orca lab ii basic setupscienide2.uwaterloo.ca/.../orca_lab_ii_basic_setup.pdf · cp file1 file2...

The Basic Computational Environment 1

1 Introduction – The Basic Computational Environment This chapter provides you with some basic introduction to your 'Computational Work

desk'. It is structured into three parts. The first one consists of some quick tutorial how

to login into your machine. The second part deals with basic steps in a UNIX-‐like

environment and introduces the 'SHELL', the UNIX command line. In the third part two

of the most used editors are presented in order to enable the user to manipulate text

files at will.

1.1 Login Into Your Computer Before you can login it is essential that you haven been provided with a username and a

password. Usually these are provided by your chemistry department or your system

administrator.

The first thing you will see is the 'login-‐screen', asking you to type in your username.

Figure 1: a typical login screen

The screen might look somewhat different, but it should be similar to the one shown

above. Once you typed in your username and pressed the <RETURN> key, the system

will ask you for your password, which you are expected to type, again followed by

<RETURN>. (The pressing of the <RETURN> key after typing in some commands or

other things is assumed from now on.) Having succeeded in providing the correct

password you are provided with your graphical desktop. All your actions will take place

in this environment. The next thing to do is to open a window containing a command-‐

line, which is usally called a 'shell'. This is nothing else than a window where you can

type in your commands. Click unto the icon on the left bottom (or top) and search for a

program called 'Konsole' or 'Terminal'. Having done so, your screen will look similar to

the one in the figure below:


Figure 2: The graphical desktop with a shell window

The following part deals with commands you can enter into this command window and

how to find your way around in a UNIX system.

1.2 The UNIX Command Line Although most computer use graphical displays and fancy graphical user interfaces

nowadays, UNIX is traditionally rooted in text based environments without any graphics,

that is, you tell the computer what to do only by typing in commands without further use

of a mouse or by clicking onto menu bars. In this it is not so different from very old

personal computers running MS-‐DOS in times when no Windows was around.

One essential feature of the shell is the administration and organisation of the files

within your home directory. Typing in the command 'pwd' the computer will tell you

where in the directory hierarchy you are at the moment, e. g. /home/frankw. Unix

directories are sperated by the slash '/' character. So /home/frankw means, the

directory 'frankw' in the 'home' directory which itself is located at the root of all

directories on this computer, called root, or '/'. When you just opened you command

window, you usually end up in your 'HOME' directory, the directory which is your own

private data space. Here you can copy files, create further directories, execute programs

and all other things usually done with a computer. When you get lost in all the

directories, 'pwd' (print working directory; you see most UNIX commands are

abbreviations or acronyms....) will tell you where you are now and a simple 'cd' (change

directory) will bring you back to the top of your HOME directory.

Some useful commands dealing with files and directories are listed in Table 1.


Table 1: Some useful unix commands for dealing with files and directories

Command Description pwd Print working directory

ls List all files in the current directory

ls *.inp List all files with extension .inp in the present directory (analogous to dir *.inp under windows)

ls -l List all files in current directory with detailed information

cp file1 file2 Copy a file with name “file1” to a file with name “file2” (analogous to the copy file1 file2 command under windows)

cp -r dir1 dir2 Copy a directory with name “dir1” to a directory with name “dir2”

mkdir calc Make the directory “calc” (same under windows) cd calc Change into the directory calc (same under windows) cd .. Change to a lower directory level rm *.tmp Remove all files with extension .tmp (CAREFUL: in unix

there is no “undelete” command – gone is gone!). mv file1 file2 Rename the file “file1” to “file2” find . -name "*.inp"

Find all files in all subdirectories with extension .inp

In the following table some commands are listed dealing with text files. Text files are

especially important since they are used almost everywhere in UNIX, for example, they

contain the input and output of your calculations, provide the system with information,

customize your shell etc. Table 2: Some useful unix commands for dealing with the contents of text files

Command Description cat file Print contents of file (without pausing on screen

boundaries) more file Print contents of file, pausing when screen end is

reached. Pressing <RETURN> scrolls down one line, <SPACE> on screen

grep -i "string" file

Search in file for "string" and print all lines containing this string

sed "s/string1/string2" file

Search in file for all occurences of string1 and replace them with string2 and print the result on the screen

Some other commands which might come in useful are listed in the following table.

Especially the man command is useful, for it provides you with a help text about other

commands. Table 3: Some more useful linux commands and tools

Command Description man ls Gives you all information about the command 'ls'.

xterm & Opens another command window. (The ‘&’ signifies that the processs xterm is to be send to the background


while you can keep on working in your present window). tar cvf file directory

Creates an archive of 'directory' into 'file'

gzip file Compresses the contents of 'file', most often used with archives

gzip -d archive.tar.gz ; tar xvf archive.tar

Uncompressed some archive (with suffix .tgz), which has been created before using tar and gzip.

There are a few other things you should know about UNIX commands.

Usually if you type in a command or start a program, which is essentially the same, it

uses some INPUT, does some work or calculation, and produces some OUTPUT. Usually

this means that all INPUT comes from the keyboard (for you to type in), and all OUTPUT

will be directed to the screen. Sometimes the OUTPUT, for example from some

calculation, becomes so large, that you would rather put it into a file for looking at it

afterwards in your own time. To do so, UNIX provides you with INPUT/OUTPUT

redirection, e. g. find . -name "*" > all_your_files

This command will 'find' all your files, from the current directory onwards (from '.') and

put them into the file 'all_your_files'. This output redirection via '>' works with all kinds

of commands.

Another important feature of the UNIX command line is the ability to put commands into

the 'background'. Usually, if you enter a command or a program name the program does

it's work and meanwhile you have to wait until it finishes. Now, if you put a '&' character

at the end of you command line, you will be greeted immediately to enter the next

command. In the meantime your program is executed invisibly in the background!

For example: orca test.inp >& output &

1.3 The Texteditor You need to use a text editor in order to edit textfiles, that is, to produce input to the

quantum chemical program packages. For this you can use the standard editors vi and

emacs or nedit. The latter is not available on all unix machines but is essentially self-‐

explanatory. The other editors are standard software but are a bit less convenient to use.

Basic familiarity with them is helpful. Some fundamental concepts and commands are

presented hereafter.


1.3.1 The VI Editor One of the most widely used editors on UNIX systems is the vi editor. Although it lacks

the look and feel of today's editors, it has the advantages of being available on all UNIX

systems and being very quick to use (and in extended versions also very powerful).

You can load a file into vi just by typing: vi filename

If the file did not exist before it will be created. One feature that is somwhat difficult to

grasp at the beginning is that editing in vi takes place in two different modes: A

command mode and an insert or edit mode. Vi starts in command mode. You can always

get back into command mode by pressing <ESC>. In this mode you can move the cursor

around on the screen and position it where you want to modify your text. For moving

around you can use the CURSOR keys or the keys h, j, k, l. Having positioned the cursor,

press i for insert mode. Now you can enter your text. Pressing <ESC> enters command-‐

mode again. In the following table are the most common keys accessible in command

mode. Table 4: usage of the vi editor

Command Description h, j, k, l Movement (left, down, up, right)

i, I Insert text before cursor position (before first character of the line)

a, A Append text after cursor position (at the end of current line)

o, O Open new line below the current line (or above current line)

X Delete charcter under cursor

Dd Delete whole line D Delete line from cursor position to the end of line

r, R Replace character under cursor (replace from cursor on onwards until leaving by <ESC>)

:wq Save file and exit vi :wfile Save current contents in 'file'. :q! Exit without saving changes

1.3.2 The EMACS Editor Another powerful editor under UNIX is the EMACS editor. You can start it by simply

calling: emacs filename

or

xemacs filename

The file will be opened in a different window, displaying the file's content. In this buffer

you can move around either by using the cursor keys or by scrolling and placing the


cursor via mouse click. Editing is done in the usual way, text is inserted before the cursor

and you can delete it by pressing the delete key repeatedly. Many functions in emacs are

accessible through the menu bar, but using key combinations is more flexible and faster.

This is just a small subset of those Table 5: Useful key-‐combinations for the emacs editor.

Command Description <CTRL>-x <CTRL>-s Save file and exit emacs <CTRL>-x <CTRL>-c Exit emacs <CTRL>-u Undo <CTRL>-k Delete line from cursor on to the end of line

(pressing <CTRL>-k repleatedly deletes lines) <CTRL>-<space> Mark beginnig of a selected region <CTRL>-w Cut region <CTRL>-y Paste region <CTRL>-x r k Cut marked rectangle <ALT>-x transient-mark-mode

Enable highlighting of selected region

If things get rough: <ALT>-x doctor

...

Quick Start into The Program Packages 7

2 Introduction – Quick Start into the Program Packages and Analysis

Tools

2.1 Calling the ORCA Program In order to run the ORCA program you need to create an input file (e.g. myinp.inp) and

then call: orca myinp.inp >myinp.out &

You can look at the progress of the calculation using tail –f myinp.out

A general form of the input file is:

(NOTE: the multiplicity is defined as 2S+1 where S is the total spin of the state under

investigation; for our purposes Mult=Number of unpaired electrons+1).

An example is:

2.2 Keywords for ORCA Below is a summary of keywords that will be used within this course. The program has,

of course, many more options – however, in this course you will essentially only need

those listed below. If you go on to do research in theoretical chemistry it is very likely

# comment lines (anywhere in input) ! Method BasisSet Additional-Keywords #Possible input blocks start with ‘%’ # for example: %scf maxiter 150 end * xyz Charge, Multiplicity Cartesian coordinates * or: * int Charge, Multiplicity Z-Matrix *

# Check H2CO optimization ! B3LYP SVP Opt TightSCF * xyz 0 1 C 0.000000 0.000000 0.000000 O 1.200000 0.000000 0.000000 H -0.550000 0.952628 0.000000 H -0.550000 -0.952628 -0.000000 *


that you need to consult the manual of the program, learn about other programs and

familiarize yourself with advanced aspects of the various program packages. Table 6: Useful Keywords for the ORCA program.

ORCA ACTIONS RHF Perform a restricted (closed-‐shell) Hartree-‐Fock calculation UHF Perform a spin-‐unrestricted open-‐shell Hartree-‐Fock calculation B3LYP/G Perform a B3LYP calculation with B3LYP being defined as in the Gaussian series of

programs. (Note for spin-‐unrestricted calculations the keyword is UKS B3LYP/G; the program automatically chooses UHF for open shell systems).

MP2 Perform a MP2 calculation on top of a RHF starting point. This is possible for energy and geometry optimization calculations.

RI-MP2 Perform a RI-‐MP2 calculation – much faster than standard MP2 but requires the input of an “auxiliary basis set” (here: SV/C if SVP; TZV/C if TZVP and TZVPP/C if TZVPP)

CCSD(T) Perform a coupled cluster calculation with single-‐ and double excitations together with a perturbative estimate of triple excitations. This is an accurate and expensive level of theory (presently only available for closed shell systems in ORCA).

SVP Use the SVP basis set. (small double zeta basis set for initial explorations; contains one set of polarization functions: p for H and d for heavier elements. With SV(P) the p functions on the hydrogens are deleted)

TZVP Use the TZVP basis set. (medium triple-‐zeta basis set ; already good for geometries and frequencies; contains one set of polarization functions: p for H and d for heavier elements)

TZVPP Use the TZVPP basis set. (Larger triple-‐zeta basis set for accurate energies. Contains three sets of polarization functions: 2p1d for H and 2d1f for heavier elements).

QZVP Large quadruple-‐zeta basis set with multiple polarization functions. Expensive but accurate for close-‐to-‐basis-‐set-‐limit results.

Opt Perform a geometry optimization NumFreq Perform a second derivative calculation (ORCA can only do numerical frequency

calculations presently). This will also automatically provide a calculated IR spectrum as well as ZPE and thermal corrections to the energy

TightSCF Request “tight” SCF convergence criteria (Necessary for geometry optimizations and frequency calculations; required input for ORCA).

%cis nroots 10 end

Absorption spectra: Calculate the first 10 excited states using configuration interaction with single excitations (appropriate for RHF or UHF SCF calculations).

%tddft nroots 10 end

Absorption spectra: Calculate the first 10 excited states using the time-‐dependent density functional theory (appropriate for a DFT SCF calculation)

%eprnmr gtensor true Nuclei = all { aiso, adip} End

ESR Spectra: Calculate the most important parameters of the ESR spectrum of S=1/2 systems. NMR chemical shifts can also be calculated.

NPA Perform a natural population analysis

In order to constrain an optimization you have to create input as in the following

example:


NOTE:

• “value” in the constraint input is optional. If you do not give a value, the present

value in the structure is constrained. For cartesian constraints you can’t give a

value, but always the initial position is constrained.

• It is recommended to use a value not too far away from your initial structure.

• It is possible to constrain whole sets of coordinates:

Relaxed surface scans can be performed as in the following example:

In the example above the value of the bond length between C and O will be changed in

12 equidistant steps from 1.35 down to 1.10 Angströms and at each point a constrained

geometry optimization will be carried out.

! RKS B3LYP/G SV(P) TightSCF Opt %geom Constraints { B 0 1 1.25 C } { A 2 0 3 120.0 C } end end * int 0 1 C 0 0 0 0.0000 0.000 0.00 O 1 0 0 1.2500 0.000 0.00 H 1 2 0 1.1075 122.016 0.00 H 1 2 3 1.1075 122.016 180.00 *

Constraining bond distances : { B N1 N2 value C } Constraining bond angles : { A N1 N2 N1 value C } Constraining dihedral angles : { D N1 N2 N3 N4 value C } Constraining cartesian coordinates : { C N1 C }

! RKS B3LYP/G SV(P) TightSCF Opt %geom Scan B 0 1 = 1.35, 1.10, 12 # C-O distance that will be scanned end end * int 0 1 C 0 0 0 0.0000 0.000 0.00 O 1 0 0 1.3500 0.000 0.00 H 1 2 0 1.1075 122.016 0.00 H 1 2 3 1.1075 122.016 180.00 *


In order to find transition states you have to have a structure that is fairly close to the

transition state itself. This can be generated by a relaxed or unrelaxed surface scan, by

chemical intition or by some other means. A suitable input is:

2.3 The MSINDO program MSINDO is a semiempirical method. It will be used for the simulation of solids and

surfaces in a later chapter. In order to run MSINDO you need to create an input file (e.g.

myinp.inp) and then call:

MSINDO < myinp.inp > myinp.out &

You can look at the progress of the calculation using tail –f myinp.out

A general form of the input file is:

! RHF SVP TightSCF SlowConv Opt PModel NumFreq %geom TS_search EF Calc_Hess true # Calculate the exact Hessian initially # Alternatively use InHess read # and InHessName "MyJob.hess" to read # a Hessian calculated at a lower level # of theory coordsys redundant Recalc_Hess 5 # re-calculate Hessian after 5 steps # Additional options: #modify_internal # { B 1 0 A } # # add a bond between atoms 0 and 10 # { B 3 1 A } # # add a bond between atoms 0 and 10 # end #Update Powell End * int 0 2 H 0 0 0 0.0 0 0 H 1 2 0 1.0 0 0 H 2 1 0 1.0 180 0 *


Due to the approximative nature of the semiempirical method, MSINDO results are in

general different from ORC or other ab initio/DFT programs. The parameterization

includes the most common bonding situations of elements H, Li -‐ F, Na -‐ Cl, K – Br.

2.4 The Molecular Editing and Visualization Program Molden Molden is a convenient visualization program for displaying molecular structures

(including animation for geometry optimizations and vibrations), electronic properties

(orbitals, electron densities) http://www.cmbi.ru.nl/molden/molden.html.

ORCA cube files can also be displayed in the <Dens. Mode>. For outputs of geometry

optimizations the starting structure is displayed. Structural changes are visualized by

<Movie>. Animations of vibrations are possible in the <Norm. Mode>. MSINDO

generates Molden inputs if the keyword

is given. This will produce a file named by the chemical formula, e.g. OCH2.molden for

the above example. The command molden OCH2.molden

PRINTOPTS=MOLDENMOS

# 1st line: Title (must include the string :NEW) CH2O :NEW # Section 1: keywords RHF or UHF MULTIP=… # closed or open shell OPT ANALY # opt. of internal coordinates CARTOPT ANALY # opt. of Cartesian coordinates # using analytical 1st derivatives NVIB=4 FULL # vibrations/heat of formation PRINTOPTS=MOLDEN # output for MOLDEN :END # end of section 1 # Section 2: atomic coordinates # Cartesian coordinates (CARTES in section 1): # Atomic number or symbol x y z (one per line) C 0.000000 0.000000 0.000000 O 1.200000 0.000000 0.000000 H -0.550000 0.952628 0.000000 H -0.550000 -0.952628 -0.000000 # Or Z-Matrix: 1 O 1 2 C RCO 1 2 3 H RCH AOCH 3 1 2 4 H RCH AOCH DHOCH :END # end of section 2 # Section 3: variables (if used in section 2) RCO = 1.20 RCH = 1.10 # Angstrom AOCH = 120 # Degrees DHOCH = 180 :END # end of section 3 END # End of input


will give the output shown below. With the <ZMAT Editor > it is possible to generate

structure definitions of simple molecules or to modify the actual Z Matrix.

Figure 3: Screenshot of the MolDen program showing the molecular structure window as well as the progress of SCF and geometry convergence and the Z-‐matrix (=structure) editor

2.5 The Visualization Program Molekel You can use the ORCA program to produce so-‐called Cube files, which contain the

information that is necessary in order to visualize molecular orbitals with either the

Molden or Molekel programs.

In order to use orca you have to invoke a small auxiliary program called orca_plot.

You have to start it with the name of a so-‐called gbw-‐file. The GBW file is a file that is

automatically made during the execution of ORCA. It contains in binary form a summary

of the calculation. For example, if you ran myjob.inp the program will produce

myjob.gbw which contains the geometry, the basis set used and the wavefunction that

was computed. Call: orca_plot myjob.gbw -i

This will give you a small “stone-‐age” menu which you can use to produce the desired

graphical information. First choose “5” to choose an output format. Select “7” to choose

“Gaussian Cube”. Then select “2” and choose the number of the MO that you want to plot.

Remember that ORCA starts counting with zero and refer to the output file to figure out

which MO you want to see. Finally choose “10” in order to produce the plot. This will

lead to a file called myjob.moXa.cube where X is the number of the MO that you

selected for plotting. After you have made all cube files that you wanted, start the


Molekel program and proceed as described below. Since the cube-‐files are ASCII files

you can also transfer them between platforms.

You can now start Molekel and load (via a right mouse click) the XYZ file (or also

directly the .cube file). Then go to the surface menu, select “Gaussian-‐cube” format and

load the surface. For orbitals click the “both signs” button and select a countour value in

the “cutoff” field. The click “create surface”. The colour schemes etc. can be adjusted at

will – try it! It’s easy and produces nice pictures. Create files via the “snapshot” feature of

Molekel. Other programs can certainly also deal with Gaussian-‐Cube files.

Figure 4: The π and π*-‐MOs of CO as visualized by Molekel.

2.6 The Data Analysis Program XMGrace For a survey over all features of xmgrace, the reader is referred to the excellent manual

provided under http:www.grace.com

2.6.1 Plotting a Graph with XMGrace Getting data Before anything can be plotted, the data must be generated. To prepare the data so that

it can be read in directly by xmgrace, one should store it in a plain text file, containing

only numbers. Decimal numbers must be written with points. To actually start xmgrace,

type

$: xmgrace datafile

while datafile is the name of the file containing the prepared data.


Figure 5: The “Getting Data” window of Xmgrace

By default, the first column is read in as the x values, while the second represents the y values. Getting even more data To load a new dataset (in short: “set” into the actual graph, select “Data -‐> Import... -‐>

ASCII” from the menu bar. Be sure to eliminate the last entry of the filter (*.dat) if you

can't see the desired file (1).

To start a completely new graph, select “File -‐> New” from the menu bar.

Getting more complicated data Data that contains more than two rows can be read in via “Data -‐> Import... -‐> ASCII”.

Selecting “Load as -‐> Block data” (2) will provide a new window where you can select

which row of data should be used for the x and the y axis.

2.6.2 Polishing the Graph: Menu Plot Graph appearance... Here one can alter the appearance of the legend, the title, the frames of the graph as well

as the legend box. It is common to select “2” for the width of all lines, in this case the

frames.

The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Restart your computer, and then open the file again. If the red x still appears, you may have to delete the image and then insert it again.


Figure 6: The “Set Appearance” window of Xmgrace

The same menu can be opened by double clicking with the left mouse button outside the

graph.

Set appearance... Here one can change the design of every single set (of data). The first part “Select set”

(1) allows to choose the set to edit. Because we normally have discrete values, we prefer

a representation of every single point over lines. This is done by going to tab “Main”,

select “Symbol properties -‐> Type: Diamonds” (for example) (2) and select “Line

properties -‐> Type: None” (3). Here you can also fill in the name of the data set for the

legend (4). The command “\s” makes all following letters to be written as a subscript,

“\N” returns to normal format. Hit “Apply” (5) to not loose this changes while going to

the next tab, “Symbols”.

Here, set the “Symbol outline -‐> width” to “2” and “Symbol fill -‐> Pattern” to the filled

black square. All other tabs are not important at the moment.

The same menu can be opened by double clicking with the left mouse button directly on

one data point (or one line).

Axis properties Here the range of the axis, the appearance of the axis bars and the title of the axis are set.



“Edit” determines which axis is to be edited. Make sure that you edit the right axis, and

that “Apply to” at the bottom is set to “Current axis” before hitting apply. Note that most

of the alterations have to be done twice.

The tab “Main” is mostly to modify the axis label. If “Symbol” must be used as the

language, open in the main menu “Window -‐> Font tool”, select “Symbol” as the

language, and click on the desired letter. The appearing string can directly be plugged

into the axis label.

To get a consistent graph, go to tab “Tick marks” and set all line width to “2” as well as

“Placement -‐> Draw on:” to “Normal side”.

The same menu can be opened by double clicking with the left mouse button directly on

one axis.

2.6.3 Evaluating the data: Fitting Procedures The most frequently used methods to search for trends in experimental or

computational data are regression analysis and the non-‐linear curve fitting.

A. Regression analysis To do a linear regression analysis, select “Data -‐> Transformation -‐> Regression ...” . This

will lead to a new window, where you can choose which data set should be analyzed, and

with which method. Furthermore, selecting “Restrictions -‐> Region ..” you can choose

which subset of data points should be used for the regression.

To define a region, go to “Edit -‐> Regions ...-‐> Define” in the main menu. Select the region

type and click “Define”. Then use the left mouse button (one click per corner/end) to

define the geometrical structure you have selected.

Back to the linear regression, click “Accept”. Now a new data set is created, which can be

treated like any data set before. Also, all information of the fitting procedure are printed

in a new window. There, go to File -‐> Save to save these results.


Figure 7: The “Nonlinear Curve Fitting” window of Xmgrace

B. Non-‐linear curve fitting

To do a non-‐linear curve fitting, select Data -‐> Transformation -‐> Non-‐linear curve

fitting. In the new window, you must select the data set (1), the fit function (2) and the

number of parameters (3) present in the fit function. Make sure that the parameters in

the fit function are labeled A0, A1 ... .

The rest is done in an analogue way to the linear regression analysis.

Note that the curve is plotted by connecting data points with the x values of the original

data set in the order of the original basis set. This can lead to quite confusing results at

first glance, so one has to switch back to 2.2 and edit the new data set accordingly, i.e., by

changing form line to point representation.

2.6.4 Printing and Saving the Results To save the whole graph, go to “File -‐> Save as ...“ in the main menu.

To print, go to “File -‐> Print setup “and disable “Output -‐> Print to file”(2). Type “lpr -‐

Plexzip” in “Output -‐> Print command” (3).



Select “File -‐> Print” back in the main menu.

To save this graph as an eps file, go to the print setup and enable “Output -‐> print to

file”(2).

Select “Device Setup -‐> Device -‐> EPS”(1).

Alter “Output -‐> File name -‐> ....eps”(4).

Select “File -‐> Print” back in the main menu.

Figure 8: The “Printing and Saving the Results” window of Xmgrace


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