zmat tutorial
DESCRIPTION
Z matriz en quimica cuanticaTRANSCRIPT
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Aces II� Z�Matrices� and Other Fun
Stu��
Sullivan Beck
Quantum Theory ProjectDepartments of Chemistry and Physics
University of FloridaGainesville� FL �����
May �� ���
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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
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Computer Facilities At This Course
Computer IBM ��� ���� ��HMemory ������ MBDisk Space ��� GB
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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�
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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
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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������
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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
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Input File� Di�erent Sections
� Restart info
� Z�Matrix
� Namelist with keywords
� Special basis set description
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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
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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�
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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�
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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�
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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
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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�
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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�
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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�
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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�
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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�
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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 � ��� � �����
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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�
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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 ��� � �����
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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
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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
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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�
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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�
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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�
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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�