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Zmat Tutorial

Aces II is a quantum chemistry program suite that can perform calculations like SCF, MBPT, and CCSD. It runs on several platforms and requires a minimum of 128 MB memory and 2 GB disk space. Users create input files with Z-matrices to define molecular geometries. Z-matrices allow defining symmetric molecules and use dummy atoms for linear portions. Keywords in the input file specify the basis set, calculation type, and other parameters. The document provides examples of writing Z-matrices for molecules like water, ethane, and borane and modifying the basis set library. Exercises are included to practice generating Z-matrices for calculations.

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Дьего Фернандо
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© © All Rights Reserved
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101 views

Zmat Tutorial

Aces II is a quantum chemistry program suite that can perform calculations like SCF, MBPT, and CCSD. It runs on several platforms and requires a minimum of 128 MB memory and 2 GB disk space. Users create input files with Z-matrices to define molecular geometries. Z-matrices allow defining symmetric molecules and use dummy atoms for linear portions. Keywords in the input file specify the basis set, calculation type, and other parameters. The document provides examples of writing Z-matrices for molecules like water, ethane, and borane and modifying the basis set library. Exercises are included to practice generating Z-matrices for calculations.

Uploaded by

Дьего Фернандо
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Aces II, Z-Matrices, and Other Fun

Stu!
Sullivan Beck
Quantum Theory Project
Departments of Chemistry and Physics
University of Florida
Gainesville, FL 32611
May 4, 1998

Overview
Computer Facilities for the Course

Aces II

{ How is it organized?
{ Where does it run?
{ What is required to run it?
{ How do you run it?

Input File
{ How is it organized?
{ Examples
{ Keywords
Basis Sets
Z-Matrices
{ Z-Matrices vs. cartesian coordinates
{ Writing a Z-matrix
{ Symmetric molecules
{ Dummy atoms
{ Aces II speci cs
{ Examples

Computer Facilities At This Course


Computer IBM 580, 590, 59H
Memory 128/256 MB
Disk Space 2/4 GB

Aces II: Organization


Aces II is a series of programs:
xjoda Reads input le and sets up calculation parameters
xvscf Performs the SCF part of the calculation
xvcc Performs the coupled cluster part of the calculation
...

They can be run individually (provided one knows the


correct sequence to run them in), or automatically using
xaces2. xaces2 determines the order in which the other
executables must be run and runs them.
A description of most of the executables is contained in
the Aces II manual.

Aces II: Where Does It Run?


Aces II has been ported to the following computers:
Cray YMP, C90, T90
IBM RS/6000
Sun
HP
SGI
DEC Alpha
NEC
Fujitsu

Aces II: What Is Required To Run It?


A lecture will be given discussing resource requirement
prediction. Recommended minimum requirements are:
Memory 128 MB
Disk Space 2 GB

Aces II was developed on the Cray and IBM RS/6000.

Aces II: How Is It Run?


Create an input le
{ Create a Z-Matrix
{ Determine the appropriate keywords
{ Check basis set
Submit the job. This is usually done by writing a
script which runs xaces2. The details of how the job
is submitted and in where it is run vary from computer
to computer. Check with the system administrator.
Analyze the output le

Input File: Dierent Sections


Restart info
Z-Matrix
Namelist with keywords
Special basis set description

Input File: Example


% JOBARC=/u/usr/beck/h2o/JOBARC
% JAINDX=/u/usr/beck/h2o/JAINDX
Water, DZP vibrational frequency calculation
H
O 1 R
H 2 R 1 A
R=0.957
A=104.51
*ACES2(CALC=SCF, VIB=EXACT, BASIS=SPECIAL)
H:PVDZ
O:PVDZ
H:PVDZ

Input File: Keywords


Some of the most commonly used keywords include:
CALC
SCF, MBPT2], CCSD, CCSDT], etc.
BASIS
STO-3G, 6-31G, DZP, SPECIAL, etc.
CHARGE
the molecular charge
MULT
the spin multiplicity
MEMORY
the number of integer words to use
REFERENCE RHF, UHF, ROHF
VIBRATION EXACT, FINDIF, etc.
See the Aces II manual for a complete list and description of the keywords.

Input File: Basis Sets


Many basis sets are available. A partial list is in the Aces
II manual under the BASIS keyword description. They
include most of the common Pople \*" and \**" basis
sets as well as a number of sets by Dunning.
For a complete list, it is necessary to actually look through
the GENBAS le. PNL distributes more than 100 basis
sets over the web. All of these are included in the Aces2
basis sets. These include guassian and ECP basis sets.
A few additional basis sets have also been added to the
GENBAS le.
If you wish to use a dierent basis set on dierent atoms
or to use ghost atoms you must use the keyword BASIS=SPECIAL and enter the basis set for each atom.

Input File: Creating Basis Sets


Make a working copy of the GENBAS le
Copy the lines for an existing basis set to use as a
template
Edit the entries for the new basis set
Test it out
A complete description of the exact format of the GENBAS le is included in the Aces II manual.

Z-Matrix: Two Types of Input


Cartesian Coordinates
{ No symmetry
{ Single point calculation
{ Very large molecule
Z-Matrix
{ Symmetric molecules
{ Geometry optimization which doesn't break symmetry
{ Smaller molecules

Z-Matrix: Writing a Z-Matrix


The Z-matrix for a simple 4-center molecule HOSF could
be written:
1>
2>
3>
4>

H
O
S
F

1 RHO
2 ROS
3 RSF

1 ASOH
2 AFSO

1 DFSOH

Figure 1:
H

O
S
F

Angles must not be 180 degrees.


Dihedral angles.
{ Between -180 and +180 degrees.
{ Both 180 and -180 are allowed.
{ Clockwise is positive.

Z-Matrix: Symmetry
No symmetry is easy: lots of possible Z-Matrices, almost all will work.
Symmetry is hard. Lots of Z-Matrices, but most will
not work.

Z-Matrix: Symmetry Must Not


Decrease
O
R OH
H

O
R OH

AOHH
R HH

R OH
AHOH

A \good" Z-Matrix will not decrease the symmetry (though


it may increase) regardless of the values for the internal
coordinates. Compare two water Z-Matrices:
O
H
H

1 ROH
1 ROH

2 AHOH

H
O
H

1 ROH
1 RHH

2 AHHO

vs.

In the rst case, symmetry may increase as AHOH approaches 0 or 180 degrees. It will never approach 0 since
that would mean merging the two hydrogen atoms.

Z-Matrix: All Present or All Absent


In a \good" Z-matrix, all occurences of an internal coordinate are present or absent in the Z-matrix.
Ammonia example:
N
H1
H2
H3

1 N-H
1 N-H
1 N-H

2 H2-N-H1
2 H2-N-H3

H3-H2-H1-N

Note: It is impossible to use 3 angles and 3 bond lengths!

Z-Matrix: Dummy Atoms


X
N
H HH
A dummy atom is a center with no charge and no basis
functions.
X
N
H
H
H

1
2
2
2

1.0
NH
NH
NH

1 XNH
1 XNH
1 XNH

3 120.0
4 120.0

Note: It is still impossible to use the three H-N-H bond


angles as one of the internal coordinates.
Note: The All Absent/Present rule only applies to optimizable internal coordinates.

Z-Matrix: Linear Molecules


X
O

Linear molecules present a special problem due to the 180


degree angles present.
CO2 example:
C
X
O
O

1 1.0
1 CO
1 CO

2 90.0
2 90.0

3 180.0

Z-Matrix: Rules and Hints


Use dummy atoms to split 180 degree angles in linear
portions.
There should always be an atom at the \center" of
the molecule.
There should always be 2 atoms along the central axis
of rotation.
Additional dummy atoms if there is a plane of symmetry.
De ne \central" atoms rst and others with respect
to those atoms.
De ne symmetry equivalents atoms as a group.

Z-Matrix: Linear Example


H

1>
2>
3>
4>
5>
6>
7>
8>
9>
10>

H
C
X
C
X
C
X
C
X
H

1
2
2
4
4
6
6
8
8

CH
1.0
CC3
1.0
CC1
1.0
CC3
1.0
CH

1
3
2
5
4
7
6
9

90.0
90.0
90.0
90.0
90.0
90.0
90.0
90.0

1
3
2
5
4
7
6

180.0
0.0
180.0
0.0
180.0
0.0
180.0

Z-Matrix: Benzene Example


17
11
23

5
18
12
24

22
16
28
3X
6

X2
10

X1
7

X4

21
15
27
8
19
13
25

20
14
26

Z-Matrix: Cubane Example


X2

N6

N7

12

16

X5

X1
H

14

10

X3
N8

15

11

X4

N9

13

17

Z-Matrix: Aces II rules


Each atom on a separate line and no blank lines.
Fields separated by a single space.
Atomic label must be 1 or 2 character atomic symbol
(or \X", \GH").
Labels may be up to 5 characters.
Labels must be present for all coordinates. You can't
include numbers.
A coordinate that will be optimized ends in a \*".
Following the Z-matrix is one blank line.
Following the blank line are initial values for the internal coordinates.
There are two special internal coordinate labels: TDA
and IHA.
In order to make things simple, name constants uniformly.

Z-Matrix: Geometry Optimization


Input
NH3 geometry optimization:
Ammonia
X
N 1 X
H 2 NH* 1 NHX*
H 2 NH* 1 NHX* 3 A120
H 2 NH* 1 NHX* 4 A120
NH=1.00259
NHX=111.08094
X=1.0
A120=120.0
*ACES2(BASIS=DZP, CALC=SCF)

Z-Matrix: Geometry Optimization


Output
The output for this (near the end) is:
Parameter dV/dR
Step
Rold
Rnew
NH
-0.000001 0.00000 1.00259 1.00259
NHX
0.000001 -0.00052 111.08094 111.08043
Minimum force: 0.000001 / RMS force: 0.000001
Note: you must modify the ZMAT le by hand to include
the optimized geometry.
Note: you should remove the \*" from the Z-matrix.

Exercises
1. Write a ZMAT le for ethane in the eclipsed conformation. Set it up to do a single point, MBPT2] calculation. Run xjoda to make sure the Z-matrix is
correct.
2. Write a ZMAT le for ethane in the staggered conformation. Set it up to do an SCF geometry optimization. Run xjoda to make sure the Z-matrix is correct.
3. Write a ZMAT le for the B2H6 molecule. It is D2h
symmetry with the two bridging hydrogens above and
below the plane containing the boron atoms and the
other four hydrogen atoms. Run xjoda to make sure
that the Z-matrix is a good one.
4. Modify the GENBAS le to add a new basis set from
the enclosed paper by Dunning. Add the boron 3s]
and hydrogen 2s] (using the exponents given in the
footnote to Table 6A) basis sets. Using the Z-matrix
for the B2H6, do a single point SCF calculation.
5. Redo exercise 3 using genzmat. Run joda and disp zmat
to test your result.

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