERSION 2010 January 2010 Important New Capabilities 1 Densities of states for
35. ot equal to unity This produced errors in the thermodynamic quantities This bug has been fixed 2 NEW FEATURE in DenSum and in Thermo particle in a box energy levels can be selected by specifying box for the type of degree of freedom see README files 3 NEW NOTE rotational and external symmetries can be handled in various ways in MultiWell Densum and Thermo To clarify the recommended way of handling symmetry numbers a new NOTE ON SYMMETRY NUMBERS has been added to the README files 4 ENHANCED OUTPUT a the number of significant digits was increased for some output quantities b zero point energies and energy differences are listed in Thermo output this is helpful for hindered rotors and it facilitates isotopic substitution simultions NEW IN VERSION 1 2 0 JANUARY 2002 1 BUG FIX the previous version applied the centrifugal corrections inconsistently when calculating Arrhenius parameters k inf was correct however and no other parts of the calculation were affected This bug has been fixed 2 NEW FEATURE can choose to apply or not apply the centrifugal corrections for any choice of k E model Thus the corrections can be applied even when using the Inverse Laplace Transform version of k E This also allows centrifugal corrections be be calculated externally and then the corrected k E or sums of states can be read from an external file NOTE THIS NEW FEATURE AFFECTS DATA FILE FORMAT AS FOLLOWS A NEW FLAG ncen
36. ple torsions instead of just one at a time NEW IN VERSION 1 4 1 September 2004 1 Please use the following citations to acknowledge results obtained using this version of MultiWell 21 MultiWell Program Suite Revision History a John R Barker Nicholas F Ortiz Jack M Preses and Lawrence L Lohr MultiWell lt version gt software http aoss engin umich edu multiwell lt date gt N B insert current lt version gt and lt date gt b John R Barker Int J Chem Kinetics 33 232 45 2001 2 MINOR REVISION MultiWell when establishing the maximum length of a simulated time period according to the number of collisions the collision frequency is now based on the collision rate constant of the initial well and not necessarily on that of well 1 3 BUG FIX Thermo fixed bug which produced incorrect values for A and B in the temperature dependent expression for Kequil when MCC units were selected The values of Kequil were correct but the values for A and B were not 4 BUG FIX Estart fixed bug that affected Pstart for thermal distribution with non zero energy offset The effect of the bug was to produce an un shifted thermal distribution Pstart with Pstart 0 at energies less than the energy offset i e with just the tail of the distribution above the energy offset NEW IN VERSION 1 3 3 October 2003 1 BUG FIX MultiWell when state densities are very sparse and hence some energy grains do not contain
37. r feedback about errors in the input file 4 ITEM OF INTEREST master equation inter comparisons A number of us who develop and use master equations are undertaking inter comparisons of the various codes This activity will help us to identify possible deficiencies in our codes as well as possible new enhancements The user community can eventually expect not only better codes but a better understanding of which codes are best suited for treating particular classes of problems So far the Master Equation Inter Comparison Group the MEIC Group includes the developers of MultiWell and MESMER Bill Green s group MIT Luc Vereecken MPI Chemie Mainz and Matthias Olzmann Karlsruhe all of whom have contributed output for inter comparison and a number of other individuals and groups who have expressed interest If you wish to be added to the list please send a message to John Barker jroarker umich edu NEW IN VERSION 2012 2 July 2012 1 USER MANUAL a A discussion of the separable rotors approximation for treating external rotations was added to Section 9 4 This discussion explains that the approximation is most ce MultiWell Program Suite Revision History accurate when the rotational constant for the K rotor is assumed to equal the unique rotational constant i e Bk A instead of the rotational constant for a symmetric top i e Bk A lt B gt b More descriptions of How to have been added to Chapt
38. reviously described as an Unsymmetrical hindered rotor hindered rotor type hrd is now described more properly as a General hindered rotation This change was made because the hrd type could always be used for any 1 D hindered internal rotation symmetrical or unsymmetrical although it is particularly useful for the latter NEW IN VERSION 2013 January 2013 1 MULTIWELL extension input for the number of stochastic trials NTRIALS can now be formatted as either REAL or INTEGER in data file multiwell dat previously it was just INTEGER It is more convenient to enter 1 e 7 instead of 10000000 2 MULTIWELL improvement A more accurate expression for the collision integral for Lennard Jones collisions has been adopted in this version Previously MultiWell used the simple version described by Troe J Chem Phys 66 4758 1977 but with this version the more accurate expression of Reid et al has been adopted Reid Prausnitz and Sherwood The Properties of Gases and Liquids Their Estimation and Correlation 3rd Edition McGraw Hill New York 1977 For T 2 300 K the two expressions give results that differ by 5 10 the differences may be larger at lower temperatures 3 THERMO improvements a The input read statements were slightly revised in order to allow users to add comments on the line for each electronic state Line 11 of input data file thermo dat b Error messages were added or revised to give bette
39. some extent d the decay of fractional population was faster than it should have been leading in some cases to rates greater than k infinity The effect of this error ranges from negligible to significant depending on the specific simulation The last effect was only detectable when k uni was large enough for multiwell to be used effectively for thermal reaction rates i e only for reactions with very loose transition states at relatively high temperatures The error was corrected and new capability was added the number of adiabatic rotations can now be selected previously it was always assumed that two rotations are adiabatic For users the only change is in the keyword calling for 6 MultiWell Program Suite Revision History centrifugal corrections Four keywords are now recognized NOCENT no centrifugal corrections CENT1 centrifugal correction assuming one adiabatic rotor CENT2 centrifugal correction assuming two adiabatic rotors this should be the usual choice CENTX legacy centrifugal correction which is incorrect and not recommended The User Manual will soon be updated to reflect these changes and to provide a more complete explanation of the centrifugal corrections If in the meantime you need more detailed information please send a message to jrbarker umich edu 2 THERMO and MOMINERT enhanced capability many more elements and isotopes are now recognized automatically by these programs The User Manual w
40. states population could get trapped in the empty grains This error in subroutine colstep f affected calculations only at very low energies and therefore did not affect most users 2 BUG FIX MultiWell an error in lower array bounds affected Estart subroutine estart f 3 BUG FIX DenSum a bug that prevented use of the Whitten Rabinovitch option in DenSum was fixed 4 ANNOUNCEMENT MultiWell the MultiWell option to use the Whitten Rabinovitch method for calculating sums and densities of states within MultiWell no longer works and is going to be eliminated It will still be possible to use DenSum to calculate sums and densities of states via the W R approximation NEW IN VERSION 1 3 2 July 2003 Thanks go to Colleen Shovelin for assistance with this distribution 1 NEW FEATURE MultiWell now can enter total concentration molecule cc in place of total pressure use Punit key word MCC 2 NEW FEATURE Densum and Thermo now can enter non symmetric hindered rotors For symmetrical hindered rotors the data file format is unchanged For each unsymmetrical hindered rotor a new line is inserted in the data file See README densum and README thermo for details 3 BUG FIX Thermo For vibrations with large negative anharmonicity the energy could become negative and the summation used in calculating the partition function would not converge at high temperature This summation is now 399 MultiWell Program Suite Revision Histor
41. though kinf itself was correct This bug did not affect any other computed output and has been fixed 2 A few minor cosmetic bugs were fixed including a problem with Thermo which did not print data for hindered internal rotations in the output file thermo out Computed output was not affected by these minor bugs NEW IN VERSION 2008 1 January 2008 1 We have changed the version numbering scheme to make it more informative From now on all of the codes in each distribution will be given the new distribution number even if some of them have not been revised The distribution number will consist of the year and the release number for that year since there may be more than one release each year e g 2008 1 is the first release of 2008 2 Previously error messages that were written in the DOS window when executing with Windows were not readable because the DOS window closed too quickly This problem with the Windows version has been fixed 3 MultiWell extension at the request of some users the default numbers of wells MaxWell product sets MaxProd and reactions MaxRxn have been increased to 50 50 and 100 respectively The defaults can be changed easily by revising file src multiwell declare1 inc and recompiling the code 4 MultiWell extension it is now possible for a user to easily change the output filenames when running multiwell If this option is not exercised the output files RI 10 DenSum new featur
42. time bin The revised version gives the exact time behavior but a larger number of stochastic trials may be needed in order to achieve the desired precision 3 A new output file MultiWell FLUX is included This file gives a record of the reactive flux for each reaction It is useful for tracing reaction pathways and for identifying quasi equilibration etc DenSum 1 A good approximation for hindered rotor energies was added Three convenient input formats can be chosen that are very convenient for using harmonic vibrational frequencies calculated by quantum chemistry programs MomInert 1 Subroutine Rotate f was revised to eliminate the errors that occurred for some molecular geometries Thermo 1 Several portions of the code were re written to make them more accurate 2 The hindered rotor options that were added to DenSum were also added to Thermo 26
43. umulative reaction probability at very low energies and in the computed partition function at temperatures below 50 K This bug probably had no effect on any users and it has been fixed 8 SCTST and THERMO modifications To improve both accuracy and convenience two modifications were made 1 the vibrational partition function which is written by SCTST to the file with suffix qcrp and used by THERMO is computed at 100 temperatures instead of the 50 used previously 2 The zero of energy for the partition function is now located at the zero point energy of the transition state instead of the ZPE of the reactant hence making it more convenient to use the same computed partition function for both the forward and reverse reactions in THERMO MultiWell Program Suite Revision History 9 ADENSUM and THERMO modifications To improve accuracy the vibrational partition function which is written by ADENSUM to the file with suffix qvb and used by THERMO is computed at 100 temperatures instead of the 50 used previously 10 MOMINERT new feature Mominert will now accept molecular Cartesian coordinates in units of either Angstroms or Bohr previously only Angstroms were accepted After the TITLE line in the data file mominert dat a new line with a keyword must be entered ANGS or BOHR all lower case is also accepted 11 DENSUM bug fix some compilers generated code that failed to execute due to the sequence of statements at the b
44. xed NEW IN VERSION 2012 1 April 2012 1 THERMO revision A minor change was made to the format of the output file thermo out The electronic partition function Qelectr is now tabulated as a function of temperature in the main output table along with the heat capacity entropy and enthalpy function The previous format was inconvenient when more than 5 temperatures were calculated This revision does not affect any numerical values 2 Gauss2multi bug fix A minor change bug prevented proper creation of data files for mominert the length units were not specified This bug was fixed by specifying ANGS for Angstrom units as default If other units are used e g Bohr Users will need to revise the mominert dat data files manually MultiWell Program Suite Revision History NEW IN VERSION 2011 2 August 2011 3 MULTIWELL bug fix The input for multiwell external data files containing k E i e __ rke type files was revised to make the order of input parameters consistent with other external files i e ___ dens files and with the User Manual In particular the order of input parameters should be as follows in Line 3 in __ rke type files Egraini imax1 Emax2 Isize Viblo Previously the input was inconsistent with the User Manual and with the other external file types Note that this ordering of parameters is not the same as in multiwell dat 4 MULTIWELL bug fix The convenient capability for using a User defined
45. y terminated at the quantum number of the highest bound level i e at vmax we 2 xe 1 2 4 MINOR FORMAT CHANGES MultiWell minor changes were made to the output file with the aim of making the debugging of data files easier Specifically the input for energy transfer parameters and reaction channels is echoed more closely in the multiwell out output file This will be helpful in spotting errors in the multiwell dat input file NEW IN VERSION 1 3 1 JAN 2003 1 BUG FIX Thermo vibrational state degeneracies were not handled correctly when not equal to unity This produced errors in the thermodynamic quantities 2 BUG FIX in Thermo fixed bug that erroneously multiplied by the particle in a box partition function when IDOF vib This caused errors in entropy and heat capacities that varied with temperature The magnitude of the error was largest for low frequency vibrations This error affected versions 1 2 1 1 2 2 and 1 2 3 3 ENHANCEMENT MultiWell In previous versions when using the ILT method for k E and simultaneously including centrifugal corrections the A factor for k infinity was equal to A inf A TSmom MolMom where A is the A factor from the input and TSmom and MolMom are the moments of inertia of transition state and molecule respectively Thus the A factor in the data file did not correspond numerically to A inf TO IMPROVE CONVENIENCE the code was revised so that the A factor in the data file should now be
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