Aces II� Z�Matrices� and Other Fun

Stu��

Sullivan Beck

Quantum Theory ProjectDepartments of Chemistry and Physics

University of FloridaGainesville� FL �����

May �� ���

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 ��� ���� ��HMemory ������ MBDisk Space ��� 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 thecorrect sequence to run them in�� or automatically usingxaces�� xaces� determines the order in which the otherexecutables must be run and runs them�

A description of most of the executables is contained inthe Aces II manual�

Aces II� Where Does It Run�

Aces II has been ported to the following computers�

� Cray YMP� C��� T��

� IBM RS�����

� Sun

� HP

� SGI

� DEC Alpha

� NEC

� Fujitsu

Aces II� What Is Required To Run It�

A lecture will be given discussing resource requirementprediction� Recommended minimum requirements are�

Memory �� MBDisk Space � GB

Aces II was developed on the Cray and IBM RS������

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 ascript which runs xaces�� The details of how the jobis submitted and in where it is run vary from computerto computer� Check with the system administrator�

� Analyze the output le

Input File� Di�erent Sections

� Restart info

� Z�Matrix

� Namelist with keywords

� Special basis set description

Input File� Example

� JOBARC��u�usr�beck�h�o�JOBARC

� JAINDX��u�usr�beck�h�o�JAINDX

Water� DZP vibrational frequency calculation

H

O � R

H � R � A

R����

A������

ACES��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� MBPT���� CCSD� CCSD�T�� etc�BASIS STO��G� ����G� DZP� SPECIAL� etc�CHARGE the molecular chargeMULT the spin multiplicityMEMORY the number of integer words to useREFERENCE RHF� UHF� ROHFVIBRATION EXACT� FINDIF� etc�

See the Aces II manual for a complete list and descrip�tion of the keywords�

Input File� Basis Sets

Many basis sets are available� A partial list is in theAcesII manual under the BASIS keyword description� Theyinclude most of the common Pople ��� and ���� basissets as well as a number of sets by Dunning�

For a complete list� it is necessary to actually look throughthe GENBAS le� PNL distributes more than ��� basissets over the web� All of these are included in the Aces�basis sets� These include guassian and ECP basis sets�A few additional basis sets have also been added to theGENBAS le�

If you wish to use a di�erent basis set on di�erent atomsor to use ghost atoms you must use the keyword BA�SIS�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 atemplate

� Edit the entries for the new basis set

� Test it out

A complete description of the exact format of the GEN�BAS 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 sym�metry

� Smaller molecules

Z�Matrix� Writing a Z�Matrix

The Z�matrix for a simple ��center molecule HOSF couldbe written�

�� H

�� O � RHO

�� S � ROS � ASOH

�� F � RSF � AFSO � DFSOH

Figure ��

F

H

O

S

� Angles must not be �� degrees�

� Dihedral angles�

� Between ��� and ��� degrees�

� Both �� and ��� are allowed�

� Clockwise is positive�

Z�Matrix� Symmetry

� No symmetry is easy� lots of possible Z�Matrices� al�most all will work�

� Symmetry is hard� Lots of Z�Matrices� but most willnot work�

Z�Matrix� Symmetry Must NotDecrease

H H

OROH

RHH

OHHA

H H

OROH ROH

AHOH

A �good� Z�Matrix will not decrease the symmetry �thoughit may increase� regardless of the values for the internalcoordinates� Compare two water Z�Matrices�

O

H � ROH

H � ROH � AHOH

vs�

H

O � ROH

H � RHH � AHHO

In the rst case� symmetry may increase as AHOH ap�proaches � or �� degrees� It will never approach � sincethat would mean merging the two hydrogen atoms�

Z�Matrix� All Present or All Absent

In a �good� Z�matrix� all occurences of an internal coor�dinate are present or absent in the Z�matrix�

Ammonia example�

N

H� � N�H

H� � N�H � H��N�H�

H� � N�H � H��N�H� � H��H��H��N

Note� It is impossible to use � angles and � bond lengths�

Z�Matrix� Dummy Atoms

N

X

HH H

A dummy atom is a center with no charge and no basisfunctions�

X

N � ���

H � NH � XNH

H � NH � XNH � �����

H � NH � XNH � �����

Note� It is still impossible to use the three H�N�H bondangles as one of the internal coordinates�

Note� The All Absent�Present rule only applies to opti�mizable internal coordinates�

Z�Matrix� Linear Molecules

X

CO OLinear molecules present a special problem due to the ��degree angles present�

CO� example�

C

X � ���

O � CO � ���

O � CO � ��� � �����

Z�Matrix� Rules and Hints

� Use dummy atoms to split �� degree angles in linearportions�

� There should always be an atom at the �center� ofthe molecule�

� There should always be � atoms along the central axisof rotation�

� Additional dummy atoms if there is a plane of sym�metry�

� De ne �central� atoms rst and others with respectto those atoms�

� De ne symmetry equivalents atoms as a group�

Z�Matrix� Linear Example

C C C C HH

XXXX

�� H

�� C � CH

�� X � ��� � ���

�� C � CC� � ��� � �����

� X � ��� � ��� � ���

�� C � CC� ��� � �����

�� X � ��� � ��� ���

�� C � CC� � ��� � �����

� X � ��� � ��� � ���

��� H � CH ��� � �����

Z�Matrix� Benzene Example

XX

X

X

511

12 13

14

15

9108

763 1

2

4

18 19

17 20

2122

23

24 25

26

272816

Z�Matrix� Cubane Example

X

X

X

X

X

N N

N N

C

C C

C

5

1

2

4

3

6 7

8 9

10 11

12 13

H

H H

H14 15

16 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 � or � character atomic symbol�or �X�� �GH���

� Labels may be up to � characters�

� Labels must be present for all coordinates� You can�tinclude 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 in�ternal coordinates�

� There are two special internal coordinate labels� TDAand IHA�

� In order to make things simple� name constants uni�formly�

Z�Matrix� Geometry OptimizationInput

NH� geometry optimization�

Ammonia

X

N � X

H � NH � NHX

H � NH � NHX � A���

H � NH � NHX � A���

NH������

NHX���������

X����

A���������

ACES��BASIS�DZP� CALC�SCF�

Z�Matrix� Geometry OptimizationOutput

The output for this �near the end� is�

Parameter dV�dR Step Rold RnewNH ��������� ������� ������� �������NHX �������� �������� �������� ��������

Minimum force� �������� � RMS force� ��������

Note� you must modify the ZMAT le by hand to includethe optimized geometry�

Note� you should remove the ��� from the Z�matrix�

Exercises

�� Write a ZMAT le for ethane in the eclipsed confor�mation� Set it up to do a single point� MBPT��� cal�culation� Run xjoda to make sure the Z�matrix iscorrect�

�� Write a ZMAT le for ethane in the staggered confor�mation� Set it up to do an SCF geometry optimiza�tion� Run xjoda to make sure the Z�matrix is correct�

�� Write a ZMAT le for the B�H� molecule� It is D�h

symmetry with the two bridging hydrogens above andbelow the plane containing the boron atoms and theother four hydrogen atoms� Run xjoda to make surethat the Z�matrix is a good one�

�� Modify the GENBAS le to add a new basis set fromthe enclosed paper by Dunning� Add the boron ��s�and hydrogen ��s� �using the exponents given in thefootnote to Table �A� basis sets� Using the Z�matrixfor the B�H�� do a single point SCF calculation�

�� Redo exercise � using genzmat� Run joda and disp zmat

to test your result�