Open Babel / Bugs / #967 moo format (Mopac output) input crashes OpenBabel-2.3.2\obgui.exe

moo format (Mopac output) input crashes OpenBabel-2.3.2\obgui.exe

#967 moo format (Mopac output) input crashes OpenBabel-2.3.2\obgui.exe

Milestone: 2.3.x

Status: open

Owner: nobody

Labels: moo (1)

Priority: 1

Updated: 2015-09-25

Created: 2015-09-25

Creator: Zoli Fekete

Private: No

Running under Win7, the following file taken as input crashes OpenBabel-2.3.2\obgui.exe:

** Site#: 87 For non-commercial use only Version 15.229W 32BITS**

** Cite this work as: **
** **
** (a) MOPAC2012, James J. P. Stewart, Stewart Computational Chemistry, **
** Version 15.229W web: HTTP://OpenMOPAC.net Days remaining: 326 **
** **
** AND **
** **
** (b) Maia, J.D.C., et al., J. Chem. Theory Comput. 2012, 8, 3072-3081. **
** DOI: 10.1021/ct3004645. **

** **
** MOPAC2012 **
** **

                          AM1 CALCULATION RESULTS

CALCULATION DONE: Fri Sep 25 16:57:23 2015 *
AM1 - The AM1 Hamiltonian to be used
T= - A TIME OF 172800.0 SECONDS REQUESTED
DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS

AM1
--- C:\MOPAC.dir\MeOH_test.pdb ---
MOPAC input generated by Facio 19.1.4
ATOM CHEMICAL X Y Z
NUMBER SYMBOL (ANGSTROMS) (ANGSTROMS) (ANGSTROMS)

 1       O          0.01000000  *  -0.00300000  *   0.00000000  *
 2       C          1.42400000  *  -0.00400000  *   0.00000000  *
 3       H          1.68600000  *   1.06200000  *   0.00100000  *
 4       H          1.80600000  *  -0.49100000  *   0.90300000  *
 5       H          1.80600000  *  -0.48900000  *  -0.90300000  *
 6       H         -0.32900000  *  -0.91900000  *  -0.00300000  *



      CARTESIAN COORDINATES

NO.       ATOM         X         Y         Z

 1         O        0.0100   -0.0030    0.0000
 2         C        1.4240   -0.0040    0.0000
 3         H        1.6860    1.0620    0.0010
 4         H        1.8060   -0.4910    0.9030
 5         H        1.8060   -0.4890   -0.9030
 6         H       -0.3290   -0.9190   -0.0030

 ===================== shared-memory parallel CPU Section ======================
 **                                                                           **
 **  MOPAC calculations will run in shared-memory parallel CPUs               **
 **                                                                           **
 **  Number of Threads =  2                                                   **
 **                                                                           **
 **                                                                           **
 **  For information on this work, see:                                       **
 **                                                                           **
 **  Maia, J.D.C., et al., J. Chem. Theory Comput. 2012, 8, 3072-3081.        **
 **        DOI: 10.1021/ct3004645.                                            **
 **                                                                           **
 ===================== shared-memory parallel CPU Section ======================

H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
C: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
O: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)

       Empirical Formula: C H4 O  =     6 atoms



  MOLECULAR POINT GROUP   :   Cs


  RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =    7

  Geometry optimization using EF

      DIAGONAL MATRIX USED AS START HESSIAN

CYCLE: 1 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 47.504 HEAT: -55.99889
CYCLE: 2 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 28.130 HEAT: -56.58412
CYCLE: 3 TIME: 0.016 TIME LEFT: 2.00D GRAD.: 16.700 HEAT: -56.88593
CYCLE: 4 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 19.239 HEAT: -56.90030
CYCLE: 5 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 19.043 HEAT: -56.91750
CYCLE: 6 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 6.533 HEAT: -57.02012
CYCLE: 7 TIME: 0.016 TIME LEFT: 2.00D GRAD.: 5.460 HEAT: -57.03173
CYCLE: 8 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 2.285 HEAT: -57.04181
CYCLE: 9 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 2.583 HEAT: -57.04692
CYCLE: 10 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 2.497 HEAT: -57.05054
CYCLE: 11 TIME: 0.000 TIME LEFT: 2.00D GRAD.: 0.673 HEAT: -57.05291

 GRADIENT =  0.67290  IS LESS THAN CUTOFF =  1.00000

AM1
--- C:\MOPAC.dir\MeOH_test.pdb ---
MOPAC input generated by Facio 19.1.4

 GEOMETRY OPTIMISED USING EIGENVECTOR FOLLOWING (EF).     
 SCF FIELD WAS ACHIEVED


                          AM1 CALCULATION
                                                   MOPAC2012 (Version: 15.229W)
                                                   Fri Sep 25 16:57:23 2015
                                                   No. of days left = 326




      FINAL HEAT OF FORMATION =        -57.05291 KCAL/MOL =    -238.70937 KJ/MOL


      TOTAL ENERGY            =       -504.00573 EV
      ELECTRONIC ENERGY       =      -1070.07688 EV  POINT GROUP:     Cs  
      CORE-CORE REPULSION     =        566.07115 EV
      COSMO AREA              =         66.14 SQUARE ANGSTROMS
      COSMO VOLUME            =         47.24 CUBIC ANGSTROMS

      GRADIENT NORM           =          0.67290
      IONIZATION POTENTIAL    =         11.134224 EV
      HOMO LUMO ENERGIES (EV) =        -11.134  3.782
      NO. OF FILLED LEVELS    =          7
      MOLECULAR WEIGHT        =         32.042

      MOLECULAR DIMENSIONS (Angstroms)

        Atom       Atom       Distance
        H     6    H     3     2.81896
        O     1    H     5     1.87905
        H     4    H     5     1.59724


      SCF CALCULATIONS        =         14

      WALL-CLOCK TIME         =          0.047 SECONDS
      COMPUTATION TIME        =          0.062 SECONDS

ATOM CHEMICAL X Y Z
NUMBER SYMBOL (ANGSTROMS) (ANGSTROMS) (ANGSTROMS)

 1       O          0.00160519  *   0.00044948  *  -0.00012544  *
 2       C          1.41171949  *  -0.00175602  *   0.00021003  *
 3       H          1.70503109  *   1.07793158  *   0.00114058  *
 4       H          1.81133147  *  -0.50897670  *   0.91375057  *
 5       H          1.81146437  *  -0.50680006  *  -0.91451558  *
 6       H         -0.28298690  *  -0.92064469  *  -0.00260083  *

                         CARTESIAN COORDINATES

1 O 0.001605191 0.000449475 -0.000125442
2 C 1.411719494 -0.001756017 0.000210032
3 H 1.705031094 1.077931583 0.001140585
4 H 1.811331472 -0.508976701 0.913750566
5 H 1.811464373 -0.506800064 -0.914515575
6 H -0.282986899 -0.920644691 -0.002600833

       Empirical Formula: C H4 O  =     6 atoms



  MOLECULAR POINT GROUP   :   Cs


              EIGENVALUES

-37.85011 -26.98114 -18.28364 -15.44859 -15.29172 -12.49759 -11.13422 3.78175
4.08962 4.22766 4.52341 6.24221

          NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS

ATOM NO. TYPE CHARGE No. of ELECS. s-Pop p-Pop
1 O -0.325646 6.3256 1.87036 4.45529
2 C -0.073412 4.0734 1.23551 2.83790
3 H 0.098038 0.9020 0.90196
4 H 0.052883 0.9471 0.94712
5 H 0.052784 0.9472 0.94722
6 H 0.195352 0.8046 0.80465
DIPOLE X Y Z TOTAL
POINT-CHG. 0.956 -0.614 -0.002 1.137
HYBRID 0.105 -0.610 -0.002 0.619
SUM 1.062 -1.225 -0.003 1.621

      ATOMIC ORBITAL ELECTRON POPULATIONS

 Atom    s        px        py        pz   
1  O   1.87036   1.19531   1.28789   1.97208
2  C   1.23551   0.82719   1.02369   0.98701
3  H   0.90196
4  H   0.94712
5  H   0.94722
6  H   0.80465

*
JOB ENDED NORMALLY *
*

TOTAL JOB TIME: 0.05 SECONDS

== MOPAC DONE ==

Discussion

Zoli Fekete - 2015-09-25

Here is the file.

MeOH_AM1.out

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

moo format (Mopac output) input crashes OpenBabel-2.3.2\obgui.exe

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#967 moo format (Mopac output) input crashes OpenBabel-2.3.2\obgui.exe

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