how to conduct a computational chemistry project

8/9/2019 How to conduct a Computational Chemistry project

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How to Conduct a ComputationalChemistry Research Project «



1.W HAT DO I W ANT TO KNO W?

2. HO W ACCURATELY ?



S earch in the literature for thelast information in a subject



Analytical chemistry S tandard deviation

Computational chemistry Practically

same results!with the exceptionof Monte Carlo

calculations .

Compare withExperimental answers or

More rigorous computations

Repetition of measurements

SUBJECT OPERATION ERROR ESTIMATION

2. HO W ACCURATELY ?F or example, compare experimental with computational chemistry




for example«

S hould I add a zero point energy (ZPE)correction ?

Is there spin contamination ?

Is spin-orbit coupling important ?

Is the effect of the solvent relevant ?

W hat do I want to consider ?



The election of the methodology«

type of calculation

basis sets

ECPs

force fields




In a imperfect world«

Many methods existbecause each is best for some situation .

The trick is to determine

which one is best for a given project .




Look at other computational researchstudies .

Perform a short study to verifythe method's accuracy .

Know merits and drawbacks of variousmethods and software packages .

in order to make an informed choice .


The election of the methodology:



This is usually done by giving some sort

of average error for a large collection of molecules .

Most of them focused on collections of organic and light main group compounds .

Look at other computational research studies .

a particular set of studies examine the accuracy of computational techniques for modelling a particularcompound or set of related compounds .



Look at the following examples that compare themethods (left column) with their calculated properties



1. The researcher examines the literature to determine that an ab initiomethod with a moderately large basis set will give the desired accuracyof results .

2. S ingle point for the monomer, 2 minutes3 . G eometry optimization for the monomer, 20 minutes

4 . The calculation scales as N 4

5 . G eometry optimization for the trimer 3 4 x 20 minutes or about 27 h .

6. W ould like to model up to a 1 5-unit chain, which would require 1 5 4 x 20 minutes or about 2 years .

7. G eometry optimization is not acceptable because«

Let¶s take an example:A researcher wants to start a study of apolymer with complex monomers:



«theresearcherwants to

complete thework in a

reasonableamount of time!



conventional integral evaluationmany ab initio programs use hard disk space to store numbers that are

computed once and used several times during the course of thecalculation .

(these are the integrals that describe the overlap between variousbasis functions)

d irect integral evaluationthe numbers are recomputed as needed .

(use less disk space at the expense of requiring more CPU time to do thecalculation)

incore algorithmstores all the integrals in RAM memory thus saving on disk space at theexpense of requiring a computer with a very large amount of memory .

s emi d irect algorithmwhich uses some disk space

and a bit more CPU time to obtain the optimal balance of both .

Calculation of integrals are usually a bottleneckin ab-initio calculations

S ome alternatives:



TIME COMPLEXITY

C = time which have to be done regardless of the size of calculation,such as initializing variables and allocating memory .

The standard matrix inversion algorithm for H F requires N 3 operations .

Computing the two-electron Coulomb and exchange integrals for a H F

calculation takes N4

operations.

At the end of the calculation, the orbital energies must be added . S incethere are N orbitals, there will be N addition operations .

total amount of CPU time required to do a H F calculation scales asN 4 + N 3 + N + C

(how the use of computer resources (CPU, time, memory, etc . ) changesas the size of the problem changes)

But if N is large then N 4 dominates .



M is the number of atoms

L the length of one side of the box containing themolecules in a calculation using periodic boundary conditions

A the number of active space orbitals

N the number of orbitals in the calculation .



Geometry optimization take s longer b ecau s e «

many calculations must be done as the geometry is changedeach iteration takes longer in order to compute energy gradients .

The amount of CPU time required for a geometry optimizationTopt ,

depends on the number of degrees of freedom, denoted as D .(degrees of freedom are the geometric variables being optimized,

such as bond lengths, angles, and the like)

As a general rule of thum b,the amount of time for a geometry optimization can be estimatedfrom the single-point energy CPU time, T single , with the equation

Topt § 5 x D 2 x T single



Ex ample

1. An ab initio method with a moderate-size basis set and minimalcorrelation may be used for optimization

2. Then a s ingle point calculation with more correlation and a largerbasis can be used for the final energy computation .

Thi s w oul d b e d enote d w itha notation like MP2/6-31 G* // cc sd( t) / cc - pV TZ.

Molecular mechanics or semiempirical calculations may be used todetermine a geometry for an ab initio calculation .

Molecular mechanics is nearly always used for conformation searching .

B ut b e careful «vibrational frequencies must be computed with the same level of theoryused to optimize the geometry .



1. Examines the literature to determine that an ab initio method with amoderately large basis set will give the desired accuracy of results .

2. S ingle point for the monomer, 2 minutes3 . G eometry optimization for the monomer, 20 minutes

4 . The calculation scales as N 4

5 . G eometry optimization for the trimer 3 4 x 20 minutes or about 27 h .

6. W ould like to model up to a 1 5-unit chain, which would require 1 5 4 x 20 minutes or about 2 years .

7. G eometry optimization is not acceptable .

8. W isely decides to stop at the 10- unit chain an d u s e geometrie s

optimize d w ith molecular mechanic s metho ds , which takes underan hour for the optimization .

9 . Obtains the d e s ire d re s ult s w ith s ingle point a b initio calculation s , which take 10 4 x 2 minutes or 2 weeks

10.feasible since she has her own work station with an uninterruptiblepower supply .



ea s ier to learn to u s e more complicate ds oft w are

than

to purcha s e a s upercomputer to solve a problem

that could bedone by a workstation with different software .

La b or co s t

(labor necessary on the part of the user)



PARALLEL COMPUTERS

Ideally, a calculation that takes an hour on a single CPUwould take half an hour on two CPUs .

This is called linear s pee d - up .

I n practice, this is not possible because the two CPU calculationsmust do extra work to divide the workload between the twoprocessors and combine results to obtain the final answer .

B ut , few types of algorithms give nearly perfectly linear scalingbecause of the nature of the algorithm and the amount of work thatthe developer did to parallelize the code .

Many Monte Carlo algorithms can be parallelized very eficiently .

Few programs for which our hypothetical hour calculation wouldtake 1. 5 hours on a two-CPU machine!

S ome of the correlated ab initio algorithms are very dificult toparallelize eficiently .



PARALLEL COMPUTERS

P ro b lem : S oftware written for single-processor computers will notautomatically use multiple CPUs .

Andcompilers are usually inefficient for sophisticated computer programs .



S ome software packages can be run on a net w orke d clu s ter of w ork s tation s a s though they w ere a multiple - proce ss or machine .

However,

the speed of data transfer across a network is not as fast as the speedof data transfer between the CPUs of a parallel computer .

( F ine-grained algorithms)

large - graine d algorithm sS ome algorithms break down the work to be done into very largechunks with a minimal amount of communication between processors

and they work as well on a cluster of workstations as on a parallelcomputer .



WH AT APPROXIMATIONS ARE BEIN G MADE?WH IC H ARE SI GNIFICANT?

M is take: e . g . investigate vibrational motions that are very anharmonicwith a calculation that uses a harmonic oscillator approximation .

To avoi d s uch mi s take s , it is important

the researcher understand the method's underlying theory

determine what software is available, what it costs, and how to properlyuse it .

Note that two programs of the same type (i . e . , ab initio) may calculatediferent properties so the user must make sure the program does exactlywhat is needed .

W hen learning how to use a program, dozens of calculations may failbecause the input was constructed incorrectly .

Do not use the project molecule to do this . Make mi s take s w ith s omething incon s equential , like a w ater

molecule .



Lis t of Computationally S ick S pecie s

http://srdata.nist

.gov/sicklist/

(unfortunately as S ep .07 the site was temporarily down)

The types of problems in the S icklist database includew rong geometrie s (see C 2 H),

unrea s ona b le vi b rational frequencie s (see N S and CH 3 ),

and b a d energetic s (see Be 2 ) .

W e are not interested in code dependent problems,such as S CF convergence problems with G AMESS

or MOLPRO for a particular molecule .



The computational chemi s try li s t ( CCL )consists of a list server and web site http://server . ccl . net/

The web site contains information about computationalchemistry and the archives from the discussion list .

S ubscribing to the list results in receiving about twenty

messages per day .

This is a good way to watch discussions of current issues .

The etiquette on the list is that you attempt to find ananswer to your question in the library and the web archivesbefore asking a question .

Once you have asked a question, please post a summary of the responses received .



Theoretical w ork is often revie w e dAdvances in Chemical Physics

Advances in Molecular ElectronicS tructureAdvances in Molecular ModellingAdvances in Quantum ChemistryAnnual Review of Physical ChemistryRecent Trends in ComputationalChemistryReviews in Computational Chemistry

R evie w s of computational w ork areChemical ReviewsChemical S ociety ReviewsS tructure and Bonding



How to Conduct a ComputationalResearch Project «

Chapter 16Computational Chemi s try: A P ractical Gui d e for Applying Technique s to R eal - W orl d P ro b lem s .

David C . Young2001 John W iley & S ons, Inc .

http://www3 . interscience . wiley . com/cgi-bin/booktoc/935 172 4 0

and how to publish it(according to the IUPAC)

Gui d eline s for P re s entation of Metho d ological Choice s in theP u b lication of Computational R e s ult s

A. Ab I nitio E lectronic S tructure Calculation s(IUPAC Recommendations 1 99 8 )

http://www . iupac . org/reports/ 1 99 8 / 700 4boggs/guidelinesa4 . pdf

how to conduct a computational chemistry project

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