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Manual for MOPAC, version 5.022mn

1. MOPAC version 5 022mn Page 36 Test run 28 The PM6G09 keyword is specified for the calculation of the single point energy of acetylene Test run 29 The DIPG09 keyword is specified for the reporting of the dipole moment of hydroxide ion via the usual MOPAC coordinate system and also in the Gaussian 09 coordinate system Test run 30 The SDAMP keyword is specified for the use of Stone s alternative damping function with the dispersion energy correction in AM1 D on the geometry optimization of a water molecule Test run 31 The MNDO D keyword is specified for calculating the single point energy of the ammonium ion Test run 32 The AM1 D keyword is specified with external parameters for optimizing the geometry of the water dimer The external parameter file is TEST32 PAR Test run 33 The PM6 keyword is specified with external parameters for calculating the single point energy of the water molecule The external parameter file is TEST33 PAR Test run 34 The AM1 D and SDAMP keywords are specified with external parameters for optimizing the water molecule geometry The external parameter file is TEST34 PAR Test run 35 The RM1 D keyword is specified for calculating the single point energy of the ammonium ion Test run 36 The PM6G09 D keyword is specified for calculating the single point energy of the acetylene molecule Test run 37 The PM6 D keyword is specified for calculating the single point energy of the ammonium ion Test run
2. SYMMETRY and TS keywords are specified for calculating the energy and optimized geometry for the transition state of the SN2 reaction of bromide methyl iodide Test run 5 The PM3 PRECISE SYMMETRY and TS keywords are specified for calculating the energy and optimized geometry of the transition state for the Diels Alder reaction of cyclopentadiene and MVK Test run 6 The C I GRADIENTS MECI PM3 ROOT SINGLET and VECTORS keywords are specified for calculating the energy and optimized geometry for the first singlet excited state of acroleine using analytical CI gradient Test run 7 The ISCF ANALYT GRADIENTS PM3 PRECISE and VECTORS keywords are specified for calculating the energy of formaldehyde with the C O bond stretched Test run 8 The AM1 CHARGE C I EF GRADIENTS PRECISE and VECTORS keywords are specified for calculating the energy and optimized geometry of the allyl cation using its ground state gradients Test run 9 The AM1 GNORM MODE PRNT RECALC SCFCRT and TS keywords are specified for calculating the energy and optimized geometry for the MeNC to MeCN transition state Test run 10 The EXTERNAL GNORM LET PM3 PRECISE TS and UHF keywords are specified for calculating the NDDO SRP in particular PM3 SRP energy and optimized geometry of the transition state of the NH3 OH reaction The input and NDDO SRP files are in mopac5022mn test test10 dat and mopac5022mn test TEST10 SRP respectively Test run 11
3. The 1SCF AM1 CHARGE C I GRADIENTS MECI PRECISE and VECTORS keywords are specified for calculating the energy and CI gradients of the allyl cation Test run 12 The GRAD MINDO3 and PRECISE keywords are specified for calculating the energy and optimized geometry of thiophene Note GRAD is a short form of GRADIENTS and has the same meaning Test run 13 The AM1 CM2 and SYMMETRY keywords are specified for calculating the CM2 charges the energy and the optimized geometry of 1 2 ethanediol MOPAC version 5 022mn Page 35 Test run 14 The CM2 PM3 and SYMMETRY keywords are specified for calculating the CM2 charges the energy and the optimized geometry of 1 2 ethanediol Test run 15 The HHON keyword is specified for calculating the energy and optimized geometry for the transition state of the CH3 CH4 reaction using AM1 CHC SRP In this test run no external HH Gaussian parameter file is specified Therefore the AM1 CHC SRP HH Gaussian is used as a default Test run 16 The HHON keyword is specified for calculating the energy and optimized geometry for the transition state of the CH3 CH reaction using PM3 CHC SRP In this test run the HH Gaussian parameters are specified in an external file explicitly The input files are mopac5022mn test test16 dat and mopac5022mn test PM3_ CHC_SRP Test run 17 The PDG and UHF keyword is specified for calculating the energy and optimized geometry of the methyl radical Test run 18 The MD
4. orbitals that are entered as just H in the input file these ordinary hydrogen atoms are automatically converted to Hp atoms This is in contrast to previous methods in MOPAC where the distinction between H and Hp atoms is preserved and are treated as two discrete types of atoms Running the PMOv1 method will run an MNDO D calculation with the MOD1 MOD2 MOD3 and MOD4 options automatically activated see Section 4 15 for details on the MODx options Additionally the parameter set has been optimized for molecules ions and clusters containing Hp and O atoms for PMOv1 If the PMOv1 keyword is used on a calculation containing any atoms other than hydrogen and oxygen the calculation will not run because the PMOv1 method is only parameterized for systems with hydrogen and oxygen atoms Currently PMOv1 and the MODx keywords do not have analytical gradients available Any calculation attempting to use the PMOv1 or the MODx keywords with the ANALYT keyword will cause the program to terminate prematurely and print an error message warning the user that this combination of keywords is not available MOPAC version 5 022mn Page 25 4 17 PMO version 2 PMO2 The PMO2 semiempirical method 28 is included in MOPAC 5 022mn PMO2 is capable of calculations on systems containing not only hydrogen and oxygen atoms like the PMOv1 method does but carbon atoms as well It is invoked by using the keyword PMO2 in the input deck The calculation sets the
5. use a Pairwise Distance Directed Gaussian PDDG modification of the PM3 and MNDO methods respectively These methods were implemented in MOPAC 5 012mn The PDDG modifications consist of a single function which is added to the existing pairwise core repulsion functions within PM3 and MNDO a reparameterized semiempirical parameter set and modified computation of the energy of formation of a gaseous atom The keywords for the PDDG PM3 and PDDG MNDO methods are PDG and MDG respectively Both PDDG methods are parameterized for H C N O F Cl Br and I MOPAC version 5 022mn Page 18 4 7 RM1 RM1 12 Recife Model 1 is a reparameterization of AM1 and was implemented in MOPAC 5 012mn Unlike AM1 and similarly to PM3 all RM1 parameters have been optimized Therefore RM has been designed with the goal of improving over AM1 and PM3 RM1 has the same analytic form and the same number of parameters for each atom as AM1 The keyword RM1 is used for this method RM1 is parameterized for H C N O P S F Cl Br and I 4 8 AM1 D PM3 D MNDO D RM1 D and PM6 D The AM1 D and PM3 D semiempirical methods developed by Hillier with his parameterization 13 with the dispersion functional form taken from Grimme 14 are modifications of the respective AM1 and PM3 methods The D dispersion methods described in this section use Grimme s version 1 dispersion functional form that also uses the suffix D1 to distinguish it from later versi
6. 0 Test 63 oat 0 0 Test 64 0 0 Test 65 ccs S 0 0 Test 66 Eee d 0 0 Test 67 eee 0 0 Test 68 e 0 0 Test 69 95 0 0 Test 70 ee 0 0 Test 71 Sas SE oes 0 0 Test 72 aoe Tan J 0 0 Test 73 zi ia 0 0 Test 74 0 0 Test 75 0 0 Test 76 rve dde 0 0 Test 77 aa ae Ese 0 0 Test 78 ie 0 0 Test 79 wee 0 0 Note 0 0 means less than 0 05 7 2 Description of test runs The input files and reference output files for the set of MOPAC version 5 022mn test runs are included in the mopac5022mn test and mopac5022 testo directories respectively Below is a brief description of each of the test runs Test run 1 The EF GRADIENTS NOINTER PRECISE and SYMMETRY keywords are specified for calculating the energy and optimized geometry of methylcyclohexane MOPAC version 5 022mn Page 34 Test run 2 The AM1 EF GNORM GRAD SCFCRT and SYMMETRY keywords are specified for calculating the energy and optimized geometry of morpholine Note GRAD is a short form of GRADIENTS and means the same thing Test run 3 The GRADIENTS MNDO PRECISE and SYMMETRY keywords are specified for calcualting the energy and optimized geometry of methyl butanoate Test run 4 The AM1 CHARGE PRECISE
7. 38 The AM1 keyword is specified for calculating the optimized bond length of the H2 molecule using the Hp atom type Test run 39 Tight optimization of the sulfur containing compound cysteine with the AM1 D method Test run 40 Tight optimization of the sulfur containing compound cysteine with the PM3 D method Test run 41 Test of MNDO D with MOD1 MOD2 MOD3 and MOD4 keywords on dihydrogen molecule The external parameter file is TEST41 PAR Test run 42 Test of MOD1 keyword with water molecule containing Hp type atoms The external parameter file is TEST42 PAR Test run 43 Test of MOD2 keyword with water molecule containing Hp type atoms The external parameter file is again TEST42 PAR MOPAC version 5 022mn Page 37 Test run 44 Test of MOD3 keyword with water molecule containing Hp type atoms Also uses the PMODS keyword in the external parameter file with the MOD3 option The external parameter file is again TEST42 PAR Test run 45 Test of MOD2 and MOD4 keywords with water molecule containing Hp type atoms The external parameter file is again TEST42 PAR Test run 46 Test of MOD1 MOD2 MOD3 and MOD4 keywords with water molecule containing Hp type atoms The external parameter file is again TEST42 PAR Test run 47 Test of MOD1 keyword with water molecule containing Hp type atoms using custom PMODS 3 and 4 parameters The external parameter file is again TEST47 PAR Test run 48 Test of PMOv1 geometry optimization of a
8. G Truhlar Modification of version 5 07mn New files PARAMS i and chgmp2 f are added to include class IV atomic charges calculated by Charge Model 2 CM2 The subroutines CHRGE WRTKEY and WRITEMO are modified and a new subroutine SCOPY is added to fromblas f Two new test runs test13 dat and test14 dat are added for evaluating partial atomic charges by the CM2A and CM2P methods respectively Version 5 09mn October 1999 Modified by P L Fast and D G Truhlar Authors J J P Stewart I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Li C J Cramer P L Fast and D G Truhlar Modification of version 5 08mn Tested make files have been provided for Compaq and Sun computers and the subroutine WRTKEY has been modified to correct a floating point error on Compaq and Sun machines The value of the parameter MAXDMP defined in SIZEZ i was increased from 3600 to 36000 Version 5 010mn December 2003 Modified by J Pu and D G Truhlar Authors J J P Stewart I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar Modification of version 5 09mn The keyword HHON is now available for adding HH repulsive Gaussian functions into AM1 and PM3 Two new test runs test15 dat and test16 dat are added for optimizing the saddle point geometry for CH3 CH4 using the AM1 CHC SRP and PM3 CHC SRP models respectively Two makefiles make altix and make linux_g77 are add
9. Qdisp The a parameter for the dispersion methods e g AM1 D ATMIP IP The atomic ionization energy for Stone s alternative damping function PMODS Pi Specify custom parameter i for use with the MODx modification options COAB Cus Coefficient used in equation 14 C1AB C TE Coefficient used in equation 14 C2AB C Cae Coefficient used in equation 14 C3AB Cus Coefficient used in equation 14 ALPPR QUB Pairwise alpha factor used in equation 14 C3PWR Pap Pairwise power of R4g used in equation 14 ALPP3 Q AB Pairwise alpha factor used in equation 14 KPRSS kav Pairwise k factor used in equation 16 s orbital on atom A and B KPRSP kuv Pairwise k factor used in equation 16 s orbital on A and p orbital on B KPRPP kav Pairwise k factor used in equation 16 p orbital on atom A and B SR6 S76 Coefficient used in the damping function for the D3 methods MOPAC version 5 022mn Page 22 S8 S8 Coefficient for the 7 terms in the D3 methods For the diatomic parameters used in PM6 for example the external file should specify the replacement parameters as follows Line 1 ALPM6 O H 1 300 Line 2 XPM6 O H 0 200 Line 3 XPM6 O O 0 540 Line 4 PMODS 1 2 250 Line 5 PMODS 2 3 100 Line 6 END The PMODS keyword changes specific parameters used by modifications to the usual semiempirical theory as discussed in Section 4 15 Using lines 4 and 5 in the example above would have the effect of setting t
10. be selected on the basis of the overlap between two following steps see OMIN If MODE 0 the eigenvector with the lowest eigenvalue will be followed regardless of the overlap with the previous optimization step MOPAC version 5 022mn Page 13 The defaults are MODE 1 TS keyword and MODE 0 EF keyword HESS n HESS n specifies how the Hessian matrix will be calculated HESS 0 The initial Hessian will be approximated as diagonal HESS 1 Calculate the Hessian using forward finite differences HESS 2 Read Hessian from disk HESS 3 Calculate the Hessian using central finite differences The default is HESS 0 for minimum optimization EF keyword and HESS 1 for transition state optimization TS keyword RECALC n In an Eigenvector Following optimization the RECALC n keyword requests the program to recalculate the Hessian every n iterations This is very effective but CPU intensive The Hessian will be recalculated using the method specified by HESS keyword DMAX n DMAX n changes the value of the starting trust radius in Angstroms in Eigenvector Following optimizations The default is DMAX 0 2 DDMIN n DDMAX m These keywords set the limits for trust radius in Angstroms in Eigenvector Following optimizations The defaults are DDMIN 0 001 and DDMAX 0 3 TS keyword or DDMAX 0 5 EF keyword RMIN n RMAX m For an Eigenvector Following step to be accepted the value of the ratio of the calculated energy to the predicted energy must b
11. calculation of overlap integrals just as the ANALYT keyword will however the program will calculate gradients numerically unlike the ANALYT keyword which will use analytical derivatives MOPAC version 5 022mn Page 40 9 REFERENCES 1 A Banerjee N Adams J Simons and R Shepard J Phys Chem 89 1985 52 2 J Baker J Comp Chem 7 1985 385 3 P Culot G Dive V H Nguyen J M Ghuysen Theor Chim Acta 82 1992 189 4 M J D Powell Math Prog 1 1971 26 5 R Fletcher Practical Methods of Optimization Unconstrained Optimization Vol 1 Wiley New York 1980 6 J C Corchado J Espinosa Garcia W P Hu I Rossi D G Truhlar J Phys Chem 99 1995 687 694 7 J Li T Zhu C J Cramer and D G Truhlar J Phys Chem A 102 1820 1831 1998 8 A Dybala Defratyka P Paneth J Pu D G Truhlar J Phys Chem A 108 2004 2475 2486 9 M P Repasky J Chandrasekhar W L Jorgensen J Comput Chem 23 2002 1601 1622 10 I Tubert Brohman C R W Guimaraes M P Repasky W L Jorgensen J Comput Chem 25 2004 138 150 11 I Tubert Brohman C R W Guimaraes W L Jorgensen J Comput Theory Chem 1 2005 817 823 12 G B Rocha R O Freire A M Simas J J P Stewart J Comput Chem 27 2006 1101 1111 13 J McNamara I Hillier Phys Chem Chem Phys 9 2007 2362 2370 14 S Grimme J Comp Chem 25 2004 1463 1473 15 J J P
12. enpart f extpar f ffhpol f flepo f fmat f fock1 f fock2d f fock2 f fock f force f formd f forsav f frame f freqcy f geout f getbet f getgeo f gethes f getsym f gmetry f gover f grid f hlelec f haddon f hcore f helect f hqrii f idamax f ijkld f ijkl f inibet f interp f iter f jab f jcarin f kab f linmin f local f locmin f lsame f mamult f matout f mecid f meci f mecih f mecip f method f moldat f molval f mopac f mstart f mtxm f mullik f mxm f nextwd f nllsq f nuchar f osinv f parsav f paths T perm f pm6de2 f pm der f pm6dpy f pm6pyr f pmodsb f pmsix f polar f powsav f powsq f pqtkl f prjfe f MOPAC version 5 022mn Page 28 prtdrc f prthes f pulay f quadr f react1 f reada f readmo f refer f repp f resetc f resetd f result f rotate 1 f rotate amsol rotate f rotate mopac rotat f rsp f sample f schmib f schmit f scopy f search f setbet f setd3 f set f setntx f setupg f solrot f spcg f spline f ss f swap f symtry f thermo f timout f tql2 f tqlrat f trbak3 f tred3 f update f updhes f util f vecprt f word f writmo f wrtkey f xerbla f xyzgeo f xyzint f Interface subroutines between subroutines MSTART and MOPAC doinit f resetc f resetd f setntx f BETxy auxiliary subroutines getbet f inibet f setbet f Machine dependent time routines date compaq f date _dec f date _hp f date_ibm f date linux f date sgi f date sun f dateclock c second_ibm f second_linux f second_sgi f Source code for BLAS subroutines used daxpy f ddot f dgemm f dscal f dswap f idamax
13. f lsame f scopy f xerbla f General machine dependent subroutines dgedi f dgefa f diag f dre f flepo f fmat f force f locmin f mullik f nllsq f powsav f powsgq f prtdre f pulay f react1 f search f tql2 f tqlrat f trbak3 f tred3 f writmo f ef f efovlp f efsav f efstr f formd f gethes f prjfc f prthes f updhes f make ifort check Remaining files SIZES i PARAMS i Makefiles make dec makefile for DEC workstations make hp makefile for HP workstations make ibm makefile for IBM RS 6000 and SP systems make sgi makefile for Silicon Graphics systems make sun makefile for Sun workstations make linux makefile for LINUX systems using f77 compiler make linux_ 77 makefile for LINUX systems using g77 compiler make pc makefile for personal computers IBM compatible make f77 makefile for f77 compilers make g77 makefile for GNU g77 compilers make ifort makefile for Intel ifort compilers make xlf makefile for IBM xlf compilers make ifort debug makefile for Intel ifort compilers with full debugging options makefile for Intel ifort compilers with run time checking enabled include file for calculation and array size limits include file for CM2 mapping parameters Directory test testsuite sh testsuite bat test01 dat testxx dat xxx PAR and xxx SRP files PM3 CHC SRP check pl Directory testo test01 out testxx out MOPAC version 5 022mn Page 29 the Bourne shell script to run the full test suite the MS DOS shell
14. is no longer accurate If the ratio is outside the interval defined by the RMIN and RMAX limits the step is rejected the trust radius reduced by a factor of two and a new step is determined The second criteria is that the eigenvector along which the energy is being maximized should not change substantially between iterations The minimum overlap of the TS eigenvector with that of the previous iteration should be larger than OMIN otherwise the step is rejected 4 2 2 New Eigenvector Following Keywords EF The Eigenvector Following routine is an alternative to the default BFGS algorithm This keyword invokes the Eigenvector Following routine to optimize to a minimum energy structure EF is particularly efficient for refining structures when the gradient is already small TS With the TS keyword the Eigenvector Following routine is invoked to optimize to a transition state The TS method is much faster and more reliable than either SADDLE or NLLSQ TS appears to work well even with Cartesian coordinates MODE n MODE n specifies that the nth Hessian eigenvector will be followed in the first step of an Eigenvector Following optimization MODE 1 means the eigenvector with the lowest eigenvalue MODE 2 the second lower and so on Note that the eigenvectors corresponding to translational and rotational motion which have zero eigenvalue are projected out of the Hessian and automatically renumbered as the last six eigenvectors The next steps will
15. m In addition to specifying the number of molecular orbitals in the active space the number of electrons can also be defined In C I n m n is the number of M O s in the active space and m is the number of doubly filled orbitals to be included in the active space Examples Keywords Number of M O s No of Electrons C L 2 2 2 1 C 1 2 1 2 2 3 C 1 3 1 3 2 3 C 1 3 2 3 4 5 C 1 3 0 OPEN 2 3 3 2 N A C 1 3 1 OPEN 2 2 3 4 N A C 1 3 1 OPEN 1 2 3 N A 3 Values for odd electron systems are given in parentheses following the number for an even number of electrons N A denotes not applicable This modification is based on the MOPAC 6 0 code 4 2 The Eigenvector Following Method for Optimization The Eigenvector Following code included in MOPAC 5 05mn and later is based on code developed by Professor Frank Jensen Department of Chemistry Aarhus University 8000 Aarhus C Denmark and is taken from the MOPAC 7 code The authors are grateful to Professor Jensen for permission to include this code in the package 4 2 1 Description of the Algorithm The EF optimization routine used here is a combination of the original EF algorithm of Simons et al 1 as implemented by Baker 2 and the QA algorithm of Culot et al 3 with some added features see RMIN RMAX and OMIN described below for improving stability MOPAC version 5 022mn Page 12 The geometry optimization is based on a second order Taylor expansi
16. new parameters consistent with hydrogen atoms with p orbitals The core charge on these atoms is 1 in order to be consistent with the way hydrogen atoms in a valence basis set are treated The exponential parameter for the 2p Slater orbitals is 0 3000 bohr It can be set to other values by defining the ZP parameter for element Hp in an external parameter file see section 2 3 in the MOPAC 5 0 manual The inclusion of p orbitals on hydrogens is necessary for the new PMO method 26 4 12 Origin for dipole moments The origin for dipole moments calculated by MOPAC is chosen to be the center of isotopic averaged masses of all atoms In the Gaussian programs the origin is chosen as the center of nuclear charge For neutral systems the results are identical however for charged systems the dipole moment depends on the choice of origin The keyword DIPG09 is used to specify that in addition to the standard MOPAC calculated dipole moment the Gaussian 09 type dipole moment is also to be reported in the output The correction necessary to convert the dipole moment of a charged system from one choice of origin x to another is m Gaussian Myopac diotal E E nae 1 The origins are calculated as a weighted average of nuclear positions R4 as given in equation 2 The weights w4 in the case of MOPAC are chosen as the isotopically averaged atomic masses the weights in the case of Gaussian 09 are the nuclear charges of the atoms atom
17. origin set as the center of nuclear charges This difference is only important for charged systems as the dipole moment of neutral systems will be invariant to the coordinate system chosen See section 4 12 for details Three new methods MNDO D RM1 D and PM6 D have been added that follow the same formalism as AM1 D and PM3 D These new methods do not occur in the literature so the dispersion parameters LRT Cs So and gn and the Uss Upp Ps Pps and a parameters chosen for them are set to equal the corresponding parameters of AM1 D for the new RM1 D method and PM3 D for the new MNDO D and PM6 D methods The elements for which these new methods have parameters are MNDO D H C N O S RM1 D H C N O S PM6 D H C N O S An alternative damping function is now available for use with the dispersion energy correction of the all the D dispersion methods The keyword SDAMP will cause this damping function to be used See section 4 13 for details Version 5 016mn July 2010 Modified L Fiedler and D G Truhlar Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar This version of MOPAC has taken the previous version of MOPAC and made the entire program into a subroutine that may be called repeatedly within a larger program framework The advantage of this modification is that version 5 016mn may be used for direc
18. parameters the polarized molecular orbital methods PMOv1 PMO2 and PMO2a class IV charges by CM2A and CM72P the eigenvector following EF algorithm for geometry optimization of equilibrium structures and saddle points improved configuration interaction options analytic gradients for the CI method and the capability to perform successive calculations with different input files and different sets of parameters The program revision date refers to the date of final modifications to all files except the manuals The date of the most recent change to the manual is given separately A change in only the manual does entail a new revision number J J P Stewart L Fiedler J Zheng I Rossi W P Hu G C Lynch Y P Liu P Zhang Y Y Chuang J Pu J Li P L Fast C J Cramer J Gao and D G Truhlar MOPAC version 5 022mn Page 2 TABLE OF CONTENTS 1 USER AGREEMENT ASR 0 SS ERRER HSS SSG SWS a Hae S 0 3 Pe CITATION S a KR a L N ear diary SM E K al Sy R N Shh N A d AR N R AR N 3 3 REVISION HISTORY 4 cs c5044 T hades Pha hedSd Pats toeesesIeoret sade 4 4 NEW CAPABILITIES 5 9 5 9 3 60 69 54 30 6N5 56455455 5 ea bo ose eS eae tesla 1 4 1 New Configuration Interaction Keyword 2 2 e ee eee eee eee 11 4 2 The Eigenvector Following Method for Optimization 1 4 2 1 Description of the Algorithm e e e d 4 2 2 New Eigenvector Following Keywords s
19. proper semiempirical parameters the dispersion settings and the MODx options specifically MOD4 MODS MOD6 and MOD7 in order to perform PMO2 calculations Examples of PMO2 calculations both with the PMO2 keyword and without the PMO2 keyword using the MODx options and external parameters explicitly given in the input deck are provided in the runs in the MOPAC 5 022mn test suite 4 18 PMO2a The PMO2a semiempirical method 29 is implemented in MOPAC 5 022mn and is invoked by the method keyword PMO2a in the input deck This method allows the use of the elements hydrogen carbon nitrogen oxygen and sulfur It is primarily intended for use on atmospheric clusters several examples of important atmospheric molecules that were used in the development and validation of the method are included in the test runs for the PMO2a keyword Like the previous polarized molecular orbital methods PMO2a automatically uses the MODn options MOD4 MODS MOD6 and MOD7 as well as specific parameters for the PMO2a method The method also must use p orbital containing hydrogens Hp atoms Examples of the PMO2a method being implemented in MOPAC with the MODn options explicitly placed in the input deck along with an external parameter file for the PMO2a parameters are given in the test runs By contrast examples of the PMO2a method being run on the same systems by only including the PMO2a keyword in the input deck are also included in the test r
20. to malfunction has been corrected The C I n m option and the Eigenvector Following optimization algorithm have been introduced as new capabilities Subroutines HIELEC ANALYT MULLIKEN and AM1 now renamed EXTPAR have been modified to use the MOPAC version 5 022mn Page 5 new NDDO SRP pairwise parameters BETSS BETSP and BETPP Relevant to this new feature is the addition to the SIZES file of the new user defined parameter MXATSP Version 5 06mn September 1997 J J P Stewart I Rossi W P Hu G C Lynch Y P Liu and D G Truhlar Modification of version 5 05mn DATA statements in the EXTPAR and ROTATE subroutines have been moved so that they are the last non executable statements in the respective subroutine to adhere to standard Fortran 77 Dummy routines date_dum f and second_dum f and the makefile make linux have been created to run MORATE under the Linux operating system Version 5 07mn December 1997 J J P Stewart I Rossi W P Hu G C Lynch Y P Liu and D G Truhlar Modification of version 5 06mn Files date_linux f second liunx f second1 c are added to replace the dummy routines for Linux operating system Some routines and makefiles for Sun DEC and HP workstations were added without testing Version 5 08mn September 1999 Modified by Y Y Chuang J Li C J Cramer and D G Truhlar Authors J J P Stewart I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Li C J Cramer and D
21. water molecule Test run 49 Test of PMOv1 single point energy and polarizability calculation of a water dimer Test run 50 Test of PMOv1 single point energy calculation on a hydronium ion H30 Test run 51 Test of PMOv1 geometry optimization of the water dimer Test run 52 Test of PM6 D3 method PM6 with D3 dispersion on acetic acid imidazole dimer with the default D3 dispersion parameters Test run 53 Test of MNDO D3 method MNDO with D3 dispersion on sandwich benzene dimer with the default dispersion parameters Test run 54 Test of AM1 D3 method AM1 with D3 dispersion on acetic acid imidazole dimer with external parameter file TEST54 PAR for dispersion parameters coming from PBEO D3 Test run 55 Test of MNDO D3 method s dispersion calculation on the system of one chlorine molecule approaching a carbon dioxide molecule Test run 56 Test of PMOv1 calculation on the geometry optimization of a water dimer using explicit keywords MOD1 MOD2 MOD3 MOD4 and MNDO D and an external parameter file for a comparison to the same calculation done using only the PMOv1 keyword Test run 57 Test of MNDO D with PMOv 1 external parameters on a water molecule for calculation of the method s complexation energy Test run 58 Test of MNDO D with PMOv 1 external parameters on a water dimer for calculation of the method s complexation energy for the water dimer Test run 59 Test of MNDO D with PMOv 1 external parameters on a water h
22. 2 0 0 Test 23 0 0 Test 24 0 0 Test 25 0 0 Test 26 0 2 Test 27 0 1 Test 28 0 0 Test 29 0 0 Test 30 0 0 Test 31 0 0 Test 32 0 0 Test 33 0 0 Test 34 0 0 Test 35 0 0 Test 36 0 0 Test 37 0 0 Test 38 0 0 Test 39 0 0 Test 40 0 0 Test 41 0 0 Test 42 0 0 Test 43 0 0 Test 44 ae ss S KE s 0 0 MOPAC version 5 022mn Page 33 Test 45 0 0 Test 46 0 0 Test 47 0 0 Test 48 0 0 Test 49 0 0 Test 50 ec ie 0 0 Test 51 sue m wae 0 0 Test 52 vee re 0 0 Test 53 0 0 Test 54 0 0 Test 55 zee e 0 0 Test 56 ao 0 0 Test 57 zi z 0 0 Test 58 sE 0 0 Test 59 z z 0 0 Test 60 ces 0 0 Test 61 e aoe 0 0 Test 62 z 0
23. G keyword is specified for calculating the energy and optimized geometry of the ethyl cation Test run 19 The RM1 and UHF keyword is specified for calculating the energy and optimized geometry for the transition state of the H FCH HF CH reaction Test run 20 The AM1 D keyword is specified for calculating the optimized geometry and ground state energy of the water dimer Test run 21 The PM3 D keyword is specified for calculating the optimized geometry and ground state energy of the water hydroxide ion complex Test run 22 The AM1 D keyword is specified for calculating the optimized geometry and ground state energy of methanethiol Test run 23 The PM3 D keyword is specified for calculating the single point energy of the ammonium ion Test run 24 The PM3 D keyword is specified for calculating the single point energy of the methane benzene van der Waals complex Test run 25 The PM6 keyword is specified for calculating the single point energy of a water molecule Test run 26 The PM6 keyword is specified for calculating the optimum geometry of a diethylamine molecule The first analytic gradient is calculated Test run 27 The EXTERNAL LET PM3 TS and UHF keywords are specified for calculating the NDDO SRP in particular PM6 SRP energy and optimized geometry of the transition state of the NH3 OH reaction The input and NDDO SRP files are in mopac5022mn test test27 dat and mopac5022mn test TEST27 SRP respectively
24. MOPAC version 5 022mn Page 1 Manual for MOPAC version 5 022mn MOPAC version 5 022mn by James J P Stewart Lucas J Fiedler Jingjing Zheng Ivan Rossi Wei Ping Hu Gillian C Lynch Yi Ping Liu Peng Zhang Yao Yuan Chuang Jingzhi Pu Jiabo Li Patton L Fast Christopher J Cramer Jiali Gao and Donald G Truhlar based on MOPAC 5 0 by James J P Stewart Program revision date June 16 2015 Date of most recent manual update June 25 2015 This version of MOPAC is based on MOPAC 5 0 but it has been extensively modified at the University of Minnesota i to be portable ii to contain additional capabilities and iii to be suitable for interfacing with molecular dynamics programs like POLYRATE With regard to i the code is fully compliant with FORTRAN 77 except that it uses the INCLUDE extension which is widely available runs on supercomputers Unix workstations and PCs running Linux The scope of this manual is to document the modifications and additions to the original MOPAC 5 0 code To learn how to use MOPAC please refer to the original MOPAC manual which is distributed as part of the MOPAC MN 5 022 package The most important additional capabilities added to the code are inclusion of PM3 as in MOPAC 6 PDDG PM3 PDDG MNDO RM1 PM6 the dispersion corrected methods AM1 D PM3 D MNDO D RM1 D and PM6 D with an alternative damping function flexible options for external modification of parameters specific reaction
25. Stewart J Mol Model 13 2007 1173 1213 16 A Misquitta A Stone Mol Phys 106 2008 1631 1643 17 K T Tang J P Toennies J Chem Phys 80 1984 3726 3741 18 A Gonzalez Lafont T N Truong D G Truhlar J Phys Chem 95 1991 4618 19 I Rossi D G Truhlar Chem Phys Lett 233 1995 231 20 Gaussian 03 Revision E 01 M J Frisch G W Trucks H B Schlegel G E Scuseria M A Robb J R Cheeseman J A Montgomery Jr T Vreven K N Kudin J C Burant J M Millam S S Iyengar J Tomasi V Barone B Mennucci M Cossi G Scalmani N Rega G A Petersson H Nakatsuji M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai M Klene X Li J E Knox H P Hratchian J B Cross V Bakken C Adamo J Jaramillo R Gomperts R E Stratmann O Yazyev A J Austin R Cammi C Pomelli J W Ochterski P Y Ayala K Morokuma G A Voth P Salvador J J Dannenberg V G Zakrzewski S Dapprich A D Daniels M C Strain O Farkas D K Malick A D Rabuck K Raghavachari J B Foresman J V Ortiz Q Cui A G Baboul S Clifford J Cioslowski B B Stefanov G Liu A Liashenko P Piskorz I Komaromi R L Martin D J Fox T Keith M A Al Laham C Y Peng A Nanayakkara M Challacombe P M W Gill B Johnson W Chen M W Wong C Gonzalez and J A Pople Gaussian Inc Wallingford CT 2004 21 Gau
26. Test of the PMO2a method using the PMO2A keyword on ammonia Test run 79 Test of the PMO2a method using the PMO2A keyword on a cluster comprising 3 sulfuric acid molecules and 2 ammonia molecules Verification of the cluster binding energy is made with this test run and those of test runs 76 and 78 MOPAC version 5 022mn Page 39 8 ADDITIONAL NOTES 8 1 Evaluation of Slater Overlap Integrals in Resonance Terms Within the Neglect of Diatomic Differential Overlap NDDO formalism the two center one electron terms are not ignored contrary to a straightforward interpretation of the meaning of NDDO Instead these terms are approximated by a resonance term Puv Suv But By 2 where Bu and By are given parameters beta parameters for the elements and orbital angular momenta corresponding to the basis functions u and v respectively The evaluation of the term S for MNDO and all later NDDO methods derived from MNDO is done using the exact overlap integral of Slater ns or np basis functions where n is valence shell s principal quantum number of the atom on which the basis functions lie However when the ANALYT keyword is specified an STO 6G basis function is used in place of the corresponding Slater basis function in order to calculate the overlap integral and the partial derivatives of the overlap integral with respect to the nuclear coordinates This is summarized in Table 2 for both MOPAC version 5 018mn and compared t
27. a Raton FL 2009 26 P Zhang L Fiedler H Leverentz D G Truhlar J Gao J Chem Theory Comp 7 2011 857 27 S Grimme J Antony S Ehrlich H Krieg J Chem Phys 132 2010 154104 28 M Isegawa L Fiedler H Leverentz Y Wang S Nachimuthu J Gao D Truhlar J Chem Theory Comp 9 2013 33 29 L Fiedler H Leverentz S Nachimuthu J Friedrich D Truhlar J Chem Theory Comp In print 2014 DOI 10 1021 ct5003169 Publication date June 16 2104 30 M J S Dewar D A Liotard J Mol Struct Theochem 206 1990 123
28. age 7 Authors J J P Stewart L Fiedler J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar Implemented analytical gradients for the PM6 method and added a keyword for PM6 PM6G09 to reproduce Gaussian 09 type calculations for PM6 since it differs from the PM6 author s software MOPAC2009 for carbon carbon triple bonds in that the Gaussian version simply adds a constant 6 0 kcal mole for each carbon carbon triple bond whereas MOPAC2009 uses the correct functional form given in the PM6 paper Version 5 015mn April 2010 Modified L Fiedler P Zhang J Gao and D G Truhlar Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar Added a new atomic symbol Hp to the program that acts as a hydrogen that contains p orbitals In effect whenever Hp atoms are specified the Hp atoms are assigned atomic number 9 the same as fluorine and the program then overwrites the fluorine parameters Additionally all fluorine atoms are considered to be Hp atoms whenever any Hp atoms have been specified in the program input A new keyword DIPG09 has been added to MOPAC in order to output both the standard MOPAC calculated dipole moment with origin set as the center of isotopic masses and the Gaussian 09 type of dipole moment calculation with
29. alculation In standard calculations the so called one electron resonance integral of NDDO theory is calculated as the overlap integral of the two atomic orbitals times a scaling factor which is defined as the mean of two atomic BETA parameters In MOPAC version 5 022mn however every scaling factor can be specified separately for every pair of atomic species 6 specifying the BETxy parameters in the EXTERNAL file as BETxy atom atom2 value where x type of orbital of atom type atom1 only S type and P type orbitals available y type of orbital of atom type atom2 only S type and P type orbitals available atom chemical symbol atom2 chemical symbol Example BETSS Cc Br 17 557832 BETPP Cc Br 8 338239 BETSP Bra iC 13 5999 32 BETSP C Br 12 336489 Note that BETSP C Br is a different parameter from BETSP Br C The value of BETxy should be in eV units Avoid tab characters in the external parameter file Also be certain that the external parameter file name is saved with all upper case characters and the file itself terminates with a blank line or the word END These parameters must be specified in the EXTERNAL file after all the other parameters See test run 10 for an example and in particular see file TEST10 SRP in the mopac5022 test directory Setting BETSS for C and Br to the average of the standard BETAS for C and Br is equivalent to doing nothing 4 4 Charge Model 2 CM2 The keyword CM2 specifies that Char
30. ating the dispersion energy with the only difference being the alternative fjamp function as given in equation 4 above Ci E disp R S5 Liamp Ry a6 6 U H e CE i ree S Here the C values are specified for individual elements by Hillier for his dispersion methods Because C and R W values for fluorine and neon were not given by Hillier values for C of 0 57 and 0 45 Jnm mol are used and values for R of 1 43 and 1 38 A are used respectively The S6 parameter is chosen as 1 4 and is common to all elements The elements H C N O F Ne and S are supported for the dispersion methods MNDO D AMI D PM3 D RM1 D and PM6 D 4 14 Additional custom parameter specifications In addition to the parameters that can be specified with a parameter file using the EXTERNAL keyword see MOPAC 5 0 manual section 2 3 there are extra parameters whose values can be specified in an external parameter file These extra parameters belong to new keywords that have been implemented in MOPAC after version 5 0 and they are described here The following list gives the parameters and the methods for which they apply ALPM6 OPM6 The a diatomic parameter for the PM6 method XPM6 XPM6 The y diatomic parameter for the PM6 method RVDW R The van der Waals radius for the dispersion methods e g AM1 D C6 Co The Ca parameter for the dispersion methods e g AM1 D S6 S6 The S parameter for the dispersion methods e g AM1 D ALPD
31. atom pairs The modified core core energy expression is given in equation 16 The default constant kpo is 0 24325 ay however it can be overridden by specifying the parameter PMODS 7 when using an external parameter file see Section 4 14 R a R ao R Ey Hp G Z uo SR al l e Hp Hpo e Y S 16 The MOD7 keyword implements pairwise beta parameters used in the calculation of the resonance integral terms The new formula is given in equation 17 Like the new core core formalism this new pairwise beta formalism allows much greater flexibility than previous semiempirical methods would allow The constant kuv has units of inverse bohrs and the constant Buv is unitless The user may specifically define the kuv constants appearing in equation 17 by using an external parameter file details are given in Section 4 14 The B constants are modified using the BETSS BETSP and BETPP keywords as described in Section 4 3 Pav B S dal uv uv 17 4 16 PMO version 1 PMOv1 A new semiempirical method called PMO is included as of version 5 018mn Calculations using PMO version 1 can be specified by using the keyword PMOv1 in the input deck Version 1 of PMO is only parameterized for systems containing Hp hydrogens with p orbitals and O atoms Future versions will extended the PMO method to carbon nitrogen and other elements If a PMOv1 calculation is run on a system with ordinary hydrogen atoms those without p
32. batch script to run full test suite MOPAC test input files see Section 7 2 for list external parameter and external specific reaction parameter files external HH Gaussian parameter file for test run 16 Perl script to verify test file output results called by testsuite sh MOPAC test output files see Section 7 2 for list MOPAC version 5 022mn Page 30 6 COMPUTERS AND OPERATING SYSTEMS ON WHICH CURRENT VERSION HAS BEEN TESTED MOPAC version 5 022mn has been tested on the following computers and operating systems as given in Table 1 Computer Processor Operating System Compiler HP Proliant BL280c Intel Nehalem CentOS 6 6 Linux ifort Intel 13 1 3 HP Linux Cluster with Haswell E5 2680v3 processors CentOS 6 6 Linux ifort Intel 13 1 3 IBM compatible PC AMD Athlon MS DOS Windows XP gfortran 4 4 0 GNU Fortran Table 1 System information for platforms on which MOPAC has been tested The compiler and loader commands are presented in the corresponding make xxx files as mentioned in Section 5 2 Some numerical problems have arisen using the Intel ifort compiler version 8 1 If you have difficulty running MOPAC version 5 022mn on your computer system such as SCF nonconvergence or inaccurate results and so on it is suggested to try turning off the compiler optimization during compilation On personal computers it may be necessary to increase the paging file size under v
33. d These modifications were intended to be used in an MNDO D calculation on a system containing Hp type hydrogen atoms Several new modifications were implemented in version 5 022mn using the keywords MODS MOD6 and MOD7 The MODS keyword introduces a more general core core energy formalism to replace the previous semiempirical formalisms Its form is given in equation 14 This expression provides more flexibility for developing new core core energy expressions and it can also be made consistent with the older semiempirical formalism by correct choice of the constants appearing in equation 14 The constants can be defined by user using an external parameter file details are in Section 4 14 Notice that the final term allows the user to specify a power for the internuclear distance factor Ey A B Z Z 8484 5358 Ras Mo Rue 4 Co eRe 4 0 Rip 1 COR ge a wa 1 14 The MOD6 keyword only applies to systems with Hp hydrogen atoms and comprises two modifications The first modification supercedes the older MOD2 keyword by replacing equation 11 with equation 15 The only difference is the removal of the unitless factor of 0 75 in equation 11 If both keywords are specified the MOD6 keyword will override the MOD2 keyword MOPAC version 5 022mn Page 24 9 i ua VR a 15 S54 PePe se LS PD la G The second modification implied by using the MOD6 keyword affects the core core energy calculation for Hp O
34. direction of the step The overlap between TS modes does not converge toward 1 but rather to a constant value which indicate how good a guess the first approximate Hessian was to the exact Hessian It appears that an updated Hessian in general is not of sufficient accuracy for reliably rejecting steps with TS overlaps much greater than 0 80 The default OMIN of 0 80 reflects the typical use of an updated Hessian and allows fairly large changes to occur and should be suitable for most uncomplicated systems If problems are encountered with many step rejections due to small TS mode overlaps try reducing OMIN maybe all the way down to 0 This most likely will work if the TS mode is the lowest Hessian eigenvector but it is doubtful that it will produce any useful results if a high lying mode is followed Note that the only way to turn off the step rejection criteria is to give suitable values to RMIN RMAX and OMIN e g the choice of RMIN 100 and RMAX 100 effectively inhibits step rejection MOPAC version 5 022mn Page 15 Similarly setting OMIN 0 disables step rejection based on large changes in the structure of the TS mode MODE The algorithm has the capability of following Hessian eigenvectors other than the one with the lowest eigenvalue see MODE keyword explanation toward a TS using the keyword MODE It is always more difficult to make such higher mode following Ideally as the optimization progresses the TS mode should at some point b
35. drocarbon fragments where a set of Gaussian parameters for AM1 and PM3 called AM1 CHC SRP and PM3 CHC SRP respectively are available To activate the HHON option the user needs to specify the keyword HHON in the MOPAC 5 022mn input file With H HONT turned on the AM1 CHC SRP and PM3 CHC SRP HH Gaussian parameters will be used as defaults for AM1 and PM3 respectively Besides using the default parameters user defined HH repulsive Gaussians can also be read from an external parameter file where the keyword HHON filename should be specified in the MOPAC 5 022mn input file The string filename following the HHON specifies the name of the parameter file containing Gaussian function parameters for hydrogen pairs The user needs to create the parameter file in the working directory for MOPAC 5 022mn Up to three Gaussian functions can be specified in the HH Gaussian parameter file with the following syntax ngauss Al r0_1 lambdal A2 r0_2 lambda A3 r0_3 lambda3 where ngauss is an integer between and 3 that specifies the number of Gaussian functions that are used and A r and lambda denote the amplitude in kcal mol the location in A and the width in A of each Gaussian function added for all hydrogen pairs The second and third Gaussians in the bracket are optional All Gaussian parameters should be floating point numbers 4 6 PDDG PM3 and PDDG MNDO The PDDG PM3 and PDDG MNDO semiempirical methods 9 10 11
36. e bracketed by the values of RMIN and RMAX Default values are RMIN 0 and RMAX 4 OMIN n During transition state optimizations the algorithm calculates the dot product between the previously followed direction and the Hessian eigenvectors The new step will be along the direction defined by the eigenvector for which this dot product is maximum if this value is greater than OMIN The default is OMIN 0 8 TS keyword and OMIN 0 0 EF keyword See also keyword MODE IUPD n IUPD n selects the Hessian updating scheme in Eigenvector Following optimizations IUPD 0 No updating IUPD 1 Powell updating scheme 4 IUPD 2 BFGS updating scheme 5 MOPAC version 5 022mn Page 14 The defaults are IUPD 1 for transition state search TS keyword and UPD 2 for a minimum energy search EF keyword RSCAL RSCAL scales the Eigenvector Following step to trust radius instead of using QA formula The default is to use QA formula for scaling NONR Skip Newton Raphson step in Eigenvector Following optimizations See Section 2 2 1 4 2 3 How to Fine Tune Optimizations RMIN and RMAX The acceptance criterion for the optimization step is that the ratio of the calculated energy to the predicted energy should be larger than RMIN and lower than RMAX If this ratio is outside this interval the step is rejected the trust radius reduced by a factor of two and a new step is predicted Setting RMIN and RMAX close to one will give a very stable but also very slo
37. ecome the lowest eigenvector Care must be taken during the optimization however that the nature of the mode does not change suddenly leading to optimization to a different TS than the one desired Note that during TS optimizations the default value MODE 1 means that mode following is active See OMIN and MODE keyword explanation This means that the TS MODE 1 will be followed and in some cases this may eventually change to some higher mode causing the optimization to fail To turn off mode following and thus following at every step the mode with lowest eigenvalue set MODE 0 Remember that following modes other than the one with the lowest eigenvalue toward a transition state indicates that the starting geometry is not a good guess of the transition state one In most cases it is better to further refine the starting geometry than to try following high lying modes There are cases however where it is very difficult to locate a starting geometry which has the desired Hessian and higher mode following may be useful Otherwise if RECALC 1 the TS mode overlap does converge toward 1 as the step size goes toward zero and in this cases there is no problems following high lying modes HESS and RECALC In certain very rigid systems or in some transition state optimizations the initial default Hessian may result to be too approximate In this case the algorithm cannot find an acceptable step larger than DDMIN so the optimization terminates after
38. ed into the mopac5010 src directory The former is for compiling MOPAC 5 010mn on SGI Altix systems with the Intel compiler efc and MOPAC version 5 022mn Page 6 the latter is for compiling MOPAC 5 010mn under the Linux operating system with the GNU Fortran compilier g77 Version 5 011mn August 2006 Modified J Zheng and D G Truhlar Authors J J P Stewart J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar Modification of version 5 010mn Three new semiempirical methods are implemented namely PDDG PM3 PDDG MNDO and RM1 The corresponding keywords are PDG PDDG PM3 MDG PDDG MNDO and RM1 RM1 Three new test runs test17 dat test 8 dat and test19 dat are added to give examples of using the PDG MDG and RM1 keywords respectively Parameters for these new methods are available for the following elements PDDG PM3 H C N O F Cl Br I PDDG MNDO H C N O F Cl Br I RM1 H C N O P S F Cl Br I A bug in the recognition of keywords for compiling with optimization is fixed The compiler ifort replaces efc in makefile make altix for compiling MOPAC 5 011mn on SGI Altix systems Version 5 012mn November 2006 Modified J Zheng and D G Truhlar Authors J J P Stewart J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar Modification of version 5 011
39. examer for calculation of the method s complexation energy for the water hexamer MOPAC version 5 022mn Page 38 Test run 60 Polarizability calculation on the dihydrogen molecule using the POLAR keyword built into MOPAC for comparison to the numerical derivative calculation of the polarizability using charged sparkles Test runs 61 69 Calculations of the dihydrogen molecule with charged sparkles at different positions around the system for the numerical calculation of the polarizability This is compared to the calculation of the polarizability done in test run 60 using the built in POLAR keyword Test run 70 Calculation of acetic acid using the PMO2 keyword Test run 71 Calculation of acetic acid using the equivalent set of keyword options and external parameter file to reproduce the results of the PMO2 method The results are compared to those of test run 70 Test run 72 Test of the PMO2 keyword on pyruvic acid Test run 73 Test of the PMO2a method using the MODx options and external parameters on the methionine dipeptide Test run 74 Test of the PMO2a method using the PMO2A keyword on the methionine dipeptide Test run 75 Test of the PMO2a method using the MODx options and external parameters on sulfuric acid Test run 76 Test of the PMO2a method using the PMO2A keyword on sulfuric acid Test run 77 Test of the PMO2a method using the MODx options and external parameters on ammonia Test run 78
40. ge Model 2 CM2 7 should be used CM2 parameterizations are available in MOPAC for either the AM1 or PM3 Hamiltonian CM2 with AM1 is called CM2A or CM2 AM1 CM2 with PM3 is called either CM2P or CM2 PM3 When the CM2 keyword is chosen in addition to the AM1 or PM3 Hamiltonian the Charge Model 2 charges and the dipole moment calculated from the CM2 charges will be be printed CM2 results will replace the Mulliken charges in the FOR12 file with MOPAC input file format CM2 is parameterized for H C N O F Si P S Cl Br and I MOPAC version 5 022mn Page 17 4 5 HH repulsive Gaussians for AM1 and PM3 The keyword HHON specifies that additional Gaussian repulsion terms are added for all hydrogen pairs 8 Analytical gradients are available with HHON and Hessians can be calculated by numerical differentiation of the analytical gradients It is well known that the PM3 Gaussian functions introduce an unphysical stabilization for HH pairs at a distance of 1 8 A The performance of PM3 can be improved by adding repulsive HH Gaussian terms of the form E HH A Exp tHH r0 lambda 2 where A is the amplitude of the Gaussian funciton rHH is the distance between a pair of hydrogens and r0 and lambda denote the location and the width of the Gaussian function A similar idea can be used for improving AM1 This option is especially useful for calculating reaction barrier heights and geometries of hydrogen atom transfer reactions between two hy
41. he ayy variable to 2 250 and the ago variable to 3 100 Further examples of specifying the above parameters can be found in test run files test32 dat test33 dat and test34 dat Also avoid tab characters in the external parameter file Be certain that the external parameter file name is saved with all upper case characters and the file itself terminates with a blank line or the word END 4 15 Modified functional forms that can be used with PMO As mentioned in Section 3 version 5 022mn includes the ability to activate specific modifications to make to the functional forms of the standard semiempirical methods The first modification MOD1 is a change to the resonance integrals that involve two different Hp hydrogen atoms or an Hp hydrogen with an oxygen atom This modification is activated by including the keyword MOD1 in a line of the input deck The MOD1 keyword activates all of the modifications given in equations 8a 10 The formulas for the modified resonance integrals are included below Poupa 8a P pusm O Ge Poss 0 Pag 3 Pe Brapa IE 2 i 10 The constant coefficients 0 03 and 0 15 that appear in equations 9 and 10 above can be modified using an external parameter file see Section 4 14 Within the external parameter file the PMODS 3 value corresponds to the coefficient of equation 9 and the PMODS 4 value corresponds to the coefficient of equation 10 The MOD1 keyword also assign
42. ing hydrogen carbon nitrogen oxygen and sulfur using other elements will not compute The programming code was also cleaned up in many places between this version and the previous version Many debugging output statements were removed that were still in the code during various phases of development The array structure was also improved for some parameters in order to switch from a packed array to a standard unpacked array that is more in line with the greater memory available on modern computer systems The name for the AM 1 core core Gaussians has been changed from GUESS to GAUSS everywhere in the code Additional commenting was placed in specific parts of the code to make it more understandable Version 5 022mn June 2015 Modified J Zheng and D G Truhlar Authors J J P Stewart L Fiedler J Zheng I Rossi W P Hu G C Lynch Y P Liu P Zhang Y Y Chuang J Pu J Li P L Fast C J Cramer J Gao and D G Truhlar Analytic gradients have for CI calculations been implemented using the method of M J S Dewar and D A Liotard 30 The code is mainly taken from AMSOL 7 1 and some modifications are made to accommodate the current MOPAC program When the CI option is turned on geometry optimization in the current version uses the CI gradient whereas they used the SCF gradient SCF gradient in the previous versions MOPAC version 5 022mn Page 11 4 NEW CAPABILITIES 4 1 New Configuration Interaction Keyword C 1 n
43. ion methods listed above by specifying the keyword SDAMP If this keyword is specified without using one of the D methods above an error will be generated Currently the SDAMP option is available for all of the same elements as the underlying dispersion method will allow The default damping function used in AM1 D and PM3 D by Hillier 13 and Grimme 14 is given in equation 3 HI R f R 1 exp 1 3 damp ij R R i J vdw Here Rj is the internuclear separation between atoms i andj The K are Hillier s parameters for each element s van der Waals radius 17 The parameter a equals 23 0 and is the same for all elements in the dispersion methods The alternative damping function specified by the SDAMP keyword used by Misquitta and Stone 16 is given in equation 4 BRY op Vom R as oh K l Here D depends on the ionization potentials of atoms i and j as given in equation 5 They are taken from the CRC Handbook of Chemistry and Physics 25 and are given for all elements in the periodic table except for astatine and those beyond atomic number 104 B V21 421 5 MOPAC version 5 022mn Page 21 In equations 4 and 5 I4 Ig fj and Ry are all in atomic units The formula for the dispersion correction used by Hillier 17 is given by equations 6 and 7 When using Stone s alternative damping function with the SDAMP keyword equations 6 and 7 still are used for calcul
44. ions are made to the theory and are implemented by the respective keywords MODI MOD2 MOD3 and MOD4 these MOD options are described in Section 4 15 The ability to use custom parameters is also included via the keyword PMODS in an external parameter file see Sections 4 14 and 4 15 The new semiempirical method PMO version can now be used in this version of the program It is activated by using the keyword PMOv1 for the method name in the input file A description of PMOvl1 is in Section 4 16 Version 5 018mn March 2011 Modified L Fiedler and D G Truhlar Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast J Gao and D G Truhlar This version of MOPAC has small changes to the input and output files The limitation on the number of text characters allowed in the input deck line has been expanded from 80 characters to 160 characters The output states for clarity that Koopmans theorem is invoked in calculating the ionization potential that appears in the summary section The new keywords MOD5 MOD6 and MOD7 are implemented in this version of the program see Section 4 15 for descriptions of each of these new modifications They provide greater flexibility in parameterizing future semiempirical methods over previous semiempirical formalisms A Perl script check pl is automatically invoked when running the test s
45. irtual memory options in order to meet the memory requirements for MOPAC version 5 022mn MOPAC version 5 022mn Page 31 7 TEST RUNS 7 1 Running test runs To run the complete test suite for MOPAC version 5 022mn change the current working directory to mopac5022mn test and execute the shell script testsuite sh as follows testsuite sh If using a personal computer the test suite can be launched as follows testsuite bat After some minutes a group of files called test out will be created in the mopac5022mn test directory You can check the results with the reference test suite outputs named test out that are in the mopac5022mn testo directory Additionally you may run the Perl script check pl located in the mopac5022mn test directory on the test out files to verify that correct calculation results were obtained The reference output files were created on an SGI Altix 3700 with Intel Itanium2 processors running the Linux 2 6 5 operating system The testsuite sh script also creates a text file called test timing containing timing information about the test runs You can compare them with the reference timings given in the table below Be aware that not all of the makefiles have been tested as of version 5 022mn but the test suite of earlier versions successfully ran the test suites as listed below The full test suite has been run successfully on the following machines in the past Computer Processors Operating system Ma
46. kefile used Compaq ES40 Alpha 500 MHz Tru64 4 0F make compaq IBM SP Power3 AIX 4 3 make ibm IBM Regatta Power4 AIX 5 1 make ibm Pentium Intel Pentium III Linux kernel 2 4 18 make linux SGI Origin 2000 R12000 IRIX 6 5 make sgi Sun Blade 2000 UltraSparc III SunOS 5 8 make sun SGI Altix 3700 Intel Itanium2 Linux kernel 2 6 5 make altix IBM compatible PC AMD Athlon Windows XP make pc HP Intel Xeon X5560 Linux kernel 2 6 32 make ifort The timings have been done using the UNIX time command bin time however timings are not yet available for the personal computer build of MOPAC version 5 022mn MOPAC version 5 022mn Page 32 User System CPU time s Compaq IBM SP Regatta Pentium Origin Sun Altix Test 1 0 5 0 8 0 3 0 7 1 1 0 7 0 2 Test 2 0 3 0 6 0 2 0 5 0 7 0 4 0 2 Test 3 0 3 0 5 0 2 0 5 0 7 0 4 0 2 Test 4 0 1 0 1 0 0 0 1 0 1 0 0 0 0 Test 5 3 4 5 9 2 1 5 8 6 7 4 9 1 5 Test 6 0 5 0 6 0 3 0 6 1 6 0 7 0 2 Test 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Test 8 0 1 0 0 0 1 0 1 0 3 0 1 0 0 Test 9 0 4 0 2 0 2 0 6 0 8 0 5 0 2 Test 10 0 2 0 6 0 1 0 1 0 1 0 1 0 1 Test 11 0 1 0 1 0 0 0 1 0 2 0 0 0 0 Test 12 0 2 0 3 0 2 0 3 0 5 0 3 0 1 Test 13 0 4 0 1 0 1 0 1 0 2 0 1 0 0 Test 14 0 8 0 2 0 1 0 2 0 3 0 2 0 0 Test 15 0 1 0 1 0 1 0 1 0 2 0 1 0 0 Test 16 0 1 0 1 0 1 0 1 0 2 0 0 0 0 Test 17 0 0 0 0 0 0 0 0 Test 18 0 0 0 1 0 0 0 0 Test 19 0 0 0 1 0 1 0 0 Test 20 0 0 Test 21 0 2 Test 2
47. lean variable LINTXT is set to true This circumvents the opening and closing of a new unit for file input output operations and replaces this with input provided by a programmer within the SETNTX subroutine Ideally this would be used for the purpose of reparameterization of a method or when invoking MOPAC for successive semiempirical calculations where terminating and relaunching the program would be highly inefficient Extensive discussion of the SETNTX subroutine and the usage of its specific common block INTEXT variables for setting up a new MOPAC calculation is provided for developers within the comment section at the beginning of the SETNTX subroutine Without making any changes to the code MOPAC 5 016mn will continue to perform identically and give the same results as past versions The launching point for the MOPAC subroutine formerly the main program unit is from the MSTART subroutine To reinitialize all variables for a new run simply call the DOINIT subroutine DOINIT reinitializes all common block variables and subroutine local variables that require resetting in order to call the MOPAC subroutine again Because STOP statements are occasionally encountered during calculations that violate common sense or represent unphysical situations the program would terminate in older versions In the current version alternate return statements are included to return the program to the top level the MSTART subroutine in order to handle these events a
48. mn The PDDG PM3 parameters for silicon phosphorus and sulfur are implemented Version 5 013mn October 2009 Modified L Fiedler and D G Truhlar Authors J J P Stewart L Fiedler J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast and D G Truhlar Implemented three new methods AM1 D PM3 D and PM6 AM1 D and PM3 D add dispersion corrections see Section 4 8 and the following elements are supported by these methods AMI D H C N O S PM3 D H C N O S PM6 is a successor to James Stewart s earlier method PM3 that has been much more extensively parameterized see Section 4 9 Because elements beyond magnesium require the inclusion of d basis functions only the elements from hydrogen to magnesium are functional is this version Analytical gradients are now available for the two dispersion methods AM1 D and PM3 D Version 5 013mn also splits the individual Fortran code files into individual files one for each of the subroutines functions data blocks etc to replace the increasingly obsolete organization of program segments of separating those subroutines that were modified from those that were not modified from when MOPAC version 5 01mn branched off from version 5 0 Version 5 013mn also contains new test runs that test single point energy calculations with AM1 D and PM3 D Version 5 014mn February 2010 Modified L Fiedler and D G Truhlar MOPAC version 5 022mn P
49. n J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast J Gao and D G Truhlar MOPAC version 5 022mn 2015 University of Minnesota Minneapolis MN 55455 MOPAC version 5 022mn Page 4 3 REVISION HISTORY As explained in the MOPAC version 5 0 manual the first two digits e g 5 0 of the MOPAC version number are constant for a given release of the program Modified versions for a given release of MOPAC should have the third digit different from zero for example a modification of version 5 0 would result in a version with the version number 5 0x where x is not equal to zero Clearly this can result in multiple versions of 5 0x in different places therefore we have added mn Minnesota to versions created at the University of Minnesota Note that starting with the release of version 5 015mn the whole program name has been given as MOPAC version 5 015mn rather than using the old system for naming This document provides the revision history for the University of Minnesota revisions leading up to this version Version 5 0 Original distributed version by James J P Stewart Version 5 01mn Modified version of MOPAC version 5 0 The modifications were made by Minnesota Supercomputer Center Inc for the Cray computers Version 5 02mn Modification of version 5 01mn In this version all the subprograms were returned to their original form
50. ncluded in distribution e 27 6 COMPUTERS AND OPERATING SYSTEMS ON WHICH CURRENT VERSION HAS BEEN TESTED pencacai roa Be R SS ee Be ee ne ae a ee ewes 30 TALES TE RUINS ar ee RR Se EG Oe SS OS OR MEE EEE RY 31 Tel RUNNING test TUS lt 6 64 oe oe Re Ro a Eee Ko eS ee TE TRS aS 31 7 2 Description of test runs Shs ob 4s Soe HES Walks HOTS Swiels VOR Side SSA Ss 33 S ADDITIONAL NOTES a SR R a R eta R a ey R RT a ae ay 39 8 1 Evaluation of Slater Overlap Integrals in Resonance Terms 39 9 REFERENCES TTT 40 MOPAC version 5 022mn Page 3 1 USER AGREEMENT This code is supplied with the following conditions The code except for unmodified code from MOPAC version 5 0 and the EF related subroutines is copyrighted by the authors who retain all rights for distribution Persons receiving the code from the authors or from authorized distributors are encouraged to share it with their co workers but are asked not to redistribute it in whole or in part in modified or unmodified form alone or as a part of another program to third parties Users may make additional copies for their own research use including usage by coworkers but are asked to retain the code name and version number author names copyright notice and user agreement notice on the output file Publications resulting from use of the MOPAC version 5 022mn code should give the reference listed in section 2 2 CITATION Citation for MOPAC version 5 022m
51. nd avoid early program termination if a set of MOPAC calculations is being carried out The ANALYT keyword previously would create a scratch directory for holding analytical derivative information To avoid the creation and deletion of a new scratch file all the file I O it would involve and the subsequent increase in time a new array was created for scratch space During the development of this version run time checking was used on all of the test runs to ensure no run time problems existed within the code Examples of these run time problems that were corrected include writing to arrays out of bounds using invalid pointers and using undefined variables Many of these run time problems existed within the code prior to version 5 016mn and each was corrected when found during development Finally the Cray workstation specific files have been removed from this distribution of MOPAC because we did not have an opportunity to test recent versions of MOPAC on Cray computers Version 5 017mn October 2010 Modified L Fiedler P Zhang J Gao and D G Truhlar MOPAC version 5 022mn Page 9 Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast J Gao and D G Truhlar This version of MOPAC has made several modifications to the semiempirical theory in order to accommodate Hp type hydrogen atoms hydrogens containing p orbitals Four modificat
52. ng directory This file should be saved and backed up for future reference or re installation Building MOPAC version 5 022mn involves two commands First type the following command cd mopac5022mn sre to change the working directory to the directory that contains all the source code Then issue the command make f make xxx mopac5022mn or to have the executable named automatically use make f make xxx where xxx is machine dependent The makefiles located in the mopac5022mn src directory distributed with MOPAC version 5 022mn are make compaq to compile on Compaq workstations make dec to compile on DEC workstations make hp to compile on Hewlett Packard workstations make ibm to compile on IBM RS 6000 SP and Regatta systems make linux to compile on LINUX systems make linux_g77 to compile on LINUX systems make sgi to compile on Silicon Graphics Origin systems make sgi_ gfortran to compile on Silicon Graphics Origin systems with GNU Fortran make sun to compile on Sun workstations make pc to compile on IBM compatible personal computers with GNU Fortran The following makefiles are specific to the type of compiler rather than the type of workstation and may be used instead based upon which compilers are available to the end user make f77 to use the 77 compiler make g77 to use the GNU Fortran g77 compiler MOPAC version 5 022mn Page 27 make ifort to use the Intel ifort compiler make ifort check
53. o the Gaussian 03 20 and Gaussian 09 21 programs MOPAC 5 and Software MOPAC version 5 022 Gaussian 03 Gaussian 09 mode Default Default AM1 OLD Default Default Slater orbitals with STO 3G with STO 3G with STO 6G with numerical derivatives analytical analytical analytical derivatives derivatives derivatives ANALYT STO 6G with analytical keyword derivatives PMOv1 or STO 6G with numerical MOD1 derivatives keyword Table 2 Methods of calculating energy and gradients of Slater overlap integral in the NDDO resonance term The method of analytical evaluation of Slater orbital overlap integrals can be found in Appendix B 4 of the book Approximate Molecular Orbital Theory 22 The method of analytical evaluation of STO nG overlap integrals which are simply linear combinations of gaussian functions on two different atom centers can be found in Appendix A of Modern Quantum Chemistry Introduction to Advanced Electronic Structure Theory 23 The STO 6G gaussian expansion coefficients used by MOPAC and the STO 3G gaussian expansion coefficients used by Gaussian 03 and Gaussian 09 with the OLD keyword can be found in Small Gaussian Expansions of Slater Type Orbitals 24 Conversions for the exponential coefficients values of alpha for the particular Slater exponents used in semiempirical methods follows equation 4 of reference 22 Using the PMOv1 or the MOD1 keyword will invoke the STO 6G
54. on of the energy around the current point At this point the energy the gradient and some estimate of the Hessian are available There are three fundamental operations in determining the next geometry based on this information o find the best step within or on the hypersphere with the current trust radius o possibly reject this step based on various criteria o update the trust radius For a minimum energy search the correct Hessian has only 3N 6 positive eigenvalues where N is the number of atoms For a Transition State TS search the correct Hessian should have exactly one negative eigenvalue and the corresponding eigenvector should be in the direction of the desired reaction coordinate The geometry step is parameterized as g s H where s is a shift factor which ensures that the step length is within or on the hypersphere If the Hessian has the correct structure a pure Newton Raphson step is attempted This corresponds to setting the shift factor to zero If this step is longer than the trust radius a P RFO step is attempted If this is also too long then the best step on the hypersphere is made via the QA formula Using the step determined the new energy and gradient are evaluated If it is a TS search two criteria are used in determining whether the step is appropriate The ratio between the actual and predicted energy change should ideally be 1 If it deviates substantially from this value the second order Taylor expansion
55. only a few cycles with the TRUST RADIUS BELOW DDMIN value warning long before the stationary point is reached In such cases RMIN could be set to some negative value thereby allowing steps which increase the energy But in general it is more useful to increase the precision of the Hessian calculation using the HESS keyword In some very difficult cases it is even necessary to recalculate the Hessian every few iterations using the RECALC keyword Unfortunately setting RECALC to low values is very expensive in terms of computer time but if used in conjecture with OMIN 0 90 or possibly an even higher value and maybe with tighter values of RMIN and RMAX it represents an option for locating transition structures that otherwise might not be possible 4 3 NDDO SRP Calculations Neglect of diatomic differential overlap NDDO molecular orbital theory with specific reaction parameters SRP 18 19 can be invoked in this program in the following way An NDDO SRP calculation which can be used in conjunction with all methods except MINDO can be invoked by using the MOPAC keyword EXTERNAL filename The parameters adjusted specifically for the given reaction should be defined in the file given in EXTERNAL filename according to the discussion in the MOPAC 5 0 manual MOPAC version 5 022mn Page 16 In order to allow the wavefunction to be more flexible three new parameters BETSS BETSP and BETPP have been defined and are recognized in an NDDO SRP c
56. ons note that D and not D1 are used for method names in MOPAC Some of the original semiempirical method parameters have been modified 13 for instance USS and UPP but most importantly additional core repulsion functions with a long range R form are included to give the method better dispersion energies for noncovalently bonded complexes The AM1 D and PM3 D methods currently are parameterized for the following elements H C N O F Ne and S The MNDO D RM1 D and PM6 D methods were not developed by Hillier and coworkers at the time that AM1 D and PM3 D were developed however they are implemented in this version using the same dispersion parameters LRT Cs Ss and Qaisp and Uss Upp Bs Bp and a as AM1 D for the RM1 D method and PM3 D for the MNDO D and the PM6 D methods Thus the same elements as listed above are available for use with MNDO D RM1 D and PM6 D The dispersion method parameters can be set using the EXTERNAL keyword and including the following lines in the external parameter file for the van der Waals radius parameters RVDW the C6 parameters C6 the Se parameter S6 and the a parameter ALPD LALO RVDW H CD H 0 160 S6 1 400 ALPD 23 000 For using the EXTERNAL keyword see Section 2 3 of the MOPAC 5th Edition user manual as well as section 4 14 of this manual for more details 4 9 PM6 The PM6 semiempirical method 15 is a successor to PM3 It is reparameterized f
57. or much of the periodic table although in MOPAC version 5 022mn only hydrogen through magnesium are currently implemented due to the requirement in PM6 of d basis functions for those elements beyond magnesium This method contains new functional forms not included in the PM3 formalism that include parameters for pairs of elements in contrast to the other semiempirical methods The two diatomic parameters aj and xj can be set using the EXTERNAL keyword and including the following lines in the external parameter file for the aj parameters ALPM6 and the xj parameters XPM6 ALPM6 H L 1 028 X DMG H C 0 217 MOPAC version 5 022mn Page 19 For using the EXTERNAL keyword see Section 2 13 of the MOPAC Sth Edition user manual 4 10 Gradients Not every method has analytic gradients available in MOPAC MN The following methods have implemented analytic gradients as of MOPAC version 5 022mn MINDO 3 MNDO AM1 PM3 RM1 AM1 D PM3 D and PM6 these methods also have analytic gradients available for CI Methods for which only numerical gradients are available in version 5 022mn are the following PDDG MNDO and PDDG PM3 4 11 Hydrogen atoms with p orbitals Hydrogen atoms containing 2p orbitals have been added to the list of available atom types The new atom symbol for such hydrogens is Hp Whenever the Hp atom symbol is used the Hp atoms are assigned the atomic number 9 fluorine and all fluorine atoms and all Hp atoms are assigned
58. s S 2 MOPAC version 5 022mn Page 20 When comparing the output files of MOPAC and Gaussian 09 be aware that the coordinate systems may differ however the dipole moment vectors will be equivalent 4 13 The D3 dispersion and alternative damping functions for dispersion Grimme s version 3 DFT dispersion 27 using the suffix D3 is available with some of the standard semiempirical methods MNDO AM1 PM3 RM1 and PM6 and all elements The dispersion includes two new parameters s and ss that can be modified with an external parameter file see Section 4 14 The choice of default values for these two parameters those for PBEsol D3 was determined by testing various DFT D3 parameters with the D3 semiempirical methods described here The damping function used with the dispersion function is the zero damping function of Grimme s goes to zero as the internuclear distance vanishes instead of the alternative Becke Johnson damping function Unlike the D dispersion methods described in Section 4 8 using the D3 dispersion does not alter the original semiempirical parameters Within the dispersion methods e g MNDO D AM1 D and PM3 D the dispersion energy correction uses a damping function to cause the R contributions to vanish as interatomic distances go to zero An alternative damping function used by Misquitta and Stone 16 and developed by Tang and Toennies 17 is offered as an option with the dispers
59. s special exponents to the orbitals used in calculating the overlap integral for the resonance integral calculation of Hp Hp atom pairs PMODS 5 value and O O atom pairs PMODS 6 value MOPAC version 5 022mn Page 23 The second modification MOD2 is a change to the 2 electron integrals SuSu pupr as follows in equation 11 It is activated by including the keyword MOD2 in the input deck E 10 756 0 Pie u Susu Papah SaSu PirP ur sandra E The third modification MOD3 alters the pairwise core core interactions that involve orbitals on two different Hp hydrogen atoms or two different oxygen atoms Itis activated by including the keyword MOD3 in the input deck R Ey LH Ln ZZ SiS ssl Te 12 Ey 0 OT ZoZo SoSo Soso 1 T az 13 By default the parameters az r and ago are equal to 2 466 A and 3 304 A respectively These two parameters can be defined differently by using the PMODS keyword in an external parameter file see Section 4 14 The PMODS value 1 corresponds to dur and the PMODS value 2 corresponds to ago A fourth modification MOD4 concerns the inclusion of quadrupole moment contributions to the 2 electron integrals of a pair of Hp atoms SHsu pypx calculated in the REPP subroutine By using the MOD4 option by including the MOD4 keyword in the input deck these quadrupole contributions are neglected Any combination of the four MODx x 1 2 3 or 4 options may be specifie
60. ss see 12 4 2 3 How to Fine Tune Optimizations e 0 eee ee eee ee eee 14 4 3 NDDO SRP Calculations 33 35 5553 e lt oo es Poets se heos she eee nse eases 15 4 4 Charge Model 2 CND ved e s s 650 es 6a dey ow ee Se ooo Soe Sw bole 16 4 5 HH repulsive Gaussians for AM1 and PM3 lt 2 e eee ee eee 17 4 6 PDDG PM3 and PDDG MNDO lt lt e Ly AT 1315 9 5 4 2 45 98 STR OS HEY WAS ERT RH SIRES SSD RRES RAS OS DORERS ARES ESS 18 4 8 AM1 D PM3 D MNDO D RM1 D and PM6 D 2 0006 18 49 PMO e kee Ke EG COKE TNE PR EEE SOS Be OER e CREE OEE SS 18 4 10 Gradients eissi arsam wie teas Peds eads Sah test erates eee ss tates 19 4 11 Hydrogen atoms with p orbitals sss T9 4 12 Origin for dipole moments e e e e e e eee eee ee ee eee te eee 19 4 13 The D3 dispersion and alternative damping functions for dispersion 20 4 14 Additional custom parameter specifications lt lt lt e e e e e e eee eee 21 4 15 Modified functional forms that can be used with PMO lt s 22 4 16 PMO version 1 PMOv1 o oo neron ereo ee ee 24 4 17 PMO version 2 PMO2 ecesas ninen 2425 an R RR a a RR 5555885 25 ATS PMO23 aan enan n TR TR AE RETR TRR A RESET RE RS 25 4 18 Analytical CI gradient wees ee Saw PA OE BR SES ew ee RE ew eS 25 S INSTALLATION dieas oe ee TT ERE RRO RRS 26 Se OMIT G lt eS esaeria did hd era TATE RT ae TER Area es dee ne ee Ge Seu a R 09 26 5 2 Files i
61. ssian 09 Revision A 02 M J Frisch G W Trucks H B Schlegel G E Scuseria M A Robb J R Cheeseman G Scalmani V Barone B Mennucci G A Petersson H Nakatsuji M Caricato X Li H P Hratchian A F Izmaylov J Bloino G Zheng J L Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven J A Montgomery Jr J E Peralta F Ogliaro M Bearpark J J Heyd E Brothers K N Kudin V N Staroverov R Kobayashi J Normand K Raghavachari A Rendell J C Burant S S Iyengar J Tomasi M Cossi N Rega J M Millam M Klene J E Knox J B Cross V Bakken C Adamo J Jaramillo R Gomperts MOPAC version 5 022mn Page 41 R E Stratmann O Yazyev A J Austin R Cammi C Pomelli J W Ochterski R L Martin K Morokuma V G Zakrzewski G A Voth P Salvador J J Dannenberg S Dapprich A D Daniels O Farkas J B Foresman J V Ortiz J Cioslowski and D J Fox Gaussian Inc Wallingford CT 2009 22 J Pople D Beveridge Approximate Molecular Orbital Theory 1 ed McGraw Hill New York 1970 pp 199 200 23 A Szabo N Ostlund Modern Quantum Chemistry Introduction to Advanced Electronic Structure Theory 1 ed rev McGraw Hill New York 1989 pp 410 412 24 R F Stewart J Chem Phys 52 1970 431 438 25 D Lide Ed CRC Handbook of Chemistry and Physics 90 ed CRC Press Boc
62. t dynamics or for parameter optimization on large sets of test molecules without having to resort to repeatedly launching it as a stand alone program Additionally it is now possible to supress all input and output from the program by setting the common block logical variable DOPRNT to FALSE by default it is set to TRUE The savings in time from avoiding repeatedly launching MOPAC and avoiding all the I O input output statements is quite substantial This is one of the principal advantages of this version MOPAC version 5 022mn Page 8 especially when carrying out direct dynamics conducting parameter optimizations or doing calculations over large sets of molecules The main changes to MOPAC 5 016mn are to the following program units File name Details mopac f Previously the main program unit now a subroutine called by MSTART mstart f The new main program unit where the program execution begins doinit f Reinitializes all subroutine and function local variables and calls RESETC and RESETD resetc f Reinitializes all common block variables to values given in BLOCK DATA resetd f Reinitializes all other common block variables setntx f Uses a virtual input file for new input deck and geometry symmetry specification It is important that if any changes are made to the block_data f file that corresponding changes are also made to the resetc f file The SETNTX subroutine can be called to use a virtual input file if the global boo
63. thods The parameters for PBEsol were chosen as the best set of D3 parameters for use with the various semiempirical methods New methods that include the D3 dispersion are MNDO D3 AM1 D3 PM3 D3 RM1 D3 and PM6 D3 Two D3 dispersion parameters are also capable of being modified MOPAC version 5 022mn Page 10 with an external parameter file to select different types of DFT D3 dispersion to use with the listed D3 semiempirical methods For more information on damping see Section 4 13 Version 5 020mn April 2013 Modified L Fiedler and D G Truhlar Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast J Gao and D G Truhlar The PMO2 semiemperical method 28 has been included as a built in keyword in this version of MOPAC It makes use of the newer MODx options in MOPAC for pairwise element parameters and uses the Hp hydrogens like its predecessor PMOv1 Version 5 021mn June 2014 Modified L Fiedler and D G Truhlar Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast J Gao and D G Truhlar A new atmospheric nucleation method 29 called PMO2a has been implemented as a built in keyword PMO2a It makes use of the Hp hydrogen atoms which contain p orbitals and is intended for atmospheric systems contain
64. uite that will confirm the expected results of all test calculations and signal the user when one of the expected results is not produced In the future this will streamline the process of ensuring no inadvertent errors slip into the code while new features are being added to MOPAC Version 5 019mn November 2011 Modified L Fiedler and D G Truhlar Authors J J P Stewart L Fiedler P Zhang J Zheng I Rossi W P Hu G C Lynch Y P Liu Y Y Chuang J Pu J Li C J Cramer P L Fast J Gao and D G Truhlar The diatomic parameter arrays were changed from compact one dimensional arrays to two or four dimensional arrays in order to simplify the program s code These changes apply to the pairwise beta and k parameters for resonance integrals using the MOD7 keyword see Section 4 15 and the pairwise core core energy parameters using the MOD5 keyword see Section 4 15 The external parameter file formats are not affected by this change Added new keyword HYBRID x xxx here x xxx is a value which should be between 0 and 1 it is 1 by default which alters the total dipole moment calculation by specifying what fraction of the hybrid dipole calculation contributes to the total dipole moment reported All three dipole calculations are still given in the output Mulliken charge dipole moment hybrid dipole moment and total dipole moment Grimme s DFT D3 dispersion 27 is now included for use with some of the semiempirical me
65. uns for verification An atmospheric cluster binding energy calculation is performed by the testsuite sh or alternatively the testsuite bat script for PCs and the check pl scripts 4 19 Analytical CI gradient Analytic gradients have been implemented for CI calculations by using the method of M J S Dewar and D A Liotard 30 No new keyword is added for this implementation When a CI calculation is performed the gradients of Cartesian coordinates are calculated using this method for the state specified in the input file When geometry optimization is required geometry is optimized using the CI gradients for the specified state See test runs 6 8 and 11 The implementation of the CI gradients has been checked against the ones calculated by AMSOL 7 1 Note that the implemented CI gradient algorithm scales as O N A more efficient algorithm by Patchkovskii and Thiel S Patchkovskii and W Thiel Theor Chim Acta 93 1996 87 has scaling as O N3 and this is under consideration for future implementation MOPAC version 5 022mn Page 26 5 INSTALLATION 5 1 Compiling The MOPAC version 5 022mn distribution package can be obtained from the University of Minnesota in one form tarred and compressed mopac5022mn tgz The mopac5022mn tgz file can be uncompressed and unarchived by typing the following tar zxvf mopac5022mn tgz This creates the directory mopac5022 in the current working directory The tar file remains in the current worki
66. used during development to check the program make ifort debug used during development to check the program make xlf to use the IBM XL Fortran xlf compiler This will create the executable file mopac5022mn After successful compilation to save disk space type make f make xxx clean where xxx is replaced by ibm sgi etc in order to remove all the object files 5 2 Files included in distribution Main directory mopac5022mn doc src test testo Directory doc mopac doc mopac5022mn doc L Directory sre Main program file mstart f directory containing the manuals directory containing the source code directory containing the test input files directory containing the test output files for comparison the original MOPAC 5 0 manual ASCH file this document Microsoft Word document Main program subroutine and function files aababc f aabacd f aabbcd f anad3 f analyt f anavib f axis f babbbc f babbcd f bangle f bfn f block_data f bonds f calpar f capcor f chgmp2 f chrge f ciparm f cnvg f coe f compfg f corgen f dang f daxpy f dcart f ddot f debug f delml2 f delmol f delri f denrot f densit f depvar f deri0 f deril f deri21 f deri22 f deri23 f deri2 f deriv f ders f dfock2 f dfpsav f dgedi f dgefa f dgemm f dhc f dhcore f diag f diagi f diagiv f diat2 f diat f digit f dihed f dijkl1 f dijkl2 f dipind f dipole f doinit f dpqtkl f drc T drcout f dscal f dswap f ef f efovlp f efsav f efstr f
67. w optimization Wide limits on RMIN and RMAX may in some cases give a faster convergence but there is always the risk that very poor steps are accepted causing the optimization to diverge The use of the default values of 0 and 4 lead to a rare rejection of steps This leads to a faster convergence but occasionally leads to the acceptance of poor steps If TS searches are found to cause problems the first try should be to change the limits of RMIN and RMAX narrowing the interval to 0 5 and 2 for example Tighter limits like 0 8 and 1 2 or even 0 9 and 1 1 will almost always slow the optimization down significantly but they may be necessary in some cases OMIN OMIN has been designed for ensuring that the nature of the TS mode only changes gradually specifically the overlap between two successive geometrical displacement should be higher than OMIN While this technique at first appears very promising it may cause problems when the Hessian is updated As the updated Hessian in each step is only approximately correct there is an upper limit on how large the TS mode overlap between steps can be To understand this consider a series of steps made from the same geometry e g at some point in the optimization but with steadily smaller step sizes The update adds corrections to the Hessian to make it a better approximation to the exact Hessian As the step size becomes small the updated Hessian converges toward the exact Hessian at least in the
68. which used the include extension and the include file SIZES This was done so that dimension changes would be much easier in MORATE In version 5 01mn the statements which made up the include file SIZES were explicitly included in all subprograms Version 5 03mn Modification of version 5 02mn The block data file was modified to include all the AM1 and PM3 parameters available in MOPAC version 6 0 Save statements were added to all the subprograms so that this version of the code does not have to be compiled with either the static or the ev option on the various Crays The include file SIZES was renamed SIZES 1 and all include statements in the FORTRAN subprograms were modified accordingly this change was made for portability purposes Version 5 04mn Modification of version 5 03mn The subprograms AM1 and MOLDAT have been modified so that the semiempirical parameters for all of the Hamiltonians MINDO 3 MNDO AM1 and PM3 can be modified by using the keyword EXTERNAL In version 5 0 only the MNDO and AM1 Hamiltonian could be modified Version 5 05mn July 1994 J J P Stewart I Rossi W P Hu G C Lynch Y P Liu and D G Truhlar Modification of version 5 04mn Several new capabilities have been added and the code has been modified to make it portable and ANSI FORTRAN 77 compliant A bug which caused the program to crash when parameter MAXORB lt NMECI 2 has been corrected A bug in ANALYT which caused PM3 analytical derivatives

Manual for MOPAC, version 5.022mn

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