The Beginner MolCAS User Manual
Contents
1. Error from SEWARD The output was EOF reached for file stdin This error was generated from the following input H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 H6 2 1 08900 1 109 471 3 180 000 End of Input Explanation The Z Matrix section must end with a black line The correct input is H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 H6 2 1 08900 1 109 471 3 180 000 35 End of Input Note that this error occurs every time the input is incomplete e g when a keyword must be followed by some number or string Error from SEWARD The output was ERROR Superimposed atoms 45 r 0 This error was generated from the following input 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 Explanation Hydrogen atoms H4 and H5 due to the same dihedral angle 120 are superimposed The correct input is e g 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 Error from SCF The output was VecFind Error in number of electrons An even number of electrons are required by RHF use UHF This error was generated from the following input ZMAT H cc pVDZ C cc pVDZ 36 C1 02 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 End of Input amp SCF amp END End of Input Expla2. 95000 95000 08900 PNNN 109 471 109 471 109 471 109 471 3 120 000 3 120 000 3 180 000 41 Appendix Input for lesson 3 amp SEWARD amp END Title And your second one ZMAT H CC pVDZ C cc pVDZ O cc pVDZ C1 02 1 1 40000 H3 1 0 95000 H4 1 0 95000 H5 1 0 95000 H6 2 1 08900 End of Input amp SCF amp END Title The SCF part KSDFT B3LYP End of Input the DFT B3LYP energy of methanol 2 109 471 2 109 471 3 120 000 2 109 471 3 120 000 1 109 471 3 180 000 42 Appendix Input for lesson 4 amp SEWARD amp END Title And the third one an MP2 calculation methanol again ZMAT H CC pVDZ C cc pVDZ O cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 H6 2 1 08900 1 109 471 3 180 000 End of Input amp SCF amp END Title The SCF part End of Input amp MBPT2 amp END Title The MP2 calculation End of Input 43 Appendix Input for lesson 5 gt gt gt Set MaxIter 5000 lt lt lt gt gt gt Do While lt lt lt amp SEWARD amp END Title Optimization of geometry methanol for the last time ZMAT H cc pVDZ C cc pVDZ O cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 H6 2 1 08900 1 109 471 3 180 000 End of Input amp SCF amp END Title The energy End of Inp
3. ZMAT H cc pVDZ C cc pVDZ O cc pVDZ N cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 Explanation The molecule does not contain any Nitrogen atom but its basis set was specified Just remove or comment the corresponding line 33 ZMAT H cc pVDZ C cc pVDZ O cc pVDZ N CC pVDZ C1 Error from SEWARD The output was ChkLbl Duplicate label Lb1 H This error was generated from the following input ZMAT H cc pVDZ C cc pVDZ O cc pVDZ C 0 1 1 40000 H 1 0 95000 H 1 0 95000 H 1 0 95000 H 2 1 08900 PNNN 109 471 109 471 109 471 109 471 3 120 000 3 120 000 3 180 000 Explanation There are more than one Hydrogen atoms therefore each one requires a unique label The input should be e g 1 0 95000 H2 1 0 95000 H3 1 0 95000 H4 2 1 08900 PNNN 109 471 109 471 109 471 109 471 3 120 000 3 120 000 3 180 000 Error from SEWARD The output was 34 BasisReader Wrong symbol in line C1 This error was generated from the following input ZMAT H cc pVDZ C cc pVDZ O cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471 Explanation The basis set sub section of the Z Matrix input must end with a black line before to start the matrix The correct input is H cc pVDZ C cc pVDZ O cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471
4. 27 CN Bond C1 N2 28 CH Bond C1 H3 29 NH Bond N2 H3 30 Vary 31 CN 32 CH 33 NH 34 RowH 35 NH 36 End of Internal 37 End Of Input Lines 12 14 Z matrix subsection of SEWARD input Shown here for the identification of the atom labels only Line 22 keyword TS to require the optimization of a transition structure Line 23 keyword PRFC Print Force Constants to require the print out of the eigenvalues and eigenvectors of the Hessian matrix Lines 24 25 maximum number of optimization steps Lines 26 36 User defined coordinates sub section Starts with keyword Internal Coordinates and finishes with keyword End of Internal 30 Lines 27 29 definition of the Primitive Internal Coordinates PICs Each label can be 8 characters long Line 30 keyword Vary followed by the list of the Internal Coordinates ICs to be optimized Lines 31 33 list of ICs In these example they correspond to the PIC therefore they use the same labels Line 34 keyword ROWH followed by the list of the ICs for which is required the numerical estimation of row and column of the Hessian matrix Line 35 IC for which the numerical estimation of row column of the Hessian matrix is required All defined ICs must be listed below Vary and Fix keywords The ICs listed below the RowH must correspond to the ones listed as above i e this list is an extra A part for the definition of PICs and ICs the output of SLAPAF is the sa
5. Angle H3 C1 H4 DH4 Dihedral 02 H3 C1 H4 CH5 Bond C1 H5 HCH5 Angle H4 C1 H5 DH5 Dihedral H3 H4 C1 H5 Vary co CH3 OCH3 CH4 HCH4 DH4 CH5 HCH5 DH5 End of Internal Explanation When using the Primitive Internal Coordinates also as Internal Coordinates CO2 in this example the second ones specified below the keyword 38 Vary must correspond to the first ones CO is a wrong IC in this case Internal Coordinates CO2 Bond C1 02 Vary C03 Error from SLAPAF The output was kkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ERROR Undefined internal ROWH coordinate in NH kkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk This error was generated from the following input C1 N2 1 1 17000 H3 1 1 16000 2 80 000 Internal Coordinates CN Bond C1 N2 CH Bond C1 H3 NH Bond N2 H3 Vary CN CH ROWH NH End of Internal The Internal Coordinates specified for the keyword ROWH must be first listed before below the keyword Vary The right input is the following Internal Coordinates CN Bond C1 N2 CH Bond C1 H3 NH Bond N2 H3 Vary CN 39 End of Internal 40 Appendix Input for lesson 2 amp SEWARD amp END Your first MolCAS calculation HF energy of methanol Title ZMAT H cc pVDZ C cc pVDZ O cc pVDZ C1 02 1 1 H3 1 0 H4 1 0 H5 1 0 H6 2 1 End of Input amp SCF amp END Title The SCF part End of Input 40000 95000
6. This file is normally located in the scratch directory but is can be easely copied by the submisio script 10 3 And your second one the DFT B3LYP energy of methanol With MolCAS you can also calculate the energy with the Density Functional Methods of course Here an example for methanol The SEWARD section of the output is the same as in the first example The SCF part of the input is the following the full input can be find in the Appendix 18 amp SCF amp End 19 Title 20 The DFT part 21 KSDFT 22 B3LYP 23 End of Input Lines 01 17 not shown are the same as in the previous one Line 18 starts the SCF input Lines 19 and 20 contain the title They can be omitted Line 21 keyword KSDFT which requires a Kohn Sham DFT calculation Line 22 keyword B3LYP which specifies the functional to be used Line 23 terminates the SCF input The output of SEWARD is the same as before In the SCF output we find again after the details of the calculation and the SCF iterations the SCF KS DFT Program Final results section Here we can find the converged energy values Total KS DFT energy 115 6513810617 One electron energy 252 6467181463 Two electron energy 951512111511 Nuclear repulsion energy 41 8441259335 Kinetic energy interpolated 115 6083888328 Virial theorem 1 0003718781 The line Total SCF energy contains the DFT B3LYP energy 115 6513810617 au The coeficients of the molecular orbitals follows Note
7. 1 the IC corresponds to the PIC CH12 Bond C7 H12 CH12 CASE 2 two ICs are linear combinations of PICs Bond 02 H4 HO5 Bond H4 05 SumR 1 0 OH4 1 0 HO5 DifR 1 0 OH4 1 0 HO5 In this example the full input can be find in the Appendix the definition of the 23 Primitive Internal Coordinates is the same used for the Z matrix input in SEWARD We can find bond distances lines 28 29 31 34 37 40 and 43 planar angles lines 30 32 35 38 41 and 44 and dihedral angles lines 33 36 39 42 and 45 The list of the Internal Coordinates as corresponding PIC follows 12 C1 13 C12 1 1 75000 14 C3 1 1 45000 2 109 471 15 H4 1 1 08900 2 109 471 3 120 000 16 H5 1 1 08900 2 109 471 3 120 000 17 H6 3 1 08900 1 109 471 2 60 000 18 H7 3 1 08900 1 109 471 6 120 000 19 H8 3 1 08900 1 109 471 6 240 000 26 amp SLAPAF amp END 27 Internal Coordinates 28 cc12 Bond C1 C12 29 CC3 Bond C1 C3 30 C1CC3 Angle C12 C1 C3 31 CH4 Bond C1 H4 32 C1CH4 Angle C12 C1 H4 33 DH4 Dihedral C3 C12 C1 H4 34 CH5 Bond C1 H5 35 C1CH5 Angle C12 C1 H5 36 DH5 Dihedral C3 C12 C1 H5 37 CH6 Bond C3 H6 38 CCH6 Angle C1 C3 H6 39 DH6 Dihedral C12 C4 C3 H6 40 CH7 Bond C3 H7 41 CCH7 Angle C1 C3 H7 42 DH7 Dihedral H6 C1 C3 H7 43 CH8 Bond C3 H8 44 CCH8 Angle C1 C3 H8 45 DH8 Dihedral H6 C4 C3 H8 46 Vary 47 CC12 48 CC3 49 ClCC3 50 CH4 51 C1CH4 52 DH4 53 CH5 54 C1CH5 55 DH5 56 CH6 57 CCH6 58 DH6 59 CH7
8. 54 CC3 Bond C1 C3 55 Vary 56 CC2 57 CCC3 58 CHA 59 CCH4 60 DH4 61 CH5 62 CCH5 63 DH5 64 CH6 65 CCH6 66 DH6 67 CH7 68 CCH7 69 DH7 70 CH8 71 CCH8 72 DH8 73 CH9 74 CCH9 75 DH9 76 CH10 77 CCH10 78 DH10 79 Fix 80 CC3 81 End of Internal 82 Iterations 83 20 84 End Of Input Lines 11 20 Z matrix subsection of SEWARD input Shown here for the identification of the atom labels only Lines 30 81 User defined coordinates sub section Starts with keyword Internal Coordinates and finishes with keyword End of Internal Lines 31 54 definition of the PIC Each label can be 8 characters long Line 55 keyword Vary followed by the list of the ICs to be optimized Each label 27 can be 8 characters long Lines 56 78 list of IC In these example they correspond to the PIC therefore they use the same labels Line 79 keyword Fix followed by the list of the ICs to be kept frozen Each label can be 8 characters long Line 80 IC to be kept frozen In these example it correspond sto the PIC therefore it uses the same label Lines 82 83 maximum number of optimization steps The output of SLAPAF after the value of the Internal Coordinates contains the gradient for each frozen IC 0 0685 for CC3 ck ckckckckckckckokckockck ck ckockck ckck ck ck ckck kok kck kck ckck ckck kckockok ck ck ck k ck kckok Value of internal coordinates au or rad ck KKK KKK KKK KKK KKK KKK KEKE
9. 60 CCH7 61 DH7 62 CH8 63 CCH8 64 DH8 65 End of Internal 66 Iterations 24 67 20 68 End of Input Lines 12 19 Z matrix subsection of SEWARD input Shown here for the identification of the atom labels only Lines 27 65 User defined coordinates sub section Starts with keyword Internal Coordinates and finishes with keyword End of Internal Lines 28 45 definition of the PIC Each label can be 8 characters long Line 46 keyword Vary followed by the list of the ICs to be optimized Each label can be 8 characters long Lines 47 64 list of IC In these example they correspond to the PIC therefore they use the same labels Lines 66 67 maximum number of optimization steps The output on SLAPAF has nothing different than the previous ones 25 9 Constrained Optimization with User defined Internal Coordinates let s go back to the potential energy curve for CH H C CH Constrained optimizations of geometries can also be performed with User defined Internal Coordinates In this example as usual the full input can be find in the Appendix we go back to the definition of the potential energy curve for the addition of the methyl radical CH to ethylene H C CH The input is the same as for the lesson 7 except for the SLAPAF section obviously The frozen coordinate is again the C1 C3 that we can define both as Primitive Internal Coordinate and as Internal Coordinate The key point of the input
10. KEKE KEKE KEKE KEKE ck k ck kckok cc2 2 7945 CCC3 1 9414 CH4 2 0451 CCH4 1 9630 DH4 2 0598 CH5 2 0451 CCH5 1 9631 DH5 2 0600 CH6 2 0324 CCH6 2 1014 DH6 1 4251 CH7 2 0324 CCH7 2 1013 DH7 1 4255 CH8 2 0448 CCH8 1 8889 DH8 3 1414 CH9 2 0435 CCH9 1 8909 DH9 2 0952 CH10 2 0436 CCH10 1 8907 DH10 2 0952 CC3 3 4015 Following internal coordinates are fixed CC3 with a gradient of 0 685E 01 is frozen and the gradient is annihilated 28 10 Optimization of a Transition Structure with User defined Internal Coordinates from HCN to CNH again The optimization of a Transition Structure TS requires a good Hessian matrix This can be easly obtained with a numerical estimation see lesson 6 but when the molecular system contains a big number of atoms this can require a very long time remember that the numerical estimation of the Hessian matrix requires 2 3N 6 gradient calculations A new feature implemented in MoICAS 7 2 allows the numerical estimation of some selected rows and columns of the Hessian matrix throughout finite differentiations of the corresponding Internal Coordinates ICs This new approach requires the usage of the User defined Internal Coordinates and of the keyword RowH In this example we will optimize again the TS for the Hydrogen migration as in the previous lesson with this new alternative approach the input file can be find in the Appendix The initial geometry is the same as in the previous
11. convergence the final predicted structure will be printed here This is not identical to the structure printed in the head of the output Nuclear coordinates of the final structure Bohr Angstrom ATOM X Y Z X Y Z c1 0 006040 0 000000 0 008402 0 003196 0 000000 0 004446 N2 0 016520 0 000000 2 204310 0 008742 0 000000 1 166471 H3 2 148300 0 000000 0 395723 1 136831 0 000000 0 209407 Nuclear coordinates in ZMAT format Angstrom and Degree C1 N2 al 1 170978 H3 1 1 159912 2 78 791420 After the optimization condition section the final geometry is printed both in Cartesian coordinates and in Z Matrix format if used in SEWARD and if the conversion is possible SLAPAF generates again the input file for molden with the geometry changes Project geo molden and due to the numerical Hessian an input file for molden with the vibrational frequencies and normal modes Project geo molden 19 7 Constrained Optimization building the potential energy curve for CH H C CH With MolCAS it is possible to define the potential energy curve along a single geometrical parameter optimizing the remaining internal coordinates throughout a constrained optimization In this example we want to define the potential energy curve for the addition of the methyl radical CH to ethylene H C CH The C1 C3 distance R will be kept frozen to 2 0 Angstroms while the remaining internal coordinate will be optimized 3 s H3C d R
12. e IH St Ta 2 The full input can be find in the Appendix The SLAPAF section of input is 28 amp SLAPAF amp END 29 Iterations 30 20 31 Constrain 32 R Bond C1 C3 33 Value 34 R 2 0 Angstrom 35 End of Constrain 36 End Of Input Lines 01 27 not shown are similar to the previous examples a part for the structure Lines 29 30 maximum number of optimization steps Lines 31 35 Constrained Optimization sub section Starts with keyword Constrain and finishes with keyword End of Constrain 20 Line 32 definition of the internal coordinate R as bond distance between atoms C1 and C3 remember to use different labels for all atoms More than one constrained coordinates can be specified here Line 33 keyword Value followed by the values of the constrained coordinates Line 34 value 2 0 Angstroms for the coordinate defined above R More details about the definition of the internal coordinate can be find in the manual 3 38 4 Note that it is not compulsory but it is advisable to give an initial geometry where the internal coordinate that has to be kept frozen is already at the required value As an example line 13 in the input could be C3 1 2 500 2 110 0 The output on SLAPAF of the last step is the following It starts with the Constrained Optimization Section where we can find the definition and the value of the constrained coordinates and the related gradient 0 048157 ConstraintsConst
13. is the list of the frozen Internal Coordinates ICs in a subsection that follows the keyword Fix This subsection follows the one with the list of ICs to be optimized started with the keyword Vary Note that in this case the frozen coordinate will keep the value originally found in the starting geometry given in SEWARD input When using IC corresponding to PIC it is advisable to use also the same order for the PICs and the ICs definitions In this example the C1 C3 bond distance PIC and IC CC3 is the last in both lists line 54 and 80 11 C1 12 C2 1 1 440 13 C3 1 2 000 2 110 0 14 H4 1 1 079 2 115 5 3 113 15 H5 1 1 079 2 115 5 3 113 16 H6 2 1 075 1 120 5 3 83 17 H7 2 1 075 1 120 5 3 83 18 H8 3 1 080 1 105 5 2 180 19 H9 3 1 079 1 106 0 8 120 20 H10 3 1 079 1 106 0 8 120 29 amp SLAPAF amp END 30 Internal Coordinates 31 CC2 Bond C1 C2 32 CCC3 Angle C2 C1 C3 33 CHA Bond C1 H4 34 CCH4 Angle C2 C1 H4 35 DH4 Dihedral C3 C2 C1 H4 36 CH5 Bond C1 H5 26 37 CCH5 Angle C2 C1 H5 38 DH5 Dihedral C3 C2 C1 H5 39 CH6 Bond C2 H6 40 CCH6 Angle C1 C2 H6 41 DH6 Dihedral C3 C1 C2 H6 42 CH7 Bond C2 H7 43 CCH7 Angle C1 C2 H7 44 DH7 Dihedral C3 C1 C2 H7 45 CH8 Bond C3 H8 46 CCH8 Angle C1 C3 H8 47 DH8 Dihedral C2 Ci C3 H8 48 CH9 Bond C3 H9 49 CCH9 Angle C1 C3 H9 50 DH9 Dihedral H8 C1 C3 H9 51 CH10 Bond C3 H10 52 CCH10 Angle C1 C3 H10 53 DH10 Dihedral H8 C1 C3 H10
14. lesson but the number of gradient calculations drops from 8 to 5 Although this is a good result it does not mean that the new approach is alway more efficient the reduction of the number of initial gradient estimations corresponding to the number of ICs for which the selected numerical Hessian is required can be compensated by the slightly less efficient algorithm for the optimization with User defined ICs H 4 s k Ci HCN CNH The differences in the input are in the SLAPAF section only obviously 29 Note that the definition of the geometry given in the SEWARD section lines 12 14 is different than that one used in the SLAPAF section in the former the position of the hydrogen atom H3 line 14 is defined throughout its distance from atom 1 N1 and its planar angle with atom 2 N2 while in the latter the position of H3 is defined throughout the two distances from N1 CH line 31 and N2 NH line 32 Also note that although the migration of the hydrogen atom would require the numerical estimation of the rows and columns of the Hessian matrix for both distances CH and NH the coupling between the two ICs introduces the necessary information in the matrix about the curvature of the Potential energy Surface PES with the differentiation of one IC only 12 C1 13 N2 1 1 17000 14 H3 1 1 16000 2 80 000 21 amp SLAPAF amp END 22 TS 23 PRFC 24 Iterations 25 10 26 Internal Coordinates
15. that SCF also generates a Project scf molden file that can be read with the program molden to see the MO 11 4 And the third one an MP2 calculation methanol again With MoICAS you can also calculate several post SCF energies like MP2 and Coupled Cluster CC The input for the first one is very simple After the SEWARD same as before and the SCF remember MP2 is a post SCF method therefore you need converged Hartree Fock wavefunction and energy you just have to add the MP2 part here named MBPT2 Many Body Perturbation Theory at 2nd order MBPT2 As usual the full input can be find in the Appendix 23 amp MBPT2 amp End 24 Title 25 The MP2 calculation 26 End of Input Lines 01 22 not shown are the same as in the first example Line 23 starts the MBPT2 MP2 input Lines 24 and 25 contain the title They can be omitted Line 26 terminates the MBPT2 input The output of SEWARD and SCF are the same as in the first example The output on MBPT2 is very simple After a few details about the calculations frozen and active occupied and external orbitals the results have given The output is the following Conventional algorithm used 114 9782183794 a u 0 3359012163 a u SCF energy Second order correlation energy 115 3141195957 a u 0 9562823661 Total energy Coefficient for the reference state The line Total energy contains the MP2 energy 115 3141195957 au 12 5 Optimization o
16. 1 75000 C3 1 1 45000 2 109 471 H4 1 1 08900 2 109 471 3 120 000 H5 1 1 08900 2 109 471 3 120 000 H6 3 1 08900 1 109 471 2 60 000 H7 3 1 08900 1 109 471 6 120 000 H8 3 1 08900 1 109 471 6 240 000 End of Input amp SCF amp END End of Input amp SLAPAF amp END Internal Coordinates ccl2 Bond C1 C12 CC3 Bond C1 C3 C1CC3 Angle C12 C1 C3 CHA Bond C1 H4 C1CH4 Angle C12 C1 H4 DH4 Dihedral C3 C12 C1 H4 CH5 Bond C1 H5 C1CH5 Angle C12 C1 H5 DH5 Dihedral C3 C12 C1 H5 CH6 Bond C3 H6 CCH6 Angle C1 C3 H6 DH6 Dihedral C12 C1 C3 H6 CH7 Bond C3 H7 CCH7 Angle C1 C3 H7 DH7 Dihedral H6 C1 C3 H7 CH8 Bond C3 H8 CCH8 Angle C1 C3 H8 DH8 Dihedral H6 C1 C3 H8 Vary ccl2 CC3 C1CC3 CH4 C1CH4 DH4 CH5 C1CH5 DH5 47 chloroethane CH6 CCH6 DH6 CH7 CCH7 DH7 CH8 CCH8 DH8 End of Internal Iterations 20 End of Input gt gt gt EndDo lt lt lt 48 Appendix Input for lesson 9 gt gt gt Set MaxIter 5000 lt lt lt gt gt gt Do While lt lt lt amp SEWARD amp END Title Energy curve of CH3 H2C CH2 ZMAT H 6 31G C 6 31G C1 C2 1 1 440 C3 t 1 800 2 110 0 H4 1 1 079 2 115 5 3 113 H5 1 1 079 2 115 5 3 113 H6 2 1 075 1 120 5 3 83 H7 2 1 075 1 120 5 3 83 H8 3 1 080 1 105 5 2 180 H9 3 1 079 1 106 0 8 120 H10 3 1 079 1 106 0 8 120 End Of Input amp SCF amp END UHF End of input amp SLAPAF amp END Internal Coordinates cc2 Bond
17. 9 RS RFO None 0 2 115 03576486 0 05754648 0 139585 0 081463 nrc003 0 166021 nrc003 115 05309080 RS RFO BFGS 0 3 115 04887247 0 01310760 0 033037 0 018068 nrc004 0 031841 nrco001 115 04938248 RS RFO BFGS 0 4 115 04958236 0 00070990 0 014454 0 007332 nrc001 0 022427 nrcoo1 115 04973174 RS RFO BFGS 0 5 115 04973289 0 00015053 0 000532 0 000357 nrcO05 0 001421 nrc005 115 04973331 RS RFO BFGS 0 Cartesian Displacements Gradient in internals Value Threshold Converged Value Threshold Converged RMS 0 7962E 03 0 1200E 02 Yes 0 1879E 03 0 3000E 03 Yes Max 0 9294E 03 0 1800E 02 Yes 0 3570E 03 0 4500E 03 Yes He Sessa ee ee a ee a DA A Heese Pao see lek eS ee E Iac Geometry is converged in 5 iterations to a minimum 15 The four condition are fullfitted Yes The SLAPAF output terminates with the final optimized geometry both in Cartesian coordinates and in Z Matrix format if used in SEWARD and if the conversion is possible This one can be used throughout an easy cut and paste to prepare a new input KAKA KR KKK KK RK KK RK RK RK kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk ck ck ck ck ck ck ck ck ck ck ck ck kk ck KEK k k kkk kkk kkk kk kk kk kkk k kk kk k k kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk
18. C1 C2 CCC3 Angle C2 C1 C3 CH4 Bond C1 H4 CCH4 Angle C2 C1 H4 DH4 Dihedral C3 C2 C1 H4 CH5 Bond C1 H5 CCH5 Angle C2 C1 H5 DH5 Dihedral C3 C2 C1 H5 CH6 Bond C2 H6 CCH6 Angle C1 C2 H6 DH6 Dihedral C3 C1 C2 H6 CH7 Bond C2 H7 CCH7 Angle C1 C2 H7 DH7 Dihedral C3 C1 C2 H7 CH8 Bond C3 H8 CCH8 Angle C1 C3 H8 DH8 Dihedral C2 C1 C3 H8 CH9 Bond C3 H9 CCH9 Angle C1 C3 H9 DH9 Dihedral H8 C1 C3 H9 CH10 Bond C3 H10 CCH10 Angle C1 C3 H10 DH10 Dihedral H8 C1 C3 H10 CC3 Bond C1 C3 Vary 49 CC2 CCC3 CH4 CCH4 DH4 CH5 CCH5 DH5 CH6 CCH6 DH6 CH7 CCH7 DH7 CH8 CCH8 DH8 CH9 CCH9 DH9 CH10 CCH10 DH10 Fix CC3 End of Internal Iterations 20 End Of Input gt gt gt EndDo lt lt lt 50 Appendix Input for lesson 10 gt gt gt Set MaxIter 5000 lt lt lt gt gt gt Do While lt lt lt amp SEWARD amp END Title Transition Structure HCN gt CNH ZMAT H cc pVDZ C cc pVDZ N cc pVDZ N2 1 1 17000 H3 1 1 16000 2 80 000 End Of Input amp SCF amp END End of input amp SLAPAF amp END TS PRFC Iterations 10 Internal Coordinates CN Bond C1 N2 CH Bond C1 H3 Bond N2 H3 End of Internal End Of Input gt gt EndDo lt lt lt 51
19. The Beginner MoICAS User Manual www teokem lu se molcas by Giovanni Ghigo www personalweb unito it giovanni ghigo Mol CAS molcas home html Dipartimento di Chimica Generale e Chimica Organica Universit di Torino E Mail giovanni ghigo unito it Version 26 March 2008 The beginner s MoICAS user Manual Version 19 March 2008 1 Introduction please read it it s short 2 Your first MoICAS calculation the HF energy of methanol 3 And your second one the DFT B3LYP energy of methanol 4 And the third one an MP2 calculation methanol again 5 Optimization of geometry methanol for the last time 6 Optimization of a Transition Structure from HCN to CNH 7 Constrained Optimization building the potential energy curve for CH H C CH 8 Optimization with User defined Internal Coordinates chloroethane 9 Constrained Optimization with User defined Internal Coordinates let s go back to the potential energy curve for CH H C CH 10 Optimization of a Transition Structure with User defined Internal Coordinates from HCN to CNH again Most frequent errors in MolCAS Appendix inputs 11 12 13 TT 20 23 26 29 32 41 1 Introduction This manual has been written to help new MolCAS users who never used the program and that like me I must confess are a bit too lazy to read the full manual Note that this manual DOES NOT substitute the official one The scope of this page
20. a planar angle with oxygen atom index 2 of 109 471 degrees and a dihedral angle with the first hydrogen atom index 3 of 120 0 degrees Fifth atom hydrogen label H5 bonded to carbon atom index 1 at distance 1 089 making a planar angle with oxygen atom index 2 of 109 471 degrees and a dihedral angle with the first hydrogen atom index 3 of 120 0 degrees A scketch of these dihedral angles is given below using a Newman s projection oxygen O2 is behind carbon C1 Hs H4 Last atom hydrogen label H6 bonded to oxygen atom index 2 at distance 0 950 making a planar angle with carbon atom index 1 of 105 000 degrees and a dihedral angle with the first hydrogen atom index 3 of 180 0 degrees Lines 08 and 15 are blank lines and are used to stop the sections In alternative to the Z Matrix format there is of course the Cartesian XYZ format to define the molecular structure see keyword BASIs in chap 3 15 2 Line 16 terminates the SEWARD input Line 17 is used just to separate the sections and can be omitted Line 18 starts the SCF input Lines 19 and 20 contain the title They can be omitted Line 21 terminates the SCF input By default SCF calculates a molecular wavefunction as singlet no unpaired electrons and neutral no charges And now let see what we can find in the output The first part contains the SEWARD output Here we can find the Cartesian coordinates both in atomic units and
21. cular structures Details about keyword ZMAT can be found in the manual chap 3 15 3 The molecule is sketched below grey line means a bond below the molecular plane Hs O H4 Hs He The full input can be find in Appendix 01 amp SEWARD amp END 02 Title 03 Your first MolCAS calculation HF energy of methanol 04 ZMAT 05 H cc pVDZ 06 C cc pVDZ 07 O cc pVDZ 08 09 C1 10 02 1 1 400 11 H3 1 1 089 2 109 471 12 H4 1 1 089 2 109 471 3 120 0 13 H5 1 1 089 2 109 471 3 120 0 14 H6 2 0 950 1 105 000 3 180 0 15 16 End of Input 17 18 amp SCF amp End 19 Title 20 The SCF part 21 End of Input Line 01 declare the program to be executed Lines 02 and 03 contain the title They can be omitted Line 04 contains the keyword ZMAT used to define the molecular structure But first the basis sets used for each single atom one definition for H one for C one for O is listed Note the dots details can be found in the manual chap 3 15 1 The molecular structure making reference to the figure above is defined in linees 09 14 as First atom carbon label C1 Second atom oxygen label 02 bonded to carbon atom index 1 at distance 1 400 Third atom hydrogen label H3 bonded to carbon atom index 1 at distance 1 089 and making a planar angle with oxygen atom index 2 of 109 471 degrees Fourth atom hydrogen label H4 bonded to carbon atom index 1 at distance 1 089 making
22. f geometry methanol for the last time MolCAS can also optimize structures Both minima and transition structures TS can be localized on the Potential Energy Surface PES The module devoted to this operation is SLAPAF This module must be preceded by the module ALASKA that yields the Cartesian gradient When the analytical derivatives are not available ALASKA automatically invokes the module NUMERICAL_GRADIENT This happens for MBPT2 CC and CASPT2 optimizations The general scheme for any geometry optimization is the following ENERGY SEWARD METHOD GRADIENT ALASKA NEW GEOMETRY SLAPAF YES FINAL ENERGY 13 Whatever the method and module used for the calculation of the energy the first module to be invoked is again SEWARD After the energy the gradient will be evaluated by ALASKA and finally module SLAPAF will define the new geometry and if the gradients and displacement fullfit the required condition it will invoke the calculation of the energy at the final geometry Otherwise the cycle will be repeated until optimization or maximum number of steps is reached Note that module ALASKA is automatically invoked by the SLAPAF module This is the preferred mode of operation In connection with numerical gradients this will ensure that the rotational and translational invariance is fully utilized in order to reduce the number of used displacements The full input for the HF optimization of methanol can be find in
23. intsConstraintsConstraints Then we find the optimization condition section and the final geometry as before The job terminates with the calculation of the final energy 22 8 Optimization with User defined Internal Coordinates chloroethane The optimization of geometry with MolCAS can also be performed with a set of User defined Internal Coordinates It must be pointed out that these coordinated included in the SLAPAF input have nothing to do with the internal coordinates implicitly defined in the Z matrix used to furnish the geometry in SEWARD input However for simple cases as in this example it can be very easy to define the internal coordinates in the same way for both input sections First a set of Primitive Internal Coordinates PIC must be given There are several types of primitive coordinates but here we will see only the most commonly used bond distances planar angles and dihedral angles More details can be find in the manual 3 38 4 The PIC must be 3N 6 N is the number of nuclei at least but they can be more this is what normally happens with the redundant auto defined coordinates All make reference to the atomic labels The Internal Coordinates IC follows These can correspond to the PIC and in this case the same label can be used see example below case 1 or they can be linear combinations of the PIC defined above see example below case 2 In any case the number of IC must be 3N 6 CASE
24. ir pwd 04 export WorkDir CurrDir scr_ Project 05 export MOLCAS progs Molcas 7 0 dev 06 export MOLCAS LINK N 07 export MOLCASMEM 1024 08 mkdir WorkDir 09 MOLCAS sbin molcas Project input Project log 2 workDir Project err Note that line 05 must contain the real MolCAS directory Line 07 must contain the maximun memory allowed 128 MBytes is enough for the examples but it can be increased for real calculations Line 08 sometime required to be commented with This will be explained in some examples Here is a version a bit more sofisticated The only difference in the gestion of the files generated by molcas and some nice printouts 01 bin sh 02 export CurrDir pwd 03 export WorkDir CurrDir scr_ Project 04 export MOLCAS progs MolCAS 7 0 dev 05 echo 06 export Project 1 07 export WorkDir CurrDir scr Project 08 echo owes ere eue See bese Sete ee ccce S 09 echo Job Project 10 echo cat MOLCAS molcashome 11 echo MolCASMem MOLCASMEM 12 echo Date date 13 echo te Iain ccot ab ccotefedcttes ee 14 mkdir WorkDir 15 MOLCAS sbin molcas Project input gt Project out 2 WorkDir Project err 16 date gt gt Project out 17 cat proc cpuinfo grep name gt gt Project out 18 rm f Project Orb autosaved Project autosaved 19 cp f WorkDir Project RunFile Project Hessian 20 cp f WorkDir Project JobIph Project JobIph 21 cp f WorkDir Project geo
25. isplacements Gradient in internals Value Threshold Converged Value Threshold Converged RMS 0 1170E 00 0 1200E 02 No 0 1178E 00 0 3000E 03 No Max 0 1374E 00 0 1800E 02 No 0 2247E 00 0 4500E 03 No SR ae ete Po ssee tee eee see etica Se ee cee SS Convergence not reached yet This is the output of the first step All parameters for the optimization maximum and RMS of both gradient and displacement are above the thresholds In this case as the maximum number of steps 20 is not reached an other optimization step is performed When all condition are fullfitted the output will be like KARR KR KAKA KR RK RK RK RK RK kk KR KR KR KR KR k kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k k kk kk kk k k kk ck ck ck ck ck ck ck ck ck ck k k ok ok kkk kkk kkk kk kk k k k k k k k k k k k k k k k k k k k k k Energy Statistics for Geometry Optimization kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk KR KKK RK RK kk kkk kkk kk k k kk KR KR KR k k k k k k k kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k k kk k k Energy Grad Grad Step Estimated Geom Hessian Iter Energy Change Norm Max Element Max Element Final Energy Update Update Index 1 114 97821838 0 00000000 0 333071 0 224740 nrc006 0 233783 nrc006 115 0205230
26. k k k k k k k k k k Energy Statistics for Geometry Optimization kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk Cokckckckckck ck ck kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k k Energy Grad Grad Step Estimated Geom Hessian Iter Energy Change Norm Max Element Max Element Final Energy Update Update Index 1 92 80720679 0 00000000 0 005379 0 003337 nrc002 0 020106 nrc003 92 80725311 RSIRFO None 1 2 92 80717119 0 00003559 0 000074 0 000052 nrc002 0 000199 nrc003 92 80717120 RSIRFO MSP 1 Cartesian Displacements Gradient in internals Value Threshold Converged Value Threshold Converged Pa Ses He ee ee Se eee ee aaa Poses tole see bec dete ee elt eee bese Ss RMS 0 1623E 03 0 1200E 02 Yes 0 4279E 04 0 3000E 03 Yes 18 FALSA RA dive RS are wien ARR PME Max 0 1667E 03 0 1800E 02 Yes 0 5203bE 04 0 4500E 03 Yes Falle ie uw uc gue du E EE ccce emen enc uendere na EUER ee cas Geometry is converged in 2 iterations to a transition state KR KR KR kkk k KKK RK RK k k k k k k KR k k KR KR KR KR KR KR KR KR k kk kk kk kk kk kk kk kk kk kk kk kk k k kk kk kk kk kk kk KR KR KR k kk kk kk kk k k kk k k kk kk k k k k ck k k k kkk kkk kkk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k k Geometrical information of the final structure NOTE on
27. kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk ck ck kk kk k k kk k k Geometrical information of the final structure NOTE on convergence the final predicted structure will be printed here This is not identical to the structure printed in the head of the output Nuclear coordinates of the final structure Bohr Angstrom ATOM C1 02 X 057685 077231 909912 973184 973184 768847 Nuclear coordinates in ZMAT NHEHHH o 397867 088946 095397 095397 944880 format BNNN Y 000000 000000 000000 679637 679637 000000 ORROOO 107 452209 112 260169 112 260169 109 092692 Angstrom and 3 3 3 Z X Y Z 0 085315 0 030526 0 000000 0 045147 2 726828 0 040869 0 000000 1 442975 0 517301 1 010682 0 000000 0 273744 0 705623 0 514987 0 888826 0 373400 0 705623 0 514987 0 888826 0 373400 3 298381 0 936034 0 000000 1 745428 Degree 118 745959 118 745959 180 000000 SLAPAF also generates an input file for molden with the geometry changes Its name is Project geo molden The calculation of the final energy terminates the job 16 6 Optimization of a Transition Structure from HCN to CNH The optimization of Transition Structure TS with MolCAS can be performed in a very easy way adding the keyword TS in the SLAPAF input In this example we optimize the TS for the reaction HCN _ CNH The full input can be find in the ap
28. me as the one in lesson 6 31 Most frequent errors in MolCAS This page contains a set of the most common errors They are collected from the output message errors and grouped by MolICAS module These are only examples the possible errors are a number and most of them will give the same messages Errors from SEWARD The output was ERROR Wrong number of basis sets Available 2 Required 3 This error was generated from the following input ZMAT H cc pVDZ C cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 H5 1 0 95000 2 109 471 3 120 000 H6 2 1 08900 1 109 471 3 180 000 Explanation The molecule contains an Oxygen atom but the basis set was not specified The following line must be added O cc pVDZ Error from SEWARD The output was BasisConsistency Atom NA 8 requires BS ERROR Basis set inconsistency This error was generated from the following input 32 ZMAT H cc pVDZ C cc pVDZ N cc pVDZ C1 02 1 1 40000 H3 1 0 95000 2 109 471 H4 1 0 95000 2 109 471 3 120 000 Explanation The molecule also contains an Oxygen atom but the basis set was specified for Nitrogen The right input is ZMAT H CC pVDZ C cc pVDZ O cc pVDZ C1 Error from SEWARD The output was ERROR Wrong number of basis sets Available 4 Required 3 This error was generated from the following input
29. molden Project geo molden 22 cp f WorkDir Project freq molden Project freq molden 23 cp f WorkDir Project scf molden Project scf molden 24 cp f WorkDir Project rasscf molden Project rasscf molden 25 if f Project geo molden then 26 if f Project rasscf molden then 27 cat Project rasscf molden gt gt Project geo molden 28 else 29 if f Project scf molden then 30 cat Project scf molden gt gt Project geo molden 31 fi 32 fi 33 fi 34 if f Project freq molden then 35 if f Project rasscf molden then 36 cat Project rasscf molden gt gt Project freq molden 37 else 38 if f Project scf molden then 39 cat Project scf molden gt gt Project freq molden 40 fi 41 fi 42 fi 43 echo 44 echo i 45 echo Job Project 46 echo Date date 47 echo 2 Your first MolCAS calculation the HF energy of methanol Assuming that the program is correctly installed we can start with the first calculation In this example we want to calculate the Hartree Fock energy of the methanol CH OH The basis set is the well known cc pVDZ First the sub program SEWARD is called to calculate the mono and bi electron integrals This program will be the first to be called almost in all cases We use the new keyword ZMAT which I prefer because more close to the chemists way of thinking the mole
30. nation This molecule is a radical or an ion but in the SCF input it was not specified The following line must be added Charge 1 if an anion or UHF if a radical Error from SCF The output was kkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkk kkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkk kkkkkkkkk kkkkkkk kkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk kkk kkk kkk kkk ERX Location gxRdRun EIR ER Unit 1209758319 PER FER RunFile does not exist hioi kkk kkk kkk kkk kkkkkkkkkkkkkkkkkkkkkkkkk kkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkk kkkkkkkkk kkkkkkk kkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk This error was generated from the following input amp SEWARD amp END ZMAT H cc pVDZ C cc pVDZ O cc pVDZ 1 40000 0 95000 2 109 471 0 95000 2 109 471 3 120 000 0 95000 2 109 471 3 120 000 BRB 37 End of Input amp SCF amp END End of Input Explanation Module SEWARD was unactivated Remove before SEWARD amp SEWARD amp END ZMAT H cc pVDZ C cc pVDZ Error from SLAPAF The output was kkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkxkkkk ERROR Undefined internal coordinate in co kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkxkkkk This error was generated from the following input Internal Coordinates c02 Bond C1 02 CH3 Bond C1 H3 OCH3 Angle 02 C1 H3 CH4 Bond C1 H4 HCH4
31. ngstroms KR KK EKER KEKE kck kck kok kok kck kck ckck kck kck kck kck kok KEKE KEKE ck kockokok Cartesian Coordinates Bohr Angstrom kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk Center Label x y Zz x y Z 1 c1 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 2 02 0 000000 0 000000 2 645617 0 000000 0 000000 1 400000 3 H3 1 692571 0 000000 0 598407 0 895670 0 000000 0 316663 4 H4 0 846285 1 465809 0 598407 0 447835 0 775673 0 316663 5 H5 0 846285 1 465809 0 598407 0 447835 0 775673 0 316663 6 H6 1 940220 0 000000 3 331580 1 026720 0 000000 1 762996 then distances and angles The otput terminates with basis set specifications and the nuclear potential energy Basis set specifications Symmetry species a Basis functions 48 Nuclear Potential Energy 41 84412593 au Then we found the SCF output After the details of the calculation and the SCF iterations we find the SCF KS DFT Program Final results section Here we can find the converged energy values Total SCF energy 114 9782183794 One electron energy 239 8194947236 Two electron energy 82 9971504107 Nuclear repulsion energy 41 8441259335 Kinetic energy interpolated 115 5406117335 Virial theorem 0 9951325050 Line Total SCF energy contains the HF energy 114 9782183794 au The coeficients of the molecular orbitals follows Note that SCF also generates a Project scf molden file that can be read with the program molden to see the MO
32. ombinations of the primitive follows The negative eigenvalue of the Hessian 0 027522 tells us that the structure is a first order saddle point i e a Transition Structure and in its corresponding eigenvector the dominating primitive coordinate is a001 the N2 C1 H3 angle which describe the movement of the hydrogen atom KAKA KR KR RK RK RK RK k k k k k k k k k k k k k k k k k k KR k k k kk k k k k k k kk kk kk k KR KR KR KR k kk kk RK RK KEKE KEKE KEKE Auto Defined Internal coordinates kkk kkk kkk kk kk kkk kkk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k Primitive Internal Coordinates b001 Bond N2 C1 b002 Bond H3 C1 a001 Angle N2 C1 H3 Internal Coordinates Vary q001 0 98690410 b001 0 09649973 b002 12925983 a001 q002 12119354 b001 0 97240208 b002 19936477 a001 q003 0 10645388 b001 0 21241937 b002 0 97136275 a001 End Of Internal Coordinates Number of redundant coordinates 3 Using old reaction mode from disk Storing new reaction mode disk Eigenvalues and Eigenvectors of the Hessian 1 2 3 Eigenvalues 0 027522 0 582963 1 721819 b001 0 121271 0 317604 0 940437 b002 0 405193 0 880738 0 245193 a001 0 906152 0 351324 0 235499 Cokckckckckck ck ck ck ck kkk kkk kkk kkk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k k kkk kkk kk k k k k k k k k k k k k k k k ck
33. pendix The the most important lines are in the SLAPAF section 21 amp SLAPAF amp End 22 TS 23 Numerical Hessian 24 PRFC 25 Iterations 26 20 27 End of Input 28 29 gt gt gt EndDo lt lt lt Lines 01 20 not shown are similar to the previous example a part for the structure Line 22 keyword TS to require the optimization of a transition structure Line 23 keyword Numerical to require the calculation of the numerical Hessian force constant matrix Line 24 keyword PRFC Print Force Constants to require the print out of the eigenvalues and eigenvectors of the Hessian matrix Line 25 keyword Iteration for specifying the maximum number of optimization steps given in line 25 20 The optimization of TS requires a good starting geometry of course but also a 17 good Hessian matrix This is why it is advisable to start the optimization with a numerical estimation of this matrix 1 2 3N 6 gradients will be estimated before to start the optimization When the structure is optimized its geometry is not enough to assure that it is a TS In order to verify its real nature of the saddle point it is advisable to check the eigenvalues and eigenvectors of its Hessian The output on SLAPAF of the last step is the following First we find the definition of the primitive internal coordinates These are defined as bonds and planar and dihedral angles among atoms The internal coordinates build as linear c
34. raintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraints ConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraints Constraints Constraints Constraints CONSTRAINTS Constraints Constraints Constraints KAKA KAKA KR KKK RK k k k k k k ck KR KR k k k k k k k KR k k KR KKK k KR KR KR KR KR KR KR KR KR KKK kk kk kk KR KK KR KR KR KR KR KR ck kk ck ck ck ck ck ck ck ck ck KEKE KEKE KEKE KE R BOND C1 C3 VALUE R 2 0 ANGSTROM KAKA KAKA KR KKK KK RK KK RK kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k KR KKK KKK KKK KKK KKK KR KKK ckok kok ckok ck ck KEKE KE Values of primitive constraints KR KKK KKK KKK KKK KKK KKK KEKE KEKE KEKE KEKE R Bond Length 2 000000 Angstrom 3 779452 bohr KR KK KKK KEK KKK KKK KK KKK KEKE KEKE KEKE ck kckokok Value of constraints au or rad KR KKK KKK KKK KKK KKK KKK KEKE KEKE KEKE KEKE KEK Label C co Cns001 3 779452 3 779452 21 KR KKK KKK KKK KKK KKK KKK KEKE KEKE kok kok KEKE KE Gradient of primitive constraints KR KK KKK KKK KKK KKK KKK KKK EKER KEKE ck ck ck ok ck ok ko R 0 048157 Constraints Constraints ConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraints ConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstraintsConstra
35. s is only to encourage the new users to adopt MolCAS as their standard quantum chemical package and to get rid of the idea that MolCAS is more difficult to use than other more famous programs Therefore in this manual you will not find a description of how to install and run the program this can be find in Chapter 9 af the official manual neither a full description of each single programs or keywords Chapter 3 The only other informations that will be assumed as well know by the users are the basic concept of quantum chemical theory Here the user will be lead through the program starting from very simple examples and guided toward more sofisticated calculations Every example will be introduced and both the input and piece of output in the boxes will be fully explained hopefully Before to start it is advisable to know a few information about olCAS files and directory Chap 1b and about submission script in Chap 1c you can find an example More details can be found in Section 2 of the manual Some new features will be available with the new 7 2 version only Every suggestion is of course welcome In case do not esitate write me 1 b The MoICAS MolCAS files and directory The name of most important MolCAS files always start with the name of the job project Project Some of them are written or transferred at the end of a job in the current directory CurrDir but most of them are located in the scratch director
36. the Appendix And these are the most important lines 01 gt gt gt Set MaxIter 5000 lt lt lt 02 gt gt gt Do While lt lt lt 26 amp SLAPAF amp End 27 Iterations 28 20 29 End of Input 30 31 gt gt gt EndDo lt lt lt Lines 01 02 and 31 are used to define the cycle Lines 03 25 not shown are the same as in the first example Lines 26 29 the SLAPAF optimization input Line 27 keyword Iterations for specifying the maximum number of optimization steps given in line 28 20 14 The output of SEWARD and SCF are the same as in the first example The output on SLAPAF starts with some details of the optimization algorithms The section with Energy Statistics follows KAKA KR KKK RK RK RK RK k k k k k k k k k k RK k k KR k kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk ck ck ck ck ck ck ck ck ck ck ck ck kk kk k k Cokckckckckckckckckckckckck k k k k k k k k k k k k k k k k k k k k Energy Statistics for Geometry Optimization kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk kkk kkk kkk kk kkk kkk kkk kkk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk kk k k Energy Grad Grad Step Estimated Geom Hessian Iter Energy Change Norm Max Element Max Element Final Energy Update Update Index 1 114 97821838 0 00000000 0 333071 0 224740 nrc006 0 233783 nrc006 115 02052309 RS RFO None 0 Cartesian D
37. ut amp SLAPAF amp END Iterations 20 End of Input gt gt gt EndDo lt lt lt 44 Appendix Input for lesson 6 gt gt gt Set MaxIter 5000 lt lt lt gt gt gt Do While lt lt lt amp SEWARD amp END Title Transition Structure HCN gt CNH ZMAT H cc pVDZ C cc pVDZ N cc pVDZ N2 1 1 17000 H3 1 1 16000 2 80 000 End Of Input amp SCF amp END End of input amp SLAPAF amp END TS Numerical Hessian PRFC Iterations 10 End Of Input gt gt gt EndDo lt lt lt 45 Appendix Input for lesson 7 gt gt gt Set MaxIter 5000 lt lt lt gt gt gt Do While lt lt lt amp SEWARD amp END Title Energy curve of CH3 H2C CH2 ZMAT H 6 31G C 6 31G C1 C2 1 1 440 C3 t 2 000 2 110 0 H4 1 1 079 2 115 5 3 113 H5 1 1 079 2 115 5 3 113 H6 2 1 075 1 120 5 3 83 H7 2 1 075 1 120 5 3 83 H8 3 1 080 1 105 5 2 180 H9 3 1 079 1 106 0 8 120 H10 3 1 079 1 106 0 8 120 End Of Input amp SCF amp END UHF End of input amp SLAPAF amp END Iterations 20 Constrain R Bond C1 C3 Value R 2 0 Angstrom End of Constrain End Of Input gt gt gt EndDo lt lt lt 46 Appendix Input for lesson 8 gt gt gt Set gt gt gt Do MaxIter 5000 lt lt lt While lt lt lt amp SEWARD amp END Title Optimization of geometry with User defined coordinates ZMAT H cc pVDZ C cc pVDZ Cl cc pVDZ C1 C12 1
38. y WorkDir whose name is scr_Project and which should be generated if not present by the submission script In the current directory the following files can be found e Project input e Project out e Project scf molden e Project rasscf molden e Project geo molden obtained in an optimization e Project freq molden e Project JobIph Communication binary input file the only user created output file input file for molden with HF SCF MO input file for molden with RASSCF MO input file for molden with molecular geometries input file for molden with frequencies MO from RASSCF binary Project RunFile These file are originally generated in WorkDir and should be copied in CurrDir at the end of the job by the submission script However sometimes this does not happen Moreover during the job some of them are copied by MolCAS in WorkDir with the final extension autosaved and removed by the submission script at the endo of the job Other useful files that can be find in WorkDir are e Project guessorb molden input file for molden with Guess MO e Project ScfOrb MO from HF SCF e Project OneInt One electron Integrals e Project OrdInt Two electron Integrals e Project JobMix MO from CASPT2 binary 1c The submission script Here is an example of the simplest shell script that can be used to run MolCAS 01 bin sh 02 export Project 1 03 export CurrD
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