| Chapter 18. A Typical Calculation | ||
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Part II. AMPAC™ 10 Examples |  |
| Chapter 18. A Typical Calculation | ||
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Part II. AMPAC™ 10 Examples | |
Table of Contents
The following is an example illustrates the features that are found in a typical calcuation. The most important features are noted below, which is helpful for new users to identify critical data sections. This example involves a geometry optimization and background information on optimization can be found in the section called “Geometry Optimization”
am1 rhf singlet gnorm=0.05 t=auto truste grad geo-okDistorted Benzene GNORM C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.500000 1 0.000000 0 0.000000 0 1 0 0 C 1.200000 1 110.000000 1 0.000000 0 2 1 0 C 1.500000 1 130.000000 1 20.000000 1 3 2 1 C 1.200000 1 105.000000 1 -20.000000 1 4 3 2 C 1.500000 1 130.000000 1 25.000000 1 5 4 3 H 0.800000 1 109.500000 1 145.000000 1 1 2 3 H 1.200000 1 130.000000 1 -135.000000 1 2 3 4 H 1.200000 1 109.500000 1 140.000000 1 3 4 5 H 0.800000 1 130.000000 1 -135.000000 1 4 5 6 H 1.200000 1 120.000000 1 -135.000000 1 5 6 1 H 0.800000 1 120.000000 1 145.000000 1 6 1 2 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
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The keyword line specifies that the AM1 Hamiltonian will be used. Specifying GNORM=0.05 tightens the criterion for optimizing the geometry. The geometry provided is very distorted, so GEO-OK is needed to allow the calculation to proceed. |
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The geometry specification section is terminated by a line of zeros. A blank line would also serve this purpose. No further data is required by the keywords, so this is the last line of the file. |
Timestamp: 2011-08-31-12-47-10-00000010A4-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Aug-31-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C6H6 
Distorted Benzene
GNORM
GEOMETRY OPTIMIZED : ENERGY MINIMIZED
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = 22.022286 kcal 
= 92.163265 kJ
ELECTRONIC ENERGY = -3253.371822 eV
CORE-CORE REPULSION = 2403.035502 eV
TOTAL ENERGY = -850.336320 eV
GRADIENT NORM = 0.110345 
RMS GRADIENT NORM = 0.020146 
UNSTABLE MODE(S) = 0 ( ESTIMATE ) 
IONIZATION POTENTIAL = 9.652544 eV 
HOMO-LUMO GAP = 10.207126 eV
DIPOLE = 0.000349 debyes 
MOLECULAR WEIGHT = 78.113400 
MOLECULAR POINT GROUP = D6h 0.100000 
NO. OF FILLED LEVELS = 15 (OCC = 2) 
TOTAL NUMBER OF ORBITALS = 30
COMPUTATION TIME = 0.27 SECONDS 
FINAL GEOMETRY OBTAINED 
CHARGE 
AM1 RHF SINGLET GNORM=0.05 T=AUTO TRUSTE GRAD GEO-OK 
Distorted Benzene
GNORM
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.1301 
C 1.395028 1 0.000000 0 0.000000 0 1 0 0 -0.1301
C 1.395067 1 120.000213 1 0.000000 0 2 1 0 -0.1301
C 1.395020 1 120.000241 1 -0.006540 1 3 2 1 -0.1301
C 1.395082 1 119.998278 1 0.001454 1 4 3 2 -0.1301
C 1.395027 1 120.001057 1 0.000382 1 5 4 3 -0.1301
H 1.099676 1 119.998309 1 180.004635 1 1 2 3 0.1301
H 1.099643 1 119.999025 1 -180.008087 1 2 3 4 0.1301
H 1.099652 1 120.001668 1 179.989239 1 3 4 5 0.1301
H 1.099696 1 119.999758 1 -179.996667 1 4 5 6 0.1301
H 1.099636 1 119.998960 1 -180.006599 1 5 6 1 0.1301
H 1.099604 1 120.000057 1 179.987363 1 6 1 2 0.1301
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
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The banner indicates which Hamiltonian (here AM1) was used to obtain the results. |
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This line gives information about which version of AMPAC (in this case 10.0) was used in this calculation. This data must be referenced when publishing results. |
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The molecular formula of the species is printed. |
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The Heat of Formation (ΔHf) begins the summary section in the
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The gradient norm (gnorm) value indicates how well the geometry has been refined. A
value of less than 1.0 is acceptable for most purposes. See discussion of the GNORM= |
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The RMS gradient norm (RMS gnorm) is another indicator of how well the geometry has been refined. It is similar to the regular gnorm but is scaled so as to be approximately independent of the system size. (See Chapter 4, Computational Procedures for an explanation of how the RMS gnorm is computed.) |
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The number of unstable modes is useful for classifying the optimized geometry. The number of modes is qualified with the statement “ESTIMATED” indicating that number of unstable modes may not in fact be correct. To get an accurate number for the unstable modes, do a FORCE (or LFORCE or HESSEI) calculation on the optimized geometry or optimize the geometry with a full Hessian method (NEWTON or LTRD). (See Chapter 4, Computational Procedures for an explanation on how to characterize stationary points.) |
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The ionization potential (as predicted by Koopman’s Theorem as the negative of the energy of the HOMO) is listed in electron volts (eV). |
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The dipole moment (in Debyes) is reported. As expected with benzene, this value is essentially zero. |
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The molecular weight as calculated from the molecular formula is given. Note that the atomic masses used in AMPAC are the isotopically averaged ones found on the Periodic Table of the Elements. |
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The molecule’s molecular point group is listed here. The number following the symmetry designation is the threshold used for determining the point group. This threshold can be changed by using the MPGCRT keyword. |
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For even electron systems, the number of doubly-occupied valence shell orbitals is noted in the summary section. Other information is presented if the calculation involved an open shell species or configuration interaction. |
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The total time for the calculation is listed here. If extensive post-SCF calculations
are performed, see the bottom of the |
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This phrase is presented at the end of most successful AMPAC runs where the calculation has been completed as requested. |
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A summary of the Coulson atomic charges as predicted by AMPAC’s analysis of the MOs is listed in the archive file. |
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The keyword line and comments are echoed back to allow the user to identify the results and interpret the calculation. |
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The final optimized geometry as predicted by the program is listed in internal coordinates in the order that the atoms were entered. If the geometry was in initially provided in internal coordinates, the connectivity remains the same as defined. If the geometry was provided as Cartesian coordinates, AMPAC will assign a connectivity pattern. |
Timestamp: 2011-08-31-12-47-10-00000010A4-win64
User Info: John Millam, Nahum,
*******************************************************************************
AM1 CALCULATION RESULTS
*******************************************************************************
* AMPAC Version 10.0.1
* Presented by:
*
* Semichem, Inc.
* www.semichem.com
*
* AM1 - THE AM1 HAMILTONIAN TO BE USED
* RHF - RESTRICTED HARTREE-FOCK CALCULATION
* TRUSTE - MINIMIZE ENERGY USING TRUST REGION METHOD
* GNORM= - OPTIMIZATION EXIT WHEN GRADIENT NORM BELOW 0.050
* GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK
* T=AUTO - AUTOMATIC DETERMINATION OF ALLOWED TIME
* GRADIENTS- ALL GRADIENTS TO BE PRINTED
* SINGLET - IS THE REQUIRED SPIN MULTIPLICITY
*******************************************************************************
AM1 RHF SINGLET GNORM=0.05 T=AUTO TRUSTE GRAD GEO-OK
Distorted Benzene
GNORM
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.50000 * 1
3 C 1.20000 * 110.00000 * 2 1
4 C 1.50000 * 130.00000 * 20.00000 * 3 2 1
5 C 1.20000 * 105.00000 * -20.00000 * 4 3 2
6 C 1.50000 * 130.00000 * 25.00000 * 5 4 3
7 H 0.80000 * 109.50000 * 145.00000 * 1 2 3
8 H 1.20000 * 130.00000 * -135.00000 * 2 3 4
9 H 1.20000 * 109.50000 * 140.00000 * 3 4 5
10 H 0.80000 * 130.00000 * -135.00000 * 4 5 6
11 H 1.20000 * 120.00000 * -135.00000 * 5 6 1
12 H 0.80000 * 120.00000 * 145.00000 * 6 1 2
MOLECULAR POINT GROUP SYMMETRY CRITERIA
C1 0.10000000
SINGLET STATE CALCULATION
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15
** REFERENCES TO PARAMETERS **
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).
CARTESIAN COORDINATES
ATOM X Y Z
1 C 0.00000000 0.00000000 0.00000000
2 C 1.50000000 0.00000000 0.00000000
3 C 1.91042417 1.12763114 0.00000000
4 C 1.22554224 2.40296821 0.39300395
5 C 0.05271549 2.15436289 0.34130475
6 C -0.66121710 0.84150901 0.47059108
7 H -0.26704549 -0.61773336 -0.43254156
8 H 2.01906721 -1.00977336 0.38849325
9 H 2.85080022 1.37788378 -0.70218695
10 H 1.61055541 2.98853186 0.77885376
11 H 0.10007627 2.90612842 1.27543833
12 H -1.35548335 1.04323500 0.12809876
STANDARD DEVIATION ON ENERGY (KCAL) 0.00000003699
STANDARD DEVIATION ON GRADIENT (KCAL/A,RD,RD) 0.00001265 0.00002233 0.00001931
AM1 RHF SINGLET GNORM=0.05 T=AUTO TRUSTE GRAD GEO-OK
Distorted Benzene
GNORM
GEOMETRY OPTIMIZED : ENERGY MINIMIZED
SCF FIELD WAS ACHIEVED
AM1 CALCULATION
VERSION 10.0.1
Aug-31-2011
FINAL HEAT OF FORMATION = 22.022286 kcal
= 92.163265 kJ
ELECTRONIC ENERGY = -3253.371822 eV
CORE-CORE REPULSION = 2403.035502 eV
TOTAL ENERGY = -850.336320 eV
GRADIENT NORM = 0.110345
RMS GRADIENT NORM = 0.020146
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 9.652544 eV
HOMO-LUMO GAP = 10.207126 eV
MOLECULAR WEIGHT = 78.113400
MOLECULAR POINT GROUP = D6h 0.100000
NO. OF FILLED LEVELS = 15 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 30
SCF CALCULATIONS = 26
COMPUTATION TIME = 0.25 SECONDS
FINAL GEOMETRY AND DERIVATIVES
PARAMETER ATOM TYPE VALUE GRADIENT
1 2 C BOND 1.395028 0.013427 kcal/angstrom
2 3 C BOND 1.395067 0.024552 kcal/angstrom
3 3 C ANGLE 120.000213 -0.015120 kcal/radian
4 4 C BOND 1.395020 -0.017856 kcal/angstrom
5 4 C ANGLE 120.000241 -0.037976 kcal/radian
6 4 C DIHEDRAL -0.006540 -0.012720 kcal/radian
7 5 C BOND 1.395082 0.045714 kcal/angstrom
8 5 C ANGLE 119.998278 -0.048351 kcal/radian
9 5 C DIHEDRAL 0.001454 -0.016369 kcal/radian
10 6 C BOND 1.395027 0.007002 kcal/angstrom
11 6 C ANGLE 120.001057 -0.018317 kcal/radian
12 6 C DIHEDRAL 0.000382 -0.018189 kcal/radian
13 7 H BOND 1.099676 0.021392 kcal/angstrom
14 7 H ANGLE 119.998309 -0.003781 kcal/radian
15 7 H DIHEDRAL 180.004635 0.000475 kcal/radian
16 8 H BOND 1.099643 -0.003342 kcal/angstrom
17 8 H ANGLE 119.999025 0.000026 kcal/radian
18 8 H DIHEDRAL -180.008087 -0.004139 kcal/radian
19 9 H BOND 1.099652 0.003205 kcal/angstrom
20 9 H ANGLE 120.001668 0.001970 kcal/radian
21 9 H DIHEDRAL 179.989239 -0.007975 kcal/radian
22 10 H BOND 1.099696 0.041440 kcal/angstrom
23 10 H ANGLE 119.999758 0.000647 kcal/radian
24 10 H DIHEDRAL -179.996667 0.003270 kcal/radian
25 11 H BOND 1.099636 -0.009138 kcal/angstrom
26 11 H ANGLE 119.998960 -0.004269 kcal/radian
27 11 H DIHEDRAL -180.006599 -0.006776 kcal/radian
28 12 H BOND 1.099604 -0.036664 kcal/angstrom
29 12 H ANGLE 120.000057 -0.000174 kcal/radian
30 12 H DIHEDRAL 179.987363 -0.005666 kcal/radian
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.39503 * 1
3 C 1.39507 * 120.00021 * 2 1
4 C 1.39502 * 120.00024 * -0.00654 * 3 2 1
5 C 1.39508 * 119.99828 * 0.00145 * 4 3 2
6 C 1.39503 * 120.00106 * 0.00038 * 5 4 3
7 H 1.09968 * 119.99831 * 180.00463 * 1 2 3
8 H 1.09964 * 119.99902 * -180.00809 * 2 3 4
9 H 1.09965 * 120.00167 * 179.98924 * 3 4 5
10 H 1.09970 * 119.99976 * -179.99667 * 4 5 6
11 H 1.09964 * 119.99896 * -180.00660 * 5 6 1
12 H 1.09960 * 120.00006 * 179.98736 * 6 1 2
MOLECULAR POINT GROUP SYMMETRY CRITERIA
D6h 0.10000000
RHF EIGENVALUES 
-39.14667 -31.36848 -31.36803 -23.06043 -23.06026 -17.85605
-16.12313 -15.40009 -14.16086 -14.16065 -13.38085 -11.88763
-11.88750 -9.65276 -9.65254 0.55458 0.55472 2.97772
4.03635 4.03654 4.04726 4.19233 4.59843 4.59857
5.12317 5.12327 5.61157 5.61163 5.72914 6.13270
NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS 
ATOM CHARGE ATOM ELECTRON DENSITY
1 C -0.1301 4.1301
2 C -0.1301 4.1301
3 C -0.1301 4.1301
4 C -0.1301 4.1301
5 C -0.1301 4.1301
6 C -0.1301 4.1301
7 H 0.1301 0.8699
8 H 0.1301 0.8699
9 H 0.1301 0.8699
10 H 0.1301 0.8699
11 H 0.1301 0.8699
12 H 0.1301 0.8699
DIPOLE (DEBYE) X Y Z TOTAL
POINT-CHG. 0.000 0.000 0.000 0.000
HYBRID 0.000 0.000 0.000 0.000
SUM 0.000 0.000 0.000 0.000
CARTESIAN COORDINATES 
ATOM X Y Z
1 C 0.00000000 0.00000000 0.00000000
2 C 1.39502833 0.00000000 0.00000000
3 C 2.09256627 1.20816077 0.00000000
4 C 1.39506581 2.41628914 -0.00013789
5 C -0.00001584 2.41625828 -0.00024513
6 C -0.69752497 1.20812680 -0.00020642
7 H -0.54981007 -0.95236388 0.00007704
8 H 1.94486259 -0.95231161 -0.00002571
9 H 3.19221826 1.20812002 -0.00009433
10 H 1.94488876 3.36866836 -0.00011301
11 H -0.54985468 3.36855913 -0.00051752
12 H -1.79712908 1.20811925 -0.00041645
ATOMIC ORBITAL ELECTRON POPULATIONS 
1.21858 0.93887 0.97267 1.00000 1.21858 0.93887
0.97266 1.00000 1.21858 0.98956 0.92198 1.00000
1.21859 0.93887 0.97266 1.00000 1.21859 0.93887
0.97266 1.00000 1.21857 0.98956 0.92198 1.00001
0.86988 0.86988 0.86988 0.86987 0.86989 0.86989
ELAPSED WALL CLOCK TIME : 0.29 SECONDS 
FULL COMPUTATION TIME : 0.27 SECONDS 
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The banner indicates which Hamiltonian (here AM1) was used to obtain the results. |
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As in the archive file, this line gives information about which version of AMPAC (in this case 10.0) was used in this calculation. This data must be referenced when publishing results. |
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The keywords that AMPAC recognized from the input file are printed here and short summaries of their functions are provided. If an expected keyword is not present in this group, check the input file for spelling or omission. |
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The keyword, title, and comment lines are echoed to the output file to help the user identify the calculation. |
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The internal coordinates of the initial geometry (whether provided to the program as internals or Cartesians) are listed. Only those geometric parameters with asterisks (*) beside them will be optimized. |
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The symmetry of the input geometry and the threshold used in determining symmetry is output here. MPGCRT can be used to adjust this threshold. |
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This short section defines the calculation that AMPAC expects to perform. In this case a singlet spin state is assumed (default if no spin multiplicity keywords are used). Open shell calculations (UHF) will show the electrons divided between alpha and beta electron spin states. |
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References to the parameters for the particular Hamiltonian chosen are listed. These citations should be used in papers. A complete bibliography may be found in Chapter 17, References. |
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The Cartesian coordinates of the initial geometry (again whether provided to the program as internals or Cartesians) are listed. This output may be suppressed by use of the NOXYZ keyword. |
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A summary of the geometry optimization methods and criteria is presented in this
section. More information, including results for each step, may be obtained by using the
PRINT= |
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Again, the keyword line, title, and comment lines are echoed to the output file. |
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This message is one of the several that AMPAC can provide to inform the user that the geometry has been properly optimized (see the section called “Geometry Optimization” for a list and description of the possible messages). Always check this line for possible failure of the geometry optimization or SCF procedure. |
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This message informs the user that SCF convergence was attained at the geometry that the optimization halted on. The results following are for the final wavefunction and geometry. |
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This summary section is almost an exact copy of that found in the archive file. See above for an explanation of its components. |
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The gradient components that are used to compute the gnorm are listed here for each optimizable parameter. This report is a result of using the keyword GRAD. The gnorm should have a low value as should each component. In the event that a geometry optimization is not converging, an examination of these components may suggest a method of redefining the geometry so that a particularly troublesome component with a high gradient value is eliminated. |
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The internal coordinates of the fully optimized geometry are printed here. Again, only those components noted with an asterisk have been optimized. |
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The symmetry of the optimized geometry and the threshold used in determining symmetry is output here. MPGCRT can be used to adjust this threshold. |
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The energy values (in eV) of the final molecular orbitals (both occupied and virtual) are listed here. In benzene, there are 15 occupied MOs, with the highest being a degenerate pair corresponding to part of the π bonding picture. Generally, occupied MOs have energies < 0.0 eV and virtuals have energies > 0.0 eV. |
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The partial charges on each atom are tabulated. This quantity is obtained by subtracting the sum of the number of core electrons and the valence electrons present on that atom as predicted by AMPAC from the atomic number (number of protons). These figures are used to compute the net dipole moment of the species. |
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The Cartesian coordinates of the final geometry are printed. This output may be suppressed by use of the NOXYZ keyword. |
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The valence orbital electron populations (the diagonal of the final density matrix) are listed for reference. |
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The wall clock time expresses the total time taken by the calculation from start ot finish as experienced by the user (or a clock on the wall). |
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The full computation time for the calculation is a measure of the time spent by the CPU in performing this calculation. It is similar to, but not the same as, the wall clock time. |
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Copyright © 1992-2013 Semichem, Inc. All rights reserved. |
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| Part II. AMPAC™ 10 Examples |  |
Chapter 19. A Large Molecule using Sparse Matrices (SPARSE, PSOLVE) |